AUTHOR=Carroll Laura M. , Pierneef Rian , Mathole Masenyabu , Matle Itumeleng 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.748611

DOI=10.3389/fmicb.2021.748611

ISSN=1664-302X

ABSTRACT=<p>In Africa, the burden of illness caused by non-typhoidal <italic>Salmonella enterica</italic> 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 <italic>Salmonella enterica</italic>, 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 <italic>Salmonella enterica</italic> 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 (<italic>n</italic> = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all <italic>S.</italic> Dublin), ST33 (all <italic>S.</italic> Hadar), ST11/ST366 (<italic>n</italic> = 12 and 1 <italic>S.</italic> Enteritidis, respectively), and ST19/ST34 (<italic>n</italic> = 23 and 1 <italic>S.</italic> 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 (<italic>n</italic> = 2,802 and 1,569 <italic>S.</italic> Dublin and Hadar genomes, respectively) and (ii) African (<italic>n</italic> = 716 and 343 <italic>S.</italic> Enteritidis and Typhimurium genomes, respectively) population. For <italic>S.</italic> 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 <italic>S.</italic> Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African <italic>S.</italic> 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. <italic>S.</italic> Typhimurium ST19/ST34 strains sequenced here were distributed across the African <italic>S.</italic> 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 <italic>Salmonella enterica</italic> 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.</p>