Table_3_Genomic Characterization of Antibiotic Resistant Escherichia coli Isolated From Domestic Chickens in Pakistan.xlsx

Poultry husbandry is important for the economic health of Pakistan, but the Pakistani poultry industry is negatively impacted by infections from Escherichia coli. We performed Illumina whole genome sequencing on 92 E. coli isolates obtained from the livers of deceased chickens originating in five Pakistani geographical regions. Our analysis indicates that the isolates are predominantly from the B1 and A clade and harbor a diverse number of antibiotic resistance and virulence genes, with no linkage between phylogeny and antibiotic resistance gene presence but some association between phylogeny and virulence gene and SNP presence for the B1 and E phylogroups. The colistin resistance gene mcr-1 and the quinolone resistance gene qnrS1 were both found in 13/92 isolates. Alarmingly, 82/92 of the E. coli strains characterized in this study are multidrug resistant with 100% (92/92) resistance to lincomycin, 81.5% (75/92) to streptomycin, 79.3% (73/92) to ampicillin and 66.3% (61/92) to ciprofloxacin. These results provide a high-resolution analysis of poultry-associated E. coli isolates in an area with a high endemic burden of antibiotic resistance. Surveillance of antibiotic resistance in poultry associated E. coli isolates is an important pillar of the One Health concept to integrate analysis of potential pathogens in human, animal, and environmental niches.

家禽养殖业对巴基斯坦的经济健康至关重要，但巴基斯坦家禽业却受到大肠杆菌（Escherichia coli）感染的负面影响。我们对源自巴基斯坦5个地理区域的病死鸡肝脏中分离得到的92株大肠杆菌菌株开展了Illumina全基因组测序。分析结果显示，这些分离菌株主要属于B1和A进化支，携带多种抗生素抗性基因与毒力基因；系统发育与抗生素抗性基因的携带情况并无关联，但针对B1和E系统发育群，系统发育与毒力基因及单核苷酸多态性（Single Nucleotide Polymorphism，简称SNP）的携带情况存在一定关联。粘菌素抗性基因mcr-1与喹诺酮类抗性基因qnrS1均在13/92株分离菌株中被检出。令人担忧的是，本研究表征的92株大肠杆菌中有82株呈多重耐药性，其中对林可霉素的耐药率达100%（92/92），对链霉素为81.5%（75/92），对氨苄西林为79.3%（73/92），对环丙沙星为66.3%（61/92）。上述结果针对抗生素抗性地方性流行负担较高的地区，完成了家禽源大肠杆菌分离菌株的高分辨率分析。对家禽源大肠杆菌分离菌株的抗生素抗性进行监测，是同一健康（One Health）理念的重要支柱，该理念旨在整合分析人类、动物与环境生态位中的潜在病原体。