{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T22:41:15Z","timestamp":1789425675603,"version":"build-2803163510"},"reference-count":43,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2017,12,1]],"date-time":"2017-12-01T00:00:00Z","timestamp":1512086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2017,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. In this study, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection. We specifically evaluated the advantages of using plasmid DNA for sequencing and the value of supplementing MinION sequences with MiSeq reads for increasing assembly accuracy. Resequencing of three plasmids in a reference\n                    <jats:named-content content-type=\"genus-species\">Klebsiella pneumoniae<\/jats:named-content>\n                    isolate demonstrated \u223c99% accuracy of draft MinION-only assembly and &gt;99.9% accuracy of assembly polished with MiSeq reads. Plasmid DNA sequencing of previously uncharacterized clinical extended-spectrum \u03b2-lactamase (ESBL)-producing\n                    <jats:named-content content-type=\"genus-species\">Escherichia coli<\/jats:named-content>\n                    and\n                    <jats:named-content content-type=\"genus-species\">K. pneumoniae<\/jats:named-content>\n                    isolates using MinION allowed successful identification of antimicrobial resistance genes in the draft assembly corresponding to all classes of observed plasmid-based phenotypic resistance. Importantly, use of plasmid DNA enabled lower depth sequencing, and assemblies sufficient for full antimicrobial resistance gene annotation were obtained with as few as 2,000 to 5,000 reads, which could be acquired in 20 min of sequencing. With a MinION-only workflow that balances accuracy against turnaround time, full annotation of plasmid resistance gene content could be obtained in under 6 h from a subcultured isolate, less time than traditional phenotypic susceptibility testing.\n                  <\/jats:p>","DOI":"10.1128\/jcm.01069-17","type":"journal-article","created":{"date-parts":[[2017,10,11]],"date-time":"2017-10-11T20:40:26Z","timestamp":1507754426000},"page":"3530-3543","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":108,"title":["Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates"],"prefix":"10.1128","volume":"55","author":[{"given":"Jamie K.","family":"Lemon","sequence":"first","affiliation":[{"name":"Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel P.","family":"Khil","sequence":"additional","affiliation":[{"name":"Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen M.","family":"Frank","sequence":"additional","affiliation":[{"name":"Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Dekker","sequence":"additional","affiliation":[{"name":"Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3380"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00742-16"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3009845"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004129"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2014.11.014"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1103-0"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3103"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000118"},{"key":"e_1_3_3_10_2","article-title":"Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology","volume":"2","author":"Judge K","year":"2016","unstructured":"Judge K Hunt M Reuter S Tracey A Quail MA Parkhill J Peacock SJ . 2016. Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology. Microb Genom2:e000085.","journal-title":"Microb Genom"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0157600"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3444"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0677-2"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01121-16"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giw018"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature22401"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-015-0220-9"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00358-17"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2017.066"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature16996"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkw397"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02483-16"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-016-0137-2"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkw318"},{"key":"e_1_3_3_25_2","article-title":"Rapid resistome mapping using nanopore sequencing","volume":"45","author":"van der Helm E","year":"2017","unstructured":"van der Helm E Imamovic L Hashim Ellabaan MM van Schaik W Koza A Sommer MOA . 2017. Rapid resistome mapping using nanopore sequencing. Nucleic Acids Res45:e61.","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14515"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-016-0111-z"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.214270.116"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks261"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-016-2847-x"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.amjmed.2006.03.013"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1097\/PAT.0000000000000237"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx067"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2016.08.001"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01030-16"},{"key":"e_1_3_3_39_2","volume-title":"M100-S27","author":"CLSI","year":"2017","unstructured":"CLSI. 2017. Performance standards for antimicrobial susceptibility testing. M100-S27. Clinical and Laboratory Standards Institute, Wayne, PA."},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu555"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0849-0"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.092759.109"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01069-17","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.01069-17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T04:51:12Z","timestamp":1646455872000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.01069-17"}},"subtitle":[],"editor":[{"given":"Alexander","family":"Mellmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":43,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["10.1128\/JCM.01069-17"],"URL":"https:\/\/doi.org\/10.1128\/jcm.01069-17","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12]]},"assertion":[{"value":"2017-07-06","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-10-03","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-11-27","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}