Comprehensive Pathogen Vocabulary
Pathogens 1-19
Haemophilus influenzae type b (Hib)
- Microbe type: Gram-negative coccobacillus.
- Virulence / pathogenesis
- Polyribitol phosphate capsule ⟶ antiphagocytic.
- Ability to invade and traverse the blood-brain barrier (BBB).
- Significance: Capsule loss (e.g., in non-type-b strains) greatly reduces invasive potential.
- Primary target: Meninges (especially in children).
- Transmission: Respiratory droplets; human reservoir.
- Treatment: Third-generation cephalosporins (e.g., ceftriaxone).
- Disease: Acute bacterial meningitis; can also cause epiglottitis, sepsis.
- Connections: Vaccination with conjugate PRP-T vaccine has shifted epidemiology toward non-typable strains.
Neisseria meningitidis
- Microbe type: Gram-negative diplococcus (kidney-bean shaped).
- Virulence / pathogenesis
- Polysaccharide capsule (serogroups A, B, C, Y, W-135).
- Endotoxin \text{LOS} ⟶ cytokine storm, septic shock, Waterhouse–Friderichsen syndrome.
- Target: Bloodstream and CNS.
- Transmission: Respiratory droplets & close contact (dormitories, barracks).
- Treatment: Empiric 3^{rd}-gen cephalosporin + vancomycin; switch to penicillin G once confirmed susceptible.
- Disease: Meningococcemia, meningitis.
- Notes: Prophylaxis with rifampin, ciprofloxacin, or ceftriaxone for close contacts.
Listeria monocytogenes
- Microbe type: Gram-positive motile rod; facultative intracellular.
- Virulence
- Listeriolysin O (LLO) perforates phagolysosomal membrane.
- “Actin rockets” for intracellular motility & cell-to-cell spread (evasion of antibodies).
- Targets: CNS (meningoencephalitis), placenta / fetus.
- Transmission: Refrigerated food (soft cheeses, deli meats), raw vegetables.
- Treatment: Ampicillin ± gentamicin (synergy).
- Diseases: Neonatal sepsis, meningitis in immunosuppressed or elderly, granulomatosis infantiseptica (in utero).
Clostridium botulinum
- Microbe type: Gram-positive, spore-forming, obligate anaerobe.
- Virulence: Botulinum neurotoxin (BoNT, A-G serotypes) ⟶ cleaves SNARE proteins, blocking ACh release at NMJ.
- Target: Peripheral motor nerves → flaccid paralysis.
- Transmission: Pre-formed toxin in improperly canned food (adult) or spores in honey (infant botulism).
- Treatment: Equine-derived polyvalent antitoxin, respiratory support.
- Disease: Botulism (descending paralysis, “floppy baby”).
- Notes: Heat-labile toxin eliminated by boiling for >10 min.
Clostridium tetani
- Microbe type: Gram-positive spore-forming anaerobe (drumstick appearance).
- Virulence: Tetanospasmin (Zn-dependent endopeptidase) blocks presynaptic release of \text{GABA} & glycine ⟶ disinhibition ⟶ spastic paralysis.
- Target: Motor neurons of anterior horn & brainstem.
- Transmission: Contaminated wounds (soil).
- Treatment: Tetanus immune globulin (TIG), metronidazole, wound debridement, benzodiazepines.
- Prevention: \text{DTaP/Tdap} toxoid vaccine (q10 years booster).
- Disease: Tetanus (trismus, risus sardonicus, opisthotonos).
Mycobacterium leprae
- Microbe type: Acid-fast rod; prefers cool temperatures (upper extremities, face).
- Virulence/pathogenesis
- Invades Schwann cells; phenolic glycolipid I suppresses immune response.
- Targets: Peripheral nerves, skin.
- Transmission: Prolonged skin contact; Armadillos = natural reservoir (U.S.).
- Treatment
- Paucibacillary: Dapsone + rifampin (6 mo).
- Multibacillary: Dapsone + rifampin + clofazimine (≥12 mo).
- Disease: Leprosy (tuberculoid vs lepromatous).
- Notes: Lepromin skin test + in tuberculoid form (Th1 response).
Trypanosoma brucei gambiense/rhodesiense
- Microbe type: Hemoflagellate protozoan.
- Virulence
- Variant surface glycoprotein (VSG) switching ⟶ antigenic variation every \approx7 days.
- Targets: Blood → lymph → CNS.
- Transmission: Tsetse fly (Glossina spp.) bite, sub-Saharan Africa.
- Treatment: Suramin for hemolymphatic stage; melarsoprol for CNS stage (arsenical).
- Disease: African trypanosomiasis (“sleeping sickness” – recurring fevers, somnolence, coma).
Naegleria fowleri
- Microbe type: Free-living amoeba (trophozoite penetrates).
- Pathogenesis: Enters via cribriform plate during water activities → rapidly necrotizing meningoencephalitis.
- Target: Frontal lobe & olfactory bulbs.
- Transmission: Warm fresh water (lakes, Neti pots).
- Treatment: Almost invariably fatal; rare success with amphotericin B + miltefosine + cooling.
- Disease: Primary Amoebic Meningoencephalitis (PAM).
Rabies virus
- Microbe type: Enveloped, bullet-shaped, negative-sense ssRNA (Rhabdoviridae).
- Pathogenesis
- Glycoprotein binds nicotinic ACh receptor on muscle → retrograde axonal transport at \approx100\,\text{mm/day} to CNS.
- Target: Hippocampus (Negri bodies), Purkinje cells, brainstem.
- Transmission: Bite of rabid mammals (dogs, bats more common in U.S.).
- Treatment: Post-exposure prophylaxis = wound cleansing + Rabies Ig (RIG) infiltrated locally + vaccine (days 0,3,7,14).
- Disease: Rabies encephalitis (hydrophobia, aerophobia, spasm, coma).
Prion disease (PrP^{\text{Sc}})
- Agent: Misfolded \beta-sheet isoform of normal PrP^{\text{C}}.
- Pathogenesis: Template-directed refolding ⟶ spongiform change & neuronal loss without inflammation.
- Target: CNS gray matter.
- Transmission: Sporadic, inherited (PRNP mutation), iatrogenic (corneal grafts), dietary (vCJD).
- Treatment: None effective.
- Disease: Creutzfeldt–Jakob disease (CJD), variant CJD.
- Notes: Rapidly progressive dementia, myoclonus, ataxia; \text{14-3-3} protein in CSF.
Streptococcus pyogenes (Immune sequelae)
- Microbe type: Gram-positive group A coccus (beta-hemolytic).
- Virulence
- M protein molecular mimicry of cardiac myosin.
- Streptococcal pyrogenic exotoxins (SPEs) ⟶ scarlet fever, STSS.
- Target: Heart valves, joints (post-infection).
- Transmission: Respiratory droplets.
- Treatment: Penicillin V or G (prevents rheumatic fever if given <10 days).
- Disease: Acute rheumatic fever (J♥NES major criteria).
Francisella tularensis
- Microbe type: Gram-negative facultative intracellular coccobacillus.
- Pathogenesis: Survives in macrophages; granuloma formation in nodes.
- Target: Regional lymph nodes → ulceroglandular disease.
- Transmission: Tick bite (Dermacentor), handling rabbits (“rabbit fever”), aerosols (biothreat).
- Treatment: Streptomycin or gentamicin.
- Disease: Tularemia (ulcer + lymphadenopathy, pneumonic form if inhaled).
Brucella spp. (B. melitensis, abortus, suis, canis)
- Microbe type: Gram-negative coccobacillus; facultative intracellular.
- Virulence: Inhibits phagolysosome fusion → persistence in reticuloendothelial system (RES).
- Target: Liver, spleen, bone marrow.
- Transmission: Unpasteurized dairy, direct animal contact (vets, farmers).
- Treatment: Doxycycline + rifampin (6 wks).
- Disease: Undulant (intermittent) fever, hepatosplenomegaly, osteomyelitis.
Bacillus anthracis
- Microbe type: Large Gram-positive spore-forming rod (capsule of poly-D-glutamate).
- Virulence
- Protective Ag (PA) delivers toxins.
- Lethal factor (LF) = Zn-dependent protease of MAPKK ⟶ necrosis.
- Edema factor (EF) = \text{Ca}^{2+}/calmodulin-dependent adenylate cyclase ⟶ ↑cAMP, edema.
- Targets: Skin (eschar), lungs (mediastinum), GI.
- Transmission: Inhalation/ingestion/skin inoculation of spores; no person-to-person respiratory spread.
- Treatment: Ciprofloxacin or doxycycline ± raxibacumab (anti-PA mAb).
- Diseases: Cutaneous anthrax, inhalational (“woolsorter’s”), GI anthrax.
Clostridium perfringens
- Microbe type: Gram-positive anaerobe, “double zone” hemolysis.
- Virulence: Alpha-toxin (lecithinase) ⟶ phospholipase C → myonecrosis & hemolysis.
- Target: Skeletal muscle; also GI (type A food poisoning).
- Transmission: Contaminated wounds, trauma.
- Treatment: Aggressive surgical debridement, hyperbaric O_2, IV penicillin.
- Disease: Gas gangrene (clostridial myonecrosis).
Bartonella henselae
- Microbe type: Fastidious Gram-negative rod.
- Pathogenesis: Intra-erythrocytic/endothelial infection ⟶ vascular proliferation (bacillary angiomatosis in AIDS).
- Target: Regional lymph nodes.
- Transmission: Cat scratch or bite, fleas.
- Treatment: Usually self-limited; azithromycin if severe or in HIV.
- Disease: Cat-scratch disease (painful adenitis), bacillary angiomatosis.
Yersinia pestis
- Microbe type: Gram-negative rod with bipolar “safety-pin” staining.
- Virulence: Yops (type III secretion) block phagocytosis, Pla protease, F1 capsule.
- Targets: Lymph nodes → buboes; lungs in pneumonic plague.
- Transmission: Flea bite from rodent reservoir; aerosol/person-to-person in pneumonic form.
- Treatment: Doxycycline or gentamicin; prophylaxis for contacts.
- Diseases: Bubonic, septicemic, pneumonic plague.
Borrelia burgdorferi
- Microbe type: Spirochete (visualized with Wright/Giemsa).
- Pathogenesis: Surface lipoprotein variation; immune complex–mediated arthritis (stage 3).
- Target: Skin → joints, heart, CNS.
- Transmission: Ixodes scapularis tick (nymph stage) from mice, deer.
- Treatment: Doxycycline (early), ceftriaxone (late neuro/cardiac).
- Disease: Lyme disease (erythema migrans, facial palsy, migratory arthralgia, encephalopathy).
Rickettsia rickettsii
- Microbe type: Obligate intracellular, weakly Gram-negative.
- Pathogenesis: Escapes phagosome, replicates in endothelial cells ⟶ vasculitis & leakage.
- Target: Small blood vessel endothelium (skin, GI, CNS).
- Transmission: Dermacentor tick bite; requires \ge24 h attachment.
- Treatment: Doxycycline (even in children).
- Disease: Rocky Mountain spotted fever (rash starting wrists/ankles → trunk, palms/soles).
Pathogens 21-40
Trypanosoma cruzi
- Microbe type: Protozoan (flagellated trypomastigote in blood; amastigote in tissue).
- Pathogenesis: Intracellular replication in cardiac & GI smooth muscle → inflammation, fibrosis.
- Targets: Heart (dilated cardiomyopathy, arrhythmia), colon & esophagus (megacolon, megaesophagus).
- Transmission: Reduviid “kissing” bug feces (posterior station).
- Treatment: Benznidazole or nifurtimox (acute); no cure for chronic stage.
- Disease: Chagas disease (Romana sign, chronic CHF, achalasia).
Toxoplasma gondii
- Microbe type: Obligate intracellular protozoan.
- Virulence: Tissue cyst formation, evades lysosomal killing.
- Targets: CNS (ring-enhancing lesions), retina, fetus (congenital).
- Transmission: Ingestion of oocysts from cat feces, cysts in undercooked meat, transplacental.
- Treatment: TMP-SMX prophylaxis (CD4<100); sulfadiazine + pyrimethamine + leucovorin for disease.
- Disease: Toxoplasmosis (encephalitis, chorioretinitis, congenital triad – chorioretinitis, hydrocephalus, intracranial calcifications).
Plasmodium spp. (falciparum, vivax, ovale, malariae)
- Microbe type: Apicomplexan protozoan.
- Pathogenesis
- Cyclic erythrocyte lysis leading to paroxysmal fevers.
- P. falciparum expresses PfEMP1 on RBCs causing cerebral malaria, placental sequestration.
- Targets: Hepatocytes (exo-erythrocytic stage), RBCs (erythrocytic stage).
- Transmission: Female Anopheles mosquito.
- Treatment: Artemisinin-based combination therapy (ACT); add primaquine for hypnozoites (vivax/ovale).
- Disease: Malaria (tertian, quartan, malignant).
Schistosoma spp. (S. mansoni, haematobium, japonicum)
- Microbe type: Trematode (fluke) helminth.
- Pathogenesis: Eggs induce granulomatous inflammation → periportal fibrosis (pipestem), bladder wall granulomas.
- Targets: Liver (portal hypertension), bladder (hematuria, SCC).
- Transmission: Skin penetration by cercariae in freshwater containing infected snails.
- Treatment: Praziquantel.
- Disease: Schistosomiasis (Katayama fever, chronic hepatic/urogenital).
Streptococcus pyogenes (Pharyngitis)
- Microbe type: Gram-positive β-hemolytic coccus.
- Virulence: Streptolysin O/S (β-hemolysis), hyaluronic acid capsule, Spe A-C (superantigens).
- Target: Oropharynx.
- Transmission: Respiratory droplets.
- Treatment: Penicillin V (10 days).
- Disease: Strep throat; complications = scarlet fever, rheumatic fever, PSGN.
Corynebacterium diphtheriae
- Microbe type: Gram-positive club-shaped rod (metachromatic granules).
- Virulence: Diphtheria toxin (exotoxin A-B) ADP-ribosylates EF-2 ⟶ inhibits protein synthesis, necrosis.
- Targets: Pharynx → myocardium, kidneys, nerves.
- Transmission: Respiratory droplets.
- Treatment: Horse antitoxin (first), penicillin or erythromycin, airway support.
- Disease: Diphtheria (pseudomembranous pharyngitis, bull neck).
- Prevention: Toxoid vaccine (Dtap/Tdap).
Bordetella pertussis
- Microbe type: Gram-negative coccobacillus.
- Virulence
- Pertussis toxin ↑cAMP in neutrophils → lymphocytosis.
- Tracheal cytotoxin kills ciliated epithelium.
- Target: Ciliated respiratory mucosa.
- Transmission: Aerosol droplets (highly contagious).
- Treatment: Macrolides (azithro); supportive.
- Disease: Whooping cough (catarrhal → paroxysmal → convalescent).
- Prevention: Acellular vaccine (aP) in DTaP/Tdap.
Mycobacterium tuberculosis
- Microbe type: Acid-fast, obligate aerobe, cord factor.
- Pathogenesis: Caseating granulomas formed by Th1 response; latent persistence.
- Target: Lung apex (primary Ghon complex in lower lobe + hilar nodes), can disseminate.
- Transmission: Airborne droplet nuclei.
- Treatment: RIPE (rifampin, isoniazid, pyrazinamide, ethambutol) for 2 mo → RI 4 mo.
- Disease: TB (primary, reactivation, miliary).
Streptococcus pneumoniae
- Microbe type: Gram-positive lancet diplococcus, α-hemolytic.
- Virulence: Polysaccharide capsule, pneumolysin O (pore former), IgA protease.
- Target: Alveoli (lobar pneumonia), meninges, middle ear.
- Transmission: Respiratory droplets, autoinoculation.
- Treatment: Penicillin G, cephalosporins; consider vanc in resistance.
- Disease: CAP pneumonia (rusty sputum), meningitis, otitis media, sinusitis.
- Prevention: PPSV23 (IgM) & PCV13 (T-cell-dependent IgG).
Chlamydia psittaci
- Microbe type: Obligate intracellular elementary/reticulate bodies.
- Pathogenesis: Atypical pneumonia with systemic reticuloendothelial involvement.
- Target: Lung interstitium.
- Transmission: Inhalation of dried bird droppings (parrots, poultry).
- Treatment: Tetracyclines (doxy).
- Disease: Psittacosis (ornithosis).
Influenza virus (A, B, C)
- Microbe type: Enveloped, segmented (8) negative-sense ssRNA, Orthomyxovirus.
- Virulence
- Hemagglutinin (HA) binds sialic acid.
- Neuraminidase (NA) cleaves budding virions.
- Antigenic drift (point mutation) vs shift (reassortment) → pandemics.
- Target: Respiratory tract epithelium.
- Transmission: Droplet, fomite; winter season.
- Treatment: Oseltamivir (NA inhibitor) if <48 h; supportive.
- Disease: Influenza (fever, myalgia); post-viral bacterial pneumonia risk.
SARS-CoV-2
- Microbe type: Enveloped +ssRNA (betacoronavirus).
- Virulence: Spike (S) protein binds ACE2; furin cleavage enhances entry.
- Target: Alveolar type II pneumocytes, endothelium.
- Transmission: Respiratory droplets, aerosols, fomite.
- Treatment: Supportive; antivirals (remdesivir), steroids, monoclonal Abs per guidelines.
- Disease: COVID-19 (ranges asymptomatic → ARDS, MIS-C).
Histoplasma capsulatum
- Microbe type: Dimorphic fungus (mold in soil, intracellular yeast at 37 °C).
- Virulence: Survives within macrophages (↓pH, Fe sequestration).
- Target: Lungs, RES; mimics TB.
- Transmission: Inhalation of microconidia in bat/bird droppings (caves).
- Treatment: Itraconazole; amphotericin B if severe.
- Disease: Histoplasmosis (calcified hilar nodes, disseminated in AIDS).
Pneumocystis jirovecii
- Microbe type: Yeast-like fungus (cannot be cultured).
- Pathogenesis: Foamy alveolar exudate ⟶ ↓diffusion capacity.
- Target: Alveoli (type I pneumocytes).
- Transmission: Airborne; latent infection reactivates in immunosuppression (CD4<200).
- Treatment/Prophylaxis: TMP-SMX; atovaquone if sulfa allergy.
- Disease: PCP pneumonia (ground-glass CXR, ↑LDH).
Escherichia coli (Uropathogenic E. coli – UPEC)
- Microbe type: Gram-negative rod, lactose +.
- Virulence: P-fimbriae (Pap) adhere to uroepithelium; hemolysin HlyA.
- Target: Urinary tract (bladder → kidney).
- Transmission: Ascending endogenous GI flora (female anatomy, catheters).
- Treatment: Nitrofurantoin for simple cystitis; fluoroquinolone for pyelonephritis.
- Disease: UTI (dysuria, urgency, pyelonephritis).
Leptospira interrogans
- Microbe type: Thin spirochete with hooked ends.
- Pathogenesis: Disseminates hematogenously → vasculitis; Weil’s disease (jaundice + renal failure + hemorrhage).
- Targets: Kidneys (interstitial nephritis), liver, lungs.
- Transmission: Contact with water/soil contaminated by animal urine (surfers, farmers).
- Treatment: Doxycycline; IV penicillin for severe.
- Disease: Leptospirosis (flu-like illness, conjunctival suffusion).
Neisseria gonorrhoeae
- Microbe type: Gram-negative diplococcus, oxidase +.
- Virulence: Pili & Opa proteins with phase/antigenic variation; IgA protease.
- Target: Columnar epithelium of genital tract, conjunctiva, pharynx.
- Transmission: Sexual contact, birth canal.
- Treatment: Ceftriaxone (single IM) + azithro/doxy (for Chlamydia).
- Diseases: Gonorrhea, PID, septic arthritis, neonatal conjunctivitis.
Chlamydia trachomatis (D–K, L1-3)
- Microbe type: Obligate intracellular; EB (infectious) / RB (replicative) cycle in inclusion.
- Virulence: Inhibits phagosome-lysosome fusion; plasmid-encoded T3SS effector CPAF.
- Target: Genital tract, eyes, joints.
- Transmission: Sexual, perinatal.
- Treatment: Doxycycline (1 wk) or azithromycin (1 dose).
- Diseases: Nongonococcal urethritis, cervicitis, PID, ectopic pregnancy, neonatal pneumonia, trachoma (A-C), LGV (L1-3).
Treponema pallidum
- Microbe type: Spirochete (dark-field microscopy, VDRL/RPR serology).
- Virulence: Corkscrew motility, ability to coat with host fibronectin (immune evasion).
- Target: Systemic (end-arteritis).
- Transmission: Sexual, transplacental.
- Treatment: Penicillin G (IM); desensitize if allergic and pregnant.
- Disease: Syphilis (primary chancre, secondary rash, tertiary gummas/aortitis, neurosyphilis, congenital).
Herpes simplex virus 2
- Microbe type: Enveloped dsDNA, icosahedral.
- Pathogenesis: Latency in sacral DRG; periodic reactivation.
- Target: Genital mucosa, sensory neurons.
- Transmission: Sexual, perinatal.
- Treatment: Acyclovir/valacyclovir (TK activation needed).
- Disease: Genital herpes (painful vesicles, neonatal HSV).
Pathogens 41-44
Human papillomavirus (HPV 6, 11, 16, 18)
- Microbe type: Non-enveloped dsDNA, circular (Papillomaviridae).
- Virulence: E6 (binds p53) & E7 (binds Rb) oncoproteins drive cell cycle.
- Targets: Stratified squamous epithelium of cervix, anus, oropharynx.
- Transmission: Sexual contact, skin-to-skin.
- Prevention: Recombinant L1 virus-like particle vaccine (Gardasil 9).
- Diseases: Low-risk (6/11) genital warts; high-risk (16/18) CIN & cancers.
Gardnerella vaginalis
- Microbe type: Gram-variable rod (facultative anaerobe).
- Pathogenesis: Disrupts normal vaginal lactobacilli → biofilm → ↑pH.
- Target: Vagina.
- Transmission: Opportunistic after dysbiosis (not strictly STI).
- Treatment: Metronidazole or clindamycin.
- Disease: Bacterial vaginosis (thin gray discharge, fishy odor, clue cells).
Candida albicans
- Microbe type: Budding yeast with pseudohyphae at 37 °C (germ tubes).
- Pathogenesis: Overgrowth when normal flora/immunity altered; adhesion proteins, hyphae invasion.
- Target: Vagina, oropharynx, bloodstream (candidemia).
- Transmission: Endogenous; risk ↑ with antibiotics, diabetes, estrogen.
- Treatment: Topical azoles for vaginitis; fluconazole or echinocandin systemic.
- Disease: Vulvovaginal candidiasis (itchy curd-like discharge).
Trichomonas vaginalis
- Microbe type: Flagellated protozoan (no cyst form).
- Pathogenesis: Adheres to squamous epithelium, causes cytolysis & inflammation.
- Target: Vagina, urethra.
- Transmission: Sexual (must treat partners).
- Treatment: Metronidazole (single 2 g dose) for patient & partner.
- Disease: Trichomoniasis (frothy green discharge, strawberry cervix, pH>4.5).
Cross-Cutting Concepts & Clinical Pearls
- Capsule vs No Capsule: Capsules (Hib, N. meningitidis, S. pneumoniae, B. anthracis) are major vaccine targets because anticapsular Ig G confers opsonization.
- Intracellular Pathogens: Require cell-mediated immunity (Th1) for control—Listeria, Brucella, Francisella, Chlamydia, Mycobacteria, Histoplasma.
- Vector Awareness: Ixodes tick co-transmits B. burgdorferi & Anaplasma; Dermacentor tick for RMSF & tularemia.
- Toxoid Vaccines: Diphtheria, tetanus, pertussis (acellular) rely on neutralizing antibody against toxin rather than organism.
- Antigenic Variation: Trypanosomes (VSG), N. gonorrhoeae pili, B. burgdorferi OspC, influenza shift/drift—complicates vaccine development.
- Post-Infectious Sequelae: S. pyogenes → rheumatic fever & PSGN; Campylobacter (not listed) → Guillain-Barré; Yersinia pestis → DIC.
- Immune Reconstitution: PCP and Toxoplasma reactivation hallmark of CD4<200 cells/μL; prophylaxis thresholds are tested.
- Classic Equations: Time to kill vs Cmax \bigl(\text{concentration-dependent killing of aminoglycosides}\bigr) guides streptomycin use in tularemia.
- Ethical/Practical: Many zoonoses involved (Brucella, Leptospira, Histo, Plague) stress One-Health approach; prion sterilization challenges call for single-use neurosurgical tools.