Clinical metagenomics of bone and joint infections: a proof of concept study

Sci Rep. 2017 Aug 10;7(1):7718. doi: 10.1038/s41598-017-07546-5.

Abstract

Bone and joint infections (BJI) are severe infections that require a tailored and protracted antibiotic treatment. Yet, the diagnostic based on culturing samples lacks sensitivity, especially for hardly culturable bacteria. Metagenomic sequencing could potentially address those limitations. Here, we assessed the performances of metagenomic sequencing on 24 BJI samples for the identification of pathogens and the prediction of their antibiotic susceptibility. For monomicrobial samples in culture (n = 8), the presence of the pathogen was confirmed by metagenomics in all cases. For polymicrobial samples (n = 16), 32/55 bacteria (58.2%) were found at the species level (and 41/55 [74.5%] at the genus level). Conversely, 273 bacteria not found in culture were identified, 182 being possible pathogens and 91 contaminants. A correct antibiotic susceptibility could be inferred in 94.1% and 76.5% cases for monomicrobial and polymicrobial samples, respectively. Altogether, we found that clinical metagenomics applied to BJI samples is a potential tool to support conventional culture.

MeSH terms

  • Aged
  • Aged, 80 and over
  • Anti-Bacterial Agents / pharmacology
  • Anti-Bacterial Agents / therapeutic use
  • Arthritis, Infectious / diagnosis
  • Arthritis, Infectious / drug therapy
  • Arthritis, Infectious / etiology
  • Arthritis, Infectious / microbiology*
  • Computational Biology / methods
  • DNA, Bacterial
  • Drug Resistance, Bacterial
  • Female
  • Humans
  • Male
  • Metagenome
  • Metagenomics* / methods
  • Middle Aged
  • Osteitis / diagnosis
  • Osteitis / drug therapy
  • Osteitis / etiology
  • Osteitis / microbiology*
  • Proof of Concept Study
  • Treatment Outcome

Substances

  • Anti-Bacterial Agents
  • DNA, Bacterial