{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T16:24:38Z","timestamp":1791390278548,"version":"4.3.3"},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2024,11,12]],"date-time":"2024-11-12T00:00:00Z","timestamp":1731369600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>Shigellosis is an acute gastroenteritis infection and one of Ethiopia\u2019s most common causes of morbidity and mortality, especially in children under five. Antimicrobial resistance (AMR) has spread quickly among <jats:italic>Shigella<\/jats:italic> species due to inappropriate antibiotic use, inadequacies of diagnostic facilities, and unhygienic conditions. This study aimed to characterize <jats:italic>Shigella sonnei (S<\/jats:italic>. <jats:italic>sonnei)<\/jats:italic> using whole genome sequence (WGS) analysis in Addis Ababa, Ethiopia.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>The raw reads were quality-filtered and trimmed, and a minimum length of 50bp was retained and taxonomically classified using MiniKraken version 1. The whole genome data were aligned with Antibiotic Resistance Gene (ARG) sequences of the Comprehensive Antibiotic Resistance Database (CARD) by Resistance Gene Identifier (RGI). Plasmids were analyzed using the PlasmidFinder tool version 2.1. Additionally, AMR and virulence genes were screened at the Centre for Genomic Epidemiology (CGE) web-based server.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Results<\/jats:title>\n<jats:p>All isolates in our investigation contained genes encoding <jats:italic>blaEC-8<\/jats:italic> and <jats:italic>blaZEG-1<\/jats:italic>. Here, 60.7% of the isolates were phenotypically sensitive to cefoxitin among the <jats:italic>blaEC-8<\/jats:italic> genes detected in the genotyping analysis, whereas all isolates were completely resistant to amoxicillin and erythromycin phenotypically. The study also identified genes that conferred resistance to trimethoprim (dfrA). Plasmid <jats:italic>Col156<\/jats:italic> and <jats:italic>Col (BS512)<\/jats:italic> types were found in all isolates, while <jats:italic>IncFII<\/jats:italic> and <jats:italic>Col (MG828)<\/jats:italic> plasmids were only identified in one isolate.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>This study found that many resistant genes were present, confirming the high variety in <jats:italic>S<\/jats:italic>. <jats:italic>sonnei<\/jats:italic> strains and hence a divergence in phylogenetic relationships. Thus, combining WGS methods for AMR prediction and strain identification into active surveillance may be beneficial for monitoring the spread of AMR in <jats:italic>S<\/jats:italic>. <jats:italic>sonnei<\/jats:italic> and detecting the potential emergence of novel variations.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0313310","type":"journal-article","created":{"date-parts":[[2024,11,12]],"date-time":"2024-11-12T18:28:53Z","timestamp":1731436133000},"page":"e0313310","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Whole genome sequencing and antimicrobial resistance among clinical isolates of Shigella sonnei in Addis Ababa, Ethiopia"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2281-7858","authenticated-orcid":true,"given":"Basha","family":"Ayele","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adane","family":"Mihret","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeleke","family":"Mekonnen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tesfaye","family":"Sisay Tessema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kalkidan","family":"Melaku","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maeruf Fetu","family":"Nassir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abaysew","family":"Ayele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dawit Hailu","family":"Alemayehu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Getenet","family":"Beyene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,11,12]]},"reference":[{"key":"pone.0313310.ref001","doi-asserted-by":"crossref","first-page":"S76","DOI":"10.1016\/j.vaccine.2022.12.037","article-title":"Vaccine value profile for Shigella","volume":"41","author":"WP Hausdorff","year":"2023","journal-title":"Vaccine"},{"issue":"31","key":"pone.0313310.ref002","doi-asserted-by":"crossref","first-page":"4792","DOI":"10.1016\/j.vaccine.2020.01.054","article-title":"Meeting Report: WHO Workshop on modelling global mortality and aetiology estimates of enteric pathogens in children under five. 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