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°C (soil), yeast at 37°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° 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° 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 & 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 & 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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