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.