摘要

      家禽饲养对巴基斯坦的经济健康发展很重要，但巴基斯坦家禽业受到大肠杆菌感染的负面影响。我们对来自巴基斯坦五个地理区域的死亡家鸡肝脏的92株大肠杆菌进行了Illumina全基因组测序。我们的分析表明，这些菌株主要来自B1和A分支，并含有多种抗生素抗性和毒力基因。对于B1和E系统群，在系统发育和抗生素抗性基因之间没有联系，但在系统发育和毒力基因、SNP之间有一定的联系。大肠杆菌素耐药基因mcr-1和喹诺酮类耐药基因qnrS1在92个分离株中均有发现。令人震惊的是，本研究所鉴定的82/92株大肠杆菌对林可霉素、链霉素、氨苄西林和环丙沙星的耐药率分别为100%（92/92）、81.5%（75/92）、79.3%（73/92）和66.3%（61/92）。这些结果提供了一个高分辨率的分析，从一个地区家禽中分离的大肠杆菌与当地高负荷的抗生素耐药性有关。家禽相关的大肠杆菌菌株的抗生素耐药性监测是综合分析人类、动物和环境生态位中潜在病原体的一个健康概念的重要支柱。

      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.

      https://www.frontiersin.org/articles/10.3389/fmicb.2019.03052/full