Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing
Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing
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DOI：
10.1371/journal.pone.0201882
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发表时间：
2018-08-13
期刊：
影响因子：
3.7
通讯作者：
Falcao, Juliana Pfrimer
中科院分区：
文献类型：
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作者：
Almeida, Fernanda;Seribelli, Amanda Aparecida;Falcao, Juliana Pfrimer
全基因组测序（WGS）已被用作分子流行病学、监测、物种和血清型鉴定、爆发源鉴定等目的的有力技术。在巴西，关于沙门氏菌的流行病学数据相对较少。在这项研究中，对90株鼠伤寒沙门氏菌菌株进行了基因组测序，以揭示1983年至2013年期间从巴西不同地理区域的人类和食品中分离出的鼠伤寒沙门氏菌的多样性。共鉴定出氨基糖苷类、四环素类、磺胺类、甲氧苄啶类、β-内酰胺类、氟喹诺酮类、苯酚类、大环内酯类等39个耐药基因，以及gyrA、gyrB、parC、帕雷等部分基因发生点突变。90例中有65例（72.2%）为阳性。研究的鼠伤寒沙门氏菌菌株对磺胺类药物表型耐药，44株（48.9%）菌株对链霉素耐药，27株（30%）菌株对四环素耐药，21株（23.3%）菌株对庆大霉素耐药，7株（7.8%）菌株对头孢曲松耐药。在gyrA基因中，观察到以下氨基酸取代：Asp（87）-> Gly，Asp（87）-> Asn，Ser（83）-> Phe，Ser（83）-> Tyr。系统发育结果将90 S.鼠伤寒沙门氏菌菌株分为两个主要分支，表明存在一个流行的亚型，可能更适应，从人类分离的菌株，在食品中的亚型有一定的多样性。在这些鼠伤寒沙门氏菌菌株中发现的耐药基因的多样性和普遍性加强了它们对人类的潜在危害和巴西食品中的风险。
Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)-> Gly, Asp(87)-> Asn, Ser(83)-> Phe, Ser(83)-> Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil.