利用比较基因组学对巴西不同来源鼠伤寒沙门氏菌分离株的流行病学见解。
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics.
作者信息
Seribelli Amanda Ap, da Silva Patrick, da Cruz Marcelo Ferreira, de Almeida Fernanda, Frazão Miliane R, Medeiros Marta I C, Rodrigues Dália Dos P, Kich Jalusa D, de Jesus Benevides Leandro, Soares Siomar de C, Allard Marc W, Falcão Juliana Pfrimer
机构信息
Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Ribeirão Preto, Brazil.
Faculdade de Ciências Farmacêuticas de Araraquara, UNESP - Departamento de Ciências Biológicas, Rodovia Araraquara-Jaú Km 1, Araraquara, SP, Brazil.
出版信息
Gut Pathog. 2021 Apr 28;13(1):27. doi: 10.1186/s13099-021-00423-7.
BACKGROUND
Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies.
RESULTS
The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes.
CONCLUSIONS
The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs' results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed.
背景
肠炎沙门氏菌肠炎亚种鼠伤寒血清型（鼠伤寒沙门氏菌）是全球重要的人畜共患病原体。本研究旨在运用不同的基因组学策略，对巴西30年间从不同来源分离出的117株鼠伤寒沙门氏菌进行基因比较。
结果
通过核心基因组多位点序列分型，117株被研究的鼠伤寒沙门氏菌菌株大多聚为一个簇（约90%）；通过单拷贝标记基因分析，约77%的菌株聚为一个簇。基于单核苷酸多态性（SNP）的系统发育分析将大多数来自人类的菌株聚为一个簇（约93%），而从食品和猪中分离出的菌株则分为三个簇。从人类和食品中分离出的一些鼠伤寒沙门氏菌发现的不同直系同源蛋白簇参与代谢和调控过程。对于来自猪的26株分离株，序列类型（ST）19和ST1921最为常见，同时也检测到了ST14、ST64、ST516和ST639。先前的结果将从人类和食品中分离出的91株鼠伤寒沙门氏菌鉴定为ST19、ST313、ST1921、ST3343和ST1649。检测到的主要前噬菌体为：79株（67.5%）含有Gifsy - 2，63株（54%）含有Gifsy - 1。所有鼠伤寒沙门氏菌分离株均含有acrA、acrB、macA、macB、mdtK、emrA、emrB、emrR和tolC外排泵基因。
结论
系统发育树将大多数来自人类的鼠伤寒沙门氏菌分离株聚为一个簇，表明在巴西存在一种流行的亚型。关于从食品和猪中分离出的菌株，SNP结果表明在该国30年间有不止一种亚型在传播。直系同源蛋白簇分析揭示了所研究菌株中的独特基因，主要与细菌代谢相关。与从人类和食品中分离出的菌株相比，来自猪的鼠伤寒沙门氏菌菌株在ST和前噬菌体方面表现出更大的多样性。该血清型中参与其毒力的独特前噬菌体的存在证实了鼠伤寒沙门氏菌菌株的致病潜力。与外排泵相关的大量抗性基因令人担忧，在需要临床治疗时可能导致治疗失败。
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