Microbiology, Infections
& Antibiotics
Shilpa Garg

Microbiology
• Microbiology - Branch of medical science,
related to the study of micro-organisms
like bacteria, viruses, parasites, fungi etc.
– Bacteriology
– Virology
– Mycology
– Parasitology

Bacteria
• All bacteria are unicellular organisms that
reproduce by binary fission.
• Bacterial cells are extremely small and are
most conveniently measured in microns.

Classification of Bacteria
• Shapes
• Cocci – Spherical or Round Shaped
• Bacilli – Rod Shaped
• Vibrios - Comma Shaped
• Spirilla – Spiral Shaped

Classification of Bacteria
• Gram Stain
– Gram Positive - Retain Primary Colour (Blue)
– Gram Negative - Retain Secondary Colour
(Pink)
• Aerobes – Require Oxygen for growth
• Anaerobes - Grow in absence of Oxygen

Bacteria
• Gram Positive Aerobes – Cocci
– Staphylococcus aureus
– Streptococcus pneumoniae
– Enterococcus
• Gram Positive Aerobes – Bacilli
– Corynebacterium
– Listeria

Bacteria
• Gram Positive Anaerobes – Cocci
– Peptococcus
– Peptostreptococcus
• Gram Positive Anaerobes – Bacilli
– Clostridium tetani
– Lactobacilli

Bacteria
• Gram Negative Aerobes – Cocci
– Neissaria gonorrhoea
– Moraxella catarrhalis
• Gram Negative Aerobes – Bacilli
– E coli
– Enterobacter
– Klebsiella
– Proteus
– Pseudomonas
– H influenza
– Salmonella
– Shigella
– H pylori

Bacteria
• Gram Negative Anaerobes – Cocci
– Veillonella
• Gram Negative Anaerobes – Bacilli
– Bacteroides fragilis
– Fusobacterium

Bacteria
• Atypical Organisms -Microorganisms that have
undergone greater changes than normal in
morphology, physiology, or cultural
characteristics
– Mycoplasma
– Chlamydia
– Ureaplasma
• Acid Fast Bacilli - Bacteria that are not
decolorised by acid-alcohol after having been
stained with dyes such as basic fuchsin.
– Mycobacterium tuberculosis

Bacteria
E Coli
E Coli

Bacteria
TB Causing Bacteria
Mycobacterium tuberculosis

Bacteria
Anthrax
Clostridium perfringes

Bacteria
E. coli
Clostridium tetani

Bacteria
Neisseria
Staph. aureus
gonorrhoeae

Bacteria
Strep
Neisseria
meningitidis

Infections
• It is defined as the successful invasion and
multiplication of micro-organisms in body
tissues.

Sources of Infection in Man
• A) Man
– Carrier-The person who harbors the
pathogenic micro-organisms without suffering
any ill effects from it.

Sources of Infection in Man
a) Man
• Healthy Carrier
• Convalescent Carrier
• Temporary Carrier
• Chronic Carrier
b) Animals
c) Insects
d) Soil and Water
e) Food

Method of Transmission
1) Contact
Contact can be direct:
e.g. Syphilis, Gonorrohoea, AIDS
Or contact can be indirect:
e.g. through fomites such as clothes,
towels, pencils etc.

Method of Transmission
2) Inhalation : (Air-borne)
Inhalation can be a method of transmission eg.
tuberculosis bacilli and influenza viruses.
3) Ingestion : (Food-borne)
Mode of infection by ingestion can be of three types:
a) Water : e.g. Cholera
b) Food :e.g. Staphylococcus food poisoning
c) Hand : e.g. bacillary dysentery

Method of Transmission
4) Inoculation:
Introduction of organisms directly into the tissue
e.g.
a) tetanus spores inoculated in wounds
b) rabies virus deposited subcutaneously by dog
bite.
5) Congenital Infection
Pathogens are able to cross the placental barrier
and infect the foetus in the uterus. This is known
as vertical transmission. e.g. congenital syphilis,
intrauterine infection.

Clinical Features of Infections
1) Fever
2) Chills
3) Myalgia
4) Photophobia
5) Lymphadenopathy
6) Splenomegaly
7) G.I.Upset

Diagnosis of Infection
A) Direct evidence of infection
i) Direct microscopic examination
a) Gram stain
b) Ziehl – Neelsen stain
ii) Cultures
B) Indirect evidence of infection
a) Blood
b) Urine analysis

Bacterial Resistance
Bacterial resistance is either
1. Natural Resistance
2. Acquired Resistance
a) Mutation
3. Cross Resistance

Infections
• Urinary Tract Infections – Microbial colonization
in urine and tissue invasion of any structure of
the urinary tract
– Complicated UTIs – Abscess, calculi, requires
prolonged therapy
– Uncomplicated UTIs – Dysuria, polyuria, simple to
treat
– Lower UTIs
– Upper UTIs
– Recurrent UTIs
• Relapse
• Reinfection

Urinary Tract Infections
• Terms used in UTIs
– Pyuria – Pus in the Urine
– Haematuria – Blood in the Urine
– Proteinuria – Proteins in the Urine
– Dysuria – Painful Urination
– Polyuria – Increased Frequency of Micturition
– Oliguria- Scanty Urine

Urinary Tract Infections
• Terms used in UTIs
– Anuria – Absence of Urine
– Urethritis- Inflammation of Urethra
– Cystitis - Inflammation of Urinary Bladder
– Pyelonephritis - Inflammation of the Kidney including
the Pelvis of the Ureter
– Prostatitis - Inflammation of the Prostrate
– Bacteriuria – Bacteria in Urine

Urinary Tract Infections
• Common Micro-organisms
– E.coli
– Proteus
– Klebseilla
– Pseudomonas
– Enterobacter

Gynaecological Infections
• Pelvic Inflammatory Disease
– Ascending spread of micro-organisms from the
vagina and cervix to endometrium, fallopian tubes
and other adjoining structures
– Polymicrobial in nature
– Streptococci, Peptostreptococci, Bacteroides,
prevotella, E.coli
– Lower abdominal pain, vaginal discharge, fever,
chills, vomiting, dyspareunia, menstrual irregularities

Gynaecological Infections
• Sequelae of PID
– Oophoritis – Inflammation of Ovary
– Salpingitis – Inflammation of Fallopian Tubes
– Endometritis – Inflammation of Endometrium
– Cervicitis – Inflammation of Cervix
– Vaginitis – Inflammation of Vagina

Gynaecological Infections
• Common Micro-organisms
– Gonococcus
– Bacteroides
– E.coli
– Chlamydia
– Streptococcus
– Klebseilla
– Enterobacter

Sexually Transmitted Diseases
• Gonorrhoea
– Neisseria gonorrhoea
– A gram-negative bacteria which is a principal cause
for sexually transmitted disease in males and
females.
– It is marked in males by urethritis with pain and
purulent discharge, but is commonly asymptomatic in
females, although it may extend to produce
suppurative salpingitis, oophoritis, tubo ovarian
abscess and peritonitis.
– Affects mucus membranes of lower genitourinary tract

Sexually Transmitted Diseases
• Chancroid
– A sexually transmitted disease caused by the
bacteria haemophilus ducreyi.
– Causes multiple painful ulcers on the penis
and the vulva often associated with tender
and enlarged inguinal lymph nodes.

Lower Respiratory Tract Infections
• Bronchitis -Inflammation of one or more bronchi
• Bronchiolitis- Inflammationof the bronchioles
• Pneumonia - Inflammation of the lungs
parenchyma
– Nosocomial Pneumonia - A type of pneumonia that is
caused by bacteria contracted during a
hospitalisation. These hospital-acquired infections
tend to be more difficult to treat due to the bacteria's
relative resistance to common forms of antibiotic
therapy.

Lower Respiratory Tract Infections
• Community Acquired Infections - Any infection
acquired in the community, that is, contrasted
with those acquired in a health care facility. An
infection would be classified as community-
acquired if the patient had not recently been in a
health care facility or been in contact with
someone who had been recently in a health care
facility.

Lower Respiratory Tract Infections
• Empyema – Pus in the Pleural Cavity
• Bronchiectasis - Persistent and progressive
dilation of bronchi or bronchioles as a
consequence of inflammatory disease (lung
infections), obstruction (tumour) or congenital
abnormality (cystic fibrosis).
– Symptoms include fetid breath and coughing,
with the expectoration of mucopurulent
matter.

Lower Respiratory Tract Infections
• Emphysema - A pathological accumulation of air
in tissues or organs, because of permanent
distension of the air spaces in the portion distal
to the terminal bronchiole. Wheezing sound.
• Cystic Fibrosis - A generalised disorder of
infants, children and young adults, in which
there is widespread dysfunction of the exocrine
glands, characterised by signs of chronic
pulmonary disease (due to excess mucus
production in the respiratory tract). There is an
ineffective immunologic defense against bacteria
in the lungs.

Lower Respiratory Tract Infections
• Common Micro-organisms
– S aureus
– S pneumoniae
– Mycobacterium
– Mycoplasma

Gastrointestinal Infections
• Typhoid Fever
– An infectious illness usually spread by
contamination of food, milk or water supplies
with Salmonella typhi, either directly by
sewage, indirectly by flies or by faulty
personal hygiene.
– Fever, diarrhoeal stools (often bloody),
abdominal pain, malaise and a rose coloured
rash on the upper abdomen are seen.

Gastrointestinal Infections
• Cholecystitis - Acute or chronic inflammation of
the gallbladder
• Cholangitis - Inflammation of a bile duct
• Peritonitis- Inflammation of the peritoneum, a
condition marked by exudations in the
peritoneum of serum, cells and pus.
• Intra-Abdominal Abscess -A localised pus-
forming bacterial infection that occurs within the
abdominal cavity as the result of a perforated
viscus or post operative complication.

Gastrointestinal Infections
• Visceral abscess – Abscess in any
abdominal organ
– Hepatic Abscess
– Splenic Abscess
– Pancreatic abscess
– Renal Abscess

Gynaecological Infections
• Common Micro-organisms
– Gonococcus
– Bacteroides
– E.coli
– Chlamydia
– Streptococcus
– Klebseilla
– Enterobacter

Bone & Joint Infections
• Osteomyelitis - Inflammation of bone
caused by a pyogenic organism. It may
remain localised or may spread through
the bone to involve the marrow, cortex and
cancellous tissue

Bone & Joint Infections
• Common Micro-organisms
– S. aureus
– Salmonella
– S pyogenes

Skin & Soft Tissue Infections
• An abscess, also called a boil or furuncle, appears as a
warm, painful swelling under the skin. A carbuncle forms
when several abscesses cluster together under the skin.
These conditions can make you feel sick and cause a
fever.
• Cellulitis is an infection that spreads under the skin. It
causes redness, swelling, and pain over a patch of skin
and can cause fever, chills, and headaches. It is
commonly seen on facial skin and the legs.
• Impetigo causes sores that are itchy and slightly painful.
Sometimes it appears as a large fluid-filled blister. The
sores leak fluid and form
yellow crusts that look like scabs. Impetigo can spread to
other people and to other parts of your body.

Skin & Soft Tissue Infections
Wound infections occur when a cut or
break in the skin allows bacteria to
enter the body.

Skin & Soft Tissue Infections
• Skin ulcers, also called pressure sores or bedsores, are
areas of damaged skin caused by a lack of blood flow.
The lack of blood flow is caused by long periods of
pressure, usually from being confined to a bed or chair
and not being able to change position easily. A bacterial
infection of skin ulcers can slow healing and even be life-
threatening if it spreads in the body.
• Deep wound infections can occur as a result of deep
cuts, bites, injuries that break the skin, and incisions
(cuts) that are made during some types of surgery.
• Uncomplicated infections can become more severe. For
example, a major abscess and cellulitis may grow into
deeper tissue and require surgical treatment.

Skin & Soft Tissue Infections

Skin & Soft Tissue Infections
• Common Micro-organisms
– Staphylococcus aureus
– Streptococcus pyogenes

Post Operative Infections
• PO Wound Infections

Antimicrobial Agent And
Chemotherapy
• Chemotherapy is the treatment of disease
with chemical agents.
•Antibacterial or Antimicrobial agent is the
drug used against micro-organisms.
• An Antiseptic is usually applied to external
surfaces such as skin e.g. iodine.
• A Disinfectant is used to sterilize
instruments commonly used for surgery
e.g.carbolic acid.

Antimicrobial Agent And
Chemotherapy
• Chemotherapeutic Agents are chemical
substances synthesized in the laboratory
which can kill (bactericidal) or inhibit
(bacteriostatic) the growth of the organisms.
• Antibiotics are substances that are derived
from micro-organisms which inhibit the
growth of or kills other micro-organisms e.g.
penicillin and it’s derivatives Ampicillin,
Amoxycillin, Cephalosporins.

Antibiotic Terminology
• Bacteriostatic :- A bacteriostatic antibiotic
is one that is able to inhibit the growth or
multiplication of bacteria.
• Bactericidal :- A bactericidal antibiotic is
one that is able to kill bacteria usually
when they are in the process of
multiplication.
• M.I.C. :- (Minimum Inhibitory
Concentration) It is the smallest amount
of antibiotic required to inhibit or suppress
the growth of the bacteria.

Antibiotic Terminology
• M.B.C. :- (Minimum Bactericidal Concentration)
It is the smallest amount of antibiotic required to
destroy or kill bacteria.
• Resistance :- Bacteria that are not susceptible
to a particular antibiotic are said to be resistant
to that antibiotic.
• Cross Resistance :- Bacteria that are resistant
to one antibiotic and also demonstrate
resistance to another different antibiotic are said
to show cross resistance. (This is normally
present in antibiotics which a similar structure).
• Spectrum :- The range of bacteria against which
an antibiotic is effective is called the
antibacterial spectrum of that antibiotic.

Classification of Anti-microbial Agents
A) Chemical Structure
1. -Lactam Antibiotics : Penicillins,
Cephalosporins, Monobactams, Carbapenems
2. Tetracyclines : Oxytetracycline, Doxycycline etc.
3. Aminoglycosides : Streptomycin, Gentamycin,
Neomycin etc.
4. Macrolide Antibiotics : Erythromycin,
Oleandomycin, Roxithromycin
5. Quinolones : Nalidixic acid, Norfloxacin,
Ciprofloxacin, Pefloxacin
6. Imidazole Derivatives : Miconazole,
Ketoconazole, Clotrimazole, Fluconazole

Classification of Anti-microbial Agents
B) Mechanism of Action
1. Inhibit Cell Wall Synthesis : Penicillins,
Cephalosporins, Cycloserine, Vancomycin, Bacitracin.
2. Inhibit Protein Synthesis : Tetracyclines,
Chloramphenicol, Erythromycin, Clindamycin
3. Interfere With DNA Function : Rifampin, Norfloxacin,
Metronidazole
4. Causing Leakage from Cell Membranes :
Amphotericin B, Nystatin

Classification of Anti-microbial Agents
C) Spectrum of Activity
1. Antibacterial : Pencillins, Aminoglycosides,
Erythromycin etc.
2. Antifungal : Griseofulvin, Amphotericin B,
Ketoconazole etc.
3. Antiviral : Idoxuridine, Acyclovir, Amantadine,
Zidovudine etc.
4. Antiprotozoal : Chloroquine, Pyrimethamine,
Metronidazole, Diloxanide etc.
5. Anthelmintic : Mebendazole, Piperazine, Pyrantel
pamoate etc.

Classification of Anti-microbial Agents
D) Type of Action
Primarily Primarily
Bacteriostatic Bactericidal
Sulfonamides Penicillins Cephalosporins
Tetracyclins Aminoglycosides Vancomycin
Chloramphernicol Polypeptides Nalidixic acid
Erythromycin Rifampin Ciprofloxacin
Ethambutol Cotrimoxazole Idoniazid

Classification of Anti-microbial Agents
E. Source
Fungi Bacteria
Penicillin Polymyxin B
Cephalosporin Colistin
Griseofulvin Bacitracin
Tyrothricin
Aztreonam

Selection of an Anti-microbial Agent
• Clinical evaluation of the probable etiology
• Identification of the causative micro-organism and
antimicrobial drugs.
• Nature of the drug
• Severity of the disease and general condition of the
patient
• Risk of toxicity of the drug
• Age of the patient
• Pregnancy and neonatal period
• Possibility of drug resistance
• History of previous allergic reactions
• Cost of the therapy

Tissue and Cell Penetration
–Success of antimicrobial therapy
depends on the concentration of
antibiotics that reaches the site of
infections
–Tissue Penetration is the amount of
drug found in tissue cells and
interstitial fluid

Combination of Antibiotics
• Normally, single antibiotics are used
• Combination therapy is necessary in
patients with mixed or life-threatening
infections

Why are Antibiotics Combined?
• To achieve an additive or synergistic
effect against a single organism
• In mixed infections with bacteria sensitive
to different drugs
• To delay the development of resistance
• To decrease the adverse reactions of an
individual drug so that the dose of a drug
can be reduced
• When the infection is severe and the body
defence is poor

Beta-lactam Antibiotics
• The discovery of Penicillin by Alexander
Fleming in his London Hospital Laboratory
in 1928 was a milestone in the battle
between human and microbes
• Penicillins, Cephalosporins – A boon to
mankind

Drug enters the bacterial cell
Binds to Penicillin Binding Proteins
No transpeptidase production
MECHANISM
OF
No crosslinking of peptidoglycan chain
ACTION
OF
PENICILLINS Weak bacterial cell wall
Lysis of the bacteria

Beta-lactam Antibiotics
-Penicillins
• Penicillin G, Penicillin V
• Penicillinase-resistant Penicillins –
Methicillin, Cloxacillin
• Aminopenicillins –Ampicillin, Amoxycillin
• Antipseudomonal Penicillins - Ticarcillin

Beta-lactam Antibiotics -
Cephalosporins
• Cephalosporins appear to inhibit
bacterial cell wall synthesis in a manner
similar to that of penicillins. Structurally
they are closely related to penicillins and
belong to the same class of b-lactam
antibiotics
• First – Generation Cephalosporins
Cefzolin, Cephalexin, Cefadroxil
These cephalosporins have good activity
against gram-positive bacteria but poor
activity against gram-negative bacteria.

Beta-lactam Antibiotics –
Cephalosporins
Second – Generation
Cephalosporins
• Cefuroxime, Cefoxitin, Cefaclor,
• The second generation
cephalosporins have increased
activity against gram-negative
micro-organisms.

Beta-lactam Antibiotics -
Cephalosporins
Third Generation Cephalosporins
• Cefotaxime, Ceftazidime, Cefoperazone,
Ceftizoxime, Ceftriaxone, Cefpodoxime
• Cefixime-oral
• These antibiotics generally have
increased potency and a wider spectrum
of activity against clinically important
gram-negative bacteria. But they are
less potent than the first generation
agents against gram-positive bacteria.

Beta-lactam Antibiotics -
Cephalosporins
Fourth Generation Cephalosporins
Cefepime is considered a fourth generation cephalosporin
due to it's intrinsic antimicrobial properties. Fourth
generation cephalosporins are projected to have many
attributes including:
 extended spectrum of activity for gram negative and gram
positive organisms (different from third generation
cephalosporins)
 minimal Beta-lactamase activity due to rapid periplasmic
penetration and high penicillin-binding protein (PBP)
access
 spectrum of activity to include gram negative organisms
with multiple drug resistance patterns (Enterobacter and
Klebsiella)

The basic mechanisms by which micro-organisms
may become resistant to beta-lactams includes:
1. Beta-lactamses
2. Permeability Resistance
3. Changes in Penicillin Binding
Proteins (PBP)
4. Mixed Mechanism of Resistance

Beta-lactamase Mediated
Resistance
• Beta-lactamases are enzymes that recognize
and attack beta-lactam ring of the antibiotics
• Penicillins are hydrolysed into bacteriologically
inactive penicilloic acid
• Intact antibiotic never reaches its target proteins
in the bacterial cell wall
• Ability to produce these enzymes is now
widespread in bacteria

Approaches to Overcome Beta-
lactamase Resistance
• Development of entirely new class of
antibiotics. Eg: Quinolones
• Development of new beta-lactam
antibiotics resisting hydrolysis by beta-
lactamase. Eg: New Cephalosporins
• Development of Beta-lactamase inhibitors.
Eg: Sulbactam and Clavulanic acid

Beta-lactamase Inhibitor
• Sulbactam
– Binds irreversibly to the beta-lactamase enzymes
– Effective against Class A & C of beta-lactamases
• Clavulanic Acid
– Binds irreversibly to the beta-lactamase enzymes
– Induces production of beta-lactamase in some
organisms
– Effective against Class A of beta-lactamases

Macrolides
• Macrolide antibiotics, include
– Azithromycin
– Clarithromycin
– Dirithromycin
– Erythromycin
– Roxithromycin

Quinolones
• Quinolones include
– Nalidixic Acid
– Norfloxacin
– Ciprofloxacin
– Sparfloxacin
– Lomefloxacin
– Ofloxacin
– Gatifloxacin
– Moxifloxacin
– Pfloxacin

3 Ds of Appropriate Antibiotic Use
• The Right Drug. Use only the antibiotic that your
healthcare professional prescribed for your
condition, and not one used by another person
or for another illness.
• The Right Dose. Take the prescribed amount of
your drug at the correct times.
• The Right Duration. Even if you start to feel
better, continue taking your drug for the full
course (the prescribed number of days) to
ensure that no bacteria can survive.