Recently, there have been reports worldwide of a multidrug-resistant, emergent Salmonella Infantis (ESI) clone with a large megaplasmid (pESI), often containing the extended-spectrum beta-lactamase gene bla_CTX-M-65. This clone also has a gyrA mutation conferring fluoroquinolone resistance, further limiting treatment options. In the United States, this clone has also been found in poultry sources, indicating a likely source of human illnesses. We conducted short-read sequencing of Salmonella enterica isolated from retail meats as part of routine surveillance by the National Antimicrobial Resistance Monitoring System (NARMS). We analyzed the resulting data temporally and geographically to determine when and where the ESI clone has spread in the United States. We found the ESI clone was first found in retail meats in Tennessee in 2014, but by 2019 was throughout the United States and comprised 29% of all Salmonella isolated from retail chickens, and 7% from retail turkey. Of these isolates, 85.0% were within 20 single nucleotide polymorphisms (SNPs) of those causing human illnesses. Long-read sequencing data indicated substantial recombination in the pESI plasmid resulting in the presence of 0–10 resistance genes, despite all their chromosomes being within 31 SNPs of one another. This work demonstrates the rapid spread of this clone of Salmonella Infantis in poultry in the United States, with the potential for increased burden of human illness attributed to this multidrug-resistant pathogen.

中文翻译：

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一种多重耐药婴儿沙门氏菌克隆正在美国传播和重组

最近，世界范围内有报道称，具有大质粒 (pESI)的多药耐药、紧急婴儿沙门氏菌(ESI) 克隆通常含有超广谱 β-内酰胺酶基因bla _CTX-M-65。该克隆还具有gyrA突变，赋予氟喹诺酮耐药性，进一步限制了治疗选择。在美国，也在家禽来源中发现了这种克隆，表明可能是人类疾病的来源。我们对沙门氏菌进行了短读长测序作为国家抗微生物药物耐药性监测系统 (NARMS) 常规监测的一部分，从零售肉类中分离出来的细菌。我们在时间和地理上分析了所得数据，以确定 ESI 克隆何时何地在美国传播。我们发现 ESI 克隆于 2014 年首次在田纳西州的零售肉类中发现，但到 2019 年遍及美国，占所有沙门氏菌的29%从零售鸡中分离，7% 来自零售火鸡。在这些分离株中，85.0% 位于导致人类疾病的那些分离株的 20 个单核苷酸多态性 (SNP) 内。长读长测序数据表明 pESI 质粒中存在大量重组，导致存在 0-10 个抗性基因，尽管它们的所有染色体都在 31 个 SNP 之内。这项工作证明了这种婴儿沙门氏菌克隆在美国家禽中的快速传播，这种多药耐药病原体可能会增加人类疾病的负担。