Detection of Prevotella species in anaerobic culture-negative multiple abscesses using next-generation sequencing

Next-generation metagenomic sequencing (mNGS) provides a comprehensive analysis of DNA and RNA in samples. In this case report, pus specimens were collected from an 86-year-old male with multiple muscle, periarticular, and bone abscesses, and osteomyelitis, without prior antimicrobial therapy. Results of bacterial culture tests, including anaerobic and intensified cultures, were negative. Despite this, mNGS using shotgun sequencing revealed a significant number of DNA and RNA nucleic acid reads from Prevotella spp. Although the subspecies could not be identified, mNGS allowed the selection of an appropriate antimicrobial agent and suggested significant oral contamination as the portal of entry. In summary, mNGS helped identify the causative organism in a case without prior antimicrobial therapy wherein culture test results were negative.