Colibacillosis, a disease caused by avian pathogenic Escherichia coli (APEC), constitutes a substantial burden to the poultry industry worldwide. APEC has been extensively characterized throughout the world, however, less is known about the genetic background of APEC isolates from Pakistan. In this study, a total of 75 E. coli isolates from colibacillosis affected dead broiler birds in Pakistan were subjected to whole genome sequencing followed by in-silico characterization. These isolates were investigated for virulence and resistance genotypes, serotypes, multi-locus sequence types, plasmid replicon types and single nucleotide polymorphism-based core genome phylogeny.

Among the APEC isolates investigated, 14 different sequence types were identified with ST117 (16 %), ST2847 (10.7 %) and ST48 (5.3 %) being the most prevalent. Of the 28 different serotypes identified in this study, O1, O2 and O78 serotypes accounted for 25.3 % of the APEC isolates. The most frequently identified virulence-associated genes (VAGs) were increased serum survival gene; iss (100 %), glutamate decarboxylase; gad (92 %) and the siderophore receptor; iroN (81.3 %). According to the previously established definition, 72 % of isolates fell within the highly pathogenic APEC category by possessing a combination of VAGs; iss, iroN, iutA, hlyF and ompT simultaneously. Of the 75 APEC isolates, 89.3 % contained the genes predicted to encode resistance against aminoglycosides, tetracyclines and sulfonamides. Notably, the acquired colistin resistance gene mcr-1 was found in 38.7 % of the APEC isolates. Our findings reveal a diverse genetic background and high virulence and resistance potentials for APEC isolates in Pakistan.

大肠杆菌病（Colibacillosis）是由禽致病性大肠杆菌（APEC）引起的疾病，对全世界的家禽业构成沉重负担。亚太经合组织已在世界范围内得到广泛表征，但是对巴基斯坦分离出的亚太经合组织的遗传背景知之甚少。在这项研究中，对巴基斯坦感染大肠杆菌病的死亡肉鸡的75株大肠杆菌分离株进行了全基因组测序，然后进行了计算机内鉴定。研究了这些分离株的毒力和抗性基因型，血清型，多基因座序列类型，质粒复制子类型和基于单核苷酸多态性的核心基因组系统发育。

在所研究的APEC分离物中，鉴定出14种不同的序列类型，其中以ST117（16％），ST2847（10.7％）和ST48（5.3％）最为普遍。在这项研究中确定的28种不同血清型中，O1，O2和O78血清型占APEC分离株的25.3％。最常见的毒力相关基因（VAGs）是血清存活基因的增加。iss（100％），谷氨酸脱羧酶；gad（92％）和铁载体受体；iroN（81.3％）。根据先前确定的定义，通过拥有VAG的组合，有72％的分离株属于高致病性APEC类别。iss，iroN，iutA，hlyF和ompT同时。在这75种APEC分离物中，有89.3％包含了预计编码对氨基糖苷类，四环素类和磺酰胺类抗药性的基因。值得注意的是，在38.7％的APEC分离物中发现了获得的大肠菌素抗性基因mcr-1。我们的发现揭示了巴基斯坦APEC分离株的多样遗传背景和高毒力和耐药潜力。