Genomic Detection of Multidrug‐Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates
- 1Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa
- 2Department of Anatomical Pathology, Faculty of Health Science University of Witwatersrand Johannesburg South Africa
Abstract
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.
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BibTeX
@article{duze2026genomic,
title = {{Genomic Detection of Multidrug‐Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates}},
author = {Sanelisiwe Thinasonke Duze and Musa Marimani and Mrudula Patel},
journal = {MicrobiologyOpen},
year = {2026},
month = oct,
doi = {10.1002/mbo3.70408},
url = {https://doi.org/10.1002/mbo3.70408},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genomic Detection of Multidrug‐Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates
AU - Sanelisiwe Thinasonke Duze
AU - Musa Marimani
AU - Mrudula Patel
PY - 2026
DA - 2026/10/27
JO - MicrobiologyOpen
DO - 10.1002/mbo3.70408
UR - https://doi.org/10.1002/mbo3.70408
AB - 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.
SN - 2045-8827
ER -