SystemWise Microbiology

High-yield organisms grouped by organ system. Use it before you start a system, and again when you revise it.

Every column header below opens that system's own page — the organism list on its own, with the WRWRT method worked through. Start with Microbiology by System, or go straight to the drugs in Antimicrobials.

Scroll sideways for more systems · headers stay pinned

USMLE Vault — SystemWise Microbiology. Cardiovascular column added 2026-08-01. Column headers link to the per-system organism lists; the method behind them is in Microbiology by System.
Microbiology	Cardiovascular	GIT	MSK	Dermat	Respiratory	Renal	Reproduction	CNS	Immunology
Bacteria	Endocarditis Staphylococcus aureus — acute, IV drug use, tricuspid Viridans group streptococci — subacute, after dental work Staphylococcus epidermidis — prosthetic valves Enterococcus — after GI/GU procedures Streptococcus gallolyticus — look for colon cancer Myocarditis / other Streptococcus pyogenes — Group A, rheumatic fever Corynebacterium diphtheriae — diphtheritic myocarditis Borrelia burgdorferi — Lyme carditis, AV block Treponema pallidum — syphilitic aortitis	Watery diarrhoea Vibrio cholerae Enterotoxigenic E. coli (ETEC) Staphylococcus aureus Clostridium perfringens Bacillus cereus Bloody diarrhoea Shigella species Enterohaemorrhagic E. coli (EHEC) Enteroinvasive E. coli (EIEC) Salmonella — especially non-typhoidal Campylobacter jejuni Yersinia enterocolitica Clostridioides difficile Stomach Helicobacter pylori — gastritis, peptic ulcer, MALT lymphoma Foodborne toxin Clostridium botulinum — ingested toxin; the illness itself is neuroparalytic (see CNS)	Gonococci Borrelia Staphylococcus Salmonella	Staphylococcus Streptococcus	Streptococcus pneumoniae Haemophilus influenzae Mycobacterium tuberculosis Bordetella pertussis Staphylococcus aureus — including MRSA Legionella pneumophila	Escherichia coli Staphylococcus saprophyticus Proteus mirabilis Klebsiella pneumoniae Enterococcus species Pseudomonas aeruginosa Serratia marcescens Streptococcus agalactiae — Group B	Neisseria gonorrhoeae — gonorrhoea, PID Chlamydia trachomatis — D–K: urethritis, PID; L1–L3: LGV Treponema pallidum — syphilis Haemophilus ducreyi — chancroid Gardnerella vaginalis — bacterial vaginosis Escherichia coli — UTIs Streptococcus agalactiae — Group B, neonatal	Neisseria meningitidis Streptococcus pneumoniae Haemophilus influenzae type B Listeria monocytogenes Group B Streptococcus — S. agalactiae Escherichia coli — K1 strain Mycobacterium tuberculosis Treponema pallidum — neurosyphilis Borrelia burgdorferi — neuroborreliosis, Lyme Clostridium botulinum Clostridium tetani	Antibody defects & asplenia — encapsulated Streptococcus pneumoniae — the classic: sepsis, meningitis, otitis Haemophilus influenzae type B — no capsular antibody, no protection Neisseria meningitidis — encapsulated — sepsis and meningitis Klebsiella pneumoniae — encapsulated Streptococcus agalactiae — Group B — encapsulated Salmonella — encapsulated; osteomyelitis in sickle cell Pseudomonas aeruginosa — encapsulated Complement defects — C5–C9 / MAC Neisseria meningitidis — recurrent meningococcaemia — the defining clue Neisseria gonorrhoeae — disseminated gonococcal infection Phagocyte defects — CGD, LAD, Chédiak-Higashi Staphylococcus aureus — catalase-positive — abscesses, poor pus Burkholderia cepacia — catalase-positive Serratia marcescens — catalase-positive Nocardia — catalase-positive T-cell defects Mycobacterium avium complex — disseminated when CD4 is very low
Viruses	Coxsackievirus B — commonest viral myocarditis Echovirus — myocarditis, pericarditis Adenovirus — myocarditis in children Parvovirus B19 — myocarditis HIV — dilated cardiomyopathy	Norovirus Rotavirus Adenovirus Cytomegalovirus — especially immunocompromised Herpes simplex virus — especially immunocompromised Hepatitis Hepatitis A virus (HAV) — faeco-oral, acute only Hepatitis B virus (HBV) — sexual/perinatal; can become chronic	Parvovirus Rubella	HSV VZV HPV Molluscum contagiosum HHV-6	Influenza virus Respiratory syncytial virus (RSV) Adenovirus	BK virus	Human papillomavirus (HPV) Herpes simplex virus — HSV-2 > HSV-1, genital herpes Human immunodeficiency virus (HIV) — opportunistic infections Cytomegalovirus (CMV) — congenital, immunosuppressed Hepatitis B virus (HBV) — sexual, perinatal	Herpes simplex virus — HSV-1, HSV-2 Varicella-zoster virus (VZV) Cytomegalovirus (CMV) Epstein-Barr virus (EBV) Human herpesvirus 6 (HHV-6) — roseola, encephalitis Rabies virus Enteroviruses — poliovirus, coxsackievirus, echovirus Mumps virus Measles virus — SSPE West Nile virus JC virus — PML	T-cell defects — DiGeorge, SCID, HIV Cytomegalovirus (CMV) — retinitis, colitis, pneumonitis Epstein–Barr virus (EBV) — lymphoproliferative disease Varicella-zoster virus (VZV) — disseminated, not dermatomal Herpes simplex virus (HSV) — severe, persistent, recurrent Severe T-cell defects JC virus — progressive multifocal leukoencephalopathy Antibody defects Enteroviruses — echovirus, poliovirus — chronic meningoencephalitis in Bruton's
Parasites	Trypanosoma cruzi — Chagas: dilated cardiomyopathy, megacolon Taenia solium — cysticercosis, rarely myocardium	Giardia lamblia Cryptosporidium parvum Entamoeba histolytica	—	—	Strongyloides stercoralis — respiratory symptoms in disseminated infection	Schistosoma haematobium	Trichomonas vaginalis — trichomoniasis	Toxoplasma gondii — toxoplasmosis Naegleria fowleri — primary amoebic meningoencephalitis Acanthamoeba species — granulomatous amoebic encephalitis Trypanosoma brucei — African sleeping sickness Taenia solium — neurocysticercosis	T-cell defects Toxoplasma gondii — ring-enhancing brain lesions Cryptosporidium — chronic watery diarrhoea IgA deficiency Giardia lamblia — no secretory IgA on the gut surface
Fungi	Candida species — endocarditis in IV drug use, prosthetic valves Aspergillus species — endocarditis in immunocompromised	—	Coccidioides	—	Pneumocystis jirovecii — especially immunocompromised Aspergillus species — invasive aspergillosis Histoplasma capsulatum Coccidioides immitis Blastomyces dermatitidis	Candida species	Candida albicans — vulvovaginal candidiasis, balanitis	Cryptococcus neoformans Coccidioides immitis Histoplasma capsulatum Blastomyces dermatitidis	T-cell defects Candida albicans — thrush, oesophagitis — mucocutaneous Pneumocystis jirovecii — pneumonia below CD4 200 Cryptococcus neoformans — meningitis Phagocyte defects — CGD Aspergillus — invasive Candida albicans — catalase-positive — invasive here, not mucosal