Microbiology Hub

Pathogens, clinical presentations, and empiric antibiotic coverage.

Viridans group Streptococci

Gram-Positive

Cocci in chains, alpha-hemolytic, optochin-resistant

Common Presentations

  • Dental caries (S. mutans)
  • Subacute infective endocarditis
  • Brain abscesses

Empiric Treatment

  • Penicillin G
  • Ceftriaxone

Bacillus cereus

Gram-Positive

Spore-forming bacilli (rods), aerobic

Common Presentations

  • Food poisoning (reheated rice syndrome - rapid onset emetic toxin)
  • Eye infections (keratitis from trauma)

Empiric Treatment

  • Supportive care (for food poisoning)

Nocardia asteroides

Gram-Positive

Weakly acid-fast, branching filamentous rods, aerobic

Common Presentations

  • Pulmonary nocardiosis (cavitary lesions in immunocompromised)
  • Cutaneous nocardiosis
  • Brain abscesses

Empiric Treatment

  • Bactrim (TMP-SMX)

Actinomyces israelii

Gram-Positive

Not acid-fast, branching filamentous rods, anaerobic

Common Presentations

  • Actinomycosis (cervicofacial lumpy jaw, pelvic infections associated with IUDs)

Empiric Treatment

  • Penicillin G (high dose, long term)

Clostridium perfringens

Gram-Positive

Spore-forming bacilli (rods), obligate anaerobe

Common Presentations

  • Gas gangrene (myonecrosis)
  • Food poisoning (late onset watery diarrhea)

Empiric Treatment

  • Penicillin G PLUS Clindamycin (to shut off toxin production)
  • Surgical debridement (crucial for gas gangrene)

Clostridium tetani

Gram-Positive

Spore-forming bacilli (rods) with terminal spores (tennis racket appearance)

Common Presentations

  • Tetanus (spastic paralysis, trismus/lockjaw, risus sardonicus, opisthotonos)

Empiric Treatment

  • Tetanus Immune Globulin (TIG)
  • Metronidazole or Penicillin G

Clostridium botulinum

Gram-Positive

Spore-forming bacilli (rods), obligate anaerobe

Common Presentations

  • Botulism (flaccid paralysis, descending weakness, cranial nerve palsies)

Empiric Treatment

  • Botulinum Antitoxin (equine-derived for adults, human-derived IG for infants)

Proteus mirabilis

Gram-Negative

Bacilli (rods), highly motile (swarming on agar), urease-positive

Common Presentations

  • UTIs
  • Struvite kidney stones (staghorn calculi due to alkaline urine)

Empiric Treatment

  • Bactrim (TMP-SMX)
  • Ampicillin

Serratia marcescens

Gram-Negative

Bacilli (rods), slow lactose fermenter, produces red pigment

Common Presentations

  • Nosocomial pneumonia
  • UTIs (catheter-associated)

Empiric Treatment

  • Cefepime
  • Meropenem

Salmonella Typhi

Gram-Negative

Bacilli (rods), flagellated, produces H2S, Vi capsule

Common Presentations

  • Typhoid fever (rose spots, stepwise fever, relative bradycardia, GI hemorrhage)

Empiric Treatment

  • Ceftriaxone
  • Ciprofloxacin

Haemophilus ducreyi

Gram-Negative

Coccobacilli, 'school of fish' appearance

Common Presentations

  • Chancroid (painful genital ulcer with exudate, inguinal lymphadenopathy)

Empiric Treatment

  • Azithromycin (single dose)

Bordetella pertussis

Gram-Negative

Coccobacilli, aerobic

Common Presentations

  • Whooping cough (catarrhal, paroxysmal, and convalescent stages)

Empiric Treatment

  • Azithromycin
  • Clarithromycin (decreases infectivity but doesn't change clinical course if started late)

Legionella pneumophila

Gram-Negative

Pleomorphic rods, requires silver stain, grows on charcoal yeast extract

Common Presentations

  • Legionnaires' disease (severe atypical pneumonia, GI symptoms, hyponatremia)
  • Pontiac fever (mild flu-like)

Empiric Treatment

  • Levofloxacin
  • Azithromycin

Brucella species

Gram-Negative

Coccobacilli, aerobic, facultative intracellular

Common Presentations

  • Brucellosis (undulant fever, night sweats, from unpasteurized dairy or animal contact)

Empiric Treatment

  • Doxycycline PLUS Rifampin

Francisella tularensis

Gram-Negative

Coccobacilli, highly infectious (potential bioweapon)

Common Presentations

  • Tularemia (ulceroglandular disease from tick/deer fly bite or rabbit handling)

Empiric Treatment

  • Streptomycin
  • Gentamicin

Pasteurella multocida

Gram-Negative

Coccobacilli, bipolar staining

Common Presentations

  • Cellulitis/osteomyelitis (from cat or dog bites)

Empiric Treatment

  • Amoxicillin-Clavulanate (Augmentin)

Bartonella henselae

Gram-Negative

Bacilli (rods), visualized with Warthin-Starry silver stain

Common Presentations

  • Cat scratch disease (regional lymphadenopathy)
  • Bacillary angiomatosis (in HIV/AIDS)

Empiric Treatment

  • Azithromycin (for cat scratch disease)

Coccidioides immitis

Fungus

Dimorphic: Spherules filled with endospores in tissue. Mold in cold.

Common Presentations

  • Valley fever (pneumonia, erythema nodosum, arthralgias - Southwestern US)

Empiric Treatment

  • Fluconazole or Itraconazole (for mild/moderate)

Blastomyces dermatitidis

Fungus

Dimorphic: Broad-based budding yeast. Mold in cold.

Common Presentations

  • Blastomycosis (pneumonia, verrucous skin lesions, bone lesions - Eastern US / Great Lakes)

Empiric Treatment

  • Itraconazole

Paracoccidioides brasiliensis

Fungus

Dimorphic: 'Captain's wheel' budding yeast. Mold in cold.

Common Presentations

  • Paracoccidioidomycosis (pneumonia, mucosal ulcers in Latin America)

Empiric Treatment

  • Itraconazole

Sporothrix schenckii

Fungus

Dimorphic: Cigar-shaped budding yeast. Rosettes of conidia on hyphae.

Common Presentations

  • Sporotrichosis (Rose gardener's disease - ascending lymphangitis from thorn prick)

Empiric Treatment

  • Itraconazole

Mucor / Rhizopus species

Fungus

Non-septate hyphae branching at wide (90-degree) angles

Common Presentations

  • Mucormycosis (rhinocerebral disease, necrotic black eschar on palate/face in DKA or neutropenic patients)

Empiric Treatment

  • Surgical debridement (URGENT)
  • Liposomal Amphotericin B

Cryptosporidium parvum

Parasite

Protozoa, acid-fast oocysts in stool

Common Presentations

  • Severe, intractable watery diarrhea in HIV/AIDS
  • Mild, self-limiting diarrhea in immunocompetent

Empiric Treatment

  • Nitazoxanide (in immunocompetent)

Entamoeba histolytica

Parasite

Protozoa, trophozoites with engulfed RBCs, cysts with up to 4 nuclei

Common Presentations

  • Amebic dysentery (bloody diarrhea, flask-shaped ulcers)
  • Amebic liver abscess ('anchovy paste' exudate)

Empiric Treatment

  • Metronidazole (or Tinidazole) PLUS Paromomycin (to eradicate luminal cysts)

Leishmania donovani / species

Parasite

Protozoa, amastigotes inside macrophages. Transmitted by sandfly.

Common Presentations

  • Visceral leishmaniasis (Kala-azar: spiking fevers, massive hepatosplenomegaly, pancytopenia)
  • Cutaneous leishmaniasis

Empiric Treatment

  • Liposomal Amphotericin B (for visceral)

Trypanosoma brucei

Parasite

Protozoa, extracellular trypomastigotes in blood. Transmitted by tsetse fly.

Common Presentations

  • African Sleeping Sickness (enlarged lymph nodes, recurring fever, coma)

Empiric Treatment

  • Suramin (for bloodborne stage)
  • Melarsoprol (for CNS involvement)

Trypanosoma cruzi

Parasite

Protozoa, C-shaped trypomastigotes in blood. Transmitted by kissing bug (Reduviid bug).

Common Presentations

  • Chagas disease (dilated cardiomyopathy with apical atrophy, megacolon, megaesophagus, Romana sign)

Empiric Treatment

  • Benznidazole

Naegleria fowleri

Parasite

Amoeba, enters through cribriform plate from warm freshwater

Common Presentations

  • Primary amebic meningoencephalitis (PAM - rapidly fatal)

Empiric Treatment

  • Amphotericin B + Miltefosine + Fluconazole (though almost universally fatal)

Ascaris lumbricoides

Parasite

Giant roundworm (Nematode)

Common Presentations

  • Ascariasis (intestinal obstruction, biliary obstruction, Loeffler syndrome/eosinophilic pneumonitis)

Empiric Treatment

  • Albendazole
  • Mebendazole

Strongyloides stercoralis

Parasite

Nematode, rhabditiform larvae in stool (can autoinfect)

Common Presentations

  • Strongyloidiasis (GI symptoms, larva currens rash, hyperinfection syndrome in immunosuppressed)

Empiric Treatment

  • Ivermectin

Varicella-Zoster Virus (VZV)

Virus

Herpesvirus (HHV-3), enveloped, dsDNA

Common Presentations

  • Chickenpox (varicella - asynchronous vesicular rash)
  • Shingles (herpes zoster - dermatomal rash)

Empiric Treatment

  • Acyclovir or Valacyclovir
  • Supportive care (for mild chickenpox in children)

Human Herpesvirus 8 (HHV-8)

Virus

Herpesvirus, enveloped, dsDNA

Common Presentations

  • Kaposi sarcoma (violaceous plaques/nodules in HIV/AIDS)
  • Primary effusion lymphoma

Empiric Treatment

  • Antiretroviral Therapy (ART) for HIV (reverses immunosuppression)

JC Virus

Virus

Polyomavirus, non-enveloped, circular dsDNA

Common Presentations

  • Progressive Multifocal Leukoencephalopathy (PML) - demyelinating disease in severe immunosuppression (HIV or Natalizumab use)

Empiric Treatment

  • No specific antiviral. Reverse immunosuppression (ART for HIV)

Rabies Virus (Duplicate to fix schema if needed)

Virus

Rhabdovirus, enveloped, bullet-shaped, negative-sense ssRNA

Common Presentations

  • Rabies (encephalitis, hydrophobia, invariably fatal once symptomatic)

Empiric Treatment

  • Post-exposure prophylaxis (PEP): Rabies Immune Globulin (RIG) + Rabies vaccine series

Staphylococcus epidermidis

Gram-Positive

Cocci in clusters, coagulase-negative, novobiocin-sensitive

Common Presentations

  • Infections of prosthetic devices (valves, joints)
  • IV catheter-associated infections
  • Endocarditis (artificial valve)

Empiric Treatment

  • Vancomycin (due to high rate of methicillin resistance)

Staphylococcus saprophyticus

Gram-Positive

Cocci in clusters, coagulase-negative, novobiocin-resistant

Common Presentations

  • Urinary tract infections (UTIs) in young, sexually active females (2nd most common cause after E. coli)

Empiric Treatment

  • Bactrim (TMP-SMX)

Streptococcus bovis (S. gallolyticus)

Gram-Positive

Cocci in chains, gamma-hemolytic

Common Presentations

  • Bacteremia
  • Subacute endocarditis (Strongly associated with colon cancer)

Empiric Treatment

  • Penicillin G
  • Ceftriaxone

Acinetobacter baumannii

Gram-Negative

Coccobacilli, aerobic, strictly non-fermenting, oxidase-negative

Common Presentations

  • Ventilator-associated pneumonia
  • Wound infections (classically combat wounds/trauma)

Empiric Treatment

  • Carbapenems (Imipenem, Meropenem) - though resistance is common

Moraxella catarrhalis

Gram-Negative

Diplococci, aerobic, oxidase-positive

Common Presentations

  • Otitis media (children)
  • COPD exacerbations (adults)
  • Sinusitis

Empiric Treatment

  • Amoxicillin-Clavulanate (Augmentin)

Yersinia pestis

Gram-Negative

Coccobacilli, bipolar staining ('safety pin'). Transmitted by flea bites (rodent reservoir)

Common Presentations

  • Bubonic plague (buboes - swollen lymph nodes)
  • Pneumonic plague (highly contagious person-to-person)

Empiric Treatment

  • Streptomycin
  • Gentamicin

Yersinia enterocolitica

Gram-Negative

Bacilli, motile at 25°C but non-motile at 37°C. (Puppy feces, contaminated milk/pork)

Common Presentations

  • Pseudoappendicitis (mesenteric adenitis, RLQ pain)
  • Inflammatory diarrhea

Empiric Treatment

  • Supportive care (often self-limiting)

Stenotrophomonas maltophilia

Gram-Negative

Bacilli, aerobic, non-fermenting

Common Presentations

  • Nosocomial pneumonia (especially in ICU/ventilator patients)
  • Bacteremia in neutropenic patients

Empiric Treatment

  • Bactrim (TMP-SMX)

Coxiella burnetii

Atypical

Obligate intracellular, survives outside host in endospore-like state. (Aerosols from sheep/cattle amniotic fluid)

Common Presentations

  • Q Fever (pneumonia, headache, culture-negative endocarditis. NO RASH.)

Empiric Treatment

  • Doxycycline

Chlamydophila psittaci

Atypical

Obligate intracellular

Common Presentations

  • Psittacosis (Parrot fever - atypical pneumonia, headache, transmitted by birds)

Empiric Treatment

  • Doxycycline

Ehrlichia chaffeensis

Atypical

Obligate intracellular, forms morulae (mulberry-like inclusions) in MONOCYTES. (Lone Star tick)

Common Presentations

  • Human monocytic ehrlichiosis (fever, headache, myalgias, thrombocytopenia, leukopenia)

Empiric Treatment

  • Doxycycline

Anaplasma phagocytophilum

Atypical

Obligate intracellular, forms morulae in GRANULOCYTES. (Ixodes tick)

Common Presentations

  • Human granulocytic anaplasmosis (fever, myalgias, cytopenias)

Empiric Treatment

  • Doxycycline

Hookworms (Necator americanus, Ancylostoma duodenale)

Parasite

Nematodes (Roundworms). Larvae penetrate skin of bare feet.

Common Presentations

  • Microcytic anemia (due to chronic blood loss in GI tract)
  • Cutaneous larva migrans (pruritic, serpiginous rash)

Empiric Treatment

  • Albendazole
  • Mebendazole

Schistosoma haematobium

Parasite

Trematode (Fluke). Eggs have a terminal spine. Snails are intermediate host.

Common Presentations

  • Squamous cell carcinoma of the bladder
  • Painless hematuria
  • Pulmonary hypertension

Empiric Treatment

  • Praziquantel

Schistosoma mansoni

Parasite

Trematode (Fluke). Eggs have a lateral spine.

Common Presentations

  • Hepatosplenomegaly
  • Portal hypertension
  • Intestinal schistosomiasis

Empiric Treatment

  • Praziquantel

Echinococcus granulosus

Parasite

Cestode (Tapeworm). Hydatid cysts. Transmitted by dog feces / sheep.

Common Presentations

  • Hydatid cyst disease (huge cysts in liver or lungs; rupture causes fatal anaphylaxis)

Empiric Treatment

  • Albendazole PLUS surgical resection

Trichinella spiralis

Parasite

Nematode. Larvae encyst in striated muscle. (Undercooked pork/bear meat)

Common Presentations

  • Trichinosis (fever, myalgias, periorbital edema, severe eosinophilia)

Empiric Treatment

  • Albendazole
  • Mebendazole

Hepatitis A Virus (HAV)

Virus

Picornavirus, non-enveloped, positive-sense ssRNA

Common Presentations

  • Acute viral hepatitis (fecal-oral transmission, jaundice, aversion to smoking)

Empiric Treatment

  • Supportive care (self-limiting, does NOT become chronic)

Hepatitis E Virus (HEV)

Virus

Hepevirus, non-enveloped, positive-sense ssRNA

Common Presentations

  • Acute viral hepatitis
  • Fulminant hepatitis in PREGNANT women (high mortality)

Empiric Treatment

  • Supportive care

Hepatitis D Virus (HDV)

Virus

Deltavirus, enveloped, circular negative-sense ssRNA. Defective virus (requires HBV surface antigen)

Common Presentations

  • Superinfection or coinfection with Hepatitis B (causes rapid, severe cirrhosis/liver failure)

Empiric Treatment

  • Pegylated Interferon alfa

Coxsackievirus A

Virus

Picornavirus (Enterovirus), non-enveloped, positive-sense ssRNA

Common Presentations

  • Hand, Foot, and Mouth Disease (vesicular rash on palms/soles, oral ulcers)
  • Herpangina

Empiric Treatment

  • Supportive care (hydration, pain control)

Coxsackievirus B

Virus

Picornavirus (Enterovirus), non-enveloped, positive-sense ssRNA

Common Presentations

  • Viral Myocarditis
  • Pericarditis
  • Pleurodynia (Bornholm disease / Devil's grip)

Empiric Treatment

  • Supportive care (heart failure management if myocarditis develops)

Adenovirus

Virus

Adenovirus, non-enveloped, linear dsDNA

Common Presentations

  • Pharyngoconjunctival fever (pink eye + sore throat)
  • Epidemic keratoconjunctivitis
  • Gastroenteritis
  • Hemorrhagic cystitis

Empiric Treatment

  • Supportive care

Rhinovirus

Virus

Picornavirus, non-enveloped, positive-sense ssRNA. Acid labile (destroyed in stomach, stays in upper respiratory tract)

Common Presentations

  • The Common Cold

Empiric Treatment

  • Supportive care (Zinc, Vitamin C, Decongestants)

Human T-lymphotropic virus (HTLV-1)

Virus

Retrovirus, enveloped, positive-sense ssRNA

Common Presentations

  • Adult T-cell leukemia/lymphoma (ATLL - lytic bone lesions, hypercalcemia)
  • Tropical spastic paraparesis (myelopathy)

Empiric Treatment

  • Zidovudine + Interferon alfa (for ATLL)

Vibrio vulnificus

Gram-Negative

Comma-shaped rod, motile, oxidase-positive. Found in warm coastal waters (oysters, marine trauma).

Common Presentations

  • Necrotizing fasciitis (from seawater exposure)
  • Rapidly fatal sepsis (especially in patients with liver disease/hemochromatosis)

Empiric Treatment

  • Doxycycline PLUS Ceftriaxone
  • Aggressive surgical debridement

Vibrio parahaemolyticus

Gram-Negative

Comma-shaped rod, motile, oxidase-positive.

Common Presentations

  • Gastroenteritis (watery diarrhea from eating raw or undercooked seafood/oysters)

Empiric Treatment

  • Supportive care (oral rehydration)

Aeromonas hydrophila

Gram-Negative

Bacilli, motile, oxidase-positive. Found in fresh or brackish water.

Common Presentations

  • Gastroenteritis
  • Wound infections (from leech therapy or freshwater trauma)
  • Necrotizing fasciitis

Empiric Treatment

  • Ciprofloxacin
  • Bactrim (TMP-SMX)

Burkholderia cepacia complex

Gram-Negative

Bacilli, aerobic, non-fermenting, catalase-positive.

Common Presentations

  • Pneumonia (highly dangerous in Cystic Fibrosis and Chronic Granulomatous Disease)

Empiric Treatment

  • Bactrim (TMP-SMX)

Burkholderia pseudomallei

Gram-Negative

Bacilli, bipolar staining ('safety pin'). Endemic to Southeast Asia / Northern Australia.

Common Presentations

  • Melioidosis (pneumonia, multiple abscesses in liver/spleen, septicemia)

Empiric Treatment

  • Ceftazidime
  • Meropenem (for intensive phase)

Leptospira interrogans

Gram-Negative

Spirochete with hook-shaped ends (question mark shape). Found in water contaminated with animal urine (rats/dogs, surfers in Hawaii).

Common Presentations

  • Leptospirosis (flu-like, conjunctival suffusion/red eyes without exudate)
  • Weil's disease (severe form: jaundice, renal failure, hemorrhage)

Empiric Treatment

  • Doxycycline
  • Penicillin G (if severe)

Borrelia recurrentis

Gram-Negative

Spirochete. Transmitted by human body louse.

Common Presentations

  • Relapsing fever (recurrent episodes of fever due to variable surface antigens)

Empiric Treatment

  • Doxycycline

Ureaplasma urealyticum

Atypical

Lacks a cell wall, requires cholesterol, urease-positive.

Common Presentations

  • Non-gonococcal urethritis
  • Struvite kidney stones

Empiric Treatment

  • Azithromycin
  • Doxycycline

Mycoplasma genitalium

Atypical

Lacks a cell wall. Smallest known genome of a free-living organism.

Common Presentations

  • Non-gonococcal urethritis (often persistent/recurrent)
  • Pelvic Inflammatory Disease (PID)

Empiric Treatment

  • Moxifloxacin (due to rising macrolide resistance)

Babesia microti

Parasite

Protozoa. 'Maltese cross' tetrads in RBCs. Transmitted by Ixodes tick (co-infection with Lyme is common).

Common Presentations

  • Babesiosis (fever, hemolytic anemia, severe in asplenic patients)

Empiric Treatment

  • Atovaquone PLUS Azithromycin

Plasmodium vivax / ovale

Parasite

Protozoa. Forms hypnozoites (dormant stage in liver) causing relapses.

Common Presentations

  • Malaria (tertian fever - every 48 hours)

Empiric Treatment

  • Chloroquine PLUS Primaquine (to kill liver hypnozoites and prevent relapse)

Wuchereria bancrofti

Parasite

Nematode (Roundworm). Transmitted by female mosquito.

Common Presentations

  • Lymphatic filariasis (Elephantiasis - severe lymphedema of lower limbs/genitals due to worms blocking lymph nodes)

Empiric Treatment

  • Diethylcarbamazine (DEC)

Loa loa

Parasite

Nematode. Transmitted by deer fly, horse fly, mango fly.

Common Presentations

  • Loiasis (transient angioedema/Calabar swellings, adult worm migrating across the conjunctiva of the eye)

Empiric Treatment

  • Diethylcarbamazine (DEC)

Onchocerca volvulus

Parasite

Nematode. Transmitted by female black fly.

Common Presentations

  • Onchocerciasis (River blindness, severe pruritus, 'leopard skin', subcutaneous nodules)

Empiric Treatment

  • Ivermectin ('Iver'mectin for 'river' blindness)

Toxocara canis

Parasite

Nematode. Transmitted by ingestion of eggs from dog/cat feces.

Common Presentations

  • Visceral larva migrans (hepatomegaly, eosinophilia)
  • Ocular larva migrans (blindness)

Empiric Treatment

  • Albendazole
  • Mebendazole

Malassezia furfur

Fungus

Lipophilic yeast. 'Spaghetti and meatballs' appearance on KOH prep.

Common Presentations

  • Tinea versicolor (hypo- or hyperpigmented skin patches, worse in summer/tanning)
  • Seborrheic dermatitis
  • Fungemia in neonates on TPN (lipid emulsions)

Empiric Treatment

  • Topical Selenium Sulfide
  • Topical Ketoconazole

Dermatophytes (Microsporum, Trichophyton, Epidermophyton)

Fungus

Branching septate hyphae visible on KOH prep with blue fungal stain.

Common Presentations

  • Tinea corporis (ringworm)
  • Tinea pedis (athlete's foot)
  • Tinea capitis (scalp)
  • Tinea unguium (onychomycosis)

Empiric Treatment

  • Topical Terbinafine or Clotrimazole (for skin)

Human Papillomavirus (HPV)

Virus

Papillomavirus, non-enveloped, circular dsDNA.

Common Presentations

  • Genital warts (Condylomata acuminata - strains 6, 11)
  • Cervical/Anal/Oropharyngeal squamous cell carcinoma (strains 16, 18)

Empiric Treatment

  • No cure. Ablation (cryotherapy, laser, trichloroacetic acid) for warts.

BK Polyomavirus

Virus

Polyomavirus, non-enveloped, circular dsDNA.

Common Presentations

  • BK virus nephropathy (transplant rejection/renal failure in kidney transplant patients)
  • Hemorrhagic cystitis

Empiric Treatment

  • Decrease immunosuppression

Molluscum contagiosum virus

Virus

Poxvirus, enveloped, linear dsDNA (largest DNA virus, replicates in cytoplasm).

Common Presentations

  • Molluscum contagiosum (flesh-colored, dome-shaped, umbilicated papules)

Empiric Treatment

  • Self-limiting in immunocompetent (resolves in months to years)

Parainfluenza virus

Virus

Paramyxovirus, enveloped, negative-sense ssRNA.

Common Presentations

  • Croup (Laryngotracheobronchitis - seal-like barking cough, inspiratory stridor, 'steeple sign' on X-ray)

Empiric Treatment

  • Supportive care (cool mist)

Staphylococcus aureus

Gram-Positive

Cocci in clusters, coagulase-positive

Common Presentations

  • Skin/soft tissue infections
  • Endocarditis
  • Osteomyelitis
  • Pneumonia
  • Toxic Shock Syndrome

Empiric Treatment

  • MSSA: Nafcillin, Oxacillin, Cefazolin
  • MRSA: Vancomycin, Daptomycin, Linezolid

Streptococcus pneumoniae

Gram-Positive

Lancet-shaped diplococci, alpha-hemolytic

Common Presentations

  • Community-acquired pneumonia
  • Meningitis
  • Otitis media
  • Sinusitis

Empiric Treatment

  • Ceftriaxone
  • High-dose Amoxicillin (for outpatient OM/sinusitis)

Pseudomonas aeruginosa

Gram-Negative

Bacilli (rods), non-lactose fermenting, oxidase-positive

Common Presentations

  • Ventilator-associated pneumonia
  • UTI (catheter-associated)
  • Burn wound infections
  • Osteomyelitis (sneaker puncture)

Empiric Treatment

  • Piperacillin-Tazobactam (Zosyn)
  • Cefepime
  • Meropenem

Escherichia coli

Gram-Negative

Bacilli (rods), lactose fermenting, indole-positive

Common Presentations

  • Urinary Tract Infections (most common cause)
  • Neonatal meningitis
  • Gastroenteritis (EHEC, ETEC)
  • Gram-negative sepsis

Empiric Treatment

  • Ceftriaxone
  • Bactrim (TMP-SMX)
  • Nitrofurantoin (for uncomplicated cystitis)

Streptococcus pyogenes (Group A Strep)

Gram-Positive

Cocci in chains, beta-hemolytic, bacitracin-sensitive

Common Presentations

  • Pharyngitis (Strep throat)
  • Cellulitis / Erysipelas
  • Necrotizing fasciitis
  • Rheumatic fever (post-infectious)

Empiric Treatment

  • Penicillin V or G
  • Amoxicillin

Streptococcus agalactiae (Group B Strep)

Gram-Positive

Cocci in chains, beta-hemolytic, bacitracin-resistant

Common Presentations

  • Neonatal sepsis / meningitis
  • Postpartum endometritis
  • UTIs in pregnancy

Empiric Treatment

  • Penicillin G
  • Ampicillin

Enterococcus faecalis / faecium

Gram-Positive

Cocci in pairs or short chains, gamma-hemolytic

Common Presentations

  • UTIs
  • Biliary tract infections
  • Endocarditis (especially post-GI/GU procedures)

Empiric Treatment

  • Ampicillin
  • Amoxicillin

Clostridioides difficile

Gram-Positive

Spore-forming bacilli (rods), obligate anaerobe

Common Presentations

  • Pseudomembranous colitis
  • Antibiotic-associated diarrhea

Empiric Treatment

  • Oral Vancomycin
  • Oral Fidaxomicin

Neisseria meningitidis

Gram-Negative

Diplococci (kidney bean shaped), encapsulated

Common Presentations

  • Meningococcemia (purpuric rash, Waterhouse-Friderichsen)
  • Bacterial meningitis

Empiric Treatment

  • Ceftriaxone
  • Penicillin G (if susceptible)

Neisseria gonorrhoeae

Gram-Negative

Diplococci, intracellular (within neutrophils)

Common Presentations

  • Gonorrhea (urethritis/cervicitis)
  • Pelvic Inflammatory Disease (PID)
  • Septic arthritis

Empiric Treatment

  • Ceftriaxone (IM)
  • PLUS Doxycycline (to cover concurrent Chlamydia)

Klebsiella pneumoniae

Gram-Negative

Bacilli (rods), thickly encapsulated, lactose fermenting

Common Presentations

  • Lobar pneumonia (currant jelly sputum, alcoholics)
  • UTIs
  • Nosocomial infections

Empiric Treatment

  • Ceftriaxone
  • Cefepime

Haemophilus influenzae

Gram-Negative

Coccobacilli, requires Factors V (NAD) and X (Hematin)

Common Presentations

  • Otitis media
  • Epiglottitis
  • Meningitis (mostly type B in unvaccinated)
  • Exacerbation of COPD

Empiric Treatment

  • Amoxicillin-Clavulanate (Augmentin)
  • Ceftriaxone (for invasive disease)

Mycobacterium tuberculosis

Gram-Positive

Acid-fast bacilli (mycolic acid cell wall)

Common Presentations

  • Pulmonary TB (cavitary lesions, apical)
  • Extrapulmonary TB (Pott disease, meningitis)

Empiric Treatment

  • RIPE Therapy (Rifampin, Isoniazid, Pyrazinamide, Ethambutol) for 2 months
  • Followed by RI for 4 months

Treponema pallidum

Gram-Negative

Spirochete (corkscrew shape), visualized on dark-field microscopy

Common Presentations

  • Syphilis (Primary: painless chancre, Secondary: maculopapular rash on palms/soles, Tertiary: neuro/cardiovascular)

Empiric Treatment

  • Penicillin G Benzathine (IM)

Influenza Virus

Virus

Orthomyxovirus, enveloped, negative-sense ssRNA, segmented

Common Presentations

  • Seasonal Flu (fever, myalgias, dry cough)
  • Viral pneumonia
  • Post-viral bacterial pneumonia (Staph aureus)

Empiric Treatment

  • Oseltamivir (Tamiflu) if started within 48 hours

Herpes Simplex Virus (HSV 1 & 2)

Virus

Herpesvirus, enveloped, linear dsDNA

Common Presentations

  • Oral herpes (Cold sores)
  • Genital herpes
  • Herpes encephalitis (temporal lobe)

Empiric Treatment

  • Acyclovir
  • Valacyclovir

Listeria monocytogenes

Gram-Positive

Bacilli (rods), intracellular, tumbling motility

Common Presentations

  • Neonatal meningitis
  • Meningitis in elderly/immunocompromised
  • Gastroenteritis (unpasteurized dairy/deli meats)

Empiric Treatment

  • Ampicillin

Corynebacterium diphtheriae

Gram-Positive

Club-shaped bacilli, metachromatic granules

Common Presentations

  • Diphtheria (pseudomembranous pharyngitis)
  • Myocarditis
  • Neuropathy

Empiric Treatment

  • Diphtheria Antitoxin
  • Erythromycin or Penicillin G

Bacillus anthracis

Gram-Positive

Large boxcar-like spore-forming bacilli

Common Presentations

  • Cutaneous Anthrax (black eschar)
  • Pulmonary Anthrax (Woolsorter's disease, hemorrhagic mediastinitis)
  • GI Anthrax

Empiric Treatment

  • Ciprofloxacin
  • Doxycycline

Helicobacter pylori

Gram-Negative

Curved rod, urease-positive

Common Presentations

  • Peptic Ulcer Disease (gastric/duodenal)
  • Gastric adenocarcinoma
  • MALT lymphoma

Empiric Treatment

  • Bismuth Quadruple Therapy (PPI + Bismuth + Metronidazole + Tetracycline) for 14 days

Campylobacter jejuni

Gram-Negative

Curved rod (comma/seagull shape), grows at 42°C

Common Presentations

  • Inflammatory diarrhea (bloody)
  • Guillain-Barré syndrome (post-infectious complication)
  • Reactive arthritis

Empiric Treatment

  • Usually self-limiting (hydration)

Salmonella enterica (non-typhoidal)

Gram-Negative

Bacilli, flagellated (motile), produces H2S

Common Presentations

  • Inflammatory diarrhea
  • Osteomyelitis (classically in Sickle Cell patients)

Empiric Treatment

  • Supportive care for uncomplicated gastroenteritis

Shigella dysenteriae

Gram-Negative

Bacilli, non-motile, Shiga toxin-producing

Common Presentations

  • Dysentery (bloody, mucoid diarrhea)
  • Hemolytic Uremic Syndrome (HUS) via Shiga toxin

Empiric Treatment

  • Azithromycin
  • Ciprofloxacin

Vibrio cholerae

Gram-Negative

Comma-shaped rod, motile, oxidase-positive

Common Presentations

  • Cholera (profuse "rice water" secretory diarrhea)
  • Severe dehydration

Empiric Treatment

  • Aggressive Oral/IV Rehydration (most critical)
  • Doxycycline (to shorten duration)

Chlamydia trachomatis

Gram-Negative

Obligate intracellular, lacks classic peptidoglycan

Common Presentations

  • Urethritis / Cervicitis
  • Pelvic Inflammatory Disease (PID)
  • Trachoma (blindness)
  • Neonatal conjunctivitis/pneumonia

Empiric Treatment

  • Doxycycline (7 days)

Mycoplasma pneumoniae

Gram-Positive

No cell wall (pleomorphic), cell membrane contains sterols

Common Presentations

  • Atypical "Walking" Pneumonia
  • Erythema multiforme / Stevens-Johnson syndrome
  • Cold agglutinin disease (IgM)

Empiric Treatment

  • Azithromycin
  • Doxycycline

Candida albicans

Fungus

Dimorphic: pseudohyphae and budding yeast at 20°C, germ tubes at 37°C

Common Presentations

  • Oral thrush
  • Vulvovaginitis
  • Diaper rash
  • Disseminated candidiasis (endocarditis in IVDU)

Empiric Treatment

  • Fluconazole (for mucosal/mild disease)

Aspergillus fumigatus

Fungus

Septate hyphae that branch at acute (45-degree) angles

Common Presentations

  • Allergic bronchopulmonary aspergillosis (ABPA)
  • Aspergilloma (fungus ball in preexisting cavity)
  • Invasive aspergillosis (immunocompromised)

Empiric Treatment

  • Voriconazole

Cryptococcus neoformans

Fungus

Heavily encapsulated yeast (not dimorphic), India ink positive

Common Presentations

  • Cryptococcal meningitis (especially in AIDS patients)
  • Cryptococcal pneumonia

Empiric Treatment

  • Amphotericin B + Flucytosine (induction phase)

Histoplasma capsulatum

Fungus

Dimorphic: mold in cold, yeast in heat. Macrophages filled with yeast

Common Presentations

  • Pneumonia (Ohio/Mississippi River Valleys, bird/bat guano)
  • Erythema nodosum
  • Disseminated disease in immunocompromised

Empiric Treatment

  • Itraconazole (mild to moderate)

Pneumocystis jirovecii

Fungus

Disc-shaped yeast on methenamine silver stain

Common Presentations

  • Pneumocystis Pneumonia (PCP) in HIV/AIDS (CD4 < 200)

Empiric Treatment

  • Bactrim (TMP-SMX) - both prophylaxis and treatment

Cytomegalovirus (CMV)

Virus

Herpesvirus (HHV-5), enveloped, dsDNA. 'Owl eye' inclusions

Common Presentations

  • CMV Retinitis (pizza pie retinopathy in AIDS)
  • CMV Mononucleosis
  • Pneumonitis in transplant patients

Empiric Treatment

  • Ganciclovir
  • Valganciclovir

Epstein-Barr Virus (EBV)

Virus

Herpesvirus (HHV-4), enveloped, dsDNA

Common Presentations

  • Infectious Mononucleosis
  • Burkitt lymphoma
  • Nasopharyngeal carcinoma
  • Oral hairy leukoplakia (in HIV)

Empiric Treatment

  • Supportive care (avoid contact sports due to splenomegaly)

Respiratory Syncytial Virus (RSV)

Virus

Paramyxovirus, enveloped, negative-sense ssRNA

Common Presentations

  • Bronchiolitis in infants
  • Pneumonia in infants and elderly

Empiric Treatment

  • Supportive care (O2, hydration)

Human Immunodeficiency Virus (HIV)

Virus

Retrovirus, enveloped, positive-sense ssRNA (diploid)

Common Presentations

  • Acute retroviral syndrome
  • AIDS (opportunistic infections when CD4 < 200)

Empiric Treatment

  • Antiretroviral Therapy (ART): 2 NRTIs + 1 Integrase Inhibitor (e.g. Biktarvy)

Rabies Virus

Virus

Rhabdovirus, enveloped, bullet-shaped, negative-sense ssRNA

Common Presentations

  • Rabies (encephalitis, hydrophobia, invariably fatal once symptomatic)

Empiric Treatment

  • Post-exposure prophylaxis (PEP): Rabies Immune Globulin (RIG) + Rabies vaccine series

SARS-CoV-2

Virus

Coronavirus, enveloped, positive-sense ssRNA, prominent spike proteins

Common Presentations

  • COVID-19 (pneumonia, ARDS, hypercoagulability)

Empiric Treatment

  • Nirmatrelvir/Ritonavir (Paxlovid) for mild-moderate in high-risk patients

Hepatitis B Virus (HBV)

Virus

Hepadnavirus, enveloped, partially dsDNA (uses reverse transcriptase)

Common Presentations

  • Acute Hepatitis
  • Chronic Hepatitis (cirrhosis, hepatocellular carcinoma)

Empiric Treatment

  • Tenofovir
  • Entecavir

Plasmodium falciparum

Parasite

Protozoa, banana-shaped gametocytes, ring form trophozoites in RBCs

Common Presentations

  • Malaria (severe: cerebral malaria, blackwater fever)

Empiric Treatment

  • Artemisinin-based combination therapy (ACT, e.g. Artemether-Lumefantrine)

Toxoplasma gondii

Parasite

Protozoa, obligate intracellular. Tachyzoites in tissues.

Common Presentations

  • Toxoplasmosis (ring-enhancing brain lesions in HIV/AIDS)
  • Congenital toxoplasmosis (chorioretinitis, hydrocephalus, intracranial calcifications)

Empiric Treatment

  • Sulfadiazine + Pyrimethamine (with Leucovorin rescue)

Trichomonas vaginalis

Parasite

Protozoa, flagellated, motile on wet mount. Cannot exist outside human host.

Common Presentations

  • Trichomoniasis (vaginitis with foul-smelling, green/yellow discharge, 'strawberry cervix')

Empiric Treatment

  • Metronidazole (treat patient AND partner)

Giardia lamblia

Parasite

Protozoa, flagellated trophozoite (looks like a face/shield) or multinucleated cyst

Common Presentations

  • Giardiasis (foul-smelling, fatty, non-bloody diarrhea after drinking stream/lake water)

Empiric Treatment

  • Metronidazole
  • Tinidazole

Enterobius vermicularis (Pinworm)

Parasite

Nematode (roundworm). Diagnosed via Scotch tape test on perianal region.

Common Presentations

  • Enterobiasis (severe perianal pruritus, especially at night in children)

Empiric Treatment

  • Mebendazole
  • Albendazole

Taenia solium

Parasite

Cestode (pork tapeworm). Scolex with hooks/suckers.

Common Presentations

  • Intestinal tapeworm (from eating undercooked pork)
  • Neurocysticercosis (from ingesting eggs from human feces - causes seizures)

Empiric Treatment

  • Praziquantel (for intestinal infection)

Borrelia burgdorferi

Atypical

Spirochete (corkscrew shape), large, visualized with Wright/Giemsa stain

Common Presentations

  • Lyme Disease (Erythema migrans rash, Bell's palsy, AV block, migratory arthritis)

Empiric Treatment

  • Doxycycline

Rickettsia rickettsii

Atypical

Obligate intracellular, weakly Gram-negative coccobacillus

Common Presentations

  • Rocky Mountain Spotted Fever (fever, headache, petechial rash starting on palms/soles spreading inward)

Empiric Treatment

  • Doxycycline (drug of choice for ALL ages, including children < 8, due to severity of disease)

Hepatitis C Virus (HCV)

Virus

Flavivirus, enveloped, positive-sense ssRNA. Lacks 3'-5' exonuclease (high mutation rate).

Common Presentations

  • Chronic Hepatitis
  • Cirrhosis
  • Hepatocellular Carcinoma
  • Cryoglobulinemia

Empiric Treatment

  • Direct-Acting Antivirals (DAAs) e.g., Sofosbuvir/Velpatasvir for 8-12 weeks (curative)

Measles Virus (Rubeola)

Virus

Paramyxovirus, enveloped, negative-sense ssRNA

Common Presentations

  • Measles (Cough, Coryza, Conjunctivitis, Koplik spots, descending maculopapular rash)
  • Subacute sclerosing panencephalitis (SSPE)

Empiric Treatment

  • Supportive care
  • Vitamin A (reduces morbidity/mortality in severe cases)

Mumps Virus

Virus

Paramyxovirus, enveloped, negative-sense ssRNA

Common Presentations

  • Mumps (Parotitis, Orchitis/epididymitis, aseptic meningitis)

Empiric Treatment

  • Supportive care

Rubella Virus (German Measles)

Virus

Togavirus, enveloped, positive-sense ssRNA

Common Presentations

  • Rubella (descending rash, postauricular lymphadenopathy)
  • Congenital Rubella Syndrome (deafness, cataracts, PDA)

Empiric Treatment

  • Supportive care

Parvovirus B19

Virus

Parvovirus, non-enveloped, single-stranded DNA (the only ssDNA virus)

Common Presentations

  • Erythema infectiosum (Fifth disease, 'slapped cheek' rash)
  • Aplastic crisis (in Sickle Cell)
  • Hydrops fetalis (in pregnancy)

Empiric Treatment

  • Supportive care

Norovirus

Virus

Calicivirus, non-enveloped, positive-sense ssRNA

Common Presentations

  • Viral gastroenteritis (cruises, schools, nursing homes - severe vomiting and watery diarrhea)

Empiric Treatment

  • Oral or IV Hydration

Rotavirus

Virus

Reovirus, non-enveloped, segmented double-stranded RNA (dsRNA)

Common Presentations

  • Severe infantile gastroenteritis (watery diarrhea leading to fatal dehydration)

Empiric Treatment

  • Aggressive oral rehydration therapy (ORT)

Dengue Virus

Virus

Flavivirus, enveloped, positive-sense ssRNA. Transmitted by Aedes mosquito.

Common Presentations

  • Breakbone fever (severe myalgias/bone pain)
  • Dengue Hemorrhagic Fever (thrombocytopenia, shock)

Empiric Treatment

  • Supportive care (IV fluids)

Zika Virus

Virus

Flavivirus, enveloped, positive-sense ssRNA. Transmitted by Aedes mosquito.

Common Presentations

  • Zika fever (maculopapular rash, conjunctivitis)
  • Congenital Zika Syndrome (microcephaly)

Empiric Treatment

  • Supportive care

Ebola Virus

Virus

Filovirus, enveloped, negative-sense ssRNA, long filamentous/shepherd's crook shape

Common Presentations

  • Ebola Virus Disease (severe hemorrhagic fever, multi-organ failure, high mortality rate)

Empiric Treatment

  • Aggressive supportive care (fluids, electrolytes, hemodynamics) in high-level isolation