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In Africa, the burden of illness caused by non-typhoidal  Salmonella enterica  is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize  Salmonella enterica , the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale. Here, we used WGS to characterize 63  Salmonella enterica  strains isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Genomes were assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium ( n  = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all  S.  Dublin), ST33 (all  S.  Hadar), ST11/ST366 ( n  = 12 and 1  S.  Enteritidis, respectively), and ST19/ST34 ( n  = 23 and 1  S.  Typhimurium, respectively; via seven-gene multi-locus sequence typing). Within-ST phylogenies were constructed using genomes sequenced in this study, plus publicly available genomes representative of each ST’s (i) global ( n  = 2,802 and 1,569  S.  Dublin and Hadar genomes, respectively) and (ii) African ( n  = 716 and 343  S.  Enteritidis and Typhimurium genomes, respectively) population. For  S.  Dublin ST10, a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa was identified, as well as a lineage that was likely recently introduced from the United States. For  S.  Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African  S.  Enteritidis ST11 could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade.  S.  Typhimurium ST19/ST34 strains sequenced here were distributed across the African  S.  Typhimurium ST19/ST34 phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides critical insights into endemic and ecdemic non-typhoidal  Salmonella enterica  lineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.

frontiers in microbiology

Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa