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Patient Microbiome Most Common Source of Surgical Infections, Sequencing Study Suggests

NEW YORK – New research suggests microbes that come from a patient's own microbiome are the most common source of surgical site infections (SSI), including infections involving antibiotic-resistant bacteria.

"These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients," first and corresponding author Dustin Long, a researcher in the University of Washington School of Medicine's anesthesiology and pain medicine department, and colleagues wrote in Science Translational Medicine on Wednesday.

The team noted that SSI "remains a leading complication of surgery," prompting them to take a closer look at potential microbial sources and their ability to dodge antibiotics and antiseptic techniques that are routinely used to prevent SSIs.

For their study, the researchers obtained pre- and post-operative skin, nasal, and rectal swab samples from 204 individuals undergoing spinal surgery.

In 14 patients who went on to develop SSIs, they sequenced the genomes of microbial isolates linked to these infections. Based on those results, they enriched the microbiome samples of these patients for the pathogen of interest using a metagenomic sequencing method called GenCap-Seq. They also determined pre-operative skin microbiome patterns from patients who did not develop infections using targeted 16S ribosomal RNA gene sequencing.

"As a team of physician-scientists, we were motivated to better understand the root causes of infection in our patients, including the factors driving resistance to the prophylactic antibiotics we give on a daily basis," Long said in an email.

Together, the team's data suggested that some 86 percent of SSI cases involved bacterial strains that had originated from microbial communities found in the patient's own microbiome prior to surgery, arguing against the notion that these infections stemmed from problems with sterility protocols or microbes in the hospital environment.

When the team looked at antibiotic resistance patterns in isolates linked to SSIs, it uncovered resistance to antibiotics used prior to surgery in 59 percent of cases. The microbial "resistome" present in patients before surgery tended to track with the antimicrobial resistance (AMR) profiles found when surgical infections did occur.

"Most of these infections were resistant to the antibiotic given during surgery, and again, the antimicrobial resistance genes conferring that resistance were 'pre-loaded' in the patient microbiome," Long explained.

Such findings suggest that infection prevention approaches might be more effectively tailored to patients by understanding the microbes they carry prior to surgery, rather than turning to the same set of pre-surgical prophylactic antibiotics for all individuals.

"In addition to shedding light on where these surgical site infections really originate from, this study shows how the principles of 'personalized medicine' can be extended to a patient's own microbiome," senior author Stephen Salipante, a researcher at the University of Washington School of Medicine, said in a statement. "It should be possible to leverage information about the microorganisms carried by an individual to improve infection outcomes after a surgical procedure."