Genetic diversity and antimicrobial resistance profiles of Salmonella enterica in the broiler supply chain in Harare, Zimbabwe: tracking transmission from farm to table

<i>Salmonella enterica</i> is a significant zoonotic pathogen, posing a serious public health threat through its presence in the food supply chain, particularly in poultry production facilities. This study aimed to investigate the genetic diversity, antimicrobial resistance (AMR) profiles and phylogenetic relationships of <i>S. enterica</i> serovars isolated from various stages of the broiler supply chain in Harare, Zimbabwe. Whole-genome sequencing was employed to analyse 28 <i>Salmonella</i> isolates from broiler farms, slaughter facilities and retail markets. The overall prevalence of <i>Salmonella</i> was 5.1% out of 552 samples tested. Contamination rates were higher at slaughter facilities, where 11% of 100 samples tested positive and at retail markets, where 20% of 20 samples were contaminated. In contrast, farms had a significantly lower prevalence, with only 3.0% of 432 samples showing <i>Salmonella</i> presence. Eight serovars were identified, with <i>S. enterica</i> subsp. <i>enterica</i> serovar Typhimurium being the most prevalent at 27.6%. Notably, 34.5% of the isolates harboured resistance genes, including <i>fosA3</i>, <i>fosA7.2</i> and <i>qnrB19</i>, and exhibited mutations in the <i>gyrA</i> and <i>parC</i> regions. An extended-spectrum beta-lactamase-producing <i>S. enterica</i> subsp. <i>enterica</i> serovar Kentucky ST198 strain was isolated from retail chicken cuts. All isolates carried virulence genes such as <i>iroC</i>, <i>iroB</i> and <i>sinH</i>, with <i>sodC1</i> present in 47.4% of the isolates. Approximately 31% of the isolates co-harboured antimicrobial, stress tolerance and virulence genes. Genomic analysis identified distinct sequence types while also revealing identical core SNPs in genomes across various stages of the supply chain. This study highlights the transmission of <i>Salmonella</i> and AMR in the broiler supply chain, emphasizing the urgent need for improved surveillance and intervention strategies to reduce public health risks from contaminated poultry products.