Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.
Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.
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DOI：
10.3389/fmicb.2021.748611
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发表时间：
2021
影响因子：
5.2
通讯作者：
Matle I
中科院分区：
文献类型：
--
作者：
Carroll LM;Pierneef R;Mathole M;Matle I
在非洲，非伤寒沙门氏菌造成的疾病负担高得不成比例；然而，全基因组测序工作压倒性地集中在负担较低的世界区域。虽然WGS在南非越来越多地被用来表征肠炎沙门氏菌，但这些努力的大部分集中在表征人类临床菌株上。因此，人们对该国动物之间在基因组规模上流通的谱系知之甚少。在这里，我们使用WGS对60年来从南非牲畜、伴生动物、野生动物和动物产品中分离的63株肠炎沙门氏菌进行了特征分析。基因组被划分为都柏林、哈达尔、肠炎和鼠伤寒沙门氏菌四种血清型(分别为18、8、13和24株)和序列类型(STS)ST10(全部都柏林沙门氏菌)、ST33(全部哈达尔沙门氏菌)、ST11/ST366(分别12和1株肠炎沙门氏菌)和ST19/ST34(n=23和1鼠伤寒沙门氏菌；通过7基因多位点序列分型)。用本研究中测序的基因组加上代表每个ST种群的公开基因组构建了Inside-ST系统发生图。(I)全球(分别为2,802和1,569个S.Dublin和Hadar基因组)和(Ii)非洲(分别为716和343个肠炎沙门氏菌和鼠伤寒杆菌基因组)。对于S.Dublin ST10，发现了一个在南非人、动物和食物中流行的主要对抗生素敏感的地方性谱系，以及一个可能是最近从美国引入的谱系。对于S.Hadar ST33，鉴定出含有链霉素和四环素耐药相关基因的多个南非谱系。非洲肠炎沙门氏菌ST11可以主要分为一个主要对抗生素敏感的分支和一个主要对多药耐药(MDR)的分支，而南非的分离株仅限于主要对抗生素敏感的分支。在此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系统发育中，代表了一系列不同的谱系，包括许多耐多药谱系。总体而言，这项研究提供了对在南非动物、食物和人类中流行的地方性和异地非伤寒肠道沙门氏菌谱系的关键见解，并展示了WGS在鉴定来自沙门氏菌高负担地区的动物相关菌株方面的效用。
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.