MICROBIOLOGY LMR

Dr SALMAN

GENERAL MICROBIOLOGY
Tumbling motility: Listeria
Gliding motility: Mycoplasma
Swarming motility: Proteus
Darting motility: Vibrio cholera (shooting star also), Campylobacter jejuni
Stately motility: Clostridium
Cork- screw motility: Spirochetes
Falling leaf motility: Giardia

Protein A of Staph Aureus, M-protein of Strep pyogenes

Mycobacterium Tuberculosis inhibit phagosome & lysosome fusion.
Capsule / Slime layer inhibits phagocytic uptake
Capsulated Organisms: Strep pneumonia, Klebsiella pneumonia, Haemophilus influenza, Pseudomonas
aeroginosa, Neisseria meningitides, Cryptococcus neoformans, B.Anthracis
Tests: Quellung Reaction, Latex particle agglutination test, India ink stain, Mcfadyen reaction are other tests

Toxins:
Exotoxin Endotoxin
Exotoxin are protein toxin Lipopolysaccharides (LPS)
Secreted by gram ve & +ve Secreted by gram ve bacteria only
Secreted outside cell wall Structural components of OM of cell wall, released only when cell is dead or during lysis
Heat labile Heat stable
Immunogenic can be toxoided Not Immunogenic

Mechanism of toxins:
Protein synthesis : Diptheria, Pseudomonas, Shigella, EHEC
Neurotoxins: C. tetani & C. botulinum
C-AMP inducers: Cholera, Anthracis, ETEC, Pertussis
Cytotoxins: St. Aureus, C.perfringens
Superantigens: St. Aureus, Str.Pyogenes

Culture media: Basic constituents of a culture media are

Peptone digested proteins
Agar Its used to solidify the media but doesn t have nutritional properties
Simple/Basal Media: They support growth of non-fastidious bacteria Ex: Peptone water, Nutrient agar, Nutrient broth
Enriched media: When basal media is added with additional nutrients like blood, serum or egg. It supports fastidious
Enrichment broth: Liquid media allow pathogens to grown and inhibit normal flora
Ex: Selenite F & Tetrathionate broth for Salmonella & Shigella, Alkaline peptone water for Vibrio cholera
Selective media: Same as Enrichment broth but it s a solid media Ex: LJ media, TCBS etc
Transport media: Keep the delicate specimens viable or store them longer
-blair, Autoclaved sea water etc
Differential media: Differentiate between 2 groups of bacteria
Ex: Mac-Conkey LF & NLF, Acid fast AF & NAF, CLED- LF & NLF for urine specimens, Gram G+ & G-
Anaerobic media:

Bacteria Culture Media, Stains

Mycobacterium TB Lowenstein Jenson media, ZN stain
C. diphtheria Potassium tellurite agar, Lofflers Serum slope, Albert stain
Vibrio cholera TCBS (Transport VR/Cary blair)
Bordetella Pertussis Regan Lowe, Bordet Genjou
Streptococci Blood agar, (transport Pikes media for S.pyogenes)
Neisseria Thayer Martin media, Blood/Chocolate agar
Haemophilus Blood agar with Satellism, Chocolate agar
Pseudomonas Cetrimide agar, Kings media (Pyocyanin & Fluorescin)
Campylobacter, Helicobacter Campys or Skirrows agar
Leishmania Romanowosky stain, Novy-mcneal-nicolle media(NNN)

Sterilization & Disinfection

Sterilization: destroys all microbes including spores
Disinfection: destroys all microbes except spores
1. Physical methods:
Heat- kills by denaturation of proteins
Dry heat (oxidative damage): Flaming, Inceneration (for biomedical waste), Hot air oven
Moist heat (coagulation & denatures protein):
a. Temp<100 C - Pasteurization, Insipissation (For egg/serum media Ex: LJ media, Lofflers serum slope)
b. Temp at 100C - Boiling, Steaming, Tyndallization (For Sugar/Gelatin containing media)
c. Temp>100C - Autoclave
Filteration: Candle filters, Membrane filters (MC used)
Radiation
a. Ionizing radiation/Cold sterilization - Sporicidal: X,Y & cosmic rays
b. Non-ionizing radiation (Non-sporicidal): UV and IR rays
2. Chemical methods:
Alcohols- Ethyl/Isopropyl alcohol
Aldehydes- Formaldehyde, Glutaraldehyde
Halogens- Iodine (Betadine Povidone iodine), Chlorine (1% Na Hypochlorite-lab disinfectant)
Oxidising agents- Hydrogen peroxide
Phenolic compounds- Lysol (surface disinfectant), Chlorhexidine Savlon, Chloroxylenol Dettol
Surface active agent- Quarternary Ammonium compounds, Soaps
Gas- Betapropionolactone (BPL), EtO(Ethylene oxide)

Dry Heat (Hot air oven): Holding temp: 160C for 2 hours
Materials sterilized:
Glassware- syringes, petri dish, flask, test tubes
Surgical instruments- scapels, scissors, forceps
Chemical-liquid parrafin, gycerol etc
Sterilization control- Nontoxic C.tetani, B.subtilis

Moist heat <100C:

Pasteurization: used for fruit/veg juices, dairy etc.
Holder method (63C for 30 mins). Coxiella burnetti survives being heat resistant
Flash method (72C for 20 seconds followed by cooling to 13C)
All non-sporing pathogens are killed
Inspissation temp: 80-850C for 30 mins for 3 consecutive days
Tyndallization temp: 1000C for 20 mins for 3 consecutive days
Moist heat >100C (Autoclave):
Temp-121C for 15 min at pressure of 15 psi
Uses- Its used for surgical instruments and culture media & those materials that

Control- B.stereothermophilus (also for Plasma sterilization)

Prions are most resistant. Recommended methods are Autoclaving at 134C for 1-1.5 hour, NaOH for 1 hour,
0.5% Na hypochlorite for 2 hours. Enveloped viruses are least resistant
Autoclaving Culture media except LJ & LSS, all sutures except catgut
Hot air oven Paraffin, Glass syringe, Flask
Isopropyl alcohol Clinical thermometers, stethescope
Formaldehyde Operation theatre, lab fumigation
Ionising radiation (X/ rays) Plastic syringe, Catgut, Catheter, Gloves, Swabs
Filteration (Membrane filter) Vaccine, Serum, Antibiotics
Orthopthaldehyde, Glutaraldehyde Bronchoscope, Cytoscope, Endoscope
Gas sterilization (Ethylene oxide) Heat sensitive items like plastic petri dishes, syringes, Heartlung machines, Dental
equipments, Respirators

Disinfectant Enveloped Bacteria Fungi Non-enveloped virus Mycobacterium Spores

virus
High level (Plasma, EtO, Sens Sens Sens Sens Sens Sens
Aldehydes)
Intermediate level (Halogens, Sens Sens Sens Sens Sens May be
Phenolic compounds)
Low level (Alcohol, Surface Sens Sens Sens Resistant Resistant Resist
active agents, Heavy metal
salts)

MYCOLOGY
Based on morphology:
Yeast is single celled. Ex: Cryptococcus neoformans, Saccharomyces
Yeast like contains pseudohyphae. Ex: Candida albicans
Moulds have branching filaments called hyphae. Ex: Dermatophytes, Aspergillus, Rhizopus, Mucor, and Penicillium
Dimorphic fungi exist in 2 forms. Yeast like in tissues [370 C] & Filamentous forms in soil & culture [250C] Ex:
Histoplasma capsulatum, Sporothrix schenckii, Blastomyces dermatitidis, Coccidiodis immitis, Paracoccidiodis
brasiliensis, Penicillium
Dx:
Direct examination: Wet mount (10% KOH/LPCB), Gram stain, India Ink preparation, PAS, H&E, GMS
Culture:

Fungal infections
Pityriasis versicolor/Tinea Versicolor:
Caused by Malassezia furfur
KOH staining shows characteristic sphegetti & meat balls/ banana & grape appearance

Dermatophytes /Tinea/Ring Worm:

Trichophyton Microsporum Epidermophyton
Tissue involved Skin, Hair, Nails Skin & Hair Skin & Nails
Microconidia Abundant Few Absent
Macroconidia Pencil shape Spindle shape Club shaped

Tinea capitis is the ringworm infection of scalp

Favus: crusty/scaly lesions by T.schonleinii
Kerion: swelling by T.mentagrophytes/verrucosum
Tinea barbae is seen in beard area, Tinea cruris involves groin area, Tinea pedis is infection around foot,
Tinea unguam is infection around nail
Sporotrichosis ( :
Caused by Sporothrix schenckii that presents with ulcers along the lymphatics and LN enlargement
Dx: On H& E Yeast form shows Cigar shaped asteroid bodies

Mycetoma:
Presents as swelling of foot, with sinuses discharging pus that contains granules
Actinomycotic/Bacterial (Actinomadurae, Nocardia)
Eumycotic/Fungal (Fusarium, Acremonium, Madurella species)
Botryomycosis mimics mycetoma caused by S.Aureus
Dx: Diagnosis is made from examination of granules
Eumycotic: black-brown (madurella), white (Fusarium, Acremonium)
Actinomycotic: white-yellow except Actinomadurae pelletri (red)

Chromoblastomycosis:
By Dematiaceae group (dark pigmented fungi) Ex: Phialophora, Cladophialophora
It causes Verrucous type lesions
Dx: On H&E: show Sclerotic/Medlar bodies that has Copper penny or Muriform appearance

Rhinosporidiosis: Strawberry/mulberry like polypoidal mass

Acquired by inhalation of spores from soil/dust contaminated with birds/bats droppings

yeast forms: narrow based budding
mold forms: tuberculate macroconidia

Coccidiomycosis/ Desert rheumatism/San Joaquin valley fever

yeast form: thick double walled spherule, filled with endospores
mold form: barrel shaped arthroconidia

Broad based budding with figure of 8 appearance

Paracoccidomycosis/South American Blastomycosis

Yeast forms show Captain/Pilot wheel/Mickey mouse appearance

Candidiasis
C.albicans (MC), C.krusei, auris are resistant to conazoles
Predisposing factors: Diabetes, AIDS, Pregnancy, Infants & elderly, prolonged administration of antibiotics,
patients on immunosuppressive drugs
Dx:
o Pse
o Chlamydospore formation on corn meal agar
o -D-glucan assay

Cryptococcosis
Acquired by contaminated soil from pigeon droppings
Meningitis in AIDS patients
India ink staining (negative staining)/Nigrosin stain for the capsule

Pneumocystis jiroveci [Pneumocystis carinii pneumonia]

Produces Plasma cell pneumonia in AIDS
On GMS: cyst (black), trophozoite (green)

Aspergillosis:
A.flavus- Aflatoxin, A.niger - Otomycosis
A.fumigatus - Allergic Broncho pulmonary aspergillosis [ABPA], Fungus ball/Aspergilloma, Otomycosis,
Oculomycosis
Dx: It shows septate hyphae with dichotomous branching (450 angle)
Mucormycosis / Zygomycosis:
Rhizopus (MC), Mucor, and Absidia are the common agents
Its angioinvasive tissue necrosis black colour
Predisposing factors: Diabetic ketoacidosis [DKA], Malignancies, Iron chelators, Steroids
It can cause ROCM (Rhino-orbital cerebral mucomycosis)
Dx: Broad aseptate ribbon like hyphae

PARASITOLOGY
Entamoeba histolytica:
Infective form is Quadrinucleate cyst by feco-oral route. Its causes amoebic dysentery
Classical lesion is inverted flask shaped ulcers with anchovy sauce

Giardia lamblia:
Transmission is by Quadrinucleate cysts through feco-oral route
It causes fatty foul smelling diarrhea and fat malabsorption (steatorrhea)
Trophozoite (tennis racket or tear drop shaped) or cysts in the stool for Dx, String/Entero test to demonstrate
trophozoites, Falling leaf motilityQ

Cryptosporidum, Cyclospora & Isospora:

Diarrhea in AIDS patients
Oocysts/Cysts are infective, For Dx Modified Acid fast (Kinyoun) oocysts are +ve

Naegleria fowleri:
It causes Primary Ameobic meningoencephalitis which presents with high fever, altered smell. Often fatal
acquired while swimming in fresh water

Acanthamoeba: It causes Keratitis in contact lens users.

Trichomonas vaginalis:
No cyst stage, only trophozoite which are sexually transmitted
It causes trichomoniasis with frothy vaginal discharge
Trophozoites with twitching/cork screw motility seen for Dx

Leishmania Donovani:
It causes Visceral Leishmaniasis or Kala azar which presents with Fever, Hepato-splenomegaly,
Hyperpigmentation, Pancytopenia, Hypergammaglobulinemia
Humans get infected with bite of a sandfly releasing promastigote forms that turns into amastigote forms in
human body and start replicating
Dx: Romanowosky stain, Novy-mcneal-nicolle media(NNN),
Compliment fixation test with WKK antigen, RK-39 antigen test by card method Q
Chopras antimony test/ Napiers aldehyde test for hypergammaglobulinemia
Montenegro skin test (Type IV HSN), LDQ bodies on biopsy

Trypanosoma Cruzi:
It causes Chagas diseaseQ (American trypanosomiasis) that presents with swelling around eyelid (Romana sign)
and Myocarditis, Megacolon, Megaesophagus, Chagoma (swelling at entry point)
Its transmitted by Reduviid bugQ (kissing bug) that transmits the trypomastigote forms
Dx is done with tryposmastigote forms in blood films

Trypanosoma Brucei: It causes sleeping sickness transmitted by tsetse fly (glossina species). It causes cervical
Q

Plasmodium
P. Vivax, P. Ovale, P. Falciparum Tertian fever
P. Malariae Quartan fever
P. Knowlesi Quotidian fever
Infective stage: Man: Sporozoite Mosquito: Gametocyte
Definitive host: Female anopheles mosquito Intermediate host: Human
Characteristics Vivax Falciparum
RBC Enlarged Not Enlarged
Accole forms Not seen Seen
Shape of gametocyte Circular/oval Banana/Crescent
Dots Maurer
Trophozoite Single large ring Multiple rings

Babesia:
It causes babesiosis which is hemolytic, malaria like disease
Giemsa stain shows maltese cross Q

Toxoplasma gondi: Def host cat, Intermediate host - Man

Congenital toxo presents with intracerebral calcifications, chorioretinitis, hydro/microcephaly
In AIDS patients it causes ring enhancing lesions and seizures

Trematodes(flukes): requires 3 hosts

Q
Intermediate host: 1st Snail, 2nd Aquatic plants,Cray/Crab fish. Def host: Man
Q
Infective stage: ingestion of Metacercaria larva for all except Schistosomes which is by skin penetration of
Cercaria larva present in contaminated water

Schistosoma Hematobium (blood fluke):

It causes shistosomiasis or bilharziasis. Symptoms associated are Allergic dermatitis d/t cercariae known as
swimmers itch. Symptoms d/t Eggs are Egg granuloma and Hematuria
It causes bladder cancer (Squamous > Transistional)
Dx for Schistoma species is done by demonstration of non operculatedQ eggs in stool or urine(hematobium).
Q*
Eggs with terminal spine (hematobium), lateral spine (mansoni), lateral knob (japonicum)
Q
All trematodes have operculated eggs (with lid) with no spine except Schistosomes who have non
operculated eggs with spines or knob

Cestodes
Taenia saginata: Intermediate host - cattle, Def host- man
Transmission is by ingesting cysticercus in uncooked beef not by ingestion of eggs
Dx is by proglottids / eggs in faeces (hexacanthembryo)
Taenia solium: Intermediate host - Pig, Def host - man
Transmitted by ingesting uncooked pork containing cysticercus causing diarrhea
Cysticercosis: transmitted by ingesting eggs in contaminated food & water. It may develop to
Neurocysticercosis which is a very common cause of seizuresQ in India

Echinococcus granulosus (Dog tapeworm): Intermediate host Man, Def host - Dog
Acquired by ingestion of eggs
It causes Hydatid cyst disease. It can involve liver and lungs. Casonis test can be done for Dx

Hymenolepis nana (Dwarf tapeworm):

Dx Non bileQ stained eggs containing central hooks and polar filaments Q

Nematodes
Transmission by eggs: Enterobius, Ascaris, Trichuris (Mnemonic EAT)
Transmission by penetration through foot, maturing in lungs: Strongyloides, Ancylostoma, Necator (Mnemonic SANd)

Enterobius vermicularis (Pin/Thread/Seatworm):

MC effect children causing perianal itching
Dx demonstration of eggs by non-bile stained eggs with tadpole shaped larva by taking a NIH swab of perianal
area by scotchtape

Trichuris trichuria (whipworm):

Its associated with rectal prolapse. Dx is by Qbarrel/dumbell shaped eggs

Ascaris lumbricoides: MC helminth worldwide and largest roundworm.

Necator Americanus (New world hookworm): Bloodsucking (0.03 ml/worm/day) leads to Anaemia

Ancylostoma duodenale (Old Hookworm):

Cutaneous larva migrans (MC seen with Ancylostoma braziliense)
Visceral larva migrans seen with Toxocara Canis, catis
Adult worm causes Iron deficiencyAnemia, blood loss (0.20 ml/worm/day)
Q
: no of hookworm eggs present per gram of faeces in population (<200 eggs is not of much
significance, >300 eggs is important health problem)

Strongyloides stercoralis: No male worms

Wuchereria bancrofti:
L3 filariform larvae transmitted by Culex(mainly), Aedes, Anopheles mosquito
Filariasis: causes fever, lymphadenitis whereas Chronic causes QElephantiasis, Hydrocele
Dx Blood smear exam (collected at night d/t nocturnal periodicity). Examination of micofilarial tail tip Q (No
nuclei in Wuchereria, 2-3 terminal nuclei in Brugia malayi)

VIROLOGY
Size of viruses: Largest Pox (300 nm), Smallest Parvo (20 nm)
Viral structure: Nucleocapsid
DNA viruses- Herpes, HBV, Adeno, Papova, Parvo& Pox
RNA viruses others
All the RNA viruses are single stranded except Reoviruses
All the DNA viruses are double stranded except Parvoviruses
Non-Enveloped virus:
Alcohol resistant, heat stable
DNA Parvo, Adeno, Papova (PAP)
RNA Picorna, Astrovirus, Calcivirus, Reovirus

Herpesviridae
Properties HSV-1 HSV-2
Transmission Direct contact with mucosa/abraded skin Sexual/ Vertical mode
Latency Trigeminal ganglia Sacral ganglia
Clinical manifestations Herpes labialis (MC), Dendritic ulcer, Encephalitis (temporal lobe), Meningitis Genital lesions
Neonatal herpes

Varicella Zoster
Chicken pox Herpes Zoster (Shingles)
Primary infection Reactivation of latent virus
MC site- spinal cord Trigeminal nerve (Opthalmic branch)
Generalized & bilateral Segmented & unilateral
Child > adult (severe) Old age

Cytomegalovirus (CMV)
Congenital: Hepatosplenomegaly, Petechiae, Microcephaly and Cerebral calcifications
Immunocompetent: Mononucleosis like syndrome
Immunocompromised: MC viral infection in organ transplant patients, In HIV it causes chorioretinitis
Dx:

Ebstein Barr virus (EBV)

EBV is transmitted through salivary secretions
It binds to CD 21 or Complement receptor 2 (CR2) on B cells
Clinical manifestations:
Dx: Paul-Bunnell test (Heterophile test)
Other manifestation are Hairy cell leukoplakia and Duncan syndrome (lympho-proliferative disorder)

HHV 6: Sixth disease/ Exanthem subitum/ Roseola infantum

HHV 8:

Poxviridae
Molluscum contagiosum:
Presents as wart like lesions
Dx Molluscum/Henderson Paterson bodies intracytoplasmic eosinophilic inclusions

Parvovirus B19
Smallest, naked, ss DNA virus
Diseases caused:
5th disease/ Erythema infectiosum- Slapped cheek appearance
Aplastic crisis in sickle cell anemia patients, Non-immune Hydrops fetalis

Human papilloma virus

1-4: Warts, 5: Epidermoplasia verruciformis
6,11: Anogenital warts (Condyloma acuminata), laryngeal warts
16,18,31,33,45,52,58: Carcinogenic. E6 (P53) & E7 (RB) facilitates in that

Orthomyxovirus (Influenza)
Influenza virus has ss-negative sense RNA virus (8 segments) that replicates in nucleus
It possess two glycoprotein antigens in the lipid envelope i.e HA (1-18) & NA (1-11)
Hemagglutinin It binds to mucin or sialic receptors on RBC causing clumping of RBC (Hemagglutination). It
facilitates viral entry
Neuraminidase Its sialidase enzyme that displaces HA from RBC reversing Hemagglutination k/a elution.
Facilitates viral release from infected cell surfaces

Paramyxoviruses
Parainfluenza virus: It s the MCC for croup (laryngotracheobronchitis)
Mumps virus: Inapparent infection>Parotitis>Orchitis is the MC presentation

Measles (Rubeola) virus

3C: Cough, Coryza, Conjunctivitis,
Complications
Secondary bacterial infections like otitis media and pneumonia are common
Subsclerosing pan encephalitis (SSPE) is the most severe complication
Dx: Multinucleated giant cells (Warthin Finkeldey cells)

Respiratory syncytial virus

Infants
Adults Influenza like URTI and causes exacerbation in COPD and Asthma
Dx characteristic syncytium formation (multinucleated giant cells)

Rubella (German measles)

It belongs to Togaviridae
Rash on day 1 on the face which lasts for 3 days, Lymphadenopathy and Forchheimer spots
Congenital rubella syndrome classical triad of Ear- Nerve deafness, Eye retinopathy, Cataract, Heart- PDA

Features HAV HBV HCV HDV HEV

Family Picorna Hepadna Flavi Calici
Route Feco-oral Sexual (MC), BT*, Parenteral Parenteral (MC), Parenteral Feco-oral
Vertical BT
Fulminant hepatitis 5-20% (superinfection) Preg - 20%
Chronicity 1-10% 90%
Oncogenic Nil Present Present Nil Nil
S gene it codes for HBsAg
C gene Pre C codes for HBeAg, C codes for HBcAg
X gene contributes to carcinogenesis by binding to p53
P gene DNA polymerase, RT, RNase activity
Refer to Hep B serology taught in class*

HIV
MC HIV in India HIV-1 Group M, Subtype C
Env (gp 120,41), Pol (RT), Gag (P24)
Sexual transmission is the MC route and Blood transfusion is the least common route
o CD4 (500-200)
o CD4 (200) PCP, Toxoplasmosis, Cryptococcosis
o CD4 (50) MAC, CMV, Lymphoma
Dx:
Recent H/O exposure or Window period P24 Ag detection (+ve by day 16)
Most sensitive test ELISA (4th gen) that can detect Antibodies against HIV-1 & HIV-2 and P24 Ag
Specific or confirmatory test Western blot
Best to determine viral load Detection of HIV RNA by NAAT(PCR)
In children HIV DNA by PCR

Picornaviruses
Rhinoviruses: It s the MCC of common cold

Coxsackie virus A Coxsackie virus B

Herpangina(Vesicular pharyngitis) Pancreatitis leading to DM
Hand foot and mouth disease (Also by Enterovirus 71) Myocarditis, Pleurodynia(Epidemic myalgia/Bornholm
Acute hemorrhagic conjunctivitis (also by Enterovirus 70) disease)

Dengue fever
-5), Aedes is the main vector
Pathogenesis: Primary dengue infection followed by secondary dengue infection due to Antibody dependant
enhancement (ADE)
Clinical manifestation:
Dengue (breakbone/saddleback/biphasic) fever High fever, Rash, Frontal headache, joint pains
Dengue hemorrhagic, Dengue shock syndrome
Dx:
ELISA is the most recommended test with good sensitivity and specificity (IgM-5days, IgG- 14 days)
NS-1 Ag detection Advantage is early detection (1st day of fever), and high specificity

Japanese Encephalitis
Culex mosquito serves as a vector. Pigs serve as an amplifier hosts

Zika virus
Its ss RNA virus that belongs to Flaviviridae and related to other virus of same family like Dengue
Transmission: Aedes mosquito (MC), Mother to child, Sexual

Rabies virus
Structure: Has Nucleoprotein, Glycoprotein G Ag
Pathogenesis: Binds to Ach receptors and spreads to CNS via peripheral nerves
Dx:
Antemortem
Sample: Hair follicles of nape of neck, Cornea
Test: DFAT (Nucleoprot Ag), PCR
Postmortem
Detect Negri bodies (Cerebellum-
Category Type of Exposure Management
I (No risk) Touching animal, Licks on intact skin No treatment needed
II (Minor risk) Minor abrasions without bleeding Local treatment
Rabies vaccine
III (Major risk) Bite with bleeding, Licks on abrasions, Bite by wild animals/bats Local treatment
HRIG
Vaccine

BACTERIOLOGY
Staphylococcus Epidermidis:
Normal Flora of skin. Coagulase ve, Novobiocin Sensitive. It produces a biofilm
MC pathogen causing endocarditis (prosthetic valves), infections in patients on catheters, cannula
Staphylococcus Saprophyticus:
It novobiocin resistance, Coagulase ve
It produces UTI in sexually active females
Staphylococcus Aureus:
Catalase (+), coagulase (+)
Its normal flora in the nose (MC site), Skin (MC route of spread is hands of healthcare workers)
Virulence: Prot A (Cowan-1 strain), Leucocidin (Panton-Valentine), Heat stable Nuclease or DNase
Diseases caused:
Org mediated: MCC of Acute endocarditis, Acute osteomyelitis, Pneumatocele, Skin & soft tissue infections
like Furuncles, Carbuncles, Boils, Bullous Impetigo, Surgical wound infection, Breast abcess, Mastitis and
Botryomycosis. It also causes Nosocomial pneumonia.
Toxin mediated: Food poisoning (Enterotoxin), TSS (Toxic shock syndrome toxin -TSST, Staphylococcal
scalded skin Syndrome (Exfoliative/Epidermolytic toxin)
Dx:
Nutrient Agar- Golden yellow colonies, Blood Agar Beta hemolysis
Selective media Mannitol salt agar, Ludlams medium
Methicillin resistance Staph Aureus [MRSA] MRSA is d/t mutation in mec-A gene
For Dx of MRSA PCR for mec-A gene (best), Cefoxitin test >> Oxacillin test

Streptococcus Pneumoniae/ Pneumococcus/ Diplococcus:

Capuslated, IgA producing Lancet/Flame shaped organisms
Dx: Draughtsman/ Carrom coin colony on blood agar

Streptococcus Viridans:
Catalase ve, alpha hemolytic, optochin resistant, bile insoluble
Strep mutans causes dental caries(MC) & produces biofilm
Strep Virdans (sanguis) is MCC of sub acute bacterial endocarditis

Streptococcus Pyogenes (GAS):

It is Beta-hemolytic, bacitracin sensitive, PYR+ve.
Lance field groups (A-V): based on carbohydrate antigen of cell wall
Griffith types (>100): based on M-proteins
Diseases caused:
SPE/Erythrogenic/Dick toxin Scarlet Fever, Streptococcal TSS
Pharyngitis (Sore throat), Skin/Soft tissue infections (Impetigo, Cellulitis, Erysipelas, Necrotising fasciitis).
Pharyngitis and SSTI can complicate as Acute Rheumatic fever (ASO titre >200 unit/ml), Acute glomerulo-
nephritis [PSGN]- Anti DNase B (>300 units/ml)

Streptococcus Agalactiae (GBS):

Reservoir is birth canal
Diseases caused: MCC of neonatal meningitis worldwide
Dx: Beta hemolytic, Bacitracin resistant, CAMP +ve, Hippurate test +ve

Enterococcus
Important species are E.faecalis (MC to cause infections), E.faecium (drug resitant)
It causes UTI, Endocarditis (Left sided-i.v drug abusers), Peritonitis etc
Dx:
Enterococcus grows in 40% bile, grows in 6.5% Nacl, PYR +ve
Bile aesculin test+ve (hydrolyses aesculin-turns agar black)
Bacillus Anthracis:
Spore forming (non-bulging), aerobic bacillus.
Virulence factors: Capsule made of polypeptide [D-glutamate] & Toxin (made of 3 factors)
o Edema factor that acts by cyclic-AMP, Lethal factor causes cell death, Protective antigen
Anthrax types:
: Malignant Pustule: Painless black necrotic eschar
: Hemorrhagic pneumonia
Dx:
Bamboo stick appearance, Medusa head colony, Christmas tree/Inverted fir tree appearance, String of pearl
appearance

Bacillus Cereus: Chinese fast-food poisoning

Clostridum Tetani:
obligate anaerobe producing terminal spherical-drum stick appearance spores (Other Clostridiums
subterminal spores). Toxin: Tetanospasmin- inhibits the release of GABA/Glycine
Dx:

Clostridium Botulinum:
Botox is coded by a prophage, acts by the release of Ach & is most potent bacterial toxin known

Clostridum Perfringens:
Gas Gangrene:
It caused by C.perfringens, C.Novyi, C.septicum
Its due to Alpha toxin (Lecithinase or Phospholipase C)
Dx: Stormy fermentation in milk media, ,
Reverse CAMP test +

Clostridium Difficile: Its responsible for antibiotic associated diarrhoea & pseudomembranous colitis

Corynebacterium diptheriae (Kleb-Loffler bacillus):

Diptheria is toxemia that acts by protein synthesis by ( EF II). Effects i.e localized (respiratory) and
systemic (damage heart, neuropathy) are toxin mediated
Diptheria: Faucial type (MC): Dirty pseudomembrane, Bull neck appearance, Myocarditis. Cause of death is
circulatory failure. Most severe type is laryngeal type of diphtheria
Dx:
Chinese letter or Cuneiform arrangement
Albert stain energy granules k/a Metachromatic/Volutin/Babes-Ernst/Polar bodies
enriched media detects growth in 6-8 hours

Listeria:
Pregnancy: leads to abortions or stillbirths
Meningitis (neonates, old age)
Dx:
Differential motility: Show tumbling motility at 25° and non-motile at 37°
Anton test, CAMP and Catalase test +ve

Actinomyces Nocardia
Anaerobic Aerobic
Normal flora of Gingiva -
Cervicofacial (lumpy jaw), Brain abcess, Actinomycetoma Pneumonia, Brain abcess, Actinomycetoma
Gram+ branching filamentous, HPE: Sunray appearance Gram+ branching filamentous, Partially acid-fast

Mycobacterium tuberculosis: Acid fast, obligate aerobe

Virulence factors: Lipoarabinomannan (LAM): impairs phagosome lysosome fusion
Dx:
Microscopy:
Acid fast stain by ZN method (heating needed)/Kinyoun (Cold method heating not needed)
Auramine-Rhodamine fluorescent dye
Culture:
Solid: Egg containing - LJ & Dorset medium, Agar Middle Brook medium
Liquid: Bactec (BacTalert, MGIT)
MPT-64 Ag test
Molecular: PCR
CBNAAT/Gene Xpert/ Gene Xpert-Rif: Rifampicin resistance can be detected
Line probe assay: Shows Multiple drug resistance can be detected

Mycobacterium Leprae ( :
Ridley & Jopling classification: TT, BT (MC in India), BB, BL, LL
Symptoms of leprosy are confined to skin & nerves. MC nerve involved is Ulnar and Cranial is Facial
Tuberculoid Leprosy (paucibacillary) Lepromatous leprosy (multibacillary)
Mild Severe
Strong CMI Weak CMI
Few lesions Multiple lesions
Lepromin test +ve Lepromin test -ve

Type I lepra reaction Type II lepra Reaction

Type IV hyper-sensitivity (Th1 predominance) Type III hypersensitivity (Th2 predominance)
Seen in border line leprosy (BB) Seen in lepromatous leprosy (LL)

Dx:
o Smear microscopy: ZN staining show globi (cigar bundle appearance) that are present in macrophages k/a
Foamy cells
o Culture: not cultivable in artificial media, but can be inoculated into armadillos, footpad of mice

Neisseria meningitidis:
Virulence: Capsule, IgA protease, Secretes Endotoxin
Meningitis: Fever, chills, nuchal rigidity, rash*
Complication: Water-
Dx:
Microscopy: lens shaped gram -ve diplococci, latex agglutination for capsule
Culture: CSF/Blood
o Blood / Chocolate agar
o Selective: Thayer-Martin or Modified New-York media
Biochemical: Oxidase +ve, Ferments maltose and glucose

Neisseria Gonorrhoea:
Virulence: Pili, IgA proteases, Outer membrane porins (OMP), Lipoligosaccharide (LOS)
Disease Caused:
Males: Urethritis (MC) Complication: Watercan Perineum
Females: Cervicitis (MC) Complication: Fitz-Hugh Curtis syndrome
Neonates: Opthalmia neonatorum
DGI (disseminated gonococcal infection): polyarthritis
Dx:
Microscopy: kidney shaped gram -ve diplococci
Culture:
o Chocolate agar, Mueller-Hinton agar
o Selective: Thayer-Martin or Modified New-York media
o Transport media Stuarts and Amies media
Biochemical: Oxidase +ve, Ferments glucose

Requires Factor V (NAD) & Factor X (Hemin) for its growth

Grows on Chocolate agar, Blood agar with Satellism
Haemophilus Ducreyi:
Disease: Chancroid (Painful)
Dx: School of fish, Tram-track, Safety-pin appearance

Treponema Pallidum:
10:Chancre (Painless), 20: Condyloma latta, Rash (copper), 30: Tabes dorsalis, Aortitis, Gummas
Dx: Dark field microscopy: Corkscrew motility
Serology: detect Ab
Non-treponemal: VDRL (for Neurosyphilis), RPR
Treponemal: Sensitive - FTA-ABS, Specific TPHA, TPI
Jarish-Herxheimer reaction seen

Borellia burgdoferi -

Chlamydia trachomatis (Energy parasite):

Obligate
Exist as Elementary body, Reticulate body
Dis: A-C: Trachoma, D-K: Genital (Urethritis), L1-L3: LGV

Cell wall is absent, Cell membrane contains Cholesterol

Culture: Fried egg col

Campylobacter Jejuni:
Transmission: Undercooked poultry. It requires low infectious dose and produces inflammatory diarrhea with
abdominal pain, fever and bloody stools
Extra-intestinal: Reactive arthritis and triggers Guillain-Barre syndrome
Dx: Gram staining: seagull wing appearance, darting motility. Transport media- Cary blair media
Culture

Enterobacteriaciae
They are Catalase +ve, Oxidase ve, Motile (except Shigella,Yersinia, Klebsiella), Nitrate to nitrites, Ferment
glucose
Lactose fermenters Non- Lactose fermenters
Citrobacter, Enterobacter, Escherichia, Klebsiella Shigella, Yersinia (Non-motile, No H2S prod)
Proteus, Salmonella ( Motile, H2S prod)

E.Coli:
Diseases caused by E.coli:
), Neonatal meningitis, Abscess, Peritonitis, Ventilator associated Pneumonia,
Scromboid fish poisoning, Diarrhea
Diarrheal strains:
ETEC:
EHEC (O157 H7): Verotoxin (shiga like) toxin blocks protein synthesis by binding to 60s ribosome and
require low infectious dose. Complications: Hemorrhagic colitis, Hemolytic uremic syndrome
UTI Dx:
Gram stain shows one bacilli/HPF indicative of UTI (Culture by CLED/Mac-Conkey is confirmatory)
Quantitative count by Kass criteria - 105 colonies/ml of urine is diagnosed as UTI

Klebsiella:
Klebsiella pneumonia -currant jelly sputum)
K.granulomatis (Calymmatobacterium granulomatis): Granuloma inguinale/venerum/Donovanosis which
presents with painless, beefy-red ulcer

Shigella:
They are gram ve, oxidase ve rods that ferment mannitol
MC Shigella worldwide is by Shigella sonnei (late lactose fermenter), in India its Shigella Flexneri
Most Severe Shigellosis is caused by Shigella Dysentery type 1.
Pathogenesis: It invades through M cells and requires low infectious dose. Shiga toxin is an exotoxin produced
by S.Dysenteriae type 1. It blocks protein synthesis by binding to 60s ribosome
Complications: HUS and HC, reactive arthritis
Dx: Transport media
Culture media (same for Shigella and Salmonella) are selective media like DCA (deoxycholate citrate agar),
XLD(Xylose lycine deoxychol), SS, HE(Hektoen Enteric) agar

Salmonella:
Typhoidal Salmonella are is S.typhi and S.paratyphi A & B
MOT: F/O route, requires high infectious dose & invade through M cells & Vi Ag plays role in virulence. Risk
factor is gastric acid
Enteric Fever presents with Step-
Dx:
1st week
2nd week- Agglutination test (Widal test)
3rd week- Stool culture
4th week- Urine culture (Wilson blair is the best media Jet black colonies seen)
Widal test (tube agglutination test):
o Ag is less immunogenic (O agglutinin titer >100) forms granular chalky clumps
o H Ag is more immunogenic (H agglutinin titer>200) forms fluffy cotton-wool clumps

Yersinia pestis:
Reservoir: Rodents. Transmission: bite of infected rat flea i.e Xenopsylla Cheopis
Bubonic Plague: MC plague characterized by regional bubos (MC inguinal LN)
Pneumonic Plague: It spreads from inhalation of bacilli from infected person/animals
Septicemic Plague:
Dx:
Wayson/Methylene blue stain demonstrate bipolar staining
On blood agar forms Dark Brown colonies
On nutrient broth with Oil/Ghee shows Stalactite growth

Proteus mirablis,vulgaris:
It causes UTI with alkaline urine (Urease +ve) which precipitates to form struvite stones/staghorn calculi.

Produces swarming motility and fishy odor on media

P.Vulgaris Ox (2,19) and P. Mirablis (Ox K) strain forms basis of Weil-Felix reaction (Heterophile)

Gardnerella:
riteria for Dx of Bacterial vaginosis:
White-grey fluid discharge from the vagina
Vaginal discharge pH >4.5
Whiff Test: Fishy odor by addition of 10% KOH to vaginal sample
Clue cells- vaginal epithelial cells coated with bacilli

Vibrio Cholera:
Serogroups based on somatic O. O1 serogroup has 2 biotypes Classical and Eltor and 3 Serotypes namely
Ogawa, Inaba and Hikojima
Cholera:
Transmission is by f/o route and is toxin mediated, requires high infectious dose
Presents with sudden onset of painless non-inflammatory diarrhea with rice watery stools
Dx:
Transport media Cary Blair or VR media
Gram staining shows comma shaped rods with darting/shooting star motility
Culture media- Alkaline bile salt agar (BSA), TCBS (best)
String test: Bile salt added to stool sample, when trying to lift with loop, string formation seen

Pseudomonas Aeroginosa:
Gram ve aerobic, oxidase +ve (change of color from white to blue), capsulated bacillus
Pseudomonas exotoxin A acts by inhibiting elongation factor EF II & inhibition of protein synthesis.
Diseases Caused:
MCC of
Ventilator associated pneumonia, Cystic fibrosis, Shanghai fever
Its catalase +ve so it causes infection in Chronic Granulomatous disease
Ecthyma Gangrenosum (black necrotic lesion seen in AIDS), MC infection in burn patients
-op patients
Green nail syndrome paronychia from prolonged submersion in water
Dx:
It produces pyocyanin (blue), pyorubin(red), pyoverdine (yellow green) pigments
Selective media- Cetrimide agar

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