Cargando…
Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies
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 (...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823515/ https://www.ncbi.nlm.nih.gov/pubmed/33406597 http://dx.doi.org/10.3390/microorganisms9010097 |
_version_ | 1783639853803503616 |
---|---|
author | Noone, J. Christopher Helmersen, Karin Leegaard, Truls Michael Skråmm, Inge Aamot, Hege Vangstein |
author_facet | Noone, J. Christopher Helmersen, Karin Leegaard, Truls Michael Skråmm, Inge Aamot, Hege Vangstein |
author_sort | Noone, J. Christopher |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7823515 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-78235152021-01-24 Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies Noone, J. Christopher Helmersen, Karin Leegaard, Truls Michael Skråmm, Inge Aamot, Hege Vangstein Microorganisms Article 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. MDPI 2021-01-04 /pmc/articles/PMC7823515/ /pubmed/33406597 http://dx.doi.org/10.3390/microorganisms9010097 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Noone, J. Christopher Helmersen, Karin Leegaard, Truls Michael Skråmm, Inge Aamot, Hege Vangstein Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies |
title | Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies |
title_full | Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies |
title_fullStr | Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies |
title_full_unstemmed | Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies |
title_short | Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies |
title_sort | rapid diagnostics of orthopaedic-implant-associated infections using nanopore shotgun metagenomic sequencing on tissue biopsies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823515/ https://www.ncbi.nlm.nih.gov/pubmed/33406597 http://dx.doi.org/10.3390/microorganisms9010097 |
work_keys_str_mv | AT noonejchristopher rapiddiagnosticsoforthopaedicimplantassociatedinfectionsusingnanoporeshotgunmetagenomicsequencingontissuebiopsies AT helmersenkarin rapiddiagnosticsoforthopaedicimplantassociatedinfectionsusingnanoporeshotgunmetagenomicsequencingontissuebiopsies AT leegaardtrulsmichael rapiddiagnosticsoforthopaedicimplantassociatedinfectionsusingnanoporeshotgunmetagenomicsequencingontissuebiopsies AT skramminge rapiddiagnosticsoforthopaedicimplantassociatedinfectionsusingnanoporeshotgunmetagenomicsequencingontissuebiopsies AT aamothegevangstein rapiddiagnosticsoforthopaedicimplantassociatedinfectionsusingnanoporeshotgunmetagenomicsequencingontissuebiopsies |