{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T07:44:11Z","timestamp":1778571851078,"version":"3.51.4"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,18]],"date-time":"2022-10-18T00:00:00Z","timestamp":1666051200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFA1202500"],"award-info":[{"award-number":["2021YFA1202500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science, Technology and Innovation Commission of Shenzhen Municipality of Basic Research Funds","award":["JCYJ20180302144721183"],"award-info":[{"award-number":["JCYJ20180302144721183"]}]},{"name":"Guangdong Natural Science Foundation for Distinguished Young Scholar","award":["2020B1515020003"],"award-info":[{"award-number":["2020B1515020003"]}]},{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology","award":["ZDSYS20200811"],"award-info":[{"award-number":["ZDSYS20200811"]}]},{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology","award":["144002008"],"award-info":[{"award-number":["144002008"]}]},{"name":"Shenzhen Science and Technology Program","award":["KQTD20 200909113758004"],"award-info":[{"award-number":["KQTD20 200909113758004"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42007216"],"award-info":[{"award-number":["42007216"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Metagenomic sequencing analysis (mNGS) has been implemented as an alternative approach for pathogen diagnosis in recent years, which is independent of cultivation and is able to identify all potential antibiotic resistance genes (ARGs). However, current mNGS methods have to deal with low amounts of prokaryotic deoxyribonucleic acid (DNA) and high amounts of host DNA in clinical samples, which significantly decrease the overall microbial detection resolution. The recently released nanopore adaptive sampling (NAS) technology facilitates immediate mapping of individual nucleotides to a given reference as each molecule is sequenced. User-defined thresholds allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. We developed a metagenomics workflow for ultra-sensitive diagnosis of bacterial pathogens and ARGs from clinical samples, which is based on the efficient selective \u2018human host depletion\u2019 NAS sequencing, real-time species identification and species-specific resistance gene prediction. Our method increased the microbial sequence yield at least 8-fold in all 21 sequenced clinical Bronchoalveolar Lavage Fluid (BALF) samples (4.5\u00a0h from sample to result) and accurately detected the ARGs at species level. The species-level positive percent agreement between metagenomic sequencing and laboratory culturing was 100% (16\/16) and negative percent agreement was 100% (5\/5) in our approach. Further work is required for a more robust validation of our approach with large sample size to allow its application to other infection types.<\/jats:p>","DOI":"10.1093\/bib\/bbac453","type":"journal-article","created":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T16:54:49Z","timestamp":1664902489000},"source":"Crossref","is-referenced-by-count":43,"title":["A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method"],"prefix":"10.1093","volume":"23","author":[{"given":"Hang","family":"Cheng","sequence":"first","affiliation":[{"name":"School of Medicine, Southern University of Science and Technology of China , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuhong","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Environmental Science & Engineering, Southern University of Science and Technology of China , Shenzhen 518055, 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518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuxin","family":"Qu","sequence":"additional","affiliation":[{"name":"Third People\u2019s Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Liu","sequence":"additional","affiliation":[{"name":"Third People\u2019s Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2362-0128","authenticated-orcid":false,"given":"Liang","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Medicine, Southern University of Science and Technology of China , Shenzhen 518055, 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