Bacteria Gram Stain & Virulence Factors Diseases Diagnostic High-Yield Notes

Shape Features
Staphylococcus Gram+ cocci in Protein A, TSST-1 TSS, pneumonia, abscess, Catalase+, MRSA = altered
aureus clusters osteomyelitis, food coagulase+, beta- PBP
poisoning hemolytic
Streptococcus Gram+ cocci in M protein, Pharyngitis, scarlet fever, ASO titer+, Can cause PSGN
pyogenes chains Streptolysin O rheumatic fever, bacitracin- after impetigo or
glomerulonephritis sensitive pharyngitis
Streptococcus Gram+ lancet Capsule, IgA Meningitis, Otitis, Optochin- Rust-colored sputum
pneumoniae diplococci protease Pneumonia, Sinusitis sensitive, bile-
(MOPS) soluble
Neisseria Gram− Capsule, LOS Meningitis, sepsis, adrenal Grows on Vaccine except type
meningitidis diplococci hemorrhage Thayer-Martin B
Neisseria Gram− Pili (antigenic Urethritis, PID, Thayer-Martin No capsule (unlike
gonorrhoeae diplococci variation) conjunctivitis, arthritis agar meningitidis)
Clostridium tetani Gram+ rod, Tetanospasmin Spastic paralysis, lockjaw Spores in soil Blocks
anaerobic GABA/glycine
release
Clostridium Gram+ rod, Botulinum toxin Flaccid paralysis, Preformed toxin Babies: spores in
botulinum anaerobic descending weakness in canned foods honey
Clostridium Gram+ rod, Toxin A Pseudomembranous colitis Detect toxin in Linked to
difficile anaerobic (enterotoxin), B stool clindamycin use
(cytotoxin)
Corynebacterium Gram+ club- Diphtheria toxin Pseudomembranous Elek test for Vaccine = DTaP
diphtheriae shaped rod (inhibits EF-2) pharyngitis toxin
Listeria Gram+ rod Actin rockets, Neonatal meningitis, Cold growth, Dairy and deli meats
monocytogenes intracellular septicemia tumbling motility
E. coli (EHEC) Gram− rod Shiga-like toxin Bloody diarrhea, HUS Does not ferment Associated with
sorbitol undercooked beef
Salmonella typhi Gram− rod Capsule (Vi Typhoid fever, constipation H2S+, motile Chronic carrier in
antigen) gallbladder
Shigella Gram− rod Shiga toxin Bloody diarrhea, tenesmus H2S−, actin Very low infectious
motility dose
Mycobacterium Acid-fast Cord factor Primary + reactivation TB Caseating PPD/IGRA
tuberculosis bacillus granulomas screening
Treponema Spirochete Immune evasion Syphilis (chancre → rash Dark-field VDRL/RPR
pallidum → CNS) microscopy (screen), FTA-ABS
(confirm)
Borrelia Spirochete Antigenic Lyme disease ELISA → Ixodes tick vector
burgdorferi variation Western blot
Chlamydia Intracellular, Elementary & STIs, neonatal Giemsa stain No peptidoglycan
trachomatis no Gram stain reticulate bodies conjunctivitis, LGV (beta-lactam
resistant)
Rickettsia rickettsii Intracellular, Obligate Rocky Mountain Spotted Rash Needs NAD+ and
Giemsa intracellular Fever wrists/ankles → CoA
trunk
High-Yield Fungi for USMLE Step 1: Cheat Sheet

Fungus Morphology / Region / Risk Key Virulence / Diseases High-Yield Clues

Stain Factor ID Feature
Histoplasma Dimorphic; yeast Ohio/Mississippi Intracellular Pulmonary TB-like, Cave, spelunking, tiny
capsulatum inside River Valley yeast, bird/bat hepatosplenomegaly yeast in macrophages
macrophages droppings
Blastomyces Broad-based Great Lakes, East Broad budding Lung, bone, skin Larger yeast than RBC,
dermatitidis budding yeast U.S. yeast infections verrucous skin lesions
Coccidioides Spherules with Southwest U.S. Spherules (not Valley fever, Dust storms,
immitis endospores (deserts) yeast) meningitis, erythema earthquakes, travel to
nodosum Arizona
Paracoccidioides Captain's wheel Latin America Multiple budding Lung, mucocutaneous Brazil, male > female
brasiliensis yeast yeast ulcers due to estrogen
inhibition
Candida albicans Pseudohyphae, Normal flora, Germ tubes at Thrush, esophagitis, White plaques in HIV
germ tubes HIV, IVDU 37°C vaginitis, endocarditis CD4 < 200
Aspergillus Septate hyphae, Neutropenia, Acute angle Fungus ball, invasive TB cavities, asthma, IgE
fumigatus acute angle cavities branching aspergillosis, ABPA ↑
Cryptococcus Encapsulated Pigeon droppings,Thick capsule, Meningitis (HIV), Soap bubble lesions in
neoformans yeast HIV India ink, pulmonary brain, CD4 < 100
mucicarmine
Mucor/Rhizopus Non-septate DKA, neutropenia Angioinvasive, Rhinocerebral DKA, black necrotic
hyphae, right black eschar mucormycosis facial lesion
angle
Dermatophytes Septate hyphae Wrestlers, Keratin digestion Tinea corporis, pedis, Annular scaling with
(T/M/E) (KOH) showers capitis central clearing
Malassezia furfur "Spaghetti & Hot/humid, oily Lipid-dependent Tinea versicolor Hypo/hyperpigmented
meatballs" skin patches
DNA viruses

Virus Type Key Diseases High-Yield Tested Topics

Enveloped Oral/genital herpes, encephalitis, Latency in ganglia, Cowdry bodies,
HSV-1/HSV-2
dsDNA neonatal HSV Tzanck smear, temporal lobe encephalitis
Varicella-Zoster Enveloped Dermatomal pattern, latency in DRG,
Chickenpox, shingles
(VZV) dsDNA postherpetic neuralgia, vaccine
Epstein-Barr Virus Enveloped Mono, Hodgkin lymphoma, Burkitt Monospot test, CD21 receptor, Downey
(EBV) dsDNA lymphoma, nasopharyngeal carcinoma cells, avoid contact sports
Cytomegalovirus Enveloped Retinitis, esophagitis in HIV; congenital Owl eye inclusions, TORCH, latent in
(CMV) dsDNA defects monocytes
Enveloped Dane particles, reverse transcriptase,
Hepatitis B (HBV) Hepatitis, hepatocellular carcinoma
partially dsDNA window period, HBsAg/anti-HBc profile
Human 16/18 → E6/E7 inhibit p53/Rb,
Naked dsDNA Warts, cervical cancer
Papillomavirus (HPV) koilocytes, Pap smear
Fifth disease, aplastic crisis, hydrops Slapped cheek rash, infects erythroid
Parvovirus B19 Naked ssDNA
fetalis precursors, TORCH

RNA Viruses: +ssRNA

Virus Type Key Diseases Step 1 Focus

Poliovirus Naked +ssRNA Flaccid paralysis Salk/Sabin vaccine, anterior horn destruction
A: Hand-foot-mouth; B:
Coxsackie A/B Naked +ssRNA Viral meningitis, dilated cardiomyopathy
myocarditis
Hepatitis A
Naked +ssRNA Acute hepatitis No chronicity, travel-related
(HAV)
Norovirus Naked +ssRNA Gastroenteritis outbreaks Cruise ships, daycares
Enveloped Congenital triad: cataracts, deafness, PDA;
Rubella virus German measles; congenital rubella
+ssRNA maculopapular rash
Enveloped Common cold, SARS/MERS,
Coronavirus Spike protein, ACE2 binding, ARDS
+ssRNA COVID-19
 Retrovirus

Virus Type Key Step 1 Focus

Diseases
HIV Enveloped +ssRNA (2 AIDS gp120/CD4 binding, reverse transcriptase, CD4 count staging, opportunistic
copies) infections

-ssRNA viruses

Virus Type Key Diseases High-Yield Clues

Influenza virus Enveloped -ssRNA, Flu, pneumonia, Reye Antigenic shift/drift, M2 protein, live vs killed
segmented syndrome vaccine
Rabies virus Enveloped -ssRNA Encephalitis, hydrophobia Bullet-shaped virus, Negri bodies, post-exposure
prophylaxis
Measles Enveloped -ssRNA Cough, coryza, conjunctivitis, Koplik spots, SSPE, vitamin A, F protein syncytia
(Rubeola) rash
Mumps virus Enveloped -ssRNA Parotitis, orchitis, meningitis Unvaccinated teens, infertility
RSV Enveloped -ssRNA Bronchiolitis in infants Palivizumab targets F protein
Parainfluenza Enveloped -ssRNA Croup (barking cough) Steeple sign on X-ray

Favorite viral themes

Topic Viruses Frequently Involved Key Concepts

Congenital infections CMV, Rubella, HSV, HIV, Parvovirus B19 Microcephaly, deafness, cataracts, heart defects
(TORCH)
Latency HSV, VZV, EBV, CMV, HIV Where the virus hides, when it reactivates
Oncogenesis EBV, HPV, HBV, HCV, HTLV-1 Mechanism of transformation (e.g., E6/E7, integration
into genome)
Vaccines HAV, HBV, HPV, MMR, VZV, Influenza, Live vs killed, contraindications, immune response
Polio
Encephalitis HSV-1 (temporal), Rabies, Arboviruses, Diagnostic clues: CSF, MRI findings, inclusion
Measles (SSPE) bodies
Serology interpretation HBV, HIV, EBV Window period, seroconversion, antigen/antibody
profiles

PARASITES : Protozoa

Parasite Transmission Disease Step 1 High-Yield Focus

Entamoeba Cysts in water Amebic dysentery, liver abscess Flask-shaped ulcers on colon biopsy, anchovy
histolytica paste abscess, bloody diarrhea
Giardia lamblia Cysts in water Fatty diarrhea Trophozoites with smiling face, no invasion, foul-
(hikers) smelling stools
Cryptosporidium Cysts in water Diarrhea (severe in AIDS) Acid-fast oocysts in stool, watery diarrhea in HIV
Toxoplasma gondii Cat feces, raw meat Congenital toxoplasmosis, brain Ring-enhancing lesions, pregnant women & cats,
abscess in AIDS TORCH
Naegleria fowleri Freshwater via Primary amebic Rapid fatal meningoencephalitis, swimming in
cribriform plate meningoencephalitis lakes, CSF shows amoebas
Trypanosoma Tsetse fly African sleeping sickness Recurrent fever, lymphadenopathy,
brucei trypomastigotes in blood, suramin/melarsoprol
Trypanosoma cruzi Reduviid bug Chagas disease Megacolon, megaesophagus, Romana sign,
trypomastigotes in blood
Plasmodium spp. Anopheles mosquito Malaria P. falciparum: irregular fever, cerebral malaria; P.
vivax/ovale: hypnozoites, cyclic fevers
Babesia microti Ixodes tick (NE Babesiosis Maltese cross in RBCs, hemolytic anemia,
U.S.) coinfection with Lyme
Leishmania Sandfly Visceral leishmaniasis Spiking fevers, hepatosplenomegaly,
donovani macrophages with amastigotes
Trichomonas STD (motile Vaginitis Green discharge, pH > 4.5, motile trophozoites,
vaginalis trophozoites) no cyst form
Helminths
 Nematodes

Parasite Transmission Disease Step 1 Highlights

Enterobius Fecal-oral Perianal itching Scotch tape test, treat entire household
vermicularis
Ascaris Fecal-oral Intestinal obstruction Migrates through lungs, giant roundworm
lumbricoides
Strongyloides Larvae in soil penetrate Autoinfection, GI & pulm Rhabditiform larvae in stool, hyperinfection in
stercoralis skin symptoms immunosuppressed
Ancylostoma / Skin penetration Iron-deficiency anemia Hookworms, blood sucking, barefoot on soil
Necator
Trichinella spiralisUndercooked pork Myositis, periorbital edema Muscle biopsy, eosinophilia
Toxocara canis Fecal-oral (puppy Visceral/ocular larva Eosinophilia, retinal granuloma
feces) migrans
Onchocerca volvulus Blackfly bite River blindness Skin nodules, hyperpigmentation, blindness
Loa loa Deer fly Eyeworm, angioedema Migrates across eye, seen under conjunctiva
Wuchereria Mosquito Elephantiasis Blocks lymphatics, eosinophilia, nighttime
bancrofti microfilariae in blood

Cestodes

Parasite Transmission Disease Step 1 Highlights

Taenia solium Pork (larvae or eggs) Neurocysticercosis Seizures, brain calcifications, ingesting eggs causes cysts
Diphyllobothrium latum Fish B12 deficiency Megaloblastic anemia, longest tapeworm
Echinococcus granulosus Dog feces Hydatid liver cysts Anaphylaxis risk with rupture, eggshell calcifications
 Trematodes

Parasite Transmission Disease Step 1 Highlights

Schistosoma Snails (skin Hematuria, portal HTN S. haematobium → bladder cancer, eggs with
penetration) spines
Clonorchis Undercooked fish Biliary disease, Pigmented gallstones
sinensis cholangiocarcinoma

Favorite step 1 themes

Theme Example Parasites What’s Tested

Eosinophilia Strongyloides, Ascaris, Trichinella, Schistosoma Seen in tissue-invasive helminths
CNS infections Taenia solium, Toxoplasma, Naegleria Imaging, route of infection, prevention
Lifecycle awareness Schistosoma, Strongyloides, Plasmodium Distinguishing stages, infective form
Blood smears Malaria, Babesia, Trypanosomes Identify morphology & diseases
Diarrhea Giardia, Entamoeba, Cryptosporidium Type of diarrhea (fatty, bloody, watery), immune status
Zoonosis Echinococcus, Toxocara, T. cruzi Route of transmission (e.g., dog, bug)

High-Yield Antimicrobials for USMLE Step 1: Master Sheet

Drug Class Example Drugs Mechanism of Clinical Uses Key Side Effects Resistance
Action Mechanism
Penicillins Penicillin G, V, Inhibits Gram-positive infections, Allergic reaction, β-lactamase, PBP
amoxicillin, transpeptidation (cell syphilis hemolytic anemia mutation
oxacillin wall synthesis)
Cephalosporins Cefazolin, Same as penicillin Broad-spectrum, surgical Hypersensitivity, β-lactamase (less
ceftriaxone, (cell wall inhibitor) prophylaxis disulfiram rxn so), altered PBPs
cefepime (cefotetan)
Carbapenems Imipenem, Broadest β-lactam, Life-threatening resistant Seizures (esp. β-lactamase
meropenem cell wall inhibitor infections imipenem) production
Monobactams Aztreonam Only Gram-negative Gram-negative infections Usually safe β-lactamase
rods in penicillin-allergic
patients
Vancomycin Vancomycin Binds D-Ala-D-Ala MRSA, C. diff (oral) Nephrotoxicity, D-Ala-D-Lac
→ inhibits cell wall ototoxicity, Red mutation
Man Syndrome
Aminoglycosides Gentamicin, 30S inhibition → Severe Gram-negative Nephro/ototoxicity, Enzyme
amikacin misreading mRNA infections NM blockade inactivation
Tetracyclines Doxycycline, 30S inhibition → Atypicals, acne, Photosensitivity, Efflux pumps
minocycline block tRNA intracellular bugs teeth discoloration
Macrolides Azithromycin, 50S inhibition → Atypicals, pertussis, QT prolongation, Methylation of
erythromycin prevent translocation strep if allergic to cholestatic hepatitis binding site
penicillin
Clindamycin Clindamycin 50S inhibition Anaerobes above C. difficile colitis Mutation of 50S
diaphragm site
Linezolid Linezolid 50S inhibition, VRE, MRSA Thrombocytopenia, rRNA point
initiation complex serotonin syndrome mutation
block
Chloramphenicol Chloramphenicol 50S Meningitis in developing Aplastic anemia, Acetyltransferase
peptidyltransferase countries Gray baby inactivation
inhibition
Sulfonamides Sulfamethoxazole Inhibits UTIs, nocardia Hypersensitivity, Altered enzyme
(SMX) dihydropteroate kernicterus
synthase
Trimethoprim Trimethoprim Inhibits dihydrofolate Combined with SMX Megaloblastic Altered DHFR
(TMP) reductase (UTIs, PCP) anemia, leukopenia
Fluoroquinolones Ciprofloxacin, Inhibits DNA Gram-negatives, UTIs, Tendon rupture, Topoisomerase
levofloxacin gyrase/topoisomerase GI QT prolongation mutation
Metronidazole Metronidazole Generates free Anaerobes below Disulfiram Rare
radicals diaphragm, protozoa reaction, metallic
taste
Rifampin Rifampin Inhibits RNA TB, prophylaxis for Orange fluids, Point mutation in
polymerase contacts CYP450 inducer RNA pol
Isoniazid Isoniazid (INH) Inhibits mycolic acid TB Hepatotoxicity, KatG mutation
synthesis neuropathy (↓ B6)
Ethambutol Ethambutol Inhibits TB Optic neuropathy Enzyme
arabinosyltransferase (red-green) mutation
Pyrazinamide Pyrazinamide Acidifies intracellular TB (especially in Hepatotoxicity, Unknown
environment phagolysosomes) hyperuricemia
Amphotericin B Amphotericin B Binds ergosterol → Severe systemic fungal Nephrotoxicity, Altered
pores infections fever/chills ergosterol
Azoles Fluconazole, Inhibits ergosterol Mucocutaneous/systemic Liver dysfunction, Efflux or CYP
itraconazole synthesis (CYP450 fungi CYP interactions mutation
inhibition)
Echinocandins Caspofungin Inhibits β-glucan Candida, Aspergillus GI upset, flushing Rare
synthesis (cell wall)
Acyclovir Acyclovir Guanosine analog → HSV, VZV Crystalluria, renal ↓ thymidine
inhibits DNA pol toxicity kinase
Ganciclovir Ganciclovir Guanosine analog → CMV Myelosuppression UL97 kinase
inhibits DNA pol mutation
Oseltamivir Oseltamivir Inhibits Influenza A/B GI upset NA mutation
neuraminidase
HAART drugs NRTIs, NNRTIs, HIV treatment HIV Class-specific Mutation in RT
protease toxicities or protease
inhibitors,
integrase
inhibitors