Wang Jingyao, Liu Xudong, Shao Yanwen, Li Runsheng, Paudel Surya
Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
Front Vet Sci. 2025 Mar 19;12:1541964. doi: 10.3389/fvets.2025.1541964. eCollection 2025.
Avian pathogenic (APEC) causes colibacillosis in poultry, which is a very important disease worldwide. Despite well-documented genomic traits and diversity of APEC, its epigenomic characteristics are less understood. This study utilized the high throughput and long-read capabilities of Oxford Nanopore Technology (ONT) to elucidate the genome structures and methylation modifications of three isolates of avian origin: one intestinal isolate from a healthy wild bird and two systemic isolates from clinically affected chickens. Three complete genomes, each comprising a single chromosome and multiple plasmids were assembled. Diverse virulence-associated genes, antimicrobial resistance genes, mobile genetic elements plasmids and integrons were characterized from the genomes. Despite a limited sample size, our whole genome sequencing (WGS) data highlighted significant genomic diversity among the strains and enriched repertoire of gene clusters related to APEC pathogenicity. From the epigenetic analysis, multiple methylation modifications, including three N5-methylcytosine (5mC), eight N6-methyladenine (6mA) and two N4-methylcytosine (4mC) modification motifs were identified within all three isolates. Furthermore, common GATC and CCWGG methylation motifs were predominantly distributed within regulatory regions, suggesting a role in epigenetic transcription regulation. This study opens the avenue for future research into pathogenesis, diagnostic and therapeutic strategies of APEC considering epigenetic analysis.
禽致病性大肠杆菌（APEC）可引起家禽大肠杆菌病，这是一种在全球范围内非常重要的疾病。尽管APEC的基因组特征和多样性已有充分记录，但其表观基因组特征却鲜为人知。本研究利用牛津纳米孔技术（ONT）的高通量和长读长能力，阐明了三株禽源分离株的基因组结构和甲基化修饰：一株来自健康野生鸟类的肠道分离株和两株来自临床发病鸡的全身感染分离株。组装了三个完整的基因组，每个基因组都包含一条染色体和多个质粒。从这些基因组中鉴定出了多种与毒力相关的基因、抗菌抗性基因、移动遗传元件质粒和整合子。尽管样本量有限，但我们的全基因组测序（WGS）数据突出了这些菌株之间显著的基因组多样性，并丰富了与APEC致病性相关的基因簇库。通过表观遗传分析，在所有三株分离株中都鉴定出了多种甲基化修饰，包括三个N5-甲基胞嘧啶（5mC）、八个N6-甲基腺嘌呤（6mA）和两个N4-甲基胞嘧啶（4mC）修饰基序。此外，常见的GATC和CCWGG甲基化基序主要分布在调控区域，表明其在表观遗传转录调控中发挥作用。本研究为今后考虑表观遗传分析的APEC发病机制、诊断和治疗策略的研究开辟了道路。
