This study identified the gut microbiome during an acute enteric infection in patients with and without inflammatory bowel disease (IBD). A cross-sectional study was performed on 260 patients who underwent stool testing and tested positive for Clostridioides difficile, Escherichia coli, or norovirus, or negative for all pathogens, and 25 healthy controls. They collected the following data from the medical record: presenting clinical symptoms, medication use, date of PCR test, PCR results, date of birth, place of PCR test, sex, race, ethnicity, presence of IBD, date of IBD diagnosis, IBD subtype, IBD therapy use, inflammatory biomarkers, and empiric and directed antimicrobial therapies for PCR results.

In addition, they collected management and outcomes after testing, including hospitalization requirement, short-term and long-term management, and outcomes and utilization including IBD medications held, added, or up titrated; requirement for steroids; colectomy; other surgery; and subsequent endoscopy, radiology, hospitalization, emergency department visit, and IBD extension or complication. They also measured the effect size of the gut microbiome on IBD characteristics and outcomes using 16S rRNA sequencing.