20 Origins of microorganisms responsible for surgical site infection following surgery for intestinal failure

Aim Surgical site infection (SSI) is the most common complication following colorectal surgery with the incidence following surgery for intestinal failure (IF) exceeding 50%. SSI is associated with a range of patient morbidity and a 200% increase in associated costs. The role of individual strains of bacteria in the pathogenesis of SSI remains uncertain. Next-generation whole-genome sequencing (WGS) and detailed bioinformatic analyses allow advanced microbial tracking with strain-level detail. A retrospective analysis in our centre previously identified Enterococcus faecium (EF), Escherichia coli (EC) and Staphylococcus aureus (SA) as the most frequent organisms isolated from SSI samples following surgery for IF. The aim of this study was to test the hypothesis that SSI following surgery for IF results from strains of EF, EC and SA originating from the patient’s commensal microbiota. Methods We conducted a prospective, observational, cohort study of adult patients scheduled to undergo elective surgery for treatment of IF or enterocutaneous fistula (ECF) at a single quaternary referral centre between January and October 2022. Swabs were collected from each patient’s nose, mouth, skin, fistula, stoma and vascular access device preoperatively. An intraoperative fascial swab was collected prior to skin closure. Patients were followed assiduously for the development of SSI, diagnosed according to the Centre for Disease Control criteria. Samples were cultured for EF, EC and SA based on presumptive identification with mass spectrometry. Isolates were cryogenically frozen and processed for Illumina sequencing. Bioinformatic analysis included identification of genes predicted to encode virulence factors (VF) and antimicrobial resistance (AMR) genes. Results Twenty-one patients were recruited with a median age of 51.5. The most frequent aetiology of IF was surgical complications (9/21) followed by inflammatory bowel disease (7/21). 71% had an ECF and 14% underwent a concomitant abdominal wall reconstruction. The SSI rate was 71%. 161 swabs were collected from which 49 pure isolates were recovered for sequencing. Species identification by WGS was superior to laboratory mass spectrometry with 6 of the 49 pure isolates confirmed as species other than EF, EC or SA on species-level (kmer-based) analysis. In three patients, identical strains of EC and EF were found preoperatively across anatomical sites. However, no exact matches were found between patients or between preoperative, intraoperative or infective strains. EC SSI isolates were predicted to encode 48% more VFs than those recovered from preoperative samples (mean 35.4 versus 24.0 per isolate). The mean number of AMR genes predicted from the preoperative, intraoperative and postoperative isolates was 41, 29 and 43, respectively. EC isolates were predicted to encode the greatest number of AMR genes on average (58), followed by Klebsiella pneumoniae (37), Enterococcus faecalis (23), SA (20) and EF (15). Conclusions This is the most detailed analysis of SSI organisms following gastrointestinal surgery to date. Strains of EC, EF, SA and other species that are genetically distinct from patient’s commensal organisms emerge during infection of the surgical site. These strains display enhanced virulence and AMR potential. WGS allows superior characterisation of pathogenic strains involved in SSI compared to standard laboratory techniques.