○​ Community-acquired​

INFECTIVE ○​ Healthcare-associated​

ENDOCARDITIS
(IE) Morphology (not needed here
since bacteria; given only for
viruses/protozoa)
Name of Disease
●​ Infective Endocarditis​ Pathogenesis
1.​ Endothelial damage of valves (due
Causative Organism to turbulent blood flow, congenital
defects, prosthetic valves).​
●​ Common: Viridans group
streptococci (Streptococcus 2.​ Platelet & fibrin deposition →
sanguis, S. mutans, S. mitis, S. sterile vegetation.​
bovis)​
3.​ Bacteremia (from dental
●​ Others: Staphylococcus aureus, procedures, IV drug use, catheter,
Enterococci, HACEK group infection focus).​
organisms, Coagulase-negative
staphylococci​ 4.​ Microbes adhere via surface
adhesins (e.g., dextran of Viridans
streptococci).​

5.​ Proliferation within vegetations →

Classification (Based on Etiology protection from host immunity &
& Clinical Course) antibiotics.​

●​ By onset:​ 6.​ Vegetations grow → valve

destruction, embolization, immune
○​ Acute IE → Staphylococcus complex formation.​
aureus (rapid, destructive)​

○​ Subacute IE → Viridans
streptococci, Enterococci​
Risk Factors
●​ By valve involved:​
●​ Pre-existing valvular heart disease
○​ Native Valve IE​ (RHD, congenital defects)​

○​ Prosthetic Valve IE​ ●​ Prosthetic heart valves​

●​ By setting:​ ●​ Intravenous drug abuse​

 ●​ Long-term intravascular catheters​
Laboratory Diagnosis
●​ Immunosuppression​

Specimen
●​ Blood (most important)​
Mode of Transmission
●​ Not person-to-person​ Possible specimens:

●​ Entry via bacteremia from:​ ●​ Blood (multiple samples)​

○​ Dental extraction, oral sepsis​ ●​ Excised valve tissue (in surgery)​

○​ Skin infections, IV drug use​

Method of Collection:
○​ Urogenital or GI procedures​
●​ 3–6 blood cultures collected from
different sites over 24 hrs (before
starting antibiotics).​

Sequence of Events Leading to Method of Transport & Preservation:

Disease – FLOWCHART
●​ Inoculated directly into blood culture
Endothelial injury → Platelet-fibrin thrombus bottles with broth media.​
→ Bacteremia → Microbial adherence to
thrombus → Vegetation formation → Valve ●​ Processed immediately; if delay →
destruction + Embolization + incubate at 37°C.​
Immune-mediated injury

Clinical Features Microscopy

●​ Acute IE (Staphylococcus aureus): ●​ Direct smear from blood → not
High fever, chills, new murmur, rapid useful (low yield).​
heart failure, embolic events.​
●​ Gram stain from excised
●​ Subacute IE (Viridans streptococci): vegetation/valve tissue may show
Low-grade fever, fatigue, weight organisms.​
loss, anemia, prolonged illness.​

●​ Peripheral signs: Osler nodes, Gram smear findings:

Janeway lesions, Roth spots,
splinter hemorrhages.​ ●​ Streptococci/Enterococci →
Gram-positive cocci in chains.​
 ●​ Staphylococcus aureus → ●​ Culture colonies → Gram stain,
Gram-positive cocci in clusters.​ biochemical tests.​

●​ HACEK group → Small

Gram-negative bacilli.​ Biochemical Tests:

●​ Catalase (Streptococci −ve,

(Draw diagrams of cocci in clusters vs Staphylococci +ve).​
chains for exams.)
●​ Coagulase (S. aureus +ve).​
Special Stains
●​ Optochin sensitivity (S. pneumoniae
●​ Silver stain (for bacteria in tissue +ve, Viridans −ve).​
sections).​
●​ Bile esculin & salt tolerance
(Enterococci +ve).​
Motility – Not applicable for
streptococci/staphylococci.
Automated Identification

●​ MALDI–TOF, VITEK 2.​

Culture
●​ Blood Culture = Gold standard.​

●​ Positive in >90% cases if no prior Special Tests

antibiotics.​
●​ Duke’s criteria include blood
culture positivity &
Culture Media: echocardiographic evidence.​

●​ Enrichment broth in automated

blood culture systems.​

●​ Chocolate agar, Blood agar (for Serology

HACEK, streptococci,
staphylococci).​ ●​ For culture-negative cases:​

○​ Coxiella burnetii – IgG phase

Enrichment broth – Brain heart infusion I antibody by ELISA/IFA.​
broth.​
Transport media – Not used (blood ○​ Bartonella spp. – Serology
inoculated directly).​ helpful.​
Selective media – For HACEK if needed.​
Differential media – Blood agar
(hemolysis patterns).

Molecular Methods
Identification
 ●​ PCR (16S rRNA gene amplification) ○​ Enterococcal: Ampicillin +
for culture-negative cases.​ Gentamicin.​

●​ Surgery if uncontrolled infection,

abscess, prosthetic valve failure.​

Non-specific Findings
●​ Normocytic normochromic anemia​

●​ Raised ESR, CRP​ Prophylaxis

●​ Microscopic hematuria​ ●​ Antibiotic prophylaxis before
dental or surgical procedures in
high-risk patients (prosthetic valves,
previous IE, congenital heart
disease).​
Antimicrobial Susceptibility ○​ Amoxicillin oral (first choice).​
Testing (AST)
●​ No vaccine available.​
●​ Performed on cultured isolates →
guides therapy.​

●​ Disc diffusion/E-test/automated MIC

detection.​ ​
You asked for Rheumatic Fever, which is
not a direct bacterial infection, but rather
a post-infectious, immune-mediated
complication following Group A
Typing Methods Streptococcal (Streptococcus pyogenes)
throat infection.
●​ Molecular typing (PFGE, MLST) in
research/outbreak settings.​ So, the causative organism is
Streptococcus pyogenes, but the disease
itself is due to an autoimmune reaction,
not direct bacterial invasion.​

Treatment
●​ Prolonged IV antibiotics (4–6 RHEUMATIC
weeks):​
FEVER
○​ Native valve (Streptococcal):
Penicillin G ± Gentamicin.​

○​ Staphylococcal: Name of Disease

Nafcillin/Oxacillin (MSSA),
Vancomycin (MRSA).​ ●​ Rheumatic Fever​
 3.​ Target sites:​

Causative Organism ○​ Heart (carditis → pancarditis)​

●​ Streptococcus pyogenes (Group A ○​ Joints (migratory

β-hemolytic streptococcus)​ polyarthritis)​

○​ CNS (Sydenham’s chorea)​

○​ Skin (erythema marginatum,

subcutaneous nodules)​
Classification
●​ Streptococcus pyogenes 4.​ Result: Inflammatory reaction
classification:​ damages valves → chronic
rheumatic heart disease.​
○​ Hemolysis: β-hemolytic​

○​ Lancefield Group: Group A​

○​ Serotyping: Based on M Risk Factors

protein (major virulence
factor)​ ●​ Untreated or recurrent streptococcal
sore throat​

●​ Poor socioeconomic conditions

(overcrowding, poor hygiene)​
Morphology (not required for
●​ Children and adolescents (5–15 yrs)​
bacteria in this section, but in
short) ●​ Genetic predisposition (certain HLA
types)​
●​ Gram-positive cocci in chains.​
(Diagram for exams: Chains of
round cocci with Gram-positive
purple stain.)​
Mode of Transmission
●​ Spread of S. pyogenes →
respiratory droplets
Pathogenesis (person-to-person).​

1.​ Initial infection: Streptococcus ●​ Rheumatic fever itself is not directly

pyogenes causes transmissible.​
pharyngitis/tonsillitis.​

2.​ Immune response: Antibodies

formed against M protein & cell
wall antigens cross-react with host Sequence of Events –
tissues (molecular mimicry).​
FLOWCHART
Streptococcal pharyngitis → Immune ●​ Blood (for serology & inflammatory
response → Cross-reacting antibodies → markers)​
Inflammation in heart, joints, CNS, skin →
Clinical Rheumatic Fever

Possible Specimens
Clinical Features (Stage-wise:
Jones Criteria) ●​ Throat swab → culture​

●​ Major Criteria:​ ●​ Serum → ASO/anti-DNase B titers​

○​ Carditis​

○​ Polyarthritis (migratory)​
Method of Collection
○​ Sydenham’s chorea​
●​ Throat swab: Taken before
○​ Erythema marginatum​ antibiotics, rubbed over tonsils &
posterior pharynx.​
○​ Subcutaneous nodules​
●​ Blood: 3–5 mL venous sample.​
●​ Minor Criteria:​

○​ Fever​

○​ Arthralgia​ Method of Transport &

Preservation
○​ Raised ESR/CRP​
●​ Throat swab → transported in
○​ Prolonged PR interval on Stuart’s / Amie’s medium if delay.​
ECG​
●​ Blood → plain tube (for serology).​
Diagnosis = Evidence of prior strep
infection + (2 major OR 1 major + 2 minor
criteria)
Microscopy
●​ Direct smear from throat swab →
LAB DIAGNOSIS Gram-positive cocci in chains.​

Gram Smear Findings

Specimen ●​ Purple cocci arranged in chains
(draw in exams).​
●​ Throat swab (for detection of S.
pyogenes)​
Special Stains
 ●​ Not needed (Gram stain sufficient).​ Special Tests
●​ ASO (Anti-streptolysin O) test​
Motility
○​ Principle: Neutralization of
●​ Non-motile.​ hemolysis of RBCs by
streptolysin O.​

○​ Observation: No hemolysis
= ASO antibodies present.​
Culture
○​ Significant: >200 Todd units
●​ Blood agar:​ (adults), >300 Todd units
(children).​
○​ β-hemolytic colonies, small, (Draw a diagram of ASO test
translucent.​ tubes for exams.)​

●​ Selective Media: Crystal violet ●​ Other Antibody Tests:​

blood agar, PNF agar.​
○​ Anti-DNase B​
●​ Enriched Media: Blood agar.​
○​ Anti-hyaluronidase​
●​ Transport Media: Stuart’s or Amie’s.​

●​ Differential Media: Blood agar

(hemolysis).​
Serology
●​ Detection of antistreptococcal
antibodies in serum by ELISA/latex
Identification agglutination.​

●​ Culture smear → Gram-positive

cocci in chains.​

●​ Biochemical Tests:​ Molecular Methods

○​ Catalase negative​ ●​ PCR for streptococcal DNA from
throat swabs.​
○​ Bacitracin sensitive​

○​ PYR test positive​

Automated Identification
Non-Specific Findings
●​ Raised ESR, CRP​
●​ MALDI-TOF / VITEK 2 for rapid
species confirmation.​
●​ Prolonged PR interval (ECG)​
 RF patients.​

Antimicrobial Susceptibility ●​ No vaccine available.​

Testing
●​ Rarely needed (Group A strep
remains penicillin-sensitive).​
Great question 🙌 .​
But here’s a very important clarification
●​ Done if macrolide resistance
first:
suspected.​
➡️ AIDS (Acquired Immunodeficiency
Syndrome) is a disease condition, not
caused directly by a virus, but it results from
chronic infection with HIV (Human
Typing Methods Immunodeficiency Virus).​
So in this format, the virus you study is
●​ M protein serotyping HIV, and the disease is AIDS.
(epidemiology).​
Let’s structure everything exam-oriented
●​ Molecular typing (emm gene and simple for recall.
sequencing).​

Treatment
AIDS (Caused by
●​ Acute infection: Penicillin V /
HIV)
Benzathine Penicillin G (IM single
dose).​

●​ Rheumatic fever: Anti-inflammatory

Name of Disease
(aspirin/steroids for carditis) +
●​ Acquired Immunodeficiency
supportive care.​
Syndrome (AIDS)​

Prophylaxis Causative Organism

●​ Primary prophylaxis: Treat every ●​ Human Immunodeficiency Virus

streptococcal sore throat with (HIV-1 and HIV-2)​
penicillin.​
●​ Family: Retroviridae​
●​ Secondary prophylaxis: Long-term
monthly Benzathine Penicillin G ●​ Genus: Lentivirus​
injections to prevent recurrence in
Classification 3.​ Fusion & Reverse Transcription:
Viral RNA → DNA via reverse
●​ Baltimore classification: Class VI transcriptase.​
(RNA viruses using reverse
transcriptase)​ 4.​ Integration: Viral DNA integrates
into host genome via integrase →
●​ Types: HIV-1 (worldwide, more latent or productive infection.​
virulent), HIV-2 (West Africa, less
transmissible)​ 5.​ Replication & Budding: Viral
proteins assembled, bud out using
host membrane.​

6.​ Immune system destruction:

Morphology of Organism (with Progressive loss of CD4+ T cells →
immunosuppression → opportunistic
DIAGRAM for exams) infections & cancers.​
●​ Enveloped virus, spherical
(100–120 nm)​

●​ Capsid: conical, made of p24

antigen​ Risk Factors

●​ Genome: two identical ●​ Unprotected sexual intercourse​

positive-sense single-stranded
RNA molecules​ ●​ Intravenous drug use (needle
sharing)​
●​ Enzymes: reverse transcriptase,
integrase, protease​ ●​ Blood transfusion (unsafe practices)​

●​ Envelope glycoproteins: gp120 ●​ Mother-to-child transmission

(attachment), gp41 (fusion/entry)​ (pregnancy, delivery, breastfeeding)​

●​ Multiple sexual partners​

(Diagram: spherical virus with lipid
envelope, gp120 spikes, RNA strands inside
with enzymes, conical capsid)

Mode of Transmission

Pathogenesis ●​ Sexual route​

1.​ Entry: Virus enters via sexual ●​ Parenteral (blood, IV drugs, unsafe
contact, blood, or vertically injections)​
(mother-to-child).​
●​ Vertical (mother → child)​
2.​ Attachment: gp120 binds to CD4
receptor + co-receptors (CCR5 or
CXCR4) on T-helper cells,
macrophages, dendritic cells.​
Sequence of Events –
FLOWCHART
Specimen
HIV entry → gp120 binds CD4 → Reverse
transcription → Integration → Gradual CD4 ●​ Blood (serum, plasma)​
destruction → ↓ Cell-mediated immunity →
Opportunistic infections & AIDS ●​ CSF (neurological involvement)​

Clinical Features (Stage-wise)

Possible Specimens
1.​ Acute HIV infection (2–4 weeks
after exposure)​ ●​ Serum → antibody & antigen testing​

○​ Fever, rash, sore throat, ●​ Plasma → viral RNA quantification​

lymphadenopathy, resembles
mononucleosis.​ ●​ PBMCs (peripheral blood
mononuclear cells) → proviral DNA​
2.​ Latent/asymptomatic phase​

○​ No symptoms, but gradual

CD4 decline; can last years.​
Method of Collection
3.​ Symptomatic HIV​
●​ Venous blood (EDTA tubes for viral
○​ Persistent lymphadenopathy, load, plain tubes for serology).​
weight loss, recurrent
infections.​
Transport & Preservation
4.​ AIDS (CD4 <200 cells/µL or
AIDS-defining illness)​ ●​ Transport at 2–8°C; plasma
separated and frozen at −70°C for
○​ Opportunistic infections: TB, long-term storage.​
Pneumocystis pneumonia,
Candidiasis, Toxoplasmosis​

○​ Malignancies: Kaposi
sarcoma, Non-Hodgkin Direct Microscopy
lymphoma​
●​ No inclusion bodies seen for HIV
○​ Neurological disease: HIV in light microscopy.​
encephalopathy​
●​ Electron microscopy shows
enveloped virions but not routine.​

LAB DIAGNOSIS
Serology
Antigen & Antibody Detection (important lymphocytes → HIV replication.​
for exams):

1.​ Screening tests (high sensitivity):​

○​ ELISA (3rd gen – antibodies; Viral Tissue Culture

4th gen – p24 antigen +
antibody combo).​ ●​ Medium: RPMI-1640 with IL-2
(supports T-cell growth).​
○​ Rapid tests / latex
agglutination (field use).​ ●​ Finding: Cytopathic effect (syncytia
formation, giant cells).​
2.​ Confirmatory test (high specificity):​

○​ Western blot (detects

antibodies to specific HIV
proteins – gp120, gp41, p24).​
Animal Inoculation
○​ Line immunoassay (newer).​ ●​ Not used routinely (HIV does not
infect standard lab animals).​
p24 Antigen – detectable early in infection
●​ Research: Chimpanzees,
before antibodies form.
humanized mice.​

Molecular Methods
●​ RT-PCR (reverse transcriptase
Embryonated Egg Inoculation
PCR) for viral RNA quantification
●​ Not used for HIV. (Egg inoculation is
(viral load).​
for poxviruses, influenza, etc.)​
●​ PCR for proviral DNA (in integrated
form, especially in infants <18
months where maternal antibodies
interfere).​
Treatment
●​ NAATs used for early detection.​
●​ Antiretroviral Therapy (ART) –
lifelong, combination therapy
(HAART):​

Virus Isolation ○​ 2 NRTIs (e.g., Tenofovir +

Lamivudine)​
●​ Possible but not routine (requires
high-level biosafety labs).​ ■​ 1 NNRTI / Integrase
inhibitor (e.g.,
●​ Peripheral blood mononuclear cells Efavirenz /
(PBMCs) co-cultured with activated Dolutegravir)​
 ●​ Prophylaxis against opportunistic Gastroenteritis, Salmonella
infections when CD4 <200 (e.g., Septicemia​
Cotrimoxazole for Pneumocystis).​

Causative Organism
Prophylaxis ●​ Salmonella enterica subspecies​
●​ Drugs:​ ○​ Salmonella enterica serovar
Typhi → Typhoid fever​
○​ Post-exposure prophylaxis
(PEP): ART for 28 days ○​ S. enterica serovar Paratyphi
within 72 hrs of exposure.​ A, B, C → Paratyphoid fever​
○​ Pre-exposure prophylaxis ○​ S. Typhimurium, S. Enteritidis
(PrEP): Tenofovir + → Gastroenteritis​
Emtricitabine daily in
high-risk individuals.​ ○​ S. Choleraesuis →
Septicemia​
●​ Vaccine: No licensed vaccine yet
(trials ongoing).​

Classification
Perfect choice✅ – Salmonella is very
frequently asked in exams.​ ●​ Family: Enterobacteriaceae​
Let’s build the complete structured
answer for Salmonella in the exact style ●​ Genus: Salmonella​
you need.
●​ Based on Kauffmann–White
scheme (antigenic classification):​

○​ O antigen → Somatic (LPS)​

SALMONELLOSIS ○​ H antigen → Flagellar​

(Enteric Fever, ○​ Vi antigen → Capsular (in S.

Typhi)​
Gastroenteritis,
Septicemia)
Morphology of Organism
●​ Gram-negative, medium-sized bacilli​
Name of Disease
●​ Enteric Fever (Typhoid &
Paratyphoid), Salmonella
 ●​ Non-capsulated (except S. Typhi ●​ Endemic areas (South Asia, Africa)​
with Vi antigen)​
●​ Children & young adults​
●​ Non-sporing​
●​ Chronic carriers (excrete Salmonella
●​ Motile (peritrichous flagella) except in stools, e.g. “Typhoid Mary”)​
S. Gallinarum & S. Pullorum​

(Diagram for exams: small Gram-negative

bacillus with peritrichous flagella) Mode of Transmission
●​ Feco-oral route​

Pathogenesis ●​ Carriers → contamination of

food/water​
1.​ Entry: Ingestion of contaminated
food/water.​ ●​ Rarely via handling infected animals
(zoonotic serotypes)​
2.​ Survival in stomach → reach small
intestine.​

3.​ Invasion: M cells of Peyer’s patches

→ taken up by macrophages.​ Sequence of Events –
FLOWCHART
4.​ Systemic spread via
reticuloendothelial system (liver, Ingestion → Intestine → Invasion of M cells
spleen, bone marrow).​ → Macrophage survival → Bacteremia →
RES organs → Peyer’s patch ulceration →
5.​ Typhoid: Multiplies in mononuclear Typhoid fever symptoms
phagocytes → persistent bacteremia
→ seeding of gallbladder & Peyer’s
patches.​

6.​ Local immune response: Clinical Features

Ulceration of Peyer’s patches →
bleeding or perforation.​ 1. Enteric (Typhoid) Fever – Stage wise

●​ Week 1: Step-ladder fever,

7.​ Endotoxin release → fever and
bacteremia, relative bradycardia,
systemic toxicity.​
toxemia​

●​ Week 2: High sustained fever,

abdominal pain, splenomegaly, “rose
spots” on abdomen​
Risk Factors
●​ Week 3: Complications – intestinal
●​ Poor sanitation, contaminated water hemorrhage, perforation,
supply​ encephalopathy​
 ●​ Week 4: Convalescence if untreated​ ●​ Blood (3–5 mL, multiple samples
before antibiotics)​

2. Paratyphoid Fever ●​ Stool (fresh sample, sterile

container)​
●​ Similar but milder and shorter course​
●​ Bone marrow aspirate (aseptic
aspiration)​
3. Gastroenteritis

●​ Incubation: 6–48 hrs → Nausea, Transport & Preservation

vomiting, diarrhea, abdominal
cramps, fever (self-limiting, 2–7 ●​ Blood → directly into bile broth /
days)​ brain heart infusion broth​

●​ Stool → Cary-Blair transport medium

4. Septicemia if delay​

●​ Fever, chills, septic shock; local

infections (osteomyelitis, meningitis
esp. in immunocompromised, sickle
cell anemia)​ Microscopy
●​ Direct Gram stain not useful (low
bacterial count in blood/stool).​

LAB DIAGNOSIS ●​ Occasionally, Gram-negative bacilli

in stool smears (non-specific).​

Gram Smear Findings (DIAGRAM)

Specimen
●​ Gram-negative bacilli (pink rods,
●​ Blood → culture (first week of slender)​
illness)​

●​ Stool & urine → culture (after 2nd Special Stains

week)​
●​ Not required routinely.​
●​ Bone marrow aspirate (high yield
even after antibiotics)​
Motility
●​ Duodenal aspirate​
●​ Actively motile (peritrichous flagella).​

Possible Specimens & Collection

Culture
 ●​ Blood culture (gold standard in first ●​ MALDI-TOF MS, VITEK 2​
week).​

●​ Stool culture (positive in 2nd–3rd

week).​
Special Tests
●​ Bone marrow culture → highest
sensitivity.​ ●​ Widal Test (serology – agglutination
test)​

Culture Media: ○​ Detects O (somatic) & H

(flagellar) antibodies in
●​ Enrichment broth: Bile broth, serum.​
Selenite F broth​
○​ Performed after 7–10 days of
●​ Enriched media: Blood agar, fever.​
Chocolate agar​
○​ Significant: Fourfold rise in
●​ Selective media: Deoxycholate titer or high single titer (e.g.,
citrate agar (DCA), XLD agar​ O ≥1:160 in endemic areas).​
(Diagram: Test tubes
●​ Differential media: MacConkey showing agglutination pattern
agar (lactose non-fermenter = pale for O & H antigens)​
colonies), Wilson–Blair bismuth
sulfite agar (black metallic sheen
colonies of S. Typhi)​

Serology
●​ Antigen/antibody detection in
Identification serum:​
●​ Culture smear findings → ○​ Widal test (traditional)​
Gram-negative bacilli​
○​ ELISA for Vi antigen / IgM
●​ Biochemical tests:​ antibodies​
○​ Triple Sugar Iron agar (TSI): ○​ Typhidot test (IgM/IgG
Alk/Acid with H2S production ELISA)​
(black butt)​

○​ Urease: Negative​

○​ Indole: Negative​
Molecular Methods
○​ Citrate: Positive​
●​ PCR for Salmonella-specific genes
(e.g., invA)​
○​ Motility: Positive​

Automated Identification
 ●​ Real-time PCR for rapid detection
from blood/stool​
Treatment
●​ Uncomplicated enteric fever:​

○​ Ceftriaxone / Azithromycin​
Non-Specific Findings ○​ Fluoroquinolones (resistance
common in Asia)​
●​ Leukopenia with relative
lymphocytosis (typhoid fever)​ ●​ MDR cases: 3rd-gen
cephalosporins, Azithromycin​
●​ Elevated ESR, CRP​
●​ XDR cases (Pakistan):
●​ Mild anemia​ Azithromycin, Meropenem​

●​ Supportive care for gastroenteritis

(rehydration, no antibiotics unless
severe).​
Antimicrobial Susceptibility
Testing (AST)
●​ Performed by Kirby–Bauer disc
diffusion, MIC methods​
Prophylaxis
●​ Detect resistance to
fluoroquinolones, cephalosporins, ●​ Vaccines:​
azithromycin​
○​ Vi capsular polysaccharide
●​ MDR Salmonella Typhi common vaccine (injectable)​
(resistant to chloramphenicol,
ampicillin, co-trimoxazole)​ ○​ Live attenuated Ty21a (oral)​

●​ Drugs: No chemoprophylaxis
recommended routinely.​

Typing Methods ●​ Public health: Safe water supply,

sanitation, food hygiene.​
●​ Serotyping by Kauffmann–White
scheme (O, H, Vi antigens)​

●​ Phage typing (historical, for

epidemiology)​
Excellent pick ✅
clarification first:
– but here’s an important

●​ Molecular typing: MLST, PFGE,

Epidemic Typhus is caused by a
WGS​
bacterium-like organism, but not a typical
free-living bacterium. It is due to Rickettsia
prowazekii, which is an obligate
intracellular bacterium (family:
Rickettsiaceae).​
So, though we study it under bacteria, its
lab diagnosis and culture methods are ●​ Stain with Giemsa or Giménez stain​
different from enteric bacteria like (Diagram for exams: small bacilli
Salmonella. inside endothelial cells, seen with
Giemsa)​
Now let’s build the complete structured
answer for Epidemic Typhus.

Pathogenesis

EPIDEMIC TYPHUS 1.​ Entry: Human body louse bites →

infected louse feces scratched into
bite wound.​

2.​ Target cells: Vascular endothelium

Name of Disease of small blood vessels.​

●​ Epidemic Typhus​ 3.​ Multiplication: Intracellular

multiplication damages endothelium.​

4.​ Vasculitis: Inflammation,

thrombosis, ischemia.​
Causative Organism
5.​ Clinical disease: High fever,
●​ Rickettsia prowazekii​ widespread rash, CNS involvement,
myocarditis.​

Classification
Risk Factors
●​ Family: Rickettsiaceae​
●​ War, famine, refugee camps
●​ Genus: Rickettsia​ (crowding, poor hygiene)​

●​ Group: Typhus group (includes R. ●​ Exposure to lice infestations​

prowazekii & R. typhi)​
●​ Immunocompromised individuals​

Morphology of Organism
Mode of Transmission
●​ Small, Gram-negative, pleomorphic
coccobacilli​ ●​ Vector-borne: Human body louse
(Pediculus humanus corporis)​
●​ Obligate intracellular organisms
(cannot grow on artificial media)​ ●​ No direct person-to-person spread.​
 ●​ Blood (serum for serology, whole
blood for molecular tests)​
Sequence of Events –
FLOWCHART
Infected louse bite → Louse feces
inoculated → Rickettsia enters bloodstream Possible Specimens & Collection
→ Multiplies in endothelial cells → Vasculitis
→ Fever + Rash + Multi-organ involvement ●​ Serum (antibody tests, ELISA, IFA)​

●​ Whole blood (PCR)​

●​ Biopsy of rash/skin lesion (rare, for

Clinical Features (Stage-wise)
histology/PCR)​
●​ Incubation period: 7–14 days​
Transport & Preservation
●​ Prodrome: Sudden high fever,
chills, severe headache, myalgia​
●​ Serum/plasma stored at 2–8 °C
short-term, −20 °C long-term.​
●​ Acute phase:​
●​ Blood in EDTA tube, transported
○​ Day 4–6: Macular rash on
cold for PCR.​
trunk → spreads to
extremities (sparing face,
palms, soles)​

○​ Delirium, stupor, hypotension

(hence called “typhus” = Microscopy
smoky/obscure state of mind)​
●​ Light microscopy: Not useful (too
●​ Complications: Myocarditis, small).​
pneumonia, CNS involvement​
●​ Giemsa stain: Intracellular bacilli
●​ Reactivation (Brill–Zinsser inside endothelial cells.​
disease): Milder recrudescent
typhus years later in previously
infected individuals​ Gram Smear Findings (Diagram)

●​ Not clearly seen by Gram stain →

appear poorly stained.​

LAB DIAGNOSIS Special Stains

●​ Giemsa stain: Blue-stained

coccobacilli inside cells​
Specimen ●​ Giménez stain: Red organisms
against green background​
Motility ○​ Rickettsia antibodies
agglutinate Proteus vulgaris
●​ Non-motile​ OX19, OX2 antigens.​

○​ Epidemic typhus: Strong

agglutination with OX19.​
(Diagram: Test tubes
Culture showing agglutination with
OX19 antigen)​
●​ Not possible on routine
bacteriological media.​

●​ Requires living cells:​

Serology
○​ Chick embryo yolk sac​
●​ Antibody detection in serum:​
○​ Tissue culture (e.g., HeLa,
Vero cells)​ ○​ IFA (Indirect
immunofluorescence
●​ Biosafety level-3 needed.​ assay) – gold standard​

○​ ELISA for IgM and IgG​

Culture Media: None artificial.​
Enrichment broth/Selective/Differential: ○​ Weil–Felix (OX19
Not applicable. agglutination) – supportive
but nonspecific​

Identification
●​ Based on antigenic structure (typhus Molecular Methods
group).​
●​ PCR targeting rickettsial DNA from
●​ Confirmed by serology or PCR.​ blood/skin biopsy.​

Biochemical tests: Not applicable (cannot

be cultured free).
Virus Isolation Equivalent (for
Automated Identification (MALDI–TOF,
VITEK): Not applicable. Rickettsia)
●​ Tissue culture or embryonated
eggs used instead of viral culture.​
Special Tests
●​ Weil–Felix test (historical, low
specificity):​
Viral Tissue Culture Equivalent
 ●​ Human cell lines (Vero, HeLa, Non-Specific Findings
fibroblasts) → cytopathic effect:
intracellular growth.​ ●​ Leukopenia​

●​ Thrombocytopenia​

●​ Elevated liver enzymes​

Animal Inoculation
●​ Guinea pigs, mice used in research
→ febrile illness.​
Antimicrobial Susceptibility
Testing
●​ Not done (intracellular organism;
Embryonated Egg Inoculation uniformly susceptible to
tetracyclines).​
●​ Yolk sac inoculation → multiplication
of R. prowazekii.​

Typing Methods
●​ Molecular typing (gene sequencing,
Treatment MLST) for epidemiology.​
●​ Drug of choice: Doxycycline (all
ages, single dose often effective)​

●​ Chloramphenicol (alternative in
pregnancy, though less effective)​
Perfect👍 – Scrub Typhus is another
Rickettsial infection, but unlike Epidemic
Typhus (lice-borne, caused by R.
prowazekii), this one is caused by Orientia
tsutsugamushi and is transmitted by
chigger mites.​
Let’s go step by step in exam-oriented
Prophylaxis detail.
●​ No vaccine in routine use (older
killed vaccine not widely available)​

●​ Prevention: Louse control

(insecticides, hygiene, delousing in
camps)​
SCRUB TYPHUS
●​ Antibiotic prophylaxis (doxycycline)
in epidemic situations sometimes
used​ Name of Disease
●​ Scrub Typhus​
 2.​ Multiplication at site → formation of
eschar (black necrotic scab).​
Causative Organism
3.​ Spreads via lymphatics & blood →
●​ Orientia tsutsugamushi (previously invades endothelial cells.​
classified under Rickettsia)​
4.​ Causes vasculitis → capillary leak,
edema, multi-organ dysfunction.​

Classification
●​ Family: Rickettsiaceae​ Risk Factors

●​ Genus: Orientia​ ●​ Rural, forest, scrubland exposure​

●​ Group: Scrub Typhus group​ ●​ Farming, military activity, outdoor

work​

●​ Poor hygiene, endemic areas

(Asia-Pacific, especially India)​
Morphology of Organism
(For Rickettsia & Orientia – DIAGRAM
recommended)
Mode of Transmission
●​ Small, pleomorphic Gram-negative
coccobacilli​ ●​ Vector-borne: chigger mite (larva
of trombiculid mite)​
●​ Obligate intracellular organism​
●​ Reservoir: rodents, mites​
●​ No typical
peptidoglycan/lipopolysaccharide ●​ No person-to-person spread​
layer (differs from other rickettsiae)​

●​ Stains: Giemsa & Giménez stain​

Sequence of Events –
(Diagram: Intracellular coccobacilli inside FLOWCHART
endothelial cell cytoplasm, stained bluish
with Giemsa) Chigger bite → Local multiplication →
Eschar → Spread via blood/lymph →
Endothelial invasion → Vasculitis → Fever,
rash, lymphadenopathy, multi-organ
Pathogenesis dysfunction

1.​ Bite of infected chigger mite (larva

of Leptotrombidium) → organism
enters skin.​ Clinical Features (Stage-wise)
 ●​ Incubation: 6–21 days​

●​ Initial: Fever, chills, severe Method of Collection

headache, myalgia, cough​
●​ Venous blood in plain tube
●​ Key sign: Eschar at bite site (black (serology) or EDTA tube (molecular)​
scab with erythematous halo,
painless) – pathognomonic​ ●​ Eschar scraping under aseptic
precautions​
●​ Progression:​

○​ Generalized Transport & Preservation

lymphadenopathy​
●​ Serum/plasma at 2–8 °C, −20 °C for
○​ Maculopapular rash (trunk → long storage​
extremities)​
●​ Blood for PCR kept cold​
○​ Hepatosplenomegaly​

●​ Severe disease: Pneumonitis,

meningoencephalitis, myocarditis,
renal/hepatic failure​ Microscopy
●​ Light microscopy not useful​

●​ Giemsa stain: intracellular bacilli in

endothelial cells (rarely done)​
LAB DIAGNOSIS

Specimen Gram Smear Findings

●​ Blood (serum for serology, whole ●​ Not well visualized; weak
blood for PCR)​ Gram-negative staining​
(Diagram: tiny intracellular rods
●​ Eschar biopsy/swab (for PCR)​ inside host cell)​

Possible Specimens Special Stains

●​ Serum → IgM ELISA, IFA​ ●​ Giemsa: Blue-stained bacilli​
●​ Whole blood → PCR​ ●​ Giménez: Red bacilli against green
background​
●​ Eschar tissue → PCR​
Type of Motility Proteus mirabilis OXK strain​

●​ Non-motile​ ○​ Scrub typhus = positive with

OXK antigen (unlike
epidemic typhus = OX19)​
(Diagram: test tube showing
agglutination with OXK
Culture antigen)​

●​ Cannot be grown on routine media​

●​ Requires tissue culture or chick

embryo yolk sac​ Serology
●​ Antibody detection in serum​
Culture Media: None artificial​
Enrichment/Selective/Differential: Not ●​ IFA (Indirect immunofluorescence
applicable assay) = gold standard​

●​ ELISA (IgM/IgG) – commonly used​

Identification ●​ Weil–Felix (OXK positive) –

supportive but less sensitive​
●​ Based on serology & molecular tests​

Molecular Methods
Biochemical Tests
●​ PCR targeting 56-kDa antigen gene
●​ Not applicable (cannot grow outside of Orientia tsutsugamushi (from
cells)​ blood or eschar)​

Automated Identification Non-Specific Findings

(MALDI-TOF / VITEK)
●​ Leukopenia, thrombocytopenia​
●​ Not applicable​
●​ Elevated liver enzymes​

●​ Raised CRP, ESR​

Special Tests
●​ Weil–Felix test:​
Antimicrobial Susceptibility
○​ Detects cross-reacting Testing
antibodies that agglutinate
 ●​ Not performed routinely (obligate Weil–Felix positive with OX19​
intracellular organism)​
●​ Scrub Typhus (O. tsutsugamushi)
●​ Sensitive to doxycycline, → transmitted by mite → Weil–Felix
azithromycin​ positive with OXK​

Typing Methods Excellent pick 👌 — Q fever is another

rickettsial disease but differs from classical
●​ Molecular typing (gene sequencing typhus/scrub typhus. It is caused by
of 56-kDa antigen gene, multilocus Coxiella burnetii, which is unique because
typing)​ it is highly infectious, forms spore-like
variants, and can spread without a vector.
●​ Useful in epidemiology (many Let’s prepare this in a structured,
antigenic variants exist)​ exam-friendly format.

Treatment Q FEVER
●​ Drug of choice: Doxycycline​

●​ Alternatives: Azithromycin Name of Disease

(pregnancy, children),
Chloramphenicol​ ●​ Q fever​

Causative Organism
Prophylaxis
●​ Coxiella burnetii​
●​ No effective vaccine​

●​ Vector control (mite avoidance,

protective clothing, insect repellents)​

●​ Doxycycline prophylaxis sometimes

Classification
used in military outbreaks​
●​ Family: Coxiellaceae​

●​ Genus: Coxiella​

✅ Key exam tip: ●​ Previously grouped under

Rickettsiales but now considered
●​ Epidemic Typhus (R. prowazekii) separate​
→ transmitted by louse →
 ●​ Intracellular, Gram-negative phagolysosome.​
bacterium​
4.​ Host response – granulomatous
●​ Two forms:​ inflammation in liver, endocardium,
lungs.​
○​ Small cell variant (SCV) –
spore-like, resistant​ 5.​ Clinical outcome – acute febrile
illness, hepatitis, pneumonia; chronic
○​ Large cell variant (LCV) – form causes endocarditis.​
metabolically active inside
host cells​

Risk Factors
Morphology of Organism ●​ Exposure to farm animals (sheep,
goats, cattle)​
(DIAGRAM useful in exams)
●​ Veterinary workers, abattoir workers,
●​ Very small pleomorphic farmers​
coccobacillus​
●​ Consumption of unpasteurized dairy
●​ Weakly Gram-negative​ products​

●​ Obligate intracellular​ ●​ Immunocompromised individuals,

pregnancy, pre-existing valvular
●​ No flagella, non-motile​ heart disease​

●​ Forms endospore-like small cell

variant for survival​

Mode of Transmission
(Diagram: small coccobacillus inside
macrophage vacuole, showing two forms ●​ Inhalation of contaminated
SCV & LCV) aerosols (main route)​

●​ Ingestion of raw milk/dairy​

Pathogenesis ●​ Direct contact with infected tissues

(placenta, birth fluids)​
1.​ Entry – inhalation of aerosols from
infected animals/products (placenta, ●​ Rare: human-to-human transmission​
milk, urine, feces).​

2.​ Survival – SCV survives harsh

environment, phagocytosed by
macrophages.​ Sequence of Events –
3.​ Inside cell – transforms to LCV,
FLOWCHART
replicates within acidic
Animal reservoir (sheep, goats, cattle)​ ●​ Blood (serum, whole blood)​
⬇​
Excretion in placenta, milk, urine, feces​ ●​ Tissue biopsy (liver, heart valve – in
⬇​ chronic cases)​
Environmental contamination (aerosols,
dust, milk)​
⬇​
Human exposure (inhalation, ingestion)​
⬇​ Possible Specimens
Infection of macrophages → replication​
⬇​ ●​ Serum → serology (antibodies)​
Vasculitis, granulomas → Acute Q fever
(pneumonia, hepatitis) or Chronic Q fever ●​ Whole blood → PCR for DNA​
(endocarditis)
●​ Tissue → histopathology & PCR​

Clinical Features
Acute Q fever (2–3 weeks incubation): Method of Collection
●​ Sudden high fever, severe ●​ Venous blood under aseptic
headache, myalgia​ precautions​

●​ Hepatitis (elevated liver enzymes, ●​ Serum separated for antibody

hepatomegaly)​ detection​

●​ Atypical pneumonia (dry cough, ●​ EDTA blood for PCR​

pleuritic pain)​

Transport & Preservation

Chronic Q fever (months–years later, esp.
with valvular heart disease): ●​ Serum at 2–8 °C short term; −20 °C
for longer storage​
●​ Subacute endocarditis
(culture-negative)​ ●​ Blood for PCR refrigerated if delay in
testing​
●​ Chronic hepatitis, osteomyelitis,
vascular infection​

Microscopy

LAB DIAGNOSIS ●​ Not visible by routine Gram stain

in clinical specimens​

●​ Requires special stains​

Specimen
Gram Smear Findings ●​ Not applicable​

●​ Weakly Gram-negative, poorly

staining coccobacilli​
(Diagram: tiny intracellular
coccobacilli in macrophage vacuole)​ Automated Identification
(MALDI-TOF/VITEK)
●​ Not useful (cannot culture routinely)​

Special Stains
●​ Giménez stain: red coccobacilli
against green background​ Special Tests
●​ Giemsa: intracellular organisms ●​ Weil–Felix test: Negative
visible​ (important exam point –
differentiates from typhus group)​

●​ Histopathology: “fibrin ring

granulomas” in liver biopsy​
Type of Motility
●​ Non-motile​ (Diagram: hepatocyte with fibrin-ring
granuloma – central fat vacuole with fibrin
ring & inflammatory cells)

Culture
Serology (sample = serum)
●​ Dangerous, requires BSL-3 labs​
●​ Indirect immunofluorescence
●​ Grown in embryonated eggs or cell assay (IFA) = gold standard​
culture (not routine)​
●​ Detects phase I and phase II
antigens:​
Culture Media: not artificial​
Enrichment/Selective/Differential: not ○​ Acute Q fever → high titers
applicable of IgG/IgM against Phase II
antigen​

○​ Chronic Q fever → high titers

Identification against Phase I antigen​

●​ By serology & PCR, not culture​ ●​ ELISA also used for screening​

Biochemical Tests Molecular Methods

 ●​ PCR (conventional/real-time) on 18–24 months for endocarditis)​
whole blood or tissue biopsy​

●​ Highly sensitive for early diagnosis​

Prophylaxis
Non-Specific Findings ●​ Vaccine: Inactivated whole-cell
vaccine available (Australia for
●​ Raised liver enzymes​ high-risk workers)​

●​ Thrombocytopenia​ ●​ Avoid raw milk, proper disposal of

animal birth products​
●​ ESR, CRP elevated​
●​ Protective clothing, masks for
high-risk occupations​

Antimicrobial Susceptibility
Testing ✅ Key Exam Tips:
●​ Not done (intracellular organism)​ ●​ Only rickettsial disease without
arthropod vector (spread by
●​ Sensitive to doxycycline, aerosols/animals).​
fluoroquinolones​
●​ Weil–Felix negative.​

●​ Phase I = chronic disease, Phase

II = acute disease antibodies.​
Typing Methods
●​ Chronic Q fever → culture-negative
●​ Phase variation antigen typing endocarditis.​
(Phase I vs Phase II)​

●​ Genotyping by PCR / sequencing

(for epidemiology)​
Perfect👍 Let’s prepare Leptospirosis in
the structured exam format you requested.
This is a zoonotic spirochetal disease
important for both theory and viva.

Treatment
●​ Acute Q fever → Doxycycline (drug
of choice) for 14 days​
LEPTOSPIROSIS
●​ Chronic Q fever → Doxycycline +
Hydroxychloroquine (long-term,
Name of Disease (Diagram: tightly coiled, hook-shaped ends
spirochete)
●​ Leptospirosis (also known as Weil’s
disease in severe cases)​

Pathogenesis
1.​ Entry via abraded skin or mucosa
Causative Organism (eye, nose, mouth) from
contaminated water/soil.​
●​ Leptospira interrogans (pathogenic
species)​ 2.​ Spread hematogenously →
leptospiremia.​

3.​ Colonization of liver, kidney, lungs,

CNS.​
Classification
4.​ Immune response → endothelial
●​ Phylum: Spirochaetes​ damage → vasculitis, capillary leak,
jaundice, renal failure, hemorrhage.​
●​ Order: Leptospirales​

●​ Family: Leptospiraceae​

●​ Genus: Leptospira​ Risk Factors

○​ Pathogenic: L. interrogans​ ●​ Occupational exposure: sewer

workers, farmers, abattoir workers,
○​ Non-pathogenic: L. biflexa​ veterinarians​

●​ Recreational exposure: swimming in

contaminated lakes/rivers​

Morphology (DIAGRAM important ●​ Tropical climates, flooding, poor

sanitation​
in exams)
●​ Very thin, tightly coiled spirochete​

●​ Ends are hooked → “question-mark

shaped” (basis of name interrogans)​ Mode of Transmission

●​ 0.1 µm thick, 6–20 µm long​ ●​ Direct/indirect contact with urine

of infected rodents, cattle, dogs​
●​ Motile by periplasmic axial
filaments (endoflagella)​ ●​ Contaminated water/soil is
commonest route​
●​ Not seen in Gram stain (too thin),
but visible by dark-field microscopy, ●​ Enters through skin abrasions or
silver stain, or immunofluorescence​ mucous membranes​
 ■​ Weil’s disease =
jaundice + renal
Sequence of Events – failure + hemorrhage​
FLOWCHART
■​ Pulmonary
Animal reservoir (rodents, cattle, dogs)​ hemorrhage
⬇​ syndrome​
Excretion of leptospires in urine​
⬇​
Contamination of soil/water​
⬇​
Human exposure via skin/mucosa​
⬇​
LAB DIAGNOSIS
Leptospiremia → systemic spread​
⬇​
Tissue invasion (liver, kidney, lungs)​
⬇​ Specimen
Immune response & endothelial damage​
⬇​ ●​ Early phase (first week) → blood,
Clinical disease (mild anicteric → severe CSF​
Weil’s disease)
●​ Later phase (after 1 week) → urine​

●​ Serum for antibody detection​

Clinical Features
Incubation: 7–12 days

Biphasic illness: Possible Specimens

1.​ Leptospiremic Phase (1st week)​ ●​ Blood → for culture/PCR (early)​

○​ Sudden high fever, chills​ ●​ CSF → in meningitic phase​

○​ Severe myalgia (calf & ●​ Urine → culture in later phase​

lumbar pain is typical)​
●​ Serum → serology (MAT, ELISA)​
○​ Headache, conjunctival
suffusion (reddening without
discharge)​

2.​ Immune Phase (2nd week Method of Collection & Transport

onwards)​
●​ Blood under aseptic precautions​
○​ Appearance of antibodies​
●​ Urine → sterile wide-mouth
○​ Meningitis, uveitis, rash​ container​

○​ Organ involvement:​
 ●​ Specimens kept at 4 °C; processed ●​ Slow-growing, 6–8 weeks​
quickly​
●​ Culture Media:​

○​ Fletcher’s medium​

Microscopy ○​ Stuart’s liquid medium​

●​ Dark-field microscopy: thin motile ○​ EMJH

spirochetes in fresh samples (low (Ellinghausen–McCullough–J
sensitivity & specificity)​ ohnson–Harris) medium –
best​
●​ Not visible in routine Gram stain​

Enrichment/Enriched Media

●​ EMJH with rabbit serum​

Gram Smear Findings (DIAGRAM)
Transport Media
●​ Not demonstrable with Gram stain
(too thin)​ ●​ Special semisolid media (EMJH or
Stuart medium)​
●​ Diagram: coiled, hook-shaped, thin
organism (seen only under special
stains)​ Selective Media

●​ EMJH with 5-Fluorouracil (inhibits

contaminants)​

Special Stains
●​ Silver impregnation (Warthin–Starry)
→ black spirochetes on yellow Identification
background​
●​ By dark-field examination, serology,
●​ Immunofluorescence stain​ PCR​

●​ Culture confirmed with specific

antisera agglutination​

Type of Motility
●​ Active, rapid, rotational motility with
flexion due to axial filaments​ Biochemical Tests
●​ Not routinely applicable​

Culture
Automated Identification
(MALDI–TOF/VITEK)
Non-Specific Findings
●​ Rarely used in routine practice (slow
growth, biosafety issues)​ ●​ Leukocytosis, thrombocytopenia​

●​ Elevated liver enzymes, bilirubin​

●​ Raised creatinine (renal

Special Tests involvement)​

●​ Microscopic Agglutination Test

(MAT) – gold standard​

○​ Live antigens + patient serum Antimicrobial Susceptibility

→ agglutination under dark Testing
field​
●​ Not routinely performed (fastidious
○​ Positive if ≥ fourfold rise in organism)​
titer​
●​ Empirical treatment with
doxycycline/penicillin​
(Diagram: showing agglutinated vs
non-agglutinated leptospires under dark
field)

Typing Methods
Serology ●​ Serotyping by MAT (over 300
serovars)​
●​ Sample = serum​
●​ Molecular typing (PFGE, MLST) for
●​ ELISA: detects IgM (early and rapid epidemiology​
diagnosis)​

●​ MAT: gold standard, species/serovar

identification​

●​ Other tests: Latex agglutination, Treatment

rapid card tests​
●​ Mild: Doxycycline​

●​ Severe (Weil’s disease): IV

Penicillin G, Ceftriaxone, or
Molecular Methods Cefotaxime​

●​ PCR (conventional or real-time) →

early detection in blood, CSF, urine​
Prophylaxis Name of Disease

●​ Chemoprophylaxis: Doxycycline ●​ Brucellosis (also called Undulant

weekly for high-risk groups (soldiers, fever, Mediterranean fever, Malta
disaster relief workers)​ fever)​

●​ Vaccines: Inactivated whole-cell

vaccines used in some countries
(not widely available)​
Causative Organism
●​ Rodent control, protective gear,
avoidance of contaminated water​ ●​ Genus Brucella​

○​ B. melitensis → goats &

sheep (most pathogenic to

✅ Key Exam Pearls: humans)​

○​ B. abortus → cattle​
●​ Hook-shaped ends → “question
mark” appearance​ ○​ B. suis → pigs​

●​ Biphasic illness (septicemic then ○​ B. canis → dogs​

immune phase)​

●​ Weil’s disease = triad of jaundice,

renal failure, hemorrhage​
Classification
●​ MAT = gold standard, IgM ELISA =
rapid test​ ●​ Phylum: Proteobacteria​

●​ Dark-field microscopy only for ●​ Class: Alphaproteobacteria​

fresh specimens, not reliable​
●​ Order: Rhizobiales​

●​ Family: Brucellaceae​
Great choice 👍 , Brucellosis is a very
important zoonotic bacterial disease often
●​ Genus: Brucella​
asked in exams because of its public health
importance and lab diagnostic challenges.
Let’s make a complete exam-oriented
structured note for you.
Morphology (Diagram not of virus
here, but of bacteria)
●​ Very small Gram-negative
coccobacilli (0.5–0.7 µm)​
BRUCELLOSIS ●​ Non-motile, non-sporing,
non-capsulated​
 ●​ Strict aerobes (except B. abortus → ●​ Zoonotic → direct contact with
requires 5–10% CO₂)​ infected animals or animal products​

●​ Intracellular pathogen of ●​ Ingestion → unpasteurized dairy

macrophages​ products​

●​ Inhalation → aerosols
(Diagram: small Gram-negative coccobacilli (slaughterhouses, labs)​
arranged singly/pairs)
●​ Inoculation through skin cuts​

Pathogenesis
1.​ Entry via skin abrasions, mucosa, Sequence of Events –
conjunctiva, or ingestion/inhalation.​ FLOWCHART
2.​ Uptake by macrophages → survive Infected animals (sheep, goats, cattle, pigs,
intracellularly by inhibiting dogs)​
phagosome-lysosome fusion.​ ⬇​
Excretion in milk, urine, placenta, aborted
3.​ Multiplication in reticuloendothelial fetus​
system (liver, spleen, bone marrow, ⬇​
lymph nodes).​ Human exposure via ingestion / inhalation /
contact​
4.​ Causes granulomatous ⬇​
inflammation.​ Entry through mucosa / skin​
⬇​
5.​ Leads to intermittent bacteremia Survival in macrophages → intracellular
→ undulant fever pattern.​ multiplication​
⬇​
Dissemination via blood (bacteremia)​
⬇​
Colonization of RES (liver, spleen, bone
Risk Factors marrow, lymph nodes)​
⬇​
●​ Farmers, veterinarians, abattoir Granulomatous lesions → clinical disease
workers, dairy workers​ (undulant fever, organ complications)

●​ Consumption of unpasteurized
milk, cheese​
Clinical Features
●​ Laboratory workers (lab-acquired
brucellosis is common)​ Incubation period: 1–3 weeks (may be
longer)

1.​ Acute stage​

Mode of Transmission ○​ Intermittent (undulant) fever,

chills, sweating (profuse,
 “mousy” odor)​ ●​ Blood: aseptic venipuncture into
blood culture bottles​
○​ Fatigue, arthralgia, myalgia,
lymphadenopathy, ●​ Bone marrow: aspirate in sterile
hepatosplenomegaly​ syringe​

2.​ Chronic stage​ ●​ Transport: biosafety precautions

(category B infectious substance),
○​ Relapsing fever​ room temperature​

○​ Arthritis, orchitis, spondylitis​

○​ Neurobrucellosis,
endocarditis (rare but fatal)​ Microscopy
●​ Type: Direct microscopy not useful
(low numbers, intracellular).​

●​ Seen as tiny Gram-negative

LAB DIAGNOSIS coccobacilli inside macrophages
(rarely).​

Specimen
●​ Blood (early stages, for Gram Smear Findings (Diagram)
culture/PCR)​
●​ Small, faintly staining Gram-negative
●​ Bone marrow aspirate (most coccobacilli, singly or in pairs​
sensitive specimen for culture)​

●​ CSF, pus, tissue biopsy (if

localized disease)​
Special Stains
●​ Serum (for antibody detection)​
●​ Modified Ziehl–Neelsen (stains red
with 1% carbol fuchsin, unlike
Mycobacteria which need stronger
decolorizer).​
Possible Specimens
●​ Blood, bone marrow, lymph node
aspirates, liver biopsy, CSF, serum​
Type of Motility
●​ Non-motile​

Method of Collection & Transport

Culture
●​ Slow-growing (2–4 weeks), small Biochemical Tests
convex translucent colonies​
●​ Catalase: positive​
●​ Strictly aerobic (except B. abortus
needs 5–10% CO₂)​ ●​ Oxidase: positive​

●​ Urease: strongly positive (within

Culture Medias: minutes, key test)​

●​ Blood agar, Chocolate agar​ ●​ H₂S production: B. abortus +, B.

melitensis –​
●​ Castaneda biphasic medium (solid +
broth in same bottle → increases
yield)​

Automated Identification
Enrichment Media:
●​ MALDI-TOF → accurate species ID​
●​ Liver infusion agar, Brucella agar
with serum​
●​ VITEK-2 → useful for biochemical
identification​
Transport Media:

●​ Castaneda biphasic medium (can

also act as transport)​
Special Tests (Important for
exams)
Selective Media:
1.​ Standard Agglutination Test
●​ Thayer-Martin, Farrell’s medium (SAT/Wright test)​
(with antibiotics)​
○​ Detects agglutinating
antibodies in serum​
Differential Media:
○​ Significant titer: ≥ 1:160 (with
●​ Not typically used​ rising titers diagnostic)​

2.​ Coombs test​

○​ Detects “blocking”
Identification non-agglutinating antibodies​

●​ Colony morphology, oxidase +, 3.​ Brucellin skin test (mallein-like)​

catalase +, urease + (rapid)​
○​ For epidemiological studies,
●​ Agglutination with monospecific not diagnosis​
antisera​
(Diagram: Tube agglutination with graded ●​ Drugs of choice:​
dilutions showing agglutination pattern)
○​ Doxycycline + Rifampicin (6
weeks)​

Serology ○​ Doxycycline + Streptomycin

(2–3 weeks streptomycin)​
●​ Sample: serum​

●​ ELISA (IgM, IgG detection – more

sensitive and specific than SAT)​
Typing Methods
●​ Rose Bengal test (rapid slide
agglutination screening test)​ ●​ Biotyping (CO₂ requirement, H₂S
production, phage typing)​
●​ Complement fixation test​
●​ Molecular: MLVA (Multiple Locus
VNTR Analysis), MLST, Whole
genome sequencing​

Molecular Methods
●​ PCR (conventional, nested,
real-time) on blood, bone marrow,
CSF, tissue​ Treatment
●​ Useful for early diagnosis and ●​ Combination therapy required (to
species differentiation​ prevent relapse):​

○​ Doxycycline + Rifampicin (6
weeks) or​

○​ Doxycycline + Streptomycin
Non-Specific Findings (2–3 weeks)​
●​ Anemia, leukopenia, relative
lymphocytosis​

●​ Raised ESR, CRP​

Prophylaxis
●​ Abnormal LFTs​
●​ No human vaccine (available only
for animals)​

●​ Pasteurization of milk​
Antimicrobial Susceptibility
Testing ●​ Animal vaccination (B. abortus strain
19, B. melitensis Rev-1)​
●​ Not routinely done (intracellular
pathogen, slow growth)​
 ●​ Protective measures for abattoir and ●​ Borrelia burgdorferi (in the U.S.)​
lab workers​
●​ Borrelia afzelii, Borrelia garinii (in
Europe & Asia)​

✅ Exam Pearls:
●​ Undulant fever pattern is classic​ Classification
●​ B. melitensis = most pathogenic to ●​ Phylum: Spirochaetota​
humans​
●​ Class: Spirochaetia​
●​ Bone marrow culture = most
sensitive​ ●​ Order: Spirochaetales​
●​ SAT (Wright’s test) = traditional ●​ Family: Spirochaetaceae​
diagnostic test​
●​ Genus: Borrelia​
●​ ELISA = best for
sensitivity/specificity​

●​ Modified ZN stain (1% H₂SO₄) →

Brucella stains red (differentiates
from Mycobacteria)​
Morphology
(for spirochetes we describe under this
heading – though bacteria, examiners
expect this)
Perfect 👍 , let’s cover Lyme disease (a
very important zoonotic bacterial infection ●​ Long, thin helical spirochete
caused by Borrelia burgdorferi). I’ll make a (~10–30 µm length, 0.2–0.5 µm
structured exam-oriented note for you. width)​

●​ Flexible, with endoflagella (axial

filaments) → corkscrew motility​

●​ Stains poorly with Gram stain →

LYME DISEASE better seen by dark-field
microscopy or silver stains​

(Diagram: thin spiral-shaped bacterium with

Name of Disease endoflagella between outer sheath and cell
wall)
●​ Lyme disease (Lyme borreliosis)​

Pathogenesis
Causative Organism
 1.​ Tick bite (Ixodes tick) introduces Local multiplication → erythema migrans
spirochetes into skin.​ (Stage I)​
⬇​
2.​ Multiply locally → characteristic Dissemination via blood & lymph​
erythema migrans rash.​ ⬇​
Involvement of heart, joints, nervous
3.​ Spread via blood/lymph → joints, system (Stage II)​
heart, nervous system.​ ⬇​
Persistent infection → chronic arthritis,
4.​ Immune response & inflammation → neuro symptoms (Stage III)
arthritis, carditis, neuroborreliosis.​

5.​ Chronic infection may persist due to

antigenic variation (VlsE protein).​ Clinical Features
Stage I – Early localized (days–weeks):

●​ Erythema migrans (target/bull’s-eye

Risk Factors rash)​

●​ Exposure to wooded or grassy areas ●​ Fever, malaise, myalgia, headache​

in endemic regions​

●​ Outdoor workers, campers, hunters​ Stage II – Early disseminated

(weeks–months):
●​ Lack of protective clothing/tick
repellent​ ●​ Multiple skin lesions​

●​ Migratory arthritis​

●​ Carditis (AV block, myocarditis)​

Mode of Transmission
●​ Neurologic: meningitis, cranial
●​ Bite of Ixodes scapularis (deer neuritis (especially facial nerve
tick) or Ixodes ricinus (Europe)​ palsy)​

●​ Reservoir: rodents (white-footed

mice), deer maintain tick population​ Stage III – Late persistent
(months–years):

●​ Chronic arthritis (large joints)​

●​ Chronic neuroborreliosis
Sequence of Events – (encephalopathy, neuropathy)​
FLOWCHART
●​ Acrodermatitis chronica atrophicans
Infected tick (Ixodes) bite​ (Europe)​
⬇​
Transmission of Borrelia burgdorferi into
human skin​
⬇​
LAB DIAGNOSIS
Gram Smear Findings (Diagram)
●​ Too thin to visualize clearly with
Specimen Gram stain → faint spiral organisms​
●​ Serum (for antibody detection –
most important)​

●​ CSF (neuroborreliosis)​
Special Stains
●​ Skin biopsy (erythema migrans)​
●​ Giemsa, Silver impregnation
●​ Blood (for PCR)​ (Warthin–Starry) → shows slender
helical spirochetes​

Possible Specimens
Type of Motility
●​ Blood, CSF, synovial fluid, skin
biopsy​ ●​ Corkscrew motility (due to axial
filaments/endoflagella)​

Method of Collection & Transport

Culture
●​ Serum: plain sterile tube​
●​ Very difficult, requires special
●​ CSF: lumbar puncture, sterile medium → rarely done in routine
screw-cap container​ labs​

●​ Synovial fluid: aspirated aseptically​

Culture Media:
●​ Transport at 4 °C, avoid repeated
freeze–thaw​ ●​ Barbour-Stoenner-Kelly (BSK)
medium → enriched medium with
serum & rabbit serum​

●​ Growth: 1–2 weeks, microaerophilic

conditions​
Microscopy
●​ Type: Dark-field microscopy Enrichment Broth/Enriched Media:
(demonstrates live motile
spirochetes from tissue)​ ●​ BSK medium itself is enriched​
●​ Silver staining of biopsy sections​
Transport Media:
 ●​ Not routinely available for Borrelia​

Special Tests
Selective Media:
●​ Two-tier serology
●​ None used routinely​ (CDC-recommended):​

1.​ ELISA or IFA (screening test)​

Differential Media:
2.​ Western blot confirmation
●​ Not applicable​
(IgM/IgG antibodies)​

(Diagram: Western blot with Borrelia

proteins and bands of IgM/IgG)
Identification
●​ Colony morphology not useful (liquid
medium preferred)​ Serology
●​ Molecular methods (PCR) used for ●​ Sample: serum (or CSF in
identification​ neuroborreliosis)​

●​ ELISA → detects IgM (early), IgG

(late) antibodies​

Culture Smear Findings ●​ C6 ELISA (detects conserved VlsE

antigen) → more specific​
●​ Same as microscopy (thin, spiral,
motile spirochetes)​

Molecular Methods
Biochemical Tests ●​ PCR → blood, CSF, synovial fluid,
skin biopsy​
●​ Not useful (fastidious organism, not
characterized by routine biochemical ●​ Used for early diagnosis & species
tests)​ typing​

Automated Identification Non-Specific Findings

●​ MALDI–TOF / VITEK → not ●​ ESR raised​
routinely applied for Borrelia (due to
culture limitations)​ ●​ Lymphocytic pleocytosis in CSF
(neuroborreliosis)​
 ●​ Prompt tick removal (ticks must feed
≥36 hrs for transmission)​
Antimicrobial Susceptibility
●​ Prophylactic single-dose doxycycline
Testing
after high-risk Ixodes bite​
●​ Not done routinely (Borrelia not
grown easily in standard conditions)​

●​ Clinical response guides therapy​

✅ Exam Pearls
●​ Erythema migrans is
pathognomonic – lab confirmation
not always needed in endemic area​
Typing Methods
●​ Two-tier serology (ELISA + Western
●​ Molecular typing: MLST (multilocus blot) is diagnostic standard​
sequence typing), PFGE, RFLP​
●​ Culture is rarely done (requires BSK
●​ Used in epidemiology to differentiate medium)​
B. burgdorferi sensu lato complex​
●​ Spirochete with corkscrew motility​

●​ Ixodes tick is the vector​

Treatment
●​ Early disease: Doxycycline (10–21
days)​
Perfect 👌 Let’s prepare Dengue Virus in
your requested Virus format step by step,
exam-oriented:
●​ Children/pregnant: Amoxicillin or
Cefuroxime​

●​ Late
disseminated/Neuroborreliosis: IV
Ceftriaxone​
🦠 Dengue Virus
• Name of Disease –​
Dengue Fever (also Dengue Hemorrhagic
Fever / Dengue Shock Syndrome in severe
cases)
Prophylaxis • Causative Organism –​
Dengue virus (DENV-1, DENV-2, DENV-3,
●​ No human vaccine (previous DENV-4 serotypes)
vaccine LYMErix withdrawn)​
• Classification (if any) –
●​ Tick avoidance (protective clothing,
repellents – DEET, permethrin)​ ●​ Family: Flaviviridae​
 ●​ Genus: Flavivirus​ • Risk Factors –

●​ Genome: Positive-sense ●​ Living in endemic tropical/subtropical

single-stranded RNA (ssRNA), ~11 regions​
kb​
●​ Poor vector control​
●​ Enveloped virus​
●​ Secondary dengue infection with
different serotype​

●​ Children & elderly more prone to

• Morphology of Organism – severe forms​

●​ Icosahedral symmetry​ ●​ Comorbidities: diabetes, asthma​

●​ ~50 nm diameter​

●​ Lipid envelope with surface

glycoproteins (E protein → • Mode of Transmission –
attachment, entry, neutralization
target)​ ●​ Bite of infected Aedes mosquitoes
(diagram would show spherical (mainly Aedes aegypti)​
enveloped virus with surface spikes)​
●​ Vertical transmission (rare, mother
→ child)​

●​ Blood transfusion / organ transplant

• Pathogenesis – (rare)​

1.​ Virus introduced via bite of infected

Aedes aegypti / Aedes albopictus.​

2.​ Virus replicates in Langerhans • Sequence of Events leading to Disease

cells, dendritic cells, monocytes, – FLOWCHART
endothelial cells.​
Infected Mosquito Bite → Viral replication in
3.​ Primary infection → usually skin dendritic cells → Spread via lymph &
self-limiting fever.​ blood → Viremia →​
Primary infection (mild dengue fever) OR
4.​ Secondary infection with different Secondary infection (ADE → cytokine storm
serotype → antibody-dependent → vascular leakage → hemorrhage/shock)
enhancement (ADE) → increased
viral replication in Fc-bearing cells.​

5.​ Cytokine storm + vascular • Clinical Features –

permeability → hemorrhage,
shock.​ Stage 1: Dengue Fever (“breakbone
fever”)

●​ High fever, severe

myalgia/arthralgia, retro-orbital pain,
 headache, rash, leukopenia.​ detect viral antigens in tissue.​

Stage 2: Dengue Hemorrhagic Fever

(DHF)
• Serology –
●​ Plasma leakage, thrombocytopenia,
hemorrhagic manifestations ●​ NS1 antigen detection
(petechiae, gum bleeding).​ (ELISA/rapid test) → useful in first
5 days of illness.​

Stage 3: Dengue Shock Syndrome (DSS) ●​ IgM ELISA → detectable from day 5
onward.​
●​ Severe hypotension, circulatory
collapse, organ failure.​ ●​ IgG ELISA → indicates past
infection; rising titer = recent
infection.​

●​ Differentiation between primary vs.

• Lab Diagnosis – secondary infection based on
IgM/IgG ratios.​
Specimen –

●​ Serum (for antigen/antibody

detection, PCR)​
• Molecular Methods –
●​ Whole blood (for viral RNA
detection)​ ●​ RT-PCR (since RNA virus) →
detects viral genome in acute phase
●​ Rare: tissue in fatal cases (liver, (day 1–7).​
spleen)​
●​ Real-time quantitative RT-PCR used
for viral load & serotyping.​
Possible Specimens – Serum, plasma,
whole blood.​
Method of Collection – Venipuncture in
sterile vacutainers.​
Transport & Preservation – • Virus Isolation –

●​ Transport on ice (2–8 °C if <24 h)​ ●​ Possible but not routine (requires
biosafety labs).​
●​ For longer: store at –70 °C (avoid
freeze-thaw).​
• Viral Tissue Culture –

●​ C6/36 mosquito cell line (Aedes

albopictus cells) → cytopathic effect
• Direct Microscopy – (CPE) after few days.​

●​ No classic inclusion bodies in cells

→ but immunofluorescence can
 ●​ Also human monocyte/macrophage ●​ Leukopenia​
cultures.​
●​ Elevated hematocrit (due to plasma
leakage)​
• Animal Inoculation –
●​ Elevated liver enzymes​
●​ Not routinely used (low yield).​

• Embryonated Egg Inoculation –

• Antimicrobial Susceptibility Testing –
●​ Not typically used for dengue virus
isolation (unlike influenza).​ ●​ Not applicable (virus, no antibiotic
sensitivity).​

• Treatment –

●​ No specific antiviral drug​

Got it✅ Let’s structure Chikungunya
Virus in your requested VIRUS format
(exam-friendly, with lab focus).
●​ Supportive management: fluid
replacement, antipyretics

🦠
(paracetamol, avoid NSAIDs due to
bleeding risk).​

●​ Monitor platelet count & hematocrit.​ Chikungunya

Virus
• Name of Disease –​
• Prophylaxis – Chikungunya Fever

●​ Vector control (eliminating • Causative Organism –​

mosquito breeding sites).​ Chikungunya virus (CHIKV)

●​ Vaccine: Dengvaxia (live • Classification –

attenuated, tetravalent vaccine) →
approved in some countries for ●​ Family: Togaviridae​
individuals with prior dengue
infection (not for dengue-naïve due ●​ Genus: Alphavirus​
to ADE risk).​
●​ Genome: Positive-sense ssRNA
(~11.8 kb)​

●​ Enveloped virus​
• Non-Specific Findings –

●​ Thrombocytopenia​

• Morphology –
 ●​ Icosahedral capsid, ~60–70 nm in ●​ Elderly (higher risk of severe
diameter​ disease)​

●​ Envelope with spike glycoproteins

(E1, E2) → mediate host cell entry​

●​ RNA genome encodes nonstructural • Mode of Transmission –

proteins (replication) + structural
proteins (capsid & envelope)​ ●​ Bite of infected Aedes
mosquitoes (day-biting mosquitoes)​

(DIAGRAM: spherical enveloped virus with ●​ Rare: vertical transmission (mother

glycoprotein spikes projecting outward, → neonate), blood transfusion​
showing capsid + RNA inside)

• Pathogenesis – • Sequence of Events – FLOWCHART

1.​ Virus enters via Aedes aegypti / Infected Mosquito Bite → Viral entry into
Aedes albopictus mosquito bite.​ skin fibroblasts → Viremia → Spread to
joints, muscles, endothelial cells →​
2.​ Initial replication in skin fibroblasts Acute phase: Fever, rash, severe
& dendritic cells.​ arthralgia →​
Chronic phase: Persistent arthritis, joint
3.​ Disseminates via bloodstream → pain in some patients
infects endothelial cells,
macrophages, joints, muscles.​

4.​ Strong innate immune response • Clinical Features –

(interferons, cytokines) → fever,
myalgia.​ Stage 1: Acute phase (2–12 days
incubation)
5.​ Persistent viral RNA in joints →
chronic arthritis-like symptoms in ●​ High fever​
some patients.​
●​ Severe polyarthralgia (“bent-over
posture”)​

●​ Maculopapular rash​
• Risk Factors –
●​ Headache, myalgia, conjunctivitis​
●​ Living in tropical/subtropical areas
with Aedes mosquitoes​
Stage 2: Chronic phase (weeks–months,
●​ Lack of mosquito control​ sometimes years)

●​ Immunocompromised individuals​ ●​ Persistent joint pain (rheumatoid

arthritis–like)​
 ●​ Fatigue, depression in some patients​ ●​ Antigen capture ELISA (less
common)​

• Lab Diagnosis –
• Molecular Methods –
Specimen –
●​ RT-PCR (since RNA virus) →
●​ Serum (for antibody, antigen, RNA detects viral genome in acute phase
detection)​ (first week)​

●​ Plasma or whole blood​ ●​ Real-time RT-PCR useful for

quantification & confirmation​

Possible Specimens – Serum, plasma,

blood​
Method of Collection – Venipuncture (2–5
mL)​ • Virus Isolation –
Transport & Preservation –
●​ Possible in specialized labs (BSL-3)​
●​ 2–8 °C if tested within 48 h​

●​ For long-term: –70 °C storage (avoid • Viral Tissue Culture –

freeze-thaw)​
●​ Vero cells (monkey kidney cells)
or BHK-21 cells (baby hamster
kidney) → show cytopathic effect
(CPE: cell rounding, syncytia
• Direct Microscopy – formation)​

●​ No typical inclusion bodies reported

for CHIKV​ • Animal Inoculation –

●​ Detection usually by ●​ Not routinely used; mice/hamsters

immunofluorescence in cell used in research models​
culture​

• Embryonated Egg Inoculation –

●​ Not routinely used for CHIKV (mainly

• Serology – for arbovirus research, not
diagnosis)​
●​ IgM ELISA (detectable from day 5,
persists for 2–3 months)​

●​ IgG ELISA (persists longer,

indicates past infection)​ • Treatment –

●​ No specific antiviral drug​

 ●​ Supportive therapy: paracetamol for
fever, fluids​

●​ NSAIDs for joint pain (after ruling out

🦠 Kyasanur
Forest Disease
dengue, as they may worsen
bleeding in dengue coinfection)​ (KFD)
• Name of Disease –​
Kyasanur Forest Disease (KFD, also called
“Monkey Fever”)
• Prophylaxis –
• Causative Organism –​
●​ No licensed vaccine yet (several Kyasanur Forest Disease Virus (KFDV)
under trial)​
• Classification –
●​ Vector control: eliminate mosquito
breeding sites, insecticide spraying, ●​ Family: Flaviviridae​
bed nets, repellents​
●​ Genus: Flavivirus​

●​ Group: Arbovirus (tick-borne)​

• Non-Specific Findings – ●​ Genome: Positive-sense
single-stranded RNA (ssRNA)​
●​ Leukopenia​

●​ Thrombocytopenia (less severe than

dengue)​
• Morphology –
●​ Elevated liver enzymes (sometimes)​
●​ Enveloped, spherical, ~40–60 nm
diameter​

●​ Icosahedral nucleocapsid​
• Antimicrobial Susceptibility Testing –
●​ Lipid envelope with glycoprotein
●​ Not applicable (virus, no antibiotics)​ spikes (for host cell binding)​

●​ RNA genome codes for structural &

non-structural proteins​
Perfect👍 Let’s do Kyasanur Forest
Disease (KFD) Virus in the VIRUS (DIAGRAM: spherical flavivirus with lipid
exam-friendly format. envelope & spikes; RNA inside icosahedral
capsid)

• Pathogenesis –
 1.​ Virus transmitted by bite of infected Spread to liver, spleen, lymph nodes →​
Haemaphysalis spinigera ticks.​ Endothelial injury + Hemorrhages → Acute
febrile illness with hemorrhage →​
2.​ Initial replication in dendritic cells Some cases → CNS involvement →
and macrophages at site of tick Meningoencephalitis
bite.​

3.​ Viremia → spreads to

reticuloendothelial system (liver, • Clinical Features –
spleen, lymph nodes).​
Stage 1: Incubation (2–7 days)
4.​ Causes endothelial damage,
capillary leakage, and ●​ Sudden high fever​
hemorrhages.​
●​ Headache, myalgia, photophobia​
5.​ CNS involvement → encephalitis in
severe cases.​ ●​ Vomiting, diarrhea​

●​ Bleeding (epistaxis, gum bleed, GI

hemorrhage)​

• Risk Factors –
Stage 2: Neurological phase (in some)
●​ People living/working in forests of
Karnataka (Western Ghats)​ ●​ After ~1–2 weeks → encephalitis
(tremors, mental confusion,
●​ Forest workers, farmers, hunters​ seizures, coma)​

●​ Exposure to ticks or contact with ●​ Mortality: 3–10%​

infected monkeys​

Stage 3: Convalescence

●​ Prolonged weakness, hair loss,

• Mode of Transmission – muscle wasting in survivors​

●​ Tick bite (Haemaphysalis ticks are

both vector & reservoir)​

●​ Handling infected animals • Lab Diagnosis –

(especially dead monkeys)​
Specimen –
●​ No person-to-person spread​
●​ Serum, plasma, CSF (if neurological
symptoms)​

• Sequence of Events – FLOWCHART Possible Specimens – Blood (for

antigen/antibody), CSF (for CNS cases),
Infected Tick Bite → Viral entry → Primary postmortem tissues
replication in dendritic cells → Viremia →
Method of Collection – ●​ Real-time RT-PCR used in outbreak
settings​
●​ Venipuncture (serum/plasma),
lumbar puncture (CSF)​

Transport & Preservation – • Virus Isolation –

●​ Keep at 2–8 °C for ≤48 h​ ●​ Possible in specialized high-level

biosafety labs​
●​ Long-term: –70 °C storage​
●​ Requires intracerebral inoculation of
●​ BSL-3/4 containment required infant mice or tissue culture​
(high-risk pathogen)​

• Viral Tissue Culture –

●​ Grows in Vero cells (monkey

• Direct Microscopy – kidney cells)​

●​ No classical inclusion bodies​ ●​ Cytopathic effect: cell rounding,

detachment​
●​ Virus not visualized directly in
routine light microscopy​
• Animal Inoculation –

●​ Infant mice (intracerebral

inoculation) → lethal encephalitis
• Serology – (used historically)​

●​ IgM ELISA (appears from ~5th day

of illness) → confirms acute infection​ • Embryonated Egg Inoculation –

●​ IgG ELISA → indicates past ●​ Rarely used for KFD (flaviviruses

exposure​ don’t typically use eggs like
orthomyxoviruses)​
●​ Hemagglutination inhibition (HI),
Complement fixation (obsolete, less
specific)​

●​ Neutralization tests (reference • Treatment –

standard in research labs)​
●​ No specific antiviral available​

●​ Supportive therapy: IV fluids,

correction of electrolyte imbalance,
• Molecular Methods – blood transfusion if hemorrhage​

●​ RT-PCR (since ssRNA virus) → ●​ Manage CNS complications

highly sensitive for acute infection​ symptomatically​
 • Name of Disease –​
Ebola Virus Disease (EVD) / Ebola
• Prophylaxis – Hemorrhagic Fever

●​ Killed formalin-inactivated KFD • Causative Organism –​

vaccine (given in endemic Ebola Virus (*species of genus Ebolavirus)
Karnataka areas)​
• Classification –
○​ Schedule: 2 doses, 1 month
apart → booster every 6–9 ●​ Family: Filoviridae​
months for 5 years​
●​ Genus: Ebolavirus​
●​ Personal protection: tick repellents,
protective clothing​ ●​ Genome: Negative-sense
single-stranded RNA (–ssRNA)​
●​ Tick control in forest areas​
●​ Notable species: Zaire ebolavirus,
Sudan ebolavirus, Bundibugyo
ebolavirus, Tai Forest ebolavirus,
Reston ebolavirus​
• Non-Specific Findings –

●​ Leukopenia​

●​ Thrombocytopenia​ • Morphology –

●​ Elevated liver enzymes​ ●​ Filamentous, pleomorphic virus

(thread-like, 800–1000 nm long)​

●​ Enveloped with helical nucleocapsid​

• Antimicrobial Susceptibility Testing – ●​ Surface covered with glycoprotein

(GP) spikes → responsible for
●​ Not applicable (virus, no antibiotics)​ attachment to host cells​

●​ RNA + nucleoprotein + polymerase

complex inside​

Alright, let’s do Ebola virus infection in the

standard exam-oriented viral disease (DIAGRAM: filamentous rod-like virus,
format. envelope with glycoprotein spikes, helical
nucleocapsid inside)

🦠 Ebola Virus
Disease (EVD)
• Pathogenesis –

1.​ Entry via mucosa, broken skin, or

parenterally (needle stick, contact
with blood/secretions).​
 2.​ Virus infects monocytes, endothelium →​
macrophages, dendritic cells → Cytokine storm + endothelial injury →
triggers cytokine storm.​ Hemorrhage + DIC → Shock, multiorgan
failure
3.​ Viremia → widespread infection of
liver, spleen, endothelial cells.​

4.​ Leads to endothelial dysfunction, • Clinical Features –

capillary leakage, hemorrhage,
DIC, multiorgan failure.​ Stage 1: Incubation (2–21 days, avg 7–10
days)

●​ Asymptomatic​

• Risk Factors –
Stage 2: Acute illness
●​ Health-care workers handling cases
without PPE​ ●​ Sudden fever, chills, malaise, severe
myalgia​
●​ Direct contact with body fluids of
infected patients​ ●​ Headache, sore throat, abdominal
pain, diarrhea, vomiting​
●​ Traditional burial practices with body
contact​ ●​ Rash (maculopapular, non-itchy) on
trunk​
●​ Bush meat handling (fruit bats,
monkeys – reservoir hosts)​
Stage 3: Hemorrhagic phase (severe
cases)

●​ Epistaxis, gum bleeding,

• Mode of Transmission – hematemesis, melena​

●​ Direct contact with blood, secretions, ●​ Conjunctival hemorrhage​

organs, or other body fluids of
infected persons/animals​ ●​ Petechiae, ecchymoses​

●​ Person-to-person spread → through ●​ Shock, multi-organ dysfunction​

skin/mucosal contact​

●​ No airborne spread proven in Stage 4: Recovery/Death

humans​
●​ High case fatality: 25–90%
depending on species​

• Sequence of Events – FLOWCHART

Infected animal → Spillover to human → • Lab Diagnosis –

Primary replication in macrophages →
Viremia → Spread to liver, spleen, Specimen –
 ●​ Blood, serum, plasma​

●​ Throat swabs, urine, tissue • Molecular Methods –

(postmortem)​
●​ RT-PCR (since Ebola is –ssRNA
virus) → gold standard for diagnosis​
Possible Specimens – Blood during acute
phase is most common ●​ Real-time RT-PCR widely used in
outbreaks​
Method of Collection –

●​ Strict biosafety precautions, PPE,

double/triple packaging​
• Virus Isolation –

Transport & Preservation – ●​ Possible but only in BSL-4 labs​

●​ Immediate processing at BSL-4 labs ●​ Very high risk → not routine​

only​

●​ Stored at –70 °C for molecular • Viral Tissue Culture –

assays​
●​ Vero E6 cells (African green monkey
kidney cells)​

●​ Findings: Cytopathic effect – cell

• Direct Microscopy – rounding, detachment, syncytia
formation​
●​ No classical inclusion bodies seen
on routine microscopy​
• Animal Inoculation –
●​ EM: filamentous particles, but not for
routine use​ ●​ Experimental use: Non-human
primates, guinea pigs, mice (for
research)​

●​ Not used diagnostically​

• Serology –

●​ ELISA for antigen detection • Embryonated Egg Inoculation –

(captures viral GP or NP antigen) –
useful early​ ●​ Not used (filoviruses do not grow
well in eggs)​
●​ IgM ELISA (appears by day 5–7)​

●​ IgG ELISA → past

infection/recovery​
• Treatment –
●​ Neutralization assay → confirmatory,
done in reference labs​
 ●​ No definitive antiviral (supportive
therapy mainstay)​
Perfect 👌 , let’s prepare a parasite-format
exam note for Malaria, since it’s one of the
most important protozoal infections for
●​ IV fluids, electrolyte correction, exams. I’ll structure it step by step exactly
oxygen support​ as per your template.

●​ Experimental drugs: Remdesivir,

🦟
monoclonal antibodies (Inmazeb,
Ebanga)​

●​ Convalescent plasma tried in Malaria

outbreaks​
(Protozoan
Disease)
• Prophylaxis – • Name of Disease –​
Malaria
●​ rVSV-ZEBOV (Ervebo®) – live
attenuated recombinant vesicular • Causative Organism –​
stomatitis virus expressing Ebola GP​ Plasmodium spp.

○​ Licensed & used in outbreak ●​ P. falciparum (most severe, cerebral

control (ring vaccination malaria)​
strategy)​
●​ P. vivax (common in India, relapsing)​
●​ Strict barrier nursing, PPE, contact
tracing​ ●​ P. malariae (quartan malaria)​

●​ P. ovale (relapsing, mainly in Africa)​

●​ P. knowlesi (zoonotic malaria,

• Non-Specific Findings – Southeast Asia)​
●​ Leukopenia, thrombocytopenia​

●​ Elevated liver enzymes, PT/APTT

prolonged​ • Classification –

●​ DIC features​ ●​ Kingdom: Protista​

●​ Phylum: Apicomplexa​

●​ Class: Sporozoa​
• Antimicrobial Susceptibility Testing –
●​ Genus: Plasmodium​
●​ Not applicable (virus)​

• Morphology (Protozoa) –
 ●​ In mosquito (definitive host):
Sporozoites, gametocytes, oocysts​
• Risk Factors –
●​ In humans (intermediate host):​
●​ Living in endemic areas​
○​ Sporozoites (infective form,
from mosquito bite)​ ●​ Lack of mosquito control​

○​ Trophozoites (ring form in ●​ Immunocompromised states​

RBCs)​
●​ Pregnancy (more severe in
○​ Schizonts (divide into falciparum malaria)​
merozoites)​
●​ Children <5 years​
○​ Gametocytes (sexual forms
taken up by mosquito)​

(DIAGRAM: RBC showing ring form, • Mode of Transmission –

trophozoite, schizont with merozoites,
crescent-shaped gametocyte in P. ●​ Bite of female Anopheles mosquito​
falciparum)
●​ Rare: blood transfusion, organ
transplant, congenital​

• Pathogenesis –

1.​ Bite of infected Anopheles mosquito

→ injection of sporozoites.​ • Sequence of Events – FLOWCHART

2.​ Sporozoites enter hepatocytes → Infected mosquito bite → Sporozoites →

exoerythrocytic schizogony Liver cells (asymptomatic schizogony) →
(asymptomatic liver stage).​ Merozoites → RBC invasion → Trophozoite
→ Schizont → RBC rupture → Clinical fever
3.​ Merozoites released → invade paroxysm → Some forms → Gametocytes
RBCs → erythrocytic cycle (for mosquito uptake).
(symptomatic stage).​

4.​ RBC rupture → release of

merozoites + hemozoin pigment → • Clinical Features (Stage-wise)
fever paroxysms.​
●​ Incubation Period:​
5.​ In P. vivax and P. ovale →
hypnozoites persist in liver → ○​ P. falciparum: 9–14 days​
relapses.​
○​ P. vivax: 12–17 days​
6.​ P. falciparum → sequestration of
parasitized RBCs in cerebral/visceral ●​ Uncomplicated Malaria:​
capillaries → severe malaria.​
○​ Fever with chills and rigors
(paroxysms periodic –
 tertian/quartan)​ Macroscopic Findings –​
No specific macroscopic changes
○​ Headache, myalgia, sweating​
Microscopic Findings (Saline Mount &
○​ Splenomegaly, anemia​ Stains) –

●​ Severe Malaria (esp. falciparum):​ ●​ Thick smear → screening (more

sensitive)​
○​ Cerebral malaria (seizures,
coma)​ ●​ Thin smear → species identification​

○​ Hypoglycemia, metabolic
acidosis​ DIAGRAM Findings:

○​ Pulmonary edema, renal ●​ P. vivax: Enlarged RBCs,

failure​ Schüffner’s dots​

○​ Hemoglobinuria (“blackwater ●​ P. falciparum: Multiple ring forms,

fever”)​ applique forms, crescent gametocyte​

●​ P. malariae: Band forms across RBC​

🔬 Lab Diagnosis
●​ P. ovale: Oval RBCs with fimbriated
edges​

• Specimen –​ Egg finding – ❌(not applicable for malaria

– only protozoan blood stages, no eggs).
Peripheral blood

• Possible Specimens –​
Capillary blood (finger prick), venous blood
If Stool – ❌ Not applicable
• Method of Collection –​
Collected at fever paroxysm and between Concentration Technique – ❌
intestinal parasites, not malaria).
(Used for
attacks (important for detection of different
stages).

• Method of Transport & Preservation –

Special Tests –
●​ Thick/thin smears prepared on the
spot​ ●​ Rapid Diagnostic Tests (RDTs):
Immunochromatographic detection
●​ EDTA blood for antigen/PCR, stored of antigens​
at 4 °C​
○​ HRP-2 (Histidine-rich protein)
→ P. falciparum​

○​ LDH or Aldolase → all

Specimen Examination species​
(Diagram: RDT strip showing control & test (to kill liver hypnozoites)​
lines for Pf/Pv)
●​ Falciparum malaria:
Artemisinin-based Combination
Therapy (ACT)​
Culture –
●​ Severe malaria: IV Artesunate​
●​ In vitro culture possible for P.
falciparum in special media (RPMI
1640), but not used for routine
diagnosis.​
• Prophylaxis –

●​ Vector control (bed nets, insecticide

spray)​
Serology –
●​ Chemoprophylaxis: Chloroquine
●​ Indirect Fluorescent Antibody Test (non-resistant areas), Mefloquine,
(IFA) or ELISA for antibodies Atovaquone-proguanil, Doxycycline
(epidemiology, not acute diagnosis).​ (travelers)​

●​ No widely available vaccine yet

(RTS,S/AS01 – under use in some
African regions).​
Molecular Methods –

●​ PCR: Highly sensitive, differentiates

👍
species, detects mixed infections​
Great pick — Kala-azar (Visceral
Leishmaniasis) is one of the most
high-yield protozoal diseases. I’ll prepare it
in your parasite-template style for exams.
Imaging Techniques & Non-Specific
Tests

●​ Splenomegaly on ultrasound​

●​ Hematology: Anemia,
thrombocytopenia​
🧬 Kala-azar
(Visceral
●​ Elevated bilirubin, LDH (due to
hemolysis)​ Leishmaniasis)
• Name of Disease –​
Kala-azar / Visceral Leishmaniasis
• Treatment –
• Causative Organism –​
Leishmania donovani complex
●​ Uncomplicated P.
vivax/ovale/malariae: Chloroquine
●​ L. donovani (India, Africa)​
(where no resistance) + Primaquine
 ●​ L. infantum / L. chagasi ■​ Infective stage for
(Mediterranean, South America)​ humans​

📌
( Diagram to draw: Amastigote inside
macrophage + Promastigote with single
• Classification – flagellum)

●​ Kingdom: Protista​

●​ Phylum: Euglenozoa​ • Pathogenesis –

●​ Class: Kinetoplastida​ 1.​ Bite of infected female Phlebotomus

(sandfly) → injects promastigotes.​
●​ Order: Trypanosomatida​
2.​ Promastigotes enter macrophages
●​ Genus: Leishmania​ → transform into amastigotes.​

●​ Species: L. donovani​ 3.​ Amastigotes multiply within

macrophages (reticuloendothelial
system: spleen, liver, bone marrow).​

4.​ Organomegaly, pancytopenia,

• Morphology – (Protozoa) hypergammaglobulinemia →
classical Kala-azar triad.​
●​ Two main forms:​

○​ Amastigote
(Leishman-Donovan body):​
• Risk Factors –
■​ Intracellular,
oval/round, 2–4 μm​ ●​ Poverty, poor housing → breeding
grounds for sandflies​
■​ Found in
macrophages ●​ Immunocompromised (esp. HIV
(spleen, liver, bone co-infection)​
marrow)​
●​ Rural endemic areas (Bihar in India,
■​ Nucleus + kinetoplast Sudan, Bangladesh)​
visible​

○​ Promastigote:​

■​ Elongated, flagellated • Mode of Transmission –

(15–20 μm)​
●​ Bite of female Phlebotomus sandfly
■​ Found in gut of (vector-borne)​
sandfly vector​
●​ Rare: congenital, blood transfusion​
 ●​ Lymph node aspirate​

• Sequence of Events – FLOWCHART ●​ Buffy coat blood​

Sandfly bite → Promastigotes injected → ●​ Skin biopsy (PKDL)​

Macrophages → Amastigotes →
Multiplication in RES → Spleen/Liver/Bone
marrow involvement → Clinical disease • Method of Collection –​
(fever, hepatosplenomegaly, anemia). Aspirates collected under aseptic
precautions

• Method of Transport & Preservation –

• Clinical Features (Stage wise)
●​ Collected material smeared, fixed in
●​ Incubation: 2–6 months​ methanol, stained
(Giemsa/Leishman).​
●​ Classical triad:​
●​ Blood: in EDTA for
1.​ Irregular fever with chills​ molecular/serology.​

2.​ Splenomegaly (massive),

hepatomegaly​

3.​ Progressive anemia, Specimen Examination

cachexia, pancytopenia​
Macroscopic Findings –​
●​ Darkening of skin ("Kala azar" = No specific gross change
black fever)​
Microscopic Findings – Saline Mount /
●​ Post-Kala-Azar Dermal Stained Smear
Leishmaniasis (PKDL): nodular skin
lesions after treatment (esp. in ●​ Amastigotes (Leishman-Donovan
India).​ bodies): Round oval 2–4 µm, inside
macrophages, with nucleus +
rod-shaped kinetoplast.​

🔬 Lab Diagnosis 📌
( Diagram: macrophage with multiple LD
bodies inside)

❌ Not applicable
• Specimen –​
Splenic aspirate (most sensitive, but risky), If Stool –

❌
Bone marrow, Lymph node aspirate, Blood
Concentration Technique – Not used
• Possible Specimens – (this is blood/tissue parasite, not intestinal).

●​ Splenic aspirate (gold standard)​

●​ Bone marrow aspirate (safer)​ Special Tests –

 ●​ Montenegro skin test (Leishmanin ●​ Hematology: pancytopenia, anemia​
test): Delayed hypersensitivity,
positive in cutaneous leishmaniasis, ●​ Hypergammaglobulinemia (↑ IgG,
usually negative in active Kala-azar.​ polyclonal rise)​

●​ rk39 Dipstick Test (Rapid test):

Detects antibodies, widely used in

💊 Treatment
endemic areas.​

●​ Aldehyde test (Napier’s test):

Nonspecific (detects
hypergammaglobulinemia).​
●​ First line (India): Liposomal
Amphotericin B​

●​ Alternatives: Miltefosine (oral),

Culture – Pentavalent antimonials (Sb⁵⁺ like
Sodium stibogluconate – resistance
●​ NNN medium in Bihar), Paromomycin.​
(Novy-MacNeal-Nicolle):
Promastigotes grow from aspirates.​

Serology –

●​ rk39 ELISA /
🛡️ Prophylaxis
●​ Vector control (sandfly eradication –
immunochromatographic test DDT spray, insecticide nets).​
(detects anti-Leishmania antibodies).​
●​ Early detection and treatment of
●​ Direct agglutination test (DAT).​ cases.​

●​ No effective vaccine yet (research

ongoing).​

Molecular Methods –

👌
●​ PCR: Highly sensitive and specific,
detects parasite DNA in Perfect Let’s do Chagas Disease
blood/tissue.​ (American Trypanosomiasis) in your
exam-template format. This one is an
important protozoan disease caused by
Trypanosoma cruzi.

Imaging Techniques & Non Specific

Tests –

●​ Ultrasound: hepatosplenomegaly​
🧬 Chagas Disease
(American
■​ Round, 2–4 µm, no
flagellum, multiplies
inside macrophages
& muscle cells.​

Trypanosomiasis) 3.​ Epimastigote (in vector

midgut).​
• Name of Disease –​
Chagas Disease (American
Trypanosomiasis) 📌
( Diagram to draw: Trypomastigote in
blood smear – “C” or “S” shaped with
• Causative Organism –​ kinetoplast & undulating membrane)
Trypanosoma cruzi

• Pathogenesis –
• Classification –
1.​ Infected reduviid bug (kissing bug)
●​ Kingdom: Protista​ defecates on skin after blood meal.​

●​ Phylum: Euglenozoa​ 2.​ Metacyclic trypomastigotes in feces

enter through bite
●​ Class: Kinetoplastida​ wound/conjunctiva.​

●​ Order: Trypanosomatida​ 3.​ Invade local macrophages →

transform to amastigotes.​
●​ Genus: Trypanosoma​
4.​ Multiply → spread via bloodstream
●​ Species: T. cruzi​ as trypomastigotes → invade
myocardium, smooth muscle,
reticuloendothelial cells.​

5.​ Chronic inflammation, granulomas,

• Morphology of Organism – fibrosis → cardiomyopathy,
megaesophagus, megacolon.​
●​ Exists in 3 morphological forms:​

1.​ Trypomastigote (blood form

– infective & diagnostic):​
• Risk Factors –
■​ Elongated, 15–20 µm,
spindle-shaped.​ ●​ Rural poor housing (mud walls,
thatched roofs → bug breeding)​
■​ Single nucleus,
posterior kinetoplast, ●​ Blood transfusion/organ transplant in
undulating endemic areas​
membrane, free
flagellum.​ ●​ Congenital transmission​

2.​ Amastigote (tissue form):​

 ●​ Immunosuppressed individuals (HIV, arrhythmias, sudden death​
transplant)​
○​ Digestive involvement:
megacolon, megaesophagus
→ dysphagia, constipation​

• Mode of Transmission – ○​ Neurological: autonomic

dysfunction​
●​ Vector-borne: bite + fecal
contamination by reduviid bug
(Triatoma, Rhodnius,

🔬 Lab Diagnosis
Panstrongylus).​

●​ Blood transfusion, organ transplant,

congenital, oral (contaminated juices
in South America).​
• Specimen –​
Blood (acute stage), Tissue biopsy (chronic
stage), CSF (if meningoencephalitis)

• Sequence of Events – FLOWCHART • Possible Specimens –

Reduviid bug bite + fecal contamination → ●​ Peripheral blood​

Entry of trypomastigotes → Amastigote
multiplication in cells → Release of ●​ Lymph node aspirate​
trypomastigotes into blood → Dissemination
→ Organ damage (heart, GIT, nervous ●​ Bone marrow aspirate​
system).
●​ Tissue biopsy (heart, esophagus,
colon)​

• Clinical Features (Stage wise)

• Method of Collection –​
1.​ Acute Stage (weeks to months):​ Venipuncture for blood, sterile aspiration for
tissue
○​ Fever, malaise,
lymphadenopathy​ • Method of Transport & Preservation –

○​ Romana’s sign: unilateral ●​ EDTA blood for

periorbital edema microscopy/molecular​
(pathognomonic)​
●​ Tissue in saline/formalin (depending
○​ Hepatosplenomegaly​ on test)​

○​ Myocarditis (tachyarrhythmia,
heart failure in severe cases)​

2.​ Chronic Stage (years later):​ Specimen Examination

○​ Cardiac involvement: Macroscopic Findings – None specific
dilated cardiomyopathy,
Microscopic Findings – chronic disease.​

●​ Acute stage (blood): motile

trypomastigotes (C- or S-shaped)
seen in thin & thick Giemsa-stained
smears.​ Molecular Methods –

●​ Chronic stage (tissue biopsy): ●​ PCR (detects parasite DNA in

amastigotes within cardiac/smooth blood/tissue, esp. in early &
muscle cells.​ congenital cases).​

📌
( Diagram: Trypomastigote in smear +
amastigotes inside cardiac cell)
Imaging & Non Specific Tests –

❌ Not applicable
●​ ECG: arrhythmias, conduction
If Stool – blocks​

Concentration Technique – ❌ Not used ●​ Echocardiography: cardiomyopathy,

ventricular dilation​

●​ Barium studies: megaesophagus,

Special Tests – megacolon​

●​ Xenodiagnosis: Allow uninfected ●​ Hematology: nonspecific anemia,

reduviid bugs to feed on patient → leukocytosis in acute stage​
dissect bug midgut later to detect
parasites.​

💊 Treatment
●​ Strout test (hemoculture
concentration).​

●​ Acute disease & congenital

Culture – cases:​

●​ Novy-MacNeal-Nicolle (NNN) ○​ Nifurtimox or Benznidazole

medium​ (effective in early phase).​

●​ Liver infusion tryptose medium​ ●​ Chronic disease:​

○​ Supportive care:
pacemakers, heart
transplant, surgery for
Serology – megaesophagus/megacolon.​
●​ ELISA, Indirect Fluorescent Antibody
(IFA), Indirect Hemagglutination
(IHA) → detect anti-T. cruzi IgG in
🛡️ Prophylaxis
●​ Vector control (insecticides, housing
●​ Family: Onchocercidae​

●​ Genus: Wuchereria​

improvement)​ ●​ Species: W. bancrofti​

●​ Screening of blood/organ donors​

●​ No vaccine available​
• Morphology of Organism –

1.​ Adult worm​

Great choice 👍 Let’s structure Wuchereria

bancrofti infection (Lymphatic
●​ Long, thread-like nematode.​

Filariasis/Elephantiasis) exactly in your ●​ Male: 4 cm, female: 8–10 cm.​

exam format.
●​ Live in lymphatic vessels/nodes.​

🪱
2.​ Microfilaria (diagnostic stage in
blood)​

Wuchereria ●​ Sheathed, 270–300 µm long.​

bancrofti ●​ Cephalic space short, nuclei

discrete, tail free of nuclei
(Lymphatic (diagnostic feature).​

Filariasis / ●​ Shows nocturnal periodicity

(appears in peripheral blood at
Elephantiasis) night).​

• Name of Disease –​
Lymphatic Filariasis (Bancroftian Filariasis, 📌 Diagram to draw in exam: Microfilaria of
W. bancrofti (with sheath, cephalic space,
Elephantiasis)
nuclei not reaching tail).
• Causative Organism –​
Wuchereria bancrofti
• Pathogenesis –

• Classification – 1.​ Inoculation of infective filariform

larvae (L3 stage) from mosquito
●​ Kingdom: Animalia​ bite.​

●​ Phylum: Nematoda (roundworms)​ 2.​ Larvae migrate to lymphatics →

develop into adult worms.​
●​ Class: Secernentea​
3.​ Adults cause lymphatic obstruction
●​ Order: Spirurida​ → lymphangitis, lymphedema.​
 4.​ Repeated episodes → fibrosis, ○​ Lymphedema​
granuloma → elephantiasis of
lower limbs, scrotum, breasts.​ ○​ Elephantiasis (limbs,
scrotum, breasts, vulva)​

○​ Hydrocele​

• Risk Factors –

🔬 Lab Diagnosis
●​ Living in tropical/subtropical areas
(India, SE Asia, Africa).​

●​ Poor housing, mosquito exposure.​

●​ Lack of vector control.​ • Specimen – Blood (night sample), urine

(for chyluria), hydrocele fluid.

• Possible Specimens –

• Mode of Transmission – ●​ Peripheral blood (best between 10

pm–2 am due to nocturnal
●​ Bite of infected female mosquito periodicity).​
(Culex, Anopheles, Aedes,
Mansonia depending on geography).​ ●​ Lymph node aspirate.​

●​ Urine/hydrocele fluid.​

• Sequence of Events – FLOWCHART • Method of Collection – Venipuncture at

night.
Mosquito bite (L3 larvae inoculated) →
Migration to lymphatics → Development into • Method of Transport & Preservation –
adult worms → Release of microfilariae into
blood → Lymphatic obstruction + ●​ EDTA/Heparinized blood.​
inflammation → Lymphedema →
Elephantiasis. ●​ Thick blood smears immediately
prepared.​

• Clinical Features (Stage wise)

1.​ Asymptomatic stage – Specimen Examination –

microfilaremia without symptoms.​
Macroscopic Findings – None specific.
2.​ Acute stage – fever, lymphangitis,
lymphadenitis, epididymo-orchitis, Microscopic Findings –
chyluria.​
●​ Saline mount (wet prep): motile
3.​ Chronic/Obstructive stage –​ microfilariae.​
 ●​ Stained smear ●​ PCR (detects W. bancrofti DNA in
(Giemsa/Leishman): sheathed blood, more sensitive than
microfilariae, nuclei not extending to microscopy).​
tail.​

📌
( Diagram: Microfilaria showing sheath &
clear tail end) Imaging Techniques & Non Specific
Tests –

If Stool – ❌ Not applicable. ●​ Ultrasound: “Filarial dance sign” in

lymphatics.​

Concentration Technique – Knott’s ●​ X-ray: Calcified dead worms.​

concentration method or membrane filtration
for microfilariae (not stool floatation). ●​ Hematology: eosinophilia, elevated
IgE.​

Special Tests –

●​ DEC Provocative Test: Single dose

diethylcarbamazine → causes
microfilariae to appear in peripheral
blood. (Rarely used now)​
💊 Treatment
●​ Diethylcarbamazine (DEC): 6
●​ Ultrasound (Filarial dance sign): mg/kg/day × 12 days → drug of
Motile adult worms in lymphatics.​ choice.​

●​ Alternatives: Ivermectin,
Albendazole (esp. in mass drug
administration programs).​
Culture – Not possible.
●​ Surgery for hydrocele/elephantiasis
in advanced cases.​
Serology –

🛡️ Prophylaxis
●​ Antigen detection: ELISA, rapid
card tests (ICT).​

●​ Antibody detection: ELISA, IFA –

useful but cannot differentiate past
vs active infection.​ ●​ Vector control (mosquito nets,
repellents, larvicides).​

●​ Mass drug administration (MDA):

DEC + Albendazole annually in
Molecular Methods – endemic areas.​
 ●​ Health education.​ ●​ Yeast: Oval budding cells
(blastoconidia).​
●​ No vaccine available.​
●​ Pseudohyphae: Elongated budding
chains.​

Perfect 👌 Let’s do Candida infection

(Candidiasis) in your exam-ready
●​ True hyphae: Seen in tissue.​

●​ Chlamydospores: Thick-walled
structured fungal template. resting spores (diagnostic for C.
albicans).​

🍄 Candida
(Candidiasis /
📌– Budding
Diagram to draw:​

structure)
yeast cell with pseudohyphae​
– Chlamydospore (large, thick-walled round

Moniliasis / Thrush)
• Pathogenesis –
• Name of Disease –​
Candidiasis (Thrush, Vulvovaginal 1.​ Candida normally commensal in
candidiasis, Candidemia, Disseminated mouth, gut, vagina.​
candidiasis)
2.​ Immunosuppression, antibiotics,
• Causative Organism –​ diabetes, steroids → overgrowth.​
Candida albicans (most common, but also
C. glabrata, C. tropicalis, C. krusei, C. auris) 3.​ Adheres via surface adhesins →
forms biofilm.​

4.​ Invasion of epithelial/mucosal barrier

• Classification – → tissue destruction → systemic
dissemination (blood, organs).​
●​ Kingdom: Fungi​

●​ Division: Ascomycota​

●​ Class: Saccharomycetes​ • Risk Factors –

●​ Order: Saccharomycetales​ ●​ Immunosuppression (HIV/AIDS,

chemotherapy, transplant)​
●​ Genus: Candida​
●​ Diabetes mellitus​
●​ Species: albicans (predominant)​
●​ Broad-spectrum antibiotics​

●​ Corticosteroid therapy​

• Morphology of Organism – ●​ IV catheters, prosthetic devices​

 ●​ Neonates, elderly​

• Mode of Transmission –
🔬 Lab Diagnosis
• Specimen – Scrapings, swabs, blood,
●​ Endogenous overgrowth (most urine, CSF, biopsy material.
common).​
• Possible Specimens –
●​ Exogenous: person-to-person (rare).​
●​ Oral/vaginal swabs​

●​ Skin/nail scrapings​

• Sequence of Events – FLOWCHART ●​ Blood cultures​

Normal commensal → Predisposing factor ●​ Urine, sputum, tissue biopsy​

(↓ immunity/antibiotics/diabetes) → Candida
overgrowth → Adherence & biofilm → Local
infection (oral/vaginal) → Invasion of tissue • Method of Collection – Sterile
→ Dissemination → Candidemia / systemic swab/aspiration/biopsy.
candidiasis.
• Transport & Preservation –

●​ Fresh samples, sent immediately.​

• Clinical Features (Stage wise)
●​ For blood: BACTEC/mycosis blood
1.​ Superficial / Mucocutaneous​ culture bottles.​

○​ Oral thrush (white curd-like

plaques)​

○​ Vaginal candidiasis (itching, • Microscopy –

cottage-cheese discharge)​
KOH Mount (10–20% KOH):
○​ Cutaneous candidiasis
(intertrigo, diaper rash, ●​ Shows budding yeast cells,
onychomycosis)​ pseudohyphae.​

2.​ Chronic mucocutaneous ●​ In tissue: true hyphae.​

candidiasis – persistent, associated
with T-cell defects.​
📌 Diagram to draw: Yeast with
pseudohyphae, budding, chlamydospore.
3.​ Systemic/Disseminated​

○​ Candidemia (fever, sepsis, Special Stains –

endocarditis, renal/hepatic
abscesses, meningitis).​ ●​ Gram stain: Gram-positive oval
budding yeast.​
 ●​ PAS (Periodic Acid Schiff): magenta • Serology –
yeast.​
●​ Detection of mannan antigen or
●​ Gomori Methenamine Silver (GMS): anti-Candida antibodies in serum
black yeast & hyphae.​ by ELISA.​

●​ (Useful in systemic candidiasis).​

• Culture –

●​ Primary medium: Sabouraud’s • Molecular Methods –

Dextrose Agar (SDA) → creamy
white smooth colonies.​ ●​ PCR (Candida DNA detection in
blood/tissue).​
●​ Special agar:​
●​ Real-time PCR for species
○​ Cornmeal agar (Dalmau identification.​
technique): shows
chlamydospore formation
(diagnostic for C. albicans).​

○​ Chromogenic agar
(CHROMagar): species
differentiation by colony color
(e.g., C. albicans = green, C.
💊 Treatment
●​ Superficial:​
tropicalis = blue, C. krusei =
pink).​
○​ Topical azoles (clotrimazole,
miconazole).​

○​ Nystatin suspension (oral

• Identification – thrush).​

●​ Lactophenol Cotton Blue Mount ●​ Systemic:​

(LPCB): budding yeast,
pseudohyphae, chlamydospore ○​ Fluconazole, Itraconazole.​
(same as KOH).​
○​ Echinocandins (caspofungin,
●​ Germ Tube Test (special test): C. micafungin) – for
albicans produces germ tubes within resistant/systemic cases.​
2–3 hrs in human/horse serum
(positive test).​ ○​ Amphotericin B
(severe/disseminated).​
●​ Sugar assimilation/fermentation
tests for species differentiation.​

🛡️ Prophylaxis
●​ Automated ID: MALDI-TOF, VITEK.​
 ●​ No vaccine.​

●​ Reduce risk factors (glycemic • Morphology – (dimorphic fungus)

control, limit antibiotics).​
●​ At 25°C (mould form, SDA):
●​ Antifungal prophylaxis (fluconazole) septate hyphae with microconidia
in high-risk immunocompromised (round, 2–4 μm) & tuberculate
patients.​ macroconidia (8–14 μm,
thick-walled, rough, “knobbed”
appearance).​

Got it✅ Let’s prepare Histoplasmosis

(Histoplasma capsulatum infection) in
●​ At 37°C (yeast form, in tissue):
small oval budding yeast (2–4 μm),
intracellular in macrophages.​
your fungal exam-template style.

📌 Diagram to draw:
🍄 Histoplasma
capsulatum
1.​ Yeast form inside macrophages.​

2.​ Tuberculate macroconidia (thick,

round with projections).​

(Histoplasmosis /
Darling’s disease) • Pathogenesis –

• Name of Disease –​ 1.​ Inhalation of microconidia from soil

Histoplasmosis enriched with bird/bat droppings.​

• Causative Organism –​ 2.​ Converts to yeast form in alveoli →

Histoplasma capsulatum (dimorphic phagocytosed by macrophages.​
fungus)
3.​ Survives intracellularly by
modulating phagolysosome pH.​

• Classification – 4.​ Spreads via reticuloendothelial

system (liver, spleen, bone marrow).​
●​ Kingdom: Fungi​
5.​ Causes granulomatous inflammation
●​ Division: Ascomycota​ → caseation, fibrosis.​

●​ Class: Eurotiomycetes​

●​ Order: Onygenales​
• Risk Factors –
●​ Genus: Histoplasma​
●​ Exposure to caves, bird roosts, bat
●​ Species: capsulatum​ guano (spelunkers, farmers).​
 ●​ Immunocompromised patients mucocutaneous ulcers,
(HIV/AIDS, transplant).​ pancytopenia.​

●​ Very young & elderly.​

• Mode of Transmission –

●​ Inhalation of microconidia from

🔬 Lab Diagnosis
• Specimen –
environment (no person-to-person
spread).​ ●​ Sputum, BAL fluid, blood, bone
marrow, lymph node biopsy, CSF.​

• Possible Specimens –
• Sequence of Events – FLOWCHART
●​ Pulmonary cases: sputum, BAL.​
Soil with bird/bat droppings → Microconidia
aerosolized → Inhalation → Yeast inside ●​ Disseminated: blood, bone marrow,
macrophages → Dissemination via RES → liver/spleen biopsy.​
Pulmonary / disseminated histoplasmosis.

• Method of Collection – Sterile

swabs/aspirates/biopsy under aseptic
• Clinical Features (Stage wise) conditions.

1.​ Acute pulmonary histoplasmosis:​ • Transport & Preservation –

○​ Flu-like illness, fever, cough, ●​ Process immediately; if delay, keep

chest pain.​ at 4°C.​

○​ Self-limiting in healthy
individuals.​

2.​ Chronic pulmonary • Microscopy –

histoplasmosis:​
●​ KOH Mount (10–20%): small
○​ Mimics tuberculosis.​ budding yeast forms.​

○​ Cavitary lung lesions, ●​ Tissue biopsy (H&E, Giemsa,

hemoptysis, weight loss.​ Wright stain): intracellular yeast
within macrophages.​
3.​ Disseminated histoplasmosis:​

○​ Occurs in 📌 Diagram to draw: Small oval yeast

clustered inside macrophages.
immunocompromised.​

○​ Fever, hepatosplenomegaly, Special Stains –

lymphadenopathy,
 ●​ PAS: red budding yeast.​ ●​ Antibody detection: Complement
fixation, immunodiffusion.​
●​ GMS: black yeast inside
macrophages.​

• Molecular Methods –

• Culture – ●​ PCR for Histoplasma DNA in

blood/tissue.​
●​ Primary: Sabouraud’s Dextrose
Agar (SDA) → white to brown,
cottony mould colonies (25°C).​

●​ Conversion test: mould (25°C) ↔

yeast (37°C) confirms dimorphism.​

• Special Agar – Brain Heart Infusion (BHI)

💊 Treatment
●​ Mild pulmonary: Itraconazole.​
agar with blood.
●​ Severe / disseminated: Amphotericin
B → followed by Itraconazole.​

• Identification – ●​ AIDS patients: lifelong suppressive

itraconazole.​
●​ LPCB mount (25°C): septate hyphae
+ microconidia + tuberculate
macroconidia.​

●​ At 37°C: yeast inside macrophages.​

🛡️ Prophylaxis
●​ No vaccine.​
• Special Tests –
●​ Avoid exposure to bat/bird guano
●​ Histoplasmin skin test (delayed contaminated sites.​
hypersensitivity) → epidemiological
only, not diagnostic.​ ●​ Itraconazole prophylaxis in high-risk
immunosuppressed patients.​

👍
• Serology –
Perfect Let’s structure
●​ Antigen detection: Histoplasma Coccidioidomycosis (Valley Fever) in
polysaccharide antigen (HPA) in your fungal exam-style template.
urine & serum by ELISA (useful in
disseminated histoplasmosis).​
🍄
Coccidioidomycosi
1.​ Barrel-shaped arthroconidia
(infective form).​

2.​ Large spherule with multiple

endospores (tissue form).​
s (Valley Fever /
San Joaquin Valley
Fever) • Pathogenesis –

1.​ Arthroconidia inhaled from dust/soil.​

• Name of Disease –​
Coccidioidomycosis
2.​ Convert to spherules in lungs →
release endospores.​
• Causative Organism –​
Coccidioides immitis & Coccidioides
3.​ Endospores spread → form new
posadasii
spherules.​

4.​ Strong host immune response (Th1,

• Classification – granulomatous inflammation).​

●​ Kingdom: Fungi​ 5.​ May disseminate (skin, bones, CNS)

especially in immunosuppressed.​
●​ Division: Ascomycota​

●​ Class: Eurotiomycetes​
• Risk Factors –
●​ Order: Onygenales​
●​ Residing/working in endemic arid
●​ Genus: Coccidioides​
regions (Southwestern USA,
Mexico).​
●​ Species: immitis, posadasii​
●​ Dust exposure (construction,
farming, military training).​

• Morphology – (dimorphic fungus) ●​ Immunocompromised (HIV/AIDS,

transplant, pregnancy, elderly).​
●​ In soil (25°C, mould phase):
septate hyphae fragment into
arthroconidia (barrel-shaped),
highly infectious.​
• Mode of Transmission –
●​ In tissue (37°C, yeast-like phase):
●​ Inhalation of airborne arthroconidia
large spherules (20–80 µm)
from contaminated soil.​
containing endospores.​
●​ ❌ No person-to-person
📌 Diagram to draw: transmission.​
 (disseminated).​

• Sequence of Events – FLOWCHART

• Method of Collection –
Soil (arthroconidia) → Inhalation → Lungs
→ Transformation to spherules → ●​ Aseptic collection of
Endospores released → Pulmonary lesions sputum/CSF/biopsy.​
± dissemination → Systemic disease.

• Transport & Preservation –

• Clinical Features (Stage wise) ●​ Process in Biosafety Level 3 lab

(arthroconidia are highly infectious).​
1.​ Primary Pulmonary
Coccidioidomycosis (“Valley ●​ If delay → refrigerate at 4°C.​
fever”):​

○​ Flu-like symptoms: fever,

cough, chest pain, erythema
nodosum (desert bumps).​ • Microscopy –

○​ Often self-limiting.​ ●​ Direct KOH mount: large spherules

with endospores (tissue).​
2.​ Chronic Pulmonary
Coccidioidomycosis:​
• KOH Mount – Diagram:​
○​ Cavitary lung lesions.​ Show thick-walled round spherule
containing endospores.
○​ Hemoptysis, weight loss,
mimics TB.​ • Special Stains –

3.​ Disseminated ●​ PAS stain: magenta spherules.​

Coccidioidomycosis:​
●​ GMS stain: black spherules &
○​ Skin, bones, joints, endospores.​
meninges.​
●​ H&E: granulomatous reaction with
○​ Meningitis → headache, spherules.​
seizures, fatal if untreated.​

🔬 Lab Diagnosis
• Culture –

●​ SDA (25°C): fluffy, white to gray

mould, arthroconidia (barrel-shaped,
alternating empty cells).​
• Specimen –
●​ ⚠️ Highly infectious: must be
handled in BSL-3 lab.​
●​ Sputum, BAL fluid, pus, tissue
biopsy, CSF (if meningitis), blood
• Special Agar – Brain Heart Infusion (BHI)
agar. 💊 Treatment
●​ Mild pulmonary: often self-limiting,
no treatment required.​
• Identification –
●​ Moderate/severe: Fluconazole or
●​ LPCB mount: barrel-shaped Itraconazole.​
arthroconidia alternating with empty
cells.​ ●​ Disseminated/meningeal:
Amphotericin B (initial) →
●​ Conversion to spherule/endospore Fluconazole lifelong for meningitis.​
form confirms Coccidioides.​

• Special Tests –

●​ Skin test (coccidioidin /

spherulin): delayed hypersensitivity
🛡️ Prophylaxis
●​ No vaccine.​
→ epidemiological only, not
diagnostic.​ ●​ Avoid dust exposure in endemic
areas.​

●​ Masks (N95) in
construction/agriculture in endemic
• Serology – zones.​
●​ Detection of antibodies in serum by ●​ Antifungal prophylaxis (fluconazole)
Complement Fixation (CF), in high-risk immunosuppressed.​
Immunodiffusion, or ELISA.​

●​ IgM → acute infection.​

●​ IgG → chronic or disseminated

infection.​

• Molecular Methods –

●​ PCR & Real-time PCR for detection

of Coccidioides DNA in
sputum/CSF/tissue.​