Rapid Review·Revision
Select any text to highlight it or add a note.
Microbiology by System
T1Must knowAll Systems: Organisms & Clues
Focus on
Use each system table to move from a classic vignette clue to the most likely organism. The page combines 155 high-yield organism-clue associations across nine body systems.
Key takeaways
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Staphylococcus aureus | Acute endocarditis; IV drug use → tricuspid valve. | Staphylococcus |
| Viridans streptococci | Subacute endocarditis after dental work, especially on damaged valves. | Streptococcus & Enterococcus |
| Staphylococcus epidermidis | Prosthetic valve endocarditis; biofilm formation. | Staphylococcus |
| Enterococcus | Endocarditis following GI/GU infection or instrumentation. | Streptococcus & Enterococcus |
| Streptococcus gallolyticus | Endocarditis + underlying colorectal neoplasia. | Streptococcus & Enterococcus |
| Streptococcus pyogenes | Migratory arthritis + carditis weeks after strep throat. | Streptococcus & Enterococcus |
| Corynebacterium diphtheriae | Pharyngeal pseudomembrane + myocarditis or arrhythmias. | Corynebacterium, Listeria & Nocardia |
| Borrelia burgdorferi | Tick exposure + fluctuating AV block. | Spirochetes: Borrelia & Leptospira |
| Treponema pallidum | Ascending aortic aneurysm or aortic regurgitation years after infection. | Treponema pallidum (Syphilis) |
| Coxsackievirus B | Young adult with chest pain or heart failure after a viral illness. | Picornaviruses & Rhinovirus |
| Echovirus | Enteroviral illness followed by myocarditis or pericarditis. | Picornaviruses & Rhinovirus |
| Adenovirus | Myocarditis following a respiratory illness, especially in children. | DNA Viruses Overview |
| Parvovirus B19 | Myocarditis associated with a recent rash or arthralgia. | DNA Viruses Overview |
| HIV | Dilated cardiomyopathy in a patient with advanced HIV. | HIV Structure & Diagnosis |
| Trypanosoma cruzi | Latin America + dilated cardiomyopathy, apical aneurysm, or megacolon. | Protozoa: Visceral & Sexually Transmitted |
| Taenia solium | Rare cardiac cysticercosis → arrhythmias in someone with cysticercosis elsewhere. | Cestodes & Trematodes |
| Candida | Endocarditis with IV drug use, prolonged IV access, or prosthetic valves. | Opportunistic Fungal Infections |
| Aspergillus | Immunocompromised patient + large vegetations and emboli; blood cultures often negative. | Opportunistic Fungal Infections |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Vibrio cholerae | Profuse “rice-water” diarrhea + severe dehydration. | Curved Rods: Campylobacter, Vibrio & H. pylori |
| Enterotoxigenic Escherichia coli (ETEC) | Traveler develops watery diarrhea without blood or significant fever. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Staphylococcus aureus | Sudden vomiting within 1–6 hours of mayonnaise-based food or cream pastries. | Staphylococcus |
| Clostridium perfringens | Cramps and diarrhea 8–16 hours after reheated meat or gravy. | Clostridia |
| Bacillus cereus | Rapid vomiting after reheated rice. | Bacillus (anthracis & cereus) |
| Shigella | Daycare exposure + fever, bloody diarrhea, and tenesmus. | Salmonella, Shigella & Yersinia |
| Enterohemorrhagic E coli (EHEC) | Bloody diarrhea after undercooked beef + little fever; may develop HUS. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Enteroinvasive E coli (EIEC) | Fever + bloody diarrhea resembling Shigella dysentery. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Nontyphoidal Salmonella | Diarrhea and fever after poultry, eggs, or reptile exposure. | Salmonella, Shigella & Yersinia |
| Campylobacter jejuni | Bloody diarrhea after poultry; may precede Guillain–Barré syndrome. | Curved Rods: Campylobacter, Vibrio & H. pylori |
| Yersinia enterocolitica | Pork exposure + RLQ pain mimicking appendicitis. | Salmonella, Shigella & Yersinia |
| Clostridioides difficile | Recent antibiotics or hospitalization + watery diarrhea and pseudomembranes. | Clostridia |
| Helicobacter pylori | Recurrent peptic ulcers; associated with gastric cancer and MALT lymphoma. | Curved Rods: Campylobacter, Vibrio & H. pylori |
| Clostridium botulinum | Home-canned food + diplopia, dysphagia, and descending paralysis. | Clostridia |
| Norovirus | Sudden vomiting and diarrhea spreading through a cruise ship, dorm, or household. | RNA Viruses Overview |
| Rotavirus | Unvaccinated infant or toddler + severe watery diarrhea and dehydration. | Rotavirus & Viral Gastroenteritis |
| Adenovirus | Prolonged watery diarrhea in a young child; enteric types 40/41. | DNA Viruses Overview |
| Cytomegalovirus | Immunocompromised patient + colitis or large linear esophageal ulcers. | Herpesviruses |
| Herpes simplex virus | Painful swallowing + small, punched-out esophageal ulcers. | Herpesviruses |
| Hepatitis A virus | Acute jaundice after contaminated food or travel; no chronic infection. | Hepatitis Viruses & HBV Serology |
| Hepatitis B virus | Hepatitis after sexual, blood, or perinatal exposure; may become chronic. | Hepatitis Viruses & HBV Serology |
| Giardia lamblia | Camping or untreated water + greasy, foul-smelling stools and bloating. | Protozoa: GI Infections |
| Cryptosporidium parvum | Swimming-pool exposure + watery diarrhea; prolonged and severe in AIDS. | Protozoa: GI Infections |
| Entamoeba histolytica | Bloody diarrhea ± liver abscess with “anchovy-paste” material. | Protozoa: GI Infections |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Neisseria gonorrhoeae | Sexually active young adult + migratory joint pain, tenosynovitis, and pustules. | Neisseria & Haemophilus influenzae |
| Borrelia burgdorferi | Tick exposure + intermittent swelling of a large joint, especially the knee. | Spirochetes: Borrelia & Leptospira |
| Staphylococcus aureus | Acutely hot, painful joint or osteomyelitis; most common bacterial cause. | Staphylococcus |
| Salmonella | Osteomyelitis in a patient with sickle cell disease. | Salmonella, Shigella & Yersinia |
| Parvovirus B19 | Acute symmetric small-joint arthritis in an adult exposed to children. | DNA Viruses Overview |
| Rubella virus | Rash + posterior auricular lymphadenopathy and arthralgia, especially in adult women. | Arboviruses & Togaviruses |
| Coccidioides | Southwestern US exposure + arthralgia and erythema nodosum; dissemination can infect bone. | Systemic Mycoses (Dimorphic Fungi) |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Staphylococcus aureus | Purulent skin abscesses, boils, or bullous impetigo. | Staphylococcus |
| Streptococcus pyogenes | Nonpurulent cellulitis or sharply demarcated erysipelas. | Streptococcus & Enterococcus |
| Herpes simplex virus | Recurrent, painful grouped vesicles on an erythematous base. | Herpesviruses |
| Varicella-zoster virus | Chickenpox lesions in different stages; shingles follows a painful unilateral dermatome. | Herpesviruses |
| Human papillomavirus | Rough skin warts or cauliflower-like genital warts. | DNA Viruses Overview |
| Molluscum contagiosum virus | Smooth, pearly papules with central umbilication. | DNA Viruses Overview |
| Human herpesvirus 6 | Infant with several days of high fever → fever resolves, then trunk rash appears. | Herpesviruses |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Streptococcus pneumoniae | Abrupt fever + pleuritic pain and lobar consolidation; classically rusty sputum. | Streptococcus & Enterococcus |
| Haemophilus influenzae | COPD exacerbation; type b also causes epiglottitis in unvaccinated children. | Neisseria & Haemophilus influenzae |
| Mycobacterium tuberculosis | Weight loss, night sweats, hemoptysis, and apical cavitation. | Mycobacteria (TB & Leprosy) |
| Bordetella pertussis | Coughing fits + inspiratory whoop or posttussive vomiting; infants may have apnea. | Bordetella & Legionella |
| Staphylococcus aureus | Severe pneumonia after influenza, often with cavitation. | Staphylococcus |
| Legionella pneumophila | Pneumonia + diarrhea and hyponatremia after hotel or water-system exposure. | Bordetella & Legionella |
| Influenza virus | Abrupt fever, prominent myalgia, headache, and dry cough. | Influenza (Orthomyxoviruses) |
| Respiratory syncytial virus | Infant in winter with bronchiolitis, wheezing, and increased work of breathing. | Paramyxoviruses (RSV, Measles & Mumps) |
| Adenovirus | Fever + pharyngitis and conjunctivitis; outbreaks among military recruits. | DNA Viruses Overview |
| Strongyloides stercoralis | Endemic exposure + GI symptoms and cough; steroids can trigger severe pulmonary hyperinfection. | Nematodes (Roundworms) |
| Pneumocystis jirovecii | HIV with CD4 <200 + subacute dry cough, hypoxemia, and diffuse ground-glass opacities. | Opportunistic Fungal Infections |
| Aspergillus | Neutropenia + lung nodules with a halo sign; a fungus ball may occupy an old cavity. | Opportunistic Fungal Infections |
| Histoplasma capsulatum | Ohio/Mississippi River valleys + bird or bat droppings; yeast inside macrophages. | Systemic Mycoses (Dimorphic Fungi) |
| Coccidioides immitis | Southwestern US dust exposure + pneumonia, erythema nodosum, and tissue spherules. | Systemic Mycoses (Dimorphic Fungi) |
| Blastomyces dermatitidis | Great Lakes or river-basin exposure + pneumonia and verrucous skin lesions; broad-based budding. | Systemic Mycoses (Dimorphic Fungi) |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Escherichia coli | Typical uncomplicated cystitis with dysuria, frequency, and nitrite-positive urine. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Staphylococcus saprophyticus | Young sexually active woman + cystitis; novobiocin resistant. | Staphylococcus |
| Proteus mirabilis | Recurrent UTI + alkaline urine and struvite/staghorn stones. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Klebsiella pneumoniae | Complicated UTI in diabetes or catheterization; mucoid lactose-fermenting colonies. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Enterococcus | UTI after instrumentation; gram-positive cocci, often nitrite-negative urine. | Streptococcus & Enterococcus |
| Pseudomonas aeruginosa | Catheter-associated UTI; oxidase-positive, non-lactose-fermenting rod. | Pseudomonas & Burkholderia |
| Serratia marcescens | Hospital or catheter-associated UTI; classically produces red pigment. | Catalase-Positive & Pigment-Producing Bacteria |
| Streptococcus agalactiae | Bacteriuria during pregnancy; Group B, CAMP-positive. | Streptococcus & Enterococcus |
| BK virus | Rising creatinine after kidney transplant; hemorrhagic cystitis after stem-cell transplant. | DNA Viruses Overview |
| Schistosoma haematobium | African freshwater exposure + terminal hematuria; bladder squamous cell carcinoma risk. | Cestodes & Trematodes |
| Candida | Yeast in urine with a catheter, diabetes, or antibiotics; often colonization. | Opportunistic Fungal Infections |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Neisseria gonorrhoeae | Purulent urethral discharge; intracellular gram-negative diplococci. | Neisseria & Haemophilus influenzae |
| Chlamydia trachomatis | D–K → urethritis/PID; L1–L3 → transient painless ulcer followed by painful inguinal nodes. | Chlamydiae |
| Treponema pallidum | Painless, indurated chancre; secondary disease causes a palm-and-sole rash. | Treponema pallidum (Syphilis) |
| Haemophilus ducreyi | Painful, ragged genital ulcer + tender, suppurative inguinal nodes. | Sexually Transmitted Infections |
| Gardnerella vaginalis | Thin gray discharge, fishy odor, clue cells, and vaginal pH >4.5. | Gardnerella vaginalis |
| Escherichia coli | Dysuria and frequency after intercourse; usually no vaginal discharge. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Streptococcus agalactiae | Maternal genital colonization → neonatal sepsis, pneumonia, or meningitis. | Streptococcus & Enterococcus |
| Human papillomavirus | Painless genital warts; types 16/18 are associated with cervical cancer. | DNA Viruses Overview |
| Herpes simplex virus | Painful grouped genital vesicles or ulcers that recur. | Herpesviruses |
| HIV | Fever, sore throat, rash, and generalized lymphadenopathy weeks after exposure. | HIV Structure & Diagnosis |
| Cytomegalovirus | Congenital infection → hearing loss, petechiae, and periventricular calcifications. | TORCH Infections |
| Hepatitis B virus | Sexual or perinatal exposure + hepatitis; neonatal infection often becomes chronic. | Hepatitis Viruses & HBV Serology |
| Trichomonas vaginalis | Frothy yellow-green discharge + strawberry cervix and motile organisms. | Protozoa: Visceral & Sexually Transmitted |
| Candida albicans | Intense itching + thick white discharge; normal vaginal pH and pseudohyphae. | Opportunistic Fungal Infections |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Neisseria meningitidis | Teenager or dorm resident + meningitis and petechial/purpuric rash. | Neisseria & Haemophilus influenzae |
| Streptococcus pneumoniae | Adult meningitis, especially after otitis, sinusitis, or a CSF leak. | Streptococcus & Enterococcus |
| Haemophilus influenzae type b | Meningitis in an unvaccinated young child. | Neisseria & Haemophilus influenzae |
| Listeria monocytogenes | Neonate, older adult, or immunocompromised patient + meningitis; unpasteurized dairy exposure. | Corynebacterium, Listeria & Nocardia |
| Group B Streptococcus | Newborn with sepsis or meningitis after maternal transmission. | Streptococcus & Enterococcus |
| Escherichia coli | Neonatal meningitis; K1 capsule. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Mycobacterium tuberculosis | Subacute meningitis + cranial nerve deficits, low CSF glucose, or hydrocephalus. | Mycobacteria (TB & Leprosy) |
| Treponema pallidum | Sensory ataxia and lightning pains, or personality changes and dementia. | Treponema pallidum (Syphilis) |
| Borrelia burgdorferi | Tick exposure + facial palsy, sometimes bilateral, and lymphocytic meningitis. | Spirochetes: Borrelia & Leptospira |
| Clostridium botulinum | Descending flaccid paralysis; honey-exposed infant with constipation and poor feeding. | Clostridia |
| Clostridium tetani | Contaminated wound + lockjaw, muscle rigidity, and painful spasms. | Clostridia |
| Herpes simplex virus | Fever, altered behavior, seizures, and temporal-lobe involvement; HSV-2 can cause recurrent meningitis. | Herpesviruses |
| Varicella-zoster virus | Meningitis or encephalitis around a shingles episode; vasculopathy can cause stroke. | Herpesviruses |
| Cytomegalovirus | Advanced AIDS + encephalitis or ascending weakness with urinary retention from polyradiculopathy. | Herpesviruses |
| Epstein–Barr virus | Rare encephalitis during mononucleosis; in AIDS, associated with primary CNS lymphoma. | Herpesviruses |
| Human herpesvirus 6 | Febrile seizures with roseola; limbic encephalitis after stem-cell transplant. | Herpesviruses |
| Rabies virus | Animal bite + hydrophobia, aerophobia, and agitation. | Rabies, Ebola & SARS-CoV-2 |
| Enteroviruses | Summer/fall aseptic meningitis; poliovirus causes asymmetric flaccid paralysis. | Picornaviruses & Rhinovirus |
| Mumps virus | Aseptic meningitis with parotitis ± orchitis in an unvaccinated patient. | Paramyxoviruses (RSV, Measles & Mumps) |
| Measles virus | Years after infection → cognitive decline and myoclonus: SSPE. | Paramyxoviruses (RSV, Measles & Mumps) |
| West Nile virus | Mosquito exposure + encephalitis, tremor, or acute flaccid paralysis. | RNA Viruses Overview |
| JC virus | Immunosuppression + progressive focal deficits and nonenhancing white-matter lesions: PML. | DNA Viruses Overview |
| Toxoplasma gondii | AIDS with CD4 <100 + seizures and multiple ring-enhancing brain lesions. | Protozoa: CNS Infections |
| Naegleria fowleri | Rapidly fatal meningoencephalitis after warm freshwater enters the nose. | Protozoa: CNS Infections |
| Acanthamoeba | Subacute granulomatous encephalitis in an immunocompromised patient. | Protozoa: CNS Infections |
| Trypanosoma brucei | Sub-Saharan Africa + tsetse fly exposure, lymphadenopathy, and sleep disturbance. | Protozoa: CNS Infections |
| Taenia solium | Seizures + brain cysts or calcifications after ingestion of tapeworm eggs. | Cestodes & Trematodes |
| Cryptococcus neoformans | AIDS + subacute headache, high opening pressure, and positive cryptococcal antigen. | Opportunistic Fungal Infections |
| Coccidioides immitis | Southwestern US exposure + chronic meningitis, sometimes with CSF eosinophilia. | Systemic Mycoses (Dimorphic Fungi) |
| Histoplasma capsulatum | Endemic exposure or disseminated histoplasmosis + chronic meningitis. | Systemic Mycoses (Dimorphic Fungi) |
| Blastomyces dermatitidis | Pulmonary or skin blastomycosis + brain abscess or meningitis. | Systemic Mycoses (Dimorphic Fungi) |
| ORGANISM | CLUE | LIBRARY PAGE |
|---|---|---|
| Streptococcus pneumoniae | Recurrent sinopulmonary infections with antibody deficiency; overwhelming sepsis with asplenia. | Streptococcus & Enterococcus |
| Haemophilus influenzae type b | Invasive infection with poor anticapsular antibody protection or asplenia. | Neisseria & Haemophilus influenzae |
| Neisseria meningitidis | Asplenia + rapidly progressive sepsis from an encapsulated organism. | Neisseria & Haemophilus influenzae |
| Klebsiella pneumoniae | Encapsulated organism; severe infections with impaired host defenses. | Enterobacteriaceae: E. coli, Klebsiella & Proteus |
| Streptococcus agalactiae | Encapsulated organism causing invasive neonatal infection. | Streptococcus & Enterococcus |
| Salmonella | Sickle cell disease + osteomyelitis; advanced HIV + recurrent bacteremia. | Salmonella, Shigella & Yersinia |
| Pseudomonas aeruginosa | Neutropenia + sepsis and ecthyma gangrenosum. | Pseudomonas & Burkholderia |
| Neisseria meningitidis | Recurrent meningococcal infections → C5–C9 deficiency. | Neisseria & Haemophilus influenzae |
| Neisseria gonorrhoeae | Recurrent disseminated infection can suggest terminal complement deficiency. | Neisseria & Haemophilus influenzae |
| Staphylococcus aureus | Recurrent deep abscesses in CGD; “cold” abscesses suggest hyper-IgE syndrome. | Staphylococcus |
| Burkholderia cepacia | Recurrent pneumonia in CGD or cystic fibrosis. | Pseudomonas & Burkholderia |
| Serratia marcescens | Unusual recurrent infections or abscesses in a child → consider CGD. | Catalase-Positive & Pigment-Producing Bacteria |
| Nocardia | Impaired cell-mediated immunity + lung infection and brain abscesses; weakly acid-fast branching rods. | Corynebacterium, Listeria & Nocardia |
| Mycobacterium avium complex | AIDS with CD4 <50 + fever, weight loss, anemia, and disseminated disease. | HIV/AIDS Opportunistic Infections by CD4 |
| Cytomegalovirus | AIDS with CD4 <50 + floaters or visual loss from hemorrhagic retinitis. | HIV/AIDS Opportunistic Infections by CD4 |
| Epstein–Barr virus | Transplant recipient + lymphadenopathy or masses → post-transplant lymphoproliferative disorder. | Herpesviruses |
| Varicella-zoster virus | Impaired T-cell immunity + widespread shingles beyond a single dermatome. | Herpesviruses |
| Herpes simplex virus | Impaired T-cell immunity + severe, persistent mucocutaneous ulcers. | Herpesviruses |
| JC virus | Immunosuppression or natalizumab exposure + progressive focal neurologic deficits. | DNA Viruses Overview |
| Enteroviruses | Chronic meningoencephalitis in a boy with absent B cells → Bruton agammaglobulinemia. | Picornaviruses & Rhinovirus |
| Toxoplasma gondii | AIDS with CD4 <100 + multiple ring-enhancing brain lesions. | Protozoa: CNS Infections |
| Cryptosporidium | Advanced HIV + persistent, profuse watery diarrhea. | Protozoa: GI Infections |
| Giardia lamblia | Recurrent greasy diarrhea in selective IgA deficiency or CVID. | Protozoa: GI Infections |
| Candida albicans | Persistent thrush and nail/skin candidiasis → impaired T-cell/IL-17 immunity. | Opportunistic Fungal Infections |
| Pneumocystis jirovecii | Infant with failure to thrive and pneumonia → SCID; adult with HIV → usually CD4 <200. | Opportunistic Fungal Infections |
| Cryptococcus neoformans | Impaired T-cell immunity, especially AIDS with CD4 <100 + meningitis. | Opportunistic Fungal Infections |
| Aspergillus | CGD or prolonged neutropenia + invasive lung infection. | Opportunistic Fungal Infections |
| Candida albicans | Neutropenia or central venous catheter + persistent fever and candidemia. | Opportunistic Fungal Infections |
How it's tested
Expect a vignette to give the exposure, host risk factor, anatomic site, or hallmark complication and ask for the organism. Start with the body system, then match the most specific clue.
You just read one page of 944
The rest of Step 1, written exactly like this.
Rapid Review is the reading layer of a full Step 1 platform: a schedule fitted to your exam date, flashcards for every page, and a mentor a message away.
Every Step 1 system
Written the same way: what to know, how it’s tested, where to go deeper.
A plan built to your exam date
Tell us when you sit, and the schedule fits the whole library and your question bank to it.
Flashcards for every page
Ready-made spaced-repetition decks linked to each topic, so nothing you read gets forgotten.
Start 14 days free
No card needed.·See pricing
