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Here, we investigated the epidemiology of <jats:italic>Shigella flexneri<\/jats:italic> serotype 1b recovered during 2016\u20132018 in Ontario, to describe the prevalence and spread of AZM resistance. We found that 72.3% (47\/65) of cases were AZM\u2013resistant (AZM<jats:sup>R<\/jats:sup>), of which 95.7% (45\/47) were among males (P\u2009&lt;\u20090.001). Whole-genome based phylogenetic analysis showed three major clusters, and 56.9% of isolates grouped within a single closely-related cluster (0\u201310 \u2206SNP). A single AZM<jats:sup>R<\/jats:sup> clonal population was persistent over 3\u00a0years and involved 67.9% (36\/53) of all male cases, and none reported international travel. In 2018, a different AZM<jats:sup>R<\/jats:sup> cluster appeared among adult males not reporting travel. A proportion of isolates (10.7%) with reduced susceptibility to ciprofloxacin (CIP) due to S83L mutation in <jats:italic>gyr<\/jats:italic>A were AZM susceptible, and 71.4% reported international travel. Resistance to AZM was due to the acquisition of <jats:italic>mph<\/jats:italic> gene-bearing <jats:italic>inc<\/jats:italic>FII plasmids having\u2009&gt;\u200995% nucleotide similarity to pKSR100. Plasmid-borne resistance limiting treatment options to AZM, ceftriaxone (CRO) and CIP was noted in a single isolate. We characterized AZM<jats:sup>R<\/jats:sup> isolates circulating locally among males and found that genomic analysis can support targeted prevention and mitigation strategies against antimicrobial-resistance.<\/jats:p>","DOI":"10.1038\/s41598-023-36733-w","type":"journal-article","created":{"date-parts":[[2023,10,3]],"date-time":"2023-10-03T10:03:22Z","timestamp":1696327402000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Whole genome sequencing of increased number of azithromycin-resistant Shigella flexneri 1b isolates in Ontario"],"prefix":"10.1038","volume":"13","author":[{"given":"Alefiya","family":"Neemuchwala","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Zittermann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dean","family":"Middleton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick J.","family":"Stapleton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vithusha","family":"Ravirajan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirby","family":"Cronin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vanessa G.","family":"Allen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samir.N.","family":"Patel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,10,3]]},"reference":[{"key":"36733_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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Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: A cross-sectional study. Lancet Infect. Dis. 15, 913\u2013921. https:\/\/doi.org\/10.1016\/S1473-3099(15)00002-X (2015).","journal-title":"Lancet Infect. Dis."},{"key":"36733_CR5","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1093\/cid\/ciz005","volume":"69","author":"DJ Ingle","year":"2019","unstructured":"Ingle, D. J. et al. Co-circulation of multidrug-resistant Shigella among men who have sex with men in Australia. Clin. Infect. Dis. 69, 1535\u20131544. https:\/\/doi.org\/10.1093\/cid\/ciz005 (2019).","journal-title":"Clin. Infect. Dis."},{"key":"36733_CR6","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01057-20","author":"EI Campos-Madueno","year":"2020","unstructured":"Campos-Madueno, E. I. et al. Rapid increase of CTX-M-producing Shigella sonnei isolates in Switzerland due to spread of common plasmids and international clones. Antimicrob. 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