{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T23:40:00Z","timestamp":1785368400789,"version":"3.55.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T00:00:00Z","timestamp":1684713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011417","name":"UK Clinical Research Collaboration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011417","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Translation"},{"name":"Infection Research Initiative Consortium","award":["G0901608"],"award-info":[{"award-number":["G0901608"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health challenge. Limitations to AMR surveillance reporting, alongside reduction in culture-based susceptibility testing, has resulted in a need for rapid diagnostics and strain detection. We investigated Nanopore sequencing time, and depth, to accurately identify closely related N. gonorrhoeae isolates, compared to Illumina sequencing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>N. gonorrhoeae strains collected from a London sexual health clinic were cultured and sequenced with MiSeq and MinION sequencing platforms. Accuracy was determined by comparing variant calls at 68 nucleotide positions (37 resistance-associated markers). Accuracy at varying MinION sequencing depths was determined through retrospective time-stamped read analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Of 22 MinION-MiSeq pairs reaching sufficient sequencing depth, agreement of variant call positions passing quality control criteria was 185\/185 (100%; 95% confidence interval [CI], 98.0%\u2013100.0%), 502\/503 (99.8%; 95% CI, 98.9%\u201399.9%), and 564\/565 (99.8%; 95% CI, 99.0%\u2013100.0%) at 10x, 30x, and 40x MinION depth, respectively. Isolates identified as closely related by MiSeq, within one yearly evolutionary distance of \u22645 single nucleotide polymorphisms, were accurately identified via MinION.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Nanopore sequencing shows utility as a rapid surveillance tool, identifying closely related N. gonorrhoeae strains, with just 10x sequencing depth, taking a median time of 29 minutes. This highlights its potential for tracking local transmission and AMR markers.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/infdis\/jiad170","type":"journal-article","created":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T22:02:21Z","timestamp":1684792941000},"page":"1179-1188","source":"Crossref","is-referenced-by-count":6,"title":["Time Required for Nanopore Whole-Genome Sequencing of <i>Neisseria gonorrhoeae<\/i> for Identification of Phylogenetic Relationships"],"prefix":"10.1093","volume":"228","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6453-0129","authenticated-orcid":false,"given":"Laura T","family":"Phillips","sequence":"first","affiliation":[{"name":"Institute for Infection and Immunity, St George\u2019s University of London , London , United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam A","family":"Witney","sequence":"additional","affiliation":[{"name":"Institute for Infection and Immunity, St George\u2019s University of London , London , United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martina","family":"Furegato","sequence":"additional","affiliation":[{"name":"Institute for Infection and Immunity, St George\u2019s University of London , London , United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken G","family":"Laing","sequence":"additional","affiliation":[{"name":"Institute for Infection and Immunity, St George\u2019s University of London , London , United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liqing","family":"Zhou","sequence":"additional","affiliation":[{"name":"Institute for Infection and Immunity, St George\u2019s University of London , London , United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S Tariq","family":"Sadiq","sequence":"additional","affiliation":[{"name":"Institute for Infection and Immunity, St George\u2019s University of London , London , United Kingdom"},{"name":"Infection Clinical Academic Group, St George's University Hospitals NHS Trust , London , United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,22]]},"reference":[{"key":"2023110719195505200_jiad170-B1","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1071\/SH19023","article-title":"World health organization global gonococcal antimicrobial surveillance program (WHO GASP): review of new data and evidence to inform international collaborative actions and research efforts","volume":"16","author":"Unemo","year":"2019","journal-title":"Sex Health"},{"key":"2023110719195505200_jiad170-B2","volume-title":"Global action plan to control the spread and impact of antimicrobial resistance in Neisseria gonorrhoeae","author":"World Health Organization","year":"2012"},{"key":"2023110719195505200_jiad170-B3","doi-asserted-by":"crossref","first-page":"e1002344","DOI":"10.1371\/journal.pmed.1002344","article-title":"Antimicrobial resistance in Neisseria gonorrhoeae: global surveillance and a call for international collaborative action","volume":"14","author":"Wi","year":"2017","journal-title":"PLoS Med"},{"key":"2023110719195505200_jiad170-B4","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/s41572-019-0128-6","article-title":"Gonorrhoea","volume":"5","author":"Unemo","year":"2019","journal-title":"Nat Rev Dis Primers"},{"key":"2023110719195505200_jiad170-B5","volume-title":"Antimicrobial resistance in Neisseria gonorrhoeae in England and Wales. Key findings from the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP 2020)","author":"UK Health Security Agency (UKHSA)","year":"2021"},{"key":"2023110719195505200_jiad170-B6","first-page":"S47","article-title":"Strengthening global surveillance for antimicrobial drug-resistant Neisseria gonorrhoeae through the enhanced gonococcal antimicrobial surveillance program","volume":"23","author":"Weston","year":"2017","journal-title":"Emerg Infect Dis"},{"key":"2023110719195505200_jiad170-B7","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1128\/CMR.00010-14","article-title":"Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future","volume":"27","author":"Unemo","year":"2014","journal-title":"Clin Microbiol"},{"key":"2023110719195505200_jiad170-B8","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.2217\/fmb.12.117","article-title":"Emergence of multidrug-resistant, extensively drug-resistant and untreatable 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