Identification of prosthetic joint infection pathogens using a shotgun metagenomics approach

Matthew J. Thoendel, Patricio R. Jeraldo, Kerryl E. Greenwood-Quaintance, Janet Z. Yao, Nicholas Chia, Arlen D. Hanssen, Matthew P. Abdel, Robin Patel

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


Background Metagenomic shotgun sequencing has the potential to change how many infections, particularly those caused by difficult-to-culture organisms, are diagnosed. Metagenomics was used to investigate prosthetic joint infections (PJIs), where pathogen detection can be challenging. Methods Four hundred eight sonicate fluid samples generated from resected hip and knee arthroplasties were tested, including 213 from subjects with infections and 195 from subjects without infection. Samples were enriched for microbial DNA using the MolYsis basic kit, whole-genome amplified, and sequenced using Illumina HiSeq 2500 instruments. A pipeline was designed to screen out human reads and analyze remaining sequences for microbial content using the Livermore Metagenomics Analysis Toolkit and MetaPhlAn2 tools. Results When compared to sonicate fluid culture, metagenomics was able to identify known pathogens in 94.8% (109/115) of culture-positive PJIs, with additional potential pathogens detected in 9.6% (11/115). New potential pathogens were detected in 43.9% (43/98) of culture-negative PJIs, 21 of which had no other positive culture sources from which these microorganisms had been detected. Detection of microorganisms in samples from uninfected aseptic failure cases was conversely rare (7/195 [3.6%] cases). The presence of human and contaminant microbial DNA from reagents was a challenge, as previously reported. Conclusions Metagenomic shotgun sequencing is a powerful tool to identify a wide range of PJI pathogens, including difficult-to-detect pathogens in culture-negative infections.

Original languageEnglish (US)
Pages (from-to)1333-1338
Number of pages6
JournalClinical Infectious Diseases
Issue number9
StatePublished - Oct 15 2018


  • diagnosis
  • infection
  • joint
  • metagenomics
  • prosthetic

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases


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