Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

Clin Microbiol Rev. 2015 Jan;28(1):3-31. doi: 10.1128/CMR.00073-14.


Bacterial gastroenteritis is a disease that is pervasive in both the developing and developed worlds. While for the most part bacterial gastroenteritis is self-limiting, identification of an etiological agent by bacterial stool culture is required for the management of patients with severe or prolonged diarrhea, symptoms consistent with invasive disease, or a history that may predict a complicated course of disease. Importantly, characterization of bacterial enteropathogens from stool cultures in clinical laboratories is one of the primary means by which public health officials identify and track outbreaks of bacterial gastroenteritis. This article provides guidance for clinical microbiology laboratories that perform stool cultures. The general characteristics, epidemiology, and clinical manifestations of key bacterial enteropathogens are summarized. Information regarding optimal specimen collection, transport, and processing and current diagnostic tests and testing algorithms is provided. This article is an update of Cumitech 12A (P. H. Gilligan, J. M. Janda, M. A. Karmali, and J. M. Miller, Cumitech 12A, Laboratory diagnosis of bacterial diarrhea, 1992).

Publication types

  • Review

MeSH terms

  • Animals
  • Bacterial Infections / diagnosis*
  • Bacterial Infections / microbiology
  • Bacterial Infections / pathology
  • Clinical Laboratory Techniques / standards
  • Diarrhea / diagnosis
  • Diarrhea / microbiology
  • Diarrhea / pathology
  • Feces / microbiology
  • Gastroenteritis / diagnosis*
  • Gastroenteritis / microbiology
  • Gastroenteritis / pathology
  • Humans
  • Specimen Handling