Related Experiment Video
Updated: Mar 2, 2026

Detection of Helicobacter pylori Infection and Antibiotic Resistance via Stool Quantitative Polymerase Chain Reaction Analysis
Published on: May 16, 2025
Enteric Infection in Relapse of Inflammatory Bowel Disease: The Utility of Stool Microbial PCR Testing
Jordan E Axelrad1, Andrew Joelson, Yael R Nobel
1*Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York; and†Department of Medicine, Columbia University Medical Center, New York, New York.
Background:
The similar presentations in relapse of inflammatory bowel disease (IBD) and enteric infection pose substantial barriers to diagnosis and treatment. The objective of this study was to investigate the incidence, etiology, predictors, and treatment of enteric infection in patients with IBD.
Methods:
We reviewed the records of 214 patients with IBD who underwent 295 gastrointestinal pathogen panel and Clostridium difficile infection (CDI) polymerase chain reaction (PCR) stool tests during an exacerbation of symptoms. We collected baseline characteristics, PCR outcomes, and medication exposures. We tested for associations via the Chi-square test and the t-test. Logistic regression analysis was used to identify predictors of enteric infection.
Results:
Of 295 PCR tests ordered during an exacerbation of symptoms, 38 (12.9%) were positive for CDI and 41 (13.8%) were positive for 14 other pathogens, with E. coli species as the most common. A previous history of CDI or colonic involvement of IBD predicted CDI, whereas a previous colectomy predicted negative testing for CDI. The majority with CDI (24, 63.2%) received oral vancomycin and 15 (37.5%) with other enteric pathogens were treated for their infection. Patients with CDI had a longer median length of hospital stay (8.5 versus 4 days, P = 0.041). Patients who tested negative for enteric infections were more likely to have IBD medications added or up-titrated (P = 0.027).
Conclusions:
Enteric infection was detected in 79 (26.8%) symptomatic patients with IBD , with CDI the most frequent followed by E. coli. Negative stool PCR testing was associated with changes in IBD management. Broad enteric PCR testing should be considered during relapse of IBD.
Insights
Enteric infections, including Clostridium difficile infection (CDI), affect over a quarter of inflammatory bowel disease (IBD) patients during symptom flares. Broad stool testing is recommended for accurate diagnosis and management of IBD relapses.
Area of Science:
- Gastroenterology
- Infectious Diseases
- Clinical Medicine
Background:
- Inflammatory bowel disease (IBD) relapse symptoms often mimic enteric infections, complicating diagnosis and treatment.
- Accurate identification of enteric infections in IBD patients is crucial for effective management.
Purpose of the Study:
- To investigate the incidence, causes, predictors, and treatment of enteric infections in patients experiencing IBD exacerbations.
- To assess the impact of enteric infections on IBD management strategies.
Main Methods:
- Retrospective review of 214 IBD patients undergoing gastrointestinal pathogen panel and Clostridium difficile infection (CDI) polymerase chain reaction (PCR) stool tests during symptom flares.
- Analysis of baseline characteristics, PCR results, medication exposures, and statistical testing for associations and predictors.
Main Results:
- Enteric infections were identified in 26.8% of symptomatic IBD patients, with CDI being most common, followed by E. coli.
- Predictors for CDI included prior CDI history or IBD colonic involvement; colectomy predicted negative CDI tests.
- Patients with CDI had longer hospital stays. Negative infection tests correlated with adjustments in IBD medication.
Conclusions:
- Enteric infections are common during IBD flares, with CDI and E. coli being frequent pathogens.
- Negative stool PCR results influenced IBD management decisions.
- Broad enteric PCR testing is recommended for symptomatic IBD patients during relapse to ensure accurate diagnosis and appropriate treatment.
More Related Videos
Related Concept Videos
Inflammatory Bowel Disease III: Diagnostic Studies and Management I-Nutritional Therapy
Diagnostic studies
A colonoscopy is the definitive screening test, distinguishing ulcerative colitis from other colon diseases with similar symptoms. During a colonoscopy test, inflamed mucosa with exudate ulcerations can be observed, and biopsies are taken to determine the histologic characteristics of the...
Serum Laboratory Studies, Stool Test, Breath Test
Inflammatory Bowel Disease V: Surgical Management
Here are some common surgical interventions for IBD:
Irritable Bowel Syndrome II: Clinical Features and Diagnostic Evaluation
Irritable Bowel Syndrome (IBS) is classified into subtypes based on the predominant bowel habits as determined by the Bristol Stool Form Scale (BSFS). The subtypes are:
Inflammatory Bowel Disease II: Crohn's Disease
Inflammatory bowel disease, commonly known as IBD, refers to a collection of disorders that lead to persistent inflammation of the gastrointestinal tract. The two types of IBD are ulcerative colitis, which impacts the colon, and Crohn's disease, which can involve any part of the gastrointestinal segment.
Crohn's disease
Crohn's disease is a chronic, systemic inflammatory bowel disease (IBD) that predominantly affects the gastrointestinal tract. It is marked by...
Inflammatory Bowel Disease I: Ulcerative Colitis
Inflammatory bowel disease, or IBD, encompasses a group of disorders characterized by chronic inflammation or ulceration of the gastrointestinal tract.
Risk Factors
The exact cause of IBD remains unclear, although it is believed to be due to a mix of genetic, environmental, microbial, and immune factors. Genetic factors are significant in determining susceptibility to IBD, with family history being a critical risk factor. Individuals with a first-degree relative who has IBD are at...

