INTRODUCTION TO

MEDICAL MICROBIOLOGY
 Learning objectives
At the end of this chapter students will be able to:
 Define what mean Microbiology and Medical Microbiology
 Scope of Microbiology
 Importance of Microorganisms
 Brief Historical background of Microbiology
 Taxonomy & classification of microorganisms
 Bacterial size, shape and arrangements
 Bacterial structures and function
 Bacterial nutrition
 Bacterial growth and generation time
 Mutation and bacterial gene transfer Mechanisms
 Introduction
 Microbiology: deals with living organisms that are individually too
small to be seen with the naked eye.

 It considers the microscopic forms of life collectively referred to

as microbes

 It deals also about their reproduction, physiology, and

participation in the process of nature, helpful and harmful

relationship with other living things, and significance in science

and industry.
 Categories of microbe studied in microbiology
i. Acellular microbes (called nonliving infectious particles)
include prions and viruses.

ii. Cellular microbes (also called living microorganisms).

 Microbes can be classified in four general groups:

1. Bacteria: Unicellular, prokaryotic organisms with no

nuclear membrane, mitochondria, Golgi bodies, or
endoplasmic reticulum.

2. Fungi: Eukaryotic organisms that contain a well-

defined nucleus, mitochondria, Golgi bodies, and
endoplasmic reticulum

3. Virus: Are the smallest infectious particles, ranging

in diameter from 18 to 600 nm (mostly <200 nm)

4. Protozoa: Are the smallest parasites 1-2 µm in

diameter (the size of many bacteria)
 What is medical microbiology??
 Medical microbiology:
• Is the study of causative agents of infectious diseases
of humans and their reactions to such infections.
• In other words it deals with medical importance
microorganisms and there pathogenesis, laboratory
diagnosis, specific treatment and control of infections.
Sub divisions of microbiology
• Bacteriology–which deals with bacteria
• Virology–studies about viruses and prions
• Mycology–which deals with fungi
• Immunology–studies mechanisms of body protection
against pathogenic microorganisms
• Phycology–Which deals with Algae
• Protozoology–which deals with Protozoa
 Scope of microbiology
 Microbiology is highly versatile science that involve in :-

• Medical Microbiology- human disease & warfare

• Veterinary Microbiology- Animal disease & probiotics
• Public Health Microbiology- in foods, water and beverages
• Industrial Microbiology-involve in production, bioremediation
• Pharmaceutical Microbiology-antibiotics production and testing
• Agriculture Microbiology-natural fertilizers, decomposing
• Plant Microbiology-plant disease and elemental cycle
Microbes are Essential for Life on Earth:
a. Production of foods: wine, beer, soft drinks through fermentation
b. Photosynthesis: Algae and some bacteria capture energy from sunlight and
convert it to food
c. Decomposers: Many microbes break down dead and decaying matter and
recycle nutrients
d. Nitrogen Fixation: Some bacteria can take nitrogen from air and
incorporate it into soil.
e. Digestion: Normal flora in digestive tract are essential for digestion and
vitamin synthesis (Vitamin K and B)
f. Drug production: Penicillin and cephalosporin drugs
g. Genetic engineering: Creating genetically modified pesticide, protein,
and vaccine
h. Bioremediation: microbes used for clean up toxic pollutants through
break down of chemicals that would be harmful to other organisms
i. In medical research: Microbes are well suited for biological and medical
research.
Distribution of microorganisms in nature
• Microorganisms: can be found nearly everywhere as
normal inhabitants of the earth (biosphere).

– They exist in soil, water, air, food, on

clothing, on the body etc.
– They survive in most unlikely environment
like cold air, in hot springs at temperatures of
900C.
– Inhabit the surface of living human and
animal bodies and grow abundantly in the
• Only a small percentage of microbes are pathogenic, few

are able to cause disease.

• The others are considered beneficial or harmless, they

cause disease only if they got opportunity like

accidentally invade or when the host immunity is low

“they are considered opportunistic”.

• Those microorganisms that live on the human body

without causing disease are called normal flora.

• Microbes are responsible for two categories
of diseases:
1. Infectious diseases pathogens
2. Microbial intoxications (poising)
 Historical Development of Microbiology
– Hippocrates, father of medicine, observed that ill health
resulted due to changes in air, winds, water, climate, food,
nature of soil and habits of people.
– Fracastorius (1500 G.C.): Proposed that the agents of communicable
diseases are living germs.
 However, microorganisms was seen for the 1 st time under
the microscope in 1764.

– Anton van Leeuwenhoek observed “animalcules” in a drop of

water.

• He was the first who properly described the different

shapes of bacteria.
 Following the discovery of Antony Van Leeuwenhoek

“father of Microbiology”, observed “animalcules”

 Question were raised - where did they originate?

 On the bases of this observation, two major theories

were formulated.

1. Theory of Abiogenesis

2. Theory of Biogenesis
 Theory of Abiogenesis deals with the theory of
spontaneous generation; stating that living things
originated “spontaneously” from non-living things.
 (e.g. maggots from meat or mushrooms from rotting
woods)
 Aristotle (384-322): The founder of a theory spontaneous
generation.
 He observed spontaneous existence of fishes from
dried ponds, when the pond was filled with rain.
 Biogenesis “Life comes from life”: States that
life comes from pre-existing life
 Francesco Redi (1626-1697): He is the scientist
who first tried to set an experiment to disprove
spontaneous generation.
• He put the meat in a bottle and covered it
with a gauze.
Observation
1) Unsealed – maggots on meat
2) Sealed – no maggots on meat
3) Gauze – few maggots on gauze, none on
meat

As a result, scientists began to doubt Aristotle’s

theory
John Needham (1749)
 Performed experiments similar to Redi’s
 Puts broth in flasks, some were sealed with corks, and some were
not.
 All flasks became cloudy, result different from Redi’s experiment.
 He suggested that life originate spontaneously from non-living
matters
• Introduced the first culture medium for microbial growth.
• Utilized infusion broth prepared by boiling meat, grain, etc.
Lazzaro Spallanzani (1776)
 Repeated Needham’s experiments to disprove
spontaneous generation in microscopic life.
 Boiled broth after placing in flasks.
 Sealed flasks by plugging with solid stopper.
 Results more consistent with Redi’s.
 Not accepted by spontaneous generation
supporters, because they said that “heating may
have destroyed, degraded “vital force” and air was
not allowed to enter”.
 Louis pasture (1822- 1895) was the scientist who
disproved the theory of abiogenesis once and for all.
 Performed experiment to disprove Theory of
spontaneous generation.
 He designed a large curved flask/swan-necked
(pasture goose neck flask) and placed a sterile
infusion broths.
 Flasks remained sterile unless tilted or neck broken.
• In ‘A’ air freely moved through the tube, but dust
particles were trapped in the curved portion of the
flask. And no microbial growth was observed.
.
• Therefore, Pasteur proved that microorganisms entered to
the broth with the air and micro organisms did not
evolve spontaneously.
 Major contribution of Louis Pasteur

• Microbial theory of fermentation: is a way of

getting energy without using oxygen
(anaerobic).
• Principles and practices of sterilization and
pasteurization.
Pasteurization: routinely used on milk to eliminate
pathogens as bovine tuberculosis and brucellosis.

• Development of vaccines against anthrax and

rabies
 The Germ Theory of
diseases
• Pasture has developed the germ theory of diseases,

which states that “a specific disease is caused by a

specific type of microorganism”.

• Stands from idea of Fracastorius

• Then Robert Koch, in 1876 established an experimental

procedure to prove the germ theory of disease.

• The scientific procedure is known as Koch’s Postulate.

Koch’s Postulate:- prove of germ theory of disease

 A Micro-organism can be accepted as a causative agent of an infectious

disease only if the following conditions are satisfied.

1. The causative agent of the disease must be present in every diseased

animal

2. The organism can be isolated from the diseased animal and grown in
pure culture

3. The pure culture will produce the disease when inoculated into a
susceptible animal

4. The same infectious agent must be re-isolated from the experimentally

infected animal.
Koch’s Postulates for Infectious Diseases
 Exceptions to Koch’s postulate
 Many healthy people carry pathogens but do not exhibit
symptoms of the disease.
 Some microbes are very difficult or impossible to grow
in vitro (in the laboratory) in artificial media. E.g..
Treponema pallidum.
 Many pathogens are species specific. E.g.. Brucella
abortus cause abortion in animals but not in humans.
 Certain diseases develop only when an opportunistic
pathogen invades immuno-compromised host.
Major achievements of Robert Koch

1. Discovery and use of solid medium in bacteriology

2. 1875-identified the germ for anthrax.

3. 1882-discovered the germ for tuberculosis (TB)

4. 1883-discovered the germ for cholera.

Taxonomy and Classification

of Microorganisms
 Taxonomy and classification of microorganisms
1. Taxonomy: is the science of classification,
identification, and nomenclature.
 Hierarchy of Taxonomy Rank: Kingdome, Phylum, Class,
Order, Family, Genus, and Species

2. Classification: is the orderly arrangement of

organisms into groups with different criteria.
 There is nothing inherent about classification
 Different groups of scientists may classify the same
organisms differently.
3. Identification:
– is the practical use of classification criteria to
distinguish certain organisms from others,
4. Nomenclature (naming):
– is the means by which the characteristics of a species
are defined and communicated among microbiologists.
– A species name should mean the same thing to all
microbiologists
 Binomial nomenclature includes:

I. Genus comes before species (e.g., Escherichia coli)

II. Genus name is always capitalized (e.g., Escherichia)
III. Species name is never capitalized (e.g., coli)
IV. Both names are always either italicized or
underlined
(e.g. Escherichia coli)

V. The genus name may be used alone, but not the

species name (i.e. saying or writing “Escherichia”
alone is legitimate while saying or writing “coli” is
not)
Criteria for microorganisms classification:-
• Classification can be phenotypic, genotypic or analytic

1. Phenotypic- Morphology (shape, size, stain reaction, cell structures) and

Biochemical activity (detection of presence or absence of particular
enzymes or metabolic pathways)

2. Genotypic classification- Composition of guanine and cytosine, DNA

hybridization, Nucleic acid sequence analysis, Plasmid analysis, Ribotyping
(analysis of rRNA genes)

3. Analytic classification-Is based upon detection of structural components

and metabolic products such as:- cell wall fatty acids, whole cell lipids,
whole cell proteins and Enzymes.
 Classification criteria for bacteria
1. Morphology
2. Motility
3. Staining
4. Growth
5. Nutritional requirement
6. Bio chemical and metabolic activity
7. Pathogenicity
8. Amino acid sequencing of proteins
9. Genetic composition
Bacterial Morphology, Size, Shape and

Arrangements
o Morphology: - Bacteria vary widely in size,
ranging from 0.2 um to 10um long
• There are three basic shapes

1. Spherical or cocci- (singular –coccus)

2. Rods or bacilli- (singular - bacillus)
3. Spirals or spirilla- (Singular - Spirillum)
• The cells of cocci may be found in various
arrangements depending on the species and the way
they divide
– Micrococcus-Cocci occurring singly
– Diplococci-Pairs of cocci
– Strepto cocci – Cocci in chain
– Staphylococci- Cocci in cluster
– Tetrads – Four cocci as in box
– Octads (sarcina) – Eight cocci
Bacterial structures and function
 Basic features of Bacterial Cell
• General property
– Typical prokaryotic cell
– Contain both DNA and RNA
– Most grow in artificial media
– Replication is by binary fission
– Contain rigid cell wall
Prokaryotic cells
– Most have haploid (single) and circular chromosomes
– Has no true nucleus and membrane bound organelles
– The nuclear body is called a nucleoid
– Histones are not present to maintain the conformation of the
DNA, and the DNA does not form nucleosomes
– The cell usually divides by binary fission
The structure of bacterial cell
• Considered at three levels.
o Cell envelope proper: Cell wall and cell membrane
o Cellular elements enclosed with in the cell envelope:

Mesosomes, ribosome, nuclear apparatus, polyamies

and cytoplasmic granules.
o Cellular element external to the cell envelope:

Flagellum, Pilus, Capsule or slime layer, and spore.

 Function of cell wall
– Provide rigid support for the cells and protect the fragile
cytoplasmic membrane
– Gives regular shapes for bacteria

– Contain strong activator of immune response

– Crucial for growth and division

– Components are unique to bacteria and used for

classification
 Function of Cell Membrane
– Regulates the transport of nutrients and waste products into and out
of the cell.
– It is selectively permeable
– Assists DNA replication
– Captures energy in ATP
 Function of Cytoplasm
– Containing a variety organic and inorganic solutes
• Water, enzymes oxygen, waste products, essential nutrients,
proteins, carbohydrates, lipids and a complex mixture of all the
materials required by the cell for its metabolic functions.
 Function of Mesosomes

– Are attached to chromosomes and are involved in DNA segregation during

cell division
– Involved in to secretion of proteins and active transport

– It is involved in respiratory enzyme-activity.

• Site of oxidative phosphorylation

 Function of Ribosomes

– Are the sites of protein synthesis

– It is composed of ribosomal RNA (rRNA) (70%) and proteins (30%)

– Prokaryotic ribosomes are 70S in size, being composed of Small (30s) and
Large ribosomal (50s) subunits.
– Where S stands sedimentation coefficient of the rRNA
 Function of plasmids

– Plasmids carry the genes for production of

• Antibiotic resistance
• Resistance to heavy metals
• Resistance to ultraviolet light
 Function of Pili (fimbriae)

– Mediate the adherence of bacteria to epithelial cells

 Types of cell wall
I. Gram positive cell wall of bacteria
– Has multiple layers of Peptidoglycan (PG) cross linked with teichoic acid.
– The PG layer comprises 50 – 90% of the cell wall and 20 – 40% of the
cell wall weight
– Teichoic acids and cell wall- associated protein are the major surface
antigens of the Gram- positive cell wall.
– The large amount of peptidoglycan make Gram- positive bacteria
susceptible to the enzyme lysozyme and penicillin.
– Penicillin specifically inhibits peptidoglycan synthesis
 II. Gram negative Cell wall of bacteria
• Is some what complex with thin peptidoglycan layer
• Has high lipopolysaccharide in the outer membrane
• Has periplasmic space.
 Outer membrane
– Contains receptors (sites) for attachment
– It participates in cell division and used in transport of materials
 Lipopolysaccharides
– Responsible for antigenicity of the outer membrane
• Powerful stimulator of immune response
– Serves as a bacterial endotoxin
 Periplasmic space
– Found between outer membrane and the cell membrane
– Mostly contain enzymes and endotoxin.
• A: gram positive bacterium, B: gram negative bacterium
III. Acid fast cell wall
– Resemble Gram positive cell wall
– Acid-fast bacteria have a cell wall with a relatively
impermeable containing a waxy lipid called mycolic acid
– Mycolic acids confer resistance to
• Desiccation
• Most antibiotics
• Phagocytosis
• Contributes to pathogenicity
IV. Bacteria with defective cell walls include:
– Mycoplasma: Highly pleomorphic bacteria naturally lacks
cell wall
– Protoplasts: Derived from Gram-positive bacteria and
totally lacking cell walls
– Spheroplast: Derived from Gram-negative bacteria non-
functional cell wall material
– L-forms: Cell wall-deficient forms of bacteria usually
produced in the laboratory
 Bacterial Nutrition, Growth,

Metabolism and Generation time

  Nutrition
• For optimal growth and multiplication, bacteria requires
nutrients, such as water, energy, carbon, nitrogen and
some inorganic salts.
• All bacteria need some form of the element Carbon, H,
O2, S, P, and N for growth.
• In most case, bacteria need small amount of salt
concentration to grow.
– Halophytes are bacteria which need high concentration
of salt for their growth.
 1. Nutrient requirement
• Depending on their nutritional requirement bacteria can
be classified primarily based on the source of carbon
• Autotrophs: - are free-living, non-pathogenic bacteria,
most of which can use carbon dioxide as their carbon
source such as the cyanobacteria.
• Heterotrophs:- are generally parasitic bacteria
– Human pathogenic bacteria are heterotrophs
– The principal source of carbon is carbohydrate
• Degraded either by oxidation in the presence of oxygen or by
fermentation in the absence of oxygen
 2. Temperature requirement
• Most pathogenic bacteria grow best at an optimum
temperature of 370C.
• Psycrophylic- are those bacteria, which grow in the range
of -5 to 200C
• Mesophilic- which grow at 20-450C and show optimum
growth at 37oC.
– pathogenic bacteria belong to this group.
• Thermophilic – are those organisms which prefer high
temperature (50-800C)
• Hyper thermophilic: those which grow at a temperature of
above 800C
 3. Oxygen requirement
Bacteria have been divided in to:
• Obligate Anaerobes-these grow only in the environment
devoid of oxygen. e.g. Clostridium
• Facultative aerobes- these can grow under both aerobic
and anaerobic conditions, e.g. enterobacteriacae
• Obligate aerobes- these cannot grow unless oxygen is
present in the medium, e.g. pseudomonas
• Microaerophilic- these organisms can grow under
conditions with low oxygen tension e.g. Clostridium
tetani.
 4. pH requirement
• Most pathogenic bacteria require a pH of 7.2-7.6 for
their optimal growth.

• Neutrophilic:- bacteria grow best at neutral pH (pH=7)

• Acidophilic: Bacterial grow best at acidic pH

(pH<7) E.g. Lactobacilli, fungi and yeast

• Alkalophilic: grow best at Alkaline pH (pH>7)

– E.g. Vibrio cholerae grow at a pH of 8.6

  Bacterial Metabolism
• Involves all the cellular processes required for the
survival and replication of the organism.
• Refers to all of the chemical reactions occurring
within a cell, including the production of energy,
intermediate products, and end products.
• Most biochemical reactions fall into two
categories: Catabolism and Anabolism.
o Catabolism: involve the breakdown of bonds of organic
compounds that results in the production of energy and
smaller molecules.
o Anabolism: involves the creation of bonds
– Refers to biosynthetic processes that use energy for
the synthesis of protoplasmic materials needed for
growth, maintenance, and other cellular functions.
– Smaller molecules are bonded together to create large
molecules
 Bacterial growth curve
• The growth cycle of bacteria has four major phases.

1. The Lag Phase: is a short duration in which bacteria

adapt themselves to new environment
– This is a period of active macro molecular synthesis
like DNA, RNA, various enzymes and other structural
components
– It is the preparation time for reproduction
– Increase in size
– No increase in cell number occurs
2. The log, or exponential phase: the population can double

approximately every 30 minutes

– It has limited duration because of:-

• Exhaustion of nutrients

• Accumulation of toxic metabolic end products

• Rise in cell density, Change in pH and

• Decrease in oxygen tension

– This phase is highly sensitive for antibiotic

3. Stationary Phase:
– It is almost a balance between the bacterial
reproduction and bacterial death
– Occur when nutrients depletion or toxic products
cause growth to slow
4. The death/decline phase:
– Due to depletion of nutrients and accumulation of
toxic end products
– The number of bacteria dying is much more than
those dividing
– There is drastic decline in viable cells.
• Factors that affect
bacterial growth in
vitro
• Nutrition
• Temperature
• Oxygen
• PH
• Salinity
• Osmotic pressure
• Light Radiation
Bacterial Genetics, Mutation and

Gene Transfer Mechanisms

 Bacterial genetics
• Most of the genetic information in a bacterial
cell is contained with in chromosome
• Bacterial inherited characteristics are encoded in
DNA (Chromosome or Extra chromosome
(Plasmid))
• Chromosome: Bacterial chromosome is circular
double stranded DNA attached to bacterial cell
membrane
• Plasmids: are self replicating extra chromosomal
DNA molecules.

• Plasmids are not essential to the life of the cell but

they may have selective advantage:
Virulence plasmids: carry virulence determining
genes
Resistance plasmids (R factor): code for drug
resistance genes
 Central dogma

• DNA replication: The identical

duplication process

• Transcription: Genetic nucleotide

sequence is transcribed into
mRNA

• Translation: Transformation of
the nucleotide sequence into the
polypeptide amino acid sequence
• Carried by the mRNA
 Genetic Variation in Bacteria
• Can occur at molecular level or intercellular level

1. Molecular Mechanism

• Bacterial mutation occur when the information in a

bacterial chromosome is altered

• There are two types of mutation

 Spontaneous mutation: takes place in nature with out
human intervention or identifiable causes
 Induced mutation: caused by exposure to chemical or
physical agent, exposure to UV light etc.
2. Intercellular Mechanisms of Genetic variability
• Gene transfer: there are three types of gene transfer that
alter the DNA gene content of bacteria
 Transformation, Transduction and Conjugation

• Transformation: occurs when fragment of exogenous DNA

is absorbed in to recipients bacterial cells

• Transduction: transfer of DNA from a donor to a receptor

cell with the help of transport bacteriophages

• Conjugation: occurs when plasmid DNA is transferred form

donor to recipient bacterium by direct contact via sex
pills
• Transduction of chromosomal DNA (A) and Plasmid (B)
• A: connection b/n two bacterial by sex pili; B: formation of specific conjugal
bridge; C: Plasmid mobilization &transfer; D: Synthesis of DNA strand
Any questions?