1.Microbiology.

Microbiology deals with microscopic organisms, the

smallest, simplest single celled organisms unseen without magnification.
Bacteria, viruses, fungi, protozoa, algae, and helminths are the major
biological groups that microbiologists study. Microbiology also studies the
natural history of microbes, aspect of microbe-human and microbe-
environmental interactions
OBJECTIVE- to impart knowledge of basic principles of
bacteriology,virology,mycology,immunology amd parisitology including nature
of pathogenic microorganisms,pathogenesis,laboratory diagnosis,
transmission,prevention and control of diseases common in the country.
TASKS Medical microbiologists provide services to aid the diagnosis and
management of infectious diseases and help ensure the safety of those at
risk of acquiring infectious diseases, both in hospitals and the community.
Although this role is laboratory-based, the microbiologist's role is
increasingly clinical.

Role of microbiology in medical practice.

One of the major areas of applied microbiology is biotechnology

Pharmaceutical industry.
Understanding the principles of microbiology and human cell
mechanisms allows pharmacists to discover antimicrobial drugs that
would prevent an escalating number of communicable diseases.
Medical devices.
Microbiology plays a significant role in medical devices, such
as fluorescent fusion, which are used for fast and precise detection
of pathogens in tissue samples.
Diagnosis
Most clinical microbiology labs will not routinely
identify Cryptococcus isolates to the species level. Although
cultures may take up to a week to become
positive, Cryptococcus spp. grow on most clinical media,
including standard radiometric blood culturing systems.

2. History and development of microbiology. L. Pasteur and R. Koch

Louis Pasteur and the germ theory. Louis Pasteur worked in the middle and
late 1800s. He performed numerous experiments to discover why wine and dairy
products became sour, and he found that bacteria were to blame. Pasteur called
attention to the importance of microorganisms in everyday life and stirred
scientists to think that if bacteria could make the wine “sick,” then perhaps they
could cause human illness.

Pasteur's attempts to prove the germ theory were unsuccessful. However, the
German scientist Robert Koch provided the proof by cultivating anthrax bacteria
apart from any other type of organism. He then injected pure cultures of the bacilli
into mice and showed that the bacilli invariably caused anthrax. The procedures
used by Koch came to be known as Koch's postulates .They provided a set of
principles whereby other microorganisms could be related to other diseases.

Work with viruses could not be effectively performed until instruments were developed to
help scientists see these disease agents. In the 1940s, the electron microscopewas
developed and perfected. In that decade, cultivation methods for viruses were also
introduced, and the knowledge of viruses developed rapidly. With the development of
vaccines in the 1950s and 1960s, such viral diseases as polio, measles, mumps, and rubella
came under control.

3. Classification and taxonomy of microorganisms

Microorganisms are a collection of organisms that share the characteristic of
being visible only with a microscope. They constitute the subject matter
of microbiology.

In the classification scheme, various species are grouped together to form

a genus. Among the bacteria, for example, the species Shigella
boydii and Shigella flexneri are in the genus Shigella because the organisms are
at least 70 percent similar. Various genera are then grouped as a family because
of similarities, and various families are placed together in an order. Continuing
the classification scheme, a number of orders are grouped as a class, and
several classes are categorized in a single phylum or division. The various
phyla or divisions are placed in the broadest classification entry, the kingdom.

Taxonomy. Includes classification, nomenclature, and identification of microorganisms.

Purpose of taxonomy is to provide useful ways for identifying and comparing organisms. The
bacteria are classified in a hierarchic system based on phenotypic, genome characteristics and
chemical composition.

4.Microorganisms as infectious agents. Prokaryotes and

eukaryotes
There are five major types of infectious
agents: bacteria, viruses, fungi, protozoa, and helminths. In addition, a new
class of infectious agents, the prions, has recently been recognized. A brief
review of the general characteristics of each of these agents and examples of
some diseases they cause follows.

Prokaryotes and eukaryotes. Because of their characteristics, microorganisms

join all other living organisms in two major groups of organisms: prokaryotes and
eukaryotes. Bacteria are prokaryotes (simple organisms having no nucleus or
organelles) because of their cellular properties, while other microorganisms such
as fungi, protozoa, and unicellular algae are eukaryotes (more complex
organisms whose cells have a nucleus and organelles). Viruses are neither
prokaryotes nor eukaryotes because of their simplicity and unique characteristics.

5. Structure of bacterial cell. Gram-positive and gram-negative

bacteria. Role of Gram staining in medical practice.
• Capsule - Some species of bacteria have a third protective covering, a capsule
made up of polysaccharides (complex carbohydrates). Capsules play a number of
roles, but the most important are to keep the bacterium from drying out and to protect
it from phagocytosis (engulfing) by larger microorganisms. The capsule is a major
virulence factor in the major disease-causing bacteria, such as Escherichia
coli and Streptococcus pneumoniae. Nonencapsulated mutants of these
organisms are avirulent, i.e. they don't cause disease.
• Cell Envelope - The cell envelope is made up of two to three layers: the interior
cytoplasmic membrane, the cell wall, and -- in some species of bacteria -- an outer
capsule.
• Cell Wall - Each bacterium is enclosed by a rigid cell wall composed of
peptidoglycan, a protein-sugar (polysaccharide) molecule. The wall gives the cell its
shape and surrounds the cytoplasmic membrane, protecting it from the environment
• Cytoplasm - The cytoplasm, or protoplasm, of bacterial cells is where the functions for
cell growth, metabolism, and replication are carried out. It is a gel-like matrix composed
of water, enzymes, nutrients, wastes, and gases and contains cell structures such as
ribosomes, a chromosome, and plasmids.
 • Flagella - Flagella (singular, flagellum) are hairlike structures that provide a means of
locomotion for those bacteria that have them
• Nucleoid - The nucleoid is a region of cytoplasm where the chromosomal DNA is
located. It is not a membrane bound nucleus, but simply an area of the cytoplasm where
the strands of DNA are found.
• Pili - Many species of bacteria have pili (singular, pilus), small hairlike projections
emerging from the outside cell surface.
• Ribosomes - Ribosomes are microscopic "factories" found in all cells, including
bacteria. They translate the genetic code from the molecular language of nucleic acid
to that of amino acids—the building blocks of proteins.

A Gram stain is a laboratory procedure used to detect the presence of bacteria

and sometimes fungi in a sample taken from the site of a suspected infection. It
gives relatively quick results as to whether bacteria or fungi are present and, if so,
the general type

A Gram stain is a test used to identify bacteria. It is one of the most common ways to quickly
diagnose bacterial infection in the body

Samples for gram staining may be collected from different areas of the
body. They include:

• Lining of the chest, belly (abdomen), and joints

• Fluid around the brain and spinal cord
• Throat
• Mucus from the lungs
• Wound drainage
• Drainage from genitals
6.L-forms of bacteria and their role in infection
L forms or L-phase variants ), protoplasts, and spheroplasts. L forms arise in vivo
spontaneously from a mutation in the wall-forming genes, or they can be induced artificially by
treatment with a chemical such as lysozyme, disrupting the cell wall, or penicillin, inhibiting cell wall
synthesis. L forms able to grow and divide. L forms can be cultivated on special media having the
right osmotic strength. L forms can be reverse or stable. Some L forms are able to resume normal
cell wall synthesis and thus can revert to the normal bacillary form upon removal of the inducing
stimulus. Others are stable and never revert. The factor that determines their capacity to revert may
be the presence of residual peptidoglycan, which normally acts as a primer in its own biosynthesis.
Medical significance of L forms. They cause chronic infections. The formation of L forms in
the host may lead to their persistence as they display low antigenicity and become sequestered in
protective regions of the body. Their reversion to the bacillary form can produce relapses of the
infection. Since L-form infections are relatively resistant to antibiotic treatment (beta-lactams), they
present special problems in chemotherapy.

7.Mycoplasma, rickettsia, spirochetes, actinomycetes, and

chlamydia.
Mycoplasmas - are bacteria that naturally lack a cell wall. The mycoplasmas have the trilaminar
cytoplasmic membrane stabilized by sterols (e.g. cholestanol or stigmasterol)., due to sterols the sell
membrane is resistant to lysis. These extremely tiny, pleomorphic cells are considered the smallest
cells, ranging from 0.1 to 0.5 µm in size. They range in shape from spherical, ovoid or pear-shaped to
branched filamentous forms. Filaments, the typical forms in young cultures under optimum
conditions, subsequently transform into chains of coccoid cells which later break up into individual
cells that are capable of passing through membrane filters of pore size 0.22 μm or 0.45 μm.
Replication of the genome may precede cytoplasmic division; hence, multinucleate‘ filaments may
exist. Most Mycoplasma spp are facultatively anaerobic.

Mycoplasmas are found in many habitats, including plants, soil, and animals. They are parasites and
pathogens in the respiratory and urogenital tracts in man and other animals. The most important
medical species is Mycoplasma pneumoniae, which adheres to the epithelial cells in the lung and
causes an atypical form of pneumonia in humans

Rickettsias. Small short rods, usually intracellular bacteria transmitted by arthropods. Rickettsias are
distinctive, very tiny, gram-negative bacteria. Unique properties of Rickettsia: 1) Pleomorohic – may
have a morphology of coccobacteria, rods, and filamentous cells; 2) circulate between a mammalian
host and blood-sucking arthropods; 3) obligate intracellular parasites – they cannot survive or
multiply outside a host cell and cannot carry out metabolism completely on their own, so they are
closely attached to their hosts; 4) can be cultured in cell cultures or laboratory animals, but not on
culture media as bacteria
Spirochetes. Flexible helical microorganisms with periplasmic flagella. They are Gram-negative
asporogenous. Due to periplasmic flagella they are motile, exhibiting rotation and flexion; can also
creep over solid surfaces. The medically important genera Treponema, Leptospira, and Borrelia have
been distinguished primarily by morphologic characters such as the nature of their spiral shape and
the arrangement of flagella. Many spirochetes are difficult to see by routine microscopy

Actinomycetes are unicellular, Gram-positive bacteria that belong to

the Order Actinomycetales.

Members of this group are widely distributed in nature and can be

found in a variety of habitats across the world. They have been shown
to share a number of characteristics with fungi (e.g. mycelial growth)
and cause the same disease as fungi in the eye

Chlamydias. Gram-negative bacteria which are obligate intracellular parasites in eukaryotic

cells with two-component life style. Because of their tiny size and obligately parasitic
lifestyle, they were at one time considered a type of virus.

1. Small size and ability to go through bacterial filters; 2. Obligate intracellular parasites
in eukaryotic cells; 3. Multiply within cytoplasmic vacuoles and form cytoplasmic
inclusion or microcolony in infected cell, these microcolonies in epithelial cell help to
diagnose Chlamydia infections microscopically after staining the smear by
Romanowsky-Giemsa; 4. Exhibit a complex developmental cycle.

8.Physiology of bacteria. Chemical content and functions of

chemicals. Types of nutrition. Transport of nutrients and
metabolites.Stages of growth
Bacterial physiology is a scientific discipline that concerns the life-supporting
functions and processes of bacteria, which allow bacterial cells to grow and
reproduce. The physiological and biochemical traits include data on growth at
different temperatures, pH values, salt concentrations, atmospheric conditions
(aerobic/anaerobic), growth in the presence of various substances such as
antimicrobial agents, and data on the presence or activity of various enzymes
9 Microbial metabolism. Destructive metabolism.
.

Classification by oxygen sensitivity. Constructive

metabolism. Constitutive and inducible enzymes
A] Microbial metabolism is the means by which a microbe obtains the energy and
nutrients (e.g. carbon) it needs to live and reproduce. Microbes use many different types
of metabolic strategies and species can often be differentiated from each other based on
metabolic characteristics. The specific metabolic properties of a microbe are the major
factors in determining that microbe's ecological niche, and often allow for that microbe to be
useful in industrial processes or responsible for biogeochemical cycles.

B] Catabolism
Catabolism is the set of metabolic processes that break down large molecules. These
include breaking down and oxidizing food molecules. The purpose of the catabolic reactions
is to provide the energy and components needed by anabolic reactions which build
molecules.[32] The exact nature of these catabolic reactions differ from organism to organism,
and organisms can be classified based on their sources of energy and carbon (their primary
nutritional groups), as shown in the table below. Organic molecules are used as a source of
energy by organotrophs, while lithotrophs use inorganic substrates, and phototrophs capture
sunlight as chemical energy.
Anabolism, or constructive metabolism: the process where the body uses
energy generated from other reactions to synthesize larger, more complex
molecules, such as carbohydrates, proteins and fats. ... The waste products are
removed from the body through the skin, kidneys, lungs, and intestines.
 It is important for the growth of new cells, the maintenance of body
tissues and the storage of energy for future use.

C] An adaptive enzyme or inducible enzyme is an enzyme that

is expressed only under conditions in which it is clearly of adaptive
value, as opposed to a constitutive enzyme which is produced all the
time. The Inducible enzyme is used for the breaking-down of things in
the cell. It is also a part of the Operon Model, which illustrates a way for
genes to turn "on" and "off". The Inducer causes the gene to turn on
(controlled by the amount of reactant which turns the gene on). Then
there's the repressor protein that turns genes off. The inducer can
remove this repressor, turning genes back on.
A constitutive gene is a gene that is transcribed continually as opposed to a
facultative gene, which is only transcribed when needed. ... An inducible gene is
a gene whose expression is either responsive to environmental change or
dependent on the position in the cell cycle.

10.Reproduction of microorganisms (viruses,

eukaryotes, prokaryotes). Bacterial fission.
 Viral replication is the formation of biological viruses during the infection process in the
target host cells. Viruses must first get into the cell before viral replication can occur.
Through the generation of abundant copies of its genome and packaging these copies,
the virus continues infecting new hosts. Replication between viruses is greatly varied and
depends on the type of genes involved in them. Most DNA viruses assemble in the
nucleus while most RNA viruses develop solely in cytoplasm.

Virus replication occurs in seven stages, namely;

1. Attachment
2. Entry,
3. Uncoating,
4. Transcription / mRNA production,
5. Synthesis of virus components,
6. Virion assembly and
7. Release (Liberation Stage).

Bacterial binary fission is the process that bacteria use to carry out cell
division. Binary fission is similar in concept to the mitosis that happens in
multicellular organisms (such as plants and animals), but its purpose is
different.

• Prokaryotes (bacteria and archaea) reproduce asexually

through binary fission. Most prokaryotes reproduce rapidly.
• Due to their fast growth and simple genetics, E. coli bacteria are
widely used in molecular biology.

• In the laboratory, a gene can be transferred into E. coli bacteria on a

small, circular DNA molecule called a plasmid. The plasmid is taken
up by the bacteria in a process called transformation.

• The transformed E. coli bacteria can be used to make many copies of

the plasmid. In some cases, they will also express the gene on the
plasmid and make protein.

11.Genetic material of viruses, eukaryotes and

prokaryotes.Extrachromosomal factors and their
role for bacteria
A virus is a small collection of genetic code, either DNA or RNA, surrounded
by a protein coat. A virus cannot replicate alone. Viruses must infect cells and
use components of the host cell to make copies of themselves.

Most prokaryotes carry a small amount of genetic material in the

form of a single molecule, or chromosome, of circular DNA.
The DNA in prokaryotes is contained in a central area of the cell
called the nucleoid, which is not surrounded by a nuclear membrane.
In eukaryotes, the cell's genetic material, or DNA, is contained within an
organelle called the nucleus, where it is organized in long molecules called
chromosomes. Eukaryotic cells also contain other organelles, including
mitochondria, which generate energy; the endoplasmic reticulum, which plays
a role in the transport of proteins; and the Golgi apparatus, which sorts and
packages proteins and lipids for transport throughout the cell.

Plasmids are self-replicating extrachromosomal DNA molecules found

in Gram-negative and Gram-positive bacteria as well as in some yeast and
other fungi. Although most of them are covalently closed circular double-
stranded DNA molecules, recently linear plasmids have been isolated from
different bacteria
Fertility F-plasmids Fertility plasmids, also known as F-plasmids, contain transfer
genes that allow genes to be transferred from one bacteria to another through
conjugation. These make up the broad category of conjugative plasmids.

Resistance PlasmidsResistance or R plasmids contain genes that help a bacterial cell

defend against environmental factors such as poisons or antibiotics. Some resistance
plasmids can transfer themselves through conjugation. When this happens, a strain
of bacteria can become resistant to antibiotics.

Virulence PlasmidsWhen a virulence plasmid is inside a bacterium, it

turns that bacterium into a pathogen, which is an agent of disease.

Col Plasmids Col plasmids contain genes that make bacteriocins (also known as
colicins), which are proteins that kill other bacteria and thus defend the host
bacterium.

Degradative Plasmids Degradative plasmids help the host bacterium to

digest compounds that are not commonly found in nature, such as
camphor, xylene, toluene, and salicylic acid.

12.Realization of genetic information

The central dogma of molecular biology describes the flow of genetic
information in cells from DNA to messenger RNA (mRNA) to protein. It states
that genes specify the sequence of mRNA molecules, which in turn specify the
sequence of proteins.

• Genes are composed of DNA arranged on chromosomes.

• Some genes encode structural or regulatory RNAs. Other genes encode
proteins.
• Replication copies DNA; transcription uses DNA to make complementary
RNAs; translation uses mRNAs to make proteins.
 • In eukaryotic cells, replication and transcription take place within the
nucleus while translation takes place in the cytoplasm.
• In prokaryotic cells, replication, transcription, and translation occur in the
cytoplasm

13.Variability of bacterial population.

Modification and
mutation.Recombination in bacteria.
The estimation of variability usually refers to the variation in the
responses of the individual cells within the population, which may be
homogeneous or heterogeneous. In a homogeneous population, the heat
resistance parameters of the individual cells are identically distributed
random variables

Genetically modified bacteria are used to produce large amounts of proteins for
industrial use. Generally the bacteria are grown to a large volume before the gene
encoding the protein is activated. The bacteria are then harvested and the desired
protein purified from them.[14] The high cost of extraction and purification has meant
that only high value products have been produced at an industrial scale.
• Genetically modified bacteria were the first organisms to be modified in the
laboratory, due to their simple genetics. These organisms are now used for several
purposes, and are particularly important in producing large amounts of pure human
proteins for use in medicine. Insulin.
• Hepatitis B vaccine.
• Tissue plasminogen activator.
• Human growth hormone.
• Ice-minus bacteria.
• Interferon.
• Bt corn.

Bacteria grow and multiply fast and can reach large numbers.
When bacteria multiply, one cell divides into two cells. Every time
the bacterium goes through this process there is a chance (or risk,
depending on the end result) that errors occur; so-called mutations. ...

Bacterial recombination is a type of genetic recombination in

bacteria characterized by DNA transfer from one organism called donor
to another organism as recipient. This process occurs in three main
ways:
• Transformation, the uptake of exogenous DNA from the surrounding environment.
• Transduction, the virus-mediated transfer of DNA between bacteria.
• Conjugation, the transfer of DNA from one bacterium to another via cell-to-cell
contact
14.Antimicrobial control. Biological factors.
Ecology of
microorganisms.Antibiotics.Bacteriophages.

Microbial control methods involve the use of physical, chemical, biological agents to eliminate or
reduce the numbers of microorganisms from a specific environment. Microbial control methods
are used to prevent the spread of infectious agents, retard spoilage, and keep commercial
products safe. Biocide is a general term describing a chemical agent.

Biocide is a general term describing a chemical agent, usually broad-spectrum, that inactivates
microorganisms.

Sterilization is complete killing, or removal, of all living and in resting (spores) organisms from a
particular object or product.

Disinfection is the destruction of pathogenic microorganisms on inanimate objects or surfaces in

order to prevent transmission of certain microorganisms

Pasteurization is the use of heat at a temperature sufficient to inactivate important pathogenic

organisms in liquids such as water or milk but at a temperature below that needed to ensure
sterilization.

Antisepsis – direct antimicrobial measures used in or on living tissue (skin, mucus membranes,
wounds) to destroy or inhibit vegetative pathogens

Sanitization is a less precise term with a meaning somewhere between disinfection and
cleanliness

Preservation is a general term for measures taken to prevent microbe caused spoilage of
susceptible products (pharmaceuticals, foods).

Decontamination is the removal or count reduction of microorganisms contaminating an object.

Asepsis - all measures aiming to prevent contamination of objects or wounds protecting from
the entry of infectious agents into sterile tissues or media and thus prevents infection or
spoilage.

Surgical asepsis involves a high level of disinfection, antisepsis, and sterilization as would be
required to maintain a microbe-free surgery. Instruments, dressings, sponges, and all other
supplies coming into contact with the patient are sterilized
 Medical asepsis includes any practice that lowers the load of infectious microbes in patients,
personnel, and the hospital environment.

BIOLOGICAL CONTROL OF MICROORGANISMS

wide variety of chemicals called antimicrobial agents are available for controlling the
growth of microbes. For example:

1. Chemotherapeutic agents, including antibiotics, are administered into the

infected body.
2. Disinfectants are chemical agents used on inanimate objects to lower the
level of microbes present on the object. These are not capable of sterilizing,
typically because they fail to kill endospores, some viruses, and organisms
such as Mycobacteriumtuberculosis.
3. Antiseptics are chemicals used on living tissue to decrease the number of
microbes present in that tissue.

Microbial ecology (or environmental microbiology) is

the ecology of microorganisms: their relationship with one another and with their
environment. It concerns the three major domains of life—Eukaryota, Archaea,
and Bacteria—as well as viruses.[2]
Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a
primary role in regulating biogeochemical systems in virtually all of our planet's
environments, including some of the most extreme, from frozen environments and acidic
lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar,
such as the human small intestine.

Antibiotics are medicines that help stop infections caused by bacteria. They do
this by killing the bacteria or by keeping them from copying themselves or
reproducing. The word antibiotic means “against life.” Any drug that kills germs
in your body is technically an antibiotic

• Alexander Fleming discovered penicillin, the first natural

antibiotic, in 1928.
• Antibiotics cannot fight viral infections.
• Fleming predicted the rise of antibiotic resistance.
• Antibiotics either kill or slow the growth of bacteria.
 A bacteriophage is a type of virus that infects bacteria. In fact, the word
"bacteriophage" literally means "bacteria eater,"
because bacteriophages destroy their host cells. All bacteriophages are
composed of a nucleic acid molecule that is surrounded by a protein structure.

15.microbial control. Chemical factors.

Aseptic, antiseptic, and disinfection
Asepsis - all measures aiming to prevent contamination of objects or wounds protecting from the
entry of infectious agents into sterile tissues or media and thus prevents infection or spoilage.

Surgical asepsis involves a high level of disinfection, antisepsis, and sterilization as would be
required to maintain a microbe-free surgery. Instruments, dressings, sponges, and all other
supplies coming into contact with the patient are sterilized

Medical asepsis includes any practice that lowers the load of infectious microbes in patients,
personnel, and the hospital environment.

Antiseptics are chemicals used on living tissue to decrease the number of microbes
present in that tissue
 direct antimicrobial measures used in or on living tissue (skin, mucus membranes, wounds) to
destroy or inhibit vegetative pathogens

Disinfectants are chemical agents used on inanimate objects to lower the level of
microbes present on the object. These are not capable of sterilizing, typically
because they fail to kill endospores, some viruses, and organisms such
as Mycobacteriumtuberculosis.

16.
Antimicrobial control. Physical factors.
Sterilization and disinfection
Sterilization is complete killing, or removal, of all living and in resting
(spores) organisms from a particular object or product. Hydrogen
peroxide, Nitrogen dioxide, Glutaraldehyde and formaldehyde
solutions, Phthalaldehyde, and Peracetic acid are other examples of
chemicals used for sterilization.

Disinfection is the destruction of pathogenic microorganisms on inanimate objects or surfaces in

order to prevent transmission of certain microorganisms

Chemical Disinfectants
• Alcohol.
• Chlorine and chlorine compounds.
• Formaldehyde.
• Glutaraldehyde.
• Hydrogen peroxide.
• Iodophors.
• Ortho-phthalaldehyde (OPA)
• Peracetic acid.