{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T05:57:10Z","timestamp":1790575030745,"version":"4.1.0"},"reference-count":68,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T00:00:00Z","timestamp":1790467200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T00:00:00Z","timestamp":1790467200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["MicrobiologyOpen"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Typhoid fever remains a major public health concern in South Africa. However, the role of urban waterways as environmental reservoirs and contributors to the spread of resistant\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Typhi remains poorly understood. This study characterized four\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi isolates recovered from the Jukskei River in Johannesburg, South Africa, using whole\u2010genome sequencing. Genomic DNA was extracted and sequenced on the Illumina NextSeq. 2000 platform, and assembled genomes were analyzed for sequence types (STs), AMR determinants, plasmids, virulence factors, and phylogenetic relatedness using 124 clinical\n                    <jats:italic>Salmonella<\/jats:italic>\n                    genomes for comparison. All isolates were confirmed as\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi, comprising ST1 (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009\n                    <jats:italic>2<\/jats:italic>\n                    ) and ST2 (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009\n                    <jats:italic>2<\/jats:italic>\n                    ). The ST1 isolates belonged to the H58 lineage (genotype 4.3.1.1), with isolate BRSA001 further classified as a sublineage 4.3.1.1. EA1. The ST1 isolates were multidrug\u2010resistant, carrying the IncQ1 plasmid and resistant genes, including\n                    <jats:italic>aph(6)\u2010Id<\/jats:italic>\n                    ,\n                    <jats:italic>aph(3\u2033)\u2010Ib<\/jats:italic>\n                    ,\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>TEM\u20101B<\/jats:italic>\n                    <\/jats:sub>\n                    ,\n                    <jats:italic>catA1<\/jats:italic>\n                    ,\n                    <jats:italic>sul1<\/jats:italic>\n                    ,\n                    <jats:italic>sul2<\/jats:italic>\n                    , and\n                    <jats:italic>dfrA7<\/jats:italic>\n                    . All isolates possessed mercury resistance genes (\n                    <jats:italic>merR<\/jats:italic>\n                    ,\n                    <jats:italic>merT<\/jats:italic>\n                    ,\n                    <jats:italic>merP<\/jats:italic>\n                    ,\n                    <jats:italic>merC<\/jats:italic>\n                    ), while ST1 isolates additionally harbored\n                    <jats:italic>qacE\u03941<\/jats:italic>\n                    . Ten\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Pathogenicity Islands (SPI\u20101 to SPI\u201010) were identified in ST1 isolates. Phylogenetic analysis revealed notable genetic diversity among the river isolates. All river isolates clustered tightly (\u2264\u20095 allele differences) with at least two clinical isolates, indicating shared epidemiological links and possible localized transmission. This study provides the first report of multidrug\u2010resistant H58\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi carrying\n                    <jats:italic>qacE\u03941<\/jats:italic>\n                    in South African surface water and highlights the Jukskei River as a potential environmental source of resistant\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi, reinforcing the need for strengthened One Health genomic surveillance.\n                  <\/jats:p>","DOI":"10.1002\/mbo3.70408","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T05:44:28Z","timestamp":1790574268000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Detection of Multidrug\u2010Resistant H58 ST1\n                    <i>Salmonella<\/i>\n                    Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates"],"prefix":"10.1002","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3909-4628","authenticated-orcid":false,"given":"Sanelisiwe Thinasonke","family":"Duze","sequence":"first","affiliation":[{"name":"Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Musa","family":"Marimani","sequence":"additional","affiliation":[{"name":"Department of Anatomical Pathology, Faculty of Health Science University of Witwatersrand Johannesburg South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8406-118X","authenticated-orcid":false,"given":"Mrudula","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,27]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0013067"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0012373"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.16291.2"},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","unstructured":"Ali N. 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