Data_Sheet_1_Whole-genome sequencing and phylogenetic analysis capture the emergence of a multi-drug resistant Salmonella enterica serovar Infantis clone from diagnostic animal samples in the United States.docx

IntroductionSalmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum β-lactamase blaCTX-M-65 on a pESI-like plasmid and a mutation in the gyrA gene has recently been found in the United States in poultry meat.
MethodsWe analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 S. infantis isolates from animal diagnostic samples.
ResultsOf these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the gyrA gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6–10 resistance genes: blaCTX-M-65, aac(3)-IVa, aadA1, aph(4)-Ia, aph(3′)-Ia, floR, sul1, dfrA14, tetA, and fosA. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybtQ and ybtP, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S.
DiscussionThis dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S.

引言：肠炎沙门氏菌（Salmonella enterica）是美国食源性疾病的主要致病原。携带大质粒（pESI）的多重耐药（MDR）新兴婴儿沙门氏菌（Salmonella Infantis，ESI）最初在以色列与意大利被鉴定，随后在全球范围内陆续被报道。近期，美国的禽肉样本中检出携带pESI样质粒且gyrA基因存在D87Y突变的ESI克隆株，该克隆株带有超广谱β-内酰胺酶blaCTX-M-65。
方法：本研究对200株来源于动物临床诊断样本的婴儿沙门氏菌分离株开展了表型与基因型抗菌耐药性、基因组学及系统发育分析。
结果：其中33.5%的分离株对至少一种抗菌药物耐药，19.5%为多重耐药（MDR）。11株来源于不同动物宿主的分离株在表型与基因型上与ESI克隆株高度相似。这些分离株的gyrA基因存在D87Y突变，可导致对环丙沙星的敏感性降低，且携带6~10种耐药基因组合：blaCTX-M-65、aac(3)-IVa、aadA1、aph(4)-Ia、aph(3′)-Ia、floR、sul1、dfrA14、tetA及fosA。这11株分离株携带Ⅰ类和Ⅱ类整合子，以及3种毒力基因：参与黏附与侵袭过程的sinH，以及与铁转运相关的ybtQ和ybtP。这些分离株彼此间仅存在7~27个单核苷酸多态性（SNP）差异，系统发育上与近期在美国发现的ESI克隆株亲缘关系密切。
讨论：本数据集记录了多重耐药（MDR）ESI克隆株在多种动物宿主中的出现情况，同时也是美国境内首次报道从马源分离株中检出pESI样质粒。