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Infectious Diseases Lecture Review

Fungal infections

  • Pneumocystosis (PCP / PJP)
    • Agent: Pneumocystis jirovecii (often called PCP pneumonia or PJP)
    • Epidemiology: most common opportunistic infection in AIDS patients; risk factors include CD4 count < 200 cells/µL and other forms of immunosuppression (e.g., chemotherapy, long-term biologics)
    • Presentation: subacute fever, dyspnea, tachypnea, nonproductive cough; exam findings may underrepresent hypoxia
    • Hypoxemia: desaturation on pulse oximetry despite seemingly good conversation; differential hypoxia for exam
    • Imaging: chest X-ray with bilateral interstitial infiltrates (but may be subtle); CT can show “ground-glass” or brown glass opacities
    • Gold standard/diagnosis: silver stain on sputum or bronchoscopy samples (historic standard)
    • Newer testing: PCR on sputum or bronchoscopy specimens is more sensitive than silver stain; still uses same sample material
    • Treatment: ext{TMP-SMX}; prednisone taper indicated if PaO_2 < 70 ext{ mmHg} on ABG
    • Visual: typical bilateral interstitial infiltrates in butterfly/basilar distribution
  • Candidiasis (Candida spp.)
    • General: yeast infections; Candida albicans vs non-albicans species; albicans typically fluconazole-susceptible
    • Fluconazole activity: Candida albicans commonly responds to fluconazole; non-albicans may be resistant
    • Vulvovaginal candidiasis
    • Common history: preceding antibiotic exposure
    • Presentation: vulvar itching, erythema, white “cottage-cheese” discharge without odor
    • Diagnostics: KOH prep showing hyphae (hyphae on wet prep)
    • Treatment: topical azoles (e.g., miconazole) for 1–7 days; or fluconazole 200 ext{ mg PO once}
    • Esophageal candidiasis
    • Risk factors: preceding antibiotic exposure; immunosuppression (steroids, chemotherapy, HIV)
    • Presentation: GERD-like symptoms, dysphagia, odynophagia
    • Diagnosis: EGD with biopsy
    • Treatment: fluconazole; IV fluconazole for severe dysphagia; note: large oral tablets may be difficult to swallow; use IV if needed
    • Esophageal candidiasis (ETD wording in transcript appears as “ETD”) description: white/blackened esophageal wall on endoscopy
  • Protozoal infections
    • Malaria (Plasmodium spp.)
    • Species: vivax, malariae, ovale, knowlesi (transcript mentions nollesi; correct name is knowlesi; five species including falciparum)
    • Epidemiology: worldwide; endemic malaria largely outside the U.S.; cases in returning travelers
    • Vectors: female Anopheles mosquito (transmitter of infection during blood meals)
    • Endemic zones and drug resistance: areas with chloroquine-resistant malaria; avoid relying on chloroquine; Mexico & Central America still have susceptibility in many areas
    • Clinical pattern: paroxysmal cycles of chills, fever, sweats (about 3 days on, 3 days off); associated with headaches, myalgia, splenomegaly
    • Diagnosis: thick and thin blood smears (speciate and guide therapy); PCR is available but less specific for species
    • Laboratory clues: anemia, leukopenia
    • Prevention: mosquito avoidance (insect repellent, bed nets) and chemoprophylaxis
    • Prophylaxis/therapy (when chloroquine resistance is present): atovaquone-proguanil (Malarone) is a preferred option; alternatives include mefloquine (Larium) and doxycycline; note adverse effects: doxycycline causes photosensitivity; mefloquine has neuropsychiatric effects; doxycycline less ideal in high sun areas
    • For chloroquine-resistant areas with hypnozoites (vivax/ovale): add primaquine or tafenoquine (stand-alone option) in addition to atovaquone-proguanil; risks: hemolysis in G6PD deficiency; not recommended in pregnancy
    • Overall: treatment decisions are complex and patient-specific; often requires referral to infectious diseases
  • Viral infections
    • Varicella-zoster virus (VZV): chickenpox and shingles
    • Transmission: primarily respiratory secretions; contact with lesions possible
    • Latency and reactivation: VZV remains dormant in dorsal root ganglia; reactivation causes herpes zoster (shingles)
    • Shingles risk factors: age, waning cell-mediated immunity, stress
    • Shingles clinical features: prodrome (burning/tingling/pain) followed by vesicular eruption in 1–3 dermatomes; can disseminate in immunocompromised or elderly
    • Non-cutaneous spread: ophthalmic involvement (herpes zoster ophthalmicus) can threaten vision
    • Postherpetic neuralgia: ~8% of patients develop persistent neuropathic pain after rash resolution
    • Diagnosis: clinical; PCR or serologies possible but slower
    • Treatment (early within 72 hours): oral acyclovir, valacyclovir, or famciclovir; IV acyclovir for severe or disseminated disease
    • Prevention: Shingrix (recombinant, non-live) vaccine; ACIP recommends 2-dose series starting at age 50; higher immunogenicity but may cause body aches, fever
    • Historical vaccine: Zostavax (live); not as immunogenic; prior Zostavax vaccination does not preclude Shingrix re-immunization
    • Coronaviruses (non-COVID strains) on PANSS blueprint
    • Recognize as non-COVID coronaviruses; often cause benign respiratory symptoms and mild illness; typically managed supportively
    • SARS-CoV-2 (COVID-19)
      • Epidemiology: first U.S. case documented Jan 2020; highly contagious
      • Presentation: highly variable; can be asymptomatic or severe; variants exist
      • High-risk groups for severe disease: age ≥ 65, immunosuppressed, underlying comorbidities (e.g., diabetes, hypertension, obesity, cardiac/pulmonary disease)
      • Testing platforms: NAAT/PCR (nasopharyngeal swab) with high sensitivity; antigen testing (home tests) is less sensitive but rapid and inexpensive
      • Imaging: not routinely used unless severe illness; CXR shows bilateral air-space consolidation; CT shows bilateral peripheral ground-glass opacities
      • Outpatient treatments (start within 5 days of symptom onset):
      • Nirmatrelvir + ritonavir (Paxlovid) with significant drug interactions; common interaction management includes holding statins; NOACs/DOACs (e.g., rivaroxaban) often contraindicated; e.g., rivaroxaban contraindicated with Paxlovid
      • Molnupiravir (Legevrio): start within 5 days; less effective than Paxlovid; contraindicated in pregnancy due to mutagenic concerns
      • Remdesivir (Veklury): IV infusion; can be started within 7 days of symptom onset; pediatric dosing begins at 28 days old and weight ≥3 kg
      • Vaccines
      • Platforms: mRNA (Pfizer-BioNTech, Moderna) and protein-based nanoparticle (Novavax)
      • Approvals: mRNA vaccines approved for ages ≥6 months; Novavax approved for ages ≥12 years; clinical guidelines may update; J&J/Janssen (viral vector) legacy vaccine no longer routinely used
      • Dosing/age considerations may change with ACIP updates
    • Influenza
    • Type: Influenza A and B; seasonal in fall/winter; high risk groups: young children, pregnant women, elderly
    • Presentation: abrupt onset of fever, cough, sore throat, rhinorrhea/congestion, body aches, headache, fatigue
    • Complications: viral or secondary bacterial pneumonia; difficult to distinguish from COVID-19 by symptoms alone
    • Diagnostics: RIDTs (rapid antigen tests) with ~70% sensitivity; PCR-based tests more sensitive (~95%); require NP swab or nasal wash
    • Treatment/Prevention: anti-influenza antivirals (oseltamivir, baloxavir, zanamivir); start within 48 hours of symptom onset; vaccine recommended for ≥6 months; high-dose vaccine recommended for ≥65
    • Mumps
    • Agent: mumps virus (paramyxovirus); spread via respiratory droplets; parotid swelling is classic
    • Incubation: ~16–18 days; prodrome with fever, myalgia, anorexia, malaise, headache
    • Complications: orchitis, meningitis, pancreatitis, myocarditis
    • Vaccination: MMR vaccination reduces risk; infection is milder if vaccinated
    • Measles
    • Note: Measles to be covered in pediatric lectures; not detailed here
    • Rubella (German measles)
    • Agent: rubella virus; elimination in U.S. 2004; travel history important
    • Presentation: mild maculopapular rash starting on face/hairline; postauricular adenopathy first; up to ~50% asymptomatic
    • Pregnancy risk: congenital rubella syndrome with miscarriage, stillbirth, congenital cataracts, heart defects, hearing impairment
    • Prevention: MMR vaccine
    • Epstein-Barr virus (EBV) – Infectious mononucleosis
    • Transmission: primarily respiratory
    • Core features: malaise, fever, severe sore throat with pharyngeal exudates, posterior cervical lymphadenopathy, splenomegaly
    • Age: acute infection often in those <20 years
    • Rash: maculopapular rash in ~10%; classic ampicillin-associated rash in EBV (up to ~90% in some datasets) when ampicillin is given (note: this is a debated association but a classic exam point)
    • Diagnosis: clinical; atypical lymphocytes on CBC; Monospot test (heterophile antibodies) detects IgM-like antibodies; alternative confirmatory tests exist
    • Management: supportive care; avoid contact sports until symptom resolution due to splenic rupture risk; steroids if airway compromise or CNS complications
    • Human Immunodeficiency Virus (HIV)
    • CDC risk: anyone sexually active or who injects drugs is at risk
    • Virology basics: retrovirus; reverse transcriptase converts RNA to proviral DNA; not curable, but suppressible with ART
    • Acute HIV syndrome: occurs 2–8 weeks after exposure; mono-like syndrome; rash in ~80% even without amino penicillin exposure; mucocutaneous ulcers common
    • Screening/testing: 4th generation HIV test (combination antibody + p24 antigen; also called EIA, antibody-antigen testing); confirm with HIV-1/2 antibody test or nucleic acid testing (HIV RNA PCR)
    • Timing of markers: p24 antigen detectable earlier (day ~10) than antibody alone (day ~21); RNA becomes detectable earliest and rises quickly after infection
    • Neonatal HIV: use HIV RNA PCR to determine infection in the newborn; maternal antibodies persist for ~6 months, so serology is not reliable for neonates
    • Screening guidelines: routine non-risk-based opt-out HIV screening recommended in many settings for ages 13–64; higher-risk groups warrant more frequent testing (every 3–6 months; annually for high risk)
    • Treatment (first-line regimens): two NRTIs backbone (emtricitabine + tenofovir) with a third agent (INSTI such as dolutegravir or bictegravir); alternative backbones include lamivudine + abacavir (subject to HLA-B*57:01 testing prior to abacavir due to hypersensitivity risk)
    • Abacavir hypersensitivity: HLA-B*57:01 testing prior to abacavir; if positive, ABACAVIR avoided due to potentially fatal hypersensitivity
    • Abacavir safety tests: HLA test required; if negative, abacavir can be used
    • Zidovudine (AZT): still used in pregnancy to prevent maternal-to-fetal transmission; adverse effect includes bone marrow suppression
    • NNRTIs: associated with rash; efavirenz has CNS side effects (dizziness, vivid dreams)
    • Integrase inhibitors: generally well tolerated; weight gain is a potential concern
    • Protease inhibitors: can cause nausea, vomiting, diarrhea, lipodystrophy; older regimens carried higher metabolic toxicity
    • First-line ART (summary from PANRS): two NRTIs + an INSTI (e.g., emtricitabine/tenofovir + dolutegravir or bictegravir); alternative: include a PI such as darunavir with ritonavir if needed
    • Opportunistic infections and HIV-specific prophylaxis (based on CD4 counts)
      • Pneumocystosis prophylaxis: TMP-SMX when CD4 < 200
      • Toxoplasmosis prophylaxis: TMP-SMX when CD4 < 100
      • Mycobacterium avium complex (MAC) prophylaxis: azithromycin when CD4 < 50
    • Rabies
    • Family of viruses: Rhabdoviridae; primarily transmitted by bite wounds from bats (U.S. context) and terrestrial mammals like skunks, foxes, coyotes; dogs are major reservoirs in developing countries
    • Rodents (mice, rats) and lagomorphs (rabbits) do not transmit rabies
    • Post-exposure prophylaxis (PEP): wound cleaning with soap and water; passive immunization with human rabies immune globulin (HRIG) infiltrated around wound; active vaccination with 4 doses on days 0, 3, 7, 14; day 0 is when HRIG and first vaccine are given; HRIG is not given again on days 3, 7, or 14; full-blown rabies is almost always fatal
    • Incubation: typically 2–4 weeks or longer before onset of symptoms
  • Bacterial infections
    • Lyme disease (Borrelia burgdorferi)
    • Vector: Ixodes ticks; most common vector-borne disease in the U.S.
    • Geography: ~95% of cases in 12 states (Northeast/Midwest)
    • Stages: Stage 1 (early localized) with erythema migrans (bull’s-eye rash) plus constitutional symptoms; Stage 2 (early disseminated) with AV block and cranial nerve involvement (e.g., Bell’s palsy) and lymphocytic meningitis; Stage 3 (late) with monoarticular oligoarthritis
    • Diagnosis: serology after exposure risk; antibodies take 4–6 weeks to develop; equivocal/positive tests require Western blot confirmation
    • Treatment: doxycycline as first line in those >8 years old; amoxicillin preferred for children <8 years or pregnancy; ceftriaxone for neurologic involvement
    • Rocky Mountain spotted fever (Rickettsia rickettsii)
    • Presentation: influenza-like prodrome followed by fever, chills, headache, myalgias; body-wide macular rash that starts at wrists/ankles and spreads centrally; petechiae in about 50% of cases
    • Treatment: doxycycline in all ages; chloramphenicol in pregnancy
    • Anaplasmosis (Anaplasma phagocytophilium)
    • Vectors: Ixodes ticks and western blacklegged tick
    • Symptoms: fever, chills, severe headache, myalgias, GI symptoms, anorexia; rash is rare unless coinfection
    • Diagnosis: history of tick exposure; labs may show anemia, thrombocytopenia, leukopenia; morulae in neutrophils on blood smear; serology and PCR available
    • Treatment: doxycycline (first-line in all ages)
    • Tetanus
    • Etiology: Clostridium tetani neurotoxin; associated with puncture wounds and wounds contaminated with organic material
    • Symptoms: trismus (jaw stiffness), risus sardonicus, muscle spasms, hyperreflexia
    • Prevention: TD (tetanus-diphtheria) booster for adults; Tdap (tetanus-diphtheria-acellular pertussis); boosters every 10 years; vaccination recommended for adults who have not received Tdap
    • Treatment: hospitalize; airway protection; control spasms (benzodiazepines like midazolam); beta-blockers for sympathetic overactivity; wound debridement; neutralizing tetanus immune globulin; penicillin G to kill bacteria and stop toxin production
  • Sexually transmitted infections (STIs)
    • Gonorrhea (Neisseria gonorrhoeae)
    • Presentation: yellow, creamy discharge; women often asymptomatic
    • Site of infection: cervix, urethra, and can involve oral, vaginal, anal mucosa
    • Diagnosis: NAAT (nucleic acid amplification testing) on discharge or urine; chlamydia NAAT often ordered separately
    • Treatment: Ceftriaxone 500 mg IM once (1 g if patient ≥150 kg)
    • Chlamydia (Chlamydia trachomatis)
    • Main cause of non-gonococcal urethritis
    • Symptoms: urethritis, cervicitis, dysuria; many women are asymptomatic; reactive arthritis possible in both sexes; PID risk if untreated
    • Diagnosis: NAAT on discharge or urine; recommends separate testing from gonorrhea
    • Treatment: doxycycline 100 mg PO BID for 7 days; azithromycin 1 g PO single dose remains an option in pregnancy; test of cure recommended after completion in pregnancy
    • Syphilis (Treponema pallidum)
    • Stages: primary (painless chancre), secondary (diffuse/maculo-papular rash including palms/soles), tertiary (neurosyphilis, cardiovascular syphilis); latent stages include early latent (
    • Diagnosis: non-treponemal tests like RPR (rapid plasma reagin) with titer; confirm with treponemal-specific tests (e.g., FTA-ABS, TP-PA, EIA)
    • Follow-up: RPR titer should decline after treatment; repeat RPR at 6 and 12 months; treponemal antibodies typically remain positive for life
    • Treatment: benzathine penicillin G (Bicillin LA) 2.4 million units IM once for primary/secondary infection; follow-up serology guidance
    • Herpes simplex virus (HSV)
    • Types: HSV-1 (oral, can cause genital lesions) and HSV-2 (genital lesions, can cause oral lesions)
    • Clinical features: painful genital ulcers; recurrences common; not curable; suppression therapy for >6 outbreaks/year
    • Diagnosis: PCR from lesion is preferred; Tzanck smear historically used but less sensitive; serology interpretation can be tricky, especially HSV-1 seropositivity with genital symptoms
    • Treatment: acyclovir, famciclovir, or valacyclovir
    • Human papillomavirus (HPV)
    • Genotypes: ~120 HPV types; ~40 infect genital tract; high-risk types 16 and 18; low-risk types 6 and 11 associated with anogenital warts
    • HPV as STI: highly prevalent; the vaccine Gardasil 9 covers 6, 11, 16, 18 plus 5 additional types (31, 33, 45, 52, 58)
    • Vaccination: recommended 9–45 years; strongly recommended for ages 9–26; shared decision-making for ages 26–45
    • Genital warts (condylomata acuminata): usually HPV 6/11; not malignant; condyloma lata refers to secondary syphilis; pearly penile papules are a normal variant (not infectious)
    • Diagnosis: acetic acid test (vinegar) turns white on HPV lesions; biopsy can be used; Pap smear screening for cervical cancer in females
    • Treatment: patient-administered therapies (e.g., imiquimod); provider-administered options include cryotherapy, laser, surgical removal
  • Orthopedic infections
    • Osteomyelitis
    • Definition: bone/marrow inflammation due to infection; inflammation with infectious etiology
    • Routes: hematogenous spread (more common in children, especially metaphyseal long bones); contiguous spread (more common in adults, e.g., diabetic foot ulcers)
    • Most common organism: Staphylococcus aureus (especially hematogenous spread)
    • Diagnosis: inflammatory markers (ESR, CRP) elevated; imaging (MRI best; plain radiographs may be early); blood cultures; if blood cultures negative, bone biopsy with culture/pathology
    • Important: rule out tumors in children (tumors can mimic osteomyelitis)
    • Treatment: long-term antibiotics, typically IV for 4–6 weeks; surgical drainage of abscesses; adjunctive therapies (revascularization, hyperbaric oxygen)
    • Infectious arthritis (pyogenic arthritis)
    • Etiology: predominantly Staphylococcus aureus (including MRSA in some cases)
    • Presentation: single hot, swollen, painful joint; fever common; rule out crystalline disease (gout, pseudogout) with joint fluid crystals
    • Diagnosis: blood cultures and joint fluid cultures
    • Treatment: joint drainage; empiric therapy with vancomycin + ceftriaxone until cultures guide therapy
    • Disseminated gonococcal infection can cause infectious arthritis; presentation: fever, migratory polyarthralgias, tenosynovitis, dermatitis; treatment: ceftriaxone 1 g IV q24h; add doxycycline 100 mg PO BID ×7 days if chlamydia not excluded
  • Cardiac infections
    • Infective endocarditis
    • Definition: microbial infection of the endocardial surface, often with vegetations on heart valves
    • Valve involvement: native valve vs prosthetic valve; left-sided disease more common; right-sided endocarditis associated with IV drug use (often S. aureus/MRSA)
    • Common organisms: native valve pathogens such as viridans group streptococci; HACEK organisms (culture-negative due to fastidious growth); Enterococci; S. aureus (including MRSA); prosthetic valve pathogens vary by time since valve placement (early < 2 months often coagulase-negative staph; late resembles native valve pathogens)
    • Clinical features: fever, new murmur, septic emboli; peripheral signs include Janeway lesions (painless), Osler nodes (tender), splinter hemorrhages
    • Diagnosis: Duke criteria (major criteria = positive blood cultures, positive echocardiography; minor criteria = fever, vascular phenomena, immunologic phenomena, risk factors, etc.);
    • Echocardiography: transthoracic echocardiogram (TTE) first-line; transesophageal echocardiogram (TEE) more sensitive but more invasive
    • Treatment: empiric IV antibiotics such as vancomycin + ceftriaxone; adjust based on cultures; sometimes gentamicin substitution if needed (toxicity considerations)
    • Dental prophylaxis: prior to dental procedures for high-risk groups; amoxicillin 2 g PO 1 hour before procedure; alternatives include cephalexin or clindamycin for penicillin allergy
  • Neurologic infections
    • Meningitis
    • Age-based pathogens for bacterial meningitis
      • Preterm to <1 month: Streptococcus agalactiae (GBS), E. coli; others
      • 1 month to 50 years: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae
      • >50 years or with comorbidities: Streptococcus pneumoniae, Listeria monocytogenes
    • Aseptic meningitis: usually viral (e.g., enteroviruses like coxsackie, echovirus)
    • Clinical features: fever, meningismus, photophobia; CSF findings help distinguish bacterial vs aseptic meningitis
    • CSF findings (bacterial): elevated opening pressure; WBC predominantly neutrophils; low glucose; high protein; Gram stain/culture often positive
    • CSF findings (aseptic): normal or mildly elevated opening pressure; WBC predominantly lymphocytes; normal glucose; normal or mildly elevated protein; Gram stain/culture negative
    • Empiric treatment (ages 1 month–50 years, general): Ceftriaxone + vancomycin; add ampicillin if risk for Listeria (older age or immunocompromised or pregnancy)
    • Dexamethasone: adjunctive to antibiotics in bacterial meningitis to reduce inflammation (timing matters; typically given with or before antibiotics)
    • Prevention: vaccines against S. pneumoniae, N. meningitidis, H. influenzae
    • Meningoencephalitis
    • Etiologies: sporadic (often viral, e.g., HSV, VZV) and seasonal (West Nile, St. Louis encephalitis, La Crosse)
    • Presentation: febrile illness with altered mental status; seizures may occur
    • Diagnostics: CSF analysis; HSV PCR; start empiric acyclovir (10 mg/kg IV q8h) while awaiting results; discontinue if HSV PCR is negative
  • Dermatologic infections
    • Erysipelas
    • Involves epidermis and upper dermis; quick progression; sharp, raised borders; common cause: Streptococcus (Group A) but can be Staphylococcus/MRSA
    • Appearance: bright red, glistening, well-demarcated area; potential sight-threatening concern
    • Treatment: penicillins; if MRSA risk, vancomycin
    • Cellulitis
    • Involves epidermis, dermis, and subcutaneous tissue; common cause: Streptococcus; MRSA possible
    • Presentation: fever, chills, erythema, edema; may be systemic
    • Treatment: elevation and compression if tolerated; empiric penicillin-based or first-generation cephalosporin or dicloxacillin unless MRSA suspected -> vancomycin
    • Abscesses (furuncle)
    • Usually Staphylococcus aureus (including MRSA)
    • Presentation: firm, tender, fluctuant nodule
    • Treatment: warm compresses; incision and drainage; antibiotics (TMP-SMX, doxycycline, clindamycin) guided by culture
    • Necrotizing skin and soft tissue infections (necrotizing fasciitis)
    • Medical emergency; surgical consultation essential; antibiotics are secondary
    • Involvement: rapid progression with subcutaneous fascia and fat destruction; limb- and life-threatening
    • Early signs: pain out of proportion to exam; borders expand rapidly
    • Management: aggressive surgical debridement; broad-spectrum antibiotics; possible repeat debridement
  • Etiologies of infectious diarrhea
    • General categorization: noninflammatory vs inflammatory diarrhea
    • Noninflammatory diarrhea
    • Large-volume watery stools; no PMNs; nausea/vomiting common
    • Common pathogens: norovirus; Staphylococcus aureus enterotoxin; Bacillus cereus; Vibrio cholerae; protozoa Giardia lamblia, Cryptosporidium
    • Management: antidiarrheal agents (Imodium, bismuth subsalicylate) can be used safely in noninflammatory cases
    • Inflammatory diarrhea
    • Small-volume, frequently bloody/mucus-containing stools; fever; abdominal pain
    • Common organisms/toxins: Enterohemorrhagic E. coli O157 (Shiga toxin), C. difficile toxins, Shigella, Campylobacter, Salmonella
    • Management: avoid antimotility agents (Imodium, Pepto-Bismol) in inflammatory diarrhea; antibiotics not always necessary and can worsen toxin release in some pathogens (e.g., EHEC)
    • Noninflammatory etiologies specifics
    • Norovirus: most common cause of gastroenteritis in the U.S.; highly contagious; self-limited
    • Cholera (Vibrio cholerae): rice-water stool; fluid management is critical; antibiotics (doxycycline or azithromycin) can shorten illness
    • Giardia and Cryptosporidium: stool antigen testing; Giardia often linked to camping/hiking and drinking unfiltered water; Cryptosporidium severe in immunocompromised (e.g., HIV)
    • Cryptosporidiosis: stool antigen testing; IV therapy/referral for severe cases; infection can be life-threatening in immunosuppressed
    • Inflammatory etiologies specifics
    • E. coli O157:H7: shiga toxin; HUS risk (hemolytic uremic syndrome); avoid antibiotics for this pathogen
    • C. difficile: associated with antibiotics/hospitalization; spectrum ranges from asymptomatic carriage to toxic megacolon; diagnosis via toxin testing or PCR on stool; treatment: oral vancomycin or fidaxomicin (not IV)
    • Shigella: abrupt onset of bloody diarrhea; contact with daycare settings; treatment with fluoroquinolones in adults or azithromycin in children
    • Campylobacter: commonly from undercooked poultry; can cause Guillain-Barré syndrome; treatment with azithromycin
    • Salmonella: two patterns – gastroenteritis (food- and water-borne) and enteric fever (typhoid); treatment with fluoroquinolones or ceftriaxone; vaccines exist (oral and injectable)
  • Sepsis
    • Definition: life-threatening organ dysfunction caused by a dysregulated host response to infection
    • Major and quick criteria for identification
    • SIRS criteria (two or more of): temperature > 38°C or < 36°C; heart rate > 90 bpm; respiratory rate > 20 breaths/min or PaCO2 < 32 mmHg; WBC > 12,000/µL or < 4,000/µL or >10% bands
    • qSOFA (quick Sequential Organ Failure Assessment): RR > 22/min; altered mentation; systolic BP ≤ 100 mmHg; any two indicate higher risk of poor outcome
    • Labs and diagnostic workup: lactate level; broad infectious workup; cultures; imaging based on suspected source
    • Management: aggressive fluid resuscitation with crystalloids, 30 mL/kg within 30–60 minutes; broad empiric antibiotics if source unknown (e.g., vancomycin + piperacillin-tazobactam); escalate or de-escalate with culture results
    • Note on definition and management: sepsis can arise from infections in any organ system; respiratory tract infections are the most common cause
  • Quick takeaways and connections
    • Immunosuppression is a recurring theme across PCP, HIV, EBV, fungal infections, and opportunistic infections; CD4 counts are critical thresholds for prophylaxis and treatment initiation
    • Gold standards in microbiology often co-exist with rapid molecular tests (e.g., silver stain historically for PCP vs PCR now)
    • Vaccines significantly alter the epidemiology of several infections (Shingrix for shingles, HPV Gardasil-9, influenza vaccination, pneumococcal vaccines, meningococcal vaccines)
    • Many conditions require staged or progressive thinking (Lyme disease stages, endocarditis Duke criteria, meningitis CSF profiles, malaria species/speciation for therapy)
    • Travel history is repeatedly emphasized (malaria, typhoid, cholera, rubella exposure, HIV testing in various populations, etc.)
  • Equations and key values (LaTeX)
    • Prophylaxis thresholds: CD4 < 200
      ightarrow ext{Pneumocystosis prophylaxis with TMP-SMX}
    • Hypoxemia threshold for PCP treatment decision: PaO_2 < 70 ext{ mmHg} on ABG
    • HIV testing timing: p24 antigen detectable earlier than antibody; clinical relevance shown by timeline in the figure: ext{p24 antigen detectable around day }
      10 ext{; HIV antibodies around day } 21; Antiretroviral therapy (ART) backbones: ext{NRTIs: } ext{emtricitabine}+ ext{tenofovir}; ext{INSTI: dolutegravir or bictegravir}
    • Endocarditis treatment empirics: ext{vancomycin} + ext{ceftriaxone}
      ightarrow ext{deescalate to culture-guided therapy}
    • Meningitis empiric coverage by age: auricular note: do not confuse with Jones criteria (Rheumatic fever) vs Duke criteria (Endocarditis) – only Duke criteria apply to endocarditis