{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T16:07:12Z","timestamp":1789142832819,"version":"build-2803163510"},"reference-count":53,"publisher":"Microbiology Society","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["206545\/Z\/17\/Z"],"award-info":[{"award-number":["206545\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,11]]},"abstract":"<jats:p>\n                    Antimicrobial resistance (AMR) in\n                    <jats:italic>Shigella<\/jats:italic>\n                    is rising globally, complicating shigellosis management. Whole-genome sequence analysis (WGSA) has advanced our understanding of AMR and transmission dynamics, yet contemporary whole-genome sequencing data from\n                    <jats:italic>Shigella<\/jats:italic>\n                    in sub-Saharan Africa remain scarce. In this study, we applied WGSA to 27\n                    <jats:italic>Shigella<\/jats:italic>\n                    isolates collected from children presenting with diarrhoea at Ndirande Health Centre in Malawi (2022\u20132023), as part of the Enterics for Global Health\n                    <jats:italic>Shigella<\/jats:italic>\n                    surveillance study. Serotyping, AMR profiling and phylogenetic analysis revealed\n                    <jats:italic>Shigella sonnei<\/jats:italic>\n                    as the dominant serogroup, with distinct genetic clustering relative to global reference strains among\n                    <jats:italic>S. sonnei<\/jats:italic>\n                    ,\n                    <jats:italic>Shigella flexneri<\/jats:italic>\n                    and\n                    <jats:italic>Shigella boydii<\/jats:italic>\n                    . We identified 16 AMR genes linked to ten antimicrobial classes with\n                    <jats:italic>qnrS1<\/jats:italic>\n                    and\n                    <jats:italic>qnrB19<\/jats:italic>\n                    genes conferring resistance to fluoroquinolone, alongside IncFIB(K) and IncFII plasmid replicon markers. Importantly, no azithromycin resistance determinants were detected both genotypically and phenotypically, providing baseline evidence that warrants continued surveillance of current first-line treatment. However, the detection of fluoroquinolone resistance genes with plasmid replicon markers in the absence of phenotypic resistance might indicate a silent reservoir with epidemic potential. This is the first contemporary\n                    <jats:italic>Shigella<\/jats:italic>\n                    data from a large-scale diarrhoea disease surveillance study in Malawi, providing essential baseline information for guiding antibiotic treatment and future vaccine development efforts, contributing to the efforts to combat shigellosis in Malawi and other similar regions.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001838","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T15:16:21Z","timestamp":1789139781000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic epidemiology and antimicrobial resistance profile of Shigella isolated from diarrhoea diseases in under-five children in Blantyre, Malawi"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8914-8874","authenticated-orcid":false,"given":"Grace Thandekire","family":"Sibande","sequence":"first","affiliation":[{"name":"Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte E.","family":"Chong","sequence":"additional","affiliation":[{"name":"Department of Genetics, Applied Microbial Genomics Laboratory, University of Cambridge, Cambridge, UK"},{"name":"Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anmol","family":"Kiran","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Western Rd, Cork, T12 CY82, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Belson","family":"Kutambe","sequence":"additional","affiliation":[{"name":"Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Charles","sequence":"additional","affiliation":[{"name":"Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Maiden","sequence":"additional","affiliation":[{"name":"Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate S.","family":"Baker","sequence":"additional","affiliation":[{"name":"Department of Genetics, Applied Microbial Genomics Laboratory, University of Cambridge, Cambridge, UK"},{"name":"Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Cornick","sequence":"additional","affiliation":[{"name":"Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK"},{"name":"Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(16)31529-X"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30475-4"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30401-3"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiad252"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)33296-8"},{"key":"R6","article-title":"Guidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1. 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