The Escherichia coli (E coli) species, specifically enteropathogenic E coli (EPEC), may have a role in the development of inflammatory bowel disease (IBD), according to a study in the Journal of Clinical Gastroenterology.

Investigators sought to determine the distribution of microbial pathogens identified from stool gastrointestinal polymerase chain reaction (GIPCR) testing in patients who ultimately developed IBD.

The retrospective study used electronic medical records of patients with IBD who were hospitalized for more than 24 hours with an episode of diarrhea. Patients of all ages who had stool testing with GIPCR from March 2015 to September 2019 were eligible.

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A total of 54 patients were included — 30 (56%) with Crohn disease and 24 (44%) with ulcerative colitis. Participants had a median age at IBD diagnosis of 35 (IQR, 18-65) years, 54% were women, and 56% were White. The median time from a positive GIPCR panel to IBD diagnosis was 3 (IQR, 2-9) months.

The researchers identified 69 unique organisms on the 54 GIPCR panels, and 42 patients had 1 positive pathogen on each stool test. Bacterial organisms were the most commonly occurring (83%), followed by viral (13%) and parasitic (4%) organisms.

The median time to IBD diagnosis from stool PCR test, when stratified according to class of organism, was 6 (IQR, 2-10) months in patients who were positive for bacteria, 3 (IQR, 1-8) months in patients positive for viruses, and 1 (IQR, 0.75-1) month in patients positive for parasites (P =.001).

The E coli species was the most frequently identified bacteria (71%), and EPEC was the most common pathogen, accounting for 38% of all unique organisms.

Enteroinvasive E coli, Vibrio, Shigella, Yersinia enterocolita, Cryptosporidium, Cyclospora cayetanensis, adenovirus, and astrovirus were not observed in stool testing for any patients.

The researchers noted that their retrospective study is exploratory and does not prove a causal association between the organisms identified on GIPCR and diagnosis of IBD. In addition, they could not rule out underdiagnosis or misdiagnosis of IBD of excluded patients. Finally, the GIPCR panel does not detect Clostridioides difficile or cytomegalovirus.

“Although there is still controversy surrounding the role of E. coli in IBD pathogenesis, we show that EPEC may serve as a predisposing factor to the development of IBD,” the study authors commented. “As such, PCR testing may be considered a potential diagnostic step for patients in whom IBD is suspected. Patients found to have positive stool PCR test, particularly with microorganisms such as EPEC, should be followed closely if clinical suspicion for IBD is high.”


Varma S, Green PH, Krishnareddy S. The distribution of gastrointestinal pathogens on stool PCR prior to the development of IBD. J Clin Gastroenterol. 2022;56(1):e52-e57. doi: 10.1097/MCG.0000000000001470