{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T16:24:08Z","timestamp":1777998248725,"version":"3.51.4"},"reference-count":24,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T00:00:00Z","timestamp":1588636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"DOI":"10.3389\/fcimb.2020.00182","type":"journal-article","created":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T04:49:46Z","timestamp":1588654186000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":28,"title":["Metagenomic Diagnosis for a Culture-Negative Sample From a Patient With Severe Pneumonia by Nanopore and Next-Generation Sequencing"],"prefix":"10.3389","volume":"10","author":[{"given":"Kaiying","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peihan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanfeng","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongbin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lang","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinhui","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tingyan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qichao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhonghong","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinying","family":"Du","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yusen","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongbin","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2020,5,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1038\/s41587-019-0156-5","article-title":"Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection","volume":"37","author":"Charalampous","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"gix120","DOI":"10.1093\/gigascience\/gix120","article-title":"SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data","volume":"7","author":"Chen","year":"2017","journal-title":"Gigascience"},{"key":"B3","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing: Twenty-Nine Informational Supplement. M100, 29th Edn","year":"2019"},{"key":"B4","doi-asserted-by":"publisher","first-page":"e0190853","DOI":"10.1371\/journal.pone.0190853","article-title":"Culture-independent analysis of liver abscess using nanopore sequencing","volume":"13","author":"Gong","year":"2018","journal-title":"PLoS ONE"},{"key":"B5","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/s13073-015-0220-9","article-title":"Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis","volume":"7","author":"Greninger","year":"2015","journal-title":"Genome Med."},{"key":"B6","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/s13073-016-0326-8","article-title":"Next-generation sequencing diagnostics of bacteremia in septic patients","volume":"8","author":"Grumaz","year":"2016","journal-title":"Genome Med."},{"key":"B7","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1001\/jama.2018.21669","article-title":"Next-generation sequencing of infectious pathogens","volume":"321","author":"Gwinn","year":"2019","journal-title":"JAMA"},{"key":"B8","doi-asserted-by":"publisher","first-page":"gkw1004","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"10","author":"Jia","year":"2016","journal-title":"Nucl. Acids Res."},{"key":"B9","doi-asserted-by":"publisher","first-page":"e104984","DOI":"10.1371\/journal.pone.0104984","article-title":"Solving the problem of comparing whole bacterial genomes across different sequencing platforms","volume":"9","author":"Kaas","year":"2014","journal-title":"PLoS ONE"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.21105\/joss.01236","article-title":"pycoQC, interactive quality control for Oxford nanopore sequencing","volume":"4","author":"Leger","year":"2019","journal-title":"JOSS"},{"key":"B13","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B14","doi-asserted-by":"publisher","first-page":"205","DOI":"10.3389\/fcimb.2018.00205","article-title":"Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing","volume":"8","author":"Li","year":"2018","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1797","DOI":"10.1128\/AAC.48.5.1797-1802.2004","article-title":"Clinical strains of Pseudomonas aeruginosa overproducing MexAB-OprM and MexXY efflux pumps simultaneously","volume":"48","author":"Llanes","year":"2004","journal-title":"Antimicrobial Agents Chemother."},{"key":"B16","doi-asserted-by":"publisher","first-page":"e00494","DOI":"10.1128\/mBio.00494-12","article-title":"Emerging infectious diseases in 2012: 20 years after the institute of medicine report","volume":"3","author":"Morens","year":"2012","journal-title":"MBio"},{"key":"B17","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1007\/s00203-016-1215-7","article-title":"Overexpression of MexAB-OprM efflux pump in carbapenem-resistant Pseudomonas aeruginosa","volume":"198","author":"Pan","year":"2016","journal-title":"Arch. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13059-018-1462-9","article-title":"From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy","volume":"19","author":"Rang","year":"2018","journal-title":"Genome Biol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1186\/s12864-018-5094-y","article-title":"Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices","volume":"19","author":"Sanderson","year":"2018","journal-title":"BMC Genom."},{"key":"B20","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1093\/jac\/dkw397","article-title":"Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing","volume":"72","author":"Schmidt","year":"2016","journal-title":"J. Antimicrobial Chemother."},{"key":"B21","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1093\/cid\/cix881","article-title":"Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases","volume":"66","author":"Simner","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"B22","doi-asserted-by":"publisher","first-page":"e00197","DOI":"10.1128\/JCM.00197-18","article-title":"Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes","volume":"56","author":"Wick","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map (SAM) format and SAMtools","volume":"25","author":"Wysoker","year":"2009","journal-title":"Bioinformatics"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1038\/nmeth.4432","article-title":"MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads","volume":"14","author":"Xiao","year":"2017","journal-title":"Nat. Methods"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fcimb.2020.00182\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T04:49:49Z","timestamp":1588654189000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fcimb.2020.00182\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,5]]},"references-count":24,"alternative-id":["10.3389\/fcimb.2020.00182"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2020.00182","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,5]]},"article-number":"182"}}