Salmonella Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging S. Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of S. Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of S. Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European S. Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes (n=82) were observed: bla CTX-M-1-positive in European isolates and bla CTX-M-65-positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals (merA) and disinfectants (qacEΔ). Worryingly, 66 % of the total isolates studied presented different gyrA chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125–0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by mph, mef and erm(B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR S. Infantis and pESI-like along the food chain in Europe.

中文翻译：

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欧洲沙门氏菌的分子流行病学：对细菌宿主及其寄生性pESI样大质粒成功的见解。

沙门氏菌 婴儿是五个血清型最常引起欧洲人类沙门氏菌病，主要是与家禽有关的一个。一个带有新兴S的结合质粒的克隆。带有多药抗性（MDR）和超广谱β-内酰胺酶（ESBL）基因的类似Infantis（pESI）的大质粒已经在意大利肉鸡业传播，也引起人类疾病。这项工作旨在阐明S的分子流行病学。使用全基因组测序和生物信息学分析，研究欧洲的Infantis和pESI样，并调查S的遗传相关性。来自九个欧洲国家的机构提供的动物，肉类，饲料和人类的Infantis克隆和pESI样。使用了两种基因分型方法：基于染色体或质粒SNP的分析以及基于核心基因组多基因座序列分型（cgMLST）的最小生成树（MST）算法。欧洲小号。婴幼儿种群似乎是异质的，在核心基因组水平上定义了不同的遗传簇。但是，在大多数国家中，有64.1％的分离株中存在pESI样变体，具有更高的遗传同源性，并能够感染不同的克隆谱系。观察到两个带有ESBL基因的不同pESI样（n = 82）：欧洲分离株中bla CTX-M-1阳性和bla CTX-M-65在美国分离株中呈阳性（研究分组）。两种变体具有毒素-抗毒素系统中，朝四环素，甲氧苄啶，磺胺类和氨基糖苷类的抗性基因，重金属（聚体A）和消毒剂（QAC EΔ）。令人担忧的是，研究的总分离株中有66％表现出与（氟）喹诺酮耐药性相关的不同的gyr A染色体点突变（MIC范围为0.125-0.5 mg / L），而18％表现出由mph，mef和erm介导的可转移的大环内酯类耐药（B ）基因。需要采取适当的干预策略来防止MDR S的进一步传播/传播。欧洲食物链中的Infantis和pESI样。