Dedicated to

My beloved Mother
&
Father Haji Muhammad Farooq.

“My Lord, have mercy upon them as they brought me up (when I was) small.”
Quran: Surah 17 Al-Israa: Verse 24.

References
 Review of Medial Microbiology & Immunology by
Warren Levinson 13th Edition.
 Medical Microbiology by
David Greenwood 16th Edition.
 Clinical Microbiology made ridiculously simple by
Mark Gladwin & Bill Trattler 3rd Edition.

Price: 450/-
 Table of contents

MICROBIOLOGY ......................................................................................... ERROR! BOOKMARK NOT DEFINED.

CELL WALL ........................................................................................................................................8
BACTERIAL GROWTH ............................................................................................................................13
MUTATION (VIVA Q) ...........................................................................................................................15
NORMAL FLORA..................................................................................................................................18
PATHOGENESIS ...................................................................................................................................20
SOME TERMINOLOGIES .........................................................................................................................21
IMMUNITY AND BACTERIAL VACCINES.......................................................................................................24
DISINFECTION & STERILIZATIONS ............................................................................................................27
LABORATORY DIAGNOSIS ......................................................................................................................32
SPECIAL BACTERIOLOGY ........................................................................................................................40
CLASSIFICATION .............................................................................................................................40
GRAM POSITIVE COCCI ................................................................................. ERROR! BOOKMARK NOT DEFINED.
STAPH AUREUS .......................................................................................... ERROR! BOOKMARK NOT DEFINED.
STREPTOCOCCUS ........................................................................................ ERROR! BOOKMARK NOT DEFINED.
GRAM NEGATIVE COCCI............................................................................... ERROR! BOOKMARK NOT DEFINED.
NEISSERIA MENINGITIDIS.............................................................................. ERROR! BOOKMARK NOT DEFINED.
NEISSERIA GONORRHOEAE............................................................................ ERROR! BOOKMARK NOT DEFINED.
GRAM POSITIVE RODS................................................................................. ERROR! BOOKMARK NOT DEFINED.
BACILLUS.................................................................................................. ERROR! BOOKMARK NOT DEFINED.
CORYNEBACTERIUM .................................................................................... ERROR! BOOKMARK NOT DEFINED.
LISTERIA ................................................................................................... ERROR! BOOKMARK NOT DEFINED.
GRAM NEGATIVE RODS ............................................................................... ERROR! BOOKMARK NOT DEFINED.
PATHOGENS BOTH WITHIN & OUTSIDE ENTERIC TRACT ....................................... ERROR! BOOKMARK NOT DEFINED.
ESCHERICHIA COLI....................................................................................... ERROR! BOOKMARK NOT DEFINED.
SHIGELLA.................................................................................................. ERROR! BOOKMARK NOT DEFINED.
V.CHOLERA ............................................................................................... ERROR! BOOKMARK NOT DEFINED.
HELICOBACTER .......................................................................................... ERROR! BOOKMARK NOT DEFINED.
PATHOGENS OUTSIDE THE ENTERIC TRACT ........................................................ ERROR! BOOKMARK NOT DEFINED.
KLEBSIELLA-ENTEROBACTER-SERRATIA (KES) GROUP ......................................... ERROR! BOOKMARK NOT DEFINED.
PROTEUS-PROVIDENCIA-MORGANELLA (PPM) GROUP ...................................... ERROR! BOOKMARK NOT DEFINED.
LEGIONELLA .............................................................................................. ERROR! BOOKMARK NOT DEFINED.
GRAM-NEGATIVE RODS RELATED TO ANIMAL SOURCES (B-FYP-B) ........................ ERROR! BOOKMARK NOT DEFINED.
BRUCELLA................................................................................................. ERROR! BOOKMARK NOT DEFINED.
FRANCISELLA ............................................................................................. ERROR! BOOKMARK NOT DEFINED.
YERSINIA .................................................................................................. ERROR! BOOKMARK NOT DEFINED.
PASTEURELLA ............................................................................................ ERROR! BOOKMARK NOT DEFINED.
BARTONELLA ............................................................................................. ERROR! BOOKMARK NOT DEFINED.
MYCOBACTERIA ......................................................................................... ERROR! BOOKMARK NOT DEFINED.
MYCOBACTERIUM TUBERCULOSIS .................................................................. ERROR! BOOKMARK NOT DEFINED.
MYCOBACTERIUM LEPRAE ............................................................................ ERROR! BOOKMARK NOT DEFINED.
ACTINOMYCETES ........................................................................................ ERROR! BOOKMARK NOT DEFINED.
MYCOPLASMA ........................................................................................... ERROR! BOOKMARK NOT DEFINED.
SPIROCHETES (TBL) .................................................................................... ERROR! BOOKMARK NOT DEFINED.
CHLAMYDIA .............................................................................................. ERROR! BOOKMARK NOT DEFINED.
PARASITOLOGY .......................................................................................... ERROR! BOOKMARK NOT DEFINED.
_ .................................................................................................. ERROR! BOOKMARK NOT DEFINED.
PARASITES ................................................................................... ERROR! BOOKMARK NOT DEFINED.
PARASITES ................................................................................... ERROR! BOOKMARK NOT DEFINED.
INTESTINAL PROTOZOA ................................................................................ ERROR! BOOKMARK NOT DEFINED.
GIARDIA LAMBLIA ...................................................................................... ERROR! BOOKMARK NOT DEFINED.
BALANTIDIUM COLI ..................................................................................... ERROR! BOOKMARK NOT DEFINED.
UROGENITAL PROTOZOA .............................................................................. ERROR! BOOKMARK NOT DEFINED.
BLOOD AND TISSUE PROTOZOA ..................................................................... ERROR! BOOKMARK NOT DEFINED.
PLASMODIUM ........................................................................................... ERROR! BOOKMARK NOT DEFINED.
TOXOPLASMA GONDII ................................................................................. ERROR! BOOKMARK NOT DEFINED.
TRYPANOSOMA ......................................................................................... ERROR! BOOKMARK NOT DEFINED.
LEISHMANIA ............................................................................... ERROR! BOOKMARK NOT DEFINED.
LEISHMANIA.............................................................................................. ERROR! BOOKMARK NOT DEFINED.
HELMINTHOLOGY ....................................................................................... ERROR! BOOKMARK NOT DEFINED.
CESTODES................................................................................................. ERROR! BOOKMARK NOT DEFINED.
.................................................................................................... ERROR! BOOKMARK NOT DEFINED.
TREMATODES ............................................................................................ ERROR! BOOKMARK NOT DEFINED.
TREATMENT ................................................................................. ERROR! BOOKMARK NOT DEFINED.
PREVENTION ................................................................................ ERROR! BOOKMARK NOT DEFINED.
NEMATODES ............................................................................................. ERROR! BOOKMARK NOT DEFINED.
TISSUE NEMATODES .................................................................................... ERROR! BOOKMARK NOT DEFINED.
CESTODES................................................................................................. ERROR! BOOKMARK NOT DEFINED.
INDEX ...............................................................................................................................................43
REFERENCES .....................................................................................................................................1
Preface
I am awfully delighted to present you this achievement of Microbiology.
Writing motivation was force of sufferings & helplessness, which I faced & every
medical student more or less have to face regarding microbiology, right in start of
session. So I decided from right that days to collect pearls from all around & start
compiling just after my exam. This book is compiled, simple, with better page
memory, with almost answers to Questions asked in medical exams. I think I did
what I could at this time, and I am thankful to Almighty Allah for this achievement.
Your suggestions & comments will be of great value and encouragement for me in
improving as well as adding other sections to this book.

For home delivery whatsapp us _ 0310-907-55-66 (Mr.najeeb)

Or Inbox us at fb-page “akhrot”.
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Dr. Muhammad Faiz Ullah Kharoti

Faiz Microbiology 5

Microbiology

Study of microscopic organisms, such as bacteria, viruses, fungi and protozoa i.e. their
sturctures, functions, classifications with ways of both exploiting and controlling their
activities__ is called microbiology

Clinical/Medical Microbiology
In addition, called applied microbiology_ is “branch of medical science concerned with the
prevention, diagnosis and treatment of infectious diseases”. This field also includes various
clinical application of microbes for improvement of health or cosmetics e.g. botulinum
toxins (botox) for wrinkles on face etc. (see botulinum p. Error! Bookmark not defined.).

Comparison of Medically important Organisms

Protozoa &
Characteristic Viruses Bacteria Fungi Helminths
Cell No Yes Yes Yes
Appropriate 0.02- 0.2 1-5 3-10 (yeasts) 15-25
(trophozoites)
diameter (um)
Nucleic acid Either DNA or RNA Both DNA RNA Both DNA RNA Both DNA RNA

Types of None Prokaryotic Eukaryotic Eukaryotic

nucleus
Ribosomes Absent 70S_ (50S+30S) 80S_ (40S+60S) 80S_
(S=Svedberg unit) (40S+60S)
Mitochondria Absent Absent Present Present

Nature of Protein Rigid wall Rigid wall Flexible

capsid and containing containing membrane
outer surface lipoprotein peptidoglycan chitin
envelope
Motility None Some None Most_ thru
flagella, cilia,
pseudopods
Methods of No binary Binary fission Budding (yeast) Mitosis
fission or
replication mitosis(mol
ds)
Faiz Microbiology 6

Prokaryotes
Microscopic single-celled organism that has neither distinct nucleus with a membrane, nor
other specialized organelles. It includes:
a) Eubacteria (true).
b) Archae-bacteria (single-celled microbes).
c) cyanobacteria (photosynthetic bacteria).

Eukaryotes
Organisms whose cells contain a nucleus and other organelles (mitochondria,lysosomes
etc) enclosed within membranes. Classified into:
a) Protozoa (unicellular)
b) Fungi
c) Parasites_ Helminths (worms).

Differences b/w Prokaryotes and Eukaryote

Characteristics Prokaryotes Eukaryotes

Nuclear membrane No Yes
Histone associated DNA No Yes
Chromosomes number 1 2
Mitotic division No Yes
Membrane bound organelles
No Yes
(mitochondria, lysosomes)
Ribosomes size 70S (50S+30S) 80S (60S+40S)
No, instead they contain flexible cell
Peptidoglycan in cell wall_ a Yes membrane (or rigid cell wall with
polymer of amino acid & sugar. chitin_ in case of fungi)
Yes (give tensile strength to prevent burst)
No (except in wall-less
Sterol in cell membranes i.e. mycoplasma)
In fungi is Ergosterol.
In human is Cholesterol.
bacteria
- Animal kingdom_ Helminths (worms)
viruses ( non-cellular,
Examples replicate only
- Protista kingdom_ protozoa
- Fungi kingdom_ fungi (yeast & molds)
within cells)
Faiz Microbiology 7

Bacterial cell structures1

 Longest bacterial rods_ are the size of
Shapes of bacteria some yeasts & human RBC (7um).
Three basic groups

1) Cocci _ rounded shape Components of bacterial cell

o Pair_ diplococcus e.g. Neisseria, (cell wall, cytoplasmic membrane, protoplasm)
S. pneumoniae.
o Chain_ streptococcus (S. pyogenes). Cell wall
o Cluster_ staphylococcus_ S. aureus.
2) Bacilli_ rods It is outermost component, common to all
o Gram +ive: clostridium, bacteria (except mycoplasma species, which are
bounded by a cell membrane, having no cell wall).
o Gram -ive: E. coli.
Some bacteria have surface features
3) Spiral shaped_ spirochetes e.g.
external to cell wall such as capsule,
Treponema
flagella & pili.
Cell wall is mainly composed of three
components with some differences in G+,
Size of bacteria G- & AFB.
 Range (1—5 um)  Peptidoglycan
 Smallest bacteria (mycoplasma_wall less)  Lipopolysaccharide
is equal to largest virus (poxvirus).  Teichoic acid.

1
Compare the cell wall of G +ive & G –ive
bacteria.
Faiz Microbiology 8

Cell wall_ components (varies in G +/-)

Gram Positive (BS.TTP) Gram Negative
Thicker peptidoglycan (retain dye_ so Blue in Gram Thinner peptidoglycan (red in Gram staining)
staining)
Teichoic acid fibers_ which protrudes outside the No teichoic acid fibers.
peptidoglycan.
Simple outer layer of peptidoglycan Complex outer layer_ Consist of
(no lipopolysaccharide i.e. no endotoxin)  Lipo-polysaccharide_ act as endotoxin.
 Lipo-protein
 Lipo-phospholipid.
No periplasmic space Lying between outer complex layer & cytoplasmic
membrane is Periplasmicspace which contains
enzyme B-lactamases, that degrade penicillin &
other B-lactam drugs.
No outer membrane Have outer membrane
No porin channels Porin channels present
BS.TTP_
Blue, Simpler, Thicker, Teichoic acid, g-
Positive.

a) Peptidoglycan alternating _
- N. acetyl-Muramic acid_NAM
- N. acetyl-Glucosamine_NAG
 Protein component (tetrapeptide)
containing D-&L-amino acids attached
to muramic acids of NAM unit.

Imp amino acids are

o Di-aminopimelic acid_ (DAP) unique to
bacterial cell wall.
o D-alanine_ involved in cross links b/w
tetrapeptides & action of penicillin.
Also called Murein molecule or
mucopeptide_ is a complex interwoven
(twisting) network that surround the entire Role of peptidoglycan
cell.
o Gives rigid support to prevent cell
It is single covalently linked macromolecule
burst.
made of sugar and protein, that form a
o Maintain shape of cell & resist media
mesh-like layer outside the plasma mem- of low osmotic pressure such as water.
brane. o Site of action of cell wall inhibitors
(antibiotics) e.g. penicillins,
 Sugar component is made of
cephalosporins, vancomycin.
Faiz Microbiology 9

wall and attach to cytoplasmic membrane,

b) Lipopolysaccharide LPS which is called_ Lipoteichoic acid, while
other anchor to peptidoglycan called_ wall
teichoic acid.
Role
 Surface antigen_ induce septic shock (as
LPS in gram-negative).
 Adhesive role i.e. mediate attachment
to mucosal surface cells.

Found in complex outer layer of cell wall in

gram-negative bacteria also called
Endotoxin (endotoxin_ b/c it is integral part of cell wall,
not actively secreted from bacteria like exotoxins).

LPS is composed of three distinct units.

Surface layer (S-layer)
1. Lipid-A (phospholipid)_ responsible for
toxic effects. Part of cell envelope found in almost all
2. Polysaccharide of 5 sugars_ linked to archaea, as well as in many types of
lipid A. bacteria. It consists of monomolecular
3. Outer polysaccharide_ about 25 sugar layer composed of identical proteins or
units_ called somatic or O-antigen_ glycoproteins. This structure is built via
used to identify certain organisms in self-assembly and encloses the whole cell
clinical lab. surface.
- Some bacteria (e.g. Neisseria) have
outer Lipo-oligo-saccharide_LOS Cell wall of Acid Fast Bacilli
(acid fast staining p:34)
instead of this outer polysaccharide
layer. 1
Mycobacteria have unusual cell wall,
which is unable to be Gram stained, i.e.
c) Teichoic acid - AFB cell wall (resembling G +ive) resists
These are fibers_ composed of polymers of decolorization, but (in contrast to G +ive) it
glycerol-phosphate or ribitol-phosphate, has additional thick layer of glycolipid
located in outer layer of gram-positive cell
wall and extend from it. 1
Name four complex lipid & the properties
Some glycerol teichoic acid penetrate cell they confer to mycobacterium.
Faiz Microbiology 10

mainly mycolic acid (long chain fatty acid) Plasmids may be_ (types)
So AFB resist decolorization with acid - Transmissible_ i.e. can be transferred
alcohol after being stained with Carbol- from cell to cell by conjugation (see p:17).
fuchsin. They are large, containing about a
- Wax-D_ enhance the immune response to many dozen genes responsible for enzymes
antigens. & sex pilus formation.
- Phosphatides_ play role in caseation necrosis. - Non-transmissible_ i.e. not transferred
- Cord factor. to other cell, and are small.

Role of plasmids
Cytoplasmic membrane - Antibiotic resistance_ mediated by
variety of enzymes.
It is same as in eukaryotes microscopically_ - Resistance to heavy metals (Hg),
i.e. phospholipid bilayer, but lack sterol, antiseptics & silver etc.
which is present in eukaryotes. (exception... - Resistance to UV light_ mediated by
mycoplasma contain sterol_ which is a wall-less bacteria).
DNA repair enzymes.
Functions - Pili (fimbriae) formation.
- Active transport of molecules into cell. - Exotoxin production.
- Energy generation by oxidative
phosphorylation. b) Inner nucleoid region_ area of
- Cell wall precursor synthesis. cytoplasm in which DNA is secreted.
- Secretion of enzymes & toxins. Being prokaryote_ the DNA is single,
- circular and __
NO nuclear membrane, NO nucleolus,
Protoplasm NO mitotic spindles, NO histones,
Two distinct areas. NO introns (non-coding segment of DNA).

a) Amorphous matrix_ contains

o Ribosomes
70s(50s+30) _ being prokaryote.
- Involves in protein synthesis
- Site of action of certain antibiotics e.g. Specialized Structures Outside
Aminoglycoside, Tetracycline (AT-30 the Cell wall
ribosomes, remaining all antiprotein antibiotics act on
50s ribosomes e.g. macrolids, chloramphenicol etc). (capsule, flagella, pilus, glycocalyx, spores)

o Nutrient granules_ stains with various *cell wall antigen… O antigen+

colors. [capsular antigen… K antigen+
o Plasmid 1 extra chromosomal, double *flagellar antigen… H antigen+
stranded circular DNA molecules,
replicate independently.

1
What are plasmids ? define its types.
Faiz Microbiology 11

- E. coli
- Pseudomonas.
- Salmonella.
- Yersinia pestis.

Flagella
Long, whip-like or thread-like appendages
extending outside from cytoplasmic
membrane or cell wall. It is main organ of
motility, that moves bacteria toward
nutrients or other stimulus __ called
Capsule chemotaxis.It is also antigenic.

Gelatinous layer covering entire bacterium,

composed of polysaccharide except in
anthrax bacillus (made of D-Glutamic acid).
Function
a) Act as virulence factor due to anti
phagocytic activity due to its negative
charge. Certain antibodies attach to
capsular polysaccharide antigen and a
large capsular molecule is formed. The
capsule appears to swell because of
increased surface tension.
This swelling phenomenon used in labs Types of flagella
to identify certain organisms _ called - Atrichous_ no flagella.
Quelling reaction (in German, swelling=quelling - Monotrichous_ single at one pole.
see p:Error! Bookmark not defined.). - Amphitrichous_ one each at two poles.
b) Capsular polysaccharide used as - Lophotrichous_ many at one pole.
antigens in certain vaccines e.g. - Peritrichous_ many, distributed around
capsule of streptococcus pneumoniae. the cell.
c) Adherence of bacteria to cause
infection.
Importance
Capsulated organisms (K-antigen)  Some motile bacteria (e.g. E. coli & Proteus)
(PMH-B-PEPSY)
- Pneumococcus_ Streptococcus are common causes of urinary tract
pneumoniae. infection “UTI” b/c flagella may play
- Meningococcus_ Neisseria meningitis. role in propelling bacteria up the
- H. Influenza_ Haemophilus influenzae. urethra into bladder.
- Bordetella  Some bacteria (e.g. Salmonella) are
- Pasteurella multocida identified in lab by flagellar “F”
antigen.
Faiz Microbiology 12

Flagellated organisms (F-antigen) SHE

- Salmonella.
- Helicobacter pylori, Bacterial spores
- E. coli, Highly resistant structures formed in
response to adverse conditions (i.e. nutrients
like carbon, nitrogen depletion) by two imp G +ive
Non-motile organisms
Klebsiella C. diphtheriae.
rods_
Shigella Bacillus anthrax,
 Bacillus
Staph+Streptococcus  Clostridium

Spores contain DNA, little cytoplasm, cell

Pilus (fimbriae) membrane, peptidoglycan, little water and
most importantly thick keratin-like coat
Hair like filament, shorter & straighter than responsible for resistance.
flagella, mainly found in Gram -ive. Spore doesn’t have metabolic activity, can
Function remain dormant for many years.
- Mediate attachment to human cell_
causing initiation of infection. Medical importance is extra-ordinary
- Attachment to other bacteria (sex resistance to heat, so boiling can’t sterilize.
pilus). Autoclaving (15lb/in2-15mint-121- C_ steam heating
under pressure_p 30) is required to sterilize.
Upon exposure to water and appropriate
Glycocalyx (slime layer) nutrients, specific enzymes degrade the
Polysaccharide coating, covers surface like coat, water and nutrients enter and
a film, which allow these bacteria to germination into potentially pathogenic
adhere firmly to various structure e.g. to bacterial cell occur.
skin, heart valves, indwelling catheters, (as
seen in staph epidermidis), prosthetic joints &
catheters. It is important component of
biofilm e.g. in Yersinia (plague).
Faiz Microbiology 13

Bacterial Growth

4) Death phase
Growth cycle Decrease in number of bacteria.
Bacteria reproduce by binary fission (i.e. a
process by which one parent cell divides to form two cells,
and each then divides to form further two, that’s why it is
called exponential/logarithmic growth).
Doubling time ranges from 18 mint
to 18 hrs. (Mycobacterium tuberculosis).
(E. coli)
Bacterial classification _on basis of
Oxygen requirement

Phases of bacterial growth cycle  Obligate aerobe

 facultative anaerobe
There are four phases mainly. If small  obligate anaerobe
number of bacteria are inoculated in a  microaerophilic
liquid nutrient medium, and counted  aero-tolerant organisms
continuously, this graph can be presented  capnophilic/carboxyphilic
as_

Obligate aerobe
Oxygen enhance metabolism, growth & act
as hydrogen accepter in final step of
energy production, which is catalyzed by
flavo-proteins & cytochromes.

Two toxic molecules (Hydrogen peroxide H2O2, free

radicle superoxide O2) are produced, so bacteria
requires two enzymes to degrade these
1) Lag phase toxic metabolites.
High metabolic activity but no division
i.e. cell count remains same.
2) Log phase 2O2 + 2H superoxide dismutase H2O2 + O2
Rapid cell division, cell count increase. 2H2O2 catalase 2H2O + O2
B-lactam drugs are effective in this
phase. Response to oxygen is important criteria to
3) Stationary phase classify bacteria and great practical
Number of cell produced balances significance for incubation.
number of cells die b/c of nutrient
depletion or toxic products. These bacteria need oxygen b/c their ATP
generating system is dependent on oxygen
Faiz Microbiology 14

as H+ accepter. They cannot ferment or

respire anaerobically.
Examples are_ Microaerophilic
- Mycobacterium tuberculosis
Require oxygen for survival but at lower
- Nocardia asteroids.
concentration than atmosphere.They are
poisoned by high concentration of oxygen.
Facultative anaerobe e.g. campylobacter grows in 5% oxygen
instead of normal 20% oxygen in
If oxygen present, is utilized. If not atmosphere.
sufficient oxygen, they use fermentation
pathway to synthesize ATP e.g.
- Staphylococcus Aero-tolerant organisms
- Enterobacteriaceae (E. coli, salmonella,
Don’t require oxygen (b/c anaerobes) but
can grow in air i.e. they are not poisoned
by oxygen.
e.g. clostridium histolyticum.
shigella).

Capnophilic/Carboxyphilic
Obligate anaerobe
Bacteria that require high carbon dioxide
These can’t grow (or even killed) in presence of
concentration for growth. Usually
oxygen, b/c they lack superoxide
microaerophilic are also Capnophilic. e.g.
dismutase or catalase or both
- Campylobacter
e.g. (ABC)
- Haemophilus influenza
- Actinomycetes
- Neisseria gonorrhoeae.
- Bacteriods
- Clostridium.
Faiz Microbiology 15

Mutation (viva Q)
1
Permanent alteration of nucleotide 2) Frame shift mutation
sequence of genome of an organism, that  When one or more base pairs are
results in insertion of different amino acid added or deleted, which shifts the
in protein, and appearance of altered reading frame on ribosome, results in
phenotype may be transmitted to incorporation of wrong amino acid,
subsequent generation. thus production of inactive proteins.
 e.g. consider sentence. “FAT CAT SAT”,
Bacteria being prokaryotes are haploid i.e. single each word represents a codon. If we
chromosome, thus a single copy of each gene, so any delete the first letter F, and read the
mutation_ results in cells that has lost that trait.
sentence “ATC ATS AT” it doesn’t make
While eukaryotes are diploid i.e. pair of each chromosome,
thus two copies of each gene, with one copy (allele) any sense.
expressed as protein_ “dominant” while the other copy not  So wrong codon produces wrong
expressed _ “recessive”, so mutation in one copy not
necessarily results in loss of that trait.
amino acid, so altered protein, e.g.
Tay-sachs disease, cystic fibrosis.

3) Insertion/deletion sequence
Types of mutation  When transposons (jumping genes) or
1) Base substitution (point mutation) newly piece of DNA is inserted in
As name shows, one nucleotide base parent DNA, will cause a profound
pair is inserted in place of another. change in length of genes into which
e.g. adenine instead of guanine. they are inserted and in adjacent
 If this base substitution causes no genes_ called insertion mutation, e.g.
change in protein synthesis_ is called Huntington’s disease.
Silent mutation.  Same is the case with deletion
 If this base substitution causes small mutation when a section of DNA is lost,
change in protein synthesis i.e. only a profound change in genes will occur,
one amino acid is changed_ is called e.g. Turner syndrome (45X0 i.e. a
Missense mutation. e.g. Sickle cell female with missing one X-
anemia (in β-Hb chain, valine (Villon) attack and chromosome, instead of normal 46XX).
replace normal glutamic acid at position 6, so instead
of normal adult Hb-A, abnormal HbS is produced).
 If this base substitution generates a
termination codon, that stop protein
synthesis prematurely_is called
Non-sense mutation which always
destroy protein function.

1
Define gene mutation. Give its types with
examples and their effects.
Faiz Microbiology 16

genome and disrupts genetic function

e.g. mutator bacteriophage_ cause
Mutagens mutation in bacterial chromosomes.
 Bacteria
“Agent causing genetic mutation”.
Helicobacter pylori_ cause
Types _ (physical, chemical, biological)
inflammation during which oxidative
species produced_ which damage DNA
and its repair system, thus increasing
1) Physical mutagens
mutations.
 Ionizing radiation (high energy)
X-ray, gamma (ϒ) rays, alpha particles_
cause DNA breakage. Transfer of DNA within
 U.V light_ (energy lower than x-ray) Bacterial cell
Cause cross linking of adjacent
pyrimidine. e.g. of thymine_ called
thymine dimers. a) Transposons (jumping gene)
 Radiation decay such as C14 in DNA, Transfer of DNA from one
which decays into Nitrogen (N14). chromosomal site to another or
plasmid. It contributes in antibiotic
2) Chemical Mutagens resistance_ as transposons can be transferred to
plasmid within same bacteria, and this plasmid is then
Chemicals may interfere directly or transferred to another bacteria by conjugation_
through metabolic processes. creating resistance.1
 Nitrous acid (HNO2) and alkylating  Some transposons move by replicating their DNA and
inserting new copy into another site_ called
agents alter the existing bases. Replicative transpositions.
 Some chemicals like 5-bromo-uracil is  Others are excised from the site without replicating
base analogue, so can be inserted in and inserted into new site_ called Direct
transpositions.
place of thymine (5-methyle Uracil),
and bind with Guanine instead of
normal Adenine.
 Reactive oxygen species, e.g. b) Programmed rearrangements
Superoxide, H2O2. “Movement of gene from a silent
 Benzpyene found in tobacco smoke, storage site where gene is not
binds to DNA base_ cause frame shift expressed to an active site where
mutation. transcription & translation occurs”. e.g.
in
3) Biological Origin - N. gonorrhoeae,
 Transposons (jumping genes) - Borrelia recurrentis (the cause of relapsing
Section of DNA that undergoes fever).
autonomous fragment - Trypanosoma.
relocation/multiplication.
 Virus
1
Virus DNA may be inserted into How transposons contribute to spread
resistance of antibiotics.
Faiz Microbiology 17

Significance_ the significance of integrate into bacterial DNA, so can

programmed rearrangement is that it acquire new traits_ called Lysogenic
provides antigenic variants to bacteria, so conversion.
that organism evades of the immune
system. Examples: diphtheria, cholera and
botulinum toxins are encoded by
bacteriophage and transferred by
transduction.

Transfer of DNA between c) Transformation

Bacterial cells Transfer of DNA itself from one cell to
another. Two methods:
 Dying bacteria release their DNA,
a) Conjugation
which may be taken by recipient cells.
Mating b/w two bacteria and DNA
 In lab, investigator may extract DNA
transferred from Donor to recipient,
from one bacterial type and introduce
controlled by F(fertility) plasmid. One of
into genetically different bacteria.
impact protein formed is pilin (which
If recipient cell is eukaryotic cell_ it is
forms sex pilus) also called conjugation
called Transfection (used in genetic
tube.
engineering procedures).
Examples: antibiotic resistance gene
Examples: DNA extracted from
usually transfer by conjugation.
encapsulated smooth pneumococci
could transform non-encapsulated
b) Transduction
rough pneumococci into encapsulated
Transfer of cell DNA by mean of
smooth organism.
bacterial virus (bacteriophage). A virus
when growing in a bacterium, get a
piece of bacterial DNA, when it attacks
another bacterium, viral DNA can
Faiz Microbiology 18

Normal Flora

- Reducing the inflammatory response.

Normal flora is term used to describe

various bacteria and fungi that are Role of normal flora members
permanent resident of certain body sites,
- They are non-pathogenic in their
that usually get benefits but not damage
normal anatomic location, but can
that host (e.g. commensals). Normal flora also
cause disease in other parts and in
called human microbiome.
immunocompromised individuals.
Virus & parasites can be present in
- They occupy attachment sites on skin
asymptomatic individuals, but these NOT
etc and interfere with pathogenic
considered as normal flora.
bacteria colonization, thus defending
host i.e. colonization resistance. If
Carrier state means presence of potential
normal flora is suppressed, pathogens
organisms without clinical signs &
will grow and cause disease.
symptoms, which is source of infection for
- They produce vit-k & several B-
others.
vitamins.
Colonization, refers to “getting of a new
organism which attaches, grow & cause Skin normal flora
infectious disease”. - Staphylococcus epidermidis (also in eye).
- Staphylococcus aureus (mainly in nose, also
Commensalism is an association b/w two in eye).
organisms in which one benefits & other - Corynebacterium diphtheria.
derives neither benefit nor harm. - Candida albicans (yeast_ a unicellular
fungus).
Opportunists are organisms that are
typically non-pathogenic, but act as Respiratory tract flora.
pathogen in certain circumstances.
 Nose (almost like skin)
1
Probiotics are living, non-pathogenic - Staphylococcus aureus_ mainly
bacteria that may be effective in treatment - Staphylococcus epidermidis
or prevention of certain human diseases, - Corynebacterium diphtheria.
on the basis of_
- Colonization resistance_ non-pathogenic
excludes pathogens from binding sites on mucosa.
- Enhancing the immune response
against pathogens.

1
Define colonization resistance.
Faiz Microbiology 19

 Throat  Intestinal tract (ECL)

- Streptococcus (pyogenes, pneumoniae, viridans) - E. coli, Enterococcus faecalis.
- Staphylococcus aureus, epidermidis. - Candida albicans.
- Neisseria meningitidis. - Lactobacilli.

GIT normal flora

 Oral cavity (ABC) Genito-Urinary Tract Normal
In gingival crevices (free space b/w enamel flora
anaerobic bacteria
and gingival epithelium)
(also ECL like intestinal, only E differs)
are found b/c oxygen concentration is
- Staphylococcus Epidermidis_ occurs at
low. Mnemonic (ABC) for anaerobes_
outermost portion of Urethra.
- Actinomycetes
- Candida albicans_ cause of candida
- Bacteroids
vaginitis if lactobacillus is suppressed
- Clostridium.
by antibiotics.
- (viridans also).
- Lactobacillus_ produce acidity in
vagina.
- Streptococcus agalactiae.
Faiz Microbiology 20

Pathogenesis

“Biological mechanism that leads to diseased state” Or

“Process of development of disease” __ is called pathogenesis.

Pathogen
A micro-organism is pathogen if it is capable of causing disease e.g. pathogenic bacteria,
virus, fungi etc.
Opportunistic pathogens are those that frequently cause infections in immune-
compromised patients. These opportunistic are frequent members of body normal flora.

Pathogenicity is the potential disease causing capacity of pathogens. It is Qualitative

measure i.e. organisms are said to be_

 Pathogenic
 Non-pathogenic.

1
Virulenceis the tendency of a pathogen to damage a host fitness. It is Quantitative
measure of pathogenicity i.e. it is measured by number of organisms required to cause
disease.

For example
- 50% Lethal dose (LD50) is the number of organisms needed to kill half the hosts.
- 50% infectious dose (ID50) is the number needed to cause infections in half the hosts.So
organisms with a lower LD50 (or ID50) are more virulent than those with a higher LD50 (or ID50) because fewer
organisms are needed to cause death or disease.
- Shigella & Salmonella both cause diarrhea, but
ID50 of Shigella_ 100 organisms.
ID50 of Salmonella_ 100,000 organisms. So Shigella is more virulent than Salmonella.

1
Define pathogenicity & virulence.
Faiz Microbiology 21

An organism is said to be more virulent than other due to its ability to produce various
factors like_

 Polysaccharide capsule_ antiphagocytic.

 Pili_ help adherence to mucus membranes.
 Exotoxin / Endotoxin production.
 Intra-cellular survival.

These factors are called virulence factors.

Infectious disease occurrence

There is a balance b/w
1) Micro-organism’s virulence i.e.
 Number of organisms_ to which person is exposed.
 Virulent factors of organisms_ higher the factors, even less number will be able to
cause disease.

2) Host defense i.e.

 Innate immunity_ may be reduced in genetic immune-deficiency e.g. agamma-
glubinemia.
 Acquired immunity_ both antibody-mediated and cell-mediated immunity_ may be
reduced in_
o AIDs (Acquired Immuno-Deficiency Syndrome)
o Drug induced immune-suppression in transplant patient.
o Diabetes.
o Auto-immune disease.
Any shift in balance i.e. either micro-organism overpowers the host defense or suppression
of host defense, leads to infectious disease. Various causes of balance shift are mentioned
in classification above.

Some terminologies

Infection
When a disease causing agent invade the body tissue, multiply and produce toxins along
with various host tissue reactions i.e. inflammation (heat, pain, red-ness, swelling, loss of function)_
called infection, but broadly, this term can be used with more than one meanings.
Faiz Microbiology 22

Subclinical / in-apparent infection

When infection occurs, but no overt symptoms develop. The person is thus an
asymptomatic carrier of microbe, intestinal parasite or virus, that usually is a pathogen causing illness at least in some
individuals.

Latent infection
The state of infection in which the infectious organisms go into dormant state but
reactivation of growth of organism & recurrence of symptoms can occur.

Communicable infections/diseases
Infections transmitted from host to host i.e. man-man, animal-animal or from environment
to man or animal, by direct contact or via vectors, fomites_ is called communicable
infections.

e.g. TB spread via airborne droplets produced by coughing.

A highly communicable disease is called contagious disease i.e. disease may even spread by
casual contact with their secretion or object touched by them or air borne e.g. flu, cold, TB
etc.

Non-contagious disease requires a special mode of transmission i.e. vector (mosquito) or non-
casual transfer of body fluids (blood transfusion, needle sharing, sexual contact).

Non-communicable Disease (NCD)

Disease that is not caused by infectious agents (i.e. non-infectious or nontransmissible), but
may transfer genetically from one generation to next generation.

Examples are_

 Heart diseases
 Stroke
 Cancers
 Diabetes.

NCDs are distinguished only by their non-infectious cause, not necessarily by their
duration_ b/c

 Some NCDs results in rapid death e.g. heart disease, kidney disease.
 Some chronic diseases of long duration may be caused by infections e.g. parasitic
Faiz Microbiology 23

diseases.

Epidemic
Rapid spread of infectious disease to large number of people within a short period of time,
OR

“unusual occurrence of a disease in a population in excess of its expected frequency (4

times) e.g. cholera epidemic etc.

If the disease is not prevalent, then presence of few cases are also called epidemic. Thus
good knowledge of base-line rate of incidence is necessary.

e.g.

- few cases of a rare disease_ epidemic.

- many cases of common disease (common cold) _ not epidemic.

Pandemic
An epidemic effecting a large proportion of population and occurring over a wide
geographic area, such as section of nation, whole nation, a continent or worldwide e.g.
influenza pandemic in 1951, CORONA virus pandemic in December 2019.

Endemic
Constant presence of a disease/infectious agent within a given geographic area or
population group, without external inputs e.g. chicken pox is endemic in UK.
Faiz Microbiology 24

Immunity and bacterial vaccines

Bacterial diseases can be prevented by Active immunity

Host defense i.e. Immunity. This immunity
can be Innate or Adaptive (acquired). Induction of immunity after exposure to
an antigen. Antibodies are created by
recipient. Active immunization can
occur_
Innate Immunity
 Naturally_ i.e. microbe or antigen attack
It is first line defense from infection in a
a person with no pre-formed antibodies
non-specific manner i.e. effective against
for defense. The immune system will
many different organisms. It comes into
create antibodies, but process is slow.
play immediately or within hours of
e.g. fighting off cold.
antigen appearance in body. e.g.
 Artificially_ i.e. modified organism or
 Physical barriers i.e. intact skin & toxoid etc injected into person before
mucus membranes, low pH of skin, they are able to take it naturally. This
stomach & vagina. doesn’t harm the person, & patient
 Respiratory tract is protected by ciliary immune system produce antibodies. This
elevator, alveolar macrophages, is the principle of Vaccine.
lysozyme, nose hairs, cough reflex etc.
 Normal flora occupies receptors, which
reduce opportunity for pathogens to
attach_ called colonization resistance.
So suppression of normal flora with
antibiotics predisposes to infections.
 Inflammation i.e. redness, swelling, Vaccine
warmth, __ are due to increased blood Vaccine is a biological preparation that
flow & increased vascular permeability, provides active acquired immunity to a
so more cells and proteins are brought particular disease.
to infections site. It is prepared from organisms (killed or
live attenuated) or their products
(capsular polysaccharide, toxoid i.e.
inactivated protein exotoxin) which induce
Adaptive (specific/acquired) immunity
active immunity.
This can be either active immunity, passive
immunity or passive-active immunity.
Types of Vaccine
[don’t mix vaccine types with immunization types].
Faiz Microbiology 25

1) Capsular Polysaccharide vaccines Neurotoxin (tetanospasmin).

This type of vaccine is made of o Coryne-bacterium diphtheria
capsular fragments taken from secretes_ diphtheria toxin.
encapsulated organism against o Bordetella pertussis secretes_
diseases caused by them, e.g. pertussis toxin.
Some encapsulated organism vaccines
and their prophylactic uses are _ Immunity for this type of pathogen
o Pneumo-coccal vaccine (Streptcoccus can be made by introducing toxoid to
pneumoniae) for various pneumococcal stimulate immune system (b/c live or
infections. (as included in EPI). killed vaccine will be useless).
o Meningo-coccal vaccine (capsular Toxoid is_ detoxified or purified toxin
polysaccharide of Neisseria meningitidis) _ for treated by heat, radiation or chemicals
meningitis. such as formalin__(formaldehyde + sterilized
o Haemophilus influenza type-b vaccine water).

(contain type-b polysaccharide of H. Examples of toxoid vaccines.

influenzae) for various infections (also Diphtheria & tetanus vaccines as
included in EPI). DTaP_ the DT are toxoids.
See details of encapsulated bacteria_ PMH-B-PEPSY
p:11
4) Purified Protein Vaccines
In this type, toxoid is combined with
2) Conjugated Vaccine
other proteins for full protection e.g.
- The response to only polysaccharide
vaccine is incomplete, may be due to
o Acellular type of pertussis vaccine_
poor antigenic properties etc.
Toxin is inactivated genetically (by
- When this weak antigen is covalently introducing two amino acid changes, that eliminate
attached to a strong antigen_ in an toxicity, but retain antigenicity) and combined
attempt to improve the with other proteins i.e.
immunological response_ is called Toxoid + filamentous hemagglutinin +
conjugated vaccine. e.g. pertactin
o Pneumococcal vaccine_ (conjugated) _ e.g. DTaP the aP show acellular
used for young children, who do not pertussis toxoid & other purified
respond well to unconjugated vaccine. proteins (in contrast to DTwP_ wP show whole-
o Meningococcal vaccine _ capsular cell inactivated pertussis organism).
polysaccharide conjugated to a carrier DTaP is recommended for all children.
protein (diphtheria toxoid) called
“menactra” _ used for high risk of o Bacillus anthracis Vaccine_ made by
meningitis, like outbreak etc. taking a strain of this bacterium &
growing it in lab, where it produces
3) Toxoid Vaccines several proteins. The protective
Some diseases are not caused by proteins are purified and used as
bacteria, but by toxin secreted by vaccines.
bacteria. e.g. Recommended only for exposed
o Clostridium tetani secretes_ individuals.
Faiz Microbiology 26

o Polio (injectable).
5) Live, attenuated vaccines o Typhoid (injectable vaccine).
This vaccine is created by reducing the o Cholera vaccine (i.e. against vibrio
virulence of a pathogen, but still cholera).
keeping it viable (or live). Attenuation
make infectious agent harmless or less
virulent. It needs to be refrigerated to
stay potent (to prevent vaccine’s bacteria from
destruction by environmental temperature).
Passive Immunity
[Live (viral MMRoP) (bacterial TToT)]
Administration of preformed
antibodies in preparations called
o Measles, Mumps, Rubella, oral Polio.
globulins_ also called Anti-toxins, e.g.
o Tuberculosis vaccine (called BCG vaccine_
Bacillus Calmette-Guerin) prepared from M. Bovis,  Tetanus anti-toxin_ for prevention
which closely related to M. tuberculosis.
(prophylaxis) of tetanus. It
o Tularemia vaccine _ contain Francisella
neutralizes any unbound toxin. It is
tularensis.
o Oral Typhoid vaccine made in human.
 Botulinum anti-toxin_ for treatment
of botulism, made in horses, so
6) Killed (inactivated) vaccine_ (3PTC) hypersensitivity may be a problem.
- Pathogens are grown in culture, then  Diphtheria anti-toxin_ for treatment
killed using heat, radiation or of diphtheria, also made in horses.
chemicals (such as formalin) _ which
destroy its ability to replicate but keep
it intact, so immune system can still
recognize it. Passive-Active Immunity
- Killed vaccine is safer, with weaker
immune response, and short term Administration of immune-globulins
protection than live vaccine. for immediate protection & vaccines to
- It doesn’t need refrigeration e.g. provide long-term protection_ called
(3PTC). Passive-Active Immunization,
e.g. _ in tetanus prevention, in non-
o Plague disease vaccine (i.e. against Yersinia
immunized person having
pestis)
contaminated wound, both tetanus
o Pertussis disease vaccine (i.e. whole-
anti-toxin & tetanus toxoid should be
cell killed Bordetella pertussis_ as
given (at different sites, so that anti-toxin doesn’t
used in DTwP) neutralize the toxoid)
Faiz Microbiology 27

Disinfection & Sterilizations

Disinfection 1 o Bandaging.
Killing of many but not all microorganism, o Suturing_ e.g. iodophor_ iodine +
i.e. some organisms and bacterial spores povidone (solubilizing agent).
may survive. These agents (disinfectants)
reduce number of bacteria to a level low
enough that disease is unlikely to occur.
Disinfectants may be corrosive e.g.
Sterilization
phenol_ used on non-living objects. Killing or removal of all microorganism,
Disinfection of water supply is done by including highly resistant bacterial spores,
chlorine. on surfaces, fluids, medications or in
compounds such as biological culture
Antiseptics_ Disinfectant mild enough media.
to use on skin, mucous membrane and Sterilization is achieved usually by heat,
other tissues_ is called antiseptics. chemicals, irradiation (UV etc), heat under
pressure (autoclave).

Principles of anti-septic techniques_ Disinfection Sterilization

(W-PNN) Definition
Decontamination Decontamination
o Always Wash hands effectively (with
process of process of killing
chlorhexidine_ a chlorinated phenol).
o Non-touch technique is used at all reducing/eliminating all micro-
times to protect key parts. harmful micro- organisms &
o Touch non-key parts with confidence. organisms. highly resistant
o Take appropriate infective Precautions. spores.
Method
Anti-septic techniques_should be used Mostly chemical Mostly physical
in procedures like_ agents. (see below) agents.

o LP & Venipuncture (puncture vein to

withdraw blood or for IV injection) _
e.g. 70% ethanol used on skin.
o Urinary catheterization.

1
Write short note on disinfection &
sterilization.
Following are the ways by which heat can be
applied for sterilization of surgical instruments
except ?
Faiz Microbiology 28

1Agents/methods used for Chlorine

decontamination It is a powerful oxidizing agent_ causes
(both Disinfection & Sterilization) cross-linking of bacterial enzymes, causing
their death.
A) Chemical agents Chlorine is used as disinfectant in_
(mostly for disinfection)
o Water supply
Chemical agents act primarily by one of
o Swimming pools
the following mechanism or their
combination as well. o Bleach_ for disinfection at home &
hospitals.
1) Disruption of cell membrane (DAP)
Iodine
 Detergents_ surface active agents
composed of both hydrophobic (lipid It is also skin anti-septic like ethanol 70%
soluble) & hydrophilic (water soluble) (but it is most effective). Action is like
groups. chloride (inactivate enzymes). Two forms
Examples are_ available_
o Povidone_ skin anti-septic.
o Benz-alkonium_ widely used as o Tincture of iodine (irritating to skin)
- skin anti-septic. it is 2% solution of iodine & potassium
- Floor disinfectant. iodide in ethanol, used for skin
disinfection before taking blood for
 Alcohol (70% ethanol) _used to culture.
disinfect skin before immunization or o Iodophor (less irritating to skin)
venipuncture. i.e. Iodine + Detergent (solubilizing
agent)
 Phenol_ damage cell membranes & e.g. Povidine-iodine (PyodineR).
denature proteins, e.g. Chlorhexidine
(chlorinated phenol) used as_ Aldehydes
o Hand disinfectant before surgery
(surgical scrub) o Formaldehyde_ (used in 37% solution
o Wound cleaning. with water_ called formalin).
o Glutaraldehyde_ with two reactive
aldehyde groups_ so 10X more
2) Modification of proteins effective & less toxic.
(CIA-e-MPA /CIMPA-EA)
These aldehydes denature protein &
nucleic acids, so used in Hospitals to
sterilize_
o Respiratory therapy equipment.
1
Which of the following is not a methods of o Endoscope.
sterilization ?
Faiz Microbiology 29

o Hemodialysis equipment. 3) Modification of Nucleic acids

Ethylene Oxide (gas) Along with aldehyde & ethylene oxide

(mentioned above in modification of proteins),
It kills micro-organisms by alkylating both there are variety of dyes, which not
proteins & nucleic acid. It is used in only stain but also interact with nucleic
hospitals for sterilization of heat-sensitive acid & thus inhibiting their growth.e.g.
materials, such as_
Crystal violet dye _ a positively
o Surgical instruments, charged dye binds to negatively
o Examination tools_ like thermometer, charged (PO4 group of) nucleic acid. It is
plastic specula/spatula for nose & ears used as skin anti-septic.
etc.
Malachite-green dye _ a component of
Lowenstein-Jensen’s (L.J) medium_
Heavy Metals used to grow Mycobacterium
tuberculosis. This dye inhibits growth
Hg (mercury) & Ag (silver) _ bind & block of unwanted organism.
enzymatic activity of bacteria_ having
antibacterial activity, e.g.

Hg containing compounds (thimerosal)_ used as skin anti- B) Physical agents

septic.
(mostly for sterilization)
AgNO3 (silver nitrate) eye drops_ prevent gonococcal
These agents act either by imparting
ophthalmia neonatorum.
energy (Heating, Radiation) or removing
Hydrogen Peroxide (H2O2) liquid. organisms through Filtration.

An oxidizing agent_ inhibit enzymatic 1) Heating1

activity, used to clean wound & disinfect Kills microbes by denaturing proteins,
contact lenses. Its effectiveness is limited damages membranes, or enzymatic
by catalase positive organisms. cleavage of DNA.

(catalase_ an enzyme that degrade H2O2 into O2 & H2O. see a) Pasteurization (for milk)2
p: Error! Bookmark not defined.)
It is Heating milk at 62 C for 30
mints(1800 sec) followed by rapid
Acids & Alkalis cooling. Flash pasteurization means
 Strong_ denature proteins, kill 72 Cfor 15 sec.
microbes e.g. NaOH (used in labs). (62 C__ 1800 sec
 Weak_ bacterio-static, used frequently 72 C__ 15 sec (flash pasteurization).
as food preservative,
e.g. benzoic acid, acetic acid.
1
Mechanism by which heat kills microbes ?
2
Write short note on pasteurization.
Faiz Microbiology 30

This process kills vegetative cells of Autoclaving

milk-borne pathogens e.g.
streptococcus, salmonella, M. bovis Most frequently used method of
but not sterilize the milk. sterilization, because it kills even highly
resistant bacterial spores (that are resistant at
b) Dry heat 100 C at sea level) due to its higher
Primarily heating up-to 180 C for 2 hrs temperature.
in form of Flaming & Hot air.
Used for glassware of clinical Principle:
instruments. The highest temperature obtained at
o Specula (Sim’s speculum, Cusco’s normal atmospheric pressure (at sea level)
speculum, Nasal/Ear specula) is 100 C, which is not sufficient to kill all
o Spatula (like tongue depressor). microbes, and specially spores of C.
botulinum.
c) Moist heat By increasing pressure, we can achieve
Can be applied in the form of: higher temp, so an autoclave chamber
o Boiling_ normal pressure, (closed vessel like pressure cooker) is used in which
o Steaming, steam at pressure of 15lb/in2_ reaches at temp
o Autoclaving_ high pressure. 121 C __ is held for 15-20-mints.
(i.e. 15-15-121 )

2) Radiation Uses
Electro-magnetic spectrum_ arranged To sterilize__
in increasing frequency, so Increasing o Theatre gown,
energy (while decreasing wavelength) o Surgical instruments
i.e. gamma rays have highest energy &
frequency. To test efficacy of autoclave
[ Radio-micro-IR-Visible-UV-X.ray-G.rays]
o Bowie-Dick test_ air removal & steam
Two types of radiation that kills penetration test.
microorganisms are_ To check whether autoclave is working
properly or not, spore forming gram +ive
a) U.V light rods_ Clostridium are used. If these
o {250-260 nm(10-9) wavelength_ is the organisms & spores are killed, it means
region of maximum absorption by autoclave is functional.
microorganism}.
o Used in hospitals to kill air-borne
o It produces thymine dimers, thus
organisms, specially in OT when not in
inhibit DNA replication & growth.
use, clinical practice area, examination
table etc.
o UV light can damage cornea & skin, so
o Spores are quite resistant to UV and
its use in medicine is limited.
require high doses.
Faiz Microbiology 31

b) X-ray_ 3) Filtration
o high energy than UV, produce free Commonly used filter is Nitro-cellulose.
radicles, thus breakage of DNA and kill It has a pore size of 0.22 um, physically
microorganism. trap organisms & spores larger than
o Vegetative cells are killed readily, but pore size.
spores are remarkably resistant due to It is preferred method for sterilizing
lower water content in spores. heat sensitive solutions b/c, even after
o X-rays used in medicine for sterilization autoclaving some solutions can still
of heat-sensitive items such as_ contain endotoxins (in cell wall of dead
 Sutures organisms) which cause disease. So
 Surgical gloves solutions are filtered to make pyrogen-
 Plastic items (syringes etc). free before autoclaving.

Clinical use of disinfection & sterilization

Clinical use Commonly used method
(disinfection/sterilization)
Disinfect surgeon hand prior to surgery Chlorhexidine
Disinfect surgical site prior to surgery iodophor
Disinfect skin prior to venipuncture or 70% ethanol
immunization
Disinfect skin prior to blood culture or Tincture of iodine followed by 70% ethanol
inserting vascular catheter or iodophor or chlorhexidine
Cleanse burn wound Silver sulfadiazine
Cleanup of blood spill from a patient with Hypochlorite (bleach, Clorox)
Hepatitis B or C (disinfect area)
Sterilize surgical instruments and heat- Ethylene oxide or glutaraldehyde.
sensitive materials (e.g. endoscope,
respiratory therapy equipment )
Sterilize non-heat sensitive materials (e.g. Autoclave
surgical gown, drapes)
Sterilize IV solution Filtration
Disinfect air in operation room (when not in use) Ultraviolet light (U.V)
Disinfect floor of operating room Benzalkonium chloride (Lysol)
Disinfect stethoscope 70% ethanol
Preservative in vaccine Thimerosal
Faiz Microbiology 32

Laboratory Diagnosis

specimen and organism.

1) Observing the organisms in
Diagnosis of infectious diseases in lab microscope after staining, e.g.
involve following approaches, i.e. Gram stain etc.
2) Obtaining a pure culture_ by
inoculating it on culture media.
 Bacteriologic Approach_ organism
3) Identifying the organism by using
is identified by staining and
 Biochemical reactions, sugar
culturing the organisms. fermentation, hemolysis etc.
 Immunologic/serologic Approach_  Growth on selective media.
organism is identified by detection  DNA probes.
of antibodies against organisms in  Specific antibody reaction, e.g.
patient’s serum. agglutination.
 Nucleic acid based methods_
amplification, sequence analysis
etc. Staining1
Each of the above is now described in much detail below.
Staining simply means coloring of micro-
organisms with dye that emphasizes
different important structures.

Bacteriologic Approach
Importance
In this approach, several steps are
performed before actual lab work (i.e.
principles of proper collection &  it highlights the structures_ allowing
submission of specimen etc.) them to be seen under microscope.
 It differentiates different organisms.
1) Choosing appropriate specimen to
 Identification of micro-organisms like
examine_ for understanding
Gram +ive, Gram –ive.
pathogenesis.
2) Obtaining the specimen properly to
avoid contamination from the normal
flora.
3) Transporting specimen with no delay,
or storing correctly.
4) Providing essential info to lab worker.

During lab work, these approaches are

usually utilized, depending on type of 1
All are the reagents of Gram staining except ?
Faiz Microbiology 33

Various types
Gram staining (ospe Q)
Staining may be_ Simple, Differential &
Special. It is very imp procedure in microbiology,
separates most bacteria in two groups, i.e.
A) Simple staining
Gram-positive_ stains blue.
 Methylene blue
Gram-negative_ stains pink.
 Carbol-fuchsin
 Crystal violet
Procedure (violet-iodinie-alcohol-safranin)
used for highlighting the total count of Specimen is taken on glass-slide &
bacteria etc. following 4-steps are done.

 Crystal violet dye_ stains all cells blue.

B) Differential staining  Iodine solution_ added, which form
 Gram staining crystal violet-iodine complexes_ is still
 Acid-fast staining. blue.
 Now slide is washed with alcohol
Used for differentiating b/w organisms. (acetone or ethanol).
This extracts more blue dye from
gram-negative bacteria (b/c of lipid
C) Special stains rich, thin walls) _ & becomes colorless.
While extracts very less dye from
o Hematoxylin & Eosin (H&E stain) _ gram-positive bacteria (b/c of lipid-
for Histology. poor, thick walls) _ & remain blue.
o Romanowsky stain_ for blood  Red dye safranin stains the colorless
smear staining & differentiating gram-negative as red/pink, while gram-
cells in pathologic specimen.We positive remains blue.
have 4 stains & can use any one of
them. Principle
 Leishman’s stain It is based on composition of cell wall i.e.
 Giemsa stain thickness & lipid components, which stain
 Field’s stain differently with stains mentioned above.
 Wright’s stain
o Periodic Acid Schiff (PAS)_ stains Interpreting Gram-staining report/result
fungi in tissue e.g. Cryptococcus. - Whether organisms are present?
o Staining of flagella, endospores, - Which type of organisms it is?(i.e. G+ive,
capsules. G-ive)

o Iron hematoxylin stain_ stain tissue - Fungi (in the form of yeast or molds) may be
component e.g. myelin & elastic present.
Bacteria that can’t be seen in Gram-stain (see p: 41)
fibers.
o Etc.
Faiz Microbiology 34

Fungi & parasites can be grown.

Acid fast stain (Ziehl-Neelson Bacterial growth needs_

staining) 1 Temperature, CO2, PH, Carbohydrates,
This is differential stain used to identify Humidity, Proteins, O2, Vitamins, Minerals.
acid-fast organisms, mainly Mycobacteria All these are provided by media.
due to unusual cell wall_ (see afb cell wall and
principle of staining p:9 ) Petri dish_ shallow cylindrical glass/plastic
(1st introduced by Dr. Paul Ehrlich, then modified by lidded dish, that biologist use to culture
bacteriologist Franz Ziehl & Pathologist Friedrich Neelson).
cells, e.g. bacteria. It contains agar.
Reagents used are_
 Carbolfuchsin (red stain_ require heating, that
soften the cell wall, so easily penetrated) Agar_is sea-weed algae_ solidified form of
 Acid-alcohol (i.e. 95% alcohol, 20% algae which contains Carbohydrates &
H2SO4) Proteins etc. Simple agar sometimes
 Methylene-blue or Malachite green. doesn’t fulfil the needs of bacteria, so it is
enriched with blood.
Acid fast bacilli become bright red after Usually sheep blood is used to enrich agar,
staining. but if in blood banks, human blood is going
to be expired, then we can add human’s
blood as well.
Cultures
Culture medium also called growth
medium is a solid or liquid substance, Types of culture media
designed to support growth of a) (on basis of physical state)
microorganisms or cells in lab (in vitro i.e. 1) Fluid culture media.
outside living body). 2) Semisolid culture media.
3) Solid culture media.

Fluid culture media Main use

Alkaline peptone water Enriched & Transport media for V.cholera
Christen’s Urea broth For detecting Urea activity of proteus
Robertson’s cooked meat medium For culturing anaerobes & maintaining control
RCMM strains of bacteria.
Tryptone water For detecting indole production specially of E.coli.

1
Heating is required in Ziehl-Neelson staining
process for.?
Faiz Microbiology 35

Semisolid media Main use

TSI agar Differentiate bacteria on fermentation basis.
Cary-Blair transport medium Transport medium for fecal pathogens (salmonella,
Shigella, vibrio, Yersinia, campylobacter).
Viral transport media Transport medium for virus.
Amie’s transport media For Neisseria & other pathogens.

Solid culture media Main uses

Blood agar Enriched medium for culturing a wide range of
pathogens & detecting hemolytic bacteria.
Crystal violet blood agar is used as selective medium for
β-hemolytic streptococci.
Chocolate agar (blood agar heated to 80 C for 10 mint)
used for H.influenza & Neisseria species.
Deoxycholate citrate agar Selective & differential medium for enteric pathogens.
DNAse agar Biochemical medium for identifying S.aureus.
Nutrient agar Basic medium for culturing bacteria that have no
special nutritional requirement.
Modified new York city Selective & enriched medium for Neisseria gonorrhea.
medium (MNYC)
Phenylalanine agar Biochemical medium for differentiating Proteus &
Providencia from other enterobacteria & excluding
Yersinia enterocolitica.
Lactose egg yolk milk Differential medium for identifying Clostridium
agar perfringens.
Sabouraud agar For culturing fungi.
Thiosulphate citrate bile Selective & differential medium for Vibrio cholera &
salt sucrose TCBS agar other vibrio species.
Xylose lysine Selective & differential medium for salmonella &
deoxycholate (XLD) Shigella species.
Mannitol salt agar Selective & differential medium for S.aureus.
MacConkey’s agar. For differentiating lactose fermenting from non-lactose
fermenting bacteria. See TSI_p: 38
Lowenstein Jensen (L. J) For culturing Mycobacterium tuberculosis.
acid medium
Loeffler serum medium Enriched medium for subculturing Corynebacterium
diphtheriae to show volutin granules.
Faiz Microbiology 36

b) (on basis of composition)  Blood agar_ differentiate hemolytic

from non-hemolytic.
1) Simple/Basic media  MacConkey’s agar_ differentiate
This media contains basic nutrients for lactose fermenters from non-lactose
bacteria that don’t have any special fermenters.
nutrition requirement. It contains  CLED medium (contains Cysteine,
(PMC-&-W): i.e. Lactose, & is Electrolyte Deficient_
Peptone, Meat extracts, NaCl & used for UTI, urine cultures.
Distilled Water.  Robertson’s cooked meat medium_
e.g. Nutrient agar (agar + distilled used for anaerobic bacteria e.g.
water), Nutrient broth. clostridium.
 Eosin-Methylene Blue EMB medium_
2) Enriched media differential medium (contain bile salts
This media contains additional which is toxic for G –ive, other than
substances to support growth of coliforms) as well as selective medium
bacteria having special nutritional (contain dyes toxic for G +ive).
requirements. These substances are [coliforms_ G -ive found in feces]

blood, plasma, serum, glucose,

vitamin, ascetic fluid (protein rich
abdominal fluid), e.g. blood agar,
chocolate agar. Working in Micr0bio-Lab
Organisms growing on Chocolate agar
Neisseria Pneumococci
Staphylococci Corynebacterium
H.influenza, Bacteria of mixed How to present culture media
infections.
First mention the type of media (blood,
3) Selective media chocolate etc), then bacterial growth or
It contains inhibitory substance (dye or colonies, then shape of colonies (mucoid
antibiotics) which discourage growth of etc), then type of hemolysis (α, β, ϒ). i.e.
all microorganisms, and allow a
Blood agar having bacterial
particular microorganism to grow, e.g.
growth/colonies, of mucoid appearance
 Lowenstein Jenson (L.J) medium to
and β-hemolysis.
grow M. tuberculosis,
Time required to culture bacteria_
 Salmonella-Shigella agar.
Usually bacteria require 24-48 hrs and
 De-oxycholate agar.
placed in incubator at 37 C, but
 EMB (differential as well).
Mycobacterium TB takes 4-6 week &
needs 7 days for fungi. (fungi grown on
Sabouraud agar).
4) Differential media
It contains dyes and indicators, used to
differentiate b/w different pathogens,
e.g.
Faiz Microbiology 37

Specimen for various Diseases Parts_

- Base or foot piece
Specimen/cultures Diseases - Body
Blood cultures Sepsis, endocarditis, - Nose piece
meningitis.
Throat cultures Pharyngitis, diphtheria,
- Stage
oral thrush. - Condenser (large convex lens)
Sputum cultures TB, pneumonia. - Eye piece
Spinal fluid cultures Meningitis, encephalitis, - Hand or arm.
brain abscess, subdural
empyema. Oil immersion Slide focusing_(exam Qs)
Stool cultures Enterocolitis.
 1st of all check the light, whether it is
Urine cultures Pyelonephritis, cyctitis.
On or Off. (turn it on)
Genital tract cultures Sexually transmitted
diseases.  Move down the stage of microscope &
Wound/abscess cultures Brain abscess, lung focus slide on 10X first.
abscess, abdomen  Put drop of oil on slide.
abscess.
 Turn lens of 100X power without
moving stage, only little bit fine focus.
Microscope
An instrument for magnifying very small
objects. Day 1: you have to do 2 things.
 Receive sample
 Put up sample for culture.
Different media are for different samples.
Unless proper media is not given to
bacteria, no colonization of the bacterium
will occur & you will miss the infectious
bacteria.

Day 2:
 You have to interpret the colonial
morphology, which have been grown
on media.
 Put bacteria on culture sensitivity (so
you will know to which antibiotic the
bacteria is sensitive).

Day 3:
See the effects of antibiotics on bacteria.
See Positivity & Negativity of biochemical
tests.
Faiz Microbiology 38

1
Organism not growing on routine of medium to the bottom of tube.
culture media_ (i.e. with negative cultures) - then, streaking on the surface of
agar slant.
- Treponema pallidum
 Leave the test tube cap ON loosely and
- Borrelia burgdorferi
incubate the tube at 35 C in moderate
- Borrelia recurrentis
- Leptospira air for 18-24 hrs.
- etc
2
Infections by the above organisms is then Interpretation
diagnosed by__ (immunological methods)
 If a bacterium is lactose (or sucrose)
- antibody detection in patient serum.
fermenter, a large amount of acid is
- Antigen detection in patient specimen.
- Nucleic acid detection in patient produced (being in larger ratio) which
specimen. turn the phenol red indicator yellow
both in butt & in in slant, e.g. (KEE).
 If a bacterium is only Glucose
Triple sugar iron(TSI) agar test fermenter (non-lactose fermenter), it
Principle: Different bacteria are will produce little acid (b/c glucose in
differentiated on the basis of their ability TSI is in smaller ratio) both in butt &
to ferment different sugars_ (thus acid slant.
production). - In comparison to slant, the butt
has less oxygen & more glucose, so
Components: This test has three sugars butt acid will turn phenol red into
(Lactose, Sucrose, Glucose in ratio L:S:G::10:10:1), Iron yellow.
(ferrous sulfate), and contain Agar as solidifying - While slant acid will be oxidized to
agent, and phenol red (indicator_ will turn yellow CO2& water, and phenol will
in acidic PH).
TSI is a semi-solid media in test tube having remain red.
Slant (angled well-oxygenated area on top), & butt - Examples of only glucose
(poorly-oxygenated in center). fermenter are_ (SSP) salmonella,
shigella, proteus.
Procedure:  If bacterium is neither Lactose/sucrose,
 With a sterilized straight inoculation nor glucose fermenter, both the butt &
needle, touch the top of a well-isolated slant will remain red.
colony. Example_ pseudomonas.
 Inoculate TSI agar by_  If H2S is produced by bacterium, black
- First stabbing through the center color of ferrous sulfide is seen.

1
All are the bacteria that can be grown on
routine culture media except ?
2
Which one of the following tests is applied
when culture is –ive.?
Faiz Microbiology 39

Lactose fermenters Slow/late fermenter Non-lactose fermenter (ShYPS)

(KEE) Non-motile Motile
Non-H2S producer H2S producer
Klebsiella, Serratia Shigella, Proteus
E. coli, Vibrio Yersinia Salmonella
Enterobacter.

Some important Exam Questions

Oxidase Positive Organisms

Urease Positive Organisms
(PUNCH) (VC-NBP-HBL)

Urease is an exo-enzyme that hydrolyze Oxidase test is used to identify bacteria,

urea to ammonia and CO2, and alkaline that produce enzyme_ Cytochrome-C
environment is created. oxidase (enzyme of bacterial electron transport chain)

Many organisms can hydrolyze urea, but When this enzyme is present, it oxidizes
only few degrade it rapidly_ called Rapid the reagent on filter paper soaked with
Urease-Positive organisms, e.g. sterile distilled water_ thus purple (bluish)
color is produced.
 Proteus
 Ureaplasma urealyticum(found in urine In absence of enzyme_ soaked filter paper
& renal calculi) is colorless.
 Nocardia
 Cryptococcus (the fungus) e.g. VC-NBP-HBL
 Helicobacter pylori.
Vibrio cholera Pasteurella
Campylobacter Helicobacter
Neisseria Brucella
Brucella Legionella

All oxidase positive are _ aerobes, not

strict aerobe.
Oxidase negative may be _ anaerobe,
aerobe or facultative.
Faiz Microbiology 40

Special bacteriology

Classification
1.A) Cocci All cocci (+,-) are non-motile, non-spore forming.

Gram +ive Staphylo-coccus Staph aureus

Staph epidermidis
Staph saprophyticus
Strepto-coccus S. pyogenes β
(PAFB) S. agalactiae β
E. faecalis αor β or none
S. bovis α or none
S. α
pneumonia
Viridans α
group
Gram –ive Neisseria N. meningitidis (meningococcus)
N. gonorrhoeae (gonococcus)
Moraxella M. catarrhalis
1.B) Rods
Gram +ive Clostridium C. tetani
(CBCL-GA) C. botulinum
(GA_ less imp)
C. perfringens
C. difficile
Bacillus B. anthracis
B. cereus
Corynebacterium C. diphtheria
Listeria L. monocytogenes
Other (less imp) Gardnerella
Actinomycetes (Actinomyces, Nocardia)
Gram –ive Mainly classified on two basis
a) Enterobacteriaceae &
Non-enterobacteriaceae. (see details)
Faiz Microbiology 41

b) Relation Enteric tract Both within - Escherichia

with & outside - Salmonella
enteric tract
Primarily -
Shigella
inside enteric -
Vibrio
tract (SVCH) -
Campylobacter
-
Helicobacter
Primarily -
Klebsiella-Enterobacter-
outside the Serratia group.
enteric tract - Proteus-Providencia-
(KES-PPM) Morganella group.
- Pseudomonas
- Bacteroids & prevotella.
Respiratory tract - Haemophilus influenza
(HBL) - Bordetella pertussis
- Legionella pneumophila
Animal sources - Brucella
(B-FYP-B) - Francisella tularensis
- Yersinia pestis
- Pasteurella multocida
- Bartonella henselae.

2)-Not readily Alternative

Gram stained Reason microscopy
Mycobacteria M.tuberculosis, Too much Acid fast stain
lipid in cell
wall, so dye
cannot
penetrate.
Mycoplasma M. No cell wall None
pneumonia
Spirochetes Treponema Too thin to see Dark filed
(spiral-shaped) Venereal microscopy
(sexually or
transmitted) fluorescence
- T. pallidum antibody
pallidum

Non-venereal
(not sexually
transmitted)
- T. pallidum
pertenue
- T. pallidum
Faiz Microbiology 42

endemicum
- T. carateum.

Leptospira Thin wall Dark filed

microscopy
Borrelia (exception, as it is stained)
Chlamydia C. Intra-cellular, Inclusion
trachomatis very small bodies in
C. cytoplasm
pneumoniae
C. psittaci
Rickettsia Cause Intra-cellular, Giemsa or
spotted very small other tissue
fever, typhus stain.
& Q-fever.
1
Mnemonic “These Rasicles M2icroscopically Lack Colors” (TRM2LC).

Chlamydia & Rickettsia__ are obligate intra-cellular parasites. Out of three spirochetes
members_ Borrelia is exception, i.e. can be stained.

1
Which of the following bacteria cannot be seen on gram stain.?
Reason for not being stained ?
 Index
Bacterial diseases transmitted Corynebacterium ................ 72
thru Insects ..................... 42 Corynebacterium diphtheria72
( Bacterial spores ..................... 8 cyanobacteria ........................ 2
Bacteroids & prevotella ....... 95 Cyclospora ......................... 146
(MTB) .................................109 barrel-shaped [Lemon shaped Cysticercus ........................ 166
...................................... 181
Base substitution ................ 11
A Beta-hemolytic ................... 54 D
Bile Esculin agar test............ 59
Acquired syphilis ................119 black-fly ............................. 182 Dark-field microscopy ....... 121
Acute Glomerulonephritis ...58 Black-water fever.............. 151 deer-fly ............................. 182
adenylyl cyclase ...................99 Blood agar ........................... 52 D-Glutamic acid ..................... 7
Adherence ...........................19 blood flukes ....................... 176 Diarrhea causing organisms 42
Aero-tolerant organisms......10 Bloody diarrhea .................. 78 Dick test ........................ 57, 59
AFB ........................................5 Bordetella ............................ 99 diecious ............................. 165
Amorphous matrix ................6 Bordet-Gengou (potato-blood- Dientamoeba fragilis ......... 142
Angiostrongylus .................185 glycerol-agar) ................ 100 diphtheria ........................... 72
Anisakis ..............................185 Bowie-Dick........................... 32 Dipylidium caninum .......... 170
Antibiotics sensitivity ...........53 Brucella.............................. 102 Disseminated Gonococcal
Antiseptics ...........................29 BTTPcellwallskecthetc See Infection DGI .................. 65
Applied microbiology ............1 dogs & cats tapeworm ...... 170
Archaebacteria ......................2 Dracunculus ...................... 183
Ascaris................................180 C Draughtsman colonies ........ 61
Ascaris pneumonia ............181 Dry heat. ............................. 32
ASO titer ..............................59 Campylobacter .................... 88 Dwarf tapeworm .............. 170
atypical pneumonia ...........117 Capnophilic .......................... 10
Auramine-rhodamine staining Capnophilic / Carboxyphilic . 10
......................................111 Capsulated organisms ........... 7 E
Autoclaving ..........................32 Capsule .................................. 7
autoinfection .....................179 Carrier state......................... 14 Endemic .............................. 18
Auto-infection ...................181 CASONI TEST ...................... 174 Endocarditis ........................ 50
Catalase test ........................ 52 Endolimax nana ................. 142
Cat-scratch disease (CSD) .. 107 Endotoxins .......................... 21
B Chagas’ disease ................. 161 Entamoeba coli ................. 142
Chemical Mutagens ............ 12 Entamoeba hartmanni ...... 142
B.TTP cell wall sketch .......4 Chinese letter arrangement. 72 Enteric fever (typhoid) ....... 81
Bacillary dysentery ..............84 Circaria .............................. 175 Enterobacteriacae ............... 76
Bacillary-Angiomatosis (BA) CLED .................................... 38 Eosin-Methylene Blue EMB . 38
......................................107 Clonorchis .......................... 176 Epidemic.............................. 18
Bacillus .................................70 Clostridium perfringes ......... 69 Epiglottitis ........................... 98
Bacillus anthracis .................70 Clostridium tetani ................ 67 Erythema nodosum .......... 110
Bacillus cereus .....................71 Coagulase test ..................... 53 Escherichia coli .................... 77
BACTEC medium ................111 Cold agglutination test ....... 45 Eubacteria ............................. 2
BACTEC medium (most rapid Colonization ........................ 14 Eukaryotes ............................ 2
& reliable test). .............111 Communicable infections .... 17 Eye worm .......................... 182
Bacterial cell structures .........3 Congenital syphilis ............ 120
Conjugation ......................... 13
 microbiome ......................... 14
F I Miliary TB.......................... 110
Miracidia ........................... 175
Facultative anaerobe ...........10 IgA protease ........................ 65 Moist heat. ......................... 32
Fasciolopsis buski ..............176 Immunofluorescence monoecious....................... 165
FCPS ...................................176 microscopy ................... 121 M-protein ............................ 56
Fe deficiency microcytic Immuno-pathogenesis ........ 20 MRSA_ Methicillin-resistant
anemia ..........................181 Incubation period ............... 21 Staph aureus .................. 51
Field’s stain ..........................35 Infection .............................. 17 Mutagens ............................ 12
Filariform ...........................179 Insertion/deletion sequence Mutation (viva Q) ................ 11
Filtration ..............................33 ........................................ 11 Mycobacteria .................... 108
fishy smell ............................93 Intracellular survival ............ 20 Mycobacteria tuberculosis 109
Flagella ...................................7 Invasion ............................... 19 Mycobacteria tuberculosis
Flagellated .............................8 (MTB)............................ 109
Flocculation test (VDRL & RPR
test)...............................121 K
Fluorescent ........................121
Frame shift mutation ..........11
N
kala-azar ............................ 162
Francisella ..........................104 Killed (inactivated) vaccine. 26 Necator ............................. 180
Neisseria.............................. 62
Niacin-production ............. 111
G L Non-chromogens .............. 109
Non-communicable Disease 17
gas gangrene .......................67 L. J medium ......................... 38 Non-motile organisms .......... 8
Gas gangrene ......................69 Lancefield ............................ 54 Novobiocin.......................... 53
Gastritis ...............................90 Largest intestinal nematode Novobiocin test ................... 53
gastro-enteritis ....................81 ...................................... 180 Nutrient agar ...................... 52
GI TB ..................................110 Legionella .......................... 100
Giema/Wayson stain ........106 Leishman’s stain .................. 35
Giemsa stain ........................35
Glycocalyx ..............................8
Leishmania donovani......... 162 O
Listeria monocytogenes ...... 74
gonococcus ..........................65 Loa loa ............................... 182
gonorrhoeae ........................65 Obligate aerobe .................... 9
Loffler’s medium ................. 73 Obligate anaerobe .............. 10
Gram –ive whole table.........46 Lowenstein-Jensen medium
Gram Negative Cocci ...........62 Oncosphere ...................... 166
...................................... 111 Ophthalmia neonatorum .... 65
Gram Negative Rods ............76 LPS ......................................... 5
Gram positive cocci .............49 Optochin disk test ............... 61
Luciferase test ................... 112 Otitis media ......................... 60
Gram Positive Rods ........ 67, 74
Gramwholetable ..................46 Oxidase test ........................ 88
Growth cycle ..........................9
M
P
mango-fly .......................... 182
H Mannitol fermentation ....... 53 Pandemic ............................ 18
Mantoux test) .................... 111 Paragonimus ..................... 176
Helicobacter ........................90 meningitides ........................ 63
Hemolytic Uremic Syndrome Parasites ............................ 131
Meningitis ......... 60, 63, 79, 98 Pasteurella ........................ 106
(HUS ................................85 Meningitis causing organisms
Hippurate hydrolysis test....59 Pasteurization ..................... 31
........................................ 43 Pathogenesis primarily within
hookworm infection ..........180 Meningococcemia ............... 63
HUS ......................................79 the Enteric tract (CVSH) . 84
Metacercariae ................... 175 PAZ_ABC ............................. 54
Microaerophilic ................... 10 PCR .................................... 100
perfringes(fastest growing Transposons ........................ 12
bacteria ...........................67
S Treponema pallidum ......... 119
Peri-anal pruritus ...............181 Triple sugar iron .................. 40
Pernicious Anemia ............169 Salmonella ........................... 80 Trypanosoma bruci ........... 160
Phage typing ........................53 Scalded skin syndrome ....... 52 Trypanosoma Cruzi ........... 160
Pharyngitis ..........................57 schizogony ......................... 150 Tuberculin ......................... 111
photo-chromogens ............109 scolex ................................ 166 typhoid................................ 81
Physical mutagens ..............12 Scotch tape test ................. 181
Pilus .......................................8 scotochromogen ............... 109
Scrofula ............................. 110
pin worm ...........................180
scrofulacium ...................... 109
U
pin worm / threadworm ....180
Plague ................................105 Seborod’s agar..................... 38
Selective nutrient agar ....... 52 Urban cycle ....................... 105
Pneumococci .......................59 UTI ....................................... 79
Pneumonia ..................... 43, 60 Septicemia .......................... 81
Sexually transmitted diseases UTI causing organisms......... 43
Pneumovax 23 .....................61
point mutation ....................11 ........................................ 44
post-streptococcal ..............58 Shigella ................................ 84
Prevnar 13 ...........................61 Simmons citrate medium .... 85 V
Probiotics .............................14 Skin normal flora ................. 14
Prodromal period ................21 Sleeping sickness ............... 161 Vaccine ................................ 26
protein level.........................64 Spirochetes ........................ 118 VAP ...................................... 43
Proteus-Providencia- spores .................................... 8 VDRL & RPR test ................ 121
Morganella group ...........93 Stages of infectious disease 21 verotoxin ............................. 78
Pseudomonas ......................94 stepladder fashion ............... 81 Vibrio ................................... 86
Pulmonary TB ....................110 Streptococcus ...................... 54 Viviparous ......................... 180
streptolysin.......................... 54 V-MOF ............................... 149
Strongyloides ..................... 180
Struvite ................................ 93
Q Sugar level ........................... 64 W
sulfur granules ................... 116
Quelling reaction ........... 61, 98 Surface layer ......................... 5
QuellingreactionOKKKKK .....44 Waterhouse-Friderichsen
swarming ............................. 93 syndrome ....................... 63
Swarming............................. 93 Watery diarrhea ................. 78
Sylvatic cycle...................... 105 whipworm infection .......... 180
R syphilis .............................. 119 Widal test ........................... 82
Wright’s ............................... 35
Radiation .............................32 Wuchereria ....................... 183
rapid growing.....................109 T
Rat tapeworm ....................170
Renal TB ............................110
Rhabditiform .....................179
tetanus extremely toxic ....... 68 Y
Thayer-Martin medium ....... 66
Rheumatic fever ..................58 threadworm ...................... 180
Robertson’s cooked meat Yersinia ............................. 105
Toxic-shock syndrome ........ 52
medium ...........................38 Toxoids ................................ 26
Round worms ....................179 Toxoplasma gondii ............ 156 Z
Transduction ....................... 13
Transformation ................... 13
Ziehl-Neelson staining ....... 111
Transmission ....................... 18
© Copy Rights 2017:All copy Rights are reserved with author. No part of this
book may be Re-printed or Reproduced in any form without written permission from
the Author. Sale of this book by photocopying is strictly prohibited.

Author :
Dr. M. Faiz Ullah Kharoti

Inspired & Supervised by:

 Dr. Noor Gul
FCPS medicine, FCPS pulmo_ Punjab Medical College, Faisalabad.

 Dr. AsadUllah
FCPS surgery_ Ayub Teaching Hospital Abbottabad.

 Dr. HinaAyub
MS (Obs&Gyne) _ Aga Khan University Medical College Karachi.

Special Thanks to:

 Dr. Khalid shah Gandapur KMC
 Dr. Noor Muhammad Kharoti KIMS
 Dr. Sadiq Amin khan Marwat GMC
 Dr. RizwanUllah Khan Marwat GMC
 Dr. Ahmed Noor Kharoti GMC
 Dr. Shams-Ur-Rehman GMC
 Dr. HaiderNiazi GMC
 Dr. Muhammad Waqas GMC
 Dr. Muhammad Ahmad Raza QMC