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Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent

Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed o...

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Autores principales: Ponraj, Diana Salomi, Lund, Michael, Lange, Jeppe, Poehlein, Anja, Himmelbach, Axel, Falstie-Jensen, Thomas, Jørgensen, Nis Pedersen, Ravn, Christen, Brüggemann, Holger
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10229904/
https://www.ncbi.nlm.nih.gov/pubmed/37265503
http://dx.doi.org/10.3389/fcimb.2023.1165017
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author Ponraj, Diana Salomi
Lund, Michael
Lange, Jeppe
Poehlein, Anja
Himmelbach, Axel
Falstie-Jensen, Thomas
Jørgensen, Nis Pedersen
Ravn, Christen
Brüggemann, Holger
author_facet Ponraj, Diana Salomi
Lund, Michael
Lange, Jeppe
Poehlein, Anja
Himmelbach, Axel
Falstie-Jensen, Thomas
Jørgensen, Nis Pedersen
Ravn, Christen
Brüggemann, Holger
author_sort Ponraj, Diana Salomi
collection PubMed
description Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.
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spelling pubmed-102299042023-06-01 Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent Ponraj, Diana Salomi Lund, Michael Lange, Jeppe Poehlein, Anja Himmelbach, Axel Falstie-Jensen, Thomas Jørgensen, Nis Pedersen Ravn, Christen Brüggemann, Holger Front Cell Infect Microbiol Cellular and Infection Microbiology Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria. Frontiers Media S.A. 2023-05-17 /pmc/articles/PMC10229904/ /pubmed/37265503 http://dx.doi.org/10.3389/fcimb.2023.1165017 Text en Copyright © 2023 Ponraj, Lund, Lange, Poehlein, Himmelbach, Falstie-Jensen, Jørgensen, Ravn and Brüggemann https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Ponraj, Diana Salomi
Lund, Michael
Lange, Jeppe
Poehlein, Anja
Himmelbach, Axel
Falstie-Jensen, Thomas
Jørgensen, Nis Pedersen
Ravn, Christen
Brüggemann, Holger
Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
title Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
title_full Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
title_fullStr Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
title_full_unstemmed Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
title_short Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent
title_sort shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with cutibacterium acnes as suspected causative agent
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10229904/
https://www.ncbi.nlm.nih.gov/pubmed/37265503
http://dx.doi.org/10.3389/fcimb.2023.1165017
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