Microbiology and Antimicrobial Resistance of Surgical Site Infection After Inflammatory Bowel Disease Surgery: Prophylaxis–Spectrum Discordance in a Retrospective Cohort from Saudi Arabia

Background/Objectives: Surgical site infection (SSI) after surgery for inflammatory bowel disease (IBD) has not been described microbiologically in the Arabian Peninsula, where extended-spectrum beta-lactamase (ESBL) prevalence is high and prophylaxis remains largely cephalosporin-based. We described the microbiology of SSI after IBD surgery and the extent to which recovered microorganisms were expected to be covered by the prophylaxis administered. Methods: We retrospectively studied consecutive gastrointestinal operations for IBD at a tertiary center in Jeddah, Saudi Arabia (April 2014 to November 2025). Of 118 eligible operations, 8 performed through a dirty/infected wound were reported separately, leaving a primary cohort of 110 operations in 91 patients. The primary outcome was deep incisional or organ/space SSI by CDC/NHSN criteria; models used cluster-robust standard errors for repeated operations. The microbiological analysis was exploratory. Results: SSI followed 33 of 110 operations (30.0%; 95% CI 22.2–39.1), of which 22 (66.7%) were deep or organ/space. Cultures were positive in 23 of 33 infections; because specimens were obtained at clinician discretion, microbiological estimates apply to this subset only. An acquired resistance phenotype was recorded in 10 of 23 (43.5%): ESBL-producing Enterobacterales in 8 and methicillin-resistant Staphylococcus aureus in 2. All operations received prophylaxis within 60 minutes of incision, but five regimens were in use. Expected non-coverage of at least one isolate, assigned from recorded phenotype and intrinsic resistance, was present in 7 of 11 culture-positive infections after cephalosporin-based prophylaxis (63.6%; 95% CI 35.4–84.8) and 0 of 12 after broader-spectrum regimens, with 5 indeterminate. Low preoperative serum albumin and absence of IBD-directed therapy were associated with deep infection after adjustment; emergent surgery was not, although it was in a sensitivity analysis that included the dirty/infected operations. Conclusions: These findings describe prophylaxis–spectrum discordance and support microbiological surveillance and locally informed review of prophylaxis policy rather than empirical broadening.