Infectious Disease Lessons | Microbiology

🔬 Infectious Disease

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🏥 Infectious Disease

Meningitis by age: Neonates (GBS+E.coli+Listeria) · Children (N.meningitidis+S.pneumo) · Adults (S.pneumo #1)

Meningitis Pathogens by Age — each age group has different most-likely organisms guiding empirical antibiotic choice

The most common bacterial meningitis pathogens shift dramatically with age

Neonates (<1 mo): Group B Strep, E. coli, Listeria — cover with ampicillin + gentamicin. Children (1 mo–18 yr): N. meningitidis, S. pneumoniae. Adults: S. pneumoniae #1, N. meningitidis. Elderly/immunocompromised: add Listeria — add ampicillin. Classic triad: fever + headache + neck stiffness. Empiric: dexamethasone + ceftriaxone + vancomycin ± ampicillin.

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🃏 🏥 Infectious Disease

Meningitis organisms by age?

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Meningitis by age: Neonates (GBS+E.coli+Listeria) · Children (N.meningitidis+S.pneumo) · Adults (S.pneumo #1)

Meningitis Pathogens by Age — each age group has different most-likely organisms guiding empirical antibiotic choice

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🏥 Infectious Disease · CSF

CSF: Bacterial=cloudy+PMNs+↑protein+↓glucose. Viral=clear+lymphs+normal glucose. TB/Fungal=between.

CSF Patterns — bacterial (WBC 1000-10000 neutrophils, protein >100, glucose <45) vs viral (WBC 10-500 lymphocytes, protein mildly ↑, glucose normal)

CSF analysis identifies meningitis type before culture results return

Bacterial: cloudy, WBC 1000-10000 (PMNs), protein >100 mg/dL, glucose <45 (CSF:serum ratio <0.6). Viral: clear, WBC 10-500 (lymphocytes), protein mildly elevated, glucose normal. TB/Fungal: lymphocytic pleocytosis, high protein, low glucose (like bacterial but slower onset). Opening pressure high in bacterial and cryptococcal meningitis.

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🃏 🏥 Infectious Disease · CSF

CSF patterns — bacterial vs viral vs TB/fungal?

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CSF: Bacterial=cloudy+PMNs+↑protein+↓glucose. Viral=clear+lymphs+normal glucose. TB/Fungal=between.

CSF Patterns — bacterial (WBC 1000-10000 neutrophils, protein >100, glucose <45) vs viral (WBC 10-500 lymphocytes, protein mildly ↑, glucose normal)

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🏥 Infectious Disease · Pneumonia

CAP: S. pneumoniae #1. Atypicals (walking pneumonia): Mycoplasma · Chlamydophila · Legionella. HAP: Gram-negatives + MRSA.

Community vs Hospital-Acquired Pneumonia — CAP typical (lobar consolidation) vs CAP atypical (interstitial, walking pneumonia) vs HAP (resistant organisms)

Different settings, different organisms — changes the antibiotic choice entirely

CAP typical: S. pneumoniae (lobar), H. influenzae (COPD), Klebsiella (alcoholics — "currant jelly sputum"). CAP atypical (Legionella: water systems, hyponatremia, high LDH; Mycoplasma: young adults, cold agglutinins; Chlamydophila: gradual). HAP/VAP: Pseudomonas, Klebsiella, MRSA. CAP treatment: azithromycin or doxycycline (outpatient), beta-lactam + macrolide (inpatient), antipseudomonal + vancomycin (ICU).

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🃏 🏥 Infectious Disease · Pneumonia

Pneumonia organisms — CAP, atypical, HAP?

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CAP: S. pneumoniae #1. Atypicals (walking pneumonia): Mycoplasma · Chlamydophila · Legionella. HAP: Gram-negatives + MRSA.

Community vs Hospital-Acquired Pneumonia — CAP typical (lobar consolidation) vs CAP atypical (interstitial, walking pneumonia) vs HAP (resistant organisms)

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🏥 Infectious Disease · UTI

UTI bugs: E. coli #1 (80%) · Staph saprophyticus (young women) · Proteus (staghorn stones) · Klebsiella (diabetics)

UTI Organisms — E. coli uses fimbriae for adhesion · S. saprophyticus is #2 in young women · Proteus urease creates struvite stones · Klebsiella in hospital/diabetic patients

Which bacteria cause UTIs and the clinical clues that identify each

E. coli: 80% community UTIs — P fimbriae for uroepithelial adhesion. S. saprophyticus: #2 in sexually active young women (novobiocin resistant). Proteus mirabilis: urease → ammonia → struvite (staghorn) kidney stones, alkaline urine. Klebsiella: diabetics, hospital. Uncomplicated: TMP-SMX or nitrofurantoin × 3-7 days.

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🃏 🏥 Infectious Disease · UTI

UTI organisms?

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UTI bugs: E. coli #1 (80%) · Staph saprophyticus (young women) · Proteus (staghorn stones) · Klebsiella (diabetics)

UTI Organisms — E. coli uses fimbriae for adhesion · S. saprophyticus is #2 in young women · Proteus urease creates struvite stones · Klebsiella in hospital/diabetic patients

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🏥 Infectious Disease · STIs

Gonorrhea (pus, Gram− diplococci) · Chlamydia (silent, intracellular) · Syphilis (painless chancre, VDRL+)

STI Triad — key features: Gonorrhea=purulent discharge+ceftriaxone · Chlamydia=asymptomatic+doxycycline · Syphilis=3 stages+penicillin G

Key features that distinguish the major STIs in clinical presentation

Gonorrhea (N. gonorrhoeae): purulent urethral discharge, Gram− intracellular diplococci, disseminated gonococcal infection (DGI — migratory polyarthritis, skin). Treat: ceftriaxone. Chlamydia (C. trachomatis): most common bacterial STI, often asymptomatic, PID, ectopic pregnancy risk. Treat: doxycycline or azithromycin. Syphilis stages: primary (painless chancre), secondary (maculopapular rash on palms/soles), tertiary (aortitis, neurosyphilis). Treat all: penicillin G.

Gonorrhea

Purulent discharge, Gram− diplococci; treat with ceftriaxone (fluoroquinolone resistance now widespread)

Chlamydia

Most common bacterial STI, often silent; obligate intracellular; doxycycline or azithromycin × 7 days

Syphilis

3 stages; screen with VDRL/RPR, confirm with FTA-ABS; treat all stages with penicillin G

HSV

Painful vesicles, recurrent (latent in sacral ganglia); acyclovir/valacyclovir suppresses outbreaks

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🃏 🏥 Infectious Disease · STIs

Gonorrhea vs chlamydia vs syphilis?

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Gonorrhea (pus, Gram− diplococci) · Chlamydia (silent, intracellular) · Syphilis (painless chancre, VDRL+)

GonorrheaPurulent discharge, Gram− diplococci; treat with ceftriaxone (fluoroquinolone resistance now widespread)

ChlamydiaMost common bacterial STI, often silent; obligate intracellular; doxycycline or azithromycin × 7 days

Syphilis3 stages; screen with VDRL/RPR, confirm with FTA-ABS; treat all stages with penicillin G

HSVPainful vesicles, recurrent (latent in sacral ganglia); acyclovir/valacyclovir suppresses outbreaks

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🏥 Infectious Disease · Vector-Borne

Tick diseases: Lyme (bull's-eye rash) · RMSF (rash starts peripherally, spreads centrally) · Ehrlichia · Babesia

Tick-Borne Pathogens — Borrelia burgdorferi (Ixodes) · Rickettsia rickettsii (Dermacentor) · Ehrlichia · Babesia — all treated with doxycycline except Babesia

Four major tick-borne infections — different ticks, different presentations

Lyme disease (Borrelia, Ixodes tick): early = erythema migrans (bull's-eye); late = arthritis, heart block, Bell's palsy. Treat: doxycycline. RMSF (Rickettsia, Dermacentor tick): fever + rash starts on wrists/ankles → spreads centrally. Treat doxycycline immediately — do NOT wait for confirmation. Babesia: hemolytic anemia, "Maltese cross" on smear — treat with atovaquone + azithromycin.

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🃏 🏥 Infectious Disease · Vector-Borne

Tick-borne diseases — key signs?

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🃏 Answer

Tick diseases: Lyme (bull's-eye rash) · RMSF (rash starts peripherally, spreads centrally) · Ehrlichia · Babesia

Tick-Borne Pathogens — Borrelia burgdorferi (Ixodes) · Rickettsia rickettsii (Dermacentor) · Ehrlichia · Babesia — all treated with doxycycline except Babesia

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🏥 Infectious Disease

Endocarditis: fever + new murmur. Viridans strep (dental). S. aureus (IVDU). Duke criteria diagnose.

Infective Endocarditis — Duke criteria: 2 major OR 1 major + 3 minor OR 5 minor criteria for definite IE

Bacterial infection of the heart valves — high morbidity, must not miss

Viridans streptococci: after dental procedures — S. mutans, S. sanguinis. S. aureus: most aggressive, IVDU (right-sided, tricuspid). S. bovis/gallolyticus: associated with colon cancer — scope all patients. IVDU valve distribution: "right-sided" (tricuspid). Classic signs: Roth spots (retinal), Janeway lesions (painless), Osler nodes (painful), splinter hemorrhages. Treat: vancomycin + ceftriaxone empirically.

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🃏 🏥 Infectious Disease

Endocarditis — presentation and organisms?

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Endocarditis: fever + new murmur. Viridans strep (dental). S. aureus (IVDU). Duke criteria diagnose.

Infective Endocarditis — Duke criteria: 2 major OR 1 major + 3 minor OR 5 minor criteria for definite IE

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🏥 Infectious Disease · Food

Food poisoning timing: Staph toxin=1-6 hr. C. perfringens=8-16 hr. Salmonella=12-48 hr. The clock tells you the bug.

Foodborne Illness Incubation Times — short incubation = preformed toxin (no growth needed) · long incubation = bacterial growth required

The time from eating to symptoms identifies the responsible organism

1-6 hr (preformed toxin): Staph aureus (mayo/potato salad, vomiting predominant), B. cereus emetic (fried rice). 8-16 hr: Clostridium perfringens (reheated meat/gravy, diarrhea no vomiting), B. cereus diarrheal. 12-72 hr: Salmonella (eggs, poultry, reptiles), E. coli O157:H7 (undercooked beef → HUS), Campylobacter (poultry → Guillain-Barré).

1-6 hours

Staph aureus or B. cereus emetic — preformed toxin already in food; no bacterial growth needed in the host

8-16 hours

C. perfringens or B. cereus diarrheal — toxin produced after bacteria colonize the gut

12-72 hours

Salmonella, E. coli O157, Campylobacter — bacterial growth and invasion required; bloody diarrhea common

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🃏 🏥 Infectious Disease · Food

Food poisoning — what does the timing tell you?

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Food poisoning timing: Staph toxin=1-6 hr. C. perfringens=8-16 hr. Salmonella=12-48 hr. The clock tells you the bug.

1-6 hoursStaph aureus or B. cereus emetic — preformed toxin already in food; no bacterial growth needed in the host

8-16 hoursC. perfringens or B. cereus diarrheal — toxin produced after bacteria colonize the gut

12-72 hoursSalmonella, E. coli O157, Campylobacter — bacterial growth and invasion required; bloody diarrhea common

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🏥 Infectious Disease · Congenital

TORCH: Toxoplasma · Other (syphilis, Zika, parvovirus) · Rubella · CMV · Herpes/HIV

Congenital Infections — T=Toxoplasma · O=Other (syphilis/Zika/parvo B19) · R=Rubella · C=CMV (most common) · H=Herpes/HIV

Infections that cross the placenta and cause congenital defects

Toxoplasma: chorioretinitis, hydrocephalus, intracranial calcifications. Rubella: "blueberry muffin" rash, cataracts, deafness, PDA (heart). CMV: most common congenital infection — periventricular calcifications, sensorineural hearing loss. Herpes: C-section if active lesions. Syphilis: saddle nose, Hutchinson's teeth, interstitial keratitis. Parvovirus B19: hydrops fetalis. Zika: microcephaly.

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🃏 🏥 Infectious Disease · Congenital

TORCH

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TORCH: Toxoplasma · Other (syphilis, Zika, parvovirus) · Rubella · CMV · Herpes/HIV

Congenital Infections — T=Toxoplasma · O=Other (syphilis/Zika/parvo B19) · R=Rubella · C=CMV (most common) · H=Herpes/HIV

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🏥 Infectious Disease · Sepsis

Sepsis = infection + organ dysfunction. qSOFA: RR≥22, AMS, SBP≤100. Lactate ≥2 = tissue hypoperfusion.

Sepsis Criteria — qSOFA = quick Sepsis-Related Organ Failure Assessment: R=Respiratory rate≥22 · A=Altered mental status · S=Systolic BP≤100

Recognize sepsis early — every hour of delay worsens mortality

Sepsis-3 definition: life-threatening organ dysfunction caused by dysregulated host response to infection. qSOFA ≥2 = high risk. Hour-1 bundle: blood cultures (before antibiotics), lactate, fluids 30 mL/kg, broad-spectrum antibiotics, vasopressors if needed. Septic shock = sepsis + vasopressor requirement + lactate >2 mmol/L.

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🃏 🏥 Infectious Disease · Sepsis

Sepsis — definition and qSOFA criteria?

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Sepsis = infection + organ dysfunction. qSOFA: RR≥22, AMS, SBP≤100. Lactate ≥2 = tissue hypoperfusion.

Sepsis Criteria — qSOFA = quick Sepsis-Related Organ Failure Assessment: R=Respiratory rate≥22 · A=Altered mental status · S=Systolic BP≤100

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🏥 Infectious Disease · HIV

HIV/AIDS CD4 thresholds: <500 (HIV symptoms) · <200 (PCP prophylaxis, AIDS) · <100 (Toxo, Crypto) · <50 (MAC, CMV retinitis)

CD4 Count Thresholds — opportunistic infections occur at predictable CD4 levels guiding prophylaxis decisions

CD4 count predicts which opportunistic infection is most likely

CD4 <500: oral candidiasis, hairy leukoplakia (EBV), recurrent bacterial infections. CD4 <200: PCP (start TMP-SMX prophylaxis — also covers Toxo). CD4 <100: Toxoplasmosis, Cryptococcal meningitis. CD4 <50: MAC (Mycobacterium avium complex — start azithromycin prophylaxis), CMV retinitis (floaters, decreased vision).

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🃏 🏥 Infectious Disease · HIV

HIV/AIDS — CD4 thresholds and their infections?

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HIV/AIDS CD4 thresholds: <500 (HIV symptoms) · <200 (PCP prophylaxis, AIDS) · <100 (Toxo, Crypto) · <50 (MAC, CMV retinitis)

CD4 Count Thresholds — opportunistic infections occur at predictable CD4 levels guiding prophylaxis decisions

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🏥 Infectious Disease · Clostridium

C. diff: pseudomembranous colitis after antibiotics. Watery diarrhea + WBC elevation + recent antibiotics = C. diff until proven otherwise.

Clostridioides difficile — toxin A (enterotoxin) and toxin B (cytotoxin) cause pseudomembranous colitis; clindamycin, fluoroquinolones, cephalosporins are highest-risk antibiotics

The most common nosocomial infection — always think about it after antibiotics

Spores survive environmental disinfectants — requires handwashing (not hand sanitizer). Toxin A + B: damage colonocytes. Pseudomembranes on colonoscopy (yellowish plaques). Diagnosis: stool PCR for toxin gene or GDH antigen + toxin EIA. First episode: oral vancomycin or fidaxomicin. Recurrence: bezlotoxumab (anti-toxin B antibody). Severe: oral vanco + IV metronidazole. Avoid antiperistaltics.

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🃏 🏥 Infectious Disease · Clostridium

C. diff — cause and classic picture?

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C. diff: pseudomembranous colitis after antibiotics. Watery diarrhea + WBC elevation + recent antibiotics = C. diff until proven otherwise.

Clostridioides difficile — toxin A (enterotoxin) and toxin B (cytotoxin) cause pseudomembranous colitis; clindamycin, fluoroquinolones, cephalosporins are highest-risk antibiotics

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