Data_Sheet_1_Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.zip

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.

在非洲，非伤寒沙门氏菌（non-typhoidal Salmonella enterica）引发的疾病负担极不成比例地偏高；然而，全基因组测序（whole-genome sequencing, WGS）的研究工作却压倒性地集中在疾病负担较低的世界区域。尽管南非越来越多地采用WGS来表征沙门氏菌，但这类工作大多集中在人类临床菌株的表征上。因此，在基因组层面上，人们对该国动物群体中流行的沙门氏菌谱系知之甚少。
本研究通过WGS对60年间从南非的家畜、伴侣动物、野生动物及动物产品中分离得到的63株沙门氏菌进行了表征。通过七基因多位点序列分型（seven-gene multi-locus sequence typing），将这些菌株分别归类为都柏林血清型（Dublin）、哈达尔血清型（Hadar）、肠炎血清型（Enteritidis）和鼠伤寒血清型（Typhimurium）（对应菌株数分别为18、8、13和24株），并归属至以下序列型（sequence types, STs）：ST10（均为都柏林沙门氏菌S. Dublin）、ST33（均为哈达尔沙门氏菌S. Hadar）、ST11/ST366（肠炎沙门氏菌分别为12株和1株），以及ST19/ST34（鼠伤寒沙门氏菌分别为23株和1株）。
基于本研究测序的基因组，结合各序列型对应的代表性公开基因组，我们构建了序列型内系统发育树：其中全球种群的都柏林沙门氏菌和哈达尔沙门氏菌基因组分别为2802和1569株，非洲种群的肠炎沙门氏菌和鼠伤寒沙门氏菌基因组分别为716和343株。
针对都柏林沙门氏菌ST10，本研究鉴定出了在南非人类、动物及食品中流行的、大多对抗菌药物敏感的地方性流行谱系，同时还发现了一条可能近期从美国传入的谱系。针对哈达尔沙门氏菌ST33，本研究鉴定出了多株携带链霉素和四环素耐药基因的南非流行谱系。
非洲肠炎沙门氏菌ST11可主要划分为两个进化枝：一个大多对抗菌药物敏感，另一个则大多为多重耐药（multidrug-resistant, MDR）型；而南非分离株均局限于抗菌药物敏感的进化枝中。本研究测序的鼠伤寒沙门氏菌ST19/ST34菌株分布于非洲鼠伤寒沙门氏菌ST19/ST34的系统发育树中，涵盖了多种不同的谱系，其中包括多个多重耐药谱系。
综上，本研究深入解析了南非动物、食品及人类群体中流行的地方性及输入性非伤寒沙门氏菌谱系，同时证实了WGS在表征高沙门氏菌病负担区域的动物关联菌株方面的应用价值。