In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–... more In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–V4 hypervariable region of 16S rRNA analysis requires sophisticated bioinformatics pipelines and validated methods that allow researchers to compare their data with confidence. Many commercial laboratories conduct extensive HTS analyses; however, there is no available information on whether the results generated by these vendors are consistent. In our study, we compared the sequencing data obtained for the same marine microbiome community sample generated by three commercial laboratories. Additionally, as a sequencing control to determine differences between commercial laboratories and two 16S rRNA databases, we also performed a “mock community” analysis of a defined number of microbial species. We also assessed the impact of the choice of two commonly used 16S rRNA databases, i.e., Greengenes and SILVA, on downstream data analysis, including taxonomic classification assignment. We demon...
In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–... more In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–V4 hypervariable region of 16S rRNA analysis requires sophisticated bioinformatics pipelines and validated methods that allow researchers to compare their data with confidence. Many commercial laboratories conduct extensive HTS analyses; however, there is no available information on whether the results generated by these vendors are consistent. In our study, we compared the sequencing data obtained for the same marine microbiome community sample generated by three commercial laboratories. Additionally, as a sequencing control to determine differences between commercial laboratories and two 16S rRNA databases, we also performed a “mock community” analysis of a defined number of microbial species. We also assessed the impact of the choice of two commonly used 16S rRNA databases, i.e., Greengenes and SILVA, on downstream data analysis, including taxonomic classification assignment. We demon...
International Journal of Environmental Research and Public Health
Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in mult... more Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health’s concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lac...
International Journal of Environmental Research and Public Health, 2022
Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in mult... more Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).
Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2006
Mutagenic pollution of the natural environment, including marine waters, is a very serious ecolog... more Mutagenic pollution of the natural environment, including marine waters, is a very serious ecological problem. However, since chemical mutagens usually occur and act at low concentrations, their detection and identification is technically difficult, laborious and time-consuming. Therefore, preliminary detection of mutagenic pollution is commonly based on biological mutagenicity assays. On the other hand, triolein-containing semi-permeable membrane devices (SPMDs) provide a method for concentration of hydrophobic organic contaminants, including a large fraction of the mutagens. Combinations of SPMDs with microbiological toxicity and mutagenicity assays have already been described, but only SPMD-derived extracts, prepared with various organic solvents, were tested in such a way to date. We found that the presence of these solvents could interfere with the Vibrio harveyi bioluminescence-based mutagenicity assay. Moreover, preparation of the extracts from SPMD takes usually at least 48h. Here, we propose a modified procedure, based on direct addition of tester bacteria cultures into SPMD. We found that this procedure is significantly (at least two times) more rapid and several times more sensitive than that based on testing the extracts. This optimization is presented in this report. Moreover, we have performed preliminary studies on samples of marine waters. Positive results (i.e. detection of mutagenic activity) were obtained when test samples came from a region known to be highly contaminated by industrial pollution, while negative results were observed in the case of samples from a region supposed to be of low risk for mutagenic pollution.
In this study, species distribution and antimicrobial susceptibility of cultivated Pseudomonas sp... more In this study, species distribution and antimicrobial susceptibility of cultivated Pseudomonas spp. were studied in influent (INF), effluent (EFF), and marine outfall (MOut) of wastewater treatment plant (WWTP). The susceptibility was tested against 8 antimicrobial classes, active against Pseudomonas spp.: aminoglycosides, carbapenems, broad-spectrum cephalosporins from the 3rd and 4th generation, extended-spectrum penicillins, as well as their combination wi th the β- lac tamase inhib i tors, monobactams, fluoroquinolones, and polymyxins. Among identified species, resistance to all antimicrobials but colistin was shown by Pseudomonas putida, the predominant species in all sampling points. In other species, resistance was observed mainly against ceftazidime, ticarcillin, ticarcillin-clavulanate, and az-treonam, although some isolates of Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas pseudoalcaligenes, and Pseudomonas protegens showed multidrug-resistance (MDR) phenotyp...
In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–... more In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–V4 hypervariable region of 16S rRNA analysis requires sophisticated bioinformatics pipelines and validated methods that allow researchers to compare their data with confidence. Many commercial laboratories conduct extensive HTS analyses; however, there is no available information on whether the results generated by these vendors are consistent. In our study, we compared the sequencing data obtained for the same marine microbiome community sample generated by three commercial laboratories. Additionally, as a sequencing control to determine differences between commercial laboratories and two 16S rRNA databases, we also performed a “mock community” analysis of a defined number of microbial species. We also assessed the impact of the choice of two commonly used 16S rRNA databases, i.e., Greengenes and SILVA, on downstream data analysis, including taxonomic classification assignment. We demon...
In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–... more In the high-throughput sequencing (HTS) era, a metabarcoding technique based on the bacterial V3–V4 hypervariable region of 16S rRNA analysis requires sophisticated bioinformatics pipelines and validated methods that allow researchers to compare their data with confidence. Many commercial laboratories conduct extensive HTS analyses; however, there is no available information on whether the results generated by these vendors are consistent. In our study, we compared the sequencing data obtained for the same marine microbiome community sample generated by three commercial laboratories. Additionally, as a sequencing control to determine differences between commercial laboratories and two 16S rRNA databases, we also performed a “mock community” analysis of a defined number of microbial species. We also assessed the impact of the choice of two commonly used 16S rRNA databases, i.e., Greengenes and SILVA, on downstream data analysis, including taxonomic classification assignment. We demon...
International Journal of Environmental Research and Public Health
Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in mult... more Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health’s concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lac...
International Journal of Environmental Research and Public Health, 2022
Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in mult... more Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).
Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2006
Mutagenic pollution of the natural environment, including marine waters, is a very serious ecolog... more Mutagenic pollution of the natural environment, including marine waters, is a very serious ecological problem. However, since chemical mutagens usually occur and act at low concentrations, their detection and identification is technically difficult, laborious and time-consuming. Therefore, preliminary detection of mutagenic pollution is commonly based on biological mutagenicity assays. On the other hand, triolein-containing semi-permeable membrane devices (SPMDs) provide a method for concentration of hydrophobic organic contaminants, including a large fraction of the mutagens. Combinations of SPMDs with microbiological toxicity and mutagenicity assays have already been described, but only SPMD-derived extracts, prepared with various organic solvents, were tested in such a way to date. We found that the presence of these solvents could interfere with the Vibrio harveyi bioluminescence-based mutagenicity assay. Moreover, preparation of the extracts from SPMD takes usually at least 48h. Here, we propose a modified procedure, based on direct addition of tester bacteria cultures into SPMD. We found that this procedure is significantly (at least two times) more rapid and several times more sensitive than that based on testing the extracts. This optimization is presented in this report. Moreover, we have performed preliminary studies on samples of marine waters. Positive results (i.e. detection of mutagenic activity) were obtained when test samples came from a region known to be highly contaminated by industrial pollution, while negative results were observed in the case of samples from a region supposed to be of low risk for mutagenic pollution.
In this study, species distribution and antimicrobial susceptibility of cultivated Pseudomonas sp... more In this study, species distribution and antimicrobial susceptibility of cultivated Pseudomonas spp. were studied in influent (INF), effluent (EFF), and marine outfall (MOut) of wastewater treatment plant (WWTP). The susceptibility was tested against 8 antimicrobial classes, active against Pseudomonas spp.: aminoglycosides, carbapenems, broad-spectrum cephalosporins from the 3rd and 4th generation, extended-spectrum penicillins, as well as their combination wi th the β- lac tamase inhib i tors, monobactams, fluoroquinolones, and polymyxins. Among identified species, resistance to all antimicrobials but colistin was shown by Pseudomonas putida, the predominant species in all sampling points. In other species, resistance was observed mainly against ceftazidime, ticarcillin, ticarcillin-clavulanate, and az-treonam, although some isolates of Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas pseudoalcaligenes, and Pseudomonas protegens showed multidrug-resistance (MDR) phenotyp...
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