{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T22:06:08Z","timestamp":1789250768680,"version":"build-2803163510"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T00:00:00Z","timestamp":1502323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T00:00:00Z","timestamp":1502323200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u00a0antibiotic susceptibility. For monomicrobial samples in culture (n\u2009=\u20098), the presence of the pathogen was confirmed by metagenomics in all cases. For polymicrobial samples (n\u2009=\u200916), 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.<\/jats:p>","DOI":"10.1038\/s41598-017-07546-5","type":"journal-article","created":{"date-parts":[[2017,8,4]],"date-time":"2017-08-04T04:56:42Z","timestamp":1501822602000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":91,"title":["Clinical metagenomics of bone and joint infections: a proof of concept study"],"prefix":"10.1038","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1178-0298","authenticated-orcid":false,"given":"Etienne","family":"Rupp\u00e9","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir","family":"Lazarevic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myriam","family":"Girard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Mouton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tristan","family":"Ferry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Laurent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Schrenzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,8,10]]},"reference":[{"key":"7546_CR1","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.jhin.2012.04.025","volume":"82","author":"L Grammatico-Guillon","year":"2012","unstructured":"Grammatico-Guillon, L. et al. Bone and joint infections in hospitalized patients in France, 2008: clinical and economic outcomes. J. Hosp. Infect. \n                           82, 40\u201348 (2012).","journal-title":"J. Hosp. Infect."},{"key":"7546_CR2","doi-asserted-by":"crossref","unstructured":"Rupp\u00e9, E., Baud, D., Schicklin, S., Guigon, G. & Schrenzel, J. Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia. Future Microbiol. Ahead of print (2015).","DOI":"10.2217\/fmb.15.144"},{"key":"7546_CR3","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/JCM.02452-13","volume":"52","author":"H Hasman","year":"2014","unstructured":"Hasman, H. et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J. Clin. Microbiol. \n                           52, 139\u2013146 (2014).","journal-title":"J. Clin. Microbiol."},{"key":"7546_CR4","doi-asserted-by":"publisher","unstructured":"Schmidt, K. et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J. Antimicrob. Chemother, doi:10.1093\/jac\/dkw397 (2016).","DOI":"10.1093\/jac\/dkw397"},{"key":"7546_CR5","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1056\/NEJMoa1401268","volume":"370","author":"MR Wilson","year":"2014","unstructured":"Wilson, M. R. et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. \n                           370, 2408\u20132417 (2014).","journal-title":"N. Engl. J. Med."},{"key":"7546_CR6","doi-asserted-by":"publisher","first-page":"e53","DOI":"10.1093\/jpids\/piv040","volume":"4","author":"M-L Fr\u00e9mond","year":"2015","unstructured":"Fr\u00e9mond, M.-L. et al. Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis. J. Pediatr. Infect. Dis. 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Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J. Antimicrob. Chemother. \n                           68, 771\u2013777 (2013).","journal-title":"J. Antimicrob. Chemother."},{"key":"7546_CR12","doi-asserted-by":"publisher","first-page":"1182","DOI":"10.1128\/JCM.03117-13","volume":"52","author":"NC Gordon","year":"2014","unstructured":"Gordon, N. C. et al. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J. Clin. Microbiol. \n                           52, 1182\u20131191 (2014).","journal-title":"J. Clin. Microbiol."},{"key":"7546_CR13","doi-asserted-by":"publisher","first-page":"2234","DOI":"10.1093\/jac\/dkt180","volume":"68","author":"N Stoesser","year":"2013","unstructured":"Stoesser, N. et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J. Antimicrob. 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(Springer New York, 2009).","DOI":"10.1007\/978-0-387-98141-3"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-07546-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-07546-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-07546-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T03:16:12Z","timestamp":1671765372000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-07546-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,10]]},"references-count":40,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["7546"],"URL":"https:\/\/doi.org\/10.1038\/s41598-017-07546-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/090530","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,10]]},"assertion":[{"value":"21 February 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 June 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 August 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"7718"}}