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However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present a method called \u2018genomic neighbour typing\u2019 for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    and\n                    <jats:italic>Neisseria gonorrhoeae<\/jats:italic>\n                    . We implemented this with rapid\n                    <jats:italic>k<\/jats:italic>\n                    -mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. This resulted in the determination of resistance within 10\u2009min (91% sensitivity and 100% specificity for\n                    <jats:italic>S. pneumoniae<\/jats:italic>\n                    and 81% sensitivity and 100% specificity for\n                    <jats:italic>N. gonorrhoeae<\/jats:italic>\n                    from isolates with a representative database) of starting sequencing, and within 4\u2009h of sample collection (75% sensitivity and 100% specificity for\n                    <jats:italic>S. pneumoniae<\/jats:italic>\n                    ) for clinical metagenomic sputum samples. This flexible approach has wide application for pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.\n                  <\/jats:p>","DOI":"10.1038\/s41564-019-0656-6","type":"journal-article","created":{"date-parts":[[2020,2,10]],"date-time":"2020-02-10T12:04:02Z","timestamp":1581336242000},"page":"455-464","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":109,"title":["Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing"],"prefix":"10.1038","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0200-557X","authenticated-orcid":false,"given":"Karel","family":"B\u0159inda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alanna","family":"Callendrello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin C.","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek R.","family":"MacFadden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8914-5868","authenticated-orcid":false,"given":"Themoula","family":"Charalampous","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robyn S.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Cowley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crista B.","family":"Wadsworth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5646-1314","authenticated-orcid":false,"given":"Yonatan H.","family":"Grad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5899-5424","authenticated-orcid":false,"given":"Gregory","family":"Kucherov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5412-7152","authenticated-orcid":false,"given":"Justin","family":"O\u2019Grady","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1303-5598","authenticated-orcid":false,"given":"Michael","family":"Baym","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6319-7336","authenticated-orcid":false,"given":"William P.","family":"Hanage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,2,10]]},"reference":[{"key":"656_CR1","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1097\/01.CCM.0000217961.75225.E9","volume":"34","author":"A Kumar","year":"2006","unstructured":"Kumar, A. et al. 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