Genomic Detection of Multidrug-Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates.

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 Salmonella Typhi remains poorly understood. This study characterized four S. Typhi isolates recovered from the Jukskei River in Johannesburg, South Africa, using whole-genome 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 Salmonella genomes for comparison. All isolates were confirmed as S. Typhi, comprising ST1 (n = 2) and ST2 (n = 2). 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-resistant, carrying the IncQ1 plasmid and resistant genes, including aph(6)-Id, aph(3″)-Ib, blaTEM-1B, catA1, sul1, sul2, and dfrA7. All isolates possessed mercury resistance genes (merR, merT, merP, merC), while ST1 isolates additionally harbored qacEΔ1. Ten Salmonella Pathogenicity Islands (SPI-1 to SPI-10) were identified in ST1 isolates. Phylogenetic analysis revealed notable genetic diversity among the river isolates. All river isolates clustered tightly (≤ 5 allele differences) with at least two clinical isolates, indicating shared epidemiological links and possible localized transmission. This study provides the first report of multidrug-resistant H58 S. Typhi carrying qacEΔ1 in South African surface water and highlights the Jukskei River as a potential environmental source of resistant S. Typhi, reinforcing the need for strengthened One Health genomic surveillance.