Comprehensive study resource covering bacteriology, virology, mycology, parasitology, antimicrobial therapy, and laboratory diagnostics. Every organism, every drug, every stain you need to know.
Gram Stain Culture Biochemical ID Pathogenesis Clinical Syndromes
Staphylococcus aureus - Catalase (+), Coagulase (+). Classic: skin abscesses, endocarditis (acute native valve), osteomyelitis, septic arthritis, pneumonia (post-viral), toxic shock syndrome (TSST-1), food poisoning (enterotoxins). MRSA: vancomycin, daptomycin, linezolid. MSSA: nafcillin, cefazolin. Key toxins: PVL (necrotizing pneumonia), TSST-1 (superantigen), enterotoxins A-E (emetic). S. epidermidis - Coagulase (-), novobiocin sensitive. Biofilm on prosthetics (catheters, joint replacements, heart valves). S. saprophyticus - Coagulase (-), novobiocin resistant. UTI in young sexually active women. Streptococcus pyogenes (GAS) - Bacitracin sensitive, PYR (+). Pharyngitis, scarlet fever (erythrogenic toxin), impetigo, cellulitis, necrotizing fasciitis, toxic shock-like syndrome. Post-streptococcal: rheumatic fever (M-protein mimicry), post-streptococcal GN. S. agalactiae (GBS) - CAMP (+), hippurate (+). Neonatal sepsis/meningitis (vertical transmission from colonized mother). Prophylaxis: intrapartum penicillin. S. pneumoniae - Optochin sensitive, bile soluble. Alpha-hemolytic, lancet-shaped diplococci. Most common cause of CAP, bacterial meningitis (adults), otitis media, sinusitis. Capsular polysaccharide vaccine (PCV15/20, PPSV23). Viridans group streptococci - Alpha-hemolytic, optochin resistant. S. sanguinis, S. mutans, S. mitis. Subacute bacterial endocarditis (damaged valves).
Bacillus anthracis - Spore-forming, non-motile, box-car shaped. Cutaneous (eschar), inhalational (mediastinal widening), GI. Ciprofloxacin, doxycycline. Bacillus cereus - Motile. Emetic (fried rice, heat-stable toxin, 1-6h) and diarrheal (heat-labile, 8-16h) food poisoning. Clostridium perfringens - Double zone hemolysis. Gas gangrene (myonecrosis), food poisoning. Treatment: surgery + PCN + clindamycin. C. tetani - Tetanospasmin blocks RIM -> spastic paralysis, trismus, opisthotonos. Prevention: DTaP. Treatment: HTIG + metronidazole. C. botulinum - Blocks ACh at NMJ -> flaccid paralysis (descending, symmetric, bulbar). Infant (honey), foodborne, wound. Antitoxin. C. difficile - Toxin A + B. Pseudomembranous colitis after antibiotics. Diagnosis: stool toxin PCR. Treatment: vancomycin PO, fidaxomicin, FMT. Listeria monocytogenes - Facultative intracellular, tumbling motility. Neonatal, pregnant (flu-like), elderly/immunocompromised meningitis. Ampicillin + gentamicin. Corynebacterium diphtheriae - Exotoxin ADP-ribosylates EF-2 -> pseudomembrane, myocarditis, polyneuritis. Antitoxin + erythromycin. Nocardia - Partially acid-fast, filamentous. Pulmonary, brain, cutaneous. TMP-SMX first-line.
Neisseria meningitidis - Oxidase (+), maltose (+). Capsule serogroups A, B, C, W, Y. Meningitis (children/young adults), meningococcemia, Waterhouse-Friderichsen. Prevention: MenACWY, MenB vaccines. Rifampin/CTX prophylaxis for contacts. Treatment: ceftriaxone. N. gonorrhoeae - Oxidase (+), glucose only. Urethritis, cervicitis, PID, disseminated (dermatitis-arthritis), ophthalmia neonatorum. Increasing FQ resistance. Treatment: ceftriaxone IM + azithromycin. Moraxella catarrhalis - Oxidase (+), DNase (+). Otitis, sinusitis, COPD exacerbation. Beta-lactamase (+).
Escherichia coli - Lactose (+), beta-glucuronidase (+). Most common UTI (UPEC), neonatal meningitis (K1 capsule), traveler's diarrhea (ETEC), HUS (STEC O157:H7, Shiga toxin). CRE emerging threat. Klebsiella pneumoniae - Capsule, mucoid, currant jelly sputum. ESBL/KPC carbapenemase. Proteus mirabilis - Swarming, urease (+), struvite stones. Salmonella enterica - Non-lactose, H2S (+). Typhi: enteric fever, rose spots, relative bradycardia. Non-typhi: gastroenteritis. Shigella - Non-lactose, non-motile. Shiga toxin -> dysentery. Low infective dose (10-100 organisms). Pseudomonas aeruginosa - Oxidase (+), grape odor. VAP, burn infection, CF, malignant otitis externa, ecthyma gangrenosum. Anti-pseudomonal BL + aminoglycoside. Campylobacter jejuni - Microaerophilic, oxidase (+), curved. Most common bacterial gastroenteritis. Associated with Guillain-Barre. Helicobacter pylori - Urease (+). Peptic ulcer, MALToma, gastric cancer. Triple therapy (PPI + clarithromycin + amoxicillin/metronidazole). Haemophilus influenzae - X+V factors. Hib: meningitis (children), epiglottitis (thumbprint), pneumonia. Non-typeable: otitis, sinusitis, COPD. Legionella pneumophila - CYE agar, silver stain. Legionnaires' (hyponatremia, confusion). Azithromycin, levofloxacin. Bordetella pertussis - Paroxysmal whooping cough. DTaP, Tdap. Azithromycin early. Brucella - Undulant fever, livestock. Doxy + rifampin. Bartonella henselae - Cat scratch disease (lymphadenitis). Bacillary angiomatosis (HIV). Azithromycin.
Mycobacterium tuberculosis - AFB, slow-growing. Ghon complex (primary), apical cavitary (reactivation), miliary, Pott disease, TB meningitis. Diagnosis: IGRA/PPD, AFB smear + GeneXpert + culture (MGIT). Treatment: 2HRZE/4HR (RIPE). MDR: BPaL. LTBI: 4R, 3HP, 9H. M. leprae - Cannot culture. Tuberculoid vs lepromatous leprosy. Dapsone + rifampin + clofazimine. MAC - Disseminated in AIDS (CD4 < 50). Clarithromycin + ethambutol + rifabutin. Nocardia - Partial AFB. Actinomyces - Sulfur granules, not AFB. PCN. Treponema pallidum - Darkfield. Syphilis: primary (chancre), secondary (rash palms/soles, condyloma lata), tertiary (neurosyphilis, gumma, aortitis). Diagnosis: VDRL/RPR + FTA-ABS/TP-PA. Treatment: benzathine PCN G (early), IV PCN G (neurosyphilis). Borrelia burgdorferi - Ixodes. Lyme: erythema migrans, AV block, Bell palsy, arthritis. Doxycycline (early), ceftriaxone (CNS). Leptospira - Weil disease. Doxycycline.
Mycoplasma pneumoniae - No cell wall, sterols in membrane. Walking pneumonia (dry cough, young adults). Cold agglutinins. Macrolide/doxycycline/FQ (NOT beta-lactams). Chlamydia trachomatis - Obligate intracellular. A-C: trachoma (blindness), D-K: urethritis/cervicitis/PID, L1-L3: LGV. NAAT test. Azithromycin/doxycycline. C. pneumoniae - Mild CAP. C. psittaci - Psittacosis (birds). Rickettsia rickettsii - RMSF: fever, headache, centripetal petechial rash (wrists/ankles). Doxycycline. R. prowazekii - Epidemic typhus (louse). Orientia tsutsugamushi - Scrub typhus. Coxiella burnetii - Q fever (livestock). Acute: flu-like, pneumonia, hepatitis (doughnut granuloma). Chronic: endocarditis. Doxycycline (acute), doxy + hydroxychloroquine (chronic). Ehrlichia/Anaplasma - Morulae in monocytes/neutrophils. Doxycycline.
DNA Viruses RNA Viruses Hepatitis HIV Prions Antivirals
All DNA viruses are dsDNA except Parvovirus (ssDNA). All replicate in nucleus except Poxvirus (cytoplasm). Mnemonic: "Papp-H" - Papilloma, Adeno, Polyoma, Parvo, Herpes, Hepadna, Pox. Herpesviridae (8 types): HSV-1 (oral, encephalitis - temporal lobe), HSV-2 (genital, neonatal). Latency in sensory ganglia. Acyclovir, valacyclovir. Acyclovir-R: foscarnet. VZV: Chickenpox, shingles. Varicella vaccine, Shingrix. EBV: Mononucleosis (fever, pharyngitis, LAD), hairy leukoplakia, PTLD, Burkitt, nasopharyngeal CA. Monospot (+), VCA IgM. CMV: Retinitis (CD4 < 50), pneumonitis, colitis, congenital (calcifications, SNHL). Ganciclovir. HHV-6: Roseola. HHV-8: Kaposi sarcoma. Adenovirus: Pharyngoconjunctival fever. HPV: 6/11 warts, 16/18 cancer. Gardasil 9. BK: Cystitis/nephropathy. JC: PML. Parvovirus B19: Fifth disease, aplastic crisis, hydrops. Pox: Molluscum, Mpox.
Picorna: Polio (asymmetric flaccid paralysis), Coxsackie A (herpangina/HFMD), B (myocarditis/pleurodynia), rhinovirus, HAV. Corona: SARS-CoV-2. Toga: Rubella (congenital: cataracts, PDA, SNHL), Chikungunya. Calici: Norovirus. Astro: Gastroenteritis. Flavi: HCV, Yellow fever, Dengue (ADE), Zika (microcephaly, GBS), West Nile (encephalitis), JE. Retro: HIV, HTLV.
All cytoplasm except Orthomyxo (nucleus). Paramyxo: Measles (Koplik, 3 Cs, SSPE), Mumps (parotitis, orchitis), RSV (bronchiolitis), Parainfluenza (croup). Rhabdo: Rabies (Negri bodies, hydrophobia). HRIG + vaccine PEP. Orthomyxo: Influenza A/B. Drift + shift. Oseltamivir, baloxavir. Filo: Ebola, Marburg. Arena: LCMV, Lassa. Bunya: Hantavirus (HPS), RVF, CCHF.
HAV: Picorna, fecal-oral, self-limited. Vaccine. HBV: Hepadna, blood/fluids. Perinatal/sexual/IVDU. Serology: HBsAg (+) = infected, anti-HBs (+) = immune, anti-HBc IgM = acute. Entecavir, tenofovir. Vaccine. HCV: Flavi, blood/IVDU. Chronic 70-85% -> cirrhosis/HCC. DAA: sofosbuvir/velpatasvir 12wk (pan-genotypic). SVR > 95%. HDV: Defective, requires HBsAg. HEV: Fecal-oral. High mortality in pregnancy.
HIV: gp120 + CD4/CCR5 or CXCR4. RT, integrase, protease. Acute: mononucleosis-like. AIDS: CD4 < 200. OIs staged by CD4. ART: INSTI + 2 NRTIs. U=U. PrEP: TAF/FTC. PEP: 28d RAL + TDF/FTC. HTLV-1: Adult T-cell leukemia, HAM/TSP. Prions: PrPSc, no nucleic acid. CJD (rapid dementia, myoclonus, PSW EEG), vCJD, kuru. MRI cortical ribboning. No treatment.
Yeasts Molds Dimorphic Superficial Systemic Opportunistic Antifungals
Dermatophytes: Trichophyton, Microsporum, Epidermophyton. Infect keratinized tissue. Tinea capitis/corporis/pedis/cruris/unguium. KOH prep (hyaline septate hyphae). Topical terbinafine/clotrimazole; systemic terbinafine/griseofulvin/itraconazole. Malassezia furfur: Pityriasis versicolor (hypopigmented patches, trunk). "Spaghetti and meatballs" on KOH. Topical ketoconazole. Candida: C. albicans (most common), C. glabrata (fluconazole-R), C. krusei (intrinsic fluconazole-R), C. auris (MDR, emerging). Superficial: thrush, esophagitis, vulvovaginitis. KOH: pseudohyphae + budding yeast. Topical nystatin/clotrimazole; oral fluconazole.
Sporothrix schenckii: Dimorphic. Lymphocutaneous sporotrichosis (rose thorn -> nodular ascending lymphangitis). Itraconazole. Chromoblastomycosis: Fonsecaea, Phialophora. Warty plaques. Itraconazole + cryosurgery. Mycetoma (eumycetoma): Madurella. Draining sinuses + grains. Itraconazole + surgery.
Mold at 25 degrees C (soil), yeast at 37 degrees C (tissue). "Mold in cold, yeast in heat." Histoplasma capsulatum: Ohio/Mississippi valleys. Bat/bird droppings. Tiny yeast within macrophages. Acute/chronic/disseminated pulmonary, mediastinal fibrosis. Urine antigen. Itraconazole (mild), L-AmB (severe). Coccidioides immitis: SW US (Valley fever). Arthroconidia. Spherules with endospores. Erythema nodosum. Fluconazole (mild), L-AmB (severe). Meningitis: lifelong fluconazole. Blastomyces dermatitidis: Ohio/Mississippi, Great Lakes. Broad-based budding yeast. Pulmonary, skin, bone. Itraconazole, L-AmB for severe. Paracoccidioides brasiliensis: Latin America. Pilot wheel yeast. Talaromyces marneffei: SE Asia. HIV-associated (CD4 < 100). Molluscum-like lesions.
Aspergillus fumigatus: Septate hyphae, 45 degrees branching. ABPA (asthma/CF, IgE, central bronchiectasis), aspergilloma (fungus ball), invasive pulmonary (neutropenic, angioinvasive -> thrombosis). Galactomannan antigen. CT: halo sign, air crescent. Voriconazole first-line. Mucorales (Rhizopus, Mucor): Broad, non-septate, 90 degrees branching. Rhinocerebral (DKA), pulmonary. L-AmB + surgical debridement. Pneumocystis jirovecii: Cystic form, previously protozoan. PCP: dyspnea, dry cough, bilateral interstitial infiltrates, hypoxemia. CD4 < 200. Silver stain (cysts). Beta-D-glucan elevated. TMP-SMX + steroids (PaO2 < 70). Prophylaxis: TMP-SMX when CD4 < 200. Candida (deep): Candidemia, intra-abdominal, hepatosplenic. Echinocandin first-line. Cryptococcus neoformans: Polysaccharide capsule. Meningitis in HIV (CD4 < 100). India ink (negative stain), CrAg antigen. L-AmB + flucytosine induction, then fluconazole. C. gattii: Pacific NW, immunocompetent, cryptococcoma.
Protozoa Nematodes Cestodes Trematodes Ectoparasites Antiparasitics
Plasmodium: P. falciparum (severe, cerebral, high parasitemia), P. vivax/ovale (hypnozoites -> relapse, primaquine needed), P. malariae (nephrotic), P. knowlesi (zoonotic, SE Asia). Vector: Anopheles. Thin/thick smear, RDT. ACT (artemether-lumefantrine) for uncomplicated falciparum. IV artesunate for severe. Chloroquine + primaquine for vivax/ovale (check G6PD). Babesia microti: Ixodes tick. Hemolytic anemia. Maltese cross (tetrad). Clindamycin + quinine. Toxoplasma gondii: Cats (oocysts). Congenital: chorioretinitis, hydrocephalus, calcifications. HIV (CD4 < 100): ring-enhancing brain lesions, single/multiple. Pyrimethamine + sulfadiazine + leucovorin. Trypanosoma cruzi: Reduviid bug. Chagas: Romaña sign, dilated cardiomyopathy (apical aneurysm), megaesophagus, megacolon. Benznidazole. T. brucei: Tsetse fly. African sleeping sickness: hemolymphatic -> CNS (somnolence). Suramin/pentamidine (early), melarsoprol/eflornithine (late). Leishmania: Sandfly. Visceral (kala-azar: fever, splenomegaly, pancytopenia), cutaneous (ulcers), mucocutaneous (espundia). L-AmB, miltefosine.
Giardia lamblia: Pear-shaped, 2 nuclei, ventral sucking disk. Foul-smelling fatty stool, bloating. Metronidazole or tinidazole. Entamoeba histolytica: Trophozoites with ingested RBCs. Dysentery, liver abscess ("anchovy paste"). Metronidazole + paromomycin. Cryptosporidium parvum: Acid-fast oocysts. Profuse watery diarrhea in HIV. Nitazoxanide. Cyclospora/Cystoisospora: Acid-fast. TMP-SMX. Trichomonas vaginalis: Motile, 5 flagella. Frothy yellow discharge, strawberry cervix. Metronidazole/tinidazole (both partners).
Enterobius vermicularis: Pinworm. Perianal pruritus (nocturnal). Scotch tape test. Albendazole. Ascaris lumbricoides: Loeffler syndrome, obstruction. Hookworm: Ground itch, iron deficiency anemia. Albendazole + iron. Strongyloides stercoralis: Autoinfection. Larva currens. Hyperinfection with steroids/immunosuppression -> gram-negative sepsis (high mortality). Ivermectin first-line. Check serology before steroids in endemic areas. Trichinella spiralis: Pork. Periorbital edema, myalgia, eosinophilia. Albendazole + steroids. Wuchereria bancrofti: Lymphatic filariasis (elephantiasis). DEC + albendazole. Loa loa: African eye worm. Calabar swellings. DEC. Toxocara: Visceral larva migrans. Albendazole. Cutaneous larva migrans: Serpiginous tunnels. Albendazole/ivermectin.
Cestodes: Taenia solium (pork, neurocysticercosis -> seizures, albendazole + praziquantel + steroids), T. saginata (beef, no cysticercosis), D. latum (fish, B12 deficiency), Echinococcus (hydatid cyst -> PAIR + albendazole). Praziquantel for most. Trematodes: Schistosoma (mansoni intestinal, haematobium bladder/hematuria/squamous cell CA, japonicum). Eggs with spines. Praziquantel. Clonorchis (cholangiocarcinoma). Fasciola (triclabendazole, NOT praziquantel). Paragonimus (lung fluke, hemoptysis).
Sarcoptes scabiei: Intense pruritus, burrows (web spaces, wrists). Permethrin 5% cream. Crusted scabies: permethrin + oral ivermectin. Pediculus humanus: Head/body/pubic lice. Permethrin. Body louse vectors typhus, trench fever, relapsing fever. Tunga penetrans: Sand flea. Demodex: Blepharitis, rosacea.
Mechanisms Spectrum Resistance Empiric Regimens Stewardship
Beta-Lactams: Penicillins (GP, spirochetes). Anti-staph (nafcillin). Aminopenicillins (ampicillin). Anti-pseudomonal (piperacillin). Beta-lactamase combos (pip-tazo, amox-clav). Cephalosporins: 1st (cefazolin, GP > GN), 2nd (cefuroxime, GP+GN+anaerobes), 3rd (ceftriaxone/cefotaxime GN > GP, ceftazidime anti-pseudomonal), 4th (cefepime GP+GN+Pseudomonas), 5th (ceftaroline MRSA). Carbapenems (meropenem, ertapenem, imipenem) - broadest. Aztreonam - GN only, safe in PCN allergy. Glycopeptides: Vancomycin (MRSA, C. diff PO). Lipopeptides: Daptomycin (MRSA, VRE - NOT for pneumonia, surfactant inactivates). Polymyxins: Colistin (last resort MDR GN). Nephro/neurotoxic.
30S: Aminoglycosides (gentamicin, amikacin - GN, synergy with cell wall agents, concentration-dependent, once-daily, oto/nephrotoxic). Tetracyclines (doxycycline, tigecycline - atypicals, Rickettsia, acne, MRSA SSTI. Avoid in children < 8). 50S: Macrolides (azithromycin - atypicals, CAP, MAC. QTc). Chloramphenicol (aplastic anemia). Linezolid (MRSA, VRE - myelosuppression, serotonin syndrome). Clindamycin (GP anaerobes, toxin suppression - C. diff risk). Quinupristin/dalfopristin (VRE faecium).
TMP-SMX: Broad (UTI, PCP, toxoplasmosis, MRSA SSTI, Nocardia, Stenotrophomonas). Sequential blockade of folate synthesis. Sulfa allergy, hyperkalemia. Fluoroquinolones: Cipro/levo (GN, Pseudomonas), moxifloxacin (anaerobes). DNA gyrase + topo IV inhibition. Tendinopathy, QTc, C. diff, neuropathy. Rifampin: RNA polymerase inhibitor. TB (RIPE), Staph biofilm, meningococcal ppx. CYP3A4 inducer. Metronidazole: Anaerobes (B. fragilis), protozoa (Giardia, E. histolytica, Trichomonas). Disulfiram-like with alcohol.
Anti-herpes: Acyclovir (HSV, VZV). Valacyclovir, famciclovir. Foscarnet (TK-independent). Anti-CMV: Ganciclovir, valganciclovir. Anti-influenza: Oseltamivir (NA inhibitor), baloxavir (cap-dependent endonuclease). Anti-COVID: Remdesivir, nirmatrelvir/ritonavir. Anti-HBV: Entecavir, tenofovir. Anti-HCV: DAA (sofosbuvir, velpatasvir). Anti-HIV: INSTI + NRTIs. Antifungals: Polyenes (Amphotericin B - ergosterol, nephrotoxicity). Azoles (fluconazole, voriconazole, isavuconazole - inhibit 14α-demethylase). Echinocandins (beta-glucan synthase - Candida first-line). Flucytosine (combination). Terbinafine (dermatophytes). Antiparasitics: ACT (malaria), metronidazole (protozoa), albendazole (nematodes), ivermectin (Strongyloides, filaria, scabies), praziquantel (cestodes, trematodes).
Beta-lactamases: Penicillinase (S. aureus), ESBL (E. coli, Klebsiella - hydrolyze 3rd gen cephalosporins), AmpC (Enterobacter - inducible), Carbapenemases (KPC, NDM, OXA-48). MRSA: mecA -> PBP2a (low affinity). VRE: VanA/VanB -> D-Ala-D-Lac. MDR-TB: R + I resistance. XDR-TB: + FQ + injectable. Efflux, target modification, porin loss. Antibiotic stewardship: right drug, right dose, right duration. De-escalate based on cultures. Shorten: CAP 5d, HAP 7d, UTI 3-5d. PCT guidance.
Stains Culture Media Biochemical Tests Serology Molecular AST
Gram Stain: CV -> iodine -> decolorizer -> safranin. GP = purple, GN = pink/red. Ziehl-Neelsen (AFB): Carbol fuchsin + heat -> acid-alcohol -> methylene blue. AFB = red. Kinyoun: Cold AFB. Modified AFB: Nocardia, Cryptosporidium. India Ink: Cryptococcus (capsule, negative stain). Silver (GMS): Fungi black, PCP cysts. Giemsa: Malaria (rings), Babesia (Maltese cross), Toxoplasma (tachyzoites), Chlamydia (inclusions). KOH: Fungal hyphae. Calcofluor White: Fluorescent fungal stain. Trichrome: Intestinal protozoa. Tzanck: Multinucleated giant cells (HSV/VZV). Darkfield: Spirochetes (Treponema).
Blood Agar: Hemolysis pattern (alpha/beta/gamma). Chocolate Agar: X+V factors (Neisseria, Haemophilus). MacConkey: Selective (GN) + differential (lactose = pink). EMB: Metallic sheen (E. coli). MSA: Selective (7.5% NaCl) + differential (mannitol = yellow for S. aureus). Thayer-Martin: VCNT (Neisseria selective). Lowenstein-Jensen: TB (egg-based, 2-8wk). MGIT: Mycobacteria liquid (1-3wk). Sabouraud Dextrose: Fungi (low pH). BCYE: Legionella (iron + cysteine). TCBS: Vibrio (yellow). CHROMagar: Candida species ID by color.
Catalase (+) -> Staph. Coagulase: S. aureus (+) vs others (-). Catalase (-) -> Strep. Hemolysis: α (pneumo: optochin S, bile S vs viridans: optochin R, bile R), β (GAS: bacitracin S, PYR + vs GBS: CAMP +, hippurate +), γ (Enterococcus). Lactose (+) MacConkey -> E. coli (indole +) vs Klebsiella/Enterobacter (indole -). Lactose (-) MacConkey -> H2S (+) Salmonella vs H2S (-) -> urease (+) Proteus vs urease (-) Shigella. Oxidase (+): Neisseria, Pseudomonas, Campylobacter, Legionella, Vibrio, Pasteurella. Urease (+): H. pylori, Proteus, Klebsiella, Yersinia. PYR (+): S. pyogenes, Enterococcus. CAMP (+): GBS. DNase (+): M. catarrhalis, S. aureus. Bile solubility (+): S. pneumoniae. MALDI-TOF: Mass spec ID in minutes.
Serology: ELISA (antigen or antibody), Western blot (confirmatory HIV, Lyme). NAAT: PCR, GeneXpert (TB + RIF resistance, MRSA, C. diff, HIV VL, COVID, CT/NG). RT-PCR for RNA viruses. Quantitative PCR: HIV, CMV, HBV, HCV viral loads. Genotyping: HIV resistance, HCV genotype, 16S rRNA, WGS. AST: Kirby-Bauer disc diffusion, broth microdilution (MIC), Etest. Automated: Vitek, MicroScan. Breakpoints per CLSI/EUCAST. D-test: Inducible clindamycin resistance (D-zone). ESBL confirmation (clavulanate synergy).
Memory Aids Organism Tables Key Associations Quick Reference
Staph (catalase+), Strep (catalase-), Enterococcus
Bacillus, Clostridium (spores), Listeria (tumbling), Nocardia (partial AFB), Corynebacterium, Actinomyces (sulfur granules)
Neisseria (meningitidis and gonorrhoeae), Moraxella catarrhalis. All oxidase (+).
Lactose (+): E. coli, Klebsiella, Enterobacter. Lactose (-): Salmonella, Shigella, Proteus, Yersinia, Pseudomonas (oxidase +).
H. influenzae (X+V), Legionella (CYE), Bordetella, Brucella, Pasteurella, Francisella.
TB, leprae, MAC, marinum, kansasii. Partial: Nocardia, Cryptosporidium, Cyclospora.
Papilloma, Adeno, Polyoma (BK/JC), Parvo (B19), Herpes (8 types), Hepadna (HBV), Pox (smallpox, molluscum, Mpox).
Picorna, Corona, Toga, Calici, Astro, Flavi, Retro.
Paramyxo, Rhabdo, Arena, Orthomyxo, Filo.
DNA: all nucleus except Pox (cytoplasm). RNA (-): all cytoplasm except Orthomyxo (nucleus). RNA (+): all cytoplasm. Retro: nucleus (integration).
Pseudomonas, S. pneumoniae, H. influenzae, Neisseria, E. coli, Salmonella, Klebsiella, Strep (GBS). Capsule = antiphagocytic. Vaccines target capsule (PCV, MenACWY, Hib). Splenectomy -> OPSI risk.
S. pneumo, N. meningitidis, Listeria ( > 50/immunocompromised)
GBS, E. coli, Listeria
S. pneumo, H. flu, M. pneumo, C. pneumo, Legionella
Acute: S. aureus. Subacute: viridans strep. Prosthetic: coag-neg Staph. HACEK.
S. aureus (most). Vertebral: TB. Sickle cell: Salmonella. Diabetic foot: polymicrobial.
E. coli (80%), S. saprophyticus (young women), Proteus, Klebsiella
1-6h: S. aureus, B. cereus (emetic). 8-16h: C. perfringens. 12-72h: Salmonella, Campylobacter, Shigella, ETEC, Norovirus. > 3d: Giardia.
Cefepime or pip-tazo or meropenem + vancomycin
India Ink (capsule)
Silver stain, BCYE agar
GMS silver stain, immunofluorescence
Ziehl-Neelsen (AFB), auramine-rhodamine
Giemsa (inclusions), NAAT
Giemsa (thick/thin), RDT
KOH, calcofluor white, GMS, PAS
Darkfield, Warthin-Starry silver
Modified AFB, Gram (beaded GPB)
Vanco + Ceftriaxone + Acyclovir +/- Ampicillin (Listeria). Dexa before abx.
Outpt: amoxicillin or doxy. Inpt: beta-lactam + macrolide. ICU: + FQ.
Nitrofurantoin or TMP-SMX (uncomplicated). Ceftriaxone (pyelo).
Cephalexin, clindamycin, TMP-SMX (MRSA concern).
Cefepime/pip-tazo + vancomycin +/- aminoglycoside.
Vancomycin PO (mild-sev). Fidaxomicin (recurrent). FMT (multiple recur).
Echinocandin. Step-down fluconazole if sensitive.
L-AmB + flucytosine induction, fluconazole consolidation.
Voriconazole. Salvage: L-AmB, isavuconazole.
L-AmB + surgery + control DKA.
TMP-SMX + steroids if PaO2 < 70.
Mild: itraconazole. Severe: L-AmB then azole.
Coagulase (+) = S. aureus. (-) = S. epi/S. saprophyticus (novobiocin R).
α: pneumo (optochin S, bile S) vs viridans (R). β: GAS (bacitracin S, PYR +) vs GBS (CAMP +). γ: Enterococcus (PYR +).
Indole (+) E. coli. Indole (-) Klebsiella, Enterobacter.
H2S (+) Salmonella. H2S (-) Urease (+) Proteus. Urease (-) Shigella, Pseudomonas.
First-Line and Alternative Regimens for Key Infections
| Infection | First-Line | Alternative | Duration |
|---|---|---|---|
| CAP (outpatient) | Amoxicillin or Doxycycline | Macrolide, FQ | 5d |
| CAP (inpatient) | Beta-lactam + Macrolide | FQ monotherapy | 5-7d |
| HAP/VAP | Antipseudomonal BL + anti-MRSA | Carbapenem + vanco/linezolid | 7d |
| UTI (uncomplicated) | Nitrofurantoin or TMP-SMX | Fosfomycin | 3-5d |
| Pyelonephritis | Ceftriaxone | FQ, carbapenem if ESBL | 7-14d |
| Cellulitis (mild) | Cephalexin | Clindamycin, TMP-SMX | 5-7d |
| MRSA SSTI | TMP-SMX or Doxycycline | Clindamycin, linezolid | 5-10d |
| Bacterial Meningitis | Vanco + Ceftriaxone + Dexa | Meropenem, moxifloxacin | 10-21d |
| Septic Arthritis | Vancomycin + Ceftriaxone | Daptomycin, FQ | 3-4wk |
| Osteomyelitis (acute) | Nafcillin/Cefazolin (MSSA), Vanco (MRSA) | Daptomycin, linezolid | 4-6wk |
| C. diff (mild-mod) | Vancomycin PO 125mg QID | Fidaxomicin | 10d |
| C. diff (severe/fulm) | Vanco PO + IV Metronidazole | Tigecycline, FMT | 14d |
| Diverticulitis (mild) | Amox-clav or TMP-SMX + Metro | Moxifloxacin | 5-7d |
| Pelvic Inflammatory Dz | Ceftriaxone + Doxy + Metro | FQ + Metro | 14d |
| Gonorrhea | Ceftriaxone 500mg IM | Gentamicin + azithromycin | Single dose |
| Syphilis (early) | Benzathine PCN G 2.4M IM x1 | Doxycycline 14d | Single dose |
| Lyme (early) | Doxycycline 100mg BID | Amoxicillin, cefuroxime | 10-14d |
| TB (active) | RIPE (Rifampin, INH, PZA, EMB) | Per resistance pattern | 6mo (2 + 4) |
| TB (latent) | 4R (rifampin 4mo) | 3HP, 9H | 4mo |
| Infection | First-Line | Alternative | Duration |
|---|---|---|---|
| Candidemia | Echinocandin (micafungin) | L-AmB, fluconazole (if sensitive) | 14d after clearance |
| Cryptococcal Meningitis | L-AmB + Flucytosine | Fluconazole high-dose | 2wk + 8wk |
| Invasive Aspergillosis | Voriconazole | L-AmB, isavuconazole | >= 12wk |
| Mucormycosis | L-AmB + Surgery | Posaconazole, isavuconazole | >= 12wk |
| PCP | TMP-SMX + Prednisone (if PaO2 < 70) | Pentamidine, atovaquone | 14-21d |
| Oropharyngeal Candidiasis | Fluconazole 200mg x1 + 100 x7d | Nystatin, itraconazole | 7-14d |
| HIV (treatment-naive) | DTG/TAF/FTC (Biktarvy) | RAL + TDF/FTC, DRV/c + TAF/FTC | Lifelong |
| Influenza | Oseltamivir (start < 48h) | Baloxavir, zanamivir | 5d |
| COVID-19 (high-risk) | Nirmatrelvir/ritonavir (Paxlovid) | Remdesivir 3d IV | 5d |
| HSV Encephalitis | Acyclovir 10mg/kg IV q8h | Foscarnet (if acyclovir-R) | 14-21d |
| HSV Genital (1st) | Valacyclovir 1g BID | Famciclovir | 7-10d |
| VZV (Shingles) | Valacyclovir 1g TID | Acyclovir, famciclovir | 7d |
| CMV Retinitis (HIV) | Valganciclovir 900mg BID | Ganciclovir IV, foscarnet | 14-21d |
| HBV (chronic) | Entecavir or TAF | PEG-IFN (selected) | Long-term |
| HCV (all genotypes) | Sofosbuvir/velpatasvir 12wk | Glecaprevir/pibrentasvir 8wk | 8-12wk |
| Infection | First-Line | Alternative | Duration |
|---|---|---|---|
| Malaria (uncomplicated falciparum) | ACT (artemether-lumefantrine) | Atovaquone-proguanil, quinine + doxy | 3d |
| Malaria (severe) | IV Artesunate | IV quinine + doxycycline | >= 24h |
| P. vivax/ovale (radical) | Chloroquine + Primaquine (G6PD!) | ACT + primaquine | 14d |
| Giardiasis | Tinidazole 2g single dose | Metronidazole 7d | 1-7d |
| Amebic Dysentery/Abscess | Tinidazole + Paromomycin | Metronidazole + diloxanide | 10d |
| Toxoplasmosis (HIV) | Pyrimethamine + Sulfadiazine + Leucovorin | TMP-SMX, atovaquone | >= 6wk |
| Trichomoniasis | Tinidazole 2g single dose | Metronidazole 500mg BID 7d | 1-7d |
| Chagas Disease | Benznidazole | Nifurtimox | 60d |
| Leishmaniasis (visceral) | L-AmB | Miltefosine | Variable |
| Ascariasis/Enterobiasis | Albendazole single dose | Mebendazole | 1-3d |
| Strongyloidiasis | Ivermectin 200 mcg/kg PO | Albendazole | 1-2d |
| Neurocysticercosis | Albendazole + Praziquantel + Steroids | Surgery (hydrocephalus) | 14d |
| Schistosomiasis | Praziquantel 40mg/kg | Oxamniquine (S. mansoni) | 1 day |
| Scabies | Permethrin 5% cream x2 | Ivermectin 200 mcg/kg PO x2 | 1-2wk apart |
TMP-SMX DS daily or 3x/wk
TMP-SMX DS daily
Azithromycin 1200mg weekly
Cefazolin <= 60min before incision
Rifampin 600mg BID 2d or CTX 250mg IM
Amoxicillin 2g PO 30-60min pre (high-risk only)
PCN G 5M then 2.5M q4h
HRIG + vaccine days 0,3,7,14
RAL + TDF/FTC x28d (within 72h)
Atovaquone-proguanil daily or doxycycline
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