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

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....

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Autores principales:	Etienne Ruppé, Vladimir Lazarevic, Myriam Girard, William Mouton, Tristan Ferry, Frédéric Laurent, Jacques Schrenzel
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4bfd5991582e4acbb10ebd7995263959
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spelling	oai:doaj.org-article:4bfd5991582e4acbb10ebd79952639592021-12-02T12:30:26ZClinical metagenomics of bone and joint infections: a proof of concept study10.1038/s41598-017-07546-52045-2322https://doaj.org/article/4bfd5991582e4acbb10ebd79952639592017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07546-5https://doaj.org/toc/2045-2322Abstract 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.Etienne RuppéVladimir LazarevicMyriam GirardWilliam MoutonTristan FerryFrédéric LaurentJacques SchrenzelNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Etienne Ruppé Vladimir Lazarevic Myriam Girard William Mouton Tristan Ferry Frédéric Laurent Jacques Schrenzel Clinical metagenomics of bone and joint infections: a proof of concept study
description	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.
format	article
author	Etienne Ruppé Vladimir Lazarevic Myriam Girard William Mouton Tristan Ferry Frédéric Laurent Jacques Schrenzel
author_facet	Etienne Ruppé Vladimir Lazarevic Myriam Girard William Mouton Tristan Ferry Frédéric Laurent Jacques Schrenzel
author_sort	Etienne Ruppé
title	Clinical metagenomics of bone and joint infections: a proof of concept study
title_short	Clinical metagenomics of bone and joint infections: a proof of concept study
title_full	Clinical metagenomics of bone and joint infections: a proof of concept study
title_fullStr	Clinical metagenomics of bone and joint infections: a proof of concept study
title_full_unstemmed	Clinical metagenomics of bone and joint infections: a proof of concept study
title_sort	clinical metagenomics of bone and joint infections: a proof of concept study
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/4bfd5991582e4acbb10ebd7995263959
work_keys_str_mv	AT etienneruppe clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy AT vladimirlazarevic clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy AT myriamgirard clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy AT williammouton clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy AT tristanferry clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy AT fredericlaurent clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy AT jacquesschrenzel clinicalmetagenomicsofboneandjointinfectionsaproofofconceptstudy
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Clinical metagenomics of bone and joint infections: a proof of concept study

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