Table_2_Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011–2016.DOCX

The emergence of plasmid-mediated colistin resistance (mcr genes) threatens the effectiveness of polymyxins, which are last-resort drugs to treat infections by multidrug- and carbapenem-resistant Gram-negative bacteria. Based on the occurrence of colistin resistance the aims of the study were to determine possible resistance mechanisms and then characterize the mcr-positive Escherichia coli. The research used material from the Polish national and EU harmonized antimicrobial resistance (AMR) monitoring programs. A total of 5,878 commensal E. coli from fecal samples of turkeys, chickens, pigs, and cattle collected in 2011–2016 were screened by minimum inhibitory concentration (MIC) determination for the presence of resistance to colistin (R) defined as R > 2 mg/L. Strains with MIC = 2 mg/L isolated in 2014–2016 were also included. A total of 128 isolates were obtained, and most (66.3%) had colistin MIC of 2 mg/L. PCR revealed mcr-1 in 80 (62.5%) isolates recovered from 61 turkeys, 11 broilers, 2 laying hens, 1 pig, and 1 bovine. No other mcr-type genes (including mcr-2 to -5) were detected. Whole-genome sequencing (WGS) of the mcr-1–positive isolates showed high diversity in the multi-locus sequence types (MLST) of E. coli, plasmid replicons, and AMR and virulence genes. Generally mcr-1.1 was detected on the same contig as the IncX4 (76.3%) and IncHI2 (6.3%) replicons. One isolate harbored mcr-1.1 on the chromosome. Various extended-spectrum beta-lactamase (blaSHV–12, blaCTX–M–1, blaCTX–M–15, blaTEM–30, blaTEM–52, and blaTEM–135) and quinolone resistance genes (qnrS1, qnrB19, and chromosomal gyrA, parC, and parE mutations) were present in the mcr-1.1–positive E. coli. A total of 49 sequence types (ST) were identified, ST354, ST359, ST48, and ST617 predominating. One isolate, identified as ST189, belonged to atypical enteropathogenic E. coli. Our findings show that mcr-1.1 has spread widely among production animals in Poland, particularly in turkeys and appears to be transferable mainly by IncX4 and IncHI2 plasmids spread across diverse E. coli lineages. Interestingly, most of these mcr-1–positive E. coli would remain undetected using phenotypic methods with the current epidemiological cut-off value (ECOFF). The appearance and spread of mcr-1 among various animals, but notably in turkeys, might be considered a food chain, and public health hazard.

噬菌体介导的粘菌素耐药性（mcr 基因）的出现，对多粘菌素的有效性构成了威胁，而多粘菌素是治疗多药耐药和碳青霉烯类耐药革兰氏阴性细菌感染的最后一道防线。基于粘菌素耐药性的发生，本研究旨在确定可能的耐药机制，并随后对阳性 mcr 的大肠杆菌进行特征描述。研究利用了来自波兰国家及欧盟协调一致的抗菌药物耐药性（AMR）监测计划的材料。2011-2016年间，从火鸡、鸡、猪和牛的粪便样本中收集了共计 5,878 株共生性大肠杆菌，通过最低抑菌浓度（MIC）测定筛选出对粘菌素（R）的耐药性，其定义为 R > 2 mg/L。2014-2016年间分离的 MIC = 2 mg/L 的菌株也被纳入研究。共获得 128 株分离株，其中大部分（66.3%）的粘菌素 MIC 为 2 mg/L。PCR 检测显示，在从 61 只火鸡、11 只肉鸡、2 只产蛋鸡、1 头猪和 1 头牛中恢复的 80 株（62.5%）分离株中存在 mcr-1。未检测到其他 mcr 型基因（包括 mcr-2 至 -5）。mcr-1 阳性分离株的全基因组测序（WGS）显示，大肠杆菌的多位点序列类型（MLST）、质粒复制子和 AMR 及致病性基因存在高度多样性。一般来说，mcr-1.1 被检测到与 IncX4（76.3%）和 IncHI2（6.3%）复制子位于同一连续片段上。一株分离株的染色体上携带 mcr-1.1。mcr-1.1 阳性大肠杆菌中存在各种广谱β-内酰胺酶（blaSHV–12、blaCTX–M–1、blaCTX–M–15、blaTEM–30、blaTEM–52 和 blaTEM–135）和喹诺酮耐药基因（qnrS1、qnrB19 和染色体上的 gyrA、parC 和 parE 突变）。共鉴定了 49 个序列类型（ST），其中 ST354、ST359、ST48 和 ST617 为主。一株被鉴定为 ST189 的分离株属于非典型肠道致病性大肠杆菌。我们的研究结果表明，mcr-1.1 在波兰的生产动物中广泛传播，尤其是在火鸡中，且主要通过 IncX4 和 IncHI2 质粒在不同大肠杆菌谱系中传播。有趣的是，这些 mcr-1 阳性大肠杆菌中的大部分在使用当前流行病学截止值（ECOFF）的表型方法时将无法被检测到。mcr-1 在各种动物（尤其是火鸡）中的出现和传播可能被视为食物链和公共卫生隐患。