Evolving bile pathogen profiles and antimicrobial resistance in patients undergoing ERCP, with a focus on acute biliary pancreatitis: a 12-year retrospective study

Long-term surveillance data on biliary pathogen profiles and antimicrobial resistance (AMR) are limited. Moreover, risk factors for multidrug resistance (MDR) in acute biliary pancreatitis (ABP) remain unclear. We retrospectively analyzed 1,377 bile culture results from patients who underwent ERCP at a tertiary care center between January 2012 and December 2023. Pathogen distribution and antimicrobial resistance trends were evaluated in the full cohort. In a predefined ABP subgroup (n = 180), risk factors for multidrug resistance (MDR) were identified using univariate and multivariable logistic regression. A total of 1,377 patients undergoing ERCP with intra-procedural bile culture were included, among whom 859 (62.4%) had positive cultures, yielding 956 non-duplicate isolates. Gram-negative bacteria predominated overall, followed by Gram-positive bacteria and fungi. Over the 12-year study period, significant temporal shifts in biliary pathogen distribution were observed, characterized by a decreasing proportion of Escherichia coli and a gradual increase in Enterococcus species. Antimicrobial resistance profiles demonstrated dynamic changes over time, including an increasing prevalence of extended-spectrum β-lactamase (ESBL)–producing Enterobacterales, whereas resistance to carbapenems remained relatively low. In the acute biliary pancreatitis (ABP) subgroup, multidrug-resistant (MDR) organisms were identified in a substantial proportion of bile culture–positive cases. This study provides long-term epidemiological insights into changes in biliary pathogen profiles and antimicrobial resistance patterns among patients undergoing ERCP. Within the ABP subgroup, several factors were found to be statistically associated with the presence of multidrug-resistant organisms. These findings highlight the potential value of integrating microbiological surveillance with individualized risk assessment to inform antimicrobial decision-making in ABP, while emphasizing that further prospective validation is required.