{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T05:00:31Z","timestamp":1775624431834,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,9,7]],"date-time":"2016-09-07T00:00:00Z","timestamp":1473206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate\u2019s ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools.<\/jats:p>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The source code and documentations are available at http:\/\/jordan.biology.gatech.edu\/page\/software\/stringMLST.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw586","type":"journal-article","created":{"date-parts":[[2016,9,8]],"date-time":"2016-09-08T00:39:31Z","timestamp":1473295171000},"page":"119-121","source":"Crossref","is-referenced-by-count":89,"title":["stringMLST: a fast k-mer based tool for multilocus sequence typing"],"prefix":"10.1093","volume":"33","author":[{"given":"Anuj","family":"Gupta","sequence":"first","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, Atlanta, GA, USA"},{"name":"Applied Bioinformatics Laboratory, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I King","family":"Jordan","sequence":"additional","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, Atlanta, GA, USA"},{"name":"Applied Bioinformatics Laboratory, Atlanta, GA, USA"},{"name":"PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lavanya","family":"Rishishwar","sequence":"additional","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, Atlanta, GA, USA"},{"name":"Applied Bioinformatics Laboratory, Atlanta, GA, USA"},{"name":"PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,7]]},"reference":[{"key":"2023020204201985100_btw586-B1","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1128\/JCM.00066-13","article-title":"Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing","volume":"51","author":"Cody","year":"2013","journal-title":"J. Clin. Microbiol"},{"key":"2023020204201985100_btw586-B2","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1128\/JCM.00133-16","article-title":"Epidemiological outbreaks of Pneumocystis jirovecii pneumonia are not limited to kidney transplant recipients: genotyping confirms common source of transmission in a liver transplantation unit","volume":"54","author":"Desoubeaux","year":"2016","journal-title":"J. Clin. Microbiol"},{"key":"2023020204201985100_btw586-B3","first-page":"282","article-title":"Notes from the field: listeriosis associated with stone fruit\u2014United States, 2014","volume":"64","author":"Jackson","year":"2015","journal-title":"MMWR Morb. Mortal. Wkly. Rep"},{"key":"2023020204201985100_btw586-B4","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1099\/ijs.0.64483-0","article-title":"DNA-DNA hybridization values and their relationship to whole-genome sequence similarities","volume":"57(Pt 1)","author":"Goris","year":"2007","journal-title":"Int. J. Syst. Evol. 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Microbiol"},{"key":"2023020204201985100_btw586-B12","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1073\/pnas.95.6.3140","article-title":"Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms","volume":"95","author":"Maiden","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020204201985100_btw586-B13","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/nrmicro3093","article-title":"MLST revisited: the gene-by-gene approach to bacterial genomics","volume":"11","author":"Maiden","year":"2013","journal-title":"Nat. Rev. Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/1\/119\/49037145\/bioinformatics_33_1_119.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/1\/119\/49037145\/bioinformatics_33_1_119.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:20:41Z","timestamp":1675311641000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/1\/119\/2525695"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,9,7]]},"references-count":13,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw586","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,1,1]]},"published":{"date-parts":[[2016,9,7]]}}}