Interpretation of Escherichia coli found in Intestinal and Fecal Samples

E. coli is normal flora in the gastrointestinal tract of mammals and is recovered in almost all fecal or intestinal cultures.

E. coli is implicated in diarrhea in three ways:

  • Virulence factor-positive strains (ETEC) causing increased fluid secretion in the small intestine leading to secretory diarrhea in neonatal animals
  • Virulence factor-positive strains (EPEC, EHEC/STEC, AEEC) causing damage to intestinal mucosa resulting in diarrhea in young animals
  • Small intestinal overgrowth of normal coli, generally associated with other co- morbidities like viral or parasitic infections, causing dysbiosis leading to malabsorption and osmotic diarrhea in young animals

The significance of an E. coli isolate is based on identification of virulence factors, histologic examination of intestinal sections when available, and compatible clinical signs. NDSU-VDL routinely performs PCR for common virulence factors on samples from ruminants younger than 14 days and small animals when indicated

Antimicrobial Susceptibility Testing

We no longer routinely perform or recommend susceptibility testing for the following reasons:

  • Poor correlation between the susceptibility data and treatment
  • Antimicrobial breakpoints for in vitro susceptibility are known only for serum achievable concentrations, and not the treatment of intra-intestinal E. coli
  • If small intestinal overgrowth due to E. coli (a significant co-morbidity in diarrhea) or bacteremia is suspected, then fecal culture is a poor representation of both sites and susceptibility data would be erroneous

Recommended samples for testing:

  • ≥ 5 grams feces
  • Fresh and fixed 5-10 cm sections of each segment of small intestine (duodenum, jejunum, ileum) and one 5-10 cm section of colon.
  • Swabs are not recommended

References for more information and for current recommended treatment strategies:

  1. Constable PD. Treatment of calf diarrhea: Antimicrobials and ancillary treatments. Vet Clin Food Anim. 2009 Mar;25(1):101-120.
  2. Radostits Veterinary Medicine: A Textbook of the Diseases of Cattle, Sheep, Pigs, Goats, and Horses. Elsevier (2007) pgs. 865-869.
  3. Smith. Large Animal Internal Medicine. Elsevier (2015) pgs. 320, 331-333.

Revised 07-2019

Printable version available here.