MICROBES AND PARASITES –BACTERIA

Organisms that cause diseases are called “pathogens,” from the Greek word pathos, or
suffering. Most pathogens are microbes, such as bacteria, protozoa, fungi or viruses.
Sometimes, we call these tiny pathogens “germs.” Pathogens cause communicable, or
infectious, diseases (diseases that can spread from one organism to another). Some diseases
are harder to catch than others, because different pathogens are transferred from one
organism to another in different ways (through droplets in air or in fluids, through contact
with a surface containing the pathogen, from insect bites, etc.). Some pathogens can make
you a lot sicker than others, and some can kill.

A widespread outbreak of a disease is called an “epidemic.” An epidemic that spreads

broadly throughout the world is referred to as a “pandemic.” This activity highlights six
microbe-based diseases with major global historical impacts: cholera, plague, malaria,
smallpox, HIV/AIDS and tuberculosis.

Of course, microbes do not cause all diseases. Invertebrates, such as hookworms, tapeworms,
etc., also can make people and animals sick. Other illnesses, such as arthritis, diabetes, heart
disease related to atherosclerosis, and some kinds of cancer, are not caused by infections. But
in some cases, diseases thought to be unrelated to microorganisms have been found to be
infectious after all. Stomach ulcers are a good example. Scientists now know that the most
common cause of peptic ulcers is infection by a bacterium called Helicobacter pylori.

A. Bacteria

Bacteria are microscopic, unicellular, prokaryotic organisms. They do not have membrane-
bound cell organelles and lack a true nucleus, hence are grouped under the domain
“Prokaryota” together with Archae.In a three-domain system, Bacteria is the largest
domain. The term ‘Bacteria’ is derived from the Ancient Greek word “backērion” meaning
“cane”, as the first bacteria observed were bacilli.

Bacteria are evolved to adapt and survive in any kind of ecological niches; from normal to
extreme environments. Hence, they are ubiquitous. They are found in every possible habitat
on the Earth; soil, air, and water.
Structure of a Bacterial Cell

Bacteria are unicellular i.e. made up of a single cell. They are prokaryotes and their cells are
different from animal and plant cells. In general, the structure of bacteria can be studied as
external and internal structures.

External Structure of a Bacteria

It includes a cell wall and all the structures outside the cell wall.

1. Flagella (sing. Flagellum)

Flagella are long hair-like filamentous structures of about 4 – 5 μm long and 0.01 – 0.03 μm
in diameter. They confer motility to the bacteria. Flagella are divided into three parts;
filament, hook, and the basal body. The filament is a threadlike part extending outside the cell
wall. It is made up of flagellin protein. The hook is a short, curved structure that joins
filament with the basal body. It produces repulsion like the propeller during the revolving of
flagella. The basal body is a set of rings embedded in the cell wall and plasma membrane.

Functions of Flagella

 Responsible for motility

 Aids in chemotaxis
 Aids in bacterial pathogenicity and survival

2. Pili/Fimbriae

They are the short, hollow, non-helical filamentous structure of about 0.5 μm in length and
0.01 μm in diameter. They are exclusively found in Gram-Negative bacteria.

They are composed of protein ‘pilin’ arranged non-helically. They are short, numerous, and
straight than flagella.Sex pili are a special kind of pili that take part in bacterial conjugation.
They are larger than usual pili; 10-20 μm in length. They are few in number, just 1-4 in
number.
Functions of Pili/Fimbriae

 Aids in adherence to host cells

 Sex pili helps in bacterial DNA transfer during bacterial conjugation

3. Capsule

It is a viscous outermost layer surrounding the cell wall. It is composed of

either polysaccharides or polypeptides of both (~2%) and water (~98%). They are present
only in some species of bacteria. The capsule is of 2 types; macro-capsule (capsule with a
thickness of 0.2 μm or more) and micro-capsule (capsule with thickness less than 0.2
μm).Instead of viscous covering, some bacteria are surrounded by amorphous/paracrystalline
colloidal protein materials called the slime layer.

Functions of Capsule

 Aids in adherence
 Prevents from desiccation
 Confer resistance against phagocytosis
 The Slime layer protects from proteolytic enzymes

4. Sheath and Prosthecae

 A sheath is a hollow tube-like structure enclosing chain-forming bacteria, mostly

aquatic bacteria. It provides mechanical strength to the chain.
 Prosthecae is a semi-rigid extension of the cell wall and plasma membrane. It
increases nutrient absorption and also helps in adhesion.

5. Cell Wall

 The cell wall is a rigid structure made up of peptidoglycan that surrounds the plasma
membrane as an external coat. It is 10 -25 μm in thickness.
 Peptidoglycan is a cross-linked polymer of alternately repeating N-Acetylmuramic
Acid (NAM) and N-Acetylglucosamine (NAG) polysaccharide sub-units.
 Based on composition, bacterial cell-wall is classified into 2 types; Gram-positive,
and Gram-negative cell walls.
Gram-positive cell wall

The gram-positive cell wall is a thick cell wall containing a large amount of peptidoglycan,
arranged in several layers. This type of cell wall also contains acidic sugars like teichoic
acids, teichuronic acids, and neutral sugars like mannose, arabinose, rhamnose, and
glucosamine as matrix substances. This type of cell wall takes up the crystal violet dye and
confer the purple color of the gram-positive bacteria in Gram staining.

Gram-negative cell wall

The gram-negative cell wall is a thin cell wall with significantly less amount of
peptidoglycan. It is comparatively more complex than the gram-positive cell wall. It contains
lipoprotein, lipopolysaccharide, and outer membrane in addition to peptidoglycan.

The outer membrane is a bilayered structure containing an inner layer resembling the plasma
membrane in composition, and an outer layer made up of lipopolysaccharide. It is rich in a
variety of proteins like ‘porin and outer membrane proteins.They lose crystal violet during
the Decolorization step and take up safranin during counterstaining, hence providing
characteristic pink color to Gram-Negative bacteria.

Gram-Positive Cell-Wall vs Gram-Negative Cell-Wall

Gram-Positive Cell-Wall Gram-Negative Cell-Wall

Thick (20 – 80 nm) Thin (10 – 15 nm)

Higher peptidoglycan content Lower peptidoglycan content

Lower lipid content (2 – 5%) Higher lipid content (15 – 20%)

The main components are peptidoglycan, The main components are peptidoglycan,
teichoic acid, and teichuronic acid lipoprotein, lipopolysaccharide, outer membrane

Very few amino acids without any Wide variety of amino acids with different
aromatic amino acids aromatic amino acids

Internal Structure of Bacteria

It includes the cell membrane and all the structures inside the cell membrane.
1. Cell membrane/Plasma membrane

 It is the innermost phospholipid bilayer, just beneath the cell wall, enclosing
cytoplasm. It is a thin (~ 5 -10 nm) semipermeable layer.
 Unlike eukaryotic plasma membrane, they lack sterols (except in Mycoplasma), and
comparatively have a higher proportion of proteins. In place of sterols, they have
sterol-like compounds, called ‘hapanoids’. They contain a wide variety of fatty acids
like usual saturated and unsaturated types and additionally methyl, hydroxyl, or cyclic
groups too.
 The plasma membrane is equipped with several porin proteins for the passive
transport of nutrients and ions.

Functions of Cell membrane/Plasma membrane

 Selective permeability regulates the inflow and outflow of nutrients, ions, and
metabolites
 Electron transport and oxidative phosphorylation

2. Cytoplasm

 It is a colourless, colloidal, viscous fluid with suspended organic and inorganic solutes
enclosed within the plasma membrane.
 Unlike eukaryotic cytoplasm, they lack membrane-bound organelles. They have
ribosomes, mesosomes, inclusion bodies, nucleic acids floating in them.

2.1 Ribosomes

Bacterial ribosomes are of 70S type and quite smaller than eukaryotic 80S types. They are
made up of 2 subunits, the 50S, and 30S. Their main role is to synthesize bacterial proteins
and enzymes. They are target sites for different antibiotics like erythromycin, macrolides,
aminoglycosides, etc.

2.2 Mesosomes
They are vesicular or branched structures formed by invaginated of the plasma membrane.
They represent the eukaryotic mitochondria in function and are the site of action of the
bacterial respiration enzymes.

2.3 Inclusion bodies

They are believed to be storage food. They are of two types; (i) organic inclusion bodies,
containing glycogen or polyhydroxybutyrate granules, and (ii) inorganic inclusion bodies,
containing polyphosphate or sulfur granules.

3. Bacterial Nucleus

They are called nucleoids. Unlike eukaryotic nuclei, they are not enclosed in the nuclear
membrane and lack nucleolus and nucleoplasm. It is represented by a dsDNA molecule either
in a closed circular form or in coiled form.Bacterial DNAs are found either in nucleoid as
chromosomal DNA or outside nucleoid as a plasmid.

Endospore of a bacteria

Some bacteria under stress form a dormant stage called an endospore. They are produced
during unfavorable environmental conditions. They grow to vegetative form when the
conditions become favorable.They have four distinct structural components; (i) core,
containing nucleoid and condensed cytoplasm, (ii) spore wall, the innermost wall of
peptidoglycan, (iii) cortex, the thickest wall with unusual peptidoglycan, and (iv) protein
coat, an outer impermeable layer made of keratin like protein.
Shapes and Arrangement of Bacteria

Basically, bacteria are of four distinct shapes, cocci, bacilli, spiral, and comma-shaped.

a. Cocci shape bacteria

They are spherical bacteria. Based on the arrangement of cells they are further sub-grouped
as;

1. Monococci; singular cocci. Eg. Micrococcus luteus,

2. Diplococci; two spherical bacteria are arranged in pairs. Eg. Neisseria spp.,
Moraxella catarrhalis, Streptococcus pneumoniae, etc.
3. Streptococci; spherical bacteria are arranged in a long chain. Eg. Streptococcus
pyogenes, S. agalactiae, etc.
4. Staphylococci; spherical bacteria arranged in irregular clusters like a bunch of grapes.
Eg. Staphylococcus aureus, S. saprophyticus, etc.
5. Tetrad; arrangement in a group of 4 cocci. Eg. Aerococcus urinae, Pediococcus spp.,
etc.
6. Sarcinae; arrangement of cocci in a group of 8. Eg. Sarcina spp., Clostridium
maximum, etc.

Shapes and Arrangement of Bacteria

b. Bacilli shape bacteria

They are rod-shaped bacteria. Based on the arrangement of cells they are also sub-grouped
as;

1. Bacillus /Mono–bacillus; single unattached rod-shaped bacteria. Eg. Salmonella

enterica serovars, Bacillus cereus, etc.
2. Diplobacilli; bacilli arranged in a pair. Eg. Moraxella bovis, Bacillus licheniformis,
etc.
3. Streptobacilli; bacilli arranged in a chain. Eg. Streptobacillus moniliform, etc.
4. Palisade; bacilli arranged in fence-like form. Eg. Corynebacterium diptheriae, etc.
5. Coccobacilli; bacilli with rounded ends or oval-shaped. Eg. Chlamydia spp., H.
influenzae, etc.
c. Spiral

They are long helical-shaped or twisted bacteria. Eg. Spirilla spp. , Spirochetes spp. , etc.

d. Comma shaped

They are comma (,) like in structure. Eg. Vibrio spp.

Besides these four basic shapes, several bacteria are found in other shapes like;

1. Filamentous (E.g. Actinobacteria, Candidatus savagella, etc. )

2. Starshaped (E.g. Stella vacuolata, Stella humosa, etc)
3. Appendaged / Budding (E.g. Hypomicrobium, Rhodomicrobium, etc.)
4. Pleomorphic (E.g. Mycoplasma spp.)
5. Chineseletterlike (E.g. Corynebacterium spp.)
6. Lobed (E.g. Sulfolobus spp.)
7. Stalked (E.g. Caulobacter crescentus )
8. Sheathed (E.g. Leptothrix, Clonothrix)

Size of Bacteria
  Bacteria are microscopic with a wide range of sizes from 0.2 μm to 100 μm.
 Cocci are generally of 0.2 to 1.0 μm.
 Bacilli are generally of 1.0 μm 5 μm in length and 0.5 to 1.0 μm in diameter.
 Spirochetes are generally 20 μm in length and 0.1 to 1.0 μm in diameter.
 The smallest bacilli are Pelagibacter ubique ( 370 – 890 nm in length and 120 – 200
nm in diameter).
 The smallest cocci are Mycoplasma genitalium with a diameter of 200 – 300 nm.
 The largest bacteria is Thiomargarita namibiensis with a diameter of 0.75 mm.

Classification of Bacteria

There are different schemes for the classification of bacteria. Some of the most common
schemes of classifications are:

a. Classification of Bacteria based on Gram Staining

It is the most common mode of classification used widely in medical and research purposes.
Bacteria are grouped into two groups as;

1. Gram-Positive Bacteria

Bacteria having a thick peptidoglycan layer and retaining the purple color of crystal violet
during Gram staining are Gram-positive bacteria. E.g. Staphylococcus, Streptococcus,
Enterococcus, Corynebacterium, Streptomyces, Bacillus, Haemophilus, Clostridium, Listeria,
etc.

2. Gram-Negative Bacteria

Bacteria having a thin peptidoglycan layer and losing crystal violet but retaining pink / red
color of counterstain safranine during Gram staining are Gram-negative bacteria. E.g.
Escherichia, Salmonella, Shigella, Neisseria, Klebsiella, Proteus, Pseudomonas,
Enterobacter, Citrobacter, etc.

Gram-Positive Bacteria Gram-Negative Bacteria

Stains violet/purple during Gram staining Stains red/pink during Gram staining
Thick cell wall Thin cell wall
Thick peptidoglycan layer Thin peptidoglycan layer
Higher mucopeptide and very low Lower mucopeptide and very high
phospholipid phospholipid
Mesosomes present Mesosomes absent (rarely present)
Fimbriae or pili absent Fimbriae or pili present
Forms endospores Forms exospores
Produce exotoxins Produce endotoxins
Teichoic acid present, Teichoic acid absent,
Lack an outer layer Presence of an outer layer

b. Classification of Bacteria based on Oxygen Requirements

Bacteria are classified into 3 types as;

1. Aerobic bacteria

They respire aerobically and can’t survive in anoxic environments. E.g. Pseudomonas
aeruginosa, Nocardia spp., Mycobacterium tuberculosis, etc.

2. Facultative aerobes

They survive in very low oxygen levels and can survive in both oxygenic and anoxic
environments. They are Microaerophiles. E.g. E. coli, Klebsiella pneumoniae, Lactobacillus
spp., Staphylococcus spp., etc.

3. Anaerobic bacteria

They respire anaerobically and can’t survive in an oxygen-rich environment. E.g. Clostridium
perfinges, Campylobacter, Listeria, Bifidobacterium, Bacteroides, etc.

c. Classification of Bacteria based on Optimum Temperature

Bacteria are classified broadly into 3 types as;

1. Psychrophiles
They have optimum growth temperature at 150C or below. E.g. Chryseobacterium,
Psychrobaceter, Polaromonas, Sphingomonas, Alteromonas, Hyphomonas, Listeria
monocytogenes, etc.

2. Mesophiles

They have optimum growth temperature at 15 – 450C. Pathogenic bacteria fall in this
category. E.g. E. coli, Staphylococcus aureus, Salmonella Typhi, Streptococcus pyogenes,
Klebsiella spp., Pseudomonas spp., etc.

3. Thermophiles

They have optimum growth temperature at above 45 0C. E.g. Bacillus thermophilus,
Methanothrix, Archaeglobus, Thermophilus aquaticus, Geogemma barosii (at 1220C),
Pyrolobus fumarii (at 1130C), Pyrococcus spp., etc.

b. Bacilli shape bacteria

They are rod-shaped bacteria. Based on the arrangement of cells they are also sub-grouped
as;

1. Bacillus /Mono–bacillus; single unattached rod-shaped bacteria. Eg. Salmonella

enterica serovars, Bacillus cereus, etc.
2. Diplobacilli; bacilli arranged in a pair. Eg. Moraxella bovis, Bacillus licheniformis,
etc.
3. Streptobacilli; bacilli arranged in a chain. Eg. Streptobacillus moniliform, etc.
4. Palisade; bacilli arranged in fence-like form. Eg. Corynebacterium diptheriae, etc.
5. Coccobacilli; bacilli with rounded ends or oval-shaped. Eg. Chlamydia spp., H.
influenzae, etc.

c. Spiral

They are long helical-shaped or twisted bacteria. Eg. Spirilla spp. , Spirochetes spp. , etc.

d. Comma shaped

They are comma (,) like in structure. Eg. Vibrio spp.

Besides these four basic shapes, several bacteria are found in other shapes like;

1. Filamentous (E.g. Actinobacteria, Candidatus savagella, etc. )

2. Starshaped (E.g. Stella vacuolata, Stella humosa, etc)
3. Appendaged / Budding (E.g. Hypomicrobium, Rhodomicrobium, etc.)
4. Pleomorphic (E.g. Mycoplasma spp.)
5. Chineseletterlike (E.g. Corynebacterium spp.)
6. Lobed (E.g. Sulfolobus spp.)
7. Stalked (E.g. Caulobacter crescentus )
8. Sheathed (E.g. Leptothrix, Clonothrix)

Size of Bacteria

Bacteria are microscopic with a wide range of sizes from 0.2 μm to 100 μm.Cocci are
generally of 0.2 to 1.0 μm.Bacilli are generally of 1.0 μm 5 μm in length and 0.5 to 1.0 μm in
diameter.Spirochetes are generally 20 μm in length and 0.1 to 1.0 μm in diameter.The
smallest bacilli are Pelagibacter ubique ( 370 – 890 nm in length and 120 – 200 nm in
diameter).The smallest cocci are Mycoplasma genitalium with a diameter of 200 – 300
nm.The largest bacteria is Thiomargarita namibiensis with a diameter of 0.75 mm.

d. Classification of Bacteria based on Arrangement of Flagella

Bacteria are classified into 5 types as;

1. Atrichous

They are bacteria without flagella. E.g. Lactobacillus spp., Bacillus anthracis,
Staphylococcus spp., Streptococcus spp., etc.

2. Monotrichous

They are bacteria with only one flagellum at one pole. E.g. Campylobacter spp., Vibrio
cholerae, etc.

3. Lophotrichus
They are bacteria with multiple flagella at one end. E.g. Spirillum, Helicobacter pylori,
Pseudomonas fluorescence, etc.

4. Peritrichous

They are bacteria with multiple flagella projecting in all directions. E.g. E. coli, Klebsiella,
Proteus, Salmonella Typhi, etc.

5. Amphitrichous

They are bacteria with one flagellum at each pole. E.g. Alcaligenes faecalis, Nitrosomonas,
etc.

e. Classification of Bacteria based on mode of nutrition

1. Autotrophic bacteria

They are bacteria capable of assimilating inorganic matters into organic matters i.e. capable
of preparing their food like plants. They are of 2 types;

Photoautotrophs; They use energy from sunlight for assimilation. It includes cyanobacteria
(Nostoc, Prochlorococcus, etc.), purple sulfur bacteria (Nitrosococcus, Thiococcus,
Halochromatium, etc.), purple non-sulfur bacteria (Rhodopseudomonas spp.), green sulfur
bacteria (Chlorobium, Chromatium, etc.)

Chemoautotrophs; They use chemical energy for assimilation. It includes sulfur bacteria
(Beggiatoa, Thiobacillus, Thiothrix, Sulfolobus, etc.), nitrogen bacteria (Nitrosomonas,
Nitrobacter, etc.), hydrogen oxidizing bacteria (H. pylori, Hydrogenbacter, Hydrogenvibrio
marinus, etc.), methanotrophs (Methylomonas, Methylococcus, etc), iron bacteria
(Thiobacillus ferroxidans, Ferrobacillus, Geobacter metallireducens, etc.)

2. Heterotrophic bacteria

They are bacteria that derive energy by consuming organic compounds, but they do not
convert organic compounds to inorganics. They are parasitic or symbiotic types. E.g. E. coli,
Rhizobium spp., Staphylococcus spp., Mycobacterium spp., Klebsiella pneumoniae, etc.
3. Saprophytic bacteria

They are bacteria that decompose organic compounds into inorganic and derive energy. They
are decomposers and feed on dead plants and animals. E.g. Cellulomonas, Clostridium
thermosaccharolyticum, Pseudomonas denitrificans, Acetobacter, etc.

Reproduction in Bacteria

Bacteria have a very short generation time i.e. they reproduce very quickly. Their
reproduction is an asexual type and can be classified into the following types: binary fission,
budding, transformation, conjugation, transduction based on environmental and other
influencing factors.

Bacterial Diseases

The bacteria that can cause infection (disease) are called pathogenic bacteria, and such
diseases are called bacterial diseases. Most of the bacteria known to us are non-pathogenic.
Only <5% are pathogenic. Some common bacterial diseases with their causative species are
listed in the table below.

Bacterial Identification

This is the method of identifying genera and species of isolated bacteria i.e. to identify which
bacteria are isolated. There are several methods designed and used for bacterial
identification.
a. Cultural Methods for Bacterial Identification

It is the method of identifying bacteria by studying their cultural characters in a specific

culture media. Several selective and indicator media are used for bacterial identification. In
this method, we study colonial characters like;

1. The shape of colonies (circular, irregular, rhizoid, etc.)

2. Size of colonies (micro, small, medium, large, etc.)
3. Pigmentation
4. Elevation of colonies (concave, convex, flat)
5. The margin of colonies (smooth, rough, dented, wavy, etc.)

b. Staining and Microscopy for Bacterial Identification

It is another useful and commonly used method for bacterial identification.

 Gram staining is the most important type of staining method used in microbiology
for bacterial identification. It is a differential staining technique used to differentiate
bacteria into two groups; Gram Positive and Gram Negative, and to study bacterial
morphology. Crystal Violet is used as the primary stain, Gram’s Iodine is used to fix
the CV stain, Acetone/Ethanol is used as a decolorizer and Safranine is used as a
counter stain.

 Besides there are other staining techniques like simple staining, negative staining,
Acid Fast Staining (ZN staining), Giemsa staining, Flagella staining, Endospore
staining, etc.
 Light microscopy, Fluorescent microscopy, Dark Field microscopy, and Electron
microscopy are used.

c. Biochemical Tests for Bacterial Identification

These tests are the methods of identifying bacteria based on their biochemical activities.
Here, we study the ability of bacteria to utilize substrate or to produce certain metabolites and
chemicals. This is a traditional method and is still widely used for the phenotypic
identification of bacteria.
Visual detection of bacterial growth and color change of media is key to identifying bacteria.
The principle of biochemical tests is that different bacteria have different physiology and
metabolism, hence showing different biochemical reactions.

Biochemical tests are easy, simple, inexpensive, and the most widely used methods.
However, they have the disadvantage of a high probability of false-positive and false-
negative results.

The most common biochemical reactions used are;

1. Indole test; is a qualitative test that detects the ability of bacteria to produce ‘indole’
by deamination and hydrolysis of ‘tryptophan’ by producing ‘tryptophanase’
enzymes. It is used to differentiate members of the Enterobacteriaceae family.
Tryptophan-containing media like Tryptophan broth, Tryptic soy broth, Sulfide Indole
Motility (SIM) medium, etc. are commonly used in this method. Bacteria are grown in
a medium containing tryptophan and incubated for 24 hours. Following incubation, an
indole reagent is added and the color change is noted. Development of red or pink
color denoted indole production.
2. Methyl-Red (MR) test; is used to detect the production of acid by fermentation of
glucose in the medium. MR-VP broth is used in this test. Bacteria are inoculated in
MR-VP broth and incubated overnight. Following incubation, a methyl red indicator
is added. If bacteria ferment glucose in the medium-producing acid, then the medium
will turn red.
3. Voges Proskauer (VP) test; is used to detect the ability of bacteria to produce neutral
products like acetoin or 2,3-butanediol. Bacteria are inoculated in MR-VP broth and
incubated overnight. Following incubation, VP reagents I and II are added and the
color change is observed. Development of cherry red / pink color indicates a positive
reaction.
4. Citrate test; is used to detect the ability of bacteria to utilize citrate as a source of
carbon. Simmon’s citrate agar is mostly used.
5. Urease test; is used to detect the ability of bacteria to ferment urea to ammonia by
producing urease enzyme. Urea containing medium like Christensen Urea Agar is
used.
6. Triple Sugar Iron (TSI) test; is used to detect the ability of bacteria to ferment
glucose and lactose or sucrose and release H2S gas. TSI agar is used for this test.
 Color change in slant and butt of TSI agar slant is studied. Change in color from red
to yellow denoted sugar fermentation. If the color of the slant is changed to yellow, it
denotes the fermentation of glucose alone. If the color of the butt is also changed to
yellow, it denotes fermentation of either sucrose, lactose, or both. If black coloration
is developed, it denoted the production of H2S.
7. Catalase test; is used to detect the ability of bacteria to produce catalase enzymes.
8. Oxidase test; is used to detect the ability of bacteria to produce the cytochrome
oxidase enzyme.
9. Sugar Fermentation test; is used to study the ability of bacteria to ferment different
types of sugars (glucose, lactose, sucrose, mannitol, sorbitol, arabinose, etc.)
10. There are several other tests used like; DNAse test, Nitrate reduction test, Esculin
hydrolysis test, Microdase test, Gelatin hydrolysis test, PYR test, ONPG test,
Decarboxylase test, Coagulase test, Sulfur reduction test, Starch hydrolysis test,
Phenylalanine deaminase test, CAMP test, Bile solubility test, etc.

d. Molecular Methods for Bacterial Identification

This test includes the study of a bacterial genome and genomic sequences. This is the most
advanced and accurate method used when very precise identification is required. We can
classify bacteria into sub-species, strains, serotypes, or pathovar levels using molecular
methods. This method includes Polymerase Chain Reactions (PCR), DNA / RNA probe tests,
Microarray, Electrophoresis, Proteomics, etc.

e. Immunological Methods for Bacterial Identification

This method is limited to the identification of pathogenic bacteria only. In this method, we
identify bacteria-specific antibodies or antigens in the body of an infected person. The
identified antibody or antigen is correlated with the identification of the infecting bacteria.

Enzyme-Linked Immunosorbent Assay (ELISA), Radio-immunoassay (RIA), Fluoro

Immuno Assay (FIA), Immuno chromatography tests, etc are commonly used tests.

Importance, Uses and Applications of Bacteria

1. They are responsible for recycling several nutrients like nitrogen, carbon, sulfur,
phosphorus, oxygen, etc. They play the most important role in assimilation and
dissimilation of the organic compounds during any biogeochemical cycle.
2. They play a very important role in regulating atmospheric oxygen levels.
Photosynthetic bacteria (Cyanobacteria, Green Sulfur bacteria) play a very important
role in the production of oxygen during photosynthesis.
3. They are responsible for biodegradation, composting, decomposition, and
bioremediation. They play a very important role in the management of organic wastes
and dead organisms and their parts.
4. Several bacteria are used industrially for the production of several enzymes. These
enzymes are used in industrial processes, medical purposes, food processing, etc.
Amylase, lipase, cellulases, proteases, hemicellulases, zymase, penicillinases,
polymerases, etc. are produced by bacteria.
5. Bacteria are genetically modified and used in biotechnological applications to produce
hormones like insulin and enzymes.
6. They are used in an anaerobic fermentation process to produce biogas (methane)
which is used as fuel.
7. Different genera of Actinomycetes and other bacteria are the source of antibiotics
used for pharmaceutical purposes.
8. Several bacterial species like Bifidobacterium, E.coli, Lactobacillus, etc. are used as
probiotics.
9. Bacteria are used in producing fermented food products like fermented dairy products,
sausages, fermented fruit juices, etc.
10. They are used in the bioremediation of oil spillage, xenobiotic, radiation wastes,
heavy metal wastes, bio-hazardous wastes, toxic wastes, and other organic and
inorganic wastes.
11. Bacteria are used in genetic engineering and molecular research. Their genes are
being used in producing different Genetically Modified Organisms (GMOs).
12. The bacterial fuel cell is new technology to convert chemical energy into electric
energy. They can be used as an alternative source of energy.
13. In agriculture, they are used as bio-pesticides, bio-fertilizers, and bio-insecticides.
14. Bacteria are the pioneer of life forms in barren lands like deserts, rocks, etc. Every
living organism living today are evolved from some eukaryotes which were
developed from bacteria some 2.0 billion years ago.
 15. Bacteria are present as normal flora in our body. They help fight against invading
pathogens, boost immune response, and help in the digestion process.

Disadvantages and Limitations of Bacteria

1. Different pathogenic bacteria are responsible for a wide variety of human diseases
from simple to life-threatening. Bacterial diseases are responsible for thousands of
death each year.
2. Bacterial spoilage of foods feeds and pharmaceutical products is another
disadvantage. The food and pharma industries have to bear huge losses due to
bacterial spoilage.
3. Several bacteria like denitrifying bacteria, sulfur-oxidizing bacteria, etc. are
responsible for decreasing the fertility of the soil, ultimately reducing crop yields.
4. Bacteria can cause disease to crop plants and domestic animals. This will reduce
agricultural production.
5. Bacteria cause deterioration and degradation of useful organic products like furniture,
textiles, etc.
 MICROBES AND PARASITES – FUNGI

Fungi are eukaryotic, non-vascular, non-motile and heterotrophic organisms. They may
be unicellular or filamentous. They reproduce by means of spores.

Characteristics of Fungi

1. Fungi is a separate kingdom

2. Fungi are Eukaryotic organism

3. Morphology:

 Fungi exists in two fundamental forms, filamentous or hyphal form (Ex. mold) and
singe celled or budding form (Ex. yeast).
 But for the classification of fungi, they are studied as mold, yeast, yeast like fungi and
dimorphic fungi.
 Yeast is Unicellular while Mold is multicellular and filamentous

4. Fungi lacks Chloroplast.

5. Mode of nutrition:

 Fungi are organotropic heterotrophs.

 Mostly Fungi are saprophytic and some are Parasitic

6. Fungi grow best in acidic environment (tolerate acidic pH).

7. Fungi can tolerate high sugar concentration and dry condition

8. Most of the fungi are Obligate aerobes (molds) and few are facultative anaerobes (yeasts)

9. Optimum temperature of growth for most saprophytic fungi is 20-30°C while 30-37°C for
parasitic fungi.

10. Growth rate of fungi is slower than that of bacteria.

11. Cell wall is composed of chitin

12. Cell membrane consists of ergosterol

13. Reproduction: both asexual and sexual mode of reproduction

 Asexual methods: fragmentation, somatic budding, fission, asexual spore formation

 Sexual methods: gametic copulation, gamate-gametangium opulation, gametangium
copulation, somatic copulation and Spermatization.

14. More than 2,00,000 fungi species are known.

15. More than 100 fungi are responsible for human infection. More than 20 species are
responsible to cause severe systemic human infection, 35 species causes less severe systemic
disease or might causes cutaneous or sub cutaneous infection and 45 species causes
superficial cutaneous infection.

17. Some fungi shows mutualistic relationship with higher plants, eg Mycorrhiza is symbiotic
associated with root of gymnosperm

Structure of kingdom Fungi

 Almost all fungi, with the exception of yeast cells, have filamentous structures.
 The chromatin threads run through the thick, translucent nucleus. A nuclear
membrane surrounds the nucleus.
 Cell walls of fungi are made of chitin and sugars.
 Protoplast, which divides into other cell parts such as the cell membrane, cell
organelles, cytoplasm, and nuclei, makes up the cell wall.
 They may be multicellular or single-celled in origin.
 The majority of fungi are made up of hyphae, which are thread-like structures.
Mycelium is the term for the structure that these hyphae produce.
Classification of fungi:

The kingdom fungi or mycota is classified into 9 division however only four division are
involved in medical mycology:

1. Ascomycetes

2. Basidiomycetes

3. Zygomycetes

4. Deuteromycetes

Ascomycetes:

 Sexual spore produced within a sac like structure called ascus and the sexual spore are
called ascospore
 Asexual reproduction occurs by single celled or multi celled conidia
 Ascomycetes are also known as sac mycetes.
 Hyphae are generally septated
 Examples: Saccharomyces, Arthroderma, Gibberella

Basidiomycetes:

 Sexual spore are produced externally on a basidium and the sexual spore are known as
basidiospore
 Asexual reproduction occurs by budding, fragmentation or conidia formation
  They are commonly called as mushroom group
 Hyphae are generally septated
 Examples: Amanita, Agaricus, Filobasidiella

Zygomycetes:

 Sexual spore are known as Zygospore

 Zygospore is formed by fusion of two similar cell.
 Asexual reproduction occurs by sporangiospore
 Hypahe are generally aseptated.
 Examples: Rhizopus, Mucor, Basidiobolus, Conidiobolus

Deuteromycetes:

 No sexual stage is present

 Deuteromycetes are also known as fungi imperfecti.
 Asexual reproduction occurs by means of conidia.
 Most of the human and animal pathogens are present in this class.
 Examples: Candida, Cryptococcus, Trichophyton, Epidermophyton, Histoplasma

Reproduction in fungi

 Fungi can reproduce both sexually and asexually. Anamorph refers to the asexual
way of reproduction while Teleomorph refers to the sexual mode of reproduction.
 Conidia, zoospores, or sporangiospores, which are spores, are used in asexual
reproduction.
 Budding, fission, and fragmentation are the three processes used in vegetative
reproduction.
 Through ascospores, basidiospores, and oospores, sexual reproduction takes place.
 In the kingdom of fungi, the usual form of sexual reproduction is not always
present. In some fungi, a diploid cell does not develop from the union of two
haploid hyphae.
 In these circumstances, a transitional stage known as dikaryophase manifests. The
emergence of diploid cells comes after this phase.

Importance of fungi:
i. Important agents for biodegradation and bio-deterioration

ii. Use in industrial fermentation process.

 Examples; Penicillium notatum is used for production of penicillin antibiotics

 Aspergillus niger is used for prodution of citric acid
 Saccharomyces cerevisiae is used for alcohol production

iii. Used in bioremediation (reduces toxic concentration)

iv. Used in agriculture, horticulture and forestry, example; biofertilizer and biopesticides

Fungal diseases in humans

Fungal infections occur when one type of fungal microbe becomes too prevalent in one area
of the body, so that the immune system is unable to defeat it. Examples include athlete’s foot
and ringworm.

Like many microbes, there are helpful fungi and harmful fungi. When harmful fungi invade
the body, they can be difficult to kill, as they can survive in the environment and re-infect the
person trying to get better.

Symptoms

Changes in the appearance of skin and itching are common symptoms of many
fungalinfections. The symptoms of a fungal infection will depend on the type, but common
symptoms include the following: skin changes, including cracking or peeling skin and
itching.

Types

The following conditions are all common types of fungal infections.

a) Athlete’s foot

Tinea pedis or athlete’s foot is a common fungal infection that affects the foot.Athlete’s foot
is commonly associated with sports and athletes because the fungus grows perfectly in warm,
moist environments, such as socks and shoes, sports equipment, and locker rooms.It is most
common in warmer climates and summer months, where it can quickly multiply.

Symptoms

Athlete’s foot is a common infection where the fungus grows in warm and moist
environments.The symptoms of athlete’s foot may vary slightly from person to person and
can look red on lighter skin tones but appear dark brown on darker skin tones. Classic
symptoms include:

 discoloration and blisters on the affected area

 the infected skin may be soft, or layers may start to break down
 peeling or cracking skin
 the skin may scale and peel away
 itching, stinging, or burning sensations in the infected area

Diagnosis, treatment, and prevention

Not all itchy feet are the result athlete’s foot. Doctors usually diagnose the infection by
scraping scaling skin off of a person and inspecting it under a microscope for evidence of any
fungus.There are a few different fungi that can cause athlete’s foot. The infection may behave
differently depending on the specific fungus that is infecting the skin.

Athlete’s foot is often treated with topical antifungal ointments. Severe infections can require
additional oral medications as well. The feet will also need to be cared for and kept dry to
help kill the fungus.Prevention methods include allowing the feet plenty of air to breathe and
keeping them clean and dry. It is a good idea to wear sandals in public showers or locker
rooms.

b) Yeast infection

Vaginal yeast infections are a common form ofCandida overgrowth in women, usually
caused by Candida albicans.An overgrowth of Candida disrupts the normal balance of the
bacteria and yeast in the vagina. This imbalance of bacteria may be due to antibiotics, stress,
hormone imbalances, or poor eating habits, among other things.Candida infections can also
commonly cause fungal toenail infections and diaper rash.
Symptoms
A yeast infection may commonly cause fungal toenail infections.Symptoms of a yeast
infection include:

 itching and swelling around the vagina

 burning sensations or pain during urination or intercourse
 redness and soreness on and surrounding the vagina
 unusual vaginal discharge, such as gray clumps that resemble cottage cheese or a very
watery discharge

A rash may develop over time in some cases. Yeast infections should be treated quickly, as
the symptoms may become severe if left untreated.

Diagnosis, treatment, and prevention

The classic symptoms of a yeast infection make them easy to diagnose. Doctors may ask
about the person’s medical history, such as any previous yeast infections or sexually
transmitted infections (STIs). They may also ask whether the person was recently taking
antibiotics.

Doctors will then examine the vaginal walls and cervix for signs of infection, taking cells
from the vagina if necessary for proper diagnosis.Treatment of yeast infections depends on
their severity. Standard treatments include creams, tablets, or suppositories. Complicated
infections may require complex treatments.

Avoiding yeast infections begins with a balanced diet and proper hygiene. Wearing loose-
fitting clothing made from natural fibers may also help prevent infection. Washing underwear
in very hot water and changing feminine products often can also help prevent fungal growth.

c) Jock itch

Tinea cruris, commonly known as jock itch, is another common fungal skin infection.These
fungi love warm and damp environments and thrive in moist areas of the body, such as the
groin, buttocks, and inner thighs. Jock itch may be more common in summer or in warm,
humid areas of the world.Jock itch is mildly contagious and is often spread through direct
contact with an infected person or an object that is carrying the fungus.
Symptoms

Thrush can affect the genital area in men as well as women.Jock itch appears on the body as
an itchy, rash that often has a circular shape to it. Symptoms include:

 groin, buttocks, or thighs can be red, flaky, or scaly, and on darker skin, the rash may
appear gray or brown
 chafing, irritation, itching, or burning in the infected area
 a rash with a circular shape and raised edges
 cracking, flaking, or dry peeling of the skin in the infected area

Diagnosis, treatment, and prevention

Jock itch has a very particular look and can usually be identified based on its appearance. If
doctors are uncertain, they may take a skin sample to inspect and confirm their
diagnosis.Treating jock itch usually involves topical antifungal ointments and proper hygiene.
Many cases of jock itch are improved by over-the-counter medications, though some require
prescription medications. Cleaning the affected area and keeping it dry can also help kill the
fungus.

Jock itch can be prevented by wearing loose-fitting natural fibers, such as cotton underwear
which is available to buy online. Avoiding contact with others who have the infection is also
important. Avoiding shared items, such as towels and sporting equipment may also help.

d) Ringworm

Tinea corporis or ringworm is a skin infection caused by a fungus that lives on dead tissues,
such as the skin, hair, and nails. Ringworm is a fungus that causes both jock itch and athlete’s
foot. When it appears anywhere else on the body, the infection is just called ringworm.

Symptoms

Ringworm is a skin infection that causes jock itch and athlete’s foot.

Ringworm is usually easy to notice because of its shape. A patch that may itch or be scaly
will often turn into a raised, ring-shaped patch of skin over time. It may even spread out into
several rings.The outside of this ring may appear red on light skin and gray or brown on skin
of color, and may also appear raised or bumpy, while the inside of the ring will appear clear
and healthy and the edges of the ring may spread outward.

Ringworm is highly contagious, and it can be transmitted by skin-to-skin contact, or from

contact with pets, such as dogs. The fungus may also survive on objects, such as towels,
clothes, and brushes.

The ringworm fungus also infects soil and mud, so people who play or work in infected dirt
may catch ringworm as well.

Diagnosis, treatment, and prevention

Other skin conditions may look like ringworm, so doctors will sometimes want to take a skin
sample to inspect for the fungus.After confirming a diagnosis, doctors will recommend a
treatment, depending on how severe the symptoms are.

Creams and medicated ointments are often sufficient to treat many cases of ringworm and
may be purchased over-the-counter or online. Ringworm of the scalp or severe ringworm
may require a prescription.Basic hygiene can help treat and prevent ringworm as well.
Keeping the skin clean and dry can help avoid infection.Safety in public includes wearing
sandals into public showers or locker rooms and avoiding shared items and towels.

Risk factors

Fungal infections are common in humans and are usually not very serious if they are treated
quickly and correctly.Anyone with a weakened immune system may be more likely to
contract a fungal infection, as well as anyone who is taking antibiotics.Cancer treatment and
diabetes may also make a person more prone to fungal infections.
 MICROBES AND PARASITES –VIRUS

Virus are very small infectious agents with size ranging from 20-300nm in diameter.Viruses
are non-cellular entities so they are also called as particles. It lacks their own independent
metabolism and cannot replicate outside the host cell. So, they are also called as obligate
intracellular parasites.Virus that infects bacteria are called bacteriophage or simply phage.
Animal virus infects animals and similarly plant virus infects plants.

Structure of virus

A basic structure of virus is nucleic acid core (either DNA or RNA but not both) surrounded
by protein coat.Central core of nucleic acid of a virus is called genome and the protein coat
surrounding is called as capsid.In some virus, an envelope made up of glycoprotein and
phospholipid bilayer is present outside the capsid.

The basic structural components of a virus are:

1. Genome:

 Virus contains either DNA or RNA as genetic material but not both. Virus which
contains DNA as genetic material are called DNA virus and those containing RNA
are called RNA virus.
  Unlike other living cell where ds DNA is always a genetic material, a viral genome
may consists of linear or circular ds DNA, single stranded DNA, ss linear RNA or ds
linear RNA.
 Examples; Reo virus is a RNA virus which contains ds RNA genome. Parvovirus
contains ss DNA, Papovavirus contains ds circular DNA as genetic materials.

2. Capsid:

Capsid is the outer layer and is referred to as coat or shell. It serves as impenetrable shell
around the nucleic acid core.Capsid also helps to introduce viral genome into host cell during
infection.The protein coat or capsid is made up of number of morphological similar sub units
called capsomere. Each capsomere is further composed of protomere.

Capsomere are arranged precisely and tightly together in a repetitive pattern to form complete
capsid.The number of capsomere in a capsid varies from virus to virus.The complete complex
of nucleic acid and protein coat of a virus particle is called as virus nucleo-capsid.Structure of
capsid give the symmetry to the virus. Virus particle may be either cubicle or helical or binal
or complex symmetry.

3. Envelope:

 Some virus contains envelope that surrounds nucleocapsid. The virus without
envelope is called naked virus.
 The envelope is a bilayer of lipoprotein and glycoprotein.
 The envelope is acquired by the progeny virus from host cell during virus release by
budding process.
 In some virus the glycoprotein projects out in the form of spike called peplomere.
Some of the peplomers or glycoprotein spike such as Haemaglutinin and
Neuraminidase which are involved in binding of virus to host cell.

4. Enzymes:

 Some virus contains enzymes which play central role during infection process. E.g.
Some bacteriophage contains an enzyme lysozyme, which makes small hole in
bacterial cell that allows viral nucleic acid to get in.
  Some virus contains their own nucleic acid polymerase which transcribe the viral
genome into mRNA during replication process. Eg. Retro virus are RNA virus that
replicates inside host cell as DNA intermediate. Theses virus possess an RNA
dependent DNA polymerase called reverse transcriptase.

Virus replication:

 Virus are the obligate intra cellular particles, they replicate inside host cell only.
 For a specific virus to replicate within a specific host cell, certain condition must be
fulfilled. Some of the criteria that are required to be fulfilled in order to viral
replication are;
o The host cell must be permissive and the virus must be compatible to host cell.
o The host cell must not degrade the virus.
o The viral genome must possess the information for multiplying utilizing the
normal metabolism of host cell.
o The virus must be able to use the metabolic capability of host cell to produce
new progeny virus particles containing replicated copy of viral genome.

A cell within which virus replicates is called host cell. Those host cell within which virus
replicates is called permissive or compatible host cell and those within which virus cannot
replicate is called non-permissive or non-compatible host cell.

Stages of virus replication:

i. Attachment (Adsorption):

 This is the first step in virus infection in which interaction of virion with a specific
receptor site on the surface of host cell occurs.
 The receptors sites are normal cell surface components of host cell such as protein,
polysaccharides or lipoprotein-polysaccharide complex to which virus attach.
 For eg. HIV binds to CD4 cell receptor of T-lymphocytes
o Rhinovirus binds to ICAM-1
o Epstein Barr virus binds to C3 complement receptor.
 Each host cell contains upto 100,000 receptor sites for a given virus.
 In general viral receptor carryout normal function in cell.
  For eg. In some bacteriophage, receptor are pilli and flagella and in other virus
receptor site may be transport binding protein etc.
 Receptor of influenza virus is glycoprotein found in RBC and on other cell of mucus
membrane of susceptible host.

ii. Penetration:

After binding of virus, virus is taken up inside the cell which is referred as penetration or
engulfment.The entry of virus into host cell may involves;

o Transfer of only genome across cytoplasmic membrane

o Transport of entire virus across cytoplasmic membrane by endocytosis
o Fusion of viral envelope with cytoplasmic membrane of host cell.

iii, Uncoating;

 Shortly after penetration, uncoating of virus take place.

 Uncoating is defined as release of viral genome from capsid and is accessible to
enzymes required to translate, transcribe and replicate it.The uncoating process vary
from virus to virus.
 Transcription of viral genome is usually the next step in all virus except in those virus
whose genome acts directly as mRNA (eg. Picorna virus).
 RNA viruses that carry minus(-) stranded RNA first transcribe their DNA to plus (+)
stranded RNA that function as mRNA.
 The transcription is catalyzed by viral RNA polymerase released during uncoating.

iv. Biosynthesis:

 The biosynthesis process of virus replication can be divided into early event and late
events.
 Early event:
o In most virus, only part of nucleic acid is initially transcribed into mRNA.
o The early mRNA codes for early proteins (enzymes) required for nucleic acid
replication
o After nucleic acid replication, many copy of progeny nucleic acids formed.
 Late event:
 o Late mRNA is transcribed from progeny genome.
o Late mRNA codes for structural proteins by the process of translation. The
translation process always occurs in cytoplasm of host cell, even if the mRNA
synthesized in nucleus, it enter cytoplasm for translation.

v. Assembly:

 When critical number of various viral components have been synthesized, they
assembled into mature virus.
 The assembly occurs in nucleus or cytoplasm of host cell depending upon types of
virus.
 DNA virus assembled in nucleus except Poxvirus and RNA viruses assembled in
cytoplasm except Influenza virus and Reo virus.

vi. Release:

 Release of mature virus from host cell is the final event in virus replication.
 The mechanism of virus release vary with types of virus.
 The naked viruses are generally released by cell lysis.
 The enveloped viruses are released by budding through special area of host cell
membrane; during which virion acquire a portion of host cell membrane.
 In some animal and plant virus, host cells are not killed, the virus release through
special channels

Types of replication cycle in virus:

 Lytic Cycle

During the lytic cycle of virulent phage, the bacteriophage takes over the cell, reproduces
new phages, and destroys the cell. There are five stages in the bacteriophage lytic cycle.
Attachment is the first stage in the infection process in which the phage interacts with
specific bacterial surface receptors. The second stage of infection is entry or penetration. This
occurs through contraction of the tail sheath, which acts like a hypodermic needle to inject
the viral genome through the cell wall and membrane. The phage head and remaining
components remain outside the bacteria.
The third stage of infection is biosynthesis of new viral components. After entering the host
cell, the virus synthesizes virus-encoded endonucleases to degrade the bacterial chromosome.
It then hijacks the host cell to replicate, transcribe, and translate the necessary viral
components (capsomeres, sheath, base plates, tail fibers, and viral enzymes) for the assembly
of new viruses. Polymerase genes are usually expressed early in the cycle, while capsid and
tail proteins are expressed later. During the maturation phase, new virions are created. To
liberate free phages, the bacterial cell wall is disrupted by phage proteins such as holin or
lysozyme. The final stage is release. Mature viruses burst out of the host cell in a process
called lysis and the progeny viruses are liberated into the environment to infect new cells.

 Lysogenic Cycle

In a lysogenic cycle, the phage genome also enters the cell through attachment and
penetration. A prime example of a phage with this type of life cycle is the lambda phage.
During the lysogenic cycle, instead of killing the host, the phage genome integrates into the
bacterial chromosome and becomes part of the host. The integrated phage genome is called a
prophage. A bacterial host with a prophage is called a lysogen. The process in which a
bacterium is infected by a temperate phage is called lysogeny. It is typical of temperate
phages to be latent or inactive within the cell. As the bacterium replicates its chromosome, it
also replicates the phage’s DNA and passes it on to new daughter cells during reproduction.
The presence of the phage may alter the phenotype of the bacterium, since it can bring in
extra genes (e.g., toxin genes that can increase bacterial virulence). This change in the host
phenotype is called lysogenic conversion or phage conversion.
Some bacteria, such as Vibrio cholerae and Clostridium botulinum, are less virulent in the
absence of the prophage. The phages infecting these bacteria carry the toxin genes in their
genome and enhance the virulence of the host when the toxin genes are expressed. In the case
of V. cholera, phage encoded toxin can cause severe diarrhea; in C. botulinum, the toxin can
cause paralysis. During lysogeny, the prophage will persist in the host chromosome until
induction, which results in the excision of the viral genome from the host chromosome. After
induction has occurred the temperate phage can proceed through a lytic cycle and then
undergo lysogeny in a newly infected cell.

Viral diseases – Refer to notes in Module 5

Prions
• Prions are unique infectious agents made up primarily of protein.

• Unlike viruses, bacteria, fungi, or parasites, prions lack genetic

material such as DNA or RNA.

• The term "prion" stands for "proteinaceous infectious particle.”

• Prions are a type of infectious agent composed of protein

material that can fold in multiple, structurally distinct ways, at
least one of which is transmissible to other prion proteins, leading
to disease in a manner that is epidemiologically similar to the
spread of viral or bacterial infections.

• These infectious proteins can induce normal proteins in the brain

to adopt their misfolded, abnormal shape.
• This misfolding process is thought to be responsible for a group of
neurodegenerative diseases known as transmissible spongiform
encephalopathies (TSEs).

• Examples of TSEs include Creutzfeldt-Jakob disease (CJD) in

humans, bovine spongiform encephalopathy (BSE or "mad cow
disease") in cattle, scrapie in sheep, and chronic wasting disease
(CWD) in deer, elk, and moose.

• The accumulation of misfolded prion proteins in the brain leads to

cell damage and ultimately cell death, causing progressive
neurological symptoms such as dementia, muscle stiffness, and
loss of coordination.
• One of the remarkable features of prions is their ability to transmit
disease across species barriers. For example, BSE in cattle is
believed to have been transmitted to humans, causing variant
Creutzfeldt-Jakob disease (vCJD).

• This ability to jump between species raises concerns about food

safety and has led to stringent measures to prevent the spread of
prion diseases in livestock and to safeguard human health.

• There is currently no cure for prion diseases, and treatment

options are limited to managing symptoms and providing
supportive care.
• Management typically involves supportive care and measures to
prevent the spread of prions, particularly in the context of food safety
and healthcare settings where transmission can occur.

Creutzfeldt-Jakob disease (CJD)

• Rare and fatal neurodegenerative disorder that belongs to the group

of diseases known as transmissible spongiform encephalopathies
(TSEs).

• It is characterized by the progressive degeneration of the brain,

leading to cognitive decline, movement disorders, and eventually
death.

• CJD occurs worldwide, affecting about 1 to 1.5 people per million

each year.
Forms of CJD:

• Sporadic CJD: This is the most common form, accounting for

about 85-90% of cases. It occurs spontaneously without any
known cause and typically affects individuals in their 60s or
older.

• Familial CJD: In this form, there is a genetic mutation that

predisposes individuals to develop the disease. Familial CJD
accounts for about 5-10% of cases, and it tends to have an
earlier onset than sporadic CJD.
• Iatrogenic CJD: This form is transmitted through medical
procedures involving contaminated surgical instruments, corneal
or dura mater transplants, or human growth hormone derived
from cadaveric pituitary glands. Iatrogenic CJD is rare but has
occurred as a result of these procedures.

• Variant CJD (vCJD): This form of the disease is linked to the

consumption of contaminated beef products, primarily during
outbreaks of bovine spongiform encephalopathy (BSE or "mad
cow disease") in the late 20th century. Variant CJD has distinct
clinical and neuropathological features compared to other forms
of CJD.
• The hallmark neuropathological features of CJD include the
accumulation of misfolded prion proteins in the brain, neuronal
loss, and the presence of spongiform changes (small holes) in
brain tissue.

• Diagnosis of CJD is challenging and often requires a combination

of clinical evaluation, imaging studies (such as MRI), cerebrospinal
fluid analysis, and sometimes brain biopsy.

• Currently, there is no cure for CJD, and treatment options are

limited to managing symptoms and providing supportive care.
Bovine spongiform encephalopathy -BSE (mad cow disease)

• Is a fatal neurodegenerative disease that affects cattle. It is caused

by the accumulation of abnormal prion proteins in the brain and
nervous system.

• The disease is believed to have originated from the practice of

feeding cattle with rendered meat and bone meal containing the
remains of infected cattle or other animals.

• BSE garnered significant attention in the 1980s and 1990s due to

its potential to cause a public health crisis.
• This concern arose because BSE can be transmitted to humans
through the consumption of contaminated beef products, leading
to a variant form of Creutzfeldt-Jakob disease (vCJD), which is also
a fatal neurodegenerative disease.

The key features of BSE include:

1. Progressive neurological symptoms in affected cattle, such as

changes in behavior, difficulty walking, and loss of coordination.

2. Accumulation of abnormal prion proteins in the brain, leading to

neuronal damage and the formation of vacuoles, which gives the
brain a spongy appearance on histological examination.
3. Long incubation periods, with affected cattle typically not showing
clinical signs until several years after infection.
• To control the spread of BSE and reduce the risk to human health,
many countries implemented strict regulations and surveillance
programs.
• These measures included banning the use of certain tissues (such
as brains and spinal cords) in the production of animal feed, as well
as the removal of specified risk materials from slaughtered cattle.
• Although the incidence of BSE has declined significantly since its
peak in the 1990s, ongoing surveillance and control measures
remain important to prevent outbreaks and protect both animal
and human health.
Scrapie in sheep

• Scrapie is a transmissible spongiform encephalopathy (TSE) that

affects sheep and goats.

• Similar to other TSEs, such as bovine spongiform encephalopathy

(BSE) in cattle and Creutzfeldt-Jakob disease (CJD) in humans,
scrapie is caused by the accumulation of abnormal prion proteins
in the brain and nervous system.
Key characteristics of scrapie include:

1. Neurological symptoms: Affected animals exhibit progressive

neurological symptoms, including changes in behavior (such as
nervousness or aggression), abnormal gait, tremors, and weight
loss. These symptoms worsen over time, ultimately leading to
death.

2. Transmissibility: Scrapie can be transmitted horizontally (from

one animal to another) and vertically (from parent to offspring).
It can spread within flocks through direct contact between
animals, as well as through contaminated environments, such as
feed and bedding.
3. Prolonged incubation period: Scrapie has a relatively long
incubation period, often lasting months to years between
infection and the onset of clinical symptoms. This prolonged
latency period complicates efforts to control the disease within
flocks.

• Scrapie has been recognized for centuries, with historical records

dating back to the 18th century.

• Control and prevention strategies for scrapie typically involve

surveillance, selective breeding for resistance, and management
practices aimed at minimizing transmission within and between
flocks.
• Many countries have implemented mandatory scrapie eradication
programs to reduce the prevalence of the disease and prevent its
spread.

• These programs often involve the identification and culling of

infected animals, as well as genetic selection for resistance traits
in breeding stock.

• Despite these efforts, scrapie remains a concern for sheep and

goat producers worldwide.