Many surgical site infections begin with the microbiome

In a study, many infections after spine surgery were found to be bacteria that had colonized the patient’s body before hospital admission.

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A new study using genetic testing of preoperative patient microbiomes shows that most surgical-site infections that emerge after major spine surgery come from bacteria already on the patients’ bodies before they enter the hospital. 

The findings expand upon those of older, more limited studies and counter conventional thinking about the source of surgical infections.

Researchers from several departments of the University of Washington School of Medicine teamed up on the study. Using genetic tests, they found that 86% of infections in patients who had surgical implants installed in their spines started from strains of bacteria carried by the patient prior to surgery. Most of these bacteria were resistant to the antibiotic administered during the procedure.

“It really just reveals the fact that we don't have clarity in this area, particularly for an event that has such a large impact on patient outcomes,” said Dr. Dustin Long, an anesthesiologist and critical-care physician at Harborview Medical Center and the paper’s lead author. “If you look at where we currently focus our efforts and a lot of the guidelines and commercial products that are out there, it's very focused on the sterility of the hospital environment. It's certainly not patient-centered or individualized in any meaningful way.”

The study appears April 10 in Science Translational Medicine. The issue also contains an outside commentary on the study.

In contrast with reductions in other complications, infection has remained a leading adverse event after surgery. It is heavily weighted in quality measures used for public reporting and insurance reimbursement. Despite health care systems’ adherence to best practices, the rates of surgical site infection have improved little in recent decades.

“Infection is now playing an oversized role in the outcomes of patients after surgery,” Long said. “It’s a big, persistent problem with the potential to be exacerbated by increasing antibiotic resistance. Part of the reason it persists is because we don't really know where to point our efforts. For many surgical procedures, there’s just a lack of good, fundamental science on where the infections come from, how they get into the wound and how they evade all the normal stuff that we do to try to stop them.”

Long and his colleagues chose to study spinal surgery for several reasons, including its complexity and resource-heavy nature. Spine surgery also is performed on similar numbers of men and women and across their lifespans, thereby making the findings applicable to larger populations. They’re also relatively clean procedures with little cross-contamination from other bodily systems.

Site infection happens in about 1 in 30 procedures. 

“We're not talking about a really rare event,” Long said. “Avoiding infection 97% of the time may sound good, but from another perspective, if one out of 30 of your units that were going down the production line blew up with no explanation, that would be a big problem. It has a major impact on that one patient and on the health system.” 

The researchers used multiple forms of genomic analysis to gain a much more detailed look at patients’ microbiomes than previously possible. The research team examined skin, nasal and rectal samples from more than 200 patients whose procedures involved the implanting of devices, and wound-infection samples from a group of 1,400 patients who underwent various spine surgeries.

The team also was able to map areas of the body where certain bacteria tend to congregate on the skin. Staphylococci, for instance, tend to be more dense on the neck and upper back, while other bacteria like E. coli are more likely found on the lower back.

“We’ve never had a ‘map’ like this of how the bacteria that live on our skin can play a role in a surgical-site infection,” added Dr. John Lynch, medical director of Harborview's Infection Prevention and Control Program and a study coauthor. “Now we can think about how to act to prevent infections at the individual patient level based on their specific bacteria or the level of their spine surgery.”

Long worked with researchers from the UW School of Medicine departments of Medicine, Division of Allergy and Infectious Diseases; Laboratory Medicine and Pathology; Orthopaedics and Sports Medicine; Microbiology; Neurological Surgery; and the UW School of Pharmacy.

“In addition to shedding light on where these infections really originate from, this study shows how the principles of ‘personalized medicine’ can be extended to a patient’s own microbiome,” said Dr. Stephen Salipante, a clinical pathologist and director of UW Medicine’s  Microbial Interactions & Microbiome Center sequencing services, who was a senior author on the study.

Long said the findings don’t absolve hospitals from taking responsibility for infection prevention. Rather, they show the need to embrace patient-centered models of infection prevention.

“We included a statement in the paper indicating that the authorship team does not see these results as an ‘out’ for hospitals,” Long said. “This should challenge us to take responsibility for better protecting patients from themselves when entering into a vulnerable state of surgery.”

Funding for the study was provided by the National Institutes of Health, National Institute of General Medical Sciences, Anesthesiology & Perioperative Medicine Research Training Program Grant (T32GM086270), a Society for Healthcare Epidemiology of America 2019 Epi Competition Award, and a National Institutes of Health, National Institute of Arthritis and Musculoskeletal and Skin Diseases Mentored Patient-Oriented Research Career Development Award (5K23AR080209-02). 


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