Surgical Site Infections and the Microbiome: Understanding the Pathogenesis of Surgical Site Infections

Surgical Site Infections and the Microbiome: Understanding the Pathogenesis of Surgical Site Infections

This is a prospective, observational study of patients undergoing open GI surgery. At the time of operation, samples will be collected from the incision site and GI tract. The study will follow patients up to 30 days postoperatively, monitoring for signs of SSI. Samples will be taken from all patients who develop SSI. Sequencing will be performed on a subset of samples based on our specific aims.

• Aim 1: conduct a case-control study of patients with SSI and age-, sex-, diagnosis-, and wound class-matched control patients without SSI, comparing microbiome alpha diversity and community composition with 16S RNA sequencing to determine the association with SSI.
• Aim 2: identify the strain of bacteria isolated from SSIs using shotgun metagenomic sequencing and determine whether the specific strain was present in the skin and gut at the time of operation.

Inclusion Criteria:

• We will include adult patients (age ≥ 18 years)
• Undergoing open abdominal surgery during the study period.
• Open abdominal surgery will include any abdominal procedure entering the peritoneal cavity through a midline incision with a skin incision that is 5cm or greater.

Exclusion Criteria:

• Patients with planned minimally invasive surgery including laparoscopic or robotic surgery as these patients have lower rates of surgical site infections (SSIs). Patients who have a laparoscopic or robotic surgery converted to open surgery will be excluded.
• Appendectomy and cholecystectomy as these patients have lower risk of SSI.
• Vascular, gynecological, obstetric, urological or transplantation.
• Trauma patients.
• Patients without source control at the index operation including those with an open abdomen, no fascial closure, or temporary abdominal closure device (such as abthera dressing).
• Pediatric patients (age<18 years).
• Patients who decline swab/specimen collection.