bacteriology

🦠 Bacteriology · Core Concepts

Comprehensive notes for USMLE Step 1 · high‑yield & clinically integrated

🔬 Gram‑positive rods

Listeria monocytogenes

🔬 Features
Small β‑hemolytic rod, tumbling motility, facultative intracellular, grows at 4°C.
🧬 Pathogenesis
Listeriolysin O (pore‑forming) enables escape from phagosome; actin‑based motility spreads cell‑to‑cell.
⚠️ Risks
Pregnant women, neonates, elderly, immunocompromised (renal transplant, lymphoma).

Clinical: Amniotic infection → granulomatosis infantiseptica (early); late‑onset meningitis (2–3 weeks). In adults: febrile gastroenteritis or meningitis.
Diagnosis: Culture on blood agar; cold enrichment; CSF shows lymphocytic predominance with some PMNs.
Treatment: Ampicillin ± gentamicin (for severe/immunocompromised).

📌 High‑yield: Third most common cause of neonatal meningitis. Avoid deli meats & soft cheese in pregnancy.

Corynebacterium diphtheriae

Morphology: Club‑shaped, pleomorphic gram‑positive rods, metachromatic granules (volutin).
Toxin: Encoded by β‑prophage; ADP‑ribosylates eEF‑2 → inhibits protein synthesis.
Disease: Gray pseudomembrane (pharynx/tonsils), “bull neck”, myocarditis, polyneuritis.
Diagnosis: Elek test (immunoprecipitation) or PCR for tox gene.
Treatment: Antitoxin + erythromycin/penicillin. Prevention: DTaP/Tdap vaccine.

🧪 Pearl: Toxin production requires lysogeny; non‑toxigenic strains can be converted by phage.

Actinomyces israelii

Anaerobic, branching gram‑positive rods, non‑acid‑fast.
Normal flora of gingiva & female genital tract; endogenous infection.
Actinomycosis: chronic, indolent, cross‑tissue planes; “sulfur granules” in pus.
Forms: Cervicofacial (“lumpy jaw”), thoracic, abdominal, pelvic (IUD), CNS abscess.
Treatment: Penicillin G + surgical drainage; metronidazole NOT effective.

Nocardia asteroides & N. brasiliensis

Aerobic, branching, partially acid‑fast (weak) gram‑positive rods.
Soil saprophyte; inhalation or traumatic implantation.
Pulmonary: cavitary pneumonia in immunocompromised; hematogenous spread → brain abscess.
Cutaneous: mycetoma or cellulitis (N. brasiliensis).
Treatment: High‑dose sulfonamides or TMP‑SMX.

📌 High‑yield: Differentiate from Actinomyces: Nocardia is aerobic, partially acid‑fast, and sulfonamide‑sensitive.

🧫 Gram‑negative cocci

Neisseria meningitidis

Features: Kidney‑bean diplococci, oxidase (+), grows on chocolate agar, ferments maltose.
Capsule: 5 serogroups (A, B, C, Y, W‑135); B is poorly immunogenic (sialic acid).
Virulence: LPS endotoxin, IgA protease, pili.
Disease: Meningitis (abrupt, petechial rash), meningococcemia, Waterhouse‑Friderichsen (adrenal hemorrhage).
Treatment: Ceftriaxone/cefotaxime; prophylaxis for contacts: rifampin/ciprofloxacin.

🧪 Pearl: Complement deficiency (C5–C9) predisposes to Neisseria bacteremia.

Neisseria gonorrhoeae

Oxidase (+), glucose fermenter, maltose (−).
Pathogenesis: Pili (antigenic variation), Opa proteins, IgA protease.
Disease: Urethritis/cervicitis, PID, neonatal ophthalmia, disseminated arthritis/dermatitis.
Diagnosis: Gram‑negative diplococci intracellular in PMNs; culture on Thayer‑Martin.
Treatment: Ceftriaxone + azithromycin (co‑treatment for Chlamydia).

📌 High‑yield: No vaccine; β‑lactamase plasmid‑mediated resistance common.

Moraxella catarrhalis

Gram‑negative diplococcus, oxidase (+), normal upper respiratory flora.
Disease: Otitis media in children, COPD exacerbations in elderly.
Treatment: Amoxicillin‑clavulanate, TMP‑SMX, or cephalosporins (most strains produce β‑lactamase).

🧪 Gram‑negative bacilli (non‑Enterobacteriaceae)

Pseudomonas aeruginosa

Features: Oxidase (+), aerobic, non‑fermenter, blue‑green pigment (pyocyanin), grape‑like odor.
Pathogenesis: Exotoxin A (ADP‑ribosylation of eEF‑2), biofilm, LPS.
Disease: Burn wound infection, pneumonia (CF, CGD), UTI (catheter), otitis externa, ecthyma gangrenosum.
Treatment: Anti‑pseudomonal β‑lactam (ceftazidime, piperacillin‑tazobactam) + aminoglycoside or fluoroquinolone.

📌 High‑yield: Intrinsic resistance due to porin loss & efflux pumps; always check susceptibilities.

Legionella pneumophila

Gram‑negative (stains poorly), requires iron & cysteine (BCYE agar), facultative intracellular.
Reservoir: Water (cooling towers, plumbing); aerosol transmission.
Disease: Legionnaires’ (atypical pneumonia, hyponatremia, diarrhea, confusion) and Pontiac fever (mild).
Diagnosis: Urinary antigen (serogroup 1), DFA, or PCR.
Treatment: Azithromycin or levofloxacin ± rifampin.

Bordetella pertussis

Small gram‑negative coccobacilli, strict aerobe.
Virulence: Pertussis toxin (ADP‑ribosylates G_i), filamentous hemagglutinin, adenylate cyclase toxin.
Stages: Catarrhal → paroxysmal (whoop) → convalescent.
Diagnosis: Culture (Regan‑Lowe), PCR, DFA.
Treatment: Macrolide (erythromycin/azithromycin), supportive care.

🧪 Pearl: Vaccine (DTaP) immunity wanes after 5–10 years; adults are a reservoir.

Haemophilus influenzae

Features: Encapsulated (type b = polyribitol phosphate), requires X (hemin) & V (NAD) factors.
Satellite phenomenon: grows around Staphylococcus aureus on blood agar.
Disease: Meningitis (children 3 mo–2 y), epiglottitis, pneumonia, otitis media (non‑typeable).
Treatment: Ceftriaxone/cefotaxime; prophylaxis with rifampin for close contacts.

📌 High‑yield: Hib conjugate vaccine (T‑cell‑dependent) has dramatically reduced disease.

🧬 Enterobacteriaceae

Key traits: Gram‑negative rods, facultative anaerobes, ferment glucose, oxidase (−), reduce nitrate.
Antigens: O (somatic), H (flagellar), K (capsular), Vi (Salmonella capsule).
Lactose fermentation: Colored on MacConkey (e.g., E. coli, Klebsiella) vs. non‑lactose (Salmonella, Shigella, Proteus).

Genus	Key features	Disease	Treatment
E. coli	Lactose (+), indole (+); ETEC, EHEC, UPEC	UTI, diarrhea, neonatal meningitis, sepsis	Cephalosporins, fluoroquinolones
Klebsiella	Lactose (+), mucoid, capsule	Pneumonia (currant‑jelly sputum), UTI	Carbapenems / extended‑spectrum cephalosporins
Salmonella	Non‑lactose, H₂S (+), motile	Enterocolitis, typhoid fever (S. Typhi)	Fluoroquinolones, ceftriaxone (typhoid)
Shigella	Non‑lactose, non‑motile, no H₂S	Inflammatory diarrhea, bacillary dysentery	Azithromycin, ciprofloxacin
Proteus	Swarming, urease (+)	UTI, stones	β‑lactams, TMP‑SMX
Yersinia	Non‑lactose, urease (+), psychrophilic	Enterocolitis, plague (Y. pestis)	Aminoglycosides, doxycycline

🧪 Pearl: Enterobacteriaceae are oxidase (−); this distinguishes them from Pseudomonas (oxidase +).

🐾 Zoonotic & atypical pathogens

Brucella

Small gram‑negative rods, facultative intracellular, zoonosis (cattle, goats, pigs).
Transmission: Unpasteurized dairy, contact with animals.
Disease: Undulant fever – septicemia, night sweats, arthralgias, hepatomegaly.
Treatment: Doxycycline + rifampin (6 weeks).

Francisella tularensis

Small gram‑negative coccobacillus, facultative intracellular, bioterrorism agent.
Reservoir: Rabbits, ticks; transmission by tick bite, skinning, aerosols.
Disease: Ulceroglandular, pneumonic, typhoidal.
Treatment: Streptomycin or gentamicin.

Campylobacter jejuni

Curved gram‑negative rod (“gull‑wing”), oxidase (+), microaerophilic, grows at 42°C.
Transmission: Poultry, raw milk; low infectious dose.
Disease: Acute inflammatory diarrhea (bloody), often self‑limiting.
Complications: Guillain‑Barré syndrome (molecular mimicry), reactive arthritis.
Treatment: Macrolide (erythromycin) if severe.

Helicobacter pylori

Spiral gram‑negative, microaerophilic, urease (+), oxidase (+).
Pathogenesis: Urease neutralizes acid, mucinase penetrates mucus; chronic gastritis.
Disease: Peptic ulcer disease, gastric adenocarcinoma, MALT lymphoma.
Diagnosis: Urea breath test, stool antigen, biopsy with silver/Giemsa.
Treatment: Triple therapy (PPI + amoxicillin + clarithromycin) or quadruple (PPI + bismuth + metronidazole + tetracycline).

📌 High‑yield: WHO class I carcinogen; associated with gastric cancer and MALToma.

🦷 Fastidious & HACEK group

Haemophilus ducreyi

Chancroid: painful, soft genital ulcer (“painful vs. syphilis’ hard chancre”).
Requires hemin (X factor) for growth, DNA probe or “school‑of‑fish” on Gram stain.
Treatment: Azithromycin, ceftriaxone, or ciprofloxacin.

HACEK organisms

Haemophilus (Aggregatibacter), Aggregatibacter, Cardiobacterium, Eikenella, Kingella.
Normal oral flora; cause ~5‑10% of subacute infective endocarditis.
Treatment: Third‑generation cephalosporin or fluoroquinolone.

Pasteurella multocida

Small gram‑negative rod, animal bite (especially cat) → rapidly spreading cellulitis/lymphadenitis.
Treatment: Amoxicillin‑clavulanate (prophylaxis for cat bites).

🧫 Mycobacteria

Mycobacterium tuberculosis

Acid‑fast, aerobic, slow‑growing (Lowenstein‑Jensen), niacin (+), catalase (heat‑labile).
Pathogenesis: Sulfatides inhibit phagolysosome fusion; cord factor (trehalose dimycolate) contributes to virulence.
Primary TB: Ghon focus → Ghon complex; latent in granulomas.
Reactivation: Upper lobe cavitary disease, hemoptysis, night sweats, weight loss.
Diagnosis: Acid‑fast smear, culture, Quantiferon‑TB (interferon‑γ release), PPD (induration interpretation).
Treatment: RIPE (rifampin, isoniazid, pyrazinamide, ethambutol) for 2 months, then rifampin + isoniazid for 4 months. MDR TB: add aminoglycosides, fluoroquinolones, bedaquiline.

📌 High‑yield: PPD ≥5 mm in HIV+; ≥10 mm in high‑risk; ≥15 mm in low‑risk. BCG not used in U.S.

MOTT (Non‑tuberculous mycobacteria)

Species	Disease	Treatment
M. avium complex (MAC)	Disseminated in AIDS (CD4 <50), pulmonary	Macrolide + ethambutol
M. kansasii	Pulmonary (chronic lung disease)	Rifampin + ethambutol + isoniazid
M. marinum	“Fish tank granuloma” (skin)	Minocycline / clarithromycin
M. ulcerans	Buruli ulcer (Africa)	Rifampin + streptomycin

Mycobacterium leprae

Obligate intracellular, cannot be cultured, grows at cooler temperatures.
Transmission: Nasal droplets; armadillos in southern U.S.
Forms: Tuberculoid (strong CMI, few lesions, nerve damage) vs. Lepromatous (weak CMI, numerous lesions, leonine facies).
Diagnosis: Punch biopsy / nasal scrapings, acid‑fast stain; lepromin test positive in tuberculoid, negative in lepromatous.
Treatment: Dapsone + rifampin; add clofazimine for lepromatous.

🌀 Vibrio & other important genera

Vibrio cholerae

Curved gram‑negative rod, oxidase (+), grows on alkaline media (TCBS).
Cholera toxin: ADP‑ribosylates G_s → persistent cAMP → massive watery diarrhea (“rice‑water”).
Treatment: Fluid/electrolyte replacement; doxycycline or azithromycin.

📌 High‑yield: Requires high inoculum if gastric acid normal; vaccine available (killed oral).

Vibrio vulnificus & V. parahaemolyticus

V. vulnificus: Seafood (oysters), brackish water; causes severe cellulitis/necrotizing fasciitis, especially in liver disease.
V. parahaemolyticus: Gastroenteritis from raw seafood; self‑limited.

Other key organisms

Burkholderia cepacia: Cystic fibrosis, CGD; TMP‑SMX treatment.
Acinetobacter baumannii: “Iraqibacter”; wound infections, highly drug‑resistant (carbapenem, polymyxin).
Eikenella corrodens: Human bite infections; bleach‑like odor; treat with 3rd‑gen cephalosporins.
Capnocytophaga canimorsus: Dog bite; asplenic patients → fulminant sepsis.
Bartonella henselae: Cat scratch disease (azithromycin), bacillary angiomatosis in AIDS.

⚡ Quick comparison · high‑yield features

Organism	Key distinctive feature	Treatment
Listeria	Cold growth, tumbling motility, intracellular	Ampicillin ± gentamicin
C. diphtheriae	ADP‑ribosylates eEF‑2, pseudomembrane	Antitoxin + erythromycin
Nocardia	Partially acid‑fast, aerobic branching	TMP‑SMX
Pseudomonas	Oxidase (+), pyocyanin, biofilm	Anti‑pseudomonal β‑lactam + AG
Legionella	BCYE agar, intracellular, hyponatremia	Azithromycin / levofloxacin
B. pertussis	Pertussis toxin (G_i ADP‑ribosylation), whoop	Macrolide
H. influenzae	X & V factors, satellite growth	Ceftriaxone
TB	Acid‑fast, niacin (+), catalase (−) at 68°C	RIPE

💡 Clinical pearl: Always consider epidemiologic clues (animal exposure, travel, occupation, immunosuppression) when approaching gram‑negative or atypical infections.