Comparative study of culture, next-generation sequencing, and immunoassay for identification of pathogen in diabetic...

Treatment of deep musculoskeletal infection (MSKI) begins with accurate identification of the offending pathogen, surgical excision/debridement, and a course of culture-directed antibiotics. Despite this, the incidence of recurrent infection continues to rise. A major contributor to this is inaccurate or negative initial cultures. Accurate identification of the main pathogen is paramount to treatment success. This is especially important in treating diabetic foot infections (DFIs) with limb salvage efforts. This study seeks to utilize standard culture, next-generation sequencing (NGS), and immunoassay for newly synthesized antibodies (NSA) to Staphylococcus aureus and Streptococcus agalactiae for diagnosis. This is a level II prospective observational study approved by our IRB. Thirty patients > 18 years of age who presented with a DFI and underwent surgical debridement or amputation by a single academic orthopedic surgeon from October 2018 to September 2019 were enrolled. Intraoperative samples were obtained from the base of the wound and sent for culture, NGS, and a peripheral blood sample was obtained at the time of diagnosis. NGS and culture were highly correlated for S. aureus (κ = 0.86) and S. agalactiae (κ = 1.0), NSA immunoassay and culture demonstrated a fair correlation for S. aureus (κ = 0.18) and S. agalactiae (κ = 0.67), and NGS and NSA immunoassay demonstrated fair correlation for S. aureus (κ = 0.1667) and S. agalactiae (κ = 0.67). Our study demonstrates a high concordance between culture and NGS in identifying the dominant pathogen in DFU. NGS may be a useful adjunct in DFI diagnosis.