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WO2025217501A1 - Panel for detecting wound pathogens - Google Patents

Panel for detecting wound pathogens

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Publication number
WO2025217501A1
WO2025217501A1 PCT/US2025/024251 US2025024251W WO2025217501A1 WO 2025217501 A1 WO2025217501 A1 WO 2025217501A1 US 2025024251 W US2025024251 W US 2025024251W WO 2025217501 A1 WO2025217501 A1 WO 2025217501A1
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WIPO (PCT)
Prior art keywords
primer pair
seq
specific
pair set
probe
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/US2025/024251
Other languages
French (fr)
Inventor
Changfu WEI
Larbi BEDRANI
Elena INGERMAN
Maidar Jamba
Elvis Huarcaya NAJARRO
Ioanna PAGANI
Pius M BRZOSKA
Kelly Li
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Life Technologies Corp
Original Assignee
Life Technologies Corp
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Publication date
Application filed by Life Technologies Corp filed Critical Life Technologies Corp
Publication of WO2025217501A1 publication Critical patent/WO2025217501A1/en
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00—Microorganisms ; Processes using microorganisms
    • C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales

Definitions

  • the gold-standard wound assessment includes direct visual inspection of the wound site under white light combined with indiscriminate collection of bacterial swabs and tissue biopsies resulting in delayed, costly, and often insensitive bacteriological results. This may affect the timing and effectiveness of treatment. Early recognition of wound pathogens may guide the detection and effectiveness of therapeutic intervention, thus reducing both morbidity and mortality while improving clinical outcomes related to wounds. Accordingly, there is a need to detect wound pathogens. The need is solved by the assays and methods described herein that detect the presence or absence of one or more of wound pathogens in individual or multiplex qPCR assays.
  • One embodiment described herein is a method for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomon
  • Primer Pair Sets comprise the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enteroc
  • the generating of the at least one amplicon comprises performing PCR.
  • the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii produced using at least one primer pair selected from SEQ ID NO: 1– 2, 4–5, or 7–8, and a sequence comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis produced using at least one primer pair selected from SEQ ID NO: 10–11, 13–14, or 16–17, and a sequence comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens produced using at least one primer pair selected from SEQ ID NO: 19–20, 22–23, or 25–26, and a sequence comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae produced using at least one primer pair selected from SEQ ID NO: 28–29, 31–32, or 34–35
  • the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae comprising at least a portion of SEQ ID NO: 427
  • the reaction mixture further comprises probes specific for the at least one amplicon.
  • the reaction mixture further comprises probes specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probes comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsi
  • the reaction mixture further contains a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample.
  • control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426.
  • the probe comprises a fluorescent reporter.
  • the probe comprises a quencher.
  • the probe is labeled at or near the 5′–end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM.
  • the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ.
  • Another embodiment described herein is a composition for individually, simultaneously, or sequentially determining the presence or absence of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia
  • Primer Pair Sets comprises the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enteroc
  • the composition further comprises a probe specific for the at least one amplicon produced using the at least one primer pair selected from one or more of Primer Pair Sets 1–44.
  • the composition further comprises a probe specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probe comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ
  • the composition further comprises a polymerase, a buffer, and deoxynucleotide triphosphates (dNTPs).
  • the composition further comprises a sample.
  • the composition further comprises a at least one control forward and reverse primer and, optionally, a control probe, that specifically amplifies a target nucleic acid of a control sample.
  • control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418– 419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426.
  • the probe contains a fluorescent reporter.
  • the probe contains a quencher.
  • the probe is labeled at or near the 5′ end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM.
  • the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ.
  • a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ.
  • Another embodiment described herein is a kit for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus
  • the composition further comprises any of the compositions described herein.
  • the kit comprises Primer Pair Sets comprising the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10– 11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44;
  • the kit further comprises probes suitable for use with specific forward and reverse primer pairs, the probes comprising one or more of: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsi
  • the kit further comprises a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample.
  • control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426.
  • the kit further comprises a control plasmid comprising one or more target sequences selected from Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia
  • control plasmid comprises one or more of nucleic acid sequences of SEQ ID NO: 427–470.
  • DESCRIPTION OF THE DRAWINGS The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
  • FIG.1 shows limits of detections for wound pathogen panel qPCR assays using Open Array (OA) or TaqManTM Array Card (TAC) platforms. DETAILED DESCRIPTION Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.
  • any nomenclatures used in connection with, and techniques of biochemistry, molecular biology, immunology, microbiology, genetics, cell and tissue culture, and protein and nucleic acid chemistry described herein are well known and commonly used in the art. In case of conflict, the present disclosure, including definitions, will control. Exemplary methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the embodiments and aspects described herein.
  • the terms “amino acid,” “nucleotide,” “polynucleotide,” “vector,” “polypeptide,” and “protein” have their common meanings as would be understood by a biochemist of ordinary skill in the art.
  • Standard single letter nucleotides A, C, G, T, U
  • standard single letter amino acids A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y
  • the terms such as “include,” “including,” “contain,” “containing,” “having,” and the like mean “comprising.”
  • the present disclosure also contemplates other embodiments “comprising,” “consisting essentially of,” and “consisting of” the embodiments or elements presented herein, whether explicitly set forth or not.
  • the term “a,” “an,” “the” and similar terms used in the context of the disclosure are to be construed to cover both the singular and plural unless otherwise indicated herein or clearly contradicted by the context.
  • “a,” “an,” or “the” means “one or more” unless otherwise specified.
  • the term “or” can be conjunctive or disjunctive.
  • the term “and/or” refers to both the conjunctive and disjunctive.
  • the term “substantially” means to a great or significant extent, but not completely.
  • the term “about” or “approximately” as applied to one or more values of interest refers to a value that is similar to a stated reference value, or within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, such as the limitations of the measurement system.
  • the term “about” refers to any values, including both integers and fractional components that are within a variation of up to ⁇ 10% of the value modified by the term “about.”
  • “about” can mean within 3 or more standard deviations, per the practice in the art.
  • the term “about” can mean within an order of magnitude, in some embodiments within 5-fold, and in some embodiments within 2-fold, of a value.
  • the symbol “ ⁇ ” means “about” or “approximately.” All ranges disclosed herein include both end points as discrete values as well as all integers and fractions specified within the range. For example, a range of 0.1–2.0 includes 0.1, 0.2, 0.3, 0.4 . . . 2.0. If the end points are modified by the term “about,” the range specified is expanded by a variation of up to ⁇ 10% of any value within the range or within 3 or more standard deviations, including the end points.
  • control As used herein, the terms “control,” or “reference” are used herein interchangeably.
  • a “reference” or “control” level may be a predetermined value or range, which is employed as a baseline or benchmark against which to assess a measured result.
  • Control also refers to control experiments.
  • the term “subject” refers to an animal. Typically, the subject is a mammal. A subject also refers to primates (e.g., humans, male or female; infant, adolescent, or adult), non- human primates, rats, mice, rabbits, pigs, cows, sheep, goats, horses, dogs, cats, fish, birds, and the like. In one embodiment, the subject is a primate.
  • the subject is a human.
  • a subject is “in need of treatment” if such subject would benefit biologically, medically, or in quality of life from such treatment.
  • a subject in need of treatment does not necessarily present symptoms, particular in the case of preventative or prophylaxis treatments.
  • the terms “inhibit,” “inhibition,” or “inhibiting” refer to the reduction or suppression of a given biological process, condition, symptom, disorder, or disease, or a significant decrease in the baseline activity of a biological activity or process.
  • treatment refers to prophylaxis of, preventing, suppressing, repressing, reversing, alleviating, ameliorating, or inhibiting the progress of biological process including a disorder or disease, or completely eliminating a disease.
  • a treatment may be either performed in an acute or chronic way.
  • the term “treatment” also refers to reducing the severity of a disease or symptoms associated with such disease prior to affliction with the disease.
  • “Repressing” or “ameliorating” a disease, disorder, or the symptoms thereof involves administering a cell, composition, or compound described herein to a subject after clinical appearance of such disease, disorder, or its symptoms.
  • wound pathogens refer to bacterial and fungal species that commonly infect wounds from either trauma, iatrogenic, or nosocomial sources.
  • the wound pathogens comprise one or more of the bacterial species: Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morg
  • the fungal pathogens comprise one or more of the fungal species: Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, and Candida tropicalis.
  • the primers, probes, and polynucleotides described herein may include variants that have substitutions, deletions, and/or additions that can involve one or more nucleotides.
  • nucleic acid molecules comprising polynucleotides having nucleotide sequences about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, and more preferably at least about 95–99% or 100% identical to (a) nucleotide sequences of SEQ ID NO: 1–470 and capable of being used as primers or probes as described herein; or (b) nucleotide sequences capable of hybridizing to the complement of any of the nucleotide sequences of SEQ ID NO: 1–470 and capable of being used as primers or probes as described herein.
  • nucleotide having a nucleotide sequence at least 90–99% “identical” to a reference nucleotide sequence indicates that the nucleotide sequence is identical to the reference sequence except that the nucleotide sequence can include up to about 10-to-1 point mutations, additions, or deletions per each 100 nucleotides of the reference nucleotide sequence.
  • nucleotide having a nucleotide sequence at least 90–99% identical to a reference nucleotide sequence up to 10% of the nucleotides in the reference sequence can be deleted, added, or substituted with another nucleotide, or a number of nucleotides up to 10% of the total nucleotides in the reference sequence can be inserted into the reference sequence.
  • mutations of the reference sequence can occur at the 5′- or 3′-terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
  • two or more polynucleotide sequences can be compared by determining their percent identity.
  • the percent identity of two sequence is generally described as the number of exact matches between two aligned sequences divided by the length of the shorter sequence and multiplied by 100.
  • Alignment for nucleic acid sequences can be performed using by the global alignment method of Needleman and Wunsch, J. Mol. Biol.48 (3): 443-453 (1970) or the local homology algorithm of Smith and Waterman, Adv. Appl. Math.2: 482-489 (1981).
  • Described herein are primers, primer sets, and probes designed for target sequences and compatible for use in an individual or multiplex qPCR determining the presence of wound pathogens.
  • Multiplex PCR presents a challenge for quantitation of the pathogen DNA: the different amplicons compete for the same PCR reaction components (such as e.g., DNA polymerase and MgCl 2 ) and this can compromise the quantitative comparison between samples. It is known in the art that there is bias in the amplification efficiencies between different template amounts or lengths so that e.g., short amplicons are favored in the expense of longer ones. At the same time, undesired cross-reactions of multiplex set oligo combinations must be avoided.
  • the selected primers and probes of the assay do not cross-react with other closely-related pathogens.
  • the disclosed detection method and assay may contain internal process control, such as Bacillus atrophaeus (BA) or a universal RNA Spike In/Reverse Transcription Control (Xeno).
  • the assay may have a real time PCR positive control.
  • the probes that target genomic regions of different pathogens utilize three distinct fluorophores, while a fourth fluorophore is designated for the process control detection. Therefore, individual or multiplex qPCR assays are described herein, wherein the detection takes place in a single-well reaction, to meet the speed and high-throughput needs for rapid clinical wound pathogen testing.
  • compositions e.g., the particular physical components of an assay such as primers and/or probes
  • kit e.g., primers and/or probes and additional buffers, reagents, etc.
  • a method e.g., a process for detecting target nucleic acids
  • embodiments are presented by describing “assays,” but it will be understood that the associated methods for the assays, and the compositions for carrying out the assays (primers, probes, and primer sets), are also intended to be part of this disclosure.
  • primer pair sets comprising one or more forward primers, reverse primers, and probes for detecting the presence or absence of one or more wound pathogens.
  • Various primer pair sets for detecting specific wound pathogens are shown in Table 1.
  • Table 1. Primer Pair Sets for Detecting Wound Pathogens Primer Pair Set Organsim 1 Acinetobacter baumannii 2 Bacteroides fragilis 3 Clostridium perfringens 4 Enterobacter cloacae 5 Enterococcus faecalis 6 Enterococcus faecium 7 Escherichia coli 8 Klebsiella pneumoniae 9 Klebsiella Oxytoca 10 Klebsiella aerogenes 11 Proteus mirabilis 12 Proteus vulgaris 13 Pseudomonas aeruginosa 14 Serratia marcescens 15 Staphylococcus aureus 16 Streptococcus agalactiae 17 Streptococcus dysgalactiae 18 Str
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 1 NO NO NO AGCCTGTGCGCGATA TGCTGCATTCTGCCC CAGCCTGCTTAATAC 1 ACA 1 CAAA 2 GAAC 3 CGTCGTGTTCAAACT GCCCAATCCTCATCT CATAACAACAGCTTA 6 GTGCAACCGTTTTAA CGGTACGGAAACCAT CACGACTTGAACCAC 3 TTGCTCGTA 7 ATTCGTTTAATG 8 AACC 9
  • Primer Pair Set 2 comprises one or more the primer pairs shown in Table 3, in a combination with a corresponding probe sequence: Table 3.
  • Primer Pair Set 3 comprises one or more the primer pairs shown in Table 4, in a combination with a corresponding probe sequence: Table 4.
  • Primer Pair Set 6 comprises one or more the primer pairs shown in Table 7, in a combination with a corresponding probe sequence: Table 7.
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 7 NO NO NO NO GGCATGGCGGATAAA GAAGGTGGGTTTCGC ACCGAAAGCGATCTC 1 TTTCAATCG 55 CTGTAT 56 C 57 GCGGATCATCGTGAC ACCGCCAGAACTTGA AAGCAATCCAGCTTC 2 GGAT 58 GCAA 59 TG 60 TGCTTCGACTTCCTG CGAGTTGCTGTCGAT TCCTGAACACCATAC 3 CAATCTTT 61 CCGTA 62 CTGTC 63
  • Primer Pair Set 8 comprises one or more the primer pairs shown in Table 9, in a combination with a corresponding probe sequence: Table 9.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 8 NO NO NO GATACGAAAGTTACC GGTCGCTGTACTGTA ACCCTGGCCCATAAT 1 TCAGGAACGT 64 CCAGAAT 65 G 66 GACGGGCGCGCATG CACCACCAGTCCGTT CAGCCGGGCAAGATG 2 67 GCT 68 69 CCTGCGGGCTGTCTC CGCCTGATGCCGGAC CCACCAGAAAATGC 3 A 70 AT 71 72 GATCGTCCAGCGAGG GATATTCCGCCGCAC 3 TCTG 79 AACCTA 80 CAGGCGGCCATTACC 81
  • Primer Pair Set 10 comprises one or more the primer pairs shown in Table 11, in a combination with a corresponding probe sequence: Table 11.
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 10 NO NO NO CGCGCTAAGCGGCAT AACGCCAATCGAATC TCCTCCACGAAAGGC 1 G 82 GATACCA 83 A 84 AAAATCCCCTTTGCG TCTTCCCAGATAGCA CACCAACGGTGGCAC 2 GAAAGC 85 ACCAAACATATTAC 86 AG 87 CGTTTCTCAATTAAT CCGGAGAAATACTCC ACTCAACTCTTTCGA 3 AACTGTGGTGACT 88 ATGACTTCTT 89 CTTTGAA 90
  • Primer Pair Set 11 comprises one or more the primer pairs shown in Table 12, in a combination with a corresponding probe sequence: Table 12.
  • Primer Pair Set 12 comprises one or more the primer pairs shown in Table 13, in a combination with a corresponding probe sequence: Table 13.
  • Primer Pair Set 13 comprises one or more the primer pairs shown in Table 14, in a combination with a corresponding probe sequence: Table 14.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 13 NO NO NO CCTGCCTGAAGATCG TCGACATGCCGGTTG CTTCGCGTTCAGTCC 1 AGGA 109 CT 110 GC 111 TTGAAGGAATTGCTT GCATCAGCAACTCCT CAGGCAGGCGAGCAT 2 GTGCATGAG 112 CGATCTT 114 GCGGGCTTTTCCAGT GCCCGGCATTCGTCC TAGCTCTGGGTGAAA 3 CAG 115 TT 116 TAG 117
  • Primer Pair Set 14 one or more the primer pairs shown in Table 15, in a combination with a corresponding probe sequence: Table 15.
  • Set 15 comprises one or more the primer pairs shown in Table 16, in a combination with a corresponding probe sequence: Table 16.
  • Primer SEQ SEQ Pair Set 16 comprises one or more the primer pairs shown in Table 17, in a combination with a corresponding probe sequence: Table 17.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 16 NO NO NO CAATGGCAGCTTCGC CTGTCCACGTCGTAT TCGCAAGTGTTCAAG 1 TATTATCAG 136 CTGTTTCTT 137 CAC 138 GCGCCAGCTTTGAAA GGTGATACCTGTTCA TTGCTCTTGTGCTAA 2 139 140 141
  • Primer Pair Set 18 comprises one or more the primer pairs shown in Table 19, in a combination with a corresponding probe sequence: Table 19.
  • Primer Pair Set 19 comprises one or more the primer pairs shown in Table 20, in a combination with a corresponding probe sequence: Table 20.
  • Streptococcus anginosus Primers and Probes (5′ ⁇ 3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 19 NO NO NO CCAGTTCCCCAGGCT CCTTCTTCCATTTAT CAGCAACACCAGTAA 1 TCTG 163 TCGCATGAAAGTT 164 ATG 165 GCACGTGATAGCCAA AGAAATTCTCGCTGC CTGGCTCTTCTCACC 2 166 167 168 in Table 21, in a combination with a corresponding probe sequence: Table 21.
  • Pair Set 21 comprises one or more the primer pairs shown in Table 22, in a combination with a corresponding probe sequence: Table 22.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 21 NO NO NO GATGGCCCCGAATCT GTTGCAGTAGTGCGA CTGCCACTATTTCCC 1 ATCCAT 181 TCCCTT 182 CTTCTAT 183 CGCTGTGGCACGAAT GCTGCCCATTAAATT CTCGCCTTGAGTTTC 2 ATGATGA 184 GACCAAGAT 185 C 186 CTTGAACCAGCGACA CAGTCTGAGGCGATA ACAACAATTCCTCCA 3 TACGGATTA 187 CCGTTAA 188 TAGTTC 189
  • Primer Pair Set 22 comprises one or more the primer pairs shown in Table 23, in a combination with a corresponding probe sequence: Table 23.
  • Pair Set 23 comprises one or more the primer pairs shown in Table 24, in a combination with a corresponding probe sequence: Table 24.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 23 NO NO NO AGAAATTATTGTCTC CGGGTTTCGATTTGG CACCCGGAAAACAG 1 TGGGCATGCT 199 ATCGGAT 200 201 GCACTCACCCTGGGA TGCCGACGCGTTGTT CCAATTCAGGGAAGA 2 CTCA 202 TG 203 CCA 204 GCGCTGACTCACTCT CCGATGAGTCCCAGG TCGTATGCCAATCAA 3 TTTCC 205 GTGA 206 TAAA 207
  • Primer Pair Set 24 comprises one or more the primer pairs shown in Table 25, in a combination with a corresponding probe sequence: Table 25.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 24 NO NO NO GGTAGCACTTACCTC CAATTCGCATAATGT TCGCAGGATGCATAC 1 TTACGCA 208 TCCCTTCCAT 209 GCA 210 GATTGTGGAAGCCGC TCGCTGGCGGCACTT CAGCGGTAATTT A CATG 211 T 212 GC 2 213 CGCGCAGTCGCTGGA GCGGTAATTTGCCCG CATGTGCGGCTTCCA 3 214 GTAAAGA 215 C 216
  • Primer Pair Set 25 comprises one or more the primer pairs shown in Table 26, in a combination with a corresponding probe sequence: Table 26.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 25 NO NO NO AAGCCCTGCACCAGC TGAGATCCAGCGAGT CTGGCCTCACTAACT 1 A 217 GTTCAG 218 GG 219 CCTCAAATCGTGTTG TGAGCCAGTTCCCGA CCACCGTCGAACAGA 2 GATCAGTTG 220 ATGTTG 221 TGT 222 CTCAAACCCTGCGCA CTTTGACCGGCGCGT TCGCTGCCACGTTGT 3 TTCC 223 TT 224 G 225
  • Primer Pair Set 26 comprises one or more the primer pairs shown in Table 27, in a combination with a corresponding probe sequence: Table 27.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 26 NO NO NO GGAACGCCTGCGTGG GTGGCGCAGTGAT CCGTTAGCTTCGATG 1 T 226 G 227 TCAAA 228 GCGTATCGAAACGCT CAGCGCTCAGACG CCGTGGTCCAGATCG 2 GTTCAC 229 230 T 231 GGCTAAAGACTACGT CTTAGCCAGCAGATC CAGCTCCATGTTAGC 3 TGACGAATCT 232 CAGACT 233 TGC 234
  • Primer Pair Set 27 comprises one or more the primer pairs shown in Table 28, in a combination with a corresponding probe sequence: Table 28.
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 27 NO NO NO GAGAGTATTATCGCC TGCAATAGGAGTTAC CAAGGCCACCGGCTC 1 TGCCCAT 235 CGCAATAGG 236 C 237 AGAAGGCGGAAGACA GATATCTCCTGTTAC AACGGATACAGACCA 2 CACAC 238 GTCTGTTGTTCT 239 CAATT 240 ACGCACGAACGGATG CCAATGTTTCGTAAA TCCCGCCGTAGCCC 3 TGA 241 CGATTTTGGATTTC 242 243
  • Primer Pair Set 28 comprises one or more the primer pairs shown in Table 29, in a combination with a corresponding probe sequence: Table 29.
  • Primer Pair Set 29 comprises one or more the primer pairs shown in Table 30, in a combination with a corresponding probe sequence: Table 30.
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 29 NO NO NO NO GACGGTACCATAGGA CGAACCCTTTACGCC ACGCTCGCCCCCTAC 1 GGAAGC 253 CAGTA 254 G 255 GGGATAGCCTCGGGA ACCGCTGTGACTTTA AACAGGCGTTACTGT 2 AACC 256 ACCACTG 257 GGTCT 258 CACGGTCCAAACTCC GGCGTCGCTGCATCA CCCCATTGTGCAAGA 3 TACGG 259 G 260 TT 261
  • Primer Pair Set 31 comprises one or more the primer pairs shown in Table 32, in a combination with a corresponding probe sequence: Table 32.
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 31 NO NO NO GCTCGCGTCTGATTA TTCATCCTCTCAGAC ACCAAGGCGACGATC 1 GCTAGTT 271 CGGCTA 272 AG 273 TGATTAGCTAGTTGG 2 74 CCGGCTACTGATCGT 2 C GGGTACGCAGGCGGT CCACTTTCCTCTCCA AAGTCGAATGTTAAA 3 C TACTCAAG 278 GATCG
  • Primer Pair Set 32 comprises one or more the primer pairs shown in Table 33, in a combination with a corresponding probe sequence: Table 33.
  • Primer SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 32 NO NO NO TGCGGTGGAACGGCT ACCTGCCCCAACTTC ACGTTGGACAAGGTT 1 AATC 280 TCTTTTAAAT 281 TTG 282 TGGGCAAATGTAGCT CACCTGCCCCAACTT CCACCGCACCATCCA 2 CATTCATTAGG 283 CTCTTT 284 A 285 CGTTGGACAAGGTTT CCCACTTGCATAAGG TTGTATCTAGCAGAT 3 TGAATTTAAAAGAGA 286 ATCATTTGGA 287 288 AATAAATAAG In another embodiment, Primer Pair Set 33 comprises one or more the primer in Table 34, in a combination with a corresponding probe sequence: Table 34.
  • Paeniclostridium sordellii (Clostridium sordellii) Primers and Probes (5′ ⁇ 3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 33 NO NO NO CTGAAGTAGTTGCTC CAGCCGCATGGAACA CTACCCCATTAGATA 1 AATACGCTAAC 289 CTATG 290 TCATTTG 291 TGAGACAGCAGTAGA GCCTTAGCAGCTTCC CCAACCCCTATTACT In Set 34 one or more in Table 35, in a combination with a corresponding probe sequence: Table 35.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 34 NO NO NO ACGGTGGATATTGGG AGTATCTGCTAGATC TTTGTTAGAGCCAGA 1 AAAATGACTT 298 ACCTTCTGAGTTT 299 AACT 300 ACAGATGATTCTAAA GATATATTGTAGAAG CAGTCTGTACATTGA 2 TAAAGCCCTTTAAGC 301 GAACTTTTTTAATAA A A 303 A ATAGTACTGAAAACA ATA ACCATTTGTAATTAT CTCAGAGCATCCATG CCCAATGATAATTAT 3 TAAATCATCTCCATC 304 305 306 GGA ATAAATGTCACT TAGTTAAAACT
  • Primer Pair Set 35 comprises one or more the primer pairs shown in Table 36, in a combination with a corresponding probe sequence: Table 36.
  • Primer SEQ SEQ Pair Set 38 comprises one or more the primer pairs shown in Table 39, in a combination with a corresponding probe sequence: Table 39.
  • Primer Pair Set 39 comprises one or more the primer pairs shown in Table 40, in a combination with a corresponding probe sequence: Table 40.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 40 NO NO NO GGAATTTACCACCCA CAGCCCCGTACCTGC CCGACGAGTCGAGTT 1 CTTAGAGCT 352 TTTT 353 GT 354 CTGTTTGAGCGTGAT ACCTGATTTGAGGCG TTGCATTCACAAAAT 2 GTCTTCTC 355 ACAACAA 356 TAC 357 3 GCCCGGCCGAAACC 358 GGAAAGATGAAAAGC A CTTTGAAAAGAGA 359 CTGGGTGCAAGCCCT 360
  • Primer Pair Set 41 comprises one or more the primer pairs shown in Table 42, in a combination with a corresponding probe sequence: Table 42.
  • Primer Pair Set 42 comprises one or more the primer pairs shown in Table 43, in a combination with a corresponding probe sequence: Table 43.
  • Candida krusei Primers and Probes (5′ ⁇ 3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 42 NO NO NO GGTATCATGGTCCCA CTTCATCGATGTTGT CAGTGAAGAATCCAA 1 CCTACAAAAT 370 TGTTGGTTCTT 371 TTGC 372 CGTCCATAGTTGAAC GAATCGATGGACTGT CTCGGGTTTCACCAA 2 373 374 375 in Table 44, in a combination with a corresponding probe sequence: Table 44.
  • Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 43 NO NO NO NO GGGTCTACAATACTG AGAGAAGGATGAGAG CAAATACATCATTCA 1 GCAACAACTA 379 CCAGTCT 380 ATAGTTCTC 381 CAATGGCTCCAAGCG ACCACCGACGGTTCT ACTCCTCGTTCAATC 2 ACTAC 382 AAATCAAT 383 CT 384 CTCCAAGCGACTACA GTCACCACCGACGGT TCGAATCTGAAAGTG 3 TCGAGAAG TCTAAA 386 TAAAGAA 387
  • Primer Pair Set 44 comprises one or more the primer pairs shown in Table 45, in a combination with a corresponding probe sequence: Table 45.
  • the method or assay includes one or more control primers and probes.
  • the control is Primer Pair Set 45 that comprises one or more the primer pairs shown in Table 46, in a combination with a corresponding probe sequence for the detection of control sample: Table 46.
  • method or assay includes one or more control primers and probes.
  • control is Primer Pair Set 46 that comprises one or more the primer pairs shown in Table 47, in a combination with a corresponding probe sequence for the detection of control sample: Table 47.
  • Bacillus subtilis atrophaeus Primers and Probes (5′ ⁇ 3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 46 NO NO NO CATCGGTGAAGAAAG CGGGTGACTTCAAAG ACGGTCCCCAGGCAT
  • the method or assay includes one or more control plasmids that contains target sequences for one or more of the target organisms.
  • the control plasmid comprises one or more the sequences shown in Table 50.
  • control plasmid for each pathogen target can include the entire corresponding amplicon sequence in Table 50 or a portion of the amplicon sequence in Table 50.
  • the portion (i.e., number of base pairs) of the amplicon sequence can vary by pathogen target.
  • the control plasmid can be used with the primers and probes of Tables 2–45 as a positive control.
  • the method and/or assay comprises a panel comprising one or more primer pairs and one or more probes for the individual, simultaneous, or sequential detection of the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis
  • the method has one or more primer pairs and one or more probes for the detection of a control sample of Bacillus atrophaeus. In another aspect, the method has one or more primer pairs and one or more probes for the detection of a universal RNA Spike In/Reverse Transcription (Xeno) Control.
  • One embodiment described herein is an individual or multiplex panel for the individual, simultaneous, or sequential detection of the presence or absence of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas malt
  • the individual or multiplex panel comprises at least one forward primer, at least one reverse primer, and at least one probe for each organism as shown in Table 42. All primer pairs (forward primers and reverse primers), and the requisite probes are consecutively numbered in multiples of three, e.g., 1, 2, 3; ... ; 370, 371, 372, as forward primer; reverse primer; and probe, respectively.
  • a primer pair and probe set could include: a forward primer such as SEQ ID NO: 1, a reverse primer such as SEQ ID NO:2, and a probe such as SEQ ID NO: 3.
  • the individual or multiplex panel comprises controls, comprising at least one forward primer, at leat one reverse primer, and a probe for the Universal RNA Spike In/Reverse Transcription Control (Xeno) as shown in Table 46 or the control organsim Bacillus atrophaeus, as shown in Table 47.
  • An additional positive control is a multisequence plasmid comprising the sequences shown in Table 50. This plasmid can be used with the primers and probes of Tables 2–45 as an amplification positive control. Table 48.
  • Organism Forward Primer Reverse Primer Probe SEQ ID NO SEQ ID NO Acinetobacter baumannii 1, 4, 7 2, 5, 8 3, 6, 9 Bacteroides fragilis 10, Clostridium perfringens 19, Enterobacter cloacae 28, 31, 34 29, 32, 35 30, 33, 36 Enterococcus faecalis 37, 40, 43 38, 41, 44 39, 42, 45 Enterococus faecium 46, 49, 52 47, 50, 53 48, 51, 54 Escherichia coli 55, 58, 61 56, 59, 62 57, 60, 63 Klebsiella pneumoniae 64, 67, 70 65, 68, 71 66, 69, 72 Klebsiella Oxytoca 73, 76, 79 74, 77, 80 75, 78, 81 Klebsiella aerogenes 82, 85, 88 83,
  • the individual or multiplex panel comprises at least one forward primer, at least one reverse primer, and at least one probe for each organism as shown in Table 49.
  • the individual or multiplex panel comprises controls, comprising at least one forward primer, at leat one reverse primer, and a probe for the Universal RNA Spike In/Reverse Transcription Control (Xeno) as shown in Table 46 or the control organsim Bacillus atrophaeus, as shown in Table 47.
  • An additional positive control is a multisequence plasmid comprising the sequences shown in Table 50. This plasmid can be used with the primers and probes of Tables 2–45 as an amplification positive control. Table 49.
  • Organism Forward Primer Reverse Primer Probe SEQ ID NO SEQ ID NO Acinetobacter baumannii 1, 4, 7 2, 5, 8 3, 6, 9 Bacteroides fragilis 10, 13, 16 11, 14, 17 12, 15, 18 Clostridium perfringens 19, 22, 25 20, 23, 26 21, 24, 27 Enterobacter cloacae 28, 31, 34 29, 32, 35 30, 33, 36 Enterococcus faecalis 37, 40, 43 38, 41, 44 39, 42, 45 Enterococcus faecium 46, 49, 52 47, 50, 53 48, 51, 54 Escherichia coli 55, 58, 61 56, 59, 62 57, 60, 63 Klebsiella pneumoniae 64, 67, 70 65, 68, 71 66, 69, 72 Klebsiella Oxytoca 73, 76, 79 74, 77, 80 75, 78, 81 Kleb
  • the amplicons are shown in Table 50.
  • the amplicon for each pathogen target i.e., organism
  • the portion (i.e., number of base pairs) of the amplicon sequence can vary by pathogen target. Table 50.
  • DNA or RNA is extracted from one or more specimen/sample, reverse transcribed if required, multiplied using real-time amplification (or RT-PCR if required), and detected using specific primers and a fluorescent reporter dye probe for one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus angi
  • the specimen/sample may comprise any number of things, including, but not limited to, include samples, swabs, or tissue samples (for example, taken during a biopsy) obtained from human patients; research samples; purified samples, such as purified genomic DNA, RNA, proteins, etc.; and raw samples (bacteria, virus, genomic DNA, etc.).
  • any experimental manipulation can have been performed on the sample before analysis.
  • the specimen/sample type for diagnosis of wound pathogens is one or more swabs of a subject’s body or of a wound. If required, nucleic acid from the sample/specimen is isolated using known techniques.
  • the sample/specimen may be treated to lyse the cells, using known lysis buffers, sonication, electroporation, etc., with purification occurring as needed, as will be appreciated by those in the art.
  • the reactions outlined herein may be accomplished in a variety of ways, as will be appreciated by those in the art. Components of the reaction may be added simultaneously, or sequentially, in any order, with preferred embodiments outlined below.
  • the reaction may include a variety of other reagents that may be included in the assays.
  • reagents like salts, buffers, neutral proteins, e.g., albumin, detergents, etc., which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions.
  • Reagents that otherwise improve the efficiency of the assay such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may be used, depending on the sample/specimen preparation methods and purity of the target wound pathogens.
  • total nucleic acid extraction from a sample or a wound swab is performed. The specimen/sample may be collected and transported in the RemelTM Cary-Blair Transport Medium by Thermo Fisher Scientific according to appropriate laboratory procedures.
  • RemelTM Cary-Blair Transport Medium is a semisolid medium recommended for use in the collection, transportation, and preservation of sample/specimens, especially wound samples and wound swabs.
  • Nucleic acids may be isolated and purified from the specimen/sample using a nucleic acid isolation, such as, e.g., the MagMAXTM Microbiome Ultra Nucleic Acid Isolation Kit with Bead Plate (Thermo Fisher Scientific). Nucleic acid extraction may be performed via an automated process using, e.g., the KingfisherTM Flex Purification System.
  • RNA viruses the RNA is reverse transcribed into cDNA. The cDNA and genomic DNA (from DNA viruses) are then subjected for amplification using the currently disclosed composition, method, or kit.
  • the disclosed kit and method of detection may further include a process control (“process control” is herein referred to, interchangeably, as “control organism” or “control sample”).
  • process control is herein referred to, interchangeably, as “control organism” or “control sample”.
  • This is an exogenous control that has the added advantage of being a bacterial lysis control in addition to being a nucleic acid extraction and recovery control.
  • Controls are treated and tested in parallel with target pathogen and are used to generate a predetermined expected result. When the expected result is reported, one or more aspects of the diagnostic test are confirmed to be working as intended, enabling the user of to verify the diagnostic test as valid.
  • the process control may be Bacillus atrophaeus, which is a gram- positive, endospore forming bacterium.
  • the process control can function as a positive control for lysis, purification and amplification within the cartridges described herein.
  • One exemplified process control is lyophilized Bacillus atrophaeus, such as, e.g., the TaqManTM Universal Extraction Control Organism by Thermo Fisher Scientific.
  • the process control may be supplied lyophilized in a quantity of 1 ⁇ 10 9 copies/vial, and reconstituted in 200 ⁇ L of 1 ⁇ PBS, pH 7.4 to a final concentration 5 ⁇ 10 6 copies/ ⁇ L.
  • 10 ⁇ L of the process control is processed as a stand-alone sample in a background of universal transport media.
  • the process control can be added to a negative extraction control.
  • the process control may be added to one or more samples/specimens at the start of the extraction process.
  • the process control is carried through the remainder of the workflow with the samples/specimens. It is recommended that at least one stand-alone control sample is run per extraction plate.
  • Another exemplified process control is a bacterial spore, such as a spore of a Bacillus species. Suitable spores can be comprised of any species of Bacillus, including, e.g., Bacillus globigii, Bacillus atrophaeus, Bacillus subtilis, or Bacillus stearothermophilus.
  • the process control may be a Bacillus atrophaeus bacterial spore.
  • vicinal oxygen chelate (VOC) genes (accession number cll463) of Bacillus atrophaeus are detected as a process control.
  • VOC vicinal oxygen chelate
  • Another exemplified process control is the TaqMan® Universal RNA Spike In/Reverse Transcription (Xeno) Control is an exogenous process control for nucleic acid isolation, reverse transcription, and preamplification.
  • the control can also be used as an internal positive control for real-time PCR.
  • the control is used with the proprietary TaqMan® assay for XenoTM sequences.
  • Positive Control the disclosed method of detection may further include a positive control to determine the validity of the assay.
  • the positive control is a mixture of plasmids of the target pathogens.
  • an exemplified positive control is a mixture of plasmids containing sequences for one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas, St
  • reaction mixture refers to a mixture of components necessary to amplify at least one amplicon from nucleic acid templates.
  • the mixture may comprise nucleotides (dNTPs, such as A, C, G, and T), a thermostable polymerase, primers, and a plurality of nucleic acid templates.
  • dNTPs nucleotides
  • the mixture may further comprise a buffer.
  • buffer refers a solution that can include multiple components such buffers that maintain a specific pH (e.g., Tris ⁇ HCl), mono and divalent salts (e.g., NaCl, KCl, (NH 4 ) 2 SO 4 , MgCl 2 , MgSO 4 ), cofactors, detergents (e.g., Polysorbate 20 (TweenTM 20), t-octylphenoxy polyethoxyethanol (TritonTM X-100), octylphenoxy polyethoxyethanol (NonidetTM P-40)), and other additives (e.g., glycerol, polyethylene glycol, betaine, formamide, dimethyl sulfoxide, dithiothreitol, tetramethylammonium chloride, bovine serum albumin, gelatin, inter alia), The working concentration range of each component is known in the art and can be optimized as needed.
  • a specific pH e.g., Tris ⁇ HCl
  • An exemplary PCR reaction mixture comprises: 50 fg to 50 ng of target DNA; 0.1–1 ⁇ M of each primer and probe; 1–2 units of Taq DNA polymerase; 0.2 mM of each dNTP; 20 mM Tris ⁇ HCl (pH 8.4), 50 mM KCl, 1.5 mM MgCl 2 , and water to the requisite volume.
  • the PCR mixture is dispensed into a PCR microtube, port or reservoir (e.g., of a TaqManTM Array Card) or plate (e.g., wells of a TaqManTM OpenArray sample plate), the mixture is mixted by vortexing, and either capped, sealed, or overlayed with mineral oil or silicone oil to prevent evaporation.
  • Amplification “Amplification” as used herein refers to the use of any amplification procedures to increase the concentration of a particular nucleic acid sequence within a mixture of nucleic acid sequences.
  • a sequence from a sample is amplified to produce a secondary target (e.g., an amplicon) that is detected, as outlined herein.
  • Amplification involves the amplification (replication) of the sequence to be detected, such that the number of copies of the sequence is increased.
  • Suitable amplification techniques include, but are not limited to, the polymerase chain reaction (PCR), strand displacement amplification (SDA), transcription mediated amplification (TMA) and nucleic acid sequence-based amplification (NASBA).
  • the amplification technique is PCR.
  • the polymerase chain reaction (PCR) is well known and involves the use of primer extension combined with thermal cycling to amplify a target sequence.
  • PCR refers to either single-plex (i.e., individual) or multiplex PCR assays, and can be real time or quantitative PCR (wherein detection occurs during amplification), end-point PCR (when detection occurs at the end amplification), or reverse transcription PCR, including but not limited to, “real-time PCR” or “quantitative PCR” or “qPCR”, “digital PCR” or “dPCR”, “reverse transcriptase PCR” or “RT-PCR”, “multiplex PCR”, “nested PCR”, “hot start PCR”, “long-range PCR”, “assembly PCR”, “asymmetric PCR”, “in situ PCR,” “single-cell PCR,” or “fast-cycling PCR,” among others.
  • An exemplary PCR amplification typically consists of 25–35 cycles of: a denaturing step a 94 °C for 30–45 seconds; an annealing step at 55 °C for 20–60 seconds; and an extension step at 72 °C for 30–90 seconds.
  • the amplification may be preceded by an initial denaturation step at 94 °C for 2–3 minutes.
  • the amplification may be followed by a final extension step at 72 °C for 10 min, and then cooled to 4 °C and maintained at this temperature until the samples are removed from the thermocycler.
  • Example embodiments of amplification are not limited to PCR.
  • amplification can include OLA followed by RCA.
  • SBE single base extension
  • OLA oligonucleotide ligation amplification
  • rolling-circle amplification can be used for amplification.
  • amplification can include OLA followed by RCA.
  • Exemplary systems include a real-time quantitative PCR (qPCR) instrument, including for example a QuantStudioTM Real-Time PCR system, such as the QuantStudioTM5 Real-Time PCR System (QS5), QuantStudioTM 7 Real-Time PCR System (QS7), QuantStudioTM 12K Flex System (QS12K), QuantStudioTM DX Real-Time PCR System (QS Dx or QS5 Dx), or a 7500 Real-Time PCR system, such as the 7500 Fast Dx system, all from Applied BiosystemsTM – a Thermo Fisher Scientific brand.
  • qPCR real-time quantitative PCR
  • amplified product or “amplicon” refer to a fragment of DNA amplified by a polymerase using a pair of primers in an amplification method such as PCR.
  • Probe “Probe” as used herein, is a non-extendable oligonucleotide attached to a fluorescent reporter dye and a quencher moiety.
  • Primer “Primer” as used herein can refer to more than one primer and refers to an oligonucleotide, whether occurring naturally or produced synthetically, which is capable of acting as an initiation- point for primer extension synthesis when placed under conditions that produce a primer extension product which is complementary to a nucleic acid strand, e.g., in the presence of nucleotides and an agent for polymerization such as DNA polymerase, at a suitable temperature for a sufficient amount of time and in the presence of a buffering agent.
  • Such conditions can include, for example, the presence of at least four different deoxyribonucleoside triphosphates (such as A, C, G, and T) and a polymerization-inducing agent such as DNA polymerase or reverse transcriptase, in a suitable buffer, and at a suitable temperature.
  • the primer may be single-stranded for maximum efficiency in amplification.
  • the primers herein are selected to be substantially complementary to the different strands of each specific sequence to be amplified. This means that the primers must be sufficiently complementary to hybridize with their respective strands.
  • a non-complementary nucleotide fragment may be attached to the 5′-end of the primer, with the remainder of the primer sequence being complementary, or partially complementary, to the target region of the target nucleic acid.
  • the primers are complementary, except when non-complementary nucleotides may be present at a predetermined sequence location, such as a primer terminus as described.
  • the complement of a nucleic acid sequence as used herein refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5′-end of one sequence is paired with the 3′-end of the other, is in “antiparallel association.” Complementarity need not be perfect; stable duplexes may contain mismatched base pairs or unmatched bases.
  • each fluorescent or detectable label may further comprise a dye, fluorescent label, or other detectable label. It should be appreciated that when using multiple fluorescent or detectable labels, particularly in an individual or multiplex format, each fluorescent or detectable label preferably differs in its spectral properties from the other detectable labels used therewith such that the labels may be distinguished from each other, or such that together the fluorescent or detectable labels emit a signal that is not emitted by either fluorescent or detectable label alone.
  • Exemplary fluorescent or detectable labels include, for instance, a fluorescent dye or fluorophore (e.g., a chemical group that can be excited by light to emit fluorescence or phosphorescence), “acceptor dyes” capable of quenching a fluorescent signal from a fluorescent donor dye, and the like, as described above.
  • a fluorescent dye or fluorophore e.g., a chemical group that can be excited by light to emit fluorescence or phosphorescence
  • acceptor dyes capable of quenching a fluorescent signal from a fluorescent donor dye, and the like, as described above.
  • Suitable fluorescent or detectable labels may include, for example, fluoresceins (e.g., 5-carboxy-2,7-dichlorofluorescein; 5-carboxyfluorescein (5-FAM); 5-hydroxy tryptamine (5-HAT); 6-JOE; 6-carboxyfluorescein (6-FAM); Mustang Purple, VIC, ABY, JUN; FITC; 6-carboxy-4′,5′-dichloro-2′,7′-dimethoxy-fluorescein (JOE)); 6-carboxy-1,4-dichloro-2′,7′- dichloro-fluorescein (TET); 6-carboxy-1,4-dichloro-2′,4′,5′,7′-tetra-chlorofluorescein (HEX); Alexa Fluor fluorophores (e.g., 350, 405, 430, 488, 500, 514, 532, 546, 555, 568, 594, 610, 633, 635
  • Exemplary fluorescent labels include but are not limited to FAM, VIC, ABY, JUN, AF647, or 6FAM.
  • the fluorescent labels include FAM, VIC, ABY, JUN, or AF647; or 6FAM, VIC, ABY, JUN, or FAM.
  • the fluorescent labels include FAM, HEX (JOE/VIC), Texas Red, and Cy5 dyes.
  • the probes are labeled with FAM.
  • Other detectable labels may be used in addition to or as an alternative to labelled probes.
  • primers can be labeled and used to both generate amplicons and to detect the presence (or concentration) of amplicons generated in the reaction, and such may be used in addition to or as an alternative to labeled probes described herein.
  • primers may be labeled and utilized as described in Nazarenko et al., Nucleic Acids Res. 30(9): e37 (2002), Hayashi et al., Nucleic Acids Res.17(9): 3605 (1989), and/or Neilan et al., Nucleic Acids Res.25(14): 2938-2939 (1997).
  • the primers and/or probes may further comprise a quencher.
  • Suitable quenchers include but are not limited to QSY (e.g., QSY7 and QSY21), BHQ (Black Hole Quencher) and DFQ (Dark Fluorescent Quencher).
  • the quencher is QSY7.
  • Detector probes may also include two probes, wherein, for example, a fluorophore is associated with one probe and a quencher is associated with a complementary probe such that hybridization of the two probes on a target quenches the fluorescent signal or hybridization on the target alters the signal signature via a change in fluorescence.
  • Detector probes may also include sulfonate derivatives of fluorescein dyes with SO3 instead of the carboxylate group, phosphoramidite forms of fluorescein, phosphoramidite forms of Cy5. Any of these systems and detectable labels, as well as many others, may be used to detect amplified target nucleic acids.
  • intercalating labels can be used such as ethidium bromide, SYBR Green I, SYBR GreenER, and PicoGreen (all products of Applied Biosystems – a brand of Thermo Fisher Scientific), thereby allowing visualization in real- time, or end point, of an amplification product in the absence of a detector probe.
  • real-time visualization may include both an intercalating detector probe and a sequence-based detector probe.
  • the detector probe is at least partially quenched when not hybridized to a complementary sequence in the amplification reaction and is at least partially unquenched when hybridized to a complementary sequence in the amplification reaction.
  • probes may further comprise various modifications such as a minor groove binder (MGB) to further provide desirable thermodynamic characteristics.
  • MGB minor groove binder
  • the amplicon is labeled by incorporation of, or hybridization to labeled primer.
  • the amplicon is labeled by hybridization to a labeled probe.
  • the amplicon is labeled by binding of a DNA-binding dye.
  • the dye may be a single-strand DNA binding dye.
  • the dye may be a double-stranded DNA binding dye.
  • the amplicon is labeled via polymerization or incorporation of labeled nucleotides in a template-dependent (or template- independent) polymerization reaction.
  • the labeled nucleotide can be added after amplifying is completed.
  • the labeled amplicon (or labeled derivative thereof) can be detected using any suitable method such as, for example, electrophoresis, hybridization-based detection (e.g., microarray, molecular beacons, and the like), chromatography, NMR, and the like.
  • the labeled amplicon is detected using qPCR.
  • a plurality of different amplicons is formed, and optionally labeled, within a single reaction volume via a single amplification reaction.
  • a multiplex reaction carried out in a single tube or reaction vessel (e.g., “single-tube” or” I-tube” or “single-vessel” reaction) can produce a plurality of amplicons that are labeled.
  • the plurality of amplicons can be differentially labeled.
  • each of the plurality of amplicons produced during amplification is labeled with a different label.
  • Assay Mixture The terms “assay mixture” or “assay mix” or “assay composition,” as used herein, include mixture containing the primer-probe pairs described above that are used in PCR.
  • the method includes: (i) contacting a sample comprising one or more target nucleic acid molecules with (a) at least one probe, such as those described herein, being sequence specific for the target nucleic acid molecule, where the at least one probe undergoes a detectable change in fluorescence upon amplification of the one or more target nucleic acid molecules; and with (b) at least one oligonucleotide primer pair; (ii) incubating the mixture of step (i) with a DNA polymerase under conditions sufficient to amplify one or more target nucleic acid molecules; and (iii) detecting the presence or absence or quantifying the amount of the amplified target nucleic acid molecules by measuring fluorescence of the probe.
  • PCR polymerase chain reaction
  • qPCR quantitative real-time polymerase chain reaction
  • the DNA polymerase comprises 5′-exonuclease activity.
  • the DNA polymerase is a Thermus aquaticus (Taq) DNA polymerase.
  • the probe is a hydrolysis probe, such as a TaqManTM probe.
  • kit for PCR such as quantitative real-time polymerase chain reaction (qPCR) and reverse transcription polymerase chain reaction (RT-PCR).
  • qPCR quantitative real-time polymerase chain reaction
  • RT-PCR reverse transcription polymerase chain reaction
  • the kit includes the assay mixture, the process control, and the positive control each described above, as well as an individual or multiplex master mix.
  • the multiplex master mix is a RT-qPCR mix that provides for sensitive, reproducible detection of a plurality of different target pathogens in a single multiplex reaction.
  • the individual master mix provides for sensitive, reproducible detection of a single target pathogen.
  • the individual or multiplex master mix may include an enzyme (for instance, DNA polymerase), a thermostable enzyme, enzyme cofactors, deoxynucleotide triphosphates (dNTPs) including dUTP, an enzyme inhibitor (for instance, RNase inhibitor), a dye and/or a buffer agent.
  • the individual or multiplex master mix can be, for instance, TaqPathTM 1-step Multiplex Master Mix by Applied Biosystems – a brand of Thermo Fisher Scientific.
  • the master mix may be concentrated.
  • the master mix may be provided at a 4 ⁇ concentration.
  • the master mix is prepared such that it requires less than a 3 ⁇ dilution prior to use in PCR, e.g., 2 ⁇ dilution, 1.5 ⁇ dilution, 1.2 ⁇ dilution, etc.
  • the kit also includes instructions for conducting the PCR, and one or more of the following: a buffering agent, deoxynucleotide triphosphates (dNTPs), an organic solvent, an enzyme, enzyme cofactors, and an enzyme inhibitor.
  • the kit for PCR comprises the described dye and/or quencher moiety, instructions for conjugating or labeling the dye and/or quencher moiety to a biomolecule, such as an oligonucleotide, instructions for conducting the PCR, and one or more of the following: a buffering agent, deoxynucleotide triphosphates (dNTPs), an organic solvent, an enzyme, enzyme cofactors, and an enzyme inhibitor.
  • the systems, compositions, methods, and devices used for nucleic acid amplification comprise a “point-of-service” (POS) system.
  • samples may be collected and/or analyzed at a “point-of-care” (POC) location.
  • POC point-of-care
  • analysis at a POC location typically does not require specialized equipment and has rapid and easy-to-read visual results.
  • analysis can be performed in the field, in a home setting, and/or by a lay person not having specialized skills.
  • the analysis of a small-volume clinical sample may be completed using a POS system in a short period of time (e.g., within hours or minutes).
  • a POS system is utilized at a location that is capable of providing a service (e.g., testing, monitoring, treatment, diagnosis, guidance, sample collection, verification of identity (ID verification), and other services) at or near the site or location of the subject.
  • a service may be a medical service, or it may be a non-medical service.
  • a POS system provides a service at a predetermined location, such as a subject’s home, school, or work, or at a grocery store, a drug store, a community center, a clinic, a doctor’s office, a hospital, an outdoor triage tent, a makeshift hospital, a border check point, etc.
  • a POS system can include one or more point of service devices, such as a portable virus/pathogen detector.
  • a POS system is a point of care system.
  • the POS system is suitable for use by non-specialized workers or personnel, such as nurses, police officers, civilian volunteers, or the patient.
  • a POC system is utilized at a location at which medical-related care (e.g., treatment, testing, monitoring, diagnosis, counseling, etc.) is provided.
  • a POC may be, e.g., at a subject’s home, work, or school, or at a grocery store, a community center, a drug store, a doctor’s office, a clinic, a hospital, an outdoor triage tent, a makeshift hospital, a border check point, etc.
  • a POC system is a system which may aid in, or may be used in, providing such medical-related care, and may be located at or near the site or location of the subject or the subject’s health care provider (e.g., subject’s home, work, or school, or at a grocery store, a community center, a drug store, a doctor’s office, a clinic, a hospital, etc.).
  • a POS system is configured to accept a clinical sample obtained from a subject at the associated POS location. In embodiments, a POS system is further configured to analyze the clinical sample at the POS location. In embodiments, the clinical sample is a small volume clinical sample. In embodiments, the clinical sample is analyzed in a short period of time. In embodiments, the short period of time is determined with respect to the time at which sample analysis began. In embodiments, the short period of time is determined with respect to the time at which the sample was inserted into a device for the analysis of the sample. In embodiments, the short period of time is determined with respect to the time at which the sample was obtained from the subject.
  • a POS system or a POC system can include the amplification- based methods, compositions and kits disclosed herein, including any of the described assays and/or assay panels. Such assays are contemplated for use with both thermal cycling amplification workflows and protocols, such as in PCR, as well as isothermal amplification workflows and protocols, such as in LAMP.
  • a POS or a POC system comprises self-collection of a biological sample.
  • the self-collection may comprise the use of a self-collection kit and/or device, such as a swab or a tube.
  • the self-collection kit comprises instructions for use, including collection instructions, sample preparation or storage instructions, and/or shipping instructions.
  • the self-collection kit and/or device may be used by an individual, such as lay person, not having specialized skills or medical expertise.
  • self-collection may be performed by the patient themselves or by any other individual in proximity to the patient, such as but not limited to a parent, a care giver, a teacher, a friend, or other family member.
  • the nucleic acid amplification protocol can be configured for rapid processing (e.g., in less than about 45 minutes) and high throughput, allowing for a minimally invasive method to quickly screen large numbers of individuals in a scalable way.
  • the disclosed embodiments can also beneficially provide a lower cost sample collection system and method that enables self-collection (reducing health care professional staffing needs) using a low-cost collection device. This eliminates the requirements for swabs, buffers, virus transmission media (or other specialized transport medium), and the like.
  • the disclosed embodiments also allow for a reduction in Personal Protective Equipment (PPE) requirements and costs. There is also a beneficial reduced dependence on supply-constrained items, and the compatibility of these methods and kit components with existing equipment improves the flexibility and simplicity of their implementation to the masses.
  • PPE Personal Protective Equipment
  • compositions, formulations, methods, processes, and applications described herein can be made without departing from the scope of any embodiments or aspects thereof.
  • the compositions and methods provided are exemplary and are not intended to limit the scope of any of the specified embodiments. All of the various embodiments, aspects, and options disclosed herein can be combined in any variations or iterations.
  • the scope of the compositions, formulations, methods, and processes described herein include all actual or potential combinations of embodiments, aspects, options, examples, and preferences herein described.
  • compositions and formulations described herein may omit any component, substitute any component disclosed herein, or include any component disclosed elsewhere herein.
  • the ratios of the mass of any component of any of the compositions or formulations disclosed herein to the mass of any other component in the formulation or to the total mass of the other components in the formulation are hereby disclosed as if they were expressly disclosed. Should the meaning of any terms in any of the patents or publications incorporated by reference conflict with the meaning of the terms used in this disclosure, the meanings of the terms or phrases in this disclosure are controlling. Furthermore, the foregoing discussion discloses and describes merely exemplary embodiments. All patents and publications cited herein are incorporated by reference herein for the specific teachings thereof.
  • Clause 1 A method for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis,
  • Primer Pair Sets comprise the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus f
  • Clause 3 The method of clause 1 or 2, wherein the generating of the at least one amplicon comprises performing PCR.
  • Clause 4 The method of any one of clauses 1–3, wherein the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii produced using at least one primer pair selected from SEQ ID NO: 1–2, 4–5, or 7–8, and a sequence comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis produced using at least one primer pair selected from SEQ ID NO: 10–11, 13–14, or 16–17, and a sequence comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens produced using at least one primer pair selected from SEQ ID NO: 19–20, 22–23, or 25–26, and a sequence comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae produced using at
  • the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae
  • Clause 6 The method any one of clauses 1–5, wherein the reaction mixture further comprises probes specific for the at least one amplicon.
  • Clause 7. The method of any one of clauses 1–6, wherein the reaction mixture further comprises probes specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probes comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia
  • Clause 8 The method of any one of clauses 1–7, wherein the reaction mixture further contains a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample.
  • the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426.
  • the probe comprises a fluorescent reporter.
  • Clause 11 The method of clause 10, wherein the probe comprises a quencher.
  • Clause 12 The method of clause 10 or 11, wherein the probe is labeled at or near the 5′–end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM.
  • Clause 13 The method of any one of clauses 10–12, wherein the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ.
  • Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8;
  • Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17;
  • Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26;
  • Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35;
  • Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44;
  • Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus fa
  • Clause 16 The composition of clause 14 or 15, further comprising a probe specific for the at least one amplicon produced using the at least one primer pair selected from one or more of Primer Pair Sets 1–44.
  • Clause 17 The composition of any one of clauses 14–16, further comprising a probe specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probe comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or
  • Clause 18 The composition of any one of clauses 14–17, further comprising a polymerase, a buffer, and deoxynucleotide triphosphates (dNTPs). Clause 19. The composition of any one of clauses 14–18, further comprising a sample. Clause 20. The composition of any one of clauses 14–19, further comprising at least one control forward and reverse primer and, optionally, a control probe, that specifically amplifies a target nucleic acid of a control sample. Clause 21.
  • control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412– 413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426.
  • Clause 22 The composition of any one of clauses 14–21, wherein the probe contains a fluorescent reporter.
  • Clause 23. The composition of clause 22, wherein the probe contains a quencher.
  • a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM.
  • Clause 25 The composition of any one of clauses 22–24, wherein the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ.
  • kit further comprises probes suitable for use with specific forward and reverse primer pairs, the probes comprising one or more of: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella pneumoniae selected
  • kits of clause 28 wherein the kit further comprises a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample.
  • the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426.
  • kit further comprises a control plasmid comprising one or more target sequences selected from Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas malt
  • Example 1 Sample Preparation A sample is obtained from a subject.
  • the sample can be a swab or sample of a wound.
  • For wound samples approximately 100 mg of sample is used to isolate genomic DNA.
  • Samples can be frozen in a storage solution at a sample to solution ratio of 1:2. Frozen samples are thawed on ice and approximately 100 mg of the sample are used to isolate nucleic acids. The frozen or samples are lysed, and genomic DNA is isolated from the lysis.
  • Example 2 Control Sample Preparation The TaqManTM Universal Extraction Control Organism (B. atrophaeus) (BA process control) was used to verify the efficacy of the sample preparation and the absence of inhibitors in the real-time PCR reaction. A 1 ⁇ solution of the control was added to each sample and negative control before extraction. The BA process control was contained a lyophilized pellet at 1 ⁇ 10 9 copies/vial.
  • a 25 ⁇ stock solution of the BA process control was prepared by adding 200 ⁇ L of 1 ⁇ phosphate buffered saline (1 ⁇ PBS: 137 mM NaCl, 2.7 mM KCl: 10 mM Na 2 HPO 4 , 1.8 mM KH 2 PO 4 , pH 7.4) to the vial containing the lyophilized pellet and vortexed until the pellet was resuspended.
  • a working 1 ⁇ stock solution was prepared by combining 24 ⁇ L of a 25 ⁇ stock solution with 576 ⁇ L 1 ⁇ PBS, pH 7.4 to achieve a total volume of 600 ⁇ L.
  • the prepared BA process control was added to the genomic DNA extraction reaction, to each sample and to the negative extraction control immediately before lysis during nucleic acid extraction.
  • Genomic DNA samples were thawed or placed on ice. All reagents were gently vortexed, briefly centrifuged to collect the liquid at the bottom of the container and kept on ice until use.
  • the amplification control was prepared by combining 495.0 ⁇ L of 1 ⁇ TE buffer (1 ⁇ TE: 10 mM Tris ⁇ HCl, 1 mM EDTA ⁇ Na 2 , pH 8.0) into a microcentrifuge tube, and adding 5.0 ⁇ L of the amplification control. The sample was mixed well and briefly centrifuged. A 5.0 ⁇ L aliquot of the diluted sample was combined with 170 ⁇ L of 1 ⁇ TE buffer, mixed, and centrifuged briefly.
  • PCR Individual or Multiplex Master Mix and Primer/Probes Component Volume per sample or Volume for n samples plus control 2 controls Master 6.25 ⁇ L 6.25 ⁇ (1.2 ⁇ n) ⁇ L 1.25 ⁇ L 1.25 ⁇ (1.2 ⁇ n) ⁇ L Total Volume 7.50 ⁇ L —
  • the Master Mix contained components for the PCR reaction (buffer, MgCl 2 , dNTPs, and DNA polymerase, inter alia) and the individual or multiplex Primer/Probe Panel contained the primer pairs and probes specific for the target organisms and controls.
  • the reaction plate was set up by dispensing 7.5 ⁇ L of the reaction mix prepared as shown in Table 51 to each well of a MicroAmpTM Optical 96-Well Reaction Plate, 0.2 mL. 17.5 ⁇ L of either the extracted materials (target DNA), the diluted amplification control, or nuclease- free water was added to the designated wells.
  • the plate was sealed thoroughly with MicroAmpTM Optical Adhesive Film, ensuring that pressure was applied across the entire plate and that there was a tight seal across every individual well.
  • the plate was vortexed at the highest setting speed for 30–60 seconds as follows: 5–10 seconds in the center of the plate, 5–10 seconds in each plate corner, and 5–10 seconds, again in the center.
  • the reaction plate was centrifuged for 1–2 minutes at ⁇ 650 ⁇ g to remove bubbles and to collect the liquid at the bottom.
  • the real-time PCR reaction plate is maintained at 2–8 °C and protected from light until it was loaded into the real-time PCR instrument.
  • the real-time PCR reaction was run within an hour after preparation of the plate.
  • the real-time PCR reaction was performed, and the results were analyzed using the software accompanying the instrument.
  • Example 3 Real-Time TaqManTM PCR with Open Array
  • the nucleic acid samples were diluted 1:10.
  • An OpenArrayTM plate was allowed to equilibrate to room temperature. Before preparing the samples, the TaqManTM OpenArrayTM Real-time PCR Master Mix was mixed but not inverted.
  • the master mix and samples were added to the wells of the OpenArrayTM Plate in a 1:1 ratio of master mix-to-pre-amplified nucleic acid.
  • the TaqManTM Amplification Control was used in place of the diluted pre-amplified nucleic acid sample.
  • the resulting mixtures were further mixed with pipetting. After mixing, the plate was sealed with aluminum foil and centrifuged at 1,200 RPM (301 ⁇ g) for 1 minute.
  • the OpenArrayTM plate is transferred to an OpenArrayTM AccuFillTM Instrument where a fraction of the samples were loaded onto a separate OpenArrayTM plate.
  • the new OpenArrayTM plate was transferred to a QuantStudioTM 12K Flex OpenArrayTM Plate Press where the plate was encased with a lid.
  • OpenArrayTM Immersion Fluid was slowly injected into the port of the encasement to minimize formation of air bubbles. After injection of the immersion fluid, the port was sealed. The encased OpenArrayTM plate was transferred to a QuantStudioTM 12K Flex Instrument where the real-time PCR reaction is performed, imaged, and analyzed. Table 52. Open Array Platform Assay Efficiency Target Name R 2 Slope Efficiency (%) A. baumannii 0.99 ⁇ 3.39 97 B. atrophaeus 0.99 ⁇ 3.42 96 B. fragilis 0.99 ⁇ 3.39 97 C. striatum 0.99 ⁇ 3.53 92 K. aerogenes 0.99 ⁇ 3.43 96 E. coli 0.99 ⁇ 3.38 98 E.
  • positive amplification control samples were added to the TaqManTM Array Card by preparing a sample containing 10 ⁇ L of TaqManTM of Amplification Control, 40 ⁇ L of nuclease free water, and 50 ⁇ L of TaqManTM Fast Advanced Master Mix for each designated control port. After the samples were added to TaqManTM Array Card, the card was centrifuged twice at 1,200 RPM (301 ⁇ g) for 1 minute. The TaqManTM Array Card was sealed and loaded into a real-time PCR instrument. Inside the instrument, the samples were activated by heating the sample to 95 °C for 10 minutes.
  • amplification was performed by holding the temperature at 95 °C for 3 seconds to allow for separation of the templates into single strands followed by reducing the temperature to 60 °C and holding the temperature for 30 second to allow for annealing and elongation. The cycling between the two temperatures is repeated 40 times.
  • the results of the real-time TaqManTM PCR reaction were analyzed using the software accompanying the instrument. The results indicate the multiplex wound pathogen detection research workflow is highly sensitive to target with a wide linear dynamic range when compared to typical culture results. Accuracy of detection with pre-determined research samples across a wide range of wound pathogens was highly comparable to a commercially available method.

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Abstract

Described herein are compositions, methods, and kits for detecting wound pathogens. One embodiment described herein is primer pairs and probes for individual, simultaneous, or sequential multiplex polymerase chain reaction (PCR) based assays for the detection of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis.

Description

PANEL FOR DETECTING WOUND PATHOGENS CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Patent Application No.63/633,339 filed on April 12, 2024, which is incorporated by reference herein in its entirety. REFERENCE TO SEQUENCE LISTING This application was filed with a Sequence Listing XML in ST.26 XML format accordance with 37 C.F.R. § 1.831. The Sequence Listing XML file submitted in the USPTO Patent Center, “215686-0159-WO01_sequence_listing_xml_27-MAR-2025.xml,” was created on 27 MAR 2025, contains 470 sequences, has a file size of 412 kilobytes (421,888 bytes), and is incorporated by reference in its entirety into the specification. BACKGROUND Wound care is a major clinical challenge. Healing and chronic non-healing wounds are associated with a number of biological tissue changes including inflammation, proliferation, remodeling of connective tissues and a common major concern, bacterial infection. A proportion of wound infections are not clinically apparent and contribute to the growing economic burden associated with wound care, especially in the aging population. Currently, the gold-standard wound assessment includes direct visual inspection of the wound site under white light combined with indiscriminate collection of bacterial swabs and tissue biopsies resulting in delayed, costly, and often insensitive bacteriological results. This may affect the timing and effectiveness of treatment. Early recognition of wound pathogens may guide the detection and effectiveness of therapeutic intervention, thus reducing both morbidity and mortality while improving clinical outcomes related to wounds. Accordingly, there is a need to detect wound pathogens. The need is solved by the assays and methods described herein that detect the presence or absence of one or more of wound pathogens in individual or multiplex qPCR assays. SUMMARY One embodiment described herein is a method for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample, the method comprising the steps of: (a) creating a reaction mixture containing the sample and one or more Primer Pair Sets, wherein the Primer Pair Sets comprise one or more of: at least one primer pair selected from Primer Pair Set 1 that specifically amplifies a portion of Acinetobacter baumannii genome; at least one primer pair selected from Primer Pair Set 2 that specifically amplifies a portion of Bacteroides fragilis genome; at least one primer pair selected from Primer Pair Set 3 that specifically amplifies a portion of Clostridium perfringens genome; at least one primer pair selected from Primer Pair Set 4 that specifically amplifies a portion of Enterobacter cloacae genome; at least one primer pair selected from Primer Pair Set 5 that specifically amplifies a portion of Enterococcus faecalis genome; at least one primer pair selected from Primer Pair Set 6 that specifically amplifies a portion of Enterococcus faecium genome; at least one primer pair selected from Primer Pair Set 7 that specifically amplifies a portion of Escherichia coli genome; at least one primer pair selected from Primer Pair Set 8 that specifically amplifies a portion of Klebsiella pneumoniae genome; at least one primer pair selected from Primer Pair Set 9 that specifically amplifies a portion of Klebsiella oxytoca genome; at least one primer pair selected from Primer Pair Set 10 that specifically amplifies a portion of Klebsiella aerogenes genome; at least one primer pair selected from Primer Pair Set 11 that specifically amplifies a portion of Proteus mirabilis genome; at least one primer pair selected from Primer Pair Set 12 that specifically amplifies a portion of Proteus vulgaris genome; at least one primer pair selected from Primer Pair Set 13 that specifically amplifies a portion of Pseudomonas aeruginosa genome; at least one primer pair selected from Primer Pair Set 14 that specifically amplifies a portion of Serratia marcescens genome; at least one primer pair selected from Primer Pair Set 15 that specifically amplifies a portion of Staphylococcus aureus genome; at least one primer pair selected from Primer Pair Set 16 that specifically amplifies a portion of Streptococcus agalactiae genome; at least one primer pair selected from Primer Pair Set 17 that specifically amplifies a portion of Streptococcus dysgalactiae genome; at least one primer pair selected from Primer Pair Set 18 that specifically amplifies a portion of Streptococcus anginosus genome; at least one primer pair selected from Primer Pair Set 19 that specifically amplifies a portion of Streptococcus pyogenes genome; at least one primer pair selected from Primer Pair Set 20 that specifically amplifies a portion of Staphylococcus lugdunensis genome; at least one primer pair selected from Primer Pair Set 21 that specifically amplifies a portion of Providencia stuartii genome; at least one primer pair selected from Primer Pair Set 22 that specifically amplifies a portion of Stenotrophomonas maltophilia genome; at least one primer pair selected from Primer Pair Set 23 that specifically amplifies a portion of Morganella morganii genome; at least one primer pair selected from Primer Pair Set 24 that specifically amplifies a portion of Citrobacter koseri genome; at least one primer pair selected from Primer Pair Set 25 that specifically amplifies a portion of Citrobacter freundii genome; at least one primer pair selected from Primer Pair Set 26 that specifically amplifies a portion of Citrobacter braakii genome; at least one primer pair selected from Primer Pair Set 27 that specifically amplifies a portion of Peptoniphilus asaccharolyticus genome; at least one primer pair selected from Primer Pair Set 28 that specifically amplifies a portion of Peptoniphilus harei genome; at least one primer pair selected from Primer Pair Set 29 that specifically amplifies a portion of Peptoniphilus ivorii genome; at least one primer pair selected from Primer Pair Set 30 that specifically amplifies a portion of Peptostreptococcus anaerobius genome; at least one primer pair selected from Primer Pair Set 31 that specifically amplifies a portion of Finegoldia magna genome; at least one primer pair selected from Primer Pair Set 32 that specifically amplifies a portion of Clostridium septicum genome; at least one primer pair selected from Primer Pair Set 33 that specifically amplifies a portion of Paeniclostridium sordellii (Clostridium sordellii) genome; at least one primer pair selected from Primer Pair Set 34 that specifically amplifies a portion of Clostridium novyi A, B genome; at least one primer pair selected from Primer Pair Set 35 that specifically amplifies a portion of Clostridium histolyticum genome; at least one primer pair selected from Primer Pair Set 36 that specifically amplifies a portion of Staphylococcus epidermidis genome; at least one primer pair selected from Primer Pair Set 37 that specifically amplifies a portion of Staphylococcus haemolyticus genome; at least one primer pair selected from Primer Pair Set 38 that specifically amplifies a portion of Corynebacterium striatum genome; at least one primer pair selected from Primer Pair Set 39 that specifically amplifies a portion of Candida albicans genome; at least one primer pair selected from Primer Pair Set 40 that specifically amplifies a portion of Candida auris genome; at least one primer pair selected from Primer Pair Set 41 that specifically amplifies a portion of Candida glabrata genome; at least one primer pair selected from Primer Pair Set 42 that specifically amplifies a portion of Candida krusei genome; at least one primer pair selected from Primer Pair Set 43 that specifically amplifies a portion of Candida parapsilosis genome; and/or at least one primer pair selected from Primer Pair Set 44 that specifically amplifies a portion of Candida tropicalis genome; and (b) subjecting the reaction mixture to reaction conditions suitable to amplify targeted nucleic acids, thereby generating at least one amplicon when the targeted nucleic acids are present in the sample; wherein the presence or absence of at least one amplicon in the sample indicates the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in the sample. In one aspect, the Primer Pair Sets comprise the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97– 98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115–116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133–134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142–143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160–161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169–170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208– 209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244– 245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289–290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301– 302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313–314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340–341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343– 344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353,355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370– 371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. In another aspect, the generating of the at least one amplicon comprises performing PCR. In another aspect, the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii produced using at least one primer pair selected from SEQ ID NO: 1– 2, 4–5, or 7–8, and a sequence comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis produced using at least one primer pair selected from SEQ ID NO: 10–11, 13–14, or 16–17, and a sequence comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens produced using at least one primer pair selected from SEQ ID NO: 19–20, 22–23, or 25–26, and a sequence comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae produced using at least one primer pair selected from SEQ ID NO: 28–29, 31–32, or 34–35, and a sequence comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis produced using at least one primer pair selected from SEQ ID NO: 37–38, 40–41, or 43–44, and a sequence comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium produced using at least one primer pair selected from SEQ ID NO: 46–47, 49–50, or 52–53, and a sequence comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli produced using at least one primer pair selected from SEQ ID NO: 55–56, 58–59, or 61–62, and a sequence comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae produced using at least one primer pair selected from SEQ ID NO: 64– 65, 67–68, or 70–71, and a sequence comprising at least a portion of SEQ ID NO: 434; an amplicon specific for Klebsiella Oxytoca produced using at least one primer pair selected from SEQ ID NO: 73–74, 76–77, or 79–80, and a sequence comprising at least a portion of SEQ ID NO: 435; an amplicon specific for Klebsiella aerogenes produced using at least one primer pair selected from SEQ ID NO: 82–83, 85–86, or 88–89, and a sequence comprising at least a portion of SEQ ID NO: 436; an amplicon specific for Proteus mirabilis produced using at least one primer pair selected from SEQ ID NO: 91–92, 94–95, or 97–98, and a sequence comprising at least a portion of SEQ ID NO: 437; an amplicon specific for Proteus vulgaris produced using at least one primer pair selected from SEQ ID NO: 100–101, 103–104, or 106–107, and a sequence comprising at least a portion of SEQ ID NO: 438; an amplicon specific for Pseudomonas aeruginosa produced using at least one primer pair selected from SEQ ID NO: 109–110, 112– 113, or 115–116, and a sequence comprising at least a portion of SEQ ID NO: 439; an amplicon specific for Serratia marcescens produced using at least one primer pair selected from SEQ ID NO: 118–119, 121–122, or 124–125, and a sequence comprising at least a portion of SEQ ID NO: 440; an amplicon specific for Staphylococcus aureus produced using at least one primer pair selected from SEQ ID NO: 127–128, 130–131, or 133–134, and a sequence comprising at least a portion of SEQ ID NO: 441; an amplicon specific for Streptococcus agalactiae produced using at least one primer pair selected from SEQ ID NO: 136–137, 139–140, or 142–143, and a sequence comprising at least a portion of SEQ ID NO: 442; an amplicon specific for Streptococcus dysgalactiae produced using at least one primer pair selected from SEQ ID NO: 145–146, 148– 149, or 151–152, and a sequence comprising at least a portion of SEQ ID NO: 443; an amplicon specific for Streptococcus anginosus produced using at least one primer pair selected from SEQ ID NO: 154–155, 157–158, or 160–161, and a sequence comprising at least a portion of SEQ ID NO: 444; an amplicon specific for Streptococcus pyogenes produced using at least one primer pair selected from SEQ ID NO: 163–164, 166–167, or 169–170, and a sequence comprising at least a portion of SEQ ID NO: 445; an amplicon specific for Staphylococcus lugdunensis produced using at least one primer pair selected from SEQ ID NO: 172–173, 175–176, or 178–179, and a sequence comprising at least a portion of SEQ ID NO: 446; an amplicon specific for Providencia stuartii produced using at least one primer pair selected from SEQ ID NO: 181–182, 184–185, or 187–188, and a sequence comprising at least a portion of SEQ ID NO: 447; an amplicon specific for Stenotrophomonas maltophilia produced using at least one primer pair selected from SEQ ID NO: 190–191, 193–194, or 196–197;, and a sequence comprising at least a portion of SEQ ID NO: 448; an amplicon specific for Morganella morganii produced using at least one primer pair selected from SEQ ID NO: 199–200, 202–203, or 205–206, and a sequence comprising at least a portion of SEQ ID NO: 449; an amplicon specific for Citrobacter koseri produced using at least one primer pair selected from SEQ ID NO: 208–209, 211–212, or 214–215, and a sequence comprising at least a portion of SEQ ID NO: 450; an amplicon specific for Citrobacter freundii produced using at least one primer pair selected from SEQ ID NO: 217–218, 220–221, or 223– 224, and a sequence comprising at least a portion of SEQ ID NO: 451; an amplicon specific for Citrobacter braakii produced using at least one primer pair selected from SEQ ID NO: 226–227, 229–230, or 232–233, and a sequence comprising at least a portion of SEQ ID NO: 452; an amplicon specific for Peptoniphilus asaccharolyticus produced using at least one primer pair selected from SEQ ID NO: 235–236, 238–239, or 241–242, and a sequence comprising at least a portion of SEQ ID NO: 453; an amplicon specific for Peptoniphilus harei produced using at least one primer pair selected from SEQ ID NO: 244–245, 247–248, or 250–251, and a sequence comprising at least a portion of SEQ ID NO: 454; an amplicon specific for Peptoniphilus ivorii produced using at least one primer pair selected from SEQ ID NO: 253–254, 256–257, or 259– 260, and a sequence comprising at least a portion of SEQ ID NO: 455; an amplicon specific for Peptostreptococcus anaerobius produced using at least one primer pair selected from SEQ ID NO: 262–263, 265–266, or 268–269, and a sequence comprising at least a portion of SEQ ID NO: 456; an amplicon specific for Finegoldia magna produced using at least one primer pair selected from SEQ ID NO: 271–272, 274–275, or 277–278, and a sequence comprising at least a portion of SEQ ID NO: 457; an amplicon specific for Clostridium septicum produced using at least one primer pair selected from SEQ ID NO: 280–281, 283–284, or 286–287, and a sequence comprising at least a portion of SEQ ID NO: 458; an amplicon specific for Paeniclostridium sordellii (Clostridium sordellii) produced using at least one primer pair selected from SEQ ID NO: 289– 290, 292–293, or 295–296, and a sequence comprising at least a portion of SEQ ID NO: 459; an amplicon specific for Clostridium novyi A, B produced using at least one primer pair selected from SEQ ID NO: 298–299, 301–302, or 304–305, and a sequence comprising at least a portion of SEQ ID NO: 460; an amplicon specific for Clostridium histolyticum produced using at least one primer pair selected from SEQ ID NO: 307–308, 310–311, or 313–314, and a sequence comprising at least a portion of SEQ ID NO: 461; an amplicon specific for Staphylococcus epidermidis produced using at least one primer pair selected from SEQ ID NO: 316–317, 319– 320, or 322–323, and a sequence comprising at least a portion of SEQ ID NO: 462; an amplicon specific for Staphylococcus haemolyticus produced using at least one primer pair selected from SEQ ID NO: 325–326, 328–329, or 331–332, and a sequence comprising at least a portion of SEQ ID NO: 463; an amplicon specific for Corynebacterium striatum produced using at least one primer pair selected from SEQ ID NO: 334–335, 337–338, or 340–341, and a sequence comprising at least a portion of SEQ ID NO: 464; an amplicon specific for Candida albicans produced using at least one primer pair selected from SEQ ID NO: 343–344, 346–347, or 349– 350, and a sequence selected from SEQ ID NO: 465; an amplicon specific for Candida auris produced using at least one primer pair selected from SEQ ID NO: 352–353,355–356, or 358– 359, and a sequence comprising at least a portion of SEQ ID NO: 466; an amplicon specific for Candida glabrata produced using at least one primer pair selected from SEQ ID NO: 361–362, 364–365, or 367–368, and a sequence comprising at least a portion of SEQ ID NO: 467; an amplicon specific for Candida krusei produced using at least one primer pair selected from SEQ ID NO: 370–371, 373–374, or 376–377, and a sequence comprising at least a portion of SEQ ID NO: 468; an amplicon specific for Candida parapsilosis produced using at least one primer pair selected from SEQ ID NO: 379–380, 382–383, or 385–386, and a sequence comprising at least a portion of SEQ ID NO: 469; and/or an amplicon specific for Candida tropicalis produced using at least one primer pair selected from SEQ ID NO: 388–389, 391–392, or 394–395, and a sequence comprising at least a portion of SEQ ID NO: 470. In another aspect, the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae comprising at least a portion of SEQ ID NO:434; an amplicon specific for Klebsiella Oxytoca comprising at least a portion of SEQ ID NO: 435; an amplicon specific for Klebsiella aerogenes comprising at least a portion of SEQ ID NO: 436; an amplicon specific for Proteus mirabilis comprising at least a portion of SEQ ID NO: 437; an amplicon specific for Proteus vulgaris comprising at least a portion of SEQ ID NO: 438; an amplicon specific for Pseudomonas aeruginosa comprising at least a portion of SEQ ID NO: 439; an amplicon specific for Serratia marcescens comprising at least a portion of SEQ ID NO: 440; an amplicon specific for Staphylococcus aureus comprising at least a portion of SEQ ID NO: 441; an amplicon specific for Streptococcus agalactiae comprising at least a portion of SEQ ID NO: 442; an amplicon specific for Streptococcus dysgalactiae comprising at least a portion of SEQ ID NO: 443; an amplicon specific for Streptococcus anginosus comprising at least a portion of SEQ ID NO: 444; an amplicon specific for Streptococcus pyogenes comprising at least a portion of SEQ ID NO: 445; an amplicon specific for Staphylococcus lugdunensis comprising at least a portion of SEQ ID NO: 446; an amplicon specific for Providencia stuartii comprising at least a portion of SEQ ID NO: 447; an amplicon specific for Stenotrophomonas maltophilia comprising at least a portion of SEQ ID NO: 448; an amplicon specific for Morganella morganii comprising at least a portion of SEQ ID NO: 449; an amplicon specific for Citrobacter koseri comprising at least a portion of SEQ ID NO: 450; an amplicon specific for Citrobacter freundii comprising at least a portion of SEQ ID NO: 451; an amplicon specific for Citrobacter braakii comprising at least a portion of SEQ ID NO: 452; an amplicon specific for Peptoniphilus asaccharolyticus comprising at least a portion of SEQ ID NO: 453; an amplicon specific for Peptoniphilus harei comprising at least a portion of SEQ ID NO: 454; an amplicon specific for Peptoniphilus ivorii comprising at least a portion of SEQ ID NO: 455; an amplicon specific for Peptostreptococcus anaerobius comprising at least a portion of SEQ ID NO: 456; an amplicon specific for Finegoldia magna comprising at least a portion of SEQ ID NO: 457; an amplicon specific for Clostridium septicum comprising at least a portion of SEQ ID NO: 458; an amplicon specific for Paeniclostridium sordellii (Clostridium sordellii) comprising at least a portion of SEQ ID NO: 459; an amplicon specific for Clostridium novyi A, B comprising at least a portion of SEQ ID NO: 460; an amplicon specific for Clostridium histolyticum comprising at least a portion of SEQ ID NO: 461; an amplicon specific for Staphylococcus epidermidis comprising at least a portion of SEQ ID NO: 462; an amplicon specific for Staphylococcus haemolyticus comprising at least a portion of SEQ ID NO: 463; an amplicon specific for Corynebacterium striatum comprising at least a portion of SEQ ID NO: 464; an amplicon specific for Candida albicans comprising at least a portion of SEQ ID NO: 465; an amplicon specific for Candida auris comprising at least a portion of SEQ ID NO: 466; an amplicon specific for Candida glabrata comprising at least a portion of SEQ ID NO: 467; an amplicon specific for Candida krusei comprising at least a portion of SEQ ID NO: 468; an amplicon specific for Candida parapsilosis comprising at least a portion of SEQ ID NO: 469; and/or an amplicon specific for Candida tropicalis comprising at least a portion of SEQ ID NO: 470. In another aspect, the reaction mixture further comprises probes specific for the at least one amplicon. In another aspect, the reaction mixture further comprises probes specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probes comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. In another aspect, the reaction mixture further contains a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample. In another aspect, the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. In another aspect, the probe comprises a fluorescent reporter. In another aspect, the probe comprises a quencher. In another aspect, the probe is labeled at or near the 5′–end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM. In another aspect, the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ. Another embodiment described herein is a composition for individually, simultaneously, or sequentially determining the presence or absence of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis comprising a plurality of Primer Pair Sets, wherein the Primer Pair Sets comprise: at least one primer pair selected from Primer Pair Set 1 that specifically amplifies a portion of Acinetobacter baumannii genome; at least one primer pair selected from Primer Pair Set 2 that specifically amplifies a portion of Bacteroides fragilis genome; at least one primer pair selected from Primer Pair Set 3 that specifically amplifies a portion of Clostridium perfringens genome; at least one primer pair selected from Primer Pair Set 4 that specifically amplifies a portion of Enterobacter cloacae genome; at least one primer pair selected from Primer Pair Set 5 that specifically amplifies a portion of Enterococcus faecalis genome; at least one primer pair selected from Primer Pair Set 6 that specifically amplifies a portion of Enterococcus faecium genome; at least one primer pair selected from Primer Pair Set 7 that specifically amplifies a portion of Escherichia coli genome; at least one primer pair selected from Primer Pair Set 8 that specifically amplifies a portion of Klebsiella pneumoniae genome; at least one primer pair selected from Primer Pair Set 9 that specifically amplifies a portion of Klebsiella oxytoca genome; at least one primer pair selected from Primer Pair Set 10 that specifically amplifies a portion of Klebsiella aerogenes genome; at least one primer pair selected from Primer Pair Set 11 that specifically amplifies a portion of Proteus mirabilis genome; at least one primer pair selected from Primer Pair Set 12 that specifically amplifies a portion of Proteus vulgaris genome; at least one primer pair selected from Primer Pair Set 13 that specifically amplifies a portion of Pseudomonas aeruginosa genome; at least one primer pair selected from Primer Pair Set 14 that specifically amplifies a portion of Serratia marcescens genome; at least one primer pair selected from Primer Pair Set 15 that specifically amplifies a portion of Staphylococcus aureus genome; at least one primer pair selected from Primer Pair Set 16 that specifically amplifies a portion of Streptococcus agalactiae genome; at least one primer pair selected from Primer Pair Set 17 that specifically amplifies a portion of Streptococcus dysgalactiae genome; at least one primer pair selected from Primer Pair Set 18 that specifically amplifies a portion of Streptococcus anginosus genome; at least one primer pair selected from Primer Pair Set 19 that specifically amplifies a portion of Streptococcus pyogenes genome; at least one primer pair selected from Primer Pair Set 20 that specifically amplifies a portion of Staphylococcus lugdunensis genome; at least one primer pair selected from Primer Pair Set 21 that specifically amplifies a portion of Providencia stuartii genome; at least one primer pair selected from Primer Pair Set 22 that specifically amplifies a portion of Stenotrophomonas maltophilia genome; at least one primer pair selected from Primer Pair Set 23 that specifically amplifies a portion of Morganella morganii genome; at least one primer pair selected from Primer Pair Set 24 that specifically amplifies a portion of Citrobacter koseri genome; at least one primer pair selected from Primer Pair Set 25 that specifically amplifies a portion of Citrobacter freundii genome; at least one primer pair selected from Primer Pair Set 26 that specifically amplifies a portion of Citrobacter braakii genome; at least one primer pair selected from Primer Pair Set 27 that specifically amplifies a portion of Peptoniphilus asaccharolyticus genome; at least one primer pair selected from Primer Pair Set 28 that specifically amplifies a portion of Peptoniphilus harei genome; at least one primer pair selected from Primer Pair Set 29 that specifically amplifies a portion of Peptoniphilus ivorii genome; at least one primer pair selected from Primer Pair Set 30 that specifically amplifies a portion of Peptostreptococcus anaerobius genome; at least one primer pair selected from Primer Pair Set 31 that specifically amplifies a portion of Finegoldia magna genome; at least one primer pair selected from Primer Pair Set 32 that specifically amplifies a portion of Clostridium septicum genome; at least one primer pair selected from Primer Pair Set 33 that specifically amplifies a portion of Paeniclostridium sordellii (Clostridium sordellii) genome; at least one primer pair selected from Primer Pair Set 34 that specifically amplifies a portion of Clostridium novyi A, B genome; at least one primer pair selected from Primer Pair Set 35 that specifically amplifies a portion of Clostridium histolyticum genome; at least one primer pair selected from Primer Pair Set 36 that specifically amplifies a portion of Staphylococcus epidermidis genome; at least one primer pair selected from Primer Pair Set 37 that specifically amplifies a portion of Staphylococcus haemolyticus genome; at least one primer pair selected from Primer Pair Set 38 that specifically amplifies a portion of Corynebacterium striatum genome; at least one primer pair selected from Primer Pair Set 39 that specifically amplifies a portion of Candida albicans genome; at least one primer pair selected from Primer Pair Set 40 that specifically amplifies a portion of Candida auris genome; at least one primer pair selected from Primer Pair Set 41 that specifically amplifies a portion of Candida glabrata genome; at least one primer pair selected from Primer Pair Set 42 that specifically amplifies a portion of Candida krusei genome; at least one primer pair selected from Primer Pair Set 43 that specifically amplifies a portion of Candida parapsilosis genome; and/or at least one primer pair selected from Primer Pair Set 44 that specifically amplifies a portion of Candida tropicalis genome. In one aspect, the Primer Pair Sets comprises the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97– 98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115–116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133–134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142–143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160–161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169–170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208– 209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244– 245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289–290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301– 302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313–314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340–341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343– 344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353,355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370– 371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. In another aspect, the composition further comprises a probe specific for the at least one amplicon produced using the at least one primer pair selected from one or more of Primer Pair Sets 1–44. In another aspect, the composition further comprises a probe specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probe comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. In another aspect, the composition further comprises a polymerase, a buffer, and deoxynucleotide triphosphates (dNTPs). In another aspect, the composition further comprises a sample. In another aspect, the composition further comprises a at least one control forward and reverse primer and, optionally, a control probe, that specifically amplifies a target nucleic acid of a control sample. In another aspect, the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418– 419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. In another aspect, the probe contains a fluorescent reporter. In another aspect, the probe contains a quencher. In another aspect, the probe is labeled at or near the 5′ end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM. In another aspect, the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ. Another embodiment described herein is a kit for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample, comprising any of the compositions described herein. In another aspect, the composition further comprises any of the compositions described herein. In another aspect, the kit comprises Primer Pair Sets comprising the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10– 11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115–116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133–134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142–143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160–161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169–170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202– 203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238– 239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274– 275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289–290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313–314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325– 326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353, 355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364– 365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. In another aspect, the kit further comprises probes suitable for use with specific forward and reverse primer pairs, the probes comprising one or more of: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; and/or a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. In another aspect, the kit further comprises a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample. In another aspect, the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. In another aspect, the kit further comprises a control plasmid comprising one or more target sequences selected from Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis. In another aspect, the control plasmid comprises one or more of nucleic acid sequences of SEQ ID NO: 427–470. DESCRIPTION OF THE DRAWINGS The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. FIG.1 shows limits of detections for wound pathogen panel qPCR assays using Open Array (OA) or TaqMan™ Array Card (TAC) platforms. DETAILED DESCRIPTION Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. For example, any nomenclatures used in connection with, and techniques of biochemistry, molecular biology, immunology, microbiology, genetics, cell and tissue culture, and protein and nucleic acid chemistry described herein are well known and commonly used in the art. In case of conflict, the present disclosure, including definitions, will control. Exemplary methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the embodiments and aspects described herein. As used herein, the terms “amino acid,” “nucleotide,” “polynucleotide,” “vector,” “polypeptide,” and “protein” have their common meanings as would be understood by a biochemist of ordinary skill in the art. Standard single letter nucleotides (A, C, G, T, U) and standard single letter amino acids (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y) are used herein. As used herein, the terms such as “include,” “including,” “contain,” “containing,” “having,” and the like mean “comprising.” The present disclosure also contemplates other embodiments “comprising,” “consisting essentially of,” and “consisting of” the embodiments or elements presented herein, whether explicitly set forth or not. As used herein, the term “a,” “an,” “the” and similar terms used in the context of the disclosure (especially in the context of the claims) are to be construed to cover both the singular and plural unless otherwise indicated herein or clearly contradicted by the context. In addition, “a,” “an,” or “the” means “one or more” unless otherwise specified. As used herein, the term “or” can be conjunctive or disjunctive. As used herein, the term “and/or” refers to both the conjunctive and disjunctive. As used herein, the term “substantially” means to a great or significant extent, but not completely. As used herein, the term “about” or “approximately” as applied to one or more values of interest, refers to a value that is similar to a stated reference value, or within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, such as the limitations of the measurement system. In one aspect, the term “about” refers to any values, including both integers and fractional components that are within a variation of up to ± 10% of the value modified by the term “about.” Alternatively, “about” can mean within 3 or more standard deviations, per the practice in the art. Alternatively, such as with respect to biological systems or processes, the term “about” can mean within an order of magnitude, in some embodiments within 5-fold, and in some embodiments within 2-fold, of a value. As used herein, the symbol “~” means “about” or “approximately.” All ranges disclosed herein include both end points as discrete values as well as all integers and fractions specified within the range. For example, a range of 0.1–2.0 includes 0.1, 0.2, 0.3, 0.4 . . . 2.0. If the end points are modified by the term “about,” the range specified is expanded by a variation of up to ±10% of any value within the range or within 3 or more standard deviations, including the end points. As used herein, the terms “control,” or “reference” are used herein interchangeably. A “reference” or “control” level may be a predetermined value or range, which is employed as a baseline or benchmark against which to assess a measured result. “Control” also refers to control experiments. As used herein, the term “subject” refers to an animal. Typically, the subject is a mammal. A subject also refers to primates (e.g., humans, male or female; infant, adolescent, or adult), non- human primates, rats, mice, rabbits, pigs, cows, sheep, goats, horses, dogs, cats, fish, birds, and the like. In one embodiment, the subject is a primate. In one embodiment, the subject is a human. As used herein, a subject is “in need of treatment” if such subject would benefit biologically, medically, or in quality of life from such treatment. A subject in need of treatment does not necessarily present symptoms, particular in the case of preventative or prophylaxis treatments. As used herein, the terms “inhibit,” “inhibition,” or “inhibiting” refer to the reduction or suppression of a given biological process, condition, symptom, disorder, or disease, or a significant decrease in the baseline activity of a biological activity or process. As used herein, “treatment” or “treating” refers to prophylaxis of, preventing, suppressing, repressing, reversing, alleviating, ameliorating, or inhibiting the progress of biological process including a disorder or disease, or completely eliminating a disease. A treatment may be either performed in an acute or chronic way. The term “treatment” also refers to reducing the severity of a disease or symptoms associated with such disease prior to affliction with the disease. “Repressing” or “ameliorating” a disease, disorder, or the symptoms thereof involves administering a cell, composition, or compound described herein to a subject after clinical appearance of such disease, disorder, or its symptoms. “Prophylaxis of” or “preventing” a disease, disorder, or the symptoms thereof involves administering a cell, composition, or compound described herein to a subject prior to onset of the disease, disorder, or the symptoms thereof. “Suppressing” a disease or disorder involves administering a cell, composition, or compound described herein to a subject after induction of the disease or disorder thereof but before its clinical appearance or symptoms thereof have manifest. As used herein, “wound pathogens” refer to bacterial and fungal species that commonly infect wounds from either trauma, iatrogenic, or nosocomial sources. In one aspect, the wound pathogens comprise one or more of the bacterial species: Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, or Corynebacterium striatum. In another aspect, the fungal pathogens comprise one or more of the fungal species: Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, and Candida tropicalis. The primers, probes, and polynucleotides described herein may include variants that have substitutions, deletions, and/or additions that can involve one or more nucleotides. Some embodiments described herein include nucleic acid molecules comprising polynucleotides having nucleotide sequences about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, and more preferably at least about 95–99% or 100% identical to (a) nucleotide sequences of SEQ ID NO: 1–470 and capable of being used as primers or probes as described herein; or (b) nucleotide sequences capable of hybridizing to the complement of any of the nucleotide sequences of SEQ ID NO: 1–470 and capable of being used as primers or probes as described herein. As used herein, a nucleotide having a nucleotide sequence at least 90–99% “identical” to a reference nucleotide sequence indicates that the nucleotide sequence is identical to the reference sequence except that the nucleotide sequence can include up to about 10-to-1 point mutations, additions, or deletions per each 100 nucleotides of the reference nucleotide sequence. In other words, to obtain a nucleotide having a nucleotide sequence at least 90–99% identical to a reference nucleotide sequence, up to 10% of the nucleotides in the reference sequence can be deleted, added, or substituted with another nucleotide, or a number of nucleotides up to 10% of the total nucleotides in the reference sequence can be inserted into the reference sequence. These mutations of the reference sequence can occur at the 5′- or 3′-terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence. These may include standard nucleotides, modified nucleotides, fluorescent dyes, linkers, or other modifications. As described above, two or more polynucleotide sequences can be compared by determining their percent identity. The percent identity of two sequence is generally described as the number of exact matches between two aligned sequences divided by the length of the shorter sequence and multiplied by 100. Alignment for nucleic acid sequences can be performed using by the global alignment method of Needleman and Wunsch, J. Mol. Biol.48 (3): 443-453 (1970) or the local homology algorithm of Smith and Waterman, Adv. Appl. Math.2: 482-489 (1981). Described herein are primers, primer sets, and probes designed for target sequences and compatible for use in an individual or multiplex qPCR determining the presence of wound pathogens. Multiplex PCR presents a challenge for quantitation of the pathogen DNA: the different amplicons compete for the same PCR reaction components (such as e.g., DNA polymerase and MgCl2) and this can compromise the quantitative comparison between samples. It is known in the art that there is bias in the amplification efficiencies between different template amounts or lengths so that e.g., short amplicons are favored in the expense of longer ones. At the same time, undesired cross-reactions of multiplex set oligo combinations must be avoided. Finding suitable primer and probe sequences for the detection of a diverse group of pathogenic microbes is far from trivial especially when designing multiplex set ups. Described herein are primer sets and probes for detecting the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis. The selected primers and probes of the assay do not cross-react with other closely-related pathogens. The disclosed detection method and assay may contain internal process control, such as Bacillus atrophaeus (BA) or a universal RNA Spike In/Reverse Transcription Control (Xeno). In addition, the assay may have a real time PCR positive control. The probes that target genomic regions of different pathogens utilize three distinct fluorophores, while a fourth fluorophore is designated for the process control detection. Therefore, individual or multiplex qPCR assays are described herein, wherein the detection takes place in a single-well reaction, to meet the speed and high-throughput needs for rapid clinical wound pathogen testing. When an exemplary “embodiment” or a particular “assay” is described herein, it will be understood that the features of that embodiment may be applicable to a composition (e.g., the particular physical components of an assay such as primers and/or probes), a kit (e.g., primers and/or probes and additional buffers, reagents, etc.), or a method (e.g., a process for detecting target nucleic acids) as appropriate. For simplicity, embodiments are presented by describing “assays,” but it will be understood that the associated methods for the assays, and the compositions for carrying out the assays (primers, probes, and primer sets), are also intended to be part of this disclosure. One embodiment described herein are primer pair sets, comprising one or more forward primers, reverse primers, and probes for detecting the presence or absence of one or more wound pathogens. Various primer pair sets for detecting specific wound pathogens are shown in Table 1. Table 1. Primer Pair Sets for Detecting Wound Pathogens Primer Pair Set Organsim 1 Acinetobacter baumannii 2 Bacteroides fragilis 3 Clostridium perfringens 4 Enterobacter cloacae 5 Enterococcus faecalis 6 Enterococcus faecium 7 Escherichia coli 8 Klebsiella pneumoniae 9 Klebsiella Oxytoca 10 Klebsiella aerogenes 11 Proteus mirabilis 12 Proteus vulgaris 13 Pseudomonas aeruginosa 14 Serratia marcescens 15 Staphylococcus aureus 16 Streptococcus agalactiae 17 Streptococcus dysgalactiae 18 Streptococcus pyogenes 19 Streptococcus anginosus 20 Staphylococcus lugdunensis 21 Providencia stuartii 22 Stenotrophomonas maltophilia 23 Morganella morganii 24 Citrobacter koseri 25 Citrobacter freundii 26 Citrobacter braakii 27 Peptoniphilus asaccharolyticus 28 Peptoniphilus harei 29 Peptoniphilus ivorii 30 Peptostreptococcus anaerobius 31 Finegoldia magna 32 Clostridium septicum 33 Paeniclostridium sordellii (Clostridium sordellii) 34 Clostridium novyi A, B 35 Clostridium histolyticum 36 Staphylococcus epidermidis 37 Staphylococcus haemolyticus 38 Corynebacterium striatum 39 Candida albicans 40 Candida auris 41 Candida glabrata 42 Candida krusei 43 Candida parapsilosis 44 Candida tropicalis In one embodiment, Primer Pair Set 1 comprises one or more the primer pairs shown in Table 2, in a combination with a corresponding probe sequence: Table 2. Acinetobacter baumannii Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 1 NO NO NO AGCCTGTGCGCGATA TGCTGCATTCTGCCC CAGCCTGCTTAATAC 1 ACA 1 CAAA 2 GAAC 3 CGTCGTGTTCAAACT GCCCAATCCTCATCT CATAACAACAGCTTA 6 GTGCAACCGTTTTAA CGGTACGGAAACCAT CACGACTTGAACCAC 3 TTGCTCGTA 7 ATTCGTTTAATG 8 AACC 9 In another embodiment, Primer Pair Set 2 comprises one or more the primer pairs shown in Table 3, in a combination with a corresponding probe sequence: Table 3. Bacteroides fragilis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 2 NO NO NO TTCCAGTGAAATCCT GAGCTAACACCATCG ACTGCTTGCCGATTT In another embodiment, Primer Pair Set 3 comprises one or more the primer pairs shown in Table 4, in a combination with a corresponding probe sequence: Table 4. Clostridium perfringens Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 3 NO NO NO CTCCTCCAACCTGCA AAGAAAGGGCGTTGT ATATACACTCCACCT 1 CTTCC 19 AAGTTCATCT 20 GGTTCAG 21 GCTCCTCCAACCTGC GAAAGGGCGTTGTAA CCTGGTTCAGAAACA 2 22 23 24 27 in Table 5, in a combination with a corresponding probe sequence: Table 5. Enterobacter cloacae Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 4 NO NO NO CTGGCACAGACAGCA GATGTTCCAGCGTTT TTTGCCATGCTTAAT 1 CAC 28 CACATAACTG 29 CTG 30 GGTGGTGATGGTGGA TCTTGACTCGCGAGC CCAGCTGACGTACGA in Table 6, in a combination with a corresponding probe sequence: Table 6. Enterococcus faecalis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 5 NO NO NO TCTTCTTGTTCCCCA CGCTCATAAAATCAA TTGGATTGCATCGCT 1 CCATGTAAAAG 37 TGGTCCAAAAGG 38 TTT 39 42 45 In another embodiment, Primer Pair Set 6 comprises one or more the primer pairs shown in Table 7, in a combination with a corresponding probe sequence: Table 7. Enterococcus faecium Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 6 NO NO NO GCTCCTACTGCTGAA TCTACACAGCCATTT ACGATCTGGTTCAAT 1 CATCCAAAT 46 CGTAATGCTT 47 ATCA 48 CAGATCGTATTTGGA ACGAGATTCCATATG CTCTTGGTTTGACTG 2 49 50 51 54 in Table 8, in a combination with a corresponding probe sequence: Table 8. Escherichia coli Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 7 NO NO NO GGCATGGCGGATAAA GAAGGTGGGTTTCGC ACCGAAAGCGATCTC 1 TTTCAATCG 55 CTGTAT 56 C 57 GCGGATCATCGTGAC ACCGCCAGAACTTGA AAGCAATCCAGCTTC 2 GGAT 58 GCAA 59 TG 60 TGCTTCGACTTCCTG CGAGTTGCTGTCGAT TCCTGAACACCATAC 3 CAATCTTT 61 CCGTA 62 CTGTC 63 In another embodiment, Primer Pair Set 8 comprises one or more the primer pairs shown in Table 9, in a combination with a corresponding probe sequence: Table 9. Klebsiella pneumoniae Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 8 NO NO NO GATACGAAAGTTACC GGTCGCTGTACTGTA ACCCTGGCCCATAAT 1 TCAGGAACGT 64 CCAGAAT 65 G 66 GACGGGCGCGCATG CACCACCAGTCCGTT CAGCCGGGCAAGATG 2 67 GCT 68 69 CCTGCGGGCTGTCTC CGCCTGATGCCGGAC CCACCAGAAAATGC 3 A 70 AT 71 72 GATCGTCCAGCGAGG GATATTCCGCCGCAC 3 TCTG 79 AACCTA 80 CAGGCGGCCATTACC 81 In another embodiment, Primer Pair Set 10 comprises one or more the primer pairs shown in Table 11, in a combination with a corresponding probe sequence: Table 11. Klebsiella aerogenes Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 10 NO NO NO CGCGCTAAGCGGCAT AACGCCAATCGAATC TCCTCCACGAAAGGC 1 G 82 GATACCA 83 A 84 AAAATCCCCTTTGCG TCTTCCCAGATAGCA CACCAACGGTGGCAC 2 GAAAGC 85 ACCAAACATATTAC 86 AG 87 CGTTTCTCAATTAAT CCGGAGAAATACTCC ACTCAACTCTTTCGA 3 AACTGTGGTGACT 88 ATGACTTCTT 89 CTTTGAA 90 In another embodiment, Primer Pair Set 11 comprises one or more the primer pairs shown in Table 12, in a combination with a corresponding probe sequence: Table 12. Proteus mirabilis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 11 NO NO NO GGCAAACTATCACAG TCAATCGGTTTGGTC TCTCACGTTGATTAT 1 TCACCACTAA 91 GGGAAAA 92 TCC 93 96 99 In another embodiment, Primer Pair Set 12 comprises one or more the primer pairs shown in Table 13, in a combination with a corresponding probe sequence: Table 13. Proteus vulgaris Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 12 NO NO NO ACCGGTTTGTTATCA AAGCTTGTTTAATCG CATTTCAGCGACATT 1 CCCAATCC 100 AAAAGGCTCAAA 101 ACC 102 In another embodiment, Primer Pair Set 13 comprises one or more the primer pairs shown in Table 14, in a combination with a corresponding probe sequence: Table 14. Pseudomonas aeruginosa Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 13 NO NO NO CCTGCCTGAAGATCG TCGACATGCCGGTTG CTTCGCGTTCAGTCC 1 AGGA 109 CT 110 GC 111 TTGAAGGAATTGCTT GCATCAGCAACTCCT CAGGCAGGCGAGCAT 2 GTGCATGAG 112 CGATCTT 114 GCGGGCTTTTCCAGT GCCCGGCATTCGTCC TAGCTCTGGGTGAAA 3 CAG 115 TT 116 TAG 117 In another embodiment, Primer Pair Set 14 one or more the primer pairs shown in Table 15, in a combination with a corresponding probe sequence: Table 15. Serratia marcescens Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 14 NO NO NO CGAAGGCGAAGCGGA GGAACGGGTTGGCGT CCGGCTCAGGCCGCC 1 GAT 118 TGTA 119 CG 120 CGCCAGCCCGTACGA CCAGTCGCCGATGTC ACCCAGTCCGGCACC 2 T 121 GAT 122 G 123 GCAGCTGACGCCGAA CACGAATGGTGGCGT CTGGACGACCTGACC 3 A 124 TGAC 125 GC 126 In another embodiment, Set 15 comprises one or more the primer pairs shown in Table 16, in a combination with a corresponding probe sequence: Table 16. Staphylococcus aureus Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 15 NO NO NO CTATAAGCCATGTTC TTCGCGAAATGAAGT CACGTGCACTAGTCA 1 TGTTCCATCGTA 127 GGTGTAGA 128 CAC 129 In another embodiment, Primer Pair Set 16 comprises one or more the primer pairs shown in Table 17, in a combination with a corresponding probe sequence: Table 17. Streptococcus agalactiae Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 16 NO NO NO CAATGGCAGCTTCGC CTGTCCACGTCGTAT TCGCAAGTGTTCAAG 1 TATTATCAG 136 CTGTTTCTT 137 CAC 138 GCGCCAGCTTTGAAA GGTGATACCTGTTCA TTGCTCTTGTGCTAA 2 139 140 141 In another embodiment, Primer Pair Set 18 comprises one or more the primer pairs shown in Table 19, in a combination with a corresponding probe sequence: Table 19. Streptococcus pyogenes Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 18 NO NO NO AAGTGCTTTTGGACA TGGCATCCATTTCAT ATAGCGATCCATAAA 1 ATGTGAAAGG 154 AAAGCCATCA 155 CCTTT 156 In another embodiment, Primer Pair Set 19 comprises one or more the primer pairs shown in Table 20, in a combination with a corresponding probe sequence: Table 20. Streptococcus anginosus Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 19 NO NO NO CCAGTTCCCCAGGCT CCTTCTTCCATTTAT CAGCAACACCAGTAA 1 TCTG 163 TCGCATGAAAGTT 164 ATG 165 GCACGTGATAGCCAA AGAAATTCTCGCTGC CTGGCTCTTCTCACC 2 166 167 168 in Table 21, in a combination with a corresponding probe sequence: Table 21. Staphylococcus lugdunensis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 20 NO NO NO AGTGCACATGTAGTG CAAACCATAACCAGT ATGAGGTAACGACCA 1 AAATTTCTAAACCT 172 TTCAGGATCT 173 ATACT 174 ATCCATCTTTCAACG GCACCGGCAATAATG ATGGAACCTGGAAAT 2 TACTCGGTTT 175 GCA 176 GT 177 TCCATCTTTCAACGT GGCATTGCACCGGCA ATGGCAGCGTTACAT 3 ACTCGGTTTT 178 A 179 TTC 180 In another embodiment, Pair Set 21 comprises one or more the primer pairs shown in Table 22, in a combination with a corresponding probe sequence: Table 22. Providencia stuartii Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 21 NO NO NO GATGGCCCCGAATCT GTTGCAGTAGTGCGA CTGCCACTATTTCCC 1 ATCCAT 181 TCCCTT 182 CTTCTAT 183 CGCTGTGGCACGAAT GCTGCCCATTAAATT CTCGCCTTGAGTTTC 2 ATGATGA 184 GACCAAGAT 185 C 186 CTTGAACCAGCGACA CAGTCTGAGGCGATA ACAACAATTCCTCCA 3 TACGGATTA 187 CCGTTAA 188 TAGTTC 189 In another embodiment, Primer Pair Set 22 comprises one or more the primer pairs shown in Table 23, in a combination with a corresponding probe sequence: Table 23. Stenotrophomonas maltophilia Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 22 NO NO NO TCAAGGCTTCGGCCA GCCTGGGTGCGGGTT TCCGGGAACTTTTCC 1 AGAT 190 191 TTG 192 CGGGCTACGGCCAAA GCCAAACGTATCAGA CTGCAATACAGCATA 2 GT 193 AACAGATGG 194 GAACT 195 ACGTTTGGCGGCTCA GTGGTTACGGAAAAT TCTGACAGTCCGACT 3 GATT 196 CATCGTTCAC 197 TTG 198 In another embodiment, Pair Set 23 comprises one or more the primer pairs shown in Table 24, in a combination with a corresponding probe sequence: Table 24. Morganella morganii Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 23 NO NO NO AGAAATTATTGTCTC CGGGTTTCGATTTGG CACCCGGAAAACAG 1 TGGGCATGCT 199 ATCGGAT 200 201 GCACTCACCCTGGGA TGCCGACGCGTTGTT CCAATTCAGGGAAGA 2 CTCA 202 TG 203 CCA 204 GCGCTGACTCACTCT CCGATGAGTCCCAGG TCGTATGCCAATCAA 3 TTTCC 205 GTGA 206 TAAA 207 In another embodiment, Primer Pair Set 24 comprises one or more the primer pairs shown in Table 25, in a combination with a corresponding probe sequence: Table 25. Citrobacter koseri Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 24 NO NO NO GGTAGCACTTACCTC CAATTCGCATAATGT TCGCAGGATGCATAC 1 TTACGCA 208 TCCCTTCCAT 209 GCA 210 GATTGTGGAAGCCGC TCGCTGGCGGCACTT CAGCGGTAATTT ACATG 211 T 212 GC 2 213 CGCGCAGTCGCTGGA GCGGTAATTTGCCCG CATGTGCGGCTTCCA 3 214 GTAAAGA 215 C 216 In another embodiment, Primer Pair Set 25 comprises one or more the primer pairs shown in Table 26, in a combination with a corresponding probe sequence: Table 26. Citrobacter freundii Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 25 NO NO NO AAGCCCTGCACCAGC TGAGATCCAGCGAGT CTGGCCTCACTAACT 1 A 217 GTTCAG 218 GG 219 CCTCAAATCGTGTTG TGAGCCAGTTCCCGA CCACCGTCGAACAGA 2 GATCAGTTG 220 ATGTTG 221 TGT 222 CTCAAACCCTGCGCA CTTTGACCGGCGCGT TCGCTGCCACGTTGT 3 TTCC 223 TT 224 G 225 In another embodiment, Primer Pair Set 26 comprises one or more the primer pairs shown in Table 27, in a combination with a corresponding probe sequence: Table 27. Citrobacter braakii Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 26 NO NO NO GGAACGCCTGCGTGG GTGGCGCGCAGTGAT CCGTTAGCTTCGATG 1 T 226 G 227 TCAAA 228 GCGTATCGAAACGCT CAGCGCGCTCAGACG CCGTGGTCCAGATCG 2 GTTCAC 229 230 T 231 GGCTAAAGACTACGT CTTAGCCAGCAGATC CAGCTCCATGTTAGC 3 TGACGAATCT 232 CAGACT 233 TGC 234 In another embodiment, Primer Pair Set 27 comprises one or more the primer pairs shown in Table 28, in a combination with a corresponding probe sequence: Table 28. Peptoniphilus asaccharolyticus Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 27 NO NO NO GAGAGTATTATCGCC TGCAATAGGAGTTAC CAAGGCCACCGGCTC 1 TGCCCAT 235 CGCAATAGG 236 C 237 AGAAGGCGGAAGACA GATATCTCCTGTTAC AACGGATACAGACCA 2 CACAC 238 GTCTGTTGTTCT 239 CAATT 240 ACGCACGAACGGATG CCAATGTTTCGTAAA TCCCGCCGTAGCCC 3 TGA 241 CGATTTTGGATTTC 242 243 In another embodiment, Primer Pair Set 28 comprises one or more the primer pairs shown in Table 29, in a combination with a corresponding probe sequence: Table 29. Peptoniphilus harei Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 28 NO NO NO CGATGAAATCTTGAC CTATCCCAATGTCTA CCG AGATCCTTCG 244 AGGCAGGTTA 245 TCCGCCGCTAAT 1 246 In another embodiment, Primer Pair Set 29 comprises one or more the primer pairs shown in Table 30, in a combination with a corresponding probe sequence: Table 30. Peptoniphilus ivorii Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 29 NO NO NO GACGGTACCATAGGA CGAACCCTTTACGCC ACGCTCGCCCCCTAC 1 GGAAGC 253 CAGTA 254 G 255 GGGATAGCCTCGGGA ACCGCTGTGACTTTA AACAGGCGTTACTGT 2 AACC 256 ACCACTG 257 GGTCT 258 CACGGTCCAAACTCC GGCGTCGCTGCATCA CCCCATTGTGCAAGA 3 TACGG 259 G 260 TT 261 In another embodiment, Primer Pair Set 31 comprises one or more the primer pairs shown in Table 32, in a combination with a corresponding probe sequence: Table 32. Finegoldia magna Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 31 NO NO NO GCTCGCGTCTGATTA TTCATCCTCTCAGAC ACCAAGGCGACGATC 1 GCTAGTT 271 CGGCTA 272 AG 273 TGATTAGCTAGTTGG 274 CCGGCTACTGATCGT 2 C GGGTACGCAGGCGGT CCACTTTCCTCTCCA AAGTCGAATGTTAAA 3 CTACTCAAG 278 GATCG In another embodiment, Primer Pair Set 32 comprises one or more the primer pairs shown in Table 33, in a combination with a corresponding probe sequence: Table 33. Clostridium septicum Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 32 NO NO NO TGCGGTGGAACGGCT ACCTGCCCCAACTTC ACGTTGGACAAGGTT 1 AATC 280 TCTTTTAAAT 281 TTG 282 TGGGCAAATGTAGCT CACCTGCCCCAACTT CCACCGCACCATCCA 2 CATTCATTAGG 283 CTCTTT 284 A 285 CGTTGGACAAGGTTT CCCACTTGCATAAGG TTGTATCTAGCAGAT 3 TGAATTTAAAAGAGA 286 ATCATTTGGA 287 288 AATAAATAAG In another embodiment, Primer Pair Set 33 comprises one or more the primer in Table 34, in a combination with a corresponding probe sequence: Table 34. Paeniclostridium sordellii (Clostridium sordellii) Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 33 NO NO NO CTGAAGTAGTTGCTC CAGCCGCATGGAACA CTACCCCATTAGATA 1 AATACGCTAAC 289 CTATG 290 TCATTTG 291 TGAGACAGCAGTAGA GCCTTAGCAGCTTCC CCAACCCCTATTACT In Set 34 one or more in Table 35, in a combination with a corresponding probe sequence: Table 35. Clostridium novyi A,B Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 34 NO NO NO ACGGTGGATATTGGG AGTATCTGCTAGATC TTTGTTAGAGCCAGA 1 AAAATGACTT 298 ACCTTCTGAGTTT 299 AACT 300 ACAGATGATTCTAAA GATATATTGTAGAAG CAGTCTGTACATTGA 2 TAAAGCCCTTTAAGC 301 GAACTTTTTTAATAA AA 303 A ATAGTACTGAAAACA ATA ACCATTTGTAATTAT CTCAGAGCATCCATG CCCAATGATAATTAT 3 TAAATCATCTCCATC 304 305 306 GGA ATAAATGTCACT TAGTTAAAACT In another embodiment, Primer Pair Set 35 comprises one or more the primer pairs shown in Table 36, in a combination with a corresponding probe sequence: Table 36. Clostridium histolyticum Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 35 NO NO NO GAGGATTCATAGGTT GCAACAAAGATTAAA TAGCCACCCCATTGC 1 CAGCATTCAAC 307 GGAGCAAATATCCA 308 C 309 TGCACTTGCAGTTAT CTTCAGTTAATAGTC CACCAACCATACCAA 2 TATGTCAGGTAT 310 CTGCAGCAGAT 311 CACC 312 GGTCTTGTATTTGCA CAGTTAATAGTCCTG TCCTATACCTGACAT 3 313 314 315 in Table 37, in a combination with a corresponding probe sequence: Table 37. Staphylococcus epidermidis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 36 NO NO NO TTACTACGCTGGTGG ATCTTCCATTGAACC CGTTATCGCCATTTT 1 AACTTCAAA 316 GCATAGC 317 G 318 GGAAAATTTAGAACA GCCAGCAGAGATGGG AAGTTTTTAGCTTCA In Set 37 one or more in Table 38, in a combination with a corresponding probe sequence: Table 38. Staphylococcus haemolyticus Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 37 NO NO NO GAGCGGCAAATAAAT CCCGTTTGTGTCATT CTGCACCAAGTTCAT 1 CAGAAGTTAATCA 325 TCCTCTTTAA 326 TCA 327 In another embodiment, Primer Pair Set 38 comprises one or more the primer pairs shown in Table 39, in a combination with a corresponding probe sequence: Table 39. Corynebacterium striatum Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 38 NO NO NO GCAGATGCGCTTCGT CGTCAGCGTCAGTAA TCCACTGGGCGTTAT 1 ATGGA 334 GAATCCAA 335 C 336 In another embodiment, Primer Pair Set 39 comprises one or more the primer pairs shown in Table 40, in a combination with a corresponding probe sequence: Table 40. Candida albicans Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 39 NO NO NO GGCAAGATTATTTAG TTTAAGTGAACCAGG ATGGGCACAGTGATA 1 CATGGACAAGTT 343 AGCATGGAAA 344 TGA 345 CATGCTCCTGGTTCA AATAAACCAAGGTGC CAAGGGCAAAACTG 2 in Table 41, in a combination with a corresponding probe sequence: Table 41. Candida auris Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 40 NO NO NO GGAATTTACCACCCA CAGCCCCGTACCTGC CCGACGAGTCGAGTT 1 CTTAGAGCT 352 TTTT 353 GT 354 CTGTTTGAGCGTGAT ACCTGATTTGAGGCG TTGCATTCACAAAAT 2 GTCTTCTC 355 ACAACAA 356 TAC 357 3 GCCCGGCCGAAACC 358 GGAAAGATGAAAAGC ACTTTGAAAAGAGA 359 CTGGGTGCAAGCCCT 360 In another embodiment, Primer Pair Set 41 comprises one or more the primer pairs shown in Table 42, in a combination with a corresponding probe sequence: Table 42. Candida glabrata Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 41 NO NO NO TTGACCAAGAATTAC GCTGCAGTAACCGAT ACACTTGGGTATCTT 1 CTGCACCT 361 GTACAAAG 362 CTG 363 In another embodiment, Primer Pair Set 42 comprises one or more the primer pairs shown in Table 43, in a combination with a corresponding probe sequence: Table 43. Candida krusei Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 42 NO NO NO GGTATCATGGTCCCA CTTCATCGATGTTGT CAGTGAAGAATCCAA 1 CCTACAAAAT 370 TGTTGGTTCTT 371 TTGC 372 CGTCCATAGTTGAAC GAATCGATGGACTGT CTCGGGTTTCACCAA 2 373 374 375 in Table 44, in a combination with a corresponding probe sequence: Table 44. Candida parapsilosis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 43 NO NO NO GGGTCTACAATACTG AGAGAAGGATGAGAG CAAATACATCATTCA 1 GCAACAACTA 379 CCAGTCT 380 ATAGTTCTC 381 CAATGGCTCCAAGCG ACCACCGACGGTTCT ACTCCTCGTTCAATC 2 ACTAC 382 AAATCAAT 383 CT 384 CTCCAAGCGACTACA GTCACCACCGACGGT TCGAATCTGAAAGTG 3 TCGAGAAG TCTAAA 386 TAAAGAA 387 In another embodiment, Primer Pair Set 44 comprises one or more the primer pairs shown in Table 45, in a combination with a corresponding probe sequence: Table 45. Candida tropicalis Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 44 NO NO NO GATGACGACGACGGA CTTGATCTTGAGTAA TCAGCACCACCACTA 1 GACTTT 388 TTGCGTCGTTG 389 ATA 390 T TCAATCAAGAGAGGC GTCGTCGTCATCTTC ACAGGCCTTATATTC 3 AGTTAAATCCAT 394 ATCATCCAAATA 395 TTCG 396 In some embodiments, the method or assay includes one or more control primers and probes. In one aspect, the control is Primer Pair Set 45 that comprises one or more the primer pairs shown in Table 46, in a combination with a corresponding probe sequence for the detection of control sample: Table 46. Xeno Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 45 NO NO NO GGCGTTTCCCGCGTT CGGCCGCAGCCTAAA ACAACAAAGGGTACT 1 TC 397 GATT 398 CGTCTAT 399 AGATCTAAGCGTGGA ACCCTTGCTAGTAGG ACGTACCAGAGGATC 2 AGTGGCTATA 400 TGTAGATTCTC 401 402 ACC CTGCGGAAGGCCCAA TTGACAGGCTCATAC 3 TTTC 403 404 ATATAA 405 CTAGCAAGGGTAGCC ATGGACGCTGCATTT 4 GATTAGTG 407 408 AC GGTTACGCGGCCAGA ACTATGGCGTACAAA 5 TGA ATTAGTATCCA 410 TAA 411 In some embodiments, method or assay includes one or more control primers and probes. In one aspect, the control is Primer Pair Set 46 that comprises one or more the primer pairs shown in Table 47, in a combination with a corresponding probe sequence for the detection of control sample: Table 47. Bacillus subtilis atrophaeus Primers and Probes (5′→3′) Primer SEQ SEQ SEQ Pair Set Forward Primer ID Reverse Primer ID Probe ID 46 NO NO NO CATCGGTGAAGAAAG CGGGTGACTTCAAAG ACGGTCCCCAGGCAT In some embodiments, the method or assay includes one or more control plasmids that contains target sequences for one or more of the target organisms. In one aspect, the control plasmid comprises one or more the sequences shown in Table 50. Specifically, the control plasmid for each pathogen target can include the entire corresponding amplicon sequence in Table 50 or a portion of the amplicon sequence in Table 50. The portion (i.e., number of base pairs) of the amplicon sequence can vary by pathogen target. The control plasmid can be used with the primers and probes of Tables 2–45 as a positive control. In one embodiment, the method and/or assay comprises a panel comprising one or more primer pairs and one or more probes for the individual, simultaneous, or sequential detection of the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample. In one aspect, the method has one or more primer pairs and one or more probes for the detection of a control sample of Bacillus atrophaeus. In another aspect, the method has one or more primer pairs and one or more probes for the detection of a universal RNA Spike In/Reverse Transcription (Xeno) Control. One embodiment described herein is an individual or multiplex panel for the individual, simultaneous, or sequential detection of the presence or absence of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalisin a sample. In one aspect, the individual or multiplex panel comprises at least one forward primer, at least one reverse primer, and at least one probe for each organism as shown in Table 42. All primer pairs (forward primers and reverse primers), and the requisite probes are consecutively numbered in multiples of three, e.g., 1, 2, 3; ... ; 370, 371, 372, as forward primer; reverse primer; and probe, respectively. As an exemplary aspect, for detecting Acinetobacter baumannii, a primer pair and probe set could include: a forward primer such as SEQ ID NO: 1, a reverse primer such as SEQ ID NO:2, and a probe such as SEQ ID NO: 3. Optionally, the individual or multiplex panel comprises controls, comprising at least one forward primer, at leat one reverse primer, and a probe for the Universal RNA Spike In/Reverse Transcription Control (Xeno) as shown in Table 46 or the control organsim Bacillus atrophaeus, as shown in Table 47. An additional positive control is a multisequence plasmid comprising the sequences shown in Table 50. This plasmid can be used with the primers and probes of Tables 2–45 as an amplification positive control. Table 48. Individual or Multiplex Panel I Open Array – Primers and Probes (38 Organisms) Organism Forward Primer Reverse Primer Probe SEQ ID NO SEQ ID NO SEQ ID NO Acinetobacter baumannii 1, 4, 7 2, 5, 8 3, 6, 9 Bacteroides fragilis 10, Clostridium perfringens 19, Enterobacter cloacae 28, 31, 34 29, 32, 35 30, 33, 36 Enterococcus faecalis 37, 40, 43 38, 41, 44 39, 42, 45 Enterococus faecium 46, 49, 52 47, 50, 53 48, 51, 54 Escherichia coli 55, 58, 61 56, 59, 62 57, 60, 63 Klebsiella pneumoniae 64, 67, 70 65, 68, 71 66, 69, 72 Klebsiella Oxytoca 73, 76, 79 74, 77, 80 75, 78, 81 Klebsiella aerogenes 82, 85, 88 83, 86, 89 84, 87, 90 Proteus mirabilis 91, 94, 97 92, 95, 98 93, 96, 99 Proteus vulgaris 100, 103, 106 101, 104, 107 102, 105, 108 Pseudomonas aeruginosa 109, 112, 115 110, 113, 116 111, 114, 117 Serraitia marcescens 118, 121, 124 119, 122, 125 120, 123, 126 Staphylococcus aureus 127, 130, 133 128, 131, 134 129, 132, 135 Streptococcus agalactiae 136, 139, 142 137, 140, 143 138, 141, 144 Streptococcus dysgalactiae 145, 148, 151 146, 149, 152 147, 150, 153 Streptococcus anginosus 154, 157, 160 155, 158, 161 156, 159, 162 Streptococcus pyogenes 163, 166, 169 164, 167, 170 165, 168, 171 Staphylococcus lugdunensis 172, 175, 178 173, 176, 179 174, 177, 180 Providencia stuartii 181, 184, 187 182, 185, 188 183, 186, 189 Stenotrophomonas maltophilia 190, 193, 196 191, 194, 197 192, 195, 198 Morganella morganii 199, 202, 205 200, 203, 206 201, 204, 207 Citrobacter koseri 208, 211, 214 209, 212, 215 210, 213, 216 Citrobacter freundii 217, 220, 223 218, 221, 224 219, 222, 225 Citrobacter braakii 226, 229, 232 227, 230, 233 227, 230, 233 Peptoniphilus asaccharolyticus 235, 238, 241 236, 239, 242 236, 239, 242 Peptoniphilus harei 244, 247, 250 245, 248, 251 245, 248, 251 Peptoniphilus ivorii 253, 256, 259 254, 257, 260 254, 257, 260 Peptostreptococcus anaerobius 262, 265, 268 263, 266, 269 263, 266, 269 Finegoldia magna 271, 274, 277 272, 275, 278 272, 275, 278 Clostridium septicum 280, 283, 286 281, 284, 287 281, 284, 287 Paeniclostridium sordellii (Clostridium sordellii) 289, 292, 295 290, 293, 296 290, 293, 296 Clostridium novyi A, B 298, 301, 304 299, 302, 305 299, 302, 305 Clostridium histolyticum 307, 310, 313 308, 311, 314 309, 312, 315 Staphylococcus epidermidis 316, 319, 322 317, 320, 323 318, 321, 324 Staphylococcus haemolyticus 325, 328, 331 326, 329, 332 327, 330, 333 Corynebacterium striatum 334, 337, 340 335, 338, 341 336, 339, 342 Candida albicans 343, 346, 349 344, 347, 350 345, 348, 351 Candida auris 352, 355, 358 353, 356, 359 354, 357, 360 Candida glabrata 361, 364, 367 362, 365, 368 363, 366, 369 Candida krusei 370, 373, 376 371, 374, 377 372, 375, 378 Candida parapsilosis 379, 382, 385 380, 383, 386 381, 384, 387 Candida tropicalis 388, 391, 394 389, 392, 395 390, 393, 396 Xeno 397, 400, 403, 406, 398, 401, 404, 407, 399, 402, 405, 408, 409 410 411 Bacillus subtilis atrophaeus 412, 415, 418, 421, 413, 416, 419, 422, 414, 417, 420, 423, 424 425 426 Another embodiment described herein is an individual or multiplex panel for the individual, simultaneous, or sequential detection of the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample. In one aspect, the individual or multiplex panel comprises at least one forward primer, at least one reverse primer, and at least one probe for each organism as shown in Table 49. Optionally, the individual or multiplex panel comprises controls, comprising at least one forward primer, at leat one reverse primer, and a probe for the Universal RNA Spike In/Reverse Transcription Control (Xeno) as shown in Table 46 or the control organsim Bacillus atrophaeus, as shown in Table 47. An additional positive control is a multisequence plasmid comprising the sequences shown in Table 50. This plasmid can be used with the primers and probes of Tables 2–45 as an amplification positive control. Table 49. Individual or Multiplex Panel II TaqMan Array – Primers and Probes (28 Organisms) Organism Forward Primer Reverse Primer Probe SEQ ID NO SEQ ID NO SEQ ID NO Acinetobacter baumannii 1, 4, 7 2, 5, 8 3, 6, 9 Bacteroides fragilis 10, 13, 16 11, 14, 17 12, 15, 18 Clostridium perfringens 19, 22, 25 20, 23, 26 21, 24, 27 Enterobacter cloacae 28, 31, 34 29, 32, 35 30, 33, 36 Enterococcus faecalis 37, 40, 43 38, 41, 44 39, 42, 45 Enterococcus faecium 46, 49, 52 47, 50, 53 48, 51, 54 Escherichia coli 55, 58, 61 56, 59, 62 57, 60, 63 Klebsiella pneumoniae 64, 67, 70 65, 68, 71 66, 69, 72 Klebsiella Oxytoca 73, 76, 79 74, 77, 80 75, 78, 81 Klebsiella aerogenes 82, 85, 88 83, 86, 89 84, 87, 90 Proteus mirabilis 91, 94, 97 92, 95, 98 93, 96, 99 Proteus vulgaris 100, 103, 106 101, 104, 107 102, 105, 108 Pseudomonas aeruginosa 109, 112, 115 110, 113, 116 111, 114, 117 Serratia marcescens 118, 121, 124 119, 122, 125 120, 123, 126 Staphylococcus aureus 127, 130, 133 128, 131, 134 129, 132, 135 Streptococcus agalactiae 136, 139, 142 137, 140, 143 138, 141, 144 Streptococcus dysgalactiae 145, 148, 151 146, 149, 152 147, 150, 153 Streptococcus anginosus 154, 157, 160 155, 158, 161 156, 159, 162 Streptococcus pyogenes 163, 166, 169 164, 167, 170 165, 168, 171 Staphylococcus lugdunensis 172, 175, 178 173, 176, 179 174, 177, 180 Providencia stuartii 181, 184, 187 182, 185, 188 183, 186, 189 Stenotrophomonas maltophilia 190, 193, 196 191, 194, 197 192, 195, 198 Morganella morganii 199, 202, 205 200, 203, 206 201, 204, 207 Citrobacter koseri 208, 211, 214 209, 212, 215 210, 213, 216 Citrobacter freundii 217, 220, 223 218, 221, 224 219, 222, 225 Citrobacter braakii 226, 229, 232 227, 230, 233 227, 230, 233 Peptoniphilus asaccharolyticus 235, 238, 241 236, 239, 242 236, 239, 242 Peptoniphilus harei 244, 247, 250 245, 248, 251 245, 248, 251 Peptoniphilus ivorii 253, 256, 259 254, 257, 260 254, 257, 260 Peptostreptococcus anaerobius 262, 265, 268 263, 266, 269 263, 266, 269 Finegoldia magna 271, 274, 277 272, 275, 278 272, 275, 278 Candida albicans 343, 346, 349 344, 347, 350 345, 348, 351 Candida auris 352, 355, 358 353, 356, 359 354, 357, 360 Candida glabrata 361, 364, 367 362, 365, 368 363, 366, 369 Candida krusei 370, 373, 376 371, 374, 377 372, 375, 378 Candida parapsilosis 379, 382, 385 380, 383, 386 381, 384, 387 Candida tropicalis 388, 391, 394 389, 392, 395 390, 393, 396 Optional Control: Xeno 397, 400, 403, 406, 398, 401, 404, 407, 399, 402, 405, 408, 409 410 411 Optional Control: Bacillus subtilis 412, 415, 418, 421, 413, 416, 419, 422, 414, 417, 420, 423, atrophaeus 424 425 426 In one embodiment, the primers pairs and probes shown in Tables 2–45 can be used to produce an amplicon. In one embodiment, the amplicons are shown in Table 50. Specifically, the amplicon for each pathogen target (i.e., organism) can include the entire corresponding amplicon sequence in Table 50 or a portion of the amplicon sequence in Table 50. The portion (i.e., number of base pairs) of the amplicon sequence can vary by pathogen target. Table 50. Amplicons Organism Amplicon Sequences (5′→3′) SEQ ID CGGTACATTTTAAACATAGTCATGGCGTCGTGTTCAAACTCTTGCTAACAT Acinetobacter GCTAAAGCATAACAACAGCTTAAAATTATGCACTAGATGAGGATTGGGCTT baumannii 427 GAACAATGAAGAGGAACGTTACT TACGAAGAAACCGTGTCCTTTGATGTTCCAGTGAAATCCTCTCAGGTTTGC Bacteroides fragilis ATAATGAATCTGAAAATCGGCAAGCAGTTGCTGTAATGACAGTACGATGGT 428 GTTAGCTCCTTTTTCTTCCAAATGTGTATAATT TCAGATTTATAATGAACAATATCTACATGTTCTCTCTGTGATGGTATTCCT Clostridium AAAATCTTATAAGCAAATTCATCTGCTAAAAGACTTTTTCCTATTCCATCC perfringens 429 TCACCAATAATTAAATGAGCATGGGAAAGT GGTGTTTGCCATGCTTAATCTGGTTCCCGGCAAGCAGTTATGTGAAACGCT Enterobacter GGAACATCTAATTCGTGAGAAAGATGCCTCTGGCATTGAAAAATACATCAG cloacae 430 CGACATTGACGCTTACGTCAAGAGCTTGCTGTAGCA TTTTCTCCATACATCGCTGTCAACACGTGCGAAGGATCCACAGTTCCCGCT Enterococcus GTACAAGCCGAGCCTGTTGAAATCGCAATACCTCTTAAGTCCAAATGCATT faecalis 431 AAGAGCAAATCACTGGGAATTCCTTTTAAATGAAGATTTAAGA CATCATTTCTGTCATTTCTTGAATCTCTACACAGCCATTTCGTAATGCTTT Enterococcus ATTATGTGTGTCCTCGATATCAGAGACGATGATATTGAACCAGATCGTATT faecium 432 TGGATGTTCAGCAGTAGGAGCAGTCAAACCAAGAGACGTGTTTTCA ACTCCAGACTGAAACCAAGTTGTCTGGCATGGCGGATAAATTTCAATCGCT Escherichia coli GGAGATCGCTTTCGGTATACAGGCGAAACCCACCTTCGGTACGTACTTCAT 433 GCTCCATCATC CTCGAAGGCGGCGGCGTATTCACCACGCCTGATGCCGGACATGCGCATTTT Klebsiella CTGGTGGAAGACGGTGAGACAGCCCGCAGGGTGCTGACCGAGGCCGGCTTT pneumoniae 434 ACGG AGAATATTAGGCAAGCGCGCAGGCAGCATCTTCGGCTCCTGCAAAGTGCCG Klebsiella Oxytoca TCGAAGTTTGGTACCCAGTCAACGGTGCCCTGCCCCAGTTCGCTCAGCAGC 435 AGTTCAGCATACTTCGACAAACGGGATTCGGTATAACGCAT TTACACCATGCTGGAGCGTTTTCTGCGTTTCTCAATTAATAACTGTGGTGA Klebsiella CTGGGGGGAGTACTGTAACTATTTACTCAACTCTTTCGACTTTGAAAAAGA aerogenes 436 AGTCATGGAGTATTTCTCCGGCATATTCAAAATCCCCTTTGCGGAA TTCAGACAGTACTAAGGTATGTAATTCAATCGGTTTGGTCGGGAAAAAATT Proteus mirabilis TGTCACATCACAAGAAACTTGACTATATTTAGGAATAATCAACGTGAGATT 437 AGTGGTGACTGTGATAGTTTGCCCATTAATACAAATCTCACCTTTTGC CGTTGAAGATGGCGCAAAAGGCTTTGCACGATTACCGACTGAAACTGAATG Proteus vulgaris GGAATTTGCGGTGCGAGGTGGCCTAAAAGTTTCAGCATCCGAATTTCGTGA 438 TACTCGTTTTCCTATGCCGGAAGG TCTGCTGGCCGGTTGCGTCAAGGGGTTGAAGGAATTGCTTGTGCATGAGCA Pseudomonas TCCGCCGATGCTCGCCTGCCTGAAGATCGAGGAGTTGCTGATGCTCTTCGC aeruginosa 439 GTTCAGTCCGCAGGGGCC CCAGCACCGGCAAGCTGCCGTCCACCGCCAGCCCGTACGATCGCGACACCC Serratia marcescens AGTCCGGCACCGAGGCGCACGCGTTTTATATCGACGATCGCATCGACATCG 440 GCGACTGGACCATCACGCCGGGCATGCGCTACG CACGTGCACTAGTCACACTGGTACTCAGGTGATAACCATCTGTCTACACCA Staphylococcus CTTCATTTCGCGAAGTGTGTCTCGTTTATACGTTGAATTCCGTTAAACAAG aureus 441 TGCTCCTAC AATAAAAAGGTACTATTGACATCGACAATGGCAGCTTCGCTATTATCAGTC Streptococcus GCAAGTGTTCAAGCACAAGAAACAGATACGACGTGGACAGCACGTACTGTT agalactiae 442 TCAGAGGTAAAGGC AGGCTAGCAAGTAAGATGACATTCTCGGAGTGGTATCAAATGTCCAAAGGC Streptococcus CAGTTTCCTCACGGCGATCGACATTGATTTCTGGCATGTTAGATAAGGCGA dysgalactiae 443 TGTCACCAGCTTCTTGATCAAA AACCTTTTTAGTCGTTACTATGTCTGTGTTGATGACGGATAGTCCCTTTAT Streptococcus TGGTACGGAAAAGACGGGCGGGATTATCTATGGCTGGGTAAATGGTTTTTG pyogenes 444 GGGGCTGTTGTCCTTTGCCATGCAGATGACTATTTTACTTGCGACAGGGA CCCTGATGGGTCTGAAAGGTCAAGTGCACGTGATAGCCAATCTAAGAGATT Streptococcus TTTAACAACTCCTGGAATTGCCCAGTTATAGGTTGGTGAGAAGAGCCAGAT anginosus 445 AGCATCAGCAGCGAGAATTTCTTCACGAGCTTTGGCAACAGCCGCAG CTCAAATTGTGTACAAAAAAATCCTCAAACCATAACCAGTTTCAGGATCTA Staphylococcus TGAGGTAACGACCAATACTTTAGATATTTATATCCAACCAATAGCAAATAG lugdunensis GTTTAGAAATTTCACTACATGTGCACTGTGTATAGTTGAAATTGCATTGAT 446 T GAGCAGTACTTGTGTTCATTCAGAACGCTGTGGCACGAATATGATGATGGA Providencia stuartii AACTCAAGGCGAGATTTACGCTTGCGATCATCAAGCAAATCAAAGTCACTA 447 TCTTGGTCAATTTAATGGGCAGCAAGGATTTAGTGATTTTGTTGAGGC ATTTCTCACGCCATCTGTTTCTGATACGTTTGGCGGCTCAGATTTTTCTGA Stenotrophomonas CAGTCCGACTTTGCCGCTAACCGGCGGTTCGATCGAGGTGAACGATGATTT maltophilia 448 TCCGTAACCACAAAGCTGTGCTTTCCGTCCTCGTCG GGGCAAATCAGCCCGGCATACCGTCAGAAATTATTGTCTCTGGGCATGCTG Morganella morganii CCCGGCTCTGTTTTCCGGGTGATCCGCAGCGCACCGCTGGGCGATCCGATC 449 CAAATCGAAACCCGGCACGTCAACCTGATGCTCAGAAAA GTTTGTTACTGTTTTATTTTTCCGGGGTAGCACTTACCTCTTACGCAGGCG Citrobacter koseri TGCGTATGCATCCTGCGATCACTGACAAACCATCATCAAAAAAACCGATGG 450 AAGGGAACATTATGCGAATTGGCATACCAAAAGAGCGGTTAACCAA CTTTATCACCTGGCAGGATGCTGGCCCTCAAATCGTGTTGGATCAGTTGCG GGCGCAAAAAGTTAACGTCGTGACGTTGCCGCGCGTACCGGCCACCGTCGA Citrobacter freundii ACAGATGTACGCCAACATTCGGGAACTGGCTCAAACCCTGCGCATTCCCGA 451 ACAAGGT TTGAATACATTGCTGGTAAAGTTGCGGCTAAAGACTACGTTGACGAATCTA Citrobacter braakii CTGGCGAGCTGATCTGCGCAGCTAACATGGAGCTGAGTCTGGATCTGCTGG 452 CTAAGCTGAGCCAGTCTGGCCACAAGCGTA CGTGTATTACATAAACCCGTAGGGGACGCACGAACGGATGTGAGGCCGTCC Peptoniphilus CGCCGTAGCCCAAGCCAAACGAAATCCAAAATCGTTTACGAAACATTGGTT asaccharolyticus 453 TTGAAAATCATCCACCAAAAATT GCGCGCTTAACACATGCAAGTCGAGCGATGAAATCTTGACAGATCCTTCGG Peptoniphilus harei GGTGAAGATAAGATGGATTAGCGGCGGACGGGTGAGTAACACGTGAGTAAC 454 CTGCCTTAGACATTGGGATAGCCTCGGGAAACCGGGATTAATACCA GCGTGAGGAACCTGCCTCTCACAACGGGATAGCCTCGGGAAACCGGGATTA Peptoniphilus ivorii ATACCGTATGAGACCACAGTAACGCCTGTTACAGTGGTTAAAGTCACAGCG 455 GTGAGAGATGGCCTCGCGTCTGATTAG GAGATGGTATCGTATGAAGTTAAAAAAGAAAGCGGTTGTTAGTGTAGCTAT Peptostreptococcus GTGTCTTTCCCTAATTTTGGTTGGACAGCCAGTATATGGGGAGACTAATAA anaerobius 456 TAATCCTGCAAAGCCA GTTGTCCGGAATTATTGGGCGTAAAGGGTACGCAGGCGGTTTAATAAGTCG Finegoldia magna AATGTTAAAGATCGGGGCTCAACCCCGTAAAGCATTGGAAACTGATAAACT 457 TGAGTAGTGGAGAGGAAAGTGGAATTCCTAGTGTAGTGGTGAAATAC AGCTCATTCATTAGGATTTGGATGGTGCGGTGGAACGGCTAATCCAAACGT Clostridium TGGACAAGGTTTTGAATTTAAAAGAGAAGTTGGGGCAGGTGGAAAAGTATC septicum 458 TTATTTATTATCTG Paeniclostridium AGGAATCAGACTATGCTACTAATGTTGAGACAGCAGTAGATCAAGGTGCTG sordellii (Clostridium ATTTAGTAATAGGGGTTGGATTTAAATTAGAAAAAGCAATAGGGGAAGCTG 459 sordellii) CTAAGGCATATCCAGAGGAAAAATTCGCATTA CTAAATCCTTGTCTAAAACATCAATAGTATCTGCTAGATCACCTTCTGAGT Clostridium novyi TTAATTTGTTAGAGCCAGAAACTATAACATTACATTTTTCAAAGTTAACTA A,B TTTTATAATTATTAAAGTCATTTTCCCAATATCCACCGTTTATTATCCATT 460 TATTATTTGTGCT GTCTTGTATTTGCAACACTTGGTATTGCACTTGCAGTTATTATGTCAGGTA Clostridium TAGGATCAGCTAGAGGTGTTGGTATGGTTGGTGAATCTGCTGCAGGACTAT histolyticum 461 TAACTGAAGAACCAGAAAAGTTTGGTAAGGCCTT TTATAATTAATCCGTTTGAAGTAGTTTACTACGCTGGTGGAACTTCAAATC Staphylococcus GTTATCGCCATTTTGCAGGGAGCTATGCGGTTCAATGGAAGATGATTAACT epidermidis 462 ATGCAATTGAACATGGT GGTTTACCTATCCTAGAAATGGATGGAGCGGCAAATAAATCAGAAGTTAAT Staphylococcus CACTTTATCAATGATGTGAATGAACTTGGTGCAGACATTAAAGAGGAAATG haemolyticus 463 ACACAAACGGGCGATAATTTTAGTTTAGCAGTATTA CGTGCTCCCTGGTGGCACGAGTAATGCAGATGCGCTTCGTATGGACGAAGC Corynebacterium CGCAGTGGAAATCGTGAAGAAGCACGTTGAGGCAGGCCGTCCACTGGGCGT striatum TATCTGCCACGGCGGTTGGATTCTTACTGACGCTGACGTGCTTAAGGACCG 464 TACTCTTACGTC CACTGCTGTATGGTTATATGTTTTCCATGCTCCTGGTTCACTTAAAGCATA CAGTTTTGCCCTTGGATTACAAAATATTTGTGGAGTTTTAACTCATTTACT Candida albicans ATTCCCCAATGCTGCACCTTGGTTTATTCATATGAATGGAGAGAATGCTAA 465 TG ATGCTTAAGTTCAGCGGGTAGTCCTACCTGATTTGAGGCGACAACAAAACG AAAAAAAAAGCGTAGATTTTTTTCGTGCAAGCTGTAATTTTGTGAATGCAA Candida auris CGCCACCGCGAAGATTGGTGAGAAGACATCACGCTCAAACAGGCATGCCTT 466 GGGGAATACCCCAAGG TATTGTCAAATATAATTGATGCATCGGCGTCTTCGCATAATCTCCTTAGAG Candida glabrata TTAGCACAGTATTGTAAGGTCCCACCACAACTTCAGATTGCTTACTGGGGA 467 ATACTGAATATGTTGTAATAAAA GTCCATCGATTCTACCCAATCCTCCTGGCGATCCCTTCATTGAATAGTTTG Candida krusei CCTTGTCCAACCCATGCAGCACTTTATACCATGGTGGAGCACATGAGAAAA 468 CCAAGTTTTGGATAATGACGCCAACCA AAGCGGGACAATGCGGGAATCAAGTGGGTCTACAATACTGGCAACAACTAG Candida CTCTAGAGCATGGAATAAACAAAGATGGAACACCAACACTGTATCCAAATA parapsilosis CATCATTCAATAGTTCTCAGACTGGCTCTCATCCTTCTCTGCAAGACTCAC 469 CACTGGGTCTGGCC TCTAGATCAAAGAGAAATTCGTAAAGGAATATTGAAATCACAACAAAGAAC ACCATTTGTTCCGTGGGCTGCTAGATCAGTTCAAGTGATACATGGTAAGAA Candida tropicalis ATCTCCTTTTATAAAGTCAAGTAATAATCTAGACGGGGTACAAATTACAAA 470 TAATACGTCAATTATC Sample or Specimen Described herein are compositions, kits, and method for the detection (i.e., the presence or absence) of wound pathogens including one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, or Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a specimen or a sample. DNA or RNA is extracted from one or more specimen/sample, reverse transcribed if required, multiplied using real-time amplification (or RT-PCR if required), and detected using specific primers and a fluorescent reporter dye probe for one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis. As will be appreciated by those in the art, the specimen/sample may comprise any number of things, including, but not limited to, include samples, swabs, or tissue samples (for example, taken during a biopsy) obtained from human patients; research samples; purified samples, such as purified genomic DNA, RNA, proteins, etc.; and raw samples (bacteria, virus, genomic DNA, etc.). As will be appreciated by those in the art, any experimental manipulation can have been performed on the sample before analysis. In some embodiments, the specimen/sample type for diagnosis of wound pathogens is one or more swabs of a subject’s body or of a wound. If required, nucleic acid from the sample/specimen is isolated using known techniques. For example, the sample/specimen may be treated to lyse the cells, using known lysis buffers, sonication, electroporation, etc., with purification occurring as needed, as will be appreciated by those in the art. In addition, the reactions outlined herein may be accomplished in a variety of ways, as will be appreciated by those in the art. Components of the reaction may be added simultaneously, or sequentially, in any order, with preferred embodiments outlined below. In addition, the reaction may include a variety of other reagents that may be included in the assays. These include reagents like salts, buffers, neutral proteins, e.g., albumin, detergents, etc., which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may be used, depending on the sample/specimen preparation methods and purity of the target wound pathogens. In some embodiments, total nucleic acid extraction from a sample or a wound swab is performed. The specimen/sample may be collected and transported in the Remel™ Cary-Blair Transport Medium by Thermo Fisher Scientific according to appropriate laboratory procedures. Remel™ Cary-Blair Transport Medium is a semisolid medium recommended for use in the collection, transportation, and preservation of sample/specimens, especially wound samples and wound swabs. Nucleic acids may be isolated and purified from the specimen/sample using a nucleic acid isolation, such as, e.g., the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit with Bead Plate (Thermo Fisher Scientific). Nucleic acid extraction may be performed via an automated process using, e.g., the Kingfisher™ Flex Purification System. For RNA viruses, the RNA is reverse transcribed into cDNA. The cDNA and genomic DNA (from DNA viruses) are then subjected for amplification using the currently disclosed composition, method, or kit. Process Control, Control Organism, or Control Sample In addition, the disclosed kit and method of detection may further include a process control (“process control” is herein referred to, interchangeably, as “control organism” or “control sample”). This is an exogenous control that has the added advantage of being a bacterial lysis control in addition to being a nucleic acid extraction and recovery control. Controls are treated and tested in parallel with target pathogen and are used to generate a predetermined expected result. When the expected result is reported, one or more aspects of the diagnostic test are confirmed to be working as intended, enabling the user of to verify the diagnostic test as valid. The process control may be Bacillus atrophaeus, which is a gram- positive, endospore forming bacterium. Preferably, the process control can function as a positive control for lysis, purification and amplification within the cartridges described herein. One exemplified process control is lyophilized Bacillus atrophaeus, such as, e.g., the TaqMan™ Universal Extraction Control Organism by Thermo Fisher Scientific. The process control may be supplied lyophilized in a quantity of 1 × 109 copies/vial, and reconstituted in 200 µL of 1× PBS, pH 7.4 to a final concentration 5 × 106 copies/µL. During nucleic acid isolation, 10 µL of the process control is processed as a stand-alone sample in a background of universal transport media. The process control can be added to a negative extraction control. The process control may be added to one or more samples/specimens at the start of the extraction process. The process control is carried through the remainder of the workflow with the samples/specimens. It is recommended that at least one stand-alone control sample is run per extraction plate. Another exemplified process control is a bacterial spore, such as a spore of a Bacillus species. Suitable spores can be comprised of any species of Bacillus, including, e.g., Bacillus globigii, Bacillus atrophaeus, Bacillus subtilis, or Bacillus stearothermophilus. In one embodiment, the process control may be a Bacillus atrophaeus bacterial spore. In one embodiment, vicinal oxygen chelate (VOC) genes (accession number cll463) of Bacillus atrophaeus are detected as a process control. Another exemplified process control is the TaqMan® Universal RNA Spike In/Reverse Transcription (Xeno) Control is an exogenous process control for nucleic acid isolation, reverse transcription, and preamplification. The control can also be used as an internal positive control for real-time PCR. The control is used with the proprietary TaqMan® assay for Xeno™ sequences. Positive Control In addition, the disclosed method of detection may further include a positive control to determine the validity of the assay. The positive control is a mixture of plasmids of the target pathogens. For instance, an exemplified positive control is a mixture of plasmids containing sequences for one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis. Reaction Mixture The terms “reaction mixture,” “amplification mixture,” or “PCR mixture” as used herein refer to a mixture of components necessary to amplify at least one amplicon from nucleic acid templates. The mixture may comprise nucleotides (dNTPs, such as A, C, G, and T), a thermostable polymerase, primers, and a plurality of nucleic acid templates. The mixture may further comprise a buffer. As used herein, “buffer” refers a solution that can include multiple components such buffers that maintain a specific pH (e.g., Tris^HCl), mono and divalent salts (e.g., NaCl, KCl, (NH4)2SO4, MgCl2, MgSO4), cofactors, detergents (e.g., Polysorbate 20 (Tween™ 20), t-octylphenoxy polyethoxyethanol (Triton™ X-100), octylphenoxy polyethoxyethanol (Nonidet™ P-40)), and other additives (e.g., glycerol, polyethylene glycol, betaine, formamide, dimethyl sulfoxide, dithiothreitol, tetramethylammonium chloride, bovine serum albumin, gelatin, inter alia), The working concentration range of each component is known in the art and can be optimized as needed. An exemplary PCR reaction mixture comprises: 50 fg to 50 ng of target DNA; 0.1–1 μM of each primer and probe; 1–2 units of Taq DNA polymerase; 0.2 mM of each dNTP; 20 mM Tris^HCl (pH 8.4), 50 mM KCl, 1.5 mM MgCl2, and water to the requisite volume. Typically, the PCR mixture is dispensed into a PCR microtube, port or reservoir (e.g., of a TaqMan™ Array Card) or plate (e.g., wells of a TaqMan™ OpenArray sample plate), the mixture is mixted by vortexing, and either capped, sealed, or overlayed with mineral oil or silicone oil to prevent evaporation. Amplification “Amplification” as used herein refers to the use of any amplification procedures to increase the concentration of a particular nucleic acid sequence within a mixture of nucleic acid sequences. In one embodiment and as describe more fully herein, a sequence from a sample is amplified to produce a secondary target (e.g., an amplicon) that is detected, as outlined herein. Amplification involves the amplification (replication) of the sequence to be detected, such that the number of copies of the sequence is increased. Suitable amplification techniques include, but are not limited to, the polymerase chain reaction (PCR), strand displacement amplification (SDA), transcription mediated amplification (TMA) and nucleic acid sequence-based amplification (NASBA). In one embodiment, the amplification technique is PCR. The polymerase chain reaction (PCR) is well known and involves the use of primer extension combined with thermal cycling to amplify a target sequence. As used herein, “PCR”, unless specifically defined, refers to either single-plex (i.e., individual) or multiplex PCR assays, and can be real time or quantitative PCR (wherein detection occurs during amplification), end-point PCR (when detection occurs at the end amplification), or reverse transcription PCR, including but not limited to, “real-time PCR” or “quantitative PCR” or “qPCR”, “digital PCR” or “dPCR”, “reverse transcriptase PCR” or “RT-PCR”, “multiplex PCR”, “nested PCR”, “hot start PCR”, “long-range PCR”, “assembly PCR”, “asymmetric PCR”, “in situ PCR,” “single-cell PCR,” or “fast-cycling PCR,” among others. An exemplary PCR amplification typically consists of 25–35 cycles of: a denaturing step a 94 °C for 30–45 seconds; an annealing step at 55 °C for 20–60 seconds; and an extension step at 72 °C for 30–90 seconds. The amplification may be preceded by an initial denaturation step at 94 °C for 2–3 minutes. The amplification may be followed by a final extension step at 72 °C for 10 min, and then cooled to 4 °C and maintained at this temperature until the samples are removed from the thermocycler. Example embodiments of amplification are not limited to PCR. For instance, signal amplification, single base extension (SBE) or minisequencing, oligonucleotide ligation amplification (OLA) and/or rolling-circle amplification can be used for amplification. In an embodiment, amplification can include OLA followed by RCA. A skilled person would be well aware of the real-time PCR systems that can be used for a multiplex detection using several dyes, or nucleic acid amplification assays as described herein. Exemplary systems include a real-time quantitative PCR (qPCR) instrument, including for example a QuantStudio™ Real-Time PCR system, such as the QuantStudio™5 Real-Time PCR System (QS5), QuantStudio™ 7 Real-Time PCR System (QS7), QuantStudio™ 12K Flex System (QS12K), QuantStudio™ DX Real-Time PCR System (QS Dx or QS5 Dx), or a 7500 Real-Time PCR system, such as the 7500 Fast Dx system, all from Applied Biosystems™ – a Thermo Fisher Scientific brand. Amplicon The terms “amplified product” or “amplicon” refer to a fragment of DNA amplified by a polymerase using a pair of primers in an amplification method such as PCR. Probe “Probe” as used herein, is a non-extendable oligonucleotide attached to a fluorescent reporter dye and a quencher moiety. Primer “Primer” as used herein can refer to more than one primer and refers to an oligonucleotide, whether occurring naturally or produced synthetically, which is capable of acting as an initiation- point for primer extension synthesis when placed under conditions that produce a primer extension product which is complementary to a nucleic acid strand, e.g., in the presence of nucleotides and an agent for polymerization such as DNA polymerase, at a suitable temperature for a sufficient amount of time and in the presence of a buffering agent. Such conditions can include, for example, the presence of at least four different deoxyribonucleoside triphosphates (such as A, C, G, and T) and a polymerization-inducing agent such as DNA polymerase or reverse transcriptase, in a suitable buffer, and at a suitable temperature. In some embodiments, the primer may be single-stranded for maximum efficiency in amplification. The primers herein are selected to be substantially complementary to the different strands of each specific sequence to be amplified. This means that the primers must be sufficiently complementary to hybridize with their respective strands. A non-complementary nucleotide fragment may be attached to the 5′-end of the primer, with the remainder of the primer sequence being complementary, or partially complementary, to the target region of the target nucleic acid. Commonly, the primers are complementary, except when non-complementary nucleotides may be present at a predetermined sequence location, such as a primer terminus as described. The complement of a nucleic acid sequence as used herein refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5′-end of one sequence is paired with the 3′-end of the other, is in “antiparallel association.” Complementarity need not be perfect; stable duplexes may contain mismatched base pairs or unmatched bases. Dyes, Detectable Labels, or Fluorescent Labels The primers and/or probes described herein may further comprise a dye, fluorescent label, or other detectable label. It should be appreciated that when using multiple fluorescent or detectable labels, particularly in an individual or multiplex format, each fluorescent or detectable label preferably differs in its spectral properties from the other detectable labels used therewith such that the labels may be distinguished from each other, or such that together the fluorescent or detectable labels emit a signal that is not emitted by either fluorescent or detectable label alone. Exemplary fluorescent or detectable labels include, for instance, a fluorescent dye or fluorophore (e.g., a chemical group that can be excited by light to emit fluorescence or phosphorescence), “acceptor dyes” capable of quenching a fluorescent signal from a fluorescent donor dye, and the like, as described above. Suitable fluorescent or detectable labels may include, for example, fluoresceins (e.g., 5-carboxy-2,7-dichlorofluorescein; 5-carboxyfluorescein (5-FAM); 5-hydroxy tryptamine (5-HAT); 6-JOE; 6-carboxyfluorescein (6-FAM); Mustang Purple, VIC, ABY, JUN; FITC; 6-carboxy-4′,5′-dichloro-2′,7′-dimethoxy-fluorescein (JOE)); 6-carboxy-1,4-dichloro-2′,7′- dichloro-fluorescein (TET); 6-carboxy-1,4-dichloro-2′,4′,5′,7′-tetra-chlorofluorescein (HEX); Alexa Fluor fluorophores (e.g., 350, 405, 430, 488, 500, 514, 532, 546, 555, 568, 594, 610, 633, 635, 647, 660, 680, 700, 750); BODIPY fluorophores (e.g., 492/515, 493/503, 500/510, 505/515, 530/550, 542/563, 558/568, 564/570, 576/589, 581/591, 630/650-X, 650/665-X, 665/676, FL, FL ATP, FI-Ceramide, R6G SE, TMR, TMR-X conjugate, TMR-X, SE, TR, TR ATP, TR-X SE), Cascade Blue, Cascade Yellow; Cy™ dyes (e.g., 3, 3.18, 3.5, 5, 5.18, 5.5, 7), cyan GFP, cyclic AMP Fluorosensor (FiCRhR), fluorescent proteins (e.g., green fluorescent protein (e.g., GFP, EGFP), blue fluorescent protein (e.g., BFP, EBFP, EBFP2, Azurite, mKalamal), cyan fluorescent protein (e.g., ECFP, Cerulean, CyPet), yellow fluorescent protein (e.g., YFP, Citrine, Venus, YPet), FRET donor/acceptor pairs (e.g., fluorescein/fluorescein, fluorescein/tetramethylrhodamine, IAEDANS/fluorescein, EDANS/dabcyl, BODIPY FL/BODIPY FL, Fluorescein/QSY7 and QSY9), LysoTracker and LysoSensor (e.g., LysoTracker Blue DND- 22, LysoTracker Blue-White DPX, LysoTracker Yellow HCK-123, LysoTracker Green DND-26, LysoTracker Red DND-99, LysoSensor Blue DND-167, LysoSensor Green DND-189, LysoSensor Green DND-153, LysoSensor Yellow/Blue DND-160, LysoSensor Yellow/Blue 10,000 MW dextran), Oregon Green (e.g., 488, 488-X, 500, 514); rhodamines (e.g., 110, 123, B, B 200, BB, BG, B extra, 5-carboxytetramethylrhodamine (5-TAMRA), 5 GLD, 6- Carboxyrhodamine 6G, Lissamine, Lissamine Rhodamine B, Phallicidin, Phalloidine, Red, Rhod- 2, ROX (6-carboxy-X-rhodamine), 5-ROX (carboxy-X-rhodamine), Sulphorhodamine B can C, Sulphorhodamine G Extra, TAMRA (6-carboxytetramethyl-rhodamine), Tetramethylrhodamine (TRITC), Texas Red, Texas Red-X, among others as would be known to those of skill in the art. Exemplary fluorescent labels include but are not limited to FAM, VIC, ABY, JUN, AF647, or 6FAM. In one exemplary individual or multiplex dye scheme, the fluorescent labels include FAM, VIC, ABY, JUN, or AF647; or 6FAM, VIC, ABY, JUN, or FAM. In another exemplary individual or multiplex dye scheme, the fluorescent labels include FAM, HEX (JOE/VIC), Texas Red, and Cy5 dyes. In one embodiment the probes are labeled with FAM. Other detectable labels may be used in addition to or as an alternative to labelled probes. For example, primers can be labeled and used to both generate amplicons and to detect the presence (or concentration) of amplicons generated in the reaction, and such may be used in addition to or as an alternative to labeled probes described herein. As a further example, primers may be labeled and utilized as described in Nazarenko et al., Nucleic Acids Res. 30(9): e37 (2002), Hayashi et al., Nucleic Acids Res.17(9): 3605 (1989), and/or Neilan et al., Nucleic Acids Res.25(14): 2938-2939 (1997). Those of skill in the art are capable of utilizing the PCR processes (and associated probe and primer design techniques) described in Zhu et al., Biotechniques (4): 317-325 (2020). In some embodiments, the primers and/or probes may further comprise a quencher. Suitable quenchers include but are not limited to QSY (e.g., QSY7 and QSY21), BHQ (Black Hole Quencher) and DFQ (Dark Fluorescent Quencher). In an exemplary embodiment, the quencher is QSY7. Detector probes may also include two probes, wherein, for example, a fluorophore is associated with one probe and a quencher is associated with a complementary probe such that hybridization of the two probes on a target quenches the fluorescent signal or hybridization on the target alters the signal signature via a change in fluorescence. Detector probes may also include sulfonate derivatives of fluorescein dyes with SO3 instead of the carboxylate group, phosphoramidite forms of fluorescein, phosphoramidite forms of Cy5. Any of these systems and detectable labels, as well as many others, may be used to detect amplified target nucleic acids. In some embodiments, intercalating labels can be used such as ethidium bromide, SYBR Green I, SYBR GreenER, and PicoGreen (all products of Applied Biosystems – a brand of Thermo Fisher Scientific), thereby allowing visualization in real- time, or end point, of an amplification product in the absence of a detector probe. In some embodiments, real-time visualization may include both an intercalating detector probe and a sequence-based detector probe. In some embodiments, the detector probe is at least partially quenched when not hybridized to a complementary sequence in the amplification reaction and is at least partially unquenched when hybridized to a complementary sequence in the amplification reaction. In some embodiments, probes may further comprise various modifications such as a minor groove binder (MGB) to further provide desirable thermodynamic characteristics. In some embodiments, the amplicon is labeled by incorporation of, or hybridization to labeled primer. In some embodiments, the amplicon is labeled by hybridization to a labeled probe. In some embodiments, the amplicon is labeled by binding of a DNA-binding dye. In some embodiments, the dye may be a single-strand DNA binding dye. In other embodiments, the dye may be a double-stranded DNA binding dye. In other embodiments, the amplicon is labeled via polymerization or incorporation of labeled nucleotides in a template-dependent (or template- independent) polymerization reaction. This can be part of the amplifying step or alternatively the labeled nucleotide can be added after amplifying is completed. The labeled amplicon (or labeled derivative thereof) can be detected using any suitable method such as, for example, electrophoresis, hybridization-based detection (e.g., microarray, molecular beacons, and the like), chromatography, NMR, and the like. In one exemplary embodiment, the labeled amplicon is detected using qPCR. In some embodiments, a plurality of different amplicons is formed, and optionally labeled, within a single reaction volume via a single amplification reaction. For example, a multiplex reaction (e.g., 4- plex) carried out in a single tube or reaction vessel (e.g., “single-tube” or” I-tube” or “single-vessel” reaction) can produce a plurality of amplicons that are labeled. In some embodiments, the plurality of amplicons can be differentially labeled. In some embodiments, each of the plurality of amplicons produced during amplification is labeled with a different label. Assay Mixture The terms “assay mixture” or “assay mix” or “assay composition,” as used herein, include mixture containing the primer-probe pairs described above that are used in PCR. Another aspect provided herein is a method of detecting or quantifying a target nucleic acid molecule in a sample by polymerase chain reaction (PCR), such as by quantitative real-time polymerase chain reaction (qPCR). In one embodiment, the method includes: (i) contacting a sample comprising one or more target nucleic acid molecules with (a) at least one probe, such as those described herein, being sequence specific for the target nucleic acid molecule, where the at least one probe undergoes a detectable change in fluorescence upon amplification of the one or more target nucleic acid molecules; and with (b) at least one oligonucleotide primer pair; (ii) incubating the mixture of step (i) with a DNA polymerase under conditions sufficient to amplify one or more target nucleic acid molecules; and (iii) detecting the presence or absence or quantifying the amount of the amplified target nucleic acid molecules by measuring fluorescence of the probe. In some embodiments, the DNA polymerase comprises 5′-exonuclease activity. In some other embodiments, the DNA polymerase is a Thermus aquaticus (Taq) DNA polymerase. In some embodiments, the probe is a hydrolysis probe, such as a TaqMan™ probe. Another aspect provided herein is a kit for PCR, such as quantitative real-time polymerase chain reaction (qPCR) and reverse transcription polymerase chain reaction (RT-PCR). In an exemplary embodiment, the kit includes the assay mixture, the process control, and the positive control each described above, as well as an individual or multiplex master mix. In an embodiment, the multiplex master mix is a RT-qPCR mix that provides for sensitive, reproducible detection of a plurality of different target pathogens in a single multiplex reaction. In another embodiment, the individual master mix provides for sensitive, reproducible detection of a single target pathogen. In an embodiment, the individual or multiplex master mix may include an enzyme (for instance, DNA polymerase), a thermostable enzyme, enzyme cofactors, deoxynucleotide triphosphates (dNTPs) including dUTP, an enzyme inhibitor (for instance, RNase inhibitor), a dye and/or a buffer agent. In an exemplary embodiment, the individual or multiplex master mix can be, for instance, TaqPath™ 1-step Multiplex Master Mix by Applied Biosystems – a brand of Thermo Fisher Scientific. In an embodiment, the master mix may be concentrated. For instance, the master mix may be provided at a 4× concentration. In some embodiments, the master mix is prepared such that it requires less than a 3× dilution prior to use in PCR, e.g., 2× dilution, 1.5× dilution, 1.2× dilution, etc. In some embodiments, the kit also includes instructions for conducting the PCR, and one or more of the following: a buffering agent, deoxynucleotide triphosphates (dNTPs), an organic solvent, an enzyme, enzyme cofactors, and an enzyme inhibitor. In another embodiment, the kit for PCR comprises the described dye and/or quencher moiety, instructions for conjugating or labeling the dye and/or quencher moiety to a biomolecule, such as an oligonucleotide, instructions for conducting the PCR, and one or more of the following: a buffering agent, deoxynucleotide triphosphates (dNTPs), an organic solvent, an enzyme, enzyme cofactors, and an enzyme inhibitor. In some embodiments, the systems, compositions, methods, and devices used for nucleic acid amplification comprise a “point-of-service” (POS) system. In some embodiments, samples may be collected and/or analyzed at a “point-of-care” (POC) location. In some embodiments, analysis at a POC location typically does not require specialized equipment and has rapid and easy-to-read visual results. In some embodiments, analysis can be performed in the field, in a home setting, and/or by a lay person not having specialized skills. In certain embodiments, for example, the analysis of a small-volume clinical sample may be completed using a POS system in a short period of time (e.g., within hours or minutes). Optionally, a POS system is utilized at a location that is capable of providing a service (e.g., testing, monitoring, treatment, diagnosis, guidance, sample collection, verification of identity (ID verification), and other services) at or near the site or location of the subject. A service may be a medical service, or it may be a non-medical service. In some situations, a POS system provides a service at a predetermined location, such as a subject’s home, school, or work, or at a grocery store, a drug store, a community center, a clinic, a doctor’s office, a hospital, an outdoor triage tent, a makeshift hospital, a border check point, etc. A POS system can include one or more point of service devices, such as a portable virus/pathogen detector. In some embodiments, a POS system is a point of care system. In some embodiments, the POS system is suitable for use by non-specialized workers or personnel, such as nurses, police officers, civilian volunteers, or the patient. In certain embodiments, a POC system is utilized at a location at which medical-related care (e.g., treatment, testing, monitoring, diagnosis, counseling, etc.) is provided. A POC may be, e.g., at a subject’s home, work, or school, or at a grocery store, a community center, a drug store, a doctor’s office, a clinic, a hospital, an outdoor triage tent, a makeshift hospital, a border check point, etc. A POC system is a system which may aid in, or may be used in, providing such medical-related care, and may be located at or near the site or location of the subject or the subject’s health care provider (e.g., subject’s home, work, or school, or at a grocery store, a community center, a drug store, a doctor’s office, a clinic, a hospital, etc.). In embodiments, a POS system is configured to accept a clinical sample obtained from a subject at the associated POS location. In embodiments, a POS system is further configured to analyze the clinical sample at the POS location. In embodiments, the clinical sample is a small volume clinical sample. In embodiments, the clinical sample is analyzed in a short period of time. In embodiments, the short period of time is determined with respect to the time at which sample analysis began. In embodiments, the short period of time is determined with respect to the time at which the sample was inserted into a device for the analysis of the sample. In embodiments, the short period of time is determined with respect to the time at which the sample was obtained from the subject. In some embodiments, a POS system or a POC system can include the amplification- based methods, compositions and kits disclosed herein, including any of the described assays and/or assay panels. Such assays are contemplated for use with both thermal cycling amplification workflows and protocols, such as in PCR, as well as isothermal amplification workflows and protocols, such as in LAMP. In some embodiments, a POS or a POC system comprises self-collection of a biological sample. In some embodiments, the self-collection may comprise the use of a self-collection kit and/or device, such as a swab or a tube. In some embodiments, the self-collection kit comprises instructions for use, including collection instructions, sample preparation or storage instructions, and/or shipping instructions. For example, the self-collection kit and/or device may be used by an individual, such as lay person, not having specialized skills or medical expertise. In some embodiments, self-collection may be performed by the patient themselves or by any other individual in proximity to the patient, such as but not limited to a parent, a care giver, a teacher, a friend, or other family member. Notably, in some embodiments, the nucleic acid amplification protocol can be configured for rapid processing (e.g., in less than about 45 minutes) and high throughput, allowing for a minimally invasive method to quickly screen large numbers of individuals in a scalable way. This can be particularly useful to perform asymptomatic testing (e.g., high frequency/widespread testing at schools, workplaces, conventions, sporting events, large social gatherings, etc.) or for epidemiological purposes. The disclosed embodiments can also beneficially provide a lower cost sample collection system and method that enables self-collection (reducing health care professional staffing needs) using a low-cost collection device. This eliminates the requirements for swabs, buffers, virus transmission media (or other specialized transport medium), and the like. The disclosed embodiments also allow for a reduction in Personal Protective Equipment (PPE) requirements and costs. There is also a beneficial reduced dependence on supply-constrained items, and the compatibility of these methods and kit components with existing equipment improves the flexibility and simplicity of their implementation to the masses. Overall, such embodiments allow for a less expensive assay that can be accomplished more quickly from sample collection through result generation. It will be apparent to one of ordinary skill in the relevant art that suitable modifications and adaptations to the compositions, formulations, methods, processes, and applications described herein can be made without departing from the scope of any embodiments or aspects thereof. The compositions and methods provided are exemplary and are not intended to limit the scope of any of the specified embodiments. All of the various embodiments, aspects, and options disclosed herein can be combined in any variations or iterations. The scope of the compositions, formulations, methods, and processes described herein include all actual or potential combinations of embodiments, aspects, options, examples, and preferences herein described. The exemplary compositions and formulations described herein may omit any component, substitute any component disclosed herein, or include any component disclosed elsewhere herein. The ratios of the mass of any component of any of the compositions or formulations disclosed herein to the mass of any other component in the formulation or to the total mass of the other components in the formulation are hereby disclosed as if they were expressly disclosed. Should the meaning of any terms in any of the patents or publications incorporated by reference conflict with the meaning of the terms used in this disclosure, the meanings of the terms or phrases in this disclosure are controlling. Furthermore, the foregoing discussion discloses and describes merely exemplary embodiments. All patents and publications cited herein are incorporated by reference herein for the specific teachings thereof. Various embodiments and aspects of the inventions described herein are summarized by the following clauses: Clause 1. A method for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample, the method comprising the steps of: (a) creating a reaction mixture containing the sample and one or more Primer Pair Sets, wherein the Primer Pair Sets comprise one or more of: at least one primer pair selected from Primer Pair Set 1 that specifically amplifies a portion of Acinetobacter baumannii genome; at least one primer pair selected from Primer Pair Set 2 that specifically amplifies a portion of Bacteroides fragilis genome; at least one primer pair selected from Primer Pair Set 3 that specifically amplifies a portion of Clostridium perfringens genome; at least one primer pair selected from Primer Pair Set 4 that specifically amplifies a portion of Enterobacter cloacae genome; at least one primer pair selected from Primer Pair Set 5 that specifically amplifies a portion of Enterococcus faecalis genome; at least one primer pair selected from Primer Pair Set 6 that specifically amplifies a portion of Enterococcus faecium genome; at least one primer pair selected from Primer Pair Set 7 that specifically amplifies a portion of Escherichia coli genome; at least one primer pair selected from Primer Pair Set 8 that specifically amplifies a portion of Klebsiella pneumoniae genome; at least one primer pair selected from Primer Pair Set 9 that specifically amplifies a portion of Klebsiella oxytoca genome; at least one primer pair selected from Primer Pair Set 10 that specifically amplifies a portion of Klebsiella aerogenes genome; at least one primer pair selected from Primer Pair Set 11 that specifically amplifies a portion of Proteus mirabilis genome; at least one primer pair selected from Primer Pair Set 12 that specifically amplifies a portion of Proteus vulgaris genome; at least one primer pair selected from Primer Pair Set 13 that specifically amplifies a portion of Pseudomonas aeruginosa genome; at least one primer pair selected from Primer Pair Set 14 that specifically amplifies a portion of Serratia marcescens genome; at least one primer pair selected from Primer Pair Set 15 that specifically amplifies a portion of Staphylococcus aureus genome; at least one primer pair selected from Primer Pair Set 16 that specifically amplifies a portion of Streptococcus agalactiae genome; at least one primer pair selected from Primer Pair Set 17 that specifically amplifies a portion of Streptococcus dysgalactiae genome; at least one primer pair selected from Primer Pair Set 18 that specifically amplifies a portion of Streptococcus anginosus genome; at least one primer pair selected from Primer Pair Set 19 that specifically amplifies a portion of Streptococcus pyogenes genome; at least one primer pair selected from Primer Pair Set 20 that specifically amplifies a portion of Staphylococcus lugdunensis genome; at least one primer pair selected from Primer Pair Set 21 that specifically amplifies a portion of Providencia stuartii genome; at least one primer pair selected from Primer Pair Set 22 that specifically amplifies a portion of Stenotrophomonas maltophilia genome; at least one primer pair selected from Primer Pair Set 23 that specifically amplifies a portion of Morganella morganii genome; at least one primer pair selected from Primer Pair Set 24 that specifically amplifies a portion of Citrobacter koseri genome; at least one primer pair selected from Primer Pair Set 25 that specifically amplifies a portion of Citrobacter freundii genome; at least one primer pair selected from Primer Pair Set 26 that specifically amplifies a portion of Citrobacter braakii genome; at least one primer pair selected from Primer Pair Set 27 that specifically amplifies a portion of Peptoniphilus asaccharolyticus genome; at least one primer pair selected from Primer Pair Set 28 that specifically amplifies a portion of Peptoniphilus harei genome; at least one primer pair selected from Primer Pair Set 29 that specifically amplifies a portion of Peptoniphilus ivorii genome; at least one primer pair selected from Primer Pair Set 30 that specifically amplifies a portion of Peptostreptococcus anaerobius genome; at least one primer pair selected from Primer Pair Set 31 that specifically amplifies a portion of Finegoldia magna genome; at least one primer pair selected from Primer Pair Set 32 that specifically amplifies a portion of Clostridium septicum genome; at least one primer pair selected from Primer Pair Set 33 that specifically amplifies a portion of Paeniclostridium sordellii (Clostridium sordellii) genome; at least one primer pair selected from Primer Pair Set 34 that specifically amplifies a portion of Clostridium novyi A, B genome; at least one primer pair selected from Primer Pair Set 35 that specifically amplifies a portion of Clostridium histolyticum genome; at least one primer pair selected from Primer Pair Set 36 that specifically amplifies a portion of Staphylococcus epidermidis genome; at least one primer pair selected from Primer Pair Set 37 that specifically amplifies a portion of Staphylococcus haemolyticus genome; at least one primer pair selected from Primer Pair Set 38 that specifically amplifies a portion of Corynebacterium striatum genome; at least one primer pair selected from Primer Pair Set 39 that specifically amplifies a portion of Candida albicans genome; at least one primer pair selected from Primer Pair Set 40 that specifically amplifies a portion of Candida auris genome; at least one primer pair selected from Primer Pair Set 41 that specifically amplifies a portion of Candida glabrata genome; at least one primer pair selected from Primer Pair Set 42 that specifically amplifies a portion of Candida krusei genome; at least one primer pair selected from Primer Pair Set 43 that specifically amplifies a portion of Candida parapsilosis genome; and/or at least one primer pair selected from Primer Pair Set 44 that specifically amplifies a portion of Candida tropicalis genome; and (b) subjecting the reaction mixture to reaction conditions suitable to amplify targeted nucleic acids, thereby generating at least one amplicon when the targeted nucleic acids are present in the sample; wherein the presence or absence of at least one amplicon in the sample indicates the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in the sample. Clause 2. The method of clause 1, wherein the Primer Pair Sets comprise the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115– 116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133– 134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142– 143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160– 161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169– 170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289– 290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313– 314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353,355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. Clause 3. The method of clause 1 or 2, wherein the generating of the at least one amplicon comprises performing PCR. Clause 4. The method of any one of clauses 1–3, wherein the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii produced using at least one primer pair selected from SEQ ID NO: 1–2, 4–5, or 7–8, and a sequence comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis produced using at least one primer pair selected from SEQ ID NO: 10–11, 13–14, or 16–17, and a sequence comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens produced using at least one primer pair selected from SEQ ID NO: 19–20, 22–23, or 25–26, and a sequence comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae produced using at least one primer pair selected from SEQ ID NO: 28–29, 31–32, or 34–35, and a sequence comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis produced using at least one primer pair selected from SEQ ID NO: 37–38, 40–41, or 43–44, and a sequence comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium produced using at least one primer pair selected from SEQ ID NO: 46–47, 49–50, or 52–53, and a sequence comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli produced using at least one primer pair selected from SEQ ID NO: 55–56, 58–59, or 61–62, and a sequence comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae produced using at least one primer pair selected from SEQ ID NO: 64–65, 67–68, or 70–71, and a sequence comprising at least a portion of SEQ ID NO: 434; an amplicon specific for Klebsiella Oxytoca produced using at least one primer pair selected from SEQ ID NO: 73–74, 76–77, or 79–80, and a sequence comprising at least a portion of SEQ ID NO: 435; an amplicon specific for Klebsiella aerogenes produced using at least one primer pair selected from SEQ ID NO: 82–83, 85–86, or 88–89, and a sequence comprising at least a portion of SEQ ID NO: 436; an amplicon specific for Proteus mirabilis produced using at least one primer pair selected from SEQ ID NO: 91–92, 94–95, or 97–98, and a sequence comprising at least a portion of SEQ ID NO: 437; an amplicon specific for Proteus vulgaris produced using at least one primer pair selected from SEQ ID NO: 100–101, 103–104, or 106–107, and a sequence comprising at least a portion of SEQ ID NO: 438; an amplicon specific for Pseudomonas aeruginosa produced using at least one primer pair selected from SEQ ID NO: 109–110, 112–113, or 115–116, and a sequence comprising at least a portion of SEQ ID NO: 439; an amplicon specific for Serratia marcescens produced using at least one primer pair selected from SEQ ID NO: 118–119, 121–122, or 124–125, and a sequence comprising at least a portion of SEQ ID NO: 440; an amplicon specific for Staphylococcus aureus produced using at least one primer pair selected from SEQ ID NO: 127–128, 130–131, or 133–134, and a sequence comprising at least a portion of SEQ ID NO: 441; an amplicon specific for Streptococcus agalactiae produced using at least one primer pair selected from SEQ ID NO: 136–137, 139–140, or 142–143, and a sequence comprising at least a portion of SEQ ID NO: 442; an amplicon specific for Streptococcus dysgalactiae produced using at least one primer pair selected from SEQ ID NO: 145–146, 148–149, or 151–152, and a sequence comprising at least a portion of SEQ ID NO: 443; an amplicon specific for Streptococcus anginosus produced using at least one primer pair selected from SEQ ID NO: 154–155, 157–158, or 160–161, and a sequence comprising at least a portion of SEQ ID NO: 444; an amplicon specific for Streptococcus pyogenesproduced using at least one primer pair selected from SEQ ID NO: 163–164, 166–167, or 169–170, and a sequence comprising at least a portion of SEQ ID NO: 445; an amplicon specific for Staphylococcus lugdunensis produced using at least one primer pair selected from SEQ ID NO: 172–173, 175–176, or 178–179, and a sequence comprising at least a portion of SEQ ID NO: 446; an amplicon specific for Providencia stuartii produced using at least one primer pair selected from SEQ ID NO: 181–182, 184–185, or 187–188, and a sequence comprising at least a portion of SEQ ID NO: 447; an amplicon specific for Stenotrophomonas maltophilia produced using at least one primer pair selected from SEQ ID NO: 190–191, 193–194, or 196–197;, and a sequence comprising at least a portion of SEQ ID NO: 448; an amplicon specific for Morganella morganii produced using at least one primer pair selected from SEQ ID NO: 199–200, 202–203, or 205–206, and a sequence comprising at least a portion of SEQ ID NO: 449; an amplicon specific for Citrobacter koseri produced using at least one primer pair selected from SEQ ID NO: 208–209, 211–212, or 214–215, and a sequence comprising at least a portion of SEQ ID NO: 450; an amplicon specific for Citrobacter freundii produced using at least one primer pair selected from SEQ ID NO: 217–218, 220–221, or 223–224, and a sequence comprising at least a portion of SEQ ID NO: 451; an amplicon specific for Citrobacter braakii produced using at least one primer pair selected from SEQ ID NO: 226–227, 229–230, or 232–233, and a sequence comprising at least a portion of SEQ ID NO: 452; an amplicon specific for Peptoniphilus asaccharolyticus produced using at least one primer pair selected from SEQ ID NO: 235–236, 238–239, or 241–242, and a sequence comprising at least a portion of SEQ ID NO: 453; an amplicon specific for Peptoniphilus harei produced using at least one primer pair selected from SEQ ID NO: 244–245, 247–248, or 250–251, and a sequence comprising at least a portion of SEQ ID NO: 454; an amplicon specific for Peptoniphilus ivorii produced using at least one primer pair selected from SEQ ID NO: 253–254, 256–257, or 259–260, and a sequence comprising at least a portion of SEQ ID NO: 455; an amplicon specific for Peptostreptococcus anaerobius produced using at least one primer pair selected from SEQ ID NO: 262–263, 265–266, or 268–269, and a sequence comprising at least a portion of SEQ ID NO: 456; an amplicon specific for Finegoldia magna produced using at least one primer pair selected from SEQ ID NO: 271–272, 274–275, or 277–278, and a sequence comprising at least a portion of SEQ ID NO: 457; an amplicon specific for Clostridium septicum produced using at least one primer pair selected from SEQ ID NO: 280–281, 283–284, or 286–287, and a sequence comprising at least a portion of SEQ ID NO: 458; an amplicon specific for Paeniclostridium sordellii (Clostridium sordellii) produced using at least one primer pair selected from SEQ ID NO: 289–290, 292–293, or 295–296, and a sequence comprising at least a portion of SEQ ID NO: 459; an amplicon specific for Clostridium novyi A, B produced using at least one primer pair selected from SEQ ID NO: 298–299, 301–302, or 304–305, and a sequence comprising at least a portion of SEQ ID NO: 460; an amplicon specific for Clostridium histolyticum produced using at least one primer pair selected from SEQ ID NO: 307–308, 310–311, or 313–314, and a sequence comprising at least a portion of SEQ ID NO: 461; an amplicon specific for Staphylococcus epidermidis produced using at least one primer pair selected from SEQ ID NO: 316–317, 319–320, or 322–323, and a sequence comprising at least a portion of SEQ ID NO: 462; an amplicon specific for Staphylococcus haemolyticus produced using at least one primer pair selected from SEQ ID NO: 325–326, 328–329, or 331–332, and a sequence comprising at least a portion of SEQ ID NO: 463; an amplicon specific for Corynebacterium striatum produced using at least one primer pair selected from SEQ ID NO: 334–335, 337–338, or 340–341, and a sequence comprising at least a portion of SEQ ID NO: 464; an amplicon specific for Candida albicans produced using at least one primer pair selected from SEQ ID NO: 343–344, 346–347, or 349–350, and a sequence selected from SEQ ID NO: 465; an amplicon specific for Candida auris produced using at least one primer pair selected from SEQ ID NO: 352–353,355–356, or 358–359, and a sequence comprising at least a portion of SEQ ID NO: 466; an amplicon specific for Candida glabrata produced using at least one primer pair selected from SEQ ID NO: 361–362, 364–365, or 367–368, and a sequence comprising at least a portion of SEQ ID NO: 467; an amplicon specific for Candida krusei produced using at least one primer pair selected from SEQ ID NO: 370–371, 373–374, or 376–377, and a sequence comprising at least a portion of SEQ ID NO: 468; an amplicon specific for Candida parapsilosis produced using at least one primer pair selected from SEQ ID NO: 379–380, 382–383, or 385–386, and a sequence comprising at least a portion of SEQ ID NO: 469; and/or an amplicon specific for Candida tropicalis produced using at least one primer pair selected from SEQ ID NO: 388–389, 391–392, or 394–395, and a sequence comprising at least a portion of SEQ ID NO: 470. Clause 5. The method of any one of clauses 1–5, wherein the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae comprising at least a portion of SEQ ID NO:434; an amplicon specific for Klebsiella Oxytoca comprising at least a portion of SEQ ID NO: 435; an amplicon specific for Klebsiella aerogenes comprising at least a portion of SEQ ID NO: 436; an amplicon specific for Proteus mirabilis comprising at least a portion of SEQ ID NO: 437; an amplicon specific for Proteus vulgaris comprising at least a portion of SEQ ID NO: 438; an amplicon specific for Pseudomonas aeruginosa comprising at least a portion of SEQ ID NO: 439; an amplicon specific for Serratia marcescens comprising at least a portion of SEQ ID NO: 440; an amplicon specific for Staphylococcus aureus comprising at least a portion of SEQ ID NO: 441; an amplicon specific for Streptococcus agalactiae comprising at least a portion of SEQ ID NO: 442; an amplicon specific for Streptococcus dysgalactiae comprising at least a portion of SEQ ID NO: 443; an amplicon specific for Streptococcus anginosus comprising at least a portion of SEQ ID NO: 444; an amplicon specific for Streptococcus pyogenes comprising at least a portion of SEQ ID NO: 445; an amplicon specific for Staphylococcus lugdunensis comprising at least a portion of SEQ ID NO: 446; an amplicon specific for Providencia stuartii comprising at least a portion of SEQ ID NO: 447; an amplicon specific for Stenotrophomonas maltophilia comprising at least a portion of SEQ ID NO: 448; an amplicon specific for Morganella morganii comprising at least a portion of SEQ ID NO: 449; an amplicon specific for Citrobacter koseri comprising at least a portion of SEQ ID NO: 450; an amplicon specific for Citrobacter freundii comprising at least a portion of SEQ ID NO: 451; an amplicon specific for Citrobacter braakii comprising at least a portion of SEQ ID NO: 452; an amplicon specific for Peptoniphilus asaccharolyticus comprising at least a portion of SEQ ID NO: 453; an amplicon specific for Peptoniphilus harei comprising at least a portion of SEQ ID NO: 454; an amplicon specific for Peptoniphilus ivorii comprising at least a portion of SEQ ID NO: 455; an amplicon specific for Peptostreptococcus anaerobius comprising at least a portion of SEQ ID NO: 456; an amplicon specific for Finegoldia magna comprising at least a portion of SEQ ID NO: 457; an amplicon specific for Clostridium septicum comprising at least a portion of SEQ ID NO: 458; an amplicon specific for Paeniclostridium sordellii (Clostridium sordellii) comprising at least a portion of SEQ ID NO: 459; an amplicon specific for Clostridium novyi A, B comprising at least a portion of SEQ ID NO: 460; an amplicon specific for Clostridium histolyticum comprising at least a portion of SEQ ID NO: 461; an amplicon specific for Staphylococcus epidermidis comprising at least a portion of SEQ ID NO: 462; an amplicon specific for Staphylococcus haemolyticus comprising at least a portion of SEQ ID NO: 463; an amplicon specific for Corynebacterium striatum comprising at least a portion of SEQ ID NO: 464; an amplicon specific for Candida albicans comprising at least a portion of SEQ ID NO: 465; an amplicon specific for Candida auris comprising at least a portion of SEQ ID NO: 466; an amplicon specific for Candida glabrata comprising at least a portion of SEQ ID NO: 467; an amplicon specific for Candida krusei comprising at least a portion of SEQ ID NO: 468; an amplicon specific for Candida parapsilosis comprising at least a portion of SEQ ID NO: 469; and/or an amplicon specific for Candida tropicalis comprising at least a portion of SEQ ID NO: 470. Clause 6. The method any one of clauses 1–5, wherein the reaction mixture further comprises probes specific for the at least one amplicon. Clause 7. The method of any one of clauses 1–6, wherein the reaction mixture further comprises probes specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probes comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. Clause 8. The method of any one of clauses 1–7, wherein the reaction mixture further contains a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample. Clause 9. The method of clause 8, wherein the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. Clause 10. The method of any one of clauses 1–9, wherein the probe comprises a fluorescent reporter. Clause 11. The method of clause 10, wherein the probe comprises a quencher. Clause 12. The method of clause 10 or 11, wherein the probe is labeled at or near the 5′–end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM. Clause 13. The method of any one of clauses 10–12, wherein the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ. Clause 14. A composition for individually, simultaneously, or sequentially determining the presence or absence of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis comprising a plurality of Primer Pair Sets, wherein the Primer Pair Sets comprise: at least one primer pair selected from Primer Pair Set 1 that specifically amplifies a portion of Acinetobacter baumannii genome; at least one primer pair selected from Primer Pair Set 2 that specifically amplifies a portion of Bacteroides fragilis genome; at least one primer pair selected from Primer Pair Set 3 that specifically amplifies a portion of Clostridium perfringens genome; at least one primer pair selected from Primer Pair Set 4 that specifically amplifies a portion of Enterobacter cloacae genome; at least one primer pair selected from Primer Pair Set 5 that specifically amplifies a portion of Enterococcus faecalis genome; at least one primer pair selected from Primer Pair Set 6 that specifically amplifies a portion of Enterococcus faecium genome; at least one primer pair selected from Primer Pair Set 7 that specifically amplifies a portion of Escherichia coli genome; at least one primer pair selected from Primer Pair Set 8 that specifically amplifies a portion of Klebsiella pneumoniae genome; at least one primer pair selected from Primer Pair Set 9 that specifically amplifies a portion of Klebsiella oxytoca genome; at least one primer pair selected from Primer Pair Set 10 that specifically amplifies a portion of Klebsiella aerogenes genome; at least one primer pair selected from Primer Pair Set 11 that specifically amplifies a portion of Proteus mirabilis genome; at least one primer pair selected from Primer Pair Set 12 that specifically amplifies a portion of Proteus vulgaris genome; at least one primer pair selected from Primer Pair Set 13 that specifically amplifies a portion of Pseudomonas aeruginosa genome; at least one primer pair selected from Primer Pair Set 14 that specifically amplifies a portion of Serratia marcescens genome; at least one primer pair selected from Primer Pair Set 15 that specifically amplifies a portion of Staphylococcus aureus genome; at least one primer pair selected from Primer Pair Set 16 that specifically amplifies a portion of Streptococcus agalactiae genome; at least one primer pair selected from Primer Pair Set 17 that specifically amplifies a portion of Streptococcus dysgalactiae genome; at least one primer pair selected from Primer Pair Set 18 that specifically amplifies a portion of Streptococcus anginosus genome; at least one primer pair selected from Primer Pair Set 19 that specifically amplifies a portion of Streptococcus pyogenes genome; at least one primer pair selected from Primer Pair Set 20 that specifically amplifies a portion of Staphylococcus lugdunensis genome; at least one primer pair selected from Primer Pair Set 21 that specifically amplifies a portion of Providencia stuartii genome; at least one primer pair selected from Primer Pair Set 22 that specifically amplifies a portion of Stenotrophomonas maltophilia genome; at least one primer pair selected from Primer Pair Set 23 that specifically amplifies a portion of Morganella morganii genome; at least one primer pair selected from Primer Pair Set 24 that specifically amplifies a portion of Citrobacter koseri genome; at least one primer pair selected from Primer Pair Set 25 that specifically amplifies a portion of Citrobacter freundii genome; at least one primer pair selected from Primer Pair Set 26 that specifically amplifies a portion of Citrobacter braakii genome; at least one primer pair selected from Primer Pair Set 27 that specifically amplifies a portion of Peptoniphilus asaccharolyticus genome; at least one primer pair selected from Primer Pair Set 28 that specifically amplifies a portion of Peptoniphilus harei genome; at least one primer pair selected from Primer Pair Set 29 that specifically amplifies a portion of Peptoniphilus ivorii genome; at least one primer pair selected from Primer Pair Set 30 that specifically amplifies a portion of Peptostreptococcus anaerobius genome; at least one primer pair selected from Primer Pair Set 31 that specifically amplifies a portion of Finegoldia magna genome; at least one primer pair selected from Primer Pair Set 32 that specifically amplifies a portion of Clostridium septicum genome; at least one primer pair selected from Primer Pair Set 33 that specifically amplifies a portion of Paeniclostridium sordellii (Clostridium sordellii) genome; at least one primer pair selected from Primer Pair Set 34 that specifically amplifies a portion of Clostridium novyi A, B genome; at least one primer pair selected from Primer Pair Set 35 that specifically amplifies a portion of Clostridium histolyticum genome; at least one primer pair selected from Primer Pair Set 36 that specifically amplifies a portion of Staphylococcus epidermidis genome; at least one primer pair selected from Primer Pair Set 37 that specifically amplifies a portion of Staphylococcus haemolyticus genome; at least one primer pair selected from Primer Pair Set 38 that specifically amplifies a portion of Corynebacterium striatum genome;at least one primer pair selected from Primer Pair Set 39 that specifically amplifies a portion of Candida albicans genome; at least one primer pair selected from Primer Pair Set 40 that specifically amplifies a portion of Candida auris genome; at least one primer pair selected from Primer Pair Set 41 that specifically amplifies a portion of Candida glabrata genome; at least one primer pair selected from Primer Pair Set 42 that specifically amplifies a portion of Candida krusei genome; at least one primer pair selected from Primer Pair Set 43 that specifically amplifies a portion of Candida parapsilosis genome; and/or at least one primer pair selected from Primer Pair Set 44 that specifically amplifies a portion of Candida tropicalis genome. Clause 15. The composition of clause 14, wherein the Primer Pair Sets comprises the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115– 116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133– 134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142– 143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160– 161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169– 170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289– 290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313– 314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353,355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. Clause 16. The composition of clause 14 or 15, further comprising a probe specific for the at least one amplicon produced using the at least one primer pair selected from one or more of Primer Pair Sets 1–44. Clause 17. The composition of any one of clauses 14–16, further comprising a probe specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probe comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. Clause 18. The composition of any one of clauses 14–17, further comprising a polymerase, a buffer, and deoxynucleotide triphosphates (dNTPs). Clause 19. The composition of any one of clauses 14–18, further comprising a sample. Clause 20. The composition of any one of clauses 14–19, further comprising at least one control forward and reverse primer and, optionally, a control probe, that specifically amplifies a target nucleic acid of a control sample. Clause 21. The composition of clause 21, wherein the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412– 413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. Clause 22. The composition of any one of clauses 14–21, wherein the probe contains a fluorescent reporter. Clause 23. The composition of clause 22, wherein the probe contains a quencher. Clause 24. The composition of any one of clauses 22 or 23, wherein the probe is labeled at or near the 5′ end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM. Clause 25. The composition of any one of clauses 22–24, wherein the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ. Clause 26. A kit for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample, comprising the compositions of any one of clauses 14–18. Clause 27. The kit of clause 29, further comprising the compositions of any one of clauses 19–25. Clause 28. The kit of clause 26 or 27, wherein the kit comprises Primer Pair Sets comprising the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115– 116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133– 134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142– 143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160– 161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169– 170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289– 290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313– 314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353, 355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. Clause 29. The kit of clause 28, wherein the kit further comprises probes suitable for use with specific forward and reverse primer pairs, the probes comprising one or more of: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; and/or a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. Clause 30. The kit of clause 28, wherein the kit further comprises a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample. Clause 31. The kit of clause 30, wherein the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. Clause 32. The kit of clause 28, wherein the kit further comprises a control plasmid comprising one or more target sequences selected from Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis. Clause 33. The control plasmid of clause 31, wherein the plasmid comprises one or more of nucleic acid sequences of SEQ ID NO: 427–470. EXAMPLES Example 1 Sample Preparation A sample is obtained from a subject. The sample can be a swab or sample of a wound. For wound samples, approximately 100 mg of sample is used to isolate genomic DNA. Samples can be frozen in a storage solution at a sample to solution ratio of 1:2. Frozen samples are thawed on ice and approximately 100 mg of the sample are used to isolate nucleic acids. The frozen or samples are lysed, and genomic DNA is isolated from the lysis. For swabs, the stick of the swab is removed and the swab containing the biological material is placed in lysis genomic extraction conditions. To each swab, the B. Atrophaeus control can be added before lysis during nucleic acid nucleic acid extraction. Example 2 Control Sample Preparation The TaqMan™ Universal Extraction Control Organism (B. atrophaeus) (BA process control) was used to verify the efficacy of the sample preparation and the absence of inhibitors in the real-time PCR reaction. A 1× solution of the control was added to each sample and negative control before extraction. The BA process control was contained a lyophilized pellet at 1 × 109 copies/vial. A 25× stock solution of the BA process control was prepared by adding 200 µL of 1× phosphate buffered saline (1× PBS: 137 mM NaCl, 2.7 mM KCl: 10 mM Na2HPO4, 1.8 mM KH2PO4, pH 7.4) to the vial containing the lyophilized pellet and vortexed until the pellet was resuspended. A working 1× stock solution was prepared by combining 24 µL of a 25× stock solution with 576 µL 1× PBS, pH 7.4 to achieve a total volume of 600 µL. The prepared BA process control was added to the genomic DNA extraction reaction, to each sample and to the negative extraction control immediately before lysis during nucleic acid extraction. Real-time PCR Reaction Preparation Genomic DNA samples were thawed or placed on ice. All reagents were gently vortexed, briefly centrifuged to collect the liquid at the bottom of the container and kept on ice until use. The amplification control was prepared by combining 495.0 µL of 1× TE buffer (1× TE: 10 mM Tris^HCl, 1 mM EDTA^Na2, pH 8.0) into a microcentrifuge tube, and adding 5.0 µL of the amplification control. The sample was mixed well and briefly centrifuged. A 5.0 µL aliquot of the diluted sample was combined with 170 µL of 1× TE buffer, mixed, and centrifuged briefly. For each 96-well plate, the following components were combined in sufficient amounts for the number of samples plus the amplification control and negative control. Table 51. PCR Individual or Multiplex Master Mix and Primer/Probes Component Volume per sample or Volume for n samples plus control 2 controls Master 6.25 µL 6.25 × (1.2 × n) µL 1.25 µL 1.25 × (1.2 × n) µL Total Volume 7.50 µL — The Master Mix contained components for the PCR reaction (buffer, MgCl2, dNTPs, and DNA polymerase, inter alia) and the individual or multiplex Primer/Probe Panel contained the primer pairs and probes specific for the target organisms and controls. The reaction plate was set up by dispensing 7.5 µL of the reaction mix prepared as shown in Table 51 to each well of a MicroAmp™ Optical 96-Well Reaction Plate, 0.2 mL. 17.5 µL of either the extracted materials (target DNA), the diluted amplification control, or nuclease- free water was added to the designated wells. The plate was sealed thoroughly with MicroAmp™ Optical Adhesive Film, ensuring that pressure was applied across the entire plate and that there was a tight seal across every individual well. The plate was vortexed at the highest setting speed for 30–60 seconds as follows: 5–10 seconds in the center of the plate, 5–10 seconds in each plate corner, and 5–10 seconds, again in the center. The reaction plate was centrifuged for 1–2 minutes at ≥ 650 × g to remove bubbles and to collect the liquid at the bottom. The real-time PCR reaction plate is maintained at 2–8 °C and protected from light until it was loaded into the real-time PCR instrument. The real-time PCR reaction was run within an hour after preparation of the plate. The real-time PCR reaction was performed, and the results were analyzed using the software accompanying the instrument. Example 3 Real-Time TaqMan™ PCR with Open Array The nucleic acid samples were diluted 1:10. An OpenArray™ plate was allowed to equilibrate to room temperature. Before preparing the samples, the TaqMan™ OpenArray™ Real-time PCR Master Mix was mixed but not inverted. The master mix and samples were added to the wells of the OpenArray™ Plate in a 1:1 ratio of master mix-to-pre-amplified nucleic acid. In separate wells, the TaqMan™ Amplification Control was used in place of the diluted pre-amplified nucleic acid sample. The resulting mixtures were further mixed with pipetting. After mixing, the plate was sealed with aluminum foil and centrifuged at 1,200 RPM (301 × g) for 1 minute. The OpenArray™ plate is transferred to an OpenArray™ AccuFill™ Instrument where a fraction of the samples were loaded onto a separate OpenArray™ plate. The new OpenArray™ plate was transferred to a QuantStudio™ 12K Flex OpenArray™ Plate Press where the plate was encased with a lid. OpenArray™ Immersion Fluid was slowly injected into the port of the encasement to minimize formation of air bubbles. After injection of the immersion fluid, the port was sealed. The encased OpenArray™ plate was transferred to a QuantStudio™ 12K Flex Instrument where the real-time PCR reaction is performed, imaged, and analyzed. Table 52. Open Array Platform Assay Efficiency Target Name R2 Slope Efficiency (%) A. baumannii 0.99 −3.39 97 B. atrophaeus 0.99 −3.42 96 B. fragilis 0.99 −3.39 97 C. striatum 0.99 −3.53 92 K. aerogenes 0.99 −3.43 96 E. coli 0.99 −3.38 98 E. faecalis 0.99 −3.44 95 E. faecium 0.99 −3.43 96 M. morganii 0.99 −3.46 95 P. aeruginosa 1.00 −3.41 96 P. stuartii 0.99 −3.45 95 S. anginosus grp. 0.99 −3.45 95 S. aureus 0.99 −3.43 96 S. lugdunensis 0.99 −3.48 94 S. marcescens 0.99 −3.40 97 S. pyogenes 0.99 −3.52 92 C. braakii, freundii,_koseri 0.99 −3.37 98 C. septicum, sordellii, novyi A, B, histolyticum 0.99 −3.36 98 C. perfringens 0.99 −3.45 95 E. cloacae 0.99 −3.43 96 F. magna, P. anaerobius 0.99 −3.40 97 K. oxytoca, pneumoniae 0.99 −3.36 99 P. asaccharolyticus, harei,_ivorii 0.99 −3.54 92 P. mirabilis,_vulgaris 0.99 −3.45 95 S. epidermidis, haemolyticus 0.99 −3.42 96 S. maltophilia 0.99 −3.48 94 S. agalactiae, dysgalactiae 0.99 −3.37 98 Xeno 0.99 −3.51 93 Example 4 Real-Time TaqMan™ PCR with TaqMan Array Card The nucleic acid samples were diluted 1:10. A TaqMan™ Array Card was allowed to equilibrate to room temperature. The TaqMan™ Fast Advanced Master Mix containing no UNG was mixed before preparing the PCR samples. A master mix containing a 2:3:5 ratio of diluted pre-amplified nucleic acid, nuclease-free water, and of TaqMan™ Fast Advanced Master Mix was prepared such that 100 µL of sample was added to each port of the TaqMan™ Array Card. Optionally, positive amplification control samples were added to the TaqMan™ Array Card by preparing a sample containing 10 µL of TaqMan™ of Amplification Control, 40 µL of nuclease free water, and 50 µL of TaqMan™ Fast Advanced Master Mix for each designated control port. After the samples were added to TaqMan™ Array Card, the card was centrifuged twice at 1,200 RPM (301 × g) for 1 minute. The TaqMan™ Array Card was sealed and loaded into a real-time PCR instrument. Inside the instrument, the samples were activated by heating the sample to 95 °C for 10 minutes. Following activation, amplification was performed by holding the temperature at 95 °C for 3 seconds to allow for separation of the templates into single strands followed by reducing the temperature to 60 °C and holding the temperature for 30 second to allow for annealing and elongation. The cycling between the two temperatures is repeated 40 times. The results of the real-time TaqMan™ PCR reaction were analyzed using the software accompanying the instrument. The results indicate the multiplex wound pathogen detection research workflow is highly sensitive to target with a wide linear dynamic range when compared to typical culture results. Accuracy of detection with pre-determined research samples across a wide range of wound pathogens was highly comparable to a commercially available method. In summary, a highly efficient, cost-effective research application for wound pathogen detection using high- performance, validated assays for wound pathogens in a high-throughput format. Table 53. TAC Platform Assay Efficiency Target Name R2 Slope Efficiency (%) A. baumannii 1.00 −3.34 99 B. atrophaeus 1.00 −3.39 97 B. fragilis 1.00 −3.41 96 C. braakii, freundii,_koseri 1.00 −3.43 96 C. perfringens 0.99 −3.35 99 E. cloacae 1.00 −3.28 102 E. faecalis 1.00 −3.39 97 E. faecium 1.00 −3.36 99 E. coli 1.00 −3.31 101 F. magna, P. anaerobius 1.00 −3.28 102 K. aerogenes 1.00 −3.35 99 K. oxytoca, pneumoniae 1.00 −3.32 100 M. morganii 1.00 −3.35 99 P. mirabilis, vulgaris 1.00 −3.34 99 P. asaccharolyticus, harei,_ivorii 1.00 −3.41 96 P. stuartii 1.00 −3.38 97 P. aeruginosa 1.00 −3.36 98 S. marcescens 1.00 −3.34 99 S. aureus 1.00 −3.37 98 S. lugdunensis 0.99 −3.47 94 S. maltophilia 1.00 −3.30 101 S. agalactiae, dysgalactiae 1.00 −3.37 98 S. pyogenes 1.00 −3.38 98 Xeno 1.00 −3.46 95 All assays showed good linearity ranging from 107 to 102 cps/uL and efficiencies ranging from 92–102%. The assays showed good performances at LoD levels in the TAC and OA platforms.

Claims

CLAIMS What is claimed: 1. A method for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample, the method comprising the steps of: (a) creating a reaction mixture containing the sample and one or more Primer Pair Sets, wherein the Primer Pair Sets comprise one or more of: at least one primer pair selected from Primer Pair Set 1 that specifically amplifies a portion of Acinetobacter baumannii genome; at least one primer pair selected from Primer Pair Set 2 that specifically amplifies a portion of Bacteroides fragilis genome; at least one primer pair selected from Primer Pair Set 3 that specifically amplifies a portion of Clostridium perfringens genome; at least one primer pair selected from Primer Pair Set 4 that specifically amplifies a portion of Enterobacter cloacae genome; at least one primer pair selected from Primer Pair Set 5 that specifically amplifies a portion of Enterococcus faecalis genome; at least one primer pair selected from Primer Pair Set 6 that specifically amplifies a portion of Enterococcus faecium genome; at least one primer pair selected from Primer Pair Set 7 that specifically amplifies a portion of Escherichia coli genome; at least one primer pair selected from Primer Pair Set 8 that specifically amplifies a portion of Klebsiella pneumoniae genome; at least one primer pair selected from Primer Pair Set 9 that specifically amplifies a portion of Klebsiella oxytoca genome; at least one primer pair selected from Primer Pair Set 10 that specifically amplifies a portion of Klebsiella aerogenes genome; at least one primer pair selected from Primer Pair Set 11 that specifically amplifies a portion of Proteus mirabilis genome; at least one primer pair selected from Primer Pair Set 12 that specifically amplifies a portion of Proteus vulgaris genome; at least one primer pair selected from Primer Pair Set 13 that specifically amplifies a portion of Pseudomonas aeruginosa genome; at least one primer pair selected from Primer Pair Set 14 that specifically amplifies a portion of Serratia marcescens genome; at least one primer pair selected from Primer Pair Set 15 that specifically amplifies a portion of Staphylococcus aureus genome; at least one primer pair selected from Primer Pair Set 16 that specifically amplifies a portion of Streptococcus agalactiae genome; at least one primer pair selected from Primer Pair Set 17 that specifically amplifies a portion of Streptococcus dysgalactiae genome; at least one primer pair selected from Primer Pair Set 18 that specifically amplifies a portion of Streptococcus anginosus genome; at least one primer pair selected from Primer Pair Set 19 that specifically amplifies a portion of Streptococcus pyogenes genome; at least one primer pair selected from Primer Pair Set 20 that specifically amplifies a portion of Staphylococcus lugdunensis genome; at least one primer pair selected from Primer Pair Set 21 that specifically amplifies a portion of Providencia stuartii genome; at least one primer pair selected from Primer Pair Set 22 that specifically amplifies a portion of Stenotrophomonas maltophilia genome; at least one primer pair selected from Primer Pair Set 23 that specifically amplifies a portion of Morganella morganii genome; at least one primer pair selected from Primer Pair Set 24 that specifically amplifies a portion of Citrobacter koseri genome; at least one primer pair selected from Primer Pair Set 25 that specifically amplifies a portion of Citrobacter freundii genome; at least one primer pair selected from Primer Pair Set 26 that specifically amplifies a portion of Citrobacter braakii genome; at least one primer pair selected from Primer Pair Set 27 that specifically amplifies a portion of Peptoniphilus asaccharolyticus genome; at least one primer pair selected from Primer Pair Set 28 that specifically amplifies a portion of Peptoniphilus harei genome; at least one primer pair selected from Primer Pair Set 29 that specifically amplifies a portion of Peptoniphilus ivorii genome; at least one primer pair selected from Primer Pair Set 30 that specifically amplifies a portion of Peptostreptococcus anaerobius genome; at least one primer pair selected from Primer Pair Set 31 that specifically amplifies a portion of Finegoldia magna genome; at least one primer pair selected from Primer Pair Set 32 that specifically amplifies a portion of Clostridium septicum genome; at least one primer pair selected from Primer Pair Set 33 that specifically amplifies a portion of Paeniclostridium sordellii (Clostridium sordellii) genome; at least one primer pair selected from Primer Pair Set 34 that specifically amplifies a portion of Clostridium novyi A, B genome; at least one primer pair selected from Primer Pair Set 35 that specifically amplifies a portion of Clostridium histolyticum genome; at least one primer pair selected from Primer Pair Set 36 that specifically amplifies a portion of Staphylococcus epidermidis genome; at least one primer pair selected from Primer Pair Set 37 that specifically amplifies a portion of Staphylococcus haemolyticus genome; at least one primer pair selected from Primer Pair Set 38 that specifically amplifies a portion of Corynebacterium striatum genome; at least one primer pair selected from Primer Pair Set 39 that specifically amplifies a portion of Candida albicans genome; at least one primer pair selected from Primer Pair Set 40 that specifically amplifies a portion of Candida auris genome; at least one primer pair selected from Primer Pair Set 41 that specifically amplifies a portion of Candida glabrata genome; at least one primer pair selected from Primer Pair Set 42 that specifically amplifies a portion of Candida krusei genome; at least one primer pair selected from Primer Pair Set 43 that specifically amplifies a portion of Candida parapsilosis genome; and/or at least one primer pair selected from Primer Pair Set 44 that specifically amplifies a portion of Candida tropicalis genome; and (b) subjecting the reaction mixture to reaction conditions suitable to amplify targeted nucleic acids, thereby generating at least one amplicon when the targeted nucleic acids are present in the sample; wherein the presence or absence of at least one amplicon in the sample indicates the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in the sample. 2. The method of claim 1, wherein the Primer Pair Sets comprise the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115– 116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133– 134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142– 143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160– 161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169– 170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289– 290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313– 314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353,355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. 3. The method of claim 1 or 2, wherein the generating of the at least one amplicon comprises performing PCR. 4. The method of any one of claims 1–3, wherein the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii produced using at least one primer pair selected from SEQ ID NO: 1–2, 4–5, or 7–8, and a sequence comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis produced using at least one primer pair selected from SEQ ID NO: 10–11, 13–14, or 16–17, and a sequence comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens produced using at least one primer pair selected from SEQ ID NO: 19–20, 22–23, or 25–26, and a sequence comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae produced using at least one primer pair selected from SEQ ID NO: 28–29, 31–32, or 34–35, and a sequence comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis produced using at least one primer pair selected from SEQ ID NO: 37–38, 40–41, or 43–44, and a sequence comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium produced using at least one primer pair selected from SEQ ID NO: 46–47, 49–50, or 52–53, and a sequence comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli produced using at least one primer pair selected from SEQ ID NO: 55–56, 58–59, or 61–62, and a sequence comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae produced using at least one primer pair selected from SEQ ID NO: 64–65, 67–68, or 70–71, and a sequence comprising at least a portion of SEQ ID NO: 434; an amplicon specific for Klebsiella Oxytoca produced using at least one primer pair selected from SEQ ID NO: 73–74, 76–77, or 79–80, and a sequence comprising at least a portion of SEQ ID NO: 435; an amplicon specific for Klebsiella aerogenes produced using at least one primer pair selected from SEQ ID NO: 82–83, 85–86, or 88–89, and a sequence comprising at least a portion of SEQ ID NO: 436; an amplicon specific for Proteus mirabilis produced using at least one primer pair selected from SEQ ID NO: 91–92, 94–95, or 97–98, and a sequence comprising at least a portion of SEQ ID NO: 437; an amplicon specific for Proteus vulgaris produced using at least one primer pair selected from SEQ ID NO: 100–101, 103–104, or 106–107, and a sequence comprising at least a portion of SEQ ID NO: 438; an amplicon specific for Pseudomonas aeruginosa produced using at least one primer pair selected from SEQ ID NO: 109–110, 112–113, or 115–116, and a sequence comprising at least a portion of SEQ ID NO: 439; an amplicon specific for Serratia marcescens produced using at least one primer pair selected from SEQ ID NO: 118–119, 121–122, or 124–125, and a sequence comprising at least a portion of SEQ ID NO: 440; an amplicon specific for Staphylococcus aureus produced using at least one primer pair selected from SEQ ID NO: 127–128, 130–131, or 133–134, and a sequence comprising at least a portion of SEQ ID NO: 441; an amplicon specific for Streptococcus agalactiae produced using at least one primer pair selected from SEQ ID NO: 136–137, 139–140, or 142–143, and a sequence comprising at least a portion of SEQ ID NO: 442; an amplicon specific for Streptococcus dysgalactiae produced using at least one primer pair selected from SEQ ID NO: 145–146, 148–149, or 151–152, and a sequence comprising at least a portion of SEQ ID NO: 443; an amplicon specific for Streptococcus anginosus produced using at least one primer pair selected from SEQ ID NO: 154–155, 157–158, or 160–161, and a sequence comprising at least a portion of SEQ ID NO: 444; an amplicon specific for Streptococcus pyogenesproduced using at least one primer pair selected from SEQ ID NO: 163–164, 166–167, or 169–170, and a sequence comprising at least a portion of SEQ ID NO: 445; an amplicon specific for Staphylococcus lugdunensis produced using at least one primer pair selected from SEQ ID NO: 172–173, 175–176, or 178–179, and a sequence comprising at least a portion of SEQ ID NO: 446; an amplicon specific for Providencia stuartii produced using at least one primer pair selected from SEQ ID NO: 181–182, 184–185, or 187–188, and a sequence comprising at least a portion of SEQ ID NO: 447; an amplicon specific for Stenotrophomonas maltophilia produced using at least one primer pair selected from SEQ ID NO: 190–191, 193–194, or 196–197;, and a sequence comprising at least a portion of SEQ ID NO: 448; an amplicon specific for Morganella morganii produced using at least one primer pair selected from SEQ ID NO: 199–200, 202–203, or 205–206, and a sequence comprising at least a portion of SEQ ID NO: 449; an amplicon specific for Citrobacter koseri produced using at least one primer pair selected from SEQ ID NO: 208–209, 211–212, or 214–215, and a sequence comprising at least a portion of SEQ ID NO: 450; an amplicon specific for Citrobacter freundii produced using at least one primer pair selected from SEQ ID NO: 217–218, 220–221, or 223–224, and a sequence comprising at least a portion of SEQ ID NO: 451; an amplicon specific for Citrobacter braakii produced using at least one primer pair selected from SEQ ID NO: 226–227, 229–230, or 232–233, and a sequence comprising at least a portion of SEQ ID NO: 452; an amplicon specific for Peptoniphilus asaccharolyticus produced using at least one primer pair selected from SEQ ID NO: 235–236, 238–239, or 241–242, and a sequence comprising at least a portion of SEQ ID NO: 453; an amplicon specific for Peptoniphilus harei produced using at least one primer pair selected from SEQ ID NO: 244–245, 247–248, or 250–251, and a sequence comprising at least a portion of SEQ ID NO: 454; an amplicon specific for Peptoniphilus ivorii produced using at least one primer pair selected from SEQ ID NO: 253–254, 256–257, or 259–260, and a sequence comprising at least a portion of SEQ ID NO: 455; an amplicon specific for Peptostreptococcus anaerobius produced using at least one primer pair selected from SEQ ID NO: 262–263, 265–266, or 268–269, and a sequence comprising at least a portion of SEQ ID NO: 456; an amplicon specific for Finegoldia magna produced using at least one primer pair selected from SEQ ID NO: 271–272, 274–275, or 277–278, and a sequence comprising at least a portion of SEQ ID NO: 457; an amplicon specific for Clostridium septicum produced using at least one primer pair selected from SEQ ID NO: 280–281, 283–284, or 286–287, and a sequence comprising at least a portion of SEQ ID NO: 458; an amplicon specific for Paeniclostridium sordellii (Clostridium sordellii) produced using at least one primer pair selected from SEQ ID NO: 289–290, 292–293, or 295–296, and a sequence comprising at least a portion of SEQ ID NO: 459; an amplicon specific for Clostridium novyi A, B produced using at least one primer pair selected from SEQ ID NO: 298–299, 301–302, or 304–305, and a sequence comprising at least a portion of SEQ ID NO: 460; an amplicon specific for Clostridium histolyticum produced using at least one primer pair selected from SEQ ID NO: 307–308, 310–311, or 313–314, and a sequence comprising at least a portion of SEQ ID NO: 461; an amplicon specific for Staphylococcus epidermidis produced using at least one primer pair selected from SEQ ID NO: 316–317, 319–320, or 322–323, and a sequence comprising at least a portion of SEQ ID NO: 462; an amplicon specific for Staphylococcus haemolyticus produced using at least one primer pair selected from SEQ ID NO: 325–326, 328–329, or 331–332, and a sequence comprising at least a portion of SEQ ID NO: 463; an amplicon specific for Corynebacterium striatum produced using at least one primer pair selected from SEQ ID NO: 334–335, 337–338, or 340–341, and a sequence comprising at least a portion of SEQ ID NO: 464; an amplicon specific for Candida albicans produced using at least one primer pair selected from SEQ ID NO: 343–344, 346–347, or 349–350, and a sequence selected from SEQ ID NO: 465; an amplicon specific for Candida auris produced using at least one primer pair selected from SEQ ID NO: 352–353,355–356, or 358–359, and a sequence comprising at least a portion of SEQ ID NO: 466; an amplicon specific for Candida glabrata produced using at least one primer pair selected from SEQ ID NO: 361–362, 364–365, or 367–368, and a sequence comprising at least a portion of SEQ ID NO: 467; an amplicon specific for Candida krusei produced using at least one primer pair selected from SEQ ID NO: 370–371, 373–374, or 376–377, and a sequence comprising at least a portion of SEQ ID NO: 468; an amplicon specific for Candida parapsilosis produced using at least one primer pair selected from SEQ ID NO: 379–380, 382–383, or 385–386, and a sequence comprising at least a portion of SEQ ID NO: 469; and/or an amplicon specific for Candida tropicalis produced using at least one primer pair selected from SEQ ID NO: 388–389, 391–392, or 394–395, and a sequence comprising at least a portion of SEQ ID NO: 470. 5. The method of any one of claims 1–5, wherein the at least one amplicon is one selected from: an amplicon specific for Acinetobacter baumannii comprising at least a portion of SEQ ID NO: 427; an amplicon specific for Bacteroides fragilis comprising at least a portion of SEQ ID NO: 428; an amplicon specific for Clostridium perfringens comprising at least a portion of SEQ ID NO: 429; an amplicon specific for Enterobacter cloacae comprising at least a portion of SEQ ID NO: 430; an amplicon specific for Enterococcus faecalis comprising at least a portion of SEQ ID NO: 431; an amplicon specific for Enterococcus faecium comprising at least a portion of SEQ ID NO: 432; an amplicon specific for Escherichia coli comprising at least a portion of SEQ ID NO: 433; an amplicon specific for Klebsiella pneumoniae comprising at least a portion of SEQ ID NO:434; an amplicon specific for Klebsiella Oxytoca comprising at least a portion of SEQ ID NO: 435; an amplicon specific for Klebsiella aerogenes comprising at least a portion of SEQ ID NO: 436; an amplicon specific for Proteus mirabilis comprising at least a portion of SEQ ID NO: 437; an amplicon specific for Proteus vulgaris comprising at least a portion of SEQ ID NO: 438; an amplicon specific for Pseudomonas aeruginosa comprising at least a portion of SEQ ID NO: 439; an amplicon specific for Serratia marcescens comprising at least a portion of SEQ ID NO: 440; an amplicon specific for Staphylococcus aureus comprising at least a portion of SEQ ID NO: 441; an amplicon specific for Streptococcus agalactiae comprising at least a portion of SEQ ID NO: 442; an amplicon specific for Streptococcus dysgalactiae comprising at least a portion of SEQ ID NO: 443; an amplicon specific for Streptococcus anginosus comprising at least a portion of SEQ ID NO: 444; an amplicon specific for Streptococcus pyogenes comprising at least a portion of SEQ ID NO: 445; an amplicon specific for Staphylococcus lugdunensis comprising at least a portion of SEQ ID NO: 446; an amplicon specific for Providencia stuartii comprising at least a portion of SEQ ID NO: 447; an amplicon specific for Stenotrophomonas maltophilia comprising at least a portion of SEQ ID NO: 448; an amplicon specific for Morganella morganii comprising at least a portion of SEQ ID NO: 449; an amplicon specific for Citrobacter koseri comprising at least a portion of SEQ ID NO: 450; an amplicon specific for Citrobacter freundii comprising at least a portion of SEQ ID NO: 451; an amplicon specific for Citrobacter braakii comprising at least a portion of SEQ ID NO: 452; an amplicon specific for Peptoniphilus asaccharolyticus comprising at least a portion of SEQ ID NO: 453; an amplicon specific for Peptoniphilus harei comprising at least a portion of SEQ ID NO: 454; an amplicon specific for Peptoniphilus ivorii comprising at least a portion of SEQ ID NO: 455; an amplicon specific for Peptostreptococcus anaerobius comprising at least a portion of SEQ ID NO: 456; an amplicon specific for Finegoldia magna comprising at least a portion of SEQ ID NO: 457; an amplicon specific for Clostridium septicum comprising at least a portion of SEQ ID NO: 458; an amplicon specific for Paeniclostridium sordellii (Clostridium sordellii) comprising at least a portion of SEQ ID NO: 459; an amplicon specific for Clostridium novyi A, B comprising at least a portion of SEQ ID NO: 460; an amplicon specific for Clostridium histolyticum comprising at least a portion of SEQ ID NO: 461; an amplicon specific for Staphylococcus epidermidis comprising at least a portion of SEQ ID NO: 462; an amplicon specific for Staphylococcus haemolyticus comprising at least a portion of SEQ ID NO: 463; an amplicon specific for Corynebacterium striatum comprising at least a portion of SEQ ID NO: 464; an amplicon specific for Candida albicans comprising at least a portion of SEQ ID NO: 465; an amplicon specific for Candida auris comprising at least a portion of SEQ ID NO: 466; an amplicon specific for Candida glabrata comprising at least a portion of SEQ ID NO: 467; an amplicon specific for Candida krusei comprising at least a portion of SEQ ID NO: 468; an amplicon specific for Candida parapsilosis comprising at least a portion of SEQ ID NO: 469; and/or an amplicon specific for Candida tropicalis comprising at least a portion of SEQ ID NO: 470. 6. The method any one of claims 1–5, wherein the reaction mixture further comprises probes specific for the at least one amplicon. 7. The method of any one of claims 1–6, wherein the reaction mixture further comprises probes specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probes comprising: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. 8. The method of any one of claims 1–7, wherein the reaction mixture further contains a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample. 9. The method of claim 8, wherein the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. 10. The method of any one of claims 1–9, wherein the probe comprises a fluorescent reporter. 11. The method of claim 10, wherein the probe comprises a quencher. 12. The method of claim 10 or 11, wherein the probe is labeled at or near the 5′–end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM. 13. The method of any one of claims 10–12, wherein the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ. 14. A composition for individually, simultaneously, or sequentially determining the presence or absence of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis comprising a plurality of Primer Pair Sets, wherein the Primer Pair Sets comprise: at least one primer pair selected from Primer Pair Set 1 that specifically amplifies a portion of Acinetobacter baumannii genome; at least one primer pair selected from Primer Pair Set 2 that specifically amplifies a portion of Bacteroides fragilis genome; at least one primer pair selected from Primer Pair Set 3 that specifically amplifies a portion of Clostridium perfringens genome; at least one primer pair selected from Primer Pair Set 4 that specifically amplifies a portion of Enterobacter cloacae genome; at least one primer pair selected from Primer Pair Set 5 that specifically amplifies a portion of Enterococcus faecalis genome; at least one primer pair selected from Primer Pair Set 6 that specifically amplifies a portion of Enterococcus faecium genome; at least one primer pair selected from Primer Pair Set 7 that specifically amplifies a portion of Escherichia coli genome; at least one primer pair selected from Primer Pair Set 8 that specifically amplifies a portion of Klebsiella pneumoniae genome; at least one primer pair selected from Primer Pair Set 9 that specifically amplifies a portion of Klebsiella oxytoca genome; at least one primer pair selected from Primer Pair Set 10 that specifically amplifies a portion of Klebsiella aerogenes genome; at least one primer pair selected from Primer Pair Set 11 that specifically amplifies a portion of Proteus mirabilis genome; at least one primer pair selected from Primer Pair Set 12 that specifically amplifies a portion of Proteus vulgaris genome; at least one primer pair selected from Primer Pair Set 13 that specifically amplifies a portion of Pseudomonas aeruginosa genome; at least one primer pair selected from Primer Pair Set 14 that specifically amplifies a portion of Serratia marcescens genome; at least one primer pair selected from Primer Pair Set 15 that specifically amplifies a portion of Staphylococcus aureus genome; at least one primer pair selected from Primer Pair Set 16 that specifically amplifies a portion of Streptococcus agalactiae genome; at least one primer pair selected from Primer Pair Set 17 that specifically amplifies a portion of Streptococcus dysgalactiae genome; at least one primer pair selected from Primer Pair Set 18 that specifically amplifies a portion of Streptococcus anginosus genome; at least one primer pair selected from Primer Pair Set 19 that specifically amplifies a portion of Streptococcus pyogenes genome; at least one primer pair selected from Primer Pair Set 20 that specifically amplifies a portion of Staphylococcus lugdunensis genome; at least one primer pair selected from Primer Pair Set 21 that specifically amplifies a portion of Providencia stuartii genome; at least one primer pair selected from Primer Pair Set 22 that specifically amplifies a portion of Stenotrophomonas maltophilia genome; at least one primer pair selected from Primer Pair Set 23 that specifically amplifies a portion of Morganella morganii genome; at least one primer pair selected from Primer Pair Set 24 that specifically amplifies a portion of Citrobacter koseri genome; at least one primer pair selected from Primer Pair Set 25 that specifically amplifies a portion of Citrobacter freundii genome; at least one primer pair selected from Primer Pair Set 26 that specifically amplifies a portion of Citrobacter braakii genome; at least one primer pair selected from Primer Pair Set 27 that specifically amplifies a portion of Peptoniphilus asaccharolyticus genome; at least one primer pair selected from Primer Pair Set 28 that specifically amplifies a portion of Peptoniphilus harei genome; at least one primer pair selected from Primer Pair Set 29 that specifically amplifies a portion of Peptoniphilus ivorii genome; at least one primer pair selected from Primer Pair Set 30 that specifically amplifies a portion of Peptostreptococcus anaerobius genome; at least one primer pair selected from Primer Pair Set 31 that specifically amplifies a portion of Finegoldia magna genome; at least one primer pair selected from Primer Pair Set 32 that specifically amplifies a portion of Clostridium septicum genome; at least one primer pair selected from Primer Pair Set 33 that specifically amplifies a portion of Paeniclostridium sordellii (Clostridium sordellii) genome; at least one primer pair selected from Primer Pair Set 34 that specifically amplifies a portion of Clostridium novyi A, B genome; at least one primer pair selected from Primer Pair Set 35 that specifically amplifies a portion of Clostridium histolyticum genome; at least one primer pair selected from Primer Pair Set 36 that specifically amplifies a portion of Staphylococcus epidermidis genome; at least one primer pair selected from Primer Pair Set 37 that specifically amplifies a portion of Staphylococcus haemolyticus genome; at least one primer pair selected from Primer Pair Set 38 that specifically amplifies a portion of Corynebacterium striatum genome;at least one primer pair selected from Primer Pair Set 39 that specifically amplifies a portion of Candida albicans genome; at least one primer pair selected from Primer Pair Set 40 that specifically amplifies a portion of Candida auris genome; at least one primer pair selected from Primer Pair Set 41 that specifically amplifies a portion of Candida glabrata genome; at least one primer pair selected from Primer Pair Set 42 that specifically amplifies a portion of Candida krusei genome; at least one primer pair selected from Primer Pair Set 43 that specifically amplifies a portion of Candida parapsilosis genome; and/or at least one primer pair selected from Primer Pair Set 44 that specifically amplifies a portion of Candida tropicalis genome. 15. The composition of claim 14, wherein the Primer Pair Sets comprises the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115– Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133– 134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142– 143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160– 161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169– 170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289– 290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313– 314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353,355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. 16. The composition of claim 14 or 15, further comprising a probe specific for for the at least one amplicon produced using the at least one primer pair selected from one or more of Primer Pair Sets 1–44. 17. The composition of any one of claims 14–16, further comprising a probe specific for the at least one amplicon and suitable for use with a Primer Pair Set, the probe comprising: probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. 18. The composition of any one of claims 14–17, further comprising a polymerase, a buffer, and deoxynucleotide triphosphates (dNTPs). 19. The composition of any one of claims 14–18, further comprising a sample. 20. The composition of any one of claims 14–19, further comprising at least one control forward and reverse primer and, optionally, a control probe, that specifically amplifies a target nucleic acid of a control sample. 21. The composition of claim 21, wherein the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418–419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. 22. The composition of any one of claims 14–21, wherein the probe contains a fluorescent reporter. 23. The composition of claim 22, wherein the probe contains a quencher. 24. The composition of any one of claims 22 or 23, wherein the probe is labeled at or near the 5′ end with a dye selected from FAM, VIC, ABY, JUN, AF647, or 6FAM. 25. The composition of any one of claims 22–24, wherein the probe is labeled at or near the 3′ end with a quencher selected from MGB, QSY7, QSY21, MGBNFQ, BHQ, or DFQ. 26. A kit for individually, simultaneously, or sequentially determining the presence or absence of one or more of Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis in a sample, comprising the compositions of any one of claims 14–18. 27. The kit of claim 29, further comprising the compositions of any one of claims 19–25. 28. The kit of claim 26 or 27, wherein the kit comprises Primer Pair Sets comprising the following sequences: Primer Pair Set 1 comprises at least one forward and reverse primer pair specific for Acinetobacter baumannii selected from SEQ ID NO: 1–2, 4–5, or 7–8; Primer Pair Set 2 comprises at least one forward and reverse primer pair specific for Bacteroides fragilis selected from SEQ ID NO: 10–11, 13–14, or 16–17; Primer Pair Set 3 comprises at least one forward and reverse primer pair specific for Clostridium perfringens selected from SEQ ID NO: 19–20, 22–23, or 25–26; Primer Pair Set 4 comprises at least one forward and reverse primer pair specific for Enterobacter cloacae selected from SEQ ID NO: 28–29, 31–32, or 34–35; Primer Pair Set 5 comprises at least one forward and reverse primer pair specific for Enterococcus faecalis selected from SEQ ID NO: 37–38, 40–41, or 43–44; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Enterococcus faecium selected from SEQ ID NO: 46–47, 49–50, or 52–53; Primer Pair Set 6 comprises at least one forward and reverse primer pair specific for Escherichia coli selected from SEQ ID NO: 55–56, 58–59, or 61–62; Primer Pair Set 8 comprises at least one forward and reverse primer pair specific for Klebsiella pneumoniae selected from SEQ ID NO: 64–65, 67–68, or 70–71; Primer Pair Set 9 comprises at least one forward and reverse primer pair specific for Klebsiella Oxytoca selected from SEQ ID NO: 73–74, 76–77, or 79–80; Primer Pair Set 10 comprises at least one forward and reverse primer pair specific for Klebsiella aerogenes selected from SEQ ID NO: 82–83, 85–86, or 88–89; Primer Pair Set 11 comprises at least one forward and reverse primer pair specific for Proteus mirabilis selected from SEQ ID NO: 91–92, 94–95, or 97–98; Primer Pair Set 12 comprises at least one forward and reverse primer pair specific for Proteus vulgaris selected from SEQ ID NO: 100–101, 103–104, or 106–107; Primer Pair Set 13 comprises at least one forward and reverse primer pair specific for Pseudomonas aeruginosa selected from SEQ ID NO: 109–110, 112–113, or 115– 116; Primer Pair Set 14 comprises at least one forward and reverse primer pair specific for Serratia marcescens selected from SEQ ID NO: 118–119, 121–122, or 124–125; Primer Pair Set 15 comprises at least one forward and reverse primer pair specific for Staphylococcus aureus selected from SEQ ID NO: 127–128, 130–131, or 133– 134; Primer Pair Set 16 comprises at least one forward and reverse primer pair specific for Streptococcus agalactiae selected from SEQ ID NO: 136–137, 139–140, or 142– 143; Primer Pair Set 17 comprises at least one forward and reverse primer pair specific for Streptococcus dysgalactiae selected from SEQ ID NO: 145–146, 148–149, or 151–152; Primer Pair Set 18 comprises at least one forward and reverse primer pair specific for Streptococcus anginosus selected from SEQ ID NO: 154–155, 157–158, or 160– 161; Primer Pair Set 19 comprises at least one forward and reverse primer pair specific for Streptococcus pyogenes selected from SEQ ID NO: 163–164, 166–167, or 169– 170; Primer Pair Set 20 comprises at least one forward and reverse primer pair specific for Staphylococcus lugdunensis selected from SEQ ID NO: 172–173, 175–176, or 178–179; Primer Pair Set 21 comprises at least one forward and reverse primer pair specific for Providencia stuartii selected from SEQ ID NO: 181–182, 184–185, or 187–188; Primer Pair Set 22 comprises at least one forward and reverse primer pair specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 190–191, 193–194, or 196–197; Primer Pair Set 23 comprises at least one forward and reverse primer pair specific for Morganella morganii selected from SEQ ID NO: 199–200, 202–203, or 205–206; Primer Pair Set 24 comprises at least one forward and reverse primer pair specific for Citrobacter koseri selected from SEQ ID NO: 208–209, 211–212, or 214–215; Primer Pair Set 25 comprises at least one forward and reverse primer pair specific for Citrobacter freundii selected from SEQ ID NO: 217–218, 220–221, or 223–224; Primer Pair Set 26 comprises at least one forward and reverse primer pair specific for Citrobacter braakii selected from SEQ ID NO: 226–227, 229–230, or 232–233; Primer Pair Set 27 comprises at least one forward and reverse primer pair specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 235–236, 238–239, or 241–242; Primer Pair Set 28 comprises at least one forward and reverse primer pair specific for Peptoniphilus harei selected from SEQ ID NO: 244–245, 247–248, or 250–251; Primer Pair Set 29 comprises at least one forward and reverse primer pair specific for Peptoniphilus ivorii selected from SEQ ID NO: 253–254, 256–257, or 259–260; Primer Pair Set 30 comprises at least one forward and reverse primer pair specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 262–263, 265–266, or 268–269; Primer Pair Set 31 comprises at least one forward and reverse primer pair specific for Finegoldia magna selected from SEQ ID NO: 271–272, 274–275, or 277–278; Primer Pair Set 32 comprises at least one forward and reverse primer pair specific for Clostridium septicum selected from SEQ ID NO: 280–281, 283–284, or 286–287; Primer Pair Set 33 comprises at least one forward and reverse primer pair specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 289– 290, 292–293, or 295–296; Primer Pair Set 34 comprises at least one forward and reverse primer pair specific for Clostridium novyi A, B selected from SEQ ID NO: 298–299, 301–302, or 304–305; Primer Pair Set 35 comprises at least one forward and reverse primer pair specific for Clostridium histolyticum selected from SEQ ID NO: 307–308, 310–311, or 313– 314; Primer Pair Set 36 comprises at least one forward and reverse primer pair specific for Staphylococcus epidermidis selected from SEQ ID NO: 316–317, 319–320, or 322–323; Primer Pair Set 37 comprises at least one forward and reverse primer pair specific for Staphylococcus haemolyticus selected from SEQ ID NO: 325–326, 328–329, or 331–332; Primer Pair Set 38 comprises at least one forward and reverse primer pair specific for Corynebacterium striatum selected from SEQ ID NO: 334–335, 337–338, or 340– 341; Primer Pair Set 39 comprises at least one forward and reverse primer pair specific for Candida albicans selected from SEQ ID NO: 343–344, 346–347, or 349–350; Primer Pair Set 40 comprises at least one forward and reverse primer pair specific for Candida auris selected from SEQ ID NO: 352–353, 355–356, or 358–359; Primer Pair Set 41 comprises at least one forward and reverse primer pair specific for Candida glabrata selected from SEQ ID NO: 361–362, 364–365, or 367–368; Primer Pair Set 42 comprises at least one forward and reverse primer pair specific for Candida krusei selected from SEQ ID NO: 370–371, 373–374, or 376–377; Primer Pair Set 43 comprises at least one forward and reverse primer pair specific for Candida parapsilosis selected from SEQ ID NO: 379–380, 382–383, or 385–386; and/or Primer Pair Set 44 comprises at least one forward and reverse primer pair specific for Candida tropicalis selected from SEQ ID NO: 388–389, 391–392, or 394–395. 29. The kit of claim 28, wherein the kit further comprises probes suitable for use with specific forward and reverse primer pairs, the probes comprising one or more of: a probe specific for Acinetobacter baumannii selected from SEQ ID NO: 3, 6, 9; a probe specific for Bacteroides fragilis selected from SEQ ID NO: 12, 15, or 18; a probe specific for Clostridium perfringens selected from SEQ ID NO: 21, 24, or 27; a probe specific for Enterobacter cloacae selected from SEQ ID NO: 30, 33, or 36; a probe specific for Enterococcus faecalis selected from SEQ ID NO: 39, 42, or 45; a probe specific for Enterococcus faecium selected from SEQ ID NO: 48, 51, or 54; a probe specific for Escherichia coli selected from SEQ ID NO: 57, 60, or 63; a probe specific for Klebsiella pneumoniae selected from SEQ ID NO: 66, 69, or 72; a probe specific for Klebsiella Oxytoca selected from SEQ ID NO: 75, 78, or 81; a probe specific for Klebsiella aerogenes selected from SEQ ID NO: 84, 87, or 90; a probe specific for Proteus mirabilis selected from SEQ ID NO: 93, 96, or 99; a probe specific for Proteus vulgaris selected from SEQ ID NO: 102, 105, or 108; a probe specific for Pseudomonas aeruginosa selected from SEQ ID NO: 111, 114, or 117; a probe specific for Serratia marcescens selected from SEQ ID NO: 120, 123, or 126; a probe specific for Staphylococcus aureus selected from SEQ ID NO: 129, 132, or 135; a probe specific for Streptococcus agalactiae selected from SEQ ID NO: 138, 141, or 144; a probe specific for Streptococcus dysgalactiae selected from SEQ ID NO: 147, 150, or 153; a probe specific for Streptococcus anginosus selected from SEQ ID NO: 156, 159, or 162; a probe specific for Streptococcus pyogenes selected from SEQ ID NO: 165, 168, or 171; a probe specific for Staphylococcus lugdunensis selected from SEQ ID NO: 174, 177, or 180; a probe specific for Providencia stuartii selected from SEQ ID NO: 183, 186, or 189; a probe specific for Stenotrophomonas maltophilia selected from SEQ ID NO: 192, 195, or 198; a probe specific for Morganella morganii selected from SEQ ID NO: 201, 204, or 207; a probe specific for Citrobacter koseri selected from SEQ ID NO: 210, 213, or 216; a probe specific for Citrobacter freundii selected from SEQ ID NO: 219, 222, or 225; a probe specific for Citrobacter braakii selected from SEQ ID NO: 228, 231, or 234; a probe specific for Peptoniphilus asaccharolyticus selected from SEQ ID NO: 237, 240, or 243; a probe specific for Peptoniphilus harei selected from SEQ ID NO: 246, 249, or 252; a probe specific for Peptoniphilus ivorii selected from SEQ ID NO: 255, 258, or 261; a probe specific for Peptostreptococcus anaerobius selected from SEQ ID NO: 264, 267, or 270; a probe specific for Finegoldia magna selected from SEQ ID NO: 273, 276, or 279; a probe specific for Clostridium septicum selected from SEQ ID NO: 282, 285, or 288; a probe specific for Paeniclostridium sordellii (Clostridium sordellii) selected from SEQ ID NO: 291, 294, or 297; a probe specific for Clostridium novyi A, B selected from SEQ ID NO: 300, 303, or 306; a probe specific for Clostridium histolyticum selected from SEQ ID NO: 309, 312, or 315; a probe specific for Staphylococcus epidermidis selected from SEQ ID NO: 318, 321, or 324; a probe specific for Staphylococcus haemolyticus selected from SEQ ID NO: 327, 330, or 333; and/or a probe specific for Corynebacterium striatum selected from SEQ ID NO: 336, 339, or 342; a probe specific for Candida albicans selected from SEQ ID NO: 345, 348, or 351; a probe specific for Candida auris selected from SEQ ID NO: 354, 357, or 360; a probe specific for Candida glabrata selected from SEQ ID NO: 363, 366, or 369; a probe specific for Candida krusei selected from SEQ ID NO: 372, 375, or 378; a probe specific for Candida parapsilosis selected from SEQ ID NO: 381, 384, or 387; and/or a probe specific for Candida tropicalis selected from SEQ ID NO: 390, 393, or 396. 30. The kit of claim 28, wherein the kit further comprises a control sample, control forward and reverse primers and, optionally, a control probe, that specifically amplifies a target nucleic acid of the control sample. 31. The kit of claim 30, wherein the control forward and reverse primer pairs are selected from SEQ ID NO: 397–398, 400–401, 403–404, 406–407, 409–410, 412–413, 415–416, 418– 419, 421–422, 424–425; and the control probe comprises a probe sequence selected from SEQ ID NO: 399, 402, 405, 408, 411, 414, 417, 420, 423, or 426. 32. The kit of claim 28, wherein the kit further comprises a control plasmid comprising one or more target sequences selected from Acinetobacter baumannii, Bacteroides fragilis, Clostridium perfringens, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Klebsiella Oxytoca, Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pyogenes, Streptococcus anginosus, Staphylococcus lugdunensis, Providencia stuartii, Stenotrophomonas maltophilia, Morganella morganii, Citrobacter koseri, Citrobacter freundii, Citrobacter braakii, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus ivorii, Peptostreptococcus anaerobius, Finegoldia magna, Clostridium septicum, Paeniclostridium sordellii (Clostridium sordellii), Clostridium novyi A, B, Clostridium histolyticum, Staphylococcus epidermidis, Staphylococcus haemolyticus, Corynebacterium striatum, Candida albicans, Candida auris, Candida glabrata, Candida krusei, Candida parapsilosis, or Candida tropicalis. 33. The control plasmid of claim 31, wherein the plasmid comprises one or more of nucleic acid sequences of SEQ ID NO: 427–470.
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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6562958B1 (en) * 1998-06-09 2003-05-13 Genome Therapeutics Corporation Nucleic acid and amino acid sequences relating to Acinetobacter baumannii for diagnostics and therapeutics
US20200340041A1 (en) * 2017-11-13 2020-10-29 Life Technologies Corporation Novel compositions, methods and kits for urinary tract microorganism detection

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6562958B1 (en) * 1998-06-09 2003-05-13 Genome Therapeutics Corporation Nucleic acid and amino acid sequences relating to Acinetobacter baumannii for diagnostics and therapeutics
US20200340041A1 (en) * 2017-11-13 2020-10-29 Life Technologies Corporation Novel compositions, methods and kits for urinary tract microorganism detection

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