Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery

Author:

Long Dustin R.1ORCID,Bryson-Cahn Chloe2,Waalkes Adam3ORCID,Holmes Elizabeth A.3ORCID,Penewit Kelsi3ORCID,Tavolaro Celeste4ORCID,Bellabarba Carlo4ORCID,Zhang Fangyi45,Chan Jeannie D.26,Fang Ferric C.378ORCID,Lynch John B.2ORCID,Salipante Stephen J.3ORCID

Affiliation:

1. Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.

2. Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.

3. Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA.

4. Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.

5. Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA.

6. Department of Pharmacy, Harborview Medical Center, University of Washington School of Pharmacy, Seattle, WA 98104, USA.

7. Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA.

8. Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA 98104, USA.

Abstract

Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient’s preoperative resistome ( P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.

Publisher

American Association for the Advancement of Science (AAAS)

Reference79 articles.

1. Costs Associated With Surgical Site Infections in Veterans Affairs Hospitals

2. Agency for Healthcare Research and Quality AHRQ National Scorecard on Hospital-Acquired Conditions Final Results for 2014 Through 2017 (Agency for Healthcare Research and Quality 2020); www.ahrq.gov/sites/default/files/wysiwyg/professionals/quality-patient-safety/pfp/Updated-hacreportFInal2017data.pdf.

3. Centers for Disease Control and Prevention 2021 National and State Healthcare-Associated Infections Progress Report (CDC 2022); www.cdc.gov/hai/data/portal/progress-report.html.

4. National Healthcare Safety Network Surgical Site Infection Event (SSI) (CDC 2023); www.cdc.gov/nhsn/pdfs/pscmanual/9pscssicurrent.pdf.

5. Surgical Site Infection Prevention

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