Primary Native Bile Culture Patterns Collected During ERCP: Microbial Profiles in Malignant Versus Benign Biliary Obstruction

Acute biliary tract infection is a serious complication of biliary obstruction, and understanding the native biliary microbiota is essential for optimizing empirical antimicrobial therapy. We retrospectively reviewed 404 patients who underwent their first endoscopic retrograde cholangiopancreatography (ERCP) for biliary obstruction between January and December 2024; bile was aspirated before any therapeutic manipulation, and microbiological characteristics were compared between benign and malignant obstruction. Among 404 patients, 365 bile samples were collected, and overall culture positivity was 68.8%. Benign obstruction demonstrated significantly higher positivity than malignant obstruction (71.9% vs. 59.3%, p = 0.04). Monomicrobial Gram-positive organisms were disproportionately more common in benign obstruction (17.2% vs. 7.7%, p = 0.03), whereas monomicrobial fungal organisms were more frequently isolated in malignant obstruction (9.9% vs. 4.4%, p = 0.07). Polymicrobial infections occurred in approximately one-quarter of cases, and anaerobes were relatively uncommon (7.9%). Bile cultures obtained during the initial ERCP revealed distinct microbial profiles associated with different etiologies of biliary obstruction, suggesting that the distribution of identified organisms varies according to the underlying cause of obstruction.