Reading File
Running Command

cd /tmp/workspace/attachments/5b878d47-e31c-40fe-a199-9fac832b4375/ && python3 -c " import pdfplumber with pdfplumber.open('DocScanner Jul 25, 2025 10-43 AM.pdf') as pdf: print(f'Pages: {len(pdf.pages)}') for i, page in enumerate(pdf.pages): text = page.extract_text() print(f'--- Page {i+1} ---') print(text) print() "

Running Command

cd /tmp/workspace/attachments/5b878d47-e31c-40fe-a199-9fac832b4375/ && python3 -c " from pypdf import PdfReader, PdfWriter import os reader = PdfReader('DocScanner Jul 25, 2025 10-43 AM.pdf') print(f'Pages: {len(reader.pages)}') # Extract individual pages as PDFs os.makedirs('/tmp/workspace/pdf_pages', exist_ok=True) for i, page in enumerate(reader.pages): writer = PdfWriter() writer.add_page(page) with open(f'/tmp/workspace/pdf_pages/page_{i+1}.pdf', 'wb') as f: writer.write(f) print('Pages extracted') "

Running Command

python3 -c " import subprocess result = subprocess.run(['python3', '-c', 'import fitz; print(fitz.__version__)'], capture_output=True, text=True) print('pymupdf:', result.stdout, result.stderr) result2 = subprocess.run(['python3', '-c', 'import pdf2image; print(\"ok\")'], capture_output=True, text=True) print('pdf2image:', result2.stdout, result2.stderr) "

Running Command

python3 -c " from pdf2image import convert_from_path import os pdf_path = '/tmp/workspace/attachments/5b878d47-e31c-40fe-a199-9fac832b4375/DocScanner Jul 25, 2025 10-43 AM.pdf' os.makedirs('/tmp/workspace/pdf_images', exist_ok=True) images = convert_from_path(pdf_path, dpi=150) print(f'Total pages converted: {len(images)}') for i, img in enumerate(images): img.save(f'/tmp/workspace/pdf_images/page_{i+1}.jpg', 'JPEG', quality=85) print(f'Saved page_{i+1}.jpg - size: {img.size}') "

Running Command

python3 -c " from PIL import Image import os # Combine pages into pairs: 1-2, 3-4, 5-6, 7-8, 9-10 pairs = [(1,2), (3,4), (5,6), (7,8), (9,10)] for p1, p2 in pairs: img1 = Image.open(f'/tmp/workspace/pdf_images/page_{p1}.jpg') img2 = Image.open(f'/tmp/workspace/pdf_images/page_{p2}.jpg') w = img1.width + img2.width h = max(img1.height, img2.height) combined = Image.new('RGB', (w, h), (255,255,255)) combined.paste(img1, (0, 0)) combined.paste(img2, (img1.width, 0)) combined.save(f'/tmp/workspace/pdf_images/combined_{p1}_{p2}.jpg', 'JPEG', quality=85) print(f'Saved combined_{p1}_{p2}.jpg') "

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Medical Microbiology Exercises - Complete Answers

Exercise MI 2.7.3 - HIV (Pages 1-2)

Clinical Case: 28-year-old promiscuous man with 6 kg weight loss over 3-5 weeks, history of mild fever, weakness, headache, lethargy, and tenesmus.
Images shown: HIV TRI-DOT rapid card test (showing two red dots = reactive for HIV-1 and/or HIV-2) + ELISA microtitre plate with colored wells indicating reactive results.

Q1. Identify and interpret the given serological test done for this patient

Test 1 - HIV TRI-DOT (Rapid Immunochromatographic test):
  • The card shows labeled positions for HIV-1 and HIV-2
  • Two dots are visible (control dot + reactive dot), indicating a positive/reactive result
  • This is a point-of-care rapid antibody detection test using recombinant HIV antigens
  • Interpretation: Reactive for HIV antibodies - consistent with HIV infection
Test 2 - ELISA (Enzyme-Linked Immunosorbent Assay) microtitre plate:
  • The orange/yellow colored wells (rows A-D, columns 1-7 approximately) indicate optical density above the cut-off = reactive wells
  • Colorless wells = non-reactive
  • The pattern seen is consistent with an indirect or sandwich ELISA for anti-HIV antibodies
  • Interpretation: ELISA positive for HIV antibodies
Together, these two reactive tests indicate HIV infection (most likely HIV-1 based on the TRI-DOT pattern). This patient is in the symptomatic HIV / early AIDS stage given his constitutional symptoms and weight loss >10%.

Q2. What are the various modes of transmission of the etiological agent (HIV)?

HIV (Human Immunodeficiency Virus, Lentivirus, Retroviridae) is transmitted by:
Sexual transmission (most common globally):
  • Unprotected heterosexual or homosexual intercourse
  • Receptive anal intercourse carries the highest per-act risk
  • Vaginal intercourse (bidirectional, female-to-male and male-to-female)
  • Oral sex (low but non-zero risk)
Blood-borne transmission:
  • Sharing contaminated intravenous drug needles/syringes
  • Blood transfusions or blood products (screened in most countries now)
  • Needlestick injuries in healthcare workers
  • Transplantation of infected organs or tissue
Mother-to-child transmission (Vertical):
  • In utero (transplacental) - especially in third trimester
  • Intrapartum (during delivery) - most common
  • Postpartum - through breastfeeding
Not transmitted by: casual contact, hugging, sharing utensils, mosquito bites, coughing, or sneezing.

Q3. What are the different modalities of diagnosis of this clinical condition?

1. Serological (Antibody detection):
  • ELISA (3rd/4th generation): Detects anti-HIV IgG/IgM antibodies (window period: 3-6 weeks for 4th gen)
  • Rapid tests / TRI-DOT / ICT: Point-of-care lateral flow assays
  • Western Blot: Confirmatory gold standard - detects antibodies to specific viral proteins (gp41, gp120, gp160, p24, p31, p51, p66)
  • Line Immunoassay (LIA): Alternative confirmatory test
2. Antigen detection:
  • p24 antigen ELISA: Detects viral core antigen; positive before antibody (during acute infection window period)
  • 4th generation combo ELISA: Detects both p24 Ag and anti-HIV antibodies simultaneously
3. Molecular (Nucleic Acid Tests):
  • HIV RNA PCR (Viral Load): Quantitative; used for monitoring treatment response and in neonates
  • HIV DNA PCR: Detects proviral DNA; used in infants born to HIV-positive mothers
  • NAAT (Nucleic Acid Amplification Test): Used for early diagnosis during window period
4. CD4+ T-cell count:
  • Not diagnostic but essential for staging and treatment decisions
  • Normal: 500-1500 cells/µL; AIDS defined as <200 cells/µL or AIDS-defining illness
5. Virus isolation / culture: Research only; not routine clinical practice
NACO (India) diagnostic algorithm:
  • Uses three rapid tests (Strategy III) for diagnosis in symptomatic individuals

Q4. Which are the various opportunistic infections that can occur in this patient?

Based on CD4 count:
CD4 CountOpportunistic Infections
<500Herpes zoster, Oral candidiasis, TB (pulmonary)
<200Pneumocystis jirovecii pneumonia (PCP), Toxoplasmosis (cerebral), Cryptococcal meningitis, Disseminated TB, Progressive multifocal leukoencephalopathy (PML)
<100Disseminated Mycobacterium avium complex (MAC), CMV retinitis, Cryptosporidiosis, Microsporidiosis
<50CMV encephalitis, Disseminated histoplasmosis, Bacillary angiomatosis
Common OIs:
  • Respiratory: PCP (Pneumocystis jirovecii), TB, Aspergillosis
  • GI: Cryptosporidiosis, Isospora, Microsporidiosis, CMV colitis, Candida esophagitis
  • CNS: Toxoplasmic encephalitis, Cryptococcal meningitis, PML (JC virus), HIV encephalopathy
  • Skin: Herpes zoster, Kaposi's sarcoma (HHV-8), Molluscum contagiosum
  • Ocular: CMV retinitis
  • Systemic: Disseminated MAC, Histoplasmosis, Penicilliosis
Tenesmus in this patient may suggest CMV colitis or cryptosporidiosis affecting the rectum.

Q5. How will you treat this condition?

Antiretroviral Therapy (ART):
ART is indicated for ALL HIV-positive individuals regardless of CD4 count (WHO/NACO guidelines).
First-line regimen (India NACO / WHO):
  • Tenofovir (TDF) + Lamivudine (3TC) + Dolutegravir (DTG)
  • TDF 300 mg + 3TC 300 mg + DTG 50 mg once daily (single-tablet regimen)
Drug classes used:
  • NRTIs (Nucleoside Reverse Transcriptase Inhibitors): TDF, 3TC, Zidovudine (AZT), Emtricitabine (FTC), Abacavir
  • NNRTIs (Non-Nucleoside RTIs): Efavirenz, Nevirapine, Rilpivirine
  • Integrase Strand Transfer Inhibitors (INSTIs): Dolutegravir, Raltegravir, Bictegravir
  • Protease Inhibitors (PIs): Lopinavir/ritonavir, Atazanavir/ritonavir
  • Entry/Fusion Inhibitors: Maraviroc (CCR5 antagonist), Enfuvirtide
OI prophylaxis:
  • CD4 <200: Co-trimoxazole (TMP-SMX) for PCP + toxoplasmosis prophylaxis
  • Fluconazole for cryptococcal prophylaxis in high-burden settings
  • INH prophylaxis therapy (IPT) for TB
Monitoring: CD4 count, viral load every 6 months; LFTs, CBC, renal function

Q6. Discuss confidentiality pertaining to patient identity in laboratory results

HIV test results are governed by strict confidentiality rules:
  • Informed consent must be obtained before testing (except in specific exceptions like blood donation screening, PPTCT programs)
  • Results must be disclosed only to the patient and authorized healthcare providers directly involved in care
  • Results must not be disclosed to employers, insurance companies, family members (without patient consent), or other institutions
  • Lab reports should use coded identifiers - patient's name should not appear on HIV result reports in India
  • Under the HIV and AIDS (Prevention and Control) Act, 2017 (India): unauthorized disclosure of HIV status is a punishable offense
  • Exceptions where disclosure is permitted: to protect a third party at risk (e.g., sexual partner), with patient's written consent, or by court order
  • Pre-test and post-test counseling is mandatory (ICTC - Integrated Counseling and Testing Centre)
  • The "need to know" principle applies - only those directly involved in treatment need the information

Q7. What is NACO Strategy I and where is it applied?

NACO Strategy I:
  • Uses a single ELISA or rapid test
  • A specimen is reported positive if the single test is reactive
  • A specimen is reported negative if the single test is non-reactive
Application:
  • Used exclusively for blood/organ/semen donor screening (transfusion safety)
  • The goal is maximum sensitivity - no blood unit that is HIV-positive should be missed
  • Not used for diagnostic purposes in symptomatic individuals
  • Donors testing positive are deferred from donation; the blood unit is discarded

Q8. What is NACO Strategy II and where is it applied?

NACO Strategy II:
  • Uses two different ELISA/rapid tests with different antigen preparations or formats
  • If Test 1 is reactive: perform Test 2
    • If Test 2 also reactive → Report as HIV positive
    • If Test 2 is non-reactive → perform Test 3 (the "tie-breaker")
  • If Test 1 is non-reactive: Report as HIV negative
Application:
  • Used for surveillance purposes (sentinel surveillance, epidemiological studies)
  • Low-prevalence settings
  • Not for individual patient diagnosis

Q9. What is NACO Strategy III and where is it applied?

NACO Strategy III:
  • Uses three different tests (ideally using different antigens/formats - one ELISA + two rapid tests OR three rapid tests)
  • Algorithm:
    • Test 1 (most sensitive): If non-reactive → Report HIV negative
    • If Test 1 reactive → Test 2: If reactive → Test 3
    • If Test 3 reactive → Report HIV positive
    • If any discordance between Test 2 and Test 3 → Report as indeterminate - repeat after 2-4 weeks
Application:
  • Mandatory for diagnosis and clinical management of symptomatic and asymptomatic individuals
  • All ICTCs (Integrated Counseling and Testing Centres) use this
  • HIV-positive pregnant women (PPTCT program)
  • Any individual presenting with clinical features suggestive of HIV/AIDS
  • This is the strategy used in this clinical case


Exercise MI3.7 AE - Hepatitis B (Pages 3-4)

Clinical Case: 40-year-old woman with multiple blood transfusions, presenting with fatigue, anorexia, nausea, vomiting, abdominal pain for 10 days. Elevated serum bilirubin and liver enzymes. HBsAg card test positive. Diagnosed with acute HBV infection.
Image: Two HBsAg rapid card tests (labeled HBsAg 130819) - both show a band in the test line and control line = positive results.

Q1. Based on the test provided, what is your diagnosis?

The HBsAg rapid card test shows two lines (control + test band) = POSITIVE for HBsAg (Hepatitis B Surface Antigen).
Diagnosis: Acute Hepatitis B Virus (HBV) infection
This is supported by:
  • Positive HBsAg (marker of active HBV infection/carrier)
  • Clinical features: jaundice (elevated bilirubin), hepatitis (elevated liver enzymes)
  • History of multiple blood transfusions (risk factor for HBV)
  • Acute presentation (10-day history)
HBsAg is the first serological marker to appear in HBV infection (4-12 weeks after exposure) and its detection is the primary test for HBV.

Q2. Suggest a test to know the infectiousness of the patient

HBeAg (Hepatitis B e-Antigen):
  • HBeAg positivity indicates active viral replication and high infectiousness
  • Derived from the precore/core region of HBV genome
  • Patients with HBeAg+ are 5-10 times more infectious than HBeAg-negative patients
HBV DNA by PCR (Viral Load):
  • The most direct and quantitative measure of infectiousness
  • Levels >20,000 IU/mL in HBeAg+ chronic hepatitis B indicate high replication
  • "Gold standard" for assessing infectiousness and treatment monitoring
If HBeAg negative but HBV DNA detectable → precore/core promoter mutant (more common in Asian patients).

Q3. Suggest a test to know if the infection is acute or chronic

TestAcute HBVChronic HBV
Anti-HBc IgMPositive (high titer)Negative (or low titer)
Anti-HBc IgGPositive (develops later)Positive
HBsAg durationPresent <6 monthsPresent >6 months
Anti-HBsDevelops at resolutionAbsent
Key test: Anti-HBc IgM (IgM antibody to Hepatitis B core antigen)
  • A high-titer anti-HBc IgM = Acute HBV infection (marker of recent infection)
  • Persists for 6-12 months after acute infection
  • In chronic HBV: anti-HBc IgG is present (total anti-HBc positive, IgM negative or very low)
Definition of chronic HBV: HBsAg positive for >6 months

Q4. Enumerate the modes of transmission of this infection

HBV is ~100 times more infectious than HIV. Transmitted via:
Parenteral/Blood-borne:
  • Blood transfusions (most common in this case - multiple transfusions)
  • Sharing contaminated needles (IV drug users)
  • Needlestick injuries (healthcare workers - occupational risk)
  • Tattooing, body piercing with unsterilized equipment
  • Sharing razors, toothbrushes
Sexual Transmission:
  • Unprotected sexual contact (heterosexual and homosexual)
  • HBsAg present in semen, vaginal secretions, saliva
Vertical (Mother-to-Child):
  • Perinatal transmission during delivery (most important route in endemic regions like Asia)
  • In utero (rare, ~2-3% of cases)
  • Breastfeeding (low risk, not a contraindication if infant vaccinated)
Close contact:
  • Within households, particularly when sharing personal items
  • HBV can survive on environmental surfaces for >7 days
Not transmitted by: fecal-oral route (unlike HAV, HEV), mosquitoes, or casual contact.

Q5. How is the general prognosis of this condition?

Acute HBV infection:
  • ~95% of immunocompetent adults recover completely with clearance of HBsAg and development of protective anti-HBs
  • ~0.1-0.5% develop fulminant hepatic failure (higher risk with co-infection with HDV)
  • ~5% progress to chronic infection (adults)
  • Neonates and infants: ~90% become chronically infected
Chronic HBV infection (~5% of adults):
  • ~15-40% develop serious complications over 5 years
  • Cirrhosis: ~20-30% of chronic HBV patients
  • Hepatocellular carcinoma (HCC): 100-fold increased risk; 15-40% of HCC worldwide is HBV-related
  • Liver failure: End-stage complication
Factors associated with poor prognosis:
  • Co-infection with HIV, HCV, or HDV
  • Alcohol consumption
  • HBeAg positivity (indicates ongoing replication)
  • High HBV DNA levels

Q6. Describe briefly the preventive measures of this condition

Active Immunization (Vaccine):
  • Recombinant HBV vaccine (HBsAg produced in yeast - Saccharomyces cerevisiae)
  • Schedule: 0, 1, 6 months (3-dose) OR 0, 1, 2, 12 months (4-dose accelerated)
  • Included in Universal Immunization Programme (UIP) of India: Birth dose + at 6, 10, 14 weeks (pentavalent vaccine)
  • Efficacy: >90% in immunocompetent adults; check anti-HBs titer 1-3 months post-vaccination
Passive Immunization:
  • Hepatitis B Immunoglobulin (HBIG): Given within 24-48 hours after exposure (post-exposure prophylaxis), also to neonates of HBsAg-positive mothers at birth
Blood Safety:
  • Mandatory HBsAg screening of all donated blood
  • Nucleic Acid Testing (NAT) to reduce window period donations
Universal Precautions:
  • Use of gloves, safe injection practices, proper needle disposal
  • Sterilization of medical/surgical instruments
Behavioral:
  • Safe sex practices (condoms)
  • Avoid sharing needles, razors, toothbrushes
  • Safe tattooing/piercing practices

Q7. Interpretation of serological markers table:

Sl.No.SymptomsHBsAgAnti-HBsAnti-HBcHBeAgAnti-HBeInterpretation
1Absent+----Early acute HBV infection ("window" before anti-HBc appears; or very early phase with HBsAg detectable before antibodies)
2Present+-IgM+-Acute HBV infection (HBsAg+, IgM anti-HBc = recent/acute infection, HBeAg+ = high infectivity)
3Present+-IgG--Chronic HBV infection (HBsAg+ for >6 months, IgG anti-HBc = long-standing infection, HBeAg negative = low/inactive replication or precore mutant)
4Absent-+IgG-+/-Past HBV infection with recovery + immunity (HBsAg cleared, anti-HBs = protective immunity, anti-HBc IgG = past exposure; OR post-vaccination - but post-vaccination only anti-HBs is positive, no anti-HBc; presence of anti-HBc IgG confirms natural infection rather than vaccination)
5Absent-+---Successful vaccination (anti-HBs only, no anti-HBc = vaccine-induced immunity without natural infection)


Exercise 19.2 - Rotavirus (Pages 5-6)

Clinical Case: 2-year-old child with abrupt onset vomiting followed by 6 episodes of watery diarrhea, fever, and abdominal pain.
Image: Electron micrograph showing multiple wheel-shaped virus particles with characteristic spoke-and-hub appearance = Rotavirus

Q1. Identify the most probable pathogen in this case

Rotavirus (Family: Reoviridae, Genus: Rotavirus)
Reasons:
  • The electron micrograph shows classic wheel-shaped (rota = wheel in Latin) double-capsid particles, ~70nm in diameter with distinct spokes radiating from a hub
  • This is the most common cause of severe dehydrating gastroenteritis in children under 5 years worldwide
  • Clinical features: abrupt onset, vomiting preceding diarrhea, watery (non-bloody) diarrhea, fever - classic rotavirus pattern
  • Peak age: 6 months to 2 years
  • Rotavirus is a double-stranded RNA virus with 11 segments enclosed in a triple-layered protein capsid

Q2. Name other tests to confirm the laboratory diagnosis

Stool antigen detection:
  • ELISA for rotavirus antigen in stool (most common clinical test) - detects group A VP6 antigen
  • Latex agglutination test - rapid, widely used
  • Rapid immunochromatographic tests (ICT/card tests) - point of care
Molecular:
  • RT-PCR - gold standard for genotyping (G and P types); detects all groups
  • Polyacrylamide gel electrophoresis (PAGE) - shows characteristic "electropherotype" (11-band pattern with 4-2-3-2 grouping)
Microscopy:
  • Electron microscopy (as shown) - morphologically diagnostic but not routine
  • Immune electron microscopy (IEM)
Cell culture:
  • Possible but technically demanding; not routine

Q3. Name the other organisms causing similar clinical manifestations (watery diarrhea with vomiting in children)

Viral:
  • Norovirus (Calicivirus) - most common cause in older children and adults; outbreaks
  • Enteric Adenovirus (types 40, 41) - second most common viral cause in children
  • Astrovirus - watery diarrhea, milder
  • Sapovirus - less common calicivirus
Bacterial:
  • Vibrio cholerae - "rice-water" stools, profuse watery diarrhea
  • Enterotoxigenic E. coli (ETEC) - traveler's diarrhea, watery
  • Cryptosporidium parvum - watery diarrhea in immunocompromised
  • Giardia lamblia - chronic watery/fatty diarrhea
Parasitic:
  • Cryptosporidium parvum
  • Giardia intestinalis

Q4. List the laboratory tests to differentiate other pathogens causing this condition

PathogenSpecific Test
RotavirusStool ELISA antigen, RT-PCR
NorovirusRT-PCR (stool) - no antigen test widely available
Adenovirus 40/41Stool ELISA, PCR
V. choleraeStool culture on TCBS agar; dark-field microscopy (shooting star motility)
ETECStool culture + virulence gene PCR
CryptosporidiumModified ZN stain (oocysts appear as pink circles), ELISA for antigen
GiardiaStool microscopy (cysts/trophozoites), ELISA antigen
AstrovirusELISA, RT-PCR
General stool workup:
  • Macroscopy: color, consistency, blood/mucus
  • Microscopy: pus cells, RBCs, parasites
  • Culture: for bacterial pathogens
  • Electron microscopy: for viral particles

Q5. Describe briefly specific preventive measures for this condition

Specific (Rotavirus vaccines):
Two oral live-attenuated vaccines licensed globally:
  • Rotarix (GSK): Human rotavirus G1P[8] strain; 2-dose oral schedule (6 and 10 weeks)
  • RotaTeq (Merck): Pentavalent human-bovine reassortant; 3-dose oral schedule (2, 4, 6 months)
India:
  • ROTAVAC (Bharat Biotech): Monovalent neonatal strain 116E; 3 doses at 6, 10, 14 weeks
  • ROTASIIL (Serum Institute): Pentavalent bovine-human reassortant
  • Introduced into Universal Immunization Programme (UIP) of India in 2016
General preventive measures (limit spread):
  • Exclusive breastfeeding in infancy (provides some passive protection via IgA)
  • Hand hygiene with soap and water (alcohol-based sanitizers less effective against rotavirus)
  • Safe water and food hygiene
  • Proper disposal of diarrheal stools
  • ORS (Oral Rehydration Solution) for management - reduces mortality but not specific prevention

Q6. A local doctor has prescribed Syp. Amoxycillin-clavulanic acid in appropriate dose and frequency for 3 days. Is it justified?

No, it is NOT justified.
Reasons:
  1. Rotavirus is a virus - antibiotics have no action against viruses
  2. Amoxicillin-clavulanic acid is an antibiotic (broad-spectrum penicillin + beta-lactamase inhibitor) - it acts on bacterial cell wall synthesis and is completely ineffective against viral gastroenteritis
  3. Prescribing antibiotics for viral diarrhea contributes to antimicrobial resistance (AMR) - a major global health concern
  4. Antibiotics may disrupt the intestinal microbiome, potentially prolonging diarrhea
  5. This represents irrational antibiotic use / antibiotic stewardship failure
Correct management of rotavirus gastroenteritis:
  • ORS (Oral Rehydration Solution) - cornerstone of treatment; prevents dehydration
  • Zinc supplementation (20 mg/day x 14 days for children >6 months) - reduces duration and severity, as per WHO/UNICEF guidelines
  • Continued feeding - do not withhold feeds
  • IV fluids only if signs of severe dehydration or failure of oral rehydration
  • Antipyretics (paracetamol) for fever
  • Antibiotics are indicated only if there is evidence of bacterial co-infection (blood in stool, high fever, elevated WBC with left shift)


Exercise MI5.2.8 AE - Rabies (Pages 7-8)

Clinical Case: 27-year-old man with anxiety, confusion, hydrophobia, hallucinations. History of stray dog bite 15 days ago with deep wounds and muscle laceration on neck and arm. Wound was cleaned but no vaccine given. Patient expired after 3 days.
Images: Two histopathology slides showing:
  • Left image: Neurons with pink cytoplasmic inclusions = Negri bodies (classic)
  • Right image: Perivascular lymphocytic cuffing and neuronal degeneration = Encephalitis

Q1. What is the diagnosis of this condition?

Rabies (Lyssa) caused by Rabies virus (Rhabdoviridae, genus Lyssavirus)
Basis for diagnosis:
  • History of dog bite (classic exposure)
  • 15-day incubation period (range: 2 weeks to 1 year; average 1-3 months; shorter for head/neck bites)
  • Prodromal phase: fever, headache, paresthesia at bite site
  • Neurological phase (furious type): hydrophobia (cardinal symptom), aerophobia, anxiety, confusion, hallucinations, agitation
  • Histopathology: Negri bodies (eosinophilic intracytoplasmic inclusions in neurons, especially Purkinje cells of cerebellum and hippocampal neurons of Ammon's horn)
  • Fatal outcome without timely post-exposure prophylaxis

Q2. Describe the lab diagnosis of the above condition

Antemortem (in living patients):
  • Direct Fluorescent Antibody Test (dFAT/FAT): Nuchal skin biopsy (nape of neck, hair follicles contain corneal nerve endings); most reliable antemortem test
  • Saliva RT-PCR: Detects rabies virus RNA; highly sensitive
  • Corneal impression smear + FAT: Corneal cells examined for viral antigen
  • CSF analysis: Mild pleocytosis, elevated protein; FAT on CSF for antigen
  • Serum and CSF antibody neutralization tests (Rapid Fluorescent Focus Inhibition Test - RFFIT)
Postmortem (definitive):
  • Demonstration of Negri bodies: H&E stained brain sections (hippocampus, cerebellum)
    • Sellar's stain: Negri bodies appear magenta/pink against blue background
    • Negri bodies: eosinophilic, round/oval intracytoplasmic inclusions, 2-10 µm
    • Specificity ~100%, but sensitivity ~80% (absent in ~20% of rabies cases)
  • Direct FAT on brain tissue: Gold standard postmortem test (WHO recommended)
  • Mouse inoculation test (MIT): Brain suspension injected into mouse footpad/intracerebrally - mice develop paralysis + Negri bodies; slower (2-3 weeks)
  • RT-PCR on brain tissue
  • Virus isolation in cell culture (BHK-21, MRC-5 cells)

Q3. What is the pre and post exposure prophylaxis?

Pre-Exposure Prophylaxis (PrEP):
  • Indicated for: veterinarians, animal handlers, lab workers, forest workers, travelers to endemic areas
  • Schedule: 3 doses of cell culture vaccine (CCV) on Days 0, 7, 21 (or 28)
  • Route: Intramuscular (1 mL) in deltoid OR intradermal (0.1 mL)
  • Booster doses: Every 2 years for high-risk groups (or check neutralizing antibody titer)
  • No immunoglobulin needed for pre-exposure prophylaxis
Post-Exposure Prophylaxis (PEP) - CRITICAL, no vaccine was given in this case leading to death:
Step 1 - Wound management (immediately):
  • Wash wound thoroughly with soap and water for minimum 15 minutes
  • Apply 70% ethanol, povidone-iodine, or quaternary ammonium compounds
  • Do NOT suture primarily if possible (or minimal suturing)
  • Tetanus prophylaxis
Step 2 - Rabies Immunoglobulin (RIG):
  • Human Rabies Immunoglobulin (HRIG): 20 IU/kg body weight - inject as much as possible into and around the wound; remainder IM at distant site
  • Equine RIG (ERIG): 40 IU/kg (requires skin test first; risk of serum sickness)
  • Passive immunity provides immediate protection
  • Given only for Category III exposures (WHO)
Step 3 - Cell Culture Vaccine (Active immunization):
  • Essen regimen (IM): Days 0, 3, 7, 14, 28 - 5 doses, 1 mL each IM in deltoid
  • Zagreb regimen (IM): Days 0 (2 sites), 7, 21 - 4 doses total
  • Updated Thai Red Cross Intradermal (TRC-ID) regimen: 0.1 mL ID at 2 sites on Days 0, 3, 7, 28
  • Previously vaccinated individuals: Only 2 doses (Days 0 and 3), no RIG needed
WHO Exposure Categories:
CategoryType of ContactManagement
ITouching/feeding animal, intact skinWash skin; no vaccine
IIMinor scratches, nibbling, abrasionWound care + vaccine
IIITransdermal bites, scratches, mucous membrane contactWound care + RIG + vaccine
This patient had Category III (deep bite wounds) and required immediate RIG + vaccine, which was not given.

Q4. What is a cell culture vaccine?

Cell culture vaccines (CCVs) for rabies replaced older nerve-tissue vaccines (Semple vaccine). Key features:
  • Produced by growing rabies virus in cell cultures (not in neural tissue)
  • Types available:
    • HDCV (Human Diploid Cell Vaccine): Grown in WI-38 or MRC-5 human diploid cells; gold standard; expensive
    • PCECV (Purified Chick Embryo Cell Vaccine): Grown in primary chick embryo cells; e.g., Rabipur/RabAvert
    • PVRV (Purified Vero cell rabies vaccine): Grown in Vero (African green monkey kidney) cells; e.g., Verorab, Abhayrab
    • PDEV (Purified Duck Embryo Vaccine): Less used now
Advantages over nerve tissue vaccines:
  • More immunogenic
  • Better safety profile (no risk of post-vaccinial encephalomyelitis/AEFI from myelin proteins)
  • Purer preparation
  • Standardized potency (≥2.5 IU/dose)

Q5. What is a subunit vaccine?

A subunit vaccine contains only specific purified antigenic component(s) of the pathogen - not the whole organism.
Types:
  • Protein subunit: Purified specific proteins (e.g., HBsAg in Hepatitis B vaccine - recombinant subunit)
  • Polysaccharide: Purified capsular polysaccharides (e.g., pneumococcal polysaccharide vaccine)
  • Conjugate: Polysaccharide linked to a carrier protein to enhance immunogenicity (e.g., Hib vaccine, meningococcal conjugate)
  • Recombinant: Antigen produced by recombinant DNA technology in yeast/bacteria/mammalian cells
  • Virus-like particles (VLPs): Self-assembling protein shells without nucleic acid (e.g., HPV vaccine - Gardasil/Cervarix)
Advantages:
  • Safe (no live pathogen; no risk of reversion)
  • Stable
  • Can be used in immunocompromised patients
Disadvantages:
  • Less immunogenic (often require adjuvants and multiple doses)
  • May not generate cellular immunity as effectively as live attenuated vaccines

Q6. Which vaccine is available in India? What is the dosage?

Rabies vaccines available in India:
VaccineTypeManufacturerRouteDose
AbhayrabPVRV (Vero cell)Indian ImmunologicalsIM/ID1 mL IM or 0.1 mL ID
Vaxirab NPVRVZydus CadilaIM1 mL
RabipurPCECVGSK/Bavarian NordicIM1 mL
VerorabPVRVSanofi PasteurIM/ID1 mL IM
IndirabPVRVBharat BiotechIM/ID1 mL IM
Dosage (Essen regimen): 1 mL IM in deltoid on Days 0, 3, 7, 14, 28 Dosage (intradermal): 0.1 mL ID at 2 sites on Days 0, 3, 7, 28
Rabies Immunoglobulin in India:
  • Berirab-P (HRIG): 20 IU/kg
  • Abhayrab HIG / Kamrab: Human RIG
  • Equine RIG (ERIG): 40 IU/kg; cheaper; test for sensitivity first

Q7. How do you differentiate a case of encephalitis from meningitis?

FeatureEncephalitisMeningitis
DefinitionInflammation of brain parenchymaInflammation of meninges
ConsciousnessAltered (confusion, drowsiness, coma)Usually preserved (except late severe)
SymptomsBehavioral changes, seizures, focal neurological signs, psychiatric symptomsSevere headache, photophobia, phonophobia, vomiting
FeverYesYes
Meningismus (neck stiffness)May be absentPresent (Kernig's sign, Brudzinski's sign positive)
CSF cellsLymphocytic pleocytosisLymphocytic (viral) or neutrophilic (bacterial) pleocytosis
CSF proteinElevatedElevated (bacterial >> viral)
CSF glucoseNormal (viral)Reduced (bacterial meningitis)
MRI/CTParenchymal changes (edema, T2 changes in temporal lobe in HSE)Meningeal enhancement
EEGAbnormal (slow waves, epileptiform)Usually normal
Common causesHSV-1, Rabies, JE, EBV, CMV, VZV, ListeriaN. meningitidis, S. pneumoniae, Cryptococcus, TB
Meningoencephalitis: Both features combined (e.g., TB meningitis, HSV, rabies).

Q8. A slide has been focused related to this disease - identify and draw a labeled diagram

Identification: The histopathology slides shown are brain tissue (neurons) demonstrating Negri bodies.
Negri Bodies (labeled diagram description):
  • Large neurons visible with distinct nucleus and nucleolus
  • In the cytoplasm: oval/round, eosinophilic (pink), sharply defined inclusions
  • Size: 2-10 µm diameter
  • Location: Preferentially in Purkinje cells of cerebellum and pyramidal neurons of hippocampus (Ammon's horn)
  • Composition: Contain aggregates of rabies virus nucleocapsid proteins (N protein + RNA)
  • Stain: Eosinophilic on H&E; magenta on Seller's stain
  • Pathognomonic of rabies (diagnostic specificity ~100%)


Exercise MI8.1.3 - Dengue (Pages 9-10)

Clinical Case: Middle-aged male with 5-day acute febrile illness, severe generalized headache, retro-orbital pain, severe myalgia (lower back, arms, legs), thrombocytopenia (<1 Lac/µL platelet count).
Images:
  1. Dengue NS1 rapid card test (labeled "DENGUE NS1 Ag") - showing positive band
  2. Dengue NS1Ag ELISA plate - showing reactive wells (yellow/orange) in the first few columns

Q1. What is the clinical diagnosis and how you arrived at it?

Diagnosis: Dengue Fever (likely Dengue with Warning Signs / Dengue Hemorrhagic Fever given thrombocytopenia)
Basis:
  • Classic Dengue Triad: High fever + severe headache + myalgia
  • Retro-orbital pain: Highly characteristic (pain behind the eyes, worsens on eye movement)
  • "Breakbone fever": Severe myalgia especially of lower back, arms, legs - classic dengue description
  • Thrombocytopenia: <1 Lac/µL (normal: 1.5-4.5 Lac/µL) - hallmark of dengue
  • NS1 antigen test positive: Dengue NS1 (Non-Structural protein 1) is detectable in blood during Days 1-9 of fever
  • ELISA for NS1 positive: High sensitivity for dengue in early febrile phase
Dengue virus: Flaviviridae, 4 serotypes (DENV-1 to DENV-4), transmitted by Aedes aegypti (and Ae. albopictus) mosquito.

Q2. Explain the mode of transmission of this disease

Vector-borne transmission:
  • Primary vector: Aedes aegypti (black/white striped mosquito; day-biting; breeds in clean stagnant water)
  • Secondary vector: Aedes albopictus (tiger mosquito)
Cycle:
  1. Mosquito bites viremic dengue patient (Day 1-5 of fever = peak viremia)
  2. Virus replicates in mosquito midgut → salivary glands (extrinsic incubation period: 8-12 days)
  3. Infected mosquito bites susceptible human → transmission via saliva
  4. Transovarial transmission in mosquito possible (virus passed to eggs)
Not transmitted:
  • Person-to-person contact
  • Through air/water
  • (Blood transfusion and needle-stick: rare but documented)
Breeding sites of Ae. aegypti: Coolers, flower pots, discarded tires, water storage containers, roof gutters - any small collection of clean water within/around homes.

Q3. Interpret the results of the laboratory test displayed

Test 1 - NS1 Rapid Antigen Card Test:
  • Shows control line (C) and test line (T) visible = POSITIVE for Dengue NS1 Antigen
  • Interpretation: Active dengue infection (viremic phase, Days 1-9)
Test 2 - Dengue NS1Ag ELISA plate:
  • Yellow/orange colored wells in the first 3-4 rows (samples) with a red/high optical density = Reactive = NS1 Antigen positive
  • The pale wells = negative controls/low samples
  • Interpretation: ELISA confirms NS1 antigen positivity - consistent with active dengue viremia
Overall interpretation: Both NS1 tests positive, combined with clinical picture → Dengue fever confirmed, early febrile phase (consistent with Day 1-5 of fever).

Q4. Suggest other microbiological tests for diagnosis of this condition

Virological (acute phase, Days 1-5):
  • NS1 antigen detection: ELISA or rapid card test (as shown; sensitivity ~80-90% in early phase)
  • Virus isolation: Aedes albopictus C6/36 cell line or Vero cells (gold standard but slow, specialized labs)
  • RT-PCR for dengue RNA: Most sensitive; allows serotyping; useful Days 1-7; reference labs
Serological (convalescent, from Day 4-5 onwards):
  • IgM ELISA: Detects dengue-specific IgM; appears Day 3-5; persists for months - gold standard serological test
  • IgG ELISA: Appears Day 7-10; high levels suggest secondary infection; persists for years
  • NS1+IgM+IgG combo rapid tests: Cover both early and late phase
  • MAC-ELISA (IgM Antibody Capture ELISA): WHO recommended for routine diagnosis
  • Haemagglutination Inhibition (HAI) test: 4-fold rise in paired sera = significant
  • Plaque Reduction Neutralization Test (PRNT): Gold standard serological confirmation; serotype-specific; reference labs only
Other supportive tests:
  • CBC (thrombocytopenia, leukopenia, rising hematocrit in DHF)
  • Liver function tests (transaminases elevated)
  • Coagulation profile if suspected DHF

Q5. Suggest treatment for this condition

Dengue has NO specific antiviral treatment. Management is entirely supportive:
Dengue Fever (uncomplicated):
  • Adequate hydration: Oral fluids (ORS, coconut water, juices) - 2-3 L/day
  • Antipyretics: Paracetamol (acetaminophen) - do NOT use aspirin, ibuprofen, or other NSAIDs (risk of bleeding, Reye's syndrome; NSAIDs reduce platelet function)
  • Rest
  • Monitor: Daily CBC for platelet count and hematocrit
  • Watch for warning signs: Abdominal pain, persistent vomiting, bleeding, fluid accumulation, rapid clinical deterioration
Dengue with Warning Signs / Severe Dengue:
  • IV fluid therapy - careful fluid management to prevent plasma leakage complications
    • Isotonic crystalloids (Ringer's lactate / NS 0.9%)
    • Rate based on clinical status and hematocrit
  • Platelet transfusion: Only if <10,000/µL or active significant bleeding (not routinely for thrombocytopenia alone)
  • Blood transfusion: For severe bleeding with anemia
  • Monitoring: Hourly urine output, vital signs, serial hematocrit
  • ICU care for dengue shock syndrome (DSS)
Dengue Vaccine:
  • Dengvaxia (CYD-TDV, Sanofi Pasteur): First licensed dengue vaccine; tetravalent; approved in some countries for seropositive individuals aged 9-45 in endemic areas; NOT recommended for seronegative individuals (risk of severe dengue on first natural infection)
  • Qdenga (TAK-003, Takeda): Newer; approved in multiple countries including EU/Indonesia; 2-dose schedule

This document covers 4 clinical case exercises in medical microbiology: Exercise MI 2.7.3 (HIV), Exercise MI3.7 AE (Hepatitis B), Exercise 19.2 (Rotavirus diarrhea), Exercise MI5.2.8 AE (Rabies), and Exercise MI8.1.3 (Dengue).
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