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USMLE (Subject) / Microbiology - Systems (Lesson)

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• Normal flora Skin – S epidermidis Nose – S epidermidis; colonized by S aureus Oropharynx – Viridans group streptococci Dental plaque – S mutans Colon – B fragilis > E coli Vagina – Lactobacillus; colonized by E coli and group B streptococci
• Bugs causing food-borne illness B cereus – Reheated rice C botulinum – Improperly canned foods (toxins), raw honey (spores) C perfringens – Reheated meat E coli O157:H7 – Undercooked meat L monocytogenes – Deli meats, soft cheeses Salmonella – Poultry, meat, eggs S aureus – Meats, mayonnaise, custard; preformed toxin V parahaemolyticus and V vulnificus – Contaminated seafood
• Bloody diarrhea Campylobacter – Comma- or S-shaped organisms; growth at 42°C E histolytica – Protozoan; amebic dysentery; liver abscess Enterohemorrhagic E coli – O157:H7; can cause HUS; makes Shiga-like toxin Enteroinvasive E coli – Invades colonic mucosa Salmonella (non-typhoidal) – Lactose ⊝; flagellar motility; has animal reservoir, especially poultry and eggs Shigella – Lactose ⊝; very low ID50; produces Shiga toxin (human reservoir only); bacillary dysentery Y enterocolitica – Day care outbreaks; pseudoappendicitis
• Watery diarrhea C difficile – Pseudomembranous colitis; associated with antibiotics and PPIs, occasionally bloody diarrhea C perfringens – Also causes gas gangrene Enterotoxigenic E coli – Travelers' diarrhea; produces heat-labile (LT) and heat-stable (ST) toxins Protozoa – Cryptosporidium, Giardia V cholerae – Comma-shaped organisms; rice-water diarrhea; often from infected seafood Viruses – Rotavirus, norovirus, enteric adenovirus
• Common causes of meningitis Newborn (0-6 months): Group B streptococci, E coli, Listeria Children (6 months-6 years): S pneumoniae, N meningitidis, H influenzae type B, enteroviruses 6-60 years: S pneumoniae, N meningitidis (#1 in teens), enteroviruses, HSV >60 years: S pneumoniae, Listeria, gram Θ rods - Give ceftriaxone and vancomycin empirically (add ampicillin if Listeria is suspected).- Viral causes of meningitis: enteroviruses (especially coxsackievirus), HSV-2 (HSV-1 = encephalitis), HIV, West Nile virus (also causes encephalitis), VZV.- In HIV: Cryptococcus spp.
• Common causes of pneumonia Neonates (<4 weeks): Group B streptococci, E coli Children (4 weeks-18 years): RSV, Mycoplasma, C trachomatis (infants-3 years), C pneumoniae (school-aged children), S pneumoniae Adults (18-40 years): Mycoplasma, C pneumoniae, S pneumoniae, viruses (eg, influenza) Adults (40-65 years): S pneumoniae, H influenzae, anaerobes, viruses, Mycoplasma Elderly: S pneumoniae, influenza virus, anaerobes, H influenzae, gram Θ rods
• Causes of pneumonia in special groups Alcoholics – Klebsiella, anaerobes usually due to aspiration (eg, Peptostreptococcus, Fusobacterium, Prevotella, Bacteroides) IV drug users – S pneumoniae, S aureus Aspiration – anaerobes Atypical – Mycoplasma, Chlamydophila, Legionella, viruses (RSV, CMV, influenza, adenovirus) Cystic fibrosis – Pseudomonas, S aureus, S pneumoniae, Burkholderia cepacia Immunocompromised – Pneumocystis jirovecii (with HIV), S aureus, enteric gram Θ rods, fungi, viruses Nosocomial – S aureus, Pseudomonas, other enteric gram Θ rods Postviral – S pneumoniae, S aureus, H influenzae
• Osteomyelitis Assume if no other information is available – S aureus Sexually active – Neisseria gonorrhoeae (rare), septic arthritis more common Sickle cell disease – Salmonella and S aureus Prosthetic joint replacement – S aureus and S epidermidis Vertebral involvement – S aureus, Mycobacterium tuberculosis (Pott disease) Cat and dog bite – Pasteurella multocida IV drug abuse – S aureus; also Pseudomonas, Candida Elevated CRP and ESR common but nonspecific.Radiographs are insensitive early but can be useful in chronic osteomyelitis. MRI is best for detecting acute infection and detailing anatomic involvement.
• Urinary tract infections Escherichia coli – Leading cause of UTI. Colonies show strong pink lactose-fermentation on MacConkey agar. Staphylococcus saprophyticus – 2nd leading cause of UTI in sexually active women. Klebsiella pneumoniae – 3rd leading cause of UTI. Large mucoid capsule and viscous colonies. Serratia marcescens – Some strains produce a red pigment; often nosocomial and drug resistant. Enterococcus – Often nosocomial and drug resistant. Proteus mirabillis – Motility caues "swarming" on agar; associated with struvite stones. Pseudomonas aeruginosa – Blue-green pigment and fruity odor; usually nosocomial and drug resistant. ⊕ Leukocyte esterase = evidence of WBC activity.⊕ Nitrate test = reduction of urinary nitrates (eg, E coli)⊕ Urease test = urease-producing bugs (eg, S saprophyticus, Proteus, Klebsiella)
• Common vaginal infections Bacterial vaginosis:- No inflammation- Thin, white discharge with fishy odor- Lab findings: Clue cells, pH >4.5- Treatment: Metronidazole or clindamycin Trichomonas vaginitis:- Inflammation ("strawberry cervix")- Frothy, yellow-green, foul-smelling discharge- Lab findings: Motile trichomonads, pH >4.5- Treatment: Metronidazole, treat sexual partner(s) Candida vulvovaginitis- Inflammation- Thick, white, "cottage cheese" discharge- Lab findings: Pseudohyphae, pH normal (4.0-4.5)- Treatment: Azoles
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• Toxoplasma gondii Mode of maternal transmission:- Cat feces- Ingestion of undercooked meat Maternal manifestations:- Usually asymptomatic- Lymphadenopathy (rarely) Neonatal manifestations:- Classic triad: Chorioretinitis, hydrocephalus, intracranial calcifications± "blueberry muffin" rash
• Rubella Mode of maternal transmission:- Respiratory droplets Maternal manifestations:- Rash, lymphadenopathy, polyarthritis, polyarthralgia Neonatal manifestations:- Classic triad: Cataract, deafness, congenital heart disease (PDA)± "blueberry muffin" rash
• Cytomegalovirus Mode of maternal transmission:- Sexual contact- Organ transplants Maternal manifestations:- Usually asymptomatic- Mononucleosis-like illness Neonatal manifestations:- Hearing loss- Seizures- Petechial rash, "blueberry muffin" rash- Chorioretinitis- Periventricular calcifications
• HIV Mode of maternal transmission:- Sexual contact- Needlestick Maternal manifestations:- Variable depending on CD4+ cell count Neonatal manifestations:- Recurrent infections- Chronic diarrhea
• Herpes simplex virus-2 Mode of maternal transmission:- Skin or mucous membrane contact Maternal manifestations:- Usually asymptomatic- Herpetic (vesicular) lesions Neonatal manifestations:- Meningoencephalitis- Herpetic (vesicular) lesions
• Syphilis Mode of maternal transmission:- Sexual contact Maternal manifestations:- Chancre (1°) and disseminated rash (2°) are the two stages likely to result in fetal infection Neonatal manifestations:- Often results in stillbirth, hydrops fetalis- Facial abnormalities (eg, notched teeth, saddle nose, short maxilla)- Saber shins- CN VIII deafness
• Sexually transmitted infections Chancroid (Haemophilus ducreyi) – Painful genital ulcer with gray to yellow exudate, inguinal adenopathy (often unilateral); can rupture and drain pus. Organisms clump in parallel strands ("school of fish"). Chlamydia (Chlamydia trachomatis D-K) – Urethritis, cervicitis, epididymitis, conjunctivitis, reactive arthritis, PID Condylomata acuminata (HPV-6, -11) – Genital warts, koilocytes Genital herpes (HSV-2) – Painful penile, vulvar, or cervical vesicles and ulcers; can cause systemic symptoms such as fever, headache, myalgia. Multinucleated giant cells and Cowdry A inclusions. Gonorrhea (Neisseria gonorrhoeae) – Urethritis, cervicitis, PID, prostatitis, epididymitis, arthritis, creamy purulent discharge Granuloma inguinale, donovanosis (Klebsiella granulomatis) – Painless, beefy red ulcer that bleeds readily on contact. No lymphadenopathy. Uncommon in US. Cytoplasmic Donovan bodies (bipolar staining) on microscopy. Lymphogranuloma venereum (Chlamydia trachomatis L1-3) – Infection of lymphatics; painless shallow genital ulcers; large, painful, coalesced lymphadenopathie (ie, buboes) Syphilis (Treponema pallidum) – 1° painless chancre (single, indurated, well-circumscribed ulcer), 2° condylomata lata, 3° gummas
• Pelvic inflammatory disease Chlamydia trachomatis (subacute, often undiagnosed), Neisseria gonorrhoeae (acute). C trachomatis – most common bacterial STI in the US. Signs:- Cervical motion tenderness- Adnexal tenderness- Purulent cervical dischargePID may include salpingitis, endometritis, hydrosalpinx, and tubo-ovarian abscess. - Salpingitis is a risk factor for ectopic pregnancy, infertility, chronic pelvic pain, and adhesions. Can lead to perihepatitis (Fitz-Hugh-Curtis syndrome) – infection and inflammation of liver capsule and "violin string" adhesions of peritoneum to liver.
• Nosocomial infections E coli (UTI) and S aureus (wound infection) are the two most common causes. Decubitus ulcers, surgical woulds, drains – S aureus (including MRSA), gram Θ anaerobes (Bacteroides, Prevotella, Fusobacterium) Intravascular catheters – S aureus, S epidermidis (long term), Enterobacter Mechanical ventilation, endotracheal intubation – Late onset: P aeruginosa, Klebsiella, Acinetobacter, S aureus- New infiltrate on CXR, ↑ sputum production; sweet odor (Pseudomonas) Renal dialysis unit, needlestick – HBV, HCV Urinary catheterization – Proteus spp, E coli, Klebsiella- Dysuria, leukocytosis, flank pain or costovertebral angle tenderness Water aerosols – Legionella
• Organisms associated with bites Eikenella corrodens: Gram-negative rods - Bleach-like odor- Transmission: Human oropharynx, human bites, or fight injuries- Cellulitis Capnocytophaga canimorsus: Gram-negative, filamentous rods- Transmission: Dog bite wounds- Cellulitis. Splenectomy → overwhelming sepsis. Bartonella henselae: Gram-negative rods- Transmission: Cats and dogs/bites, scratches, fleas- Cat scratch fever, bacillary angiomatosis (AIDS)
• HACEK group infections Group of gram-negative fastidious rods- Aggregatibacter aphrophilus (formerly Haemophilus aphrophilus)- Aggregatibacter actinomcetemcomitans- Cardiobacterium hominis- Eikenella corrodens- Kingella kingae - HACEK organisms usually responsible for 5-10% of infective endocarditis (usually subacute) - Most common cause of gram-negative endocarditis in non-IV drug users - All part of normal oral flora Treatment: third-generation cephaosporin or fluoroquinolone
• Subcutaneous granulomas/ulcers/cellulitis Tropical fish enthusiasts; granulomatous lesion – Mycobacterium marinum (fish tank granuloma) Cellulitis following contact with saltwater or oysters – Vibrio vulnificu
• Malignant pustule Pustule → dark red fluid-filled, tumor-like lesion → necrosis → black eschar surrounded by red margin – Bacillus anthracis Ecthyma gangrenosum – Pseudomonas septicemia
• Wounds Surgical wounds (clean) – S aureus Surgical wounds (dirty) – S aureus, Enterobacteriaceae, anaerobes Trauma – Clostridium, Enterobacteriaceae, Pseudomonas Shallow puncture wound through tennis shoe sole – Pseudomonas aeruginosa
• Animal bites Various – Pasteurella multocida Human bites, fist fight – Eikenella corrodens Dog bites – Capnocytophaga canimorsus Rat bites – Streptobacillus moniliformis, Spirillum minus Cat scratches resulting in lymphadenopathy with stellate granulomas – Bartonella henselae
• Acute otitis media Red, bulging tympanic membrane, fever 102-103°; pain goes away if drum ruptures or ear tubes are patent: - Streptococcus pneumoniae- H. influenzae (often nontypeable)- Moraxella catarrhalis- RSV- Rhinovirus
• Otitis externa Ear pain Often mixed infections:- Staph aureus- Candida albicans- Proteus (water organism)- Pseudomonas (water) Malignant otitis externa: Severe ear pain in diabetic, life threatening – Pseudomonas aeruginosa
• Sore throat Inflammed tonsils/pharynx, which may be purulent and may develop abscesses; cervical lymphadenopathy, fever, stomach upset; sandpaper rash – Streptococcus pyogenes- Rash indicates presence of erythrogenic exotoxin A White papules with red base on posterior palate and pharynx, fever – Coxsackie A Throat looking like Strep with severe fatigue, lymphadenopathy, fever, fash; heterophile ⊕; Downey type II cells – Epstein-Barr virus Low-grade fever with a 1-2 day gradual onset of membranous nasopharyngitis and/or obstructive laryngotracheitis; bull neck from lymphadenopathy; elevated BUN; abnormal ECG; little change in WBC (toxin). Exudate bleeds profusely when dislodged – Corynebacterium diphtheriae
• Common cold Rhinitis, sneezing, coughing - Rhinovirus (summer-fall)- Coronavirus (winter-spring)- Adenovirus
• Eyelid infection Bilateral eye lid swelling, >10% eosinophilia, fever, muscle pain, earlier GI symptoms – Trichinella Unilateral inflammation at bite site often around eye or mouth; travel to Mexico, Central or South America – Trypanosoma cruzi
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• Conjunctivitis neonate Red itchy eye(s)/pus; onset 2-5 days – Neisseria gonorrhoeae Red itchy eye(s)/pus; onset 5-10 days – Chlamydia trachomatis (serotypes D-K) Neonate with "sticky eye" – Staphylococcus aureus
• Conjunctivitis (other age groups) Red itchy eye(s), thin exudate; pain, photophobia – Viral pink eye: adenovirus Red eye, pus:- Staphylococcus aureus- Streptococcus pyogenes- Streptococcus pneumoniae- Haemophilus influenzae Red eye, pus, presence of inclusion bodies in scrapings – Chlamydia trachomatis serotypes D-K (inclusion conjunctivitis) Granulomas and inturned eye lashes, corneal scarring, blindness – Chlamydia trachomatis serotypes A-C (trachoma)
• Chorioretinitis Neonate or AIDS - Toxoplasma - CMV 
• Bronchitis Wheezy; infant or child ≤5 years – RSV >5 years – Haemophilus influenzae, Myocplasma pneumoniae, Chlamydophila pneumoniae With cough >2 weeks, afebrile, >9 years – Bordetella pertussis
• Acute pneumonia with chronic cough with weight loss, night sweats, calcifying lesions Over 55, HIV+, or immigrant from developing countries – Mycobacterium tuberculosis Dusty environment with bird or bat fecal contamination  (Missouri chicken farmers), yeasts packed into phagocytic cells – Histoplasma capsulatum Desert sand, Southwest US – Coccidioides immitis Rotting contaminated wood, North and South Carolina – Blastomyces dermatitidis
• Acid fast organisms - Mycobacterium - Nocardia (partially acid fast) - Cryptosporidium oocysts
• Non-motile gram-positive rods - Corynebacterium diphtheriae - Nocardia - Clostridium perfringens (rest of the pathogenic Clostridia are motile) - Bacillus anthracis
• Bacteria and fungi with capsules - Streptococcus pneumoniae- Klebsiella pneumoniae- Haemophilus influenzae- Neisseria meningitidis- Pseudomonas aeruginosa- Cryptococcus neoformans (only encapsulated fungal pathogen)- Bordetella pertussis - E. coli meningeal strains have capsule, mostly K1- Bacillus antrhracis – poly D-glutamate capsule- Salmonella enterica subsp. typhi – Vi capsular antigen
• Unique morphology/staining Metachromic staining – Corynebacterium  Lancet-shaped diplococci – Pneumococcus Kidney bean-shaped diplococci – Neisseriae Bipolar staining – Yersinia pestis Gulls wings – Campylobacter
• Metabolism Aerobes:- Mycobacterium- Corynebacterium- Pseudomonas- Bacillus- Nocardia Anaerobes:- Bacteroides- Actinomyces- Clostridium- Fusobacterium - Prevotella- Propionibacterium- Lactobacillus Microaerophilic:- Helicobacter- Campylobacter
• Urease positive - Proteus - Helicobacter - Ureaplasma - Nocardia - Cryptococcus
• Parotitis Risk factors: Decreased salivary flow- Medications (eg, anticholinergics)- Obstruction (eg, calculi, neoplasm)- Dehydration, postsurgical/intubation Microbiology: Staphylococcus aureus, anaerobes Presentation:- Firm, erythematous pre/postauricular swelling- Trismus, dysphagia, systemic findings (fever, chills) Diagnosis: - Imaging (ultrasound/CT): Ductal inflammation/obstruction, frank abscess- Laboratory: Elevated serum amylase without pancreatitis
• Stool findings in acute diarrhea Watery diarrhea: Noninflammatory (enterotoxin)- No fecal leukocytes, no red cells- Vibrio cholerae, ETEC, Bacillus cereus, S aureus, some viruses, Giardia lamblia, Cryptosporidium Dysentery or inflammatory diarrhea: Invasion or cytotoxin- Fecal polymorphonuclear leukocytes, with or without red cells- Shigella, Salmonella, Campylobacter jejuni, EIEC, Yersinia enterocolitica, Clostridium difficile, Entamoeba histolytica Enteric fever: Penetration & possible dissemination- Fecal mononuclear leukocytes- Salmonella Typhi
• Gonococcal cervicitis Clinical features:- Purulent or mucopurulent discharge- Friable cervix with easy bleeding (eg, intermenstrual or postcoital bleeding) Diagnosis: - Nucleic acid amplification testing Empiric treatment: 3rd-generation cephalosporin + azithromycin/doxycycline

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