Abstract
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
,
bla
TEM‐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.