{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T12:19:54Z","timestamp":1790079594859,"version":"4.0.1"},"reference-count":22,"publisher":"Microbiology Society","issue":"2","license":[{"start":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T00:00:00Z","timestamp":1645574400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006714-01"],"award-info":[{"award-number":["1U18 FD006714-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006593-01"],"award-info":[{"award-number":["1U18 FD006593-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006445-01"],"award-info":[{"award-number":["1U18 FD006445-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18FD006671-01"],"award-info":[{"award-number":["1U18FD006671-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006460-01"],"award-info":[{"award-number":["1U18 FD006460-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006444-01"],"award-info":[{"award-number":["1U18 FD006444-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006866-01"],"award-info":[{"award-number":["1U18 FD006866-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18FD006866-01"],"award-info":[{"award-number":["1U18FD006866-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["5U18FD006160-02"],"award-info":[{"award-number":["5U18FD006160-02"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006568-01"],"award-info":[{"award-number":["1U18 FD006568-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006859-01"],"award-info":[{"award-number":["1U18 FD006859-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18FD006714-01"],"award-info":[{"award-number":["1U18FD006714-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006719-01"],"award-info":[{"award-number":["1U18 FD006719-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000038","name":"u.s. food and drug administration","doi-asserted-by":"crossref","award":["1U18 FD006555-01"],"award-info":[{"award-number":["1U18 FD006555-01"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,23]]},"abstract":"<jats:p>\n                    There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-defined bioinformatic protocols, the technological capability to incorporate this technique for real-time surveillance and genomic epidemiology has greatly expanded. There is a need, however, to ensure that data are of high quality. The goal of this study was to assess the utility of a small benchtop sequencing platform using a multi-laboratory verification approach. Thirteen laboratories were provided the same equipment, reagents, protocols and bacterial reference strains. The Illumina DNA Prep and Nextera XT library preparation kits were compared, and 2\u00d7150\u2009bp iSeq i100 chemistry was used for sequencing. Analyses comparing the sequences produced from this study with closed genomes from the provided strains were performed using open-source programs. A detailed, step-by-step protocol is publicly available via protocols.io (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.protocols.io\/view\/iseq-bacterial-wgs-protocol-bij8kcrw\" xlink:type=\"simple\">https:\/\/www.protocols.io\/view\/iseq-bacterial-wgs-protocol-bij8kcrw<\/jats:ext-link>\n                    ). The throughput for this method is approximately 4\u20136 bacterial isolates per sequencing run (20\u201326\u2009Mb total load). The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations. The Prep method produced more consistent coverage compared to XT, and when coverage benchmarks were met, nearly all AMR, virulence and subtyping gene targets were correctly identified. Because it reduces the technical and financial barriers to generating WGS data, the iSeq platform is a viable option for small laboratories interested in genomic surveillance of microbial pathogens.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000717","type":"journal-article","created":{"date-parts":[[2022,2,3]],"date-time":"2022-02-03T14:17:36Z","timestamp":1643897856000},"source":"Crossref","is-referenced-by-count":12,"title":["Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria"],"prefix":"10.1099","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6848-0846","authenticated-orcid":false,"given":"Patrick K.","family":"Mitchell","sequence":"first","affiliation":[{"name":"Cornell University, College of Veterinary Medicine, Ithaca, NY, 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Veterinary Medicine, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shipra","family":"Mohan","sequence":"additional","affiliation":[{"name":"Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5826-3933","authenticated-orcid":false,"given":"Lijuan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Sanchez","sequence":"additional","affiliation":[{"name":"Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paula","family":"Bartlett","sequence":"additional","affiliation":[{"name":"Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary 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M.","family":"Hengesbach","sequence":"additional","affiliation":[{"name":"Michigan State University, Veterinary Diagnostic Laboratory, Lansing, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Gresch","sequence":"additional","affiliation":[{"name":"University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9102-0039","authenticated-orcid":false,"given":"Katie","family":"Wright","sequence":"additional","affiliation":[{"name":"University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1112-088X","authenticated-orcid":false,"given":"Sunil","family":"Mor","sequence":"additional","affiliation":[{"name":"University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, 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Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000717?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T16:23:37Z","timestamp":1702571017000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000717"}},"subtitle":["&lt;xhtml:span xmlns:xhtml=\"http:\/\/www.w3.org\/1999\/xhtml\" xml:lang=\"en\"&gt;This article is part of the &lt;a href=\"https:\/\/www.microbiologyresearch.org\/content\/implementation-of-genomics-in-clinical-and-public-health-microbiology\" rel=\"noopener noreferrer\" target=\"_blank\"&gt;Implementation of Genomics in Clinical and Public Health Microbiology collection&lt;\/a&gt;&amp;#160;\n&lt;\/xhtml:span&gt;"],"short-title":[],"issued":{"date-parts":[[2022,2,23]]},"references-count":22,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,2,23]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000717","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,23]]}}}