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Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for\n                    <jats:italic>S. sonnei<\/jats:italic>\n                    outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for\n                    <jats:italic>S. sonnei<\/jats:italic>\n                    to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse &gt;4,000\u2009\n                    <jats:italic>S. sonnei<\/jats:italic>\n                    isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant\n                    <jats:italic>S. sonnei<\/jats:italic>\n                    clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.\n                  <\/jats:p>","DOI":"10.1038\/s41467-021-22700-4","type":"journal-article","created":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T06:04:54Z","timestamp":1620713094000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":118,"title":["Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9661-5293","authenticated-orcid":false,"given":"Jane","family":"Hawkey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kalani","family":"Paranagama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate S.","family":"Baker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca J.","family":"Bengtsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9941-5799","authenticated-orcid":false,"given":"Fran\u00e7ois-Xavier","family":"Weill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4432-8505","authenticated-orcid":false,"given":"Nicholas R.","family":"Thomson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1308-5755","authenticated-orcid":false,"given":"Stephen","family":"Baker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4495-2615","authenticated-orcid":false,"given":"Louise","family":"Cerdeira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8466-7547","authenticated-orcid":false,"given":"Zamin","family":"Iqbal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Hunt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danielle J.","family":"Ingle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Dallman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Jenkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7363-6665","authenticated-orcid":false,"given":"Deborah A.","family":"Williamson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3949-2471","authenticated-orcid":false,"given":"Kathryn E.","family":"Holt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,11]]},"reference":[{"key":"22700_CR1","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1016\/S0140-6736(17)33296-8","volume":"391","author":"KL Kotloff","year":"2018","unstructured":"Kotloff, K. 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