{"doi":"10.3389/fmicb.2021.748611","title":"Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa","abstract":"\n In Africa, the burden of illness caused by non-typhoidal\n Salmonella enterica\n 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\n Salmonella enterica\n , 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\n Salmonella enterica\n 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 n\n = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all\n S.\n Dublin), ST33 (all\n S.\n Hadar), ST11/ST366 (\n n\n = 12 and 1\n S.\n Enteritidis, respectively), and ST19/ST34 (\n n\n = 23 and 1\n S.\n 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 n\n = 2,802 and 1,569\n S.\n Dublin and Hadar genomes, respectively) and (ii) African (\n n\n = 716 and 343\n S.\n Enteritidis and Typhimurium genomes, respectively) population. For\n S.\n 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\n S.\n Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African\n S.\n 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.\n S.\n Typhimurium ST19/ST34 strains sequenced here were distributed across the African\n S.\n 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\n Salmonella enterica\n 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.\n ","journal":"Frontiers in Microbiology","year":2021,"id":681914,"datarank":0.47670807455219194,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"self_citation_contribution":0.47670807455219194,"citation_network_contribution":0.0,"self_endowment_contribution":0.47670807455219194,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":23,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1781597,"name":"Rian Pierneef","orcid":null,"position":1,"is_corresponding":false},{"id":1781599,"name":"Masenyabu Mathole","orcid":null,"position":2,"is_corresponding":false},{"id":1781601,"name":"Itumeleng Matle","orcid":null,"position":3,"is_corresponding":false},{"id":829286,"name":"Laura M. Carroll","orcid":"0000-0002-3677-0192","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa","abstract":"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.","is_dataset_classified":null,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"34671335","pmcid":"PMC8521152","openalex_id":"https://openalex.org/W3163450007","authors":[],"funders":[{"funder_name":"Gauteng Department of Agriculture and Rural Development","grant_id":"","title":null}],"total_grants":1,"fwci":2.2406,"citation_percentile":0.86837394,"influential_citations":0,"citation_trend":[{"year":2021,"count":1},{"year":2022,"count":3},{"year":2023,"count":7},{"year":2024,"count":4},{"year":2025,"count":5},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.3389/fmicb.2021.748611","host_type":"journal"},{"url":"https://doi.org/10.3389/fmicb.2021.748611","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/34671335","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8521152","host_type":"repository"},{"url":"https://doaj.org/article/aa951bd4acf04518a6e8be868a637923","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8521152","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8521152?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Salmonella and Campylobacter epidemiology","Genomics and Phylogenetic Studies","Bacteriophages and microbial interactions"],"mesh_terms":[],"keywords":["Salmonella enterica","Biology","Salmonella","Genome","Lineage (genetic)","Serotype","Genetics","Population","Whole genome sequencing","Microbiology","Gene","Bacteria","Salmonella typhimurium","Africa","Antimicrobial resistance","Salmonella enteritidis","Whole-genome Sequencing","Foodborne Illness","Salmonella Hadar","Salmonella Dublin"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"bioproject"},{"name":"gen"},{"name":"refseq"},{"name":"doi"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-17T18:58:16.283855Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}