摘要
出身背景
大肠杆菌病是由禽类致病性大肠杆菌（APEC）引起的，是世界范围内影响禽类的最严重的传染病之一。
目标
本研究旨在通过全基因组测序（WGS）测定从蛋鸡中分离的亚太经合组织MTR_BAU02菌株的基因组多样性、毒力因子基因（VFGs）和抗微生物耐药性基因（ARGs）。
方法
使用Illumina MiSeq测序仪（Illumina，San Diego，CA）进行配对末端（2×250）WGS，并使用SPAdes进行从头组装。使用BacWGSTdb 2.0服务器对亚太经合组织MTR_BAU02和从国家生物技术信息中心（NCBI）GenBank数据库检索的所有ST1196大肠杆菌菌株进行核心基因组多点序列分型（cgMLST）分析。我们利用不同的数据库来检测亚太经合组织MTR_BAU02菌株的ARGs、VFG和基因组功能特征。
后果
APC-MTR_BAU02的全基因组由94个重叠群组成，包括4924680bp（鸟嘌呤-胞嘧啶[GC]含量为51.1%），包括4681个蛋白质编码序列、一条染色体和一个质粒，并归属于ST1196。亚太经合组织MTR_BAU02的近亲是来自孟加拉国人类临床标本（腹泻粪便）的四个分离株和来自印度鸡的两个临床分离株，它们在694个核心基因组多点序列分型（cgMLST）等位基因上存在差异。在亚太经合组织MTR_BAU02基因组中鉴定出122个ARG和92个VFG。代谢功能注释检测到380个SEED子系统，包括编码碳水化合物代谢、蛋白质代谢、辅因子、维生素、辅基和色素、呼吸、膜转运、应激反应、运动性和趋化性以及毒力、疾病和防御的基因。
结论
这项研究报告了从孟加拉国蛋鸡中分离出的一种耐多药亚太经合组织菌株的基因组序列。ARGs和VFGs广泛存在于亚太经合组织MTR_BAU02中，与人类分离株中发现的ARGs相似，并突显了家禽和人类抗微生物耐药性的日益严重的威胁。
ABSTRACT
Background
Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide.

Objectives
This study aimed to determine the genomic diversity, virulence factor genes (VFGs), and antimicrobial resistance genes (ARGs) in the APEC MTR_BAU02 strain isolated from a layer chicken using whole-genome sequencing (WGS).

Methods
Paired-end (2 × 250) WGS was performed using Illumina MiSeq sequencer (Illumina, San Diego, CA) and de novo assembly was performed using SPAdes. Core genome multilocus sequence typing (cgMLST) analysis between APEC MTR_BAU02 and all of the ST1196 E. coli strains retrieved from the National Center for Biotechnology Information (NCBI) GenBank database was performed using the BacWGSTdb 2.0 server. We utilized different databases to detect ARGs, VFGs, and genomic functional features of the APEC MTR_BAU02 strain.

Results
The complete genome of APEC MTR_BAU02 consists of 94 contigs comprising 4,924,680 bp (51.1% guanine-cytosine [GC] content), including 4681 protein-coding sequences, one chromosome, and one plasmid, and was assigned to ST1196. The closest relatives of APEC MTR_BAU02 were four isolates originating from human clinical specimens (diarrhetic stool) in Bangladesh and two clinical isolates originating from chicken in India, which differed by 694 core genome multilocus sequence typing (cgMLST) alleles. One hundred and twenty-two ARGs and 92 VFGs were identified in the APEC MTR_BAU02 genome. Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups and pigments, respiration, membrane transport, stress response, motility and chemotaxis, and virulence, disease, and defense.

Conclusion
This study reports the genome sequence of a multidrug-resistant APEC strain isolated from layer birds in Bangladesh. The ARGs and VFGs, widespread in APEC MTR_BAU02, are similar to those found in human isolates, and highlight the growing threat of antimicrobial resistance in both poultry and humans.

https://www.sciencedirect.com/science/article/pii/S2213716522001345