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Bovine Enteric Aerobic Culture and E. coli Genotyping PCR

Enterotoxigenic E. coli in Calves

E. coli is a normal intestinal tract commensal organism in calves and its growth on aerobic culture is expected in both scouring and healthy calves. Pathogenic enterotoxigenic E. coli (ETEC) is the most common type of E. coli implicated in causing diarrhea in young calves under 2 weeks of age. 

The pathogenicity of ETEC is linked to fimbriae, such as F17A, F41, F5(K99), that facilitate attachment to the intestinal mucosa and enterotoxins that stimulate a secretory response by intestinal crypt cells, including heat stable enterotoxin Sta.

E. coli of Zoonotic Concern

Attaching and Effacing E. coli (AEEC) and shigatoxin-producing E. coli (STEC) have been demonstrated to be less influential in the pathogenesis of calf diarrhea but do pose a public health concern as zoonotic pathogens linked to disease in people. AEEC express the EAE gene allowing microvillus effacement and intimate attachment of the bacterium to enterocytes, resulting in attaching and effacing lesions. Enteropathogenic (EPEC) and Enterohemorrhagic E. coli (EHEC) are classes of AEEC considered to be human pathogens for which cattle are a major reservoir. EPEC express the EAE gene, while EHEC express both EAE and toxins responsible for cytotoxic damage to the intestinal lumen (STX1 and STX2).

Although less common, AEEC and STEC have been associated with diarrhea in calves up to several months of age, and diarrhea associated with STEC can be hemorrhagic.

The diagnosis of AEEC or STEC as a cause of diarrhea in calves can be made through identification of characteristic histologic gastrointestinal lesions in combination with EAE or shigatoxin positive E. coli genotyping PCR.

Submission Strategy for Bovine Enteric Aerobic Culture

Fresh feces, intestinal contents, fresh intestine and colon or a swab of either can be submitted in appropriate transport medium for bovine enteric aerobic culture from calves less than 2 weeks of age or older calves with hemorrhagic diarrhea.

While a variety of E. coli types can colonize the GI tract of calves, ETEC can be diagnosed through identification of virulence factors in a group of E. coli colonies grown in aerobic culture using molecular-based E. coli genotyping PCR. Enteric aerobic culture should always be performed in combination with E. coli genotyping PCR and whenever possible histopathology should be performed on representative sections of gastrointestinal tract (small intestine, abomasum, cecum, colon) to determine the relevance of E. coli growth.

The AHDC offers a genotyping PCR panel specifically for the diagnosis of ETEC (insert name and code of panel here once determined), as well as a separate panel for the identification of EAE/STX1/STX2 (insert name and code of panel here once determined).

Due to the diversity and large number of E. coli colony types present in most fecal samples, antimicrobial susceptibility testing of a single E. coli colony is not recommended because the results may not be clinically relevant. Please contact Veterinary Support Services for more information regarding bacterin production (; (607) 253-3412).

ETEC Genotyping PCR Interpretation Guidance for Bovine Species

The AHDC offers separate E. coli genotyping PCR panels for ETEC and EAE/STX1/STX2. Results for enteric E. coli genotyping PCR reflect the genes present in a group of colonies grown on aerobic culture. The detection of genes alone does not confirm E. coli as the causative agent of diarrhea. It is important to consider and rule out other common causes of diarrhea in this age group of calves, including but not limited to Salmonella, beta coronavirus, rotavirus, bovine viral diarrhea virus, Cryptosporidium and Clostridium. Please see the Bovine Diarrhea Calf Acute Diagnostic Plan for additional diagnostic guidance.

The CNF gene included in this panel is expressed by necrotoxigenic E. coli (NTEC) and has been associated with septicemia and diarrhea in calves. 

E. coli Diagnostics in Non-bovine species

For guidance or interpretation of E. coli genotyping results in non-bovine species, please contact the AHDC Veterinary Support Services team (607) 253-3900 or

Bacterin Production

For more information on the process and additional fees associated with identification of E. coli isolates for bacterin production, please contact the AHDC Veterinary Support Services team (607) 253-3900 or