Micro 9/17

  • Enterics overview
    • Group of gram-negative rods commonly identified in clinical labs; many pathogens fall into this group. They are generally not distinguished from each other by a simple Gram stain.
    • Taxonomy changes: the order Enterobacterialis has been adopted; previously many organisms were grouped under Enterobacteriaceae. For quick reference, we still call the group “enterics.”
    • Key Families: the enterics are divided into seven families based on biochemical characteristics. ( memorize flowcharts rather than every single biochemical for every organism; the class uses a shared biochemical panel to identify them.)
    • Common clinical relevance: many are normal GI flora or opportunistic pathogens; they can cause a variety of diseases depending on the organism (GI, urinary, wound infections, bacteremia, meningitis in newborns, etc.).
  • General characteristics of enterics
    • Gram-negative rods; generally non-spore-forming; not filamentous; often lack distinctive Gram-stain features to separate one from another.
    • Bipolar staining may occur in some, which can be mistaken for multiple organisms if not interpreted correctly.
    • Metabolism: facultative anaerobes; grow in CO2 and in ambient air; not fastidious; grow on routine media (blood agar, MacConkey, etc.).
    • Habitat: mostly GI tract; many are normal flora or opportunistic infections; some pathogens are not normally found in humans (e.g., certain yersinia or pleisomonas species).
  • Enteric antigens: what helps differentiate and identify
    • O antigens: cell wall antigens; used to confirm identification of Salmonella and Shigella via O-antigen typing.
    • H antigens: flagellar antigens; present in most enterics; some organisms have prominent H-antigens contributing to virulence.
    • K antigens: capsular antigens; some organisms have thick capsules that can mask other antigens; capsule denaturation may be required to expose O antigens for testing.
    • VI (surface) antigens: sometimes present and related to virulence.
    • F (pili) antigens: related to adherence; have role in virulence.
    • Main takeaway for testing: the major focus is on O, H, and K antigens as part of serotyping; E. coli, Salmonella, Shigella commonly tested this way.
  • Common biochemical traits to know
    • Glucose fermentation: all enterics ferment glucose (fermentation is anaerobic but can also occur aerobically); this is a baseline test.
    • Lactose fermentation: variable among enterics; makes identifying via media easier when combined with color changes.
    • Oxidase test: all enterics are oxidase-negative (negative oxidase test) with one notable exception discussed here.
    • Nitrate reduction: all enterics reduce nitrate to nitrite (nitrate positive) with a few environmental exceptions; Moraxella and some others outside the enterics may differ.
    • Special note: Pleisomonas (Plesiomonas) is oxidase-positive, which is an exception to the typical enteric rule and important for differential testing.
  • Notable exceptions and special cases
    • Pleisomonas (Plesiomonas) shigelloides: oxidase-positive enteric organism; environmental; not part of standard enteric rules; important to recognize as an exception.
    • Escherichia coli O157:H7: a Shiga toxin-producing E. coli (STEC); important cause of hemorrhagic colitis and HUS; does not ferment sorbitol on SMAC plate (see SMAC detail below).
    • Yersinia enterocolitica: grows on CIN agar with distinctive bull’s-eye colonies; cold-tolerant; often misdiagnosed as appendicitis due to RLQ pain.
  • Escherichia coli (E. coli) – the big picture
    • Normal intestinal flora in humans; many strains exist.
    • E. coli O157:H7: a pathogenic strain producing Shiga-like toxin; causes hemorrhagic colitis and potentially hemolytic uremic syndrome (HUS).
    • Traveler’s diarrhea and urinary tract infections (UTIs) are commonly caused by various E. coli strains.
    • E. coli O157:H7 testing: Sorbitol MacConkey (SMAC) is used to differentiate; O157:H7 cannot ferment sorbitol, so colonies that remain colorless on SMAC are presumptively O157:H7; confirm with PCR or serology testing.
    • Other notable E. coli topics: normal fecal flora is not typically tested for in stool cultures unless clinically suspected; carriers exist and can spread infection.
  • Shigella – key disease and identification points
    • Causes bacillary dysentery; four species commonly discussed (A, B, C, D; dysenteriae, flexneri, boydii, sonnei).
    • Transmission: fecal-oral; strongly associated with food, water, and poor hygiene; four Fs mnemonic: Food, Fingers, Feces, Flies.
    • Toxins: Shiga toxin contributes to severe disease and dysentery; Shigella, like some other enterics, can be highly virulent.
    • Identification: Shigella agglutination tests use O-antigen antisera; if initial antisera are negative across A–D, boil the isolate for at least 15 minutes to denature the capsule, retest, and look for agglutination (capsule masking can cause false negatives).
    • Public health: isolates are often confirmed or followed up by the state health department; outbreak tracking relies on serogrouping and serology tests.
  • Salmonella – key disease and identification points
    • Salmonella spp. are not normal human flora; transmitted via fecal-oral route and animals (foodborne illness).
    • Two main species used to be highlighted: Salmonella enterica and Salmonella bongori; there are >2,000 serotypes of Salmonella based on O, H, and BI antigens (serotyping by serogroup/antigen testing).
    • Typhoidal Salmonella (S. enterica serotypes Typhi and others) cause typhoid fever; Typhi historically had carrier cases (e.g., Typhoid Mary).
    • Outbreak tracking and public health: laboratories report Salmonella serogroups and serotypes to health departments for surveillance.
    • H2S production: Salmonella is typically H2S positive on select media; this helps differentiate from other non-H2S producers on certain plates.
    • Colony morphology: despite similar appearances to Shigella and E. coli on many plates, Salmonella can be distinguished by its H2S production and sometimes by lysine utilization on certain media (see XLD discussion).
    • Vaccination: there is a vaccine for Salmonella Typhi (not routinely used in the U.S. for general population).
  • Klebsiella species – focus on two common pathogens
    • Klebsiella pneumoniae: classically produces very mucoid colonies (often described as “mucoid” and can overwhelm a plate); associated with community-acquired pneumonia and abscesses, UTIs, wound infections.
    • Klebsiella oxytoca: also mucoid but generally less so than K. pneumoniae.
    • Differentiation: indole test helps distinguish the two: K. pneumoniae is indole-negative; K. oxytoca is indole-positive (a red color indicates a positive indole test).
    • Endol test: endol (tryptophanase) test helps differentiate K. pneumoniae (endol negative) from K. oxytoca (endol positive).
    • Motility: Klebsiella species are typically nonmotile; recent taxonomy changes have placed some related species differently, so be aware of potential nonmotile results in panel interpretation.
  • Proteus species – hallmark features
    • Proteus mirabilis: known for a strong, distinctive (burnt chocolate-like) odor on certain plates; swarming motility on solid media can complicate isolation of other organisms.
    • Proteus mirabilis also tends to be H2S positive on reporters; associated with UTIs and wound infections.
    • Proteus vulgaris: indole-positive variant; some strains are sucrose fermenters.
    • On multichannel media: Proteus vulgaris may appear yellow on certain media due to sucrose fermentation with H2S production (context-dependent on the plate and indicators).
  • Plesiomonas shigelloides – an enteric exception
    • Formerly classified with nonfermenters, now considered part of the enteric family by some classifications.
    • Oxidase-positive, unlike most enterics; environmental organism typically associated with aquatic sources and animal contact.
    • Infections present as GI illness; important to recognize as an enteric exception (oxidase-positive) in testing panels.
  • Yersinia species