Abstract
Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diagnostic protocol with regard to (a) pathogen identification, (b) time to pathogen identification, and (c) identification of antimicrobial resistance (AMR). This prospective proof-of-concept study included soft tissue biopsies from 32 patients with OIAIs undergoing first revision surgery at Akershus University Hospital, Norway. The biopsies were divided into two segments. Nanopore shotgun metagenomic sequencing and pathogen and antimicrobial resistance gene identification using the EPI2ME analysis platform (Oxford Nanopore Technologies) were performed on one segment. Conventional culture-based diagnostics were performed on the other. Microbial identification matched in 23/32 OIAI patients (72%). Sequencing detected additional microbes in 9/32 patients. Pathogens detected by culturing were identified by sequencing within a median of 1 h of sequencing start [range 1–18 h]. Phenotypic AMR was explained by the detection of resistance genes in 11/23 patients (48%). Diagnostics of OIAIs using shotgun metagenomics sequencing are possible within 24 h from biopsy using nanopore technology. Sequencing outperformed culturing with respect to speed and pathogen detection where pathogens were at sufficient concentration, whereas culture-based methods had an advantage at lower pathogen concentrations. Sequencing-based AMR detection may not yet be a suitable replacement for culture-based antibiotic susceptibility testing.
Highlights
Introduction nal affiliationsOrthopaedic-implant-associated infections (OIAIs) are associated with a fivefold increased risk of 30-days to one-year mortality compared to aseptic implant failures [1]
Results of all cultivation and shotgun metagenomic sequencing are detailed in the Supplementary
(blaTEM-4 ), and 57% (APH(30 )-Ia(3)) of patients and controls. This proof-of-concept study demonstrates that rapid diagnostics of orthopaedic-implant-associated infections (OIAIs) using nanopore shotgun metagenomic sequencing on tissue biopsies are possible
Summary
Orthopaedic-implant-associated infections (OIAIs) are associated with a fivefold increased risk of 30-days to one-year mortality compared to aseptic implant failures [1]. Late and/or poorly targeted OIAI treatment can, in addition, lead to selection for antimicrobialresistant bacterial strains, need of revision surgery, removal of the implant device, and loss of functionality [2,3]. Conventional culture-based diagnostic methods are comprehensive and often require several days to diagnose an OIAI. Detection is dependent on cultivating microbes, occasionally requiring growth conditions not reproduced in a laboratory setting. Culture-based methods are, impracticable for expedient routine diagnostics, extending the time to microbial identification and recommended targeted treatment [4,5].
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