生物技术通报 ›› 2023, Vol. 39 ›› Issue (12): 287-299.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0578

• 研究报告 • 上一篇    下一篇

猪源致病性大肠杆菌基因组比较与毒力因子分析

吴莉丹1(), 冉雪琴2, 牛熙1, 黄世会2, 李升1, 王嘉福1()   

  1. 1.贵州大学生命科学学院 农业生物工程研究院 山地植物资源保护与种质创新教育部重点实验室,贵阳 550025
    2.贵州大学动物科学学院,高原山地动物遗传育种与繁殖教育部重点实验室,贵阳 550025
  • 收稿日期:2023-06-16 出版日期:2023-12-26 发布日期:2024-01-11
  • 通讯作者: 王嘉福,男,教授,研究方向:生物化学与分子生物学;E-mail: jfwang@gzu.edu.cn
  • 作者简介:吴莉丹,女,硕士研究生,研究方向:微生物学;E-mail: 1848642537@qq.com
  • 基金资助:
    国家自然科学基金项目(31960641);贵州省科技创新人才团队项目(黔科合平台人才[2019]5615)

Genome Comparison and Virulence Factor Analysis of Pathogenic Escherichia coli from Porcine

WU Li-dan1(), RAN Xue-qin2, NIU Xi1, HUANG Shi-hui2, LI Sheng1, WANG Jia-fu1()   

  1. 1. College of Life Sciences, Institute of Agricultural Bioengineering, Key Laboratory of Conservation of Mountain Plant Resources and Germplasm Innovation, Ministry of Education, Guizhou University, Guiyang 550025
    2. College of Animal Science, Guizhou University, Key Laboratory of Genetic Breeding and Reproduction of Plateau Mountain Animals, Ministry of Education, Guiyang 550025
  • Received:2023-06-16 Published:2023-12-26 Online:2024-01-11

摘要:

不同菌株猪源致病性大肠杆菌的致病力有较大差异,通过着重研究菌株基因组中携带的毒力因子种类和数量,以解析猪源大肠杆菌致病的分子机制。利用二代高通量DNA测序技术测定猪源致病性大肠杆菌的基因组DNA序列,通过生物信息学方法,分析不同毒力菌株的基因组结构特征、进化类型、携带的毒力因子基因及其碱基变异,采用PCR方法对候选毒力因子基因进行验证。猪源致病性大肠杆菌不同毒力菌株的基因组全长范围为4.62-5.3 Mb,含有3 364-3 557个编码基因,菌株的系统进化群和多位点序列分型多属于A群和ST10克隆复合群。6株菌携带112-280个毒力因子基因,强毒菌株的毒力因子基因尤其是毒素基因多于弱毒菌株,且各菌株分泌系统基因的数量变异较大。此外,毒力因子基因中检测到插入缺失、移码突变和无义突变等高影响碱基变异。采用PCR验证了代表性毒力因子基因及其变异。猪源致病性大肠杆菌的毒力与基因组长度、编码基因的数量和变异相关,与GC含量、前噬菌体和CRISPR序列没有必然联系。

关键词: 猪源致病性大肠杆菌, 致病力, 全基因组, 基因分型, 毒力因子基因

Abstract:

The pathogenicity of different strains of porcine-derived Escherichia coli varies greatly. By focusing on the types and quantities of virulence factors carried in the genomes of the strains, we can analyze the molecular mechanism of porcine-derived E. coli causing disease. Next-generation high-throughput DNA sequencing technology was used to determine the genomic DNA sequence of porcine-derived pathogenic E. coli, and bioinformatics methods were adapted to analyze the genome structural characteristics, evolutionary types, virulence factor genes and base variation of different virulent strains. PCR method was to verify the candidate virulence factor genes. The full lengths of the genomes from different virulent strains of porcine pathogenic E. coli ranged from 4.62 Mb to 5.3 Mb, containing 3 364 to 3 557 coding genes. Most phylogenetic groups and multi-locus sequence typing of strains belonged to group A and ST10 clonal complex groups. Six virulent strains carried 112 to 280 virulence factor genes. Virulence factor genes, especially toxin genes, in strong virulent strains were more than that in the weak virulent strains, and the number of genes in the secretion system of each strain varied greatly. In addition, there were high-impact variations(e.g., insertion deletion, frameshift mutation, and nonsense mutation)in virulence factor genes. And representative virulence factor genes and their mutations were confirmed by PCR method. The virulence of porcine-derived pathogenic E. coli was correlated with genome size and number and variation in coding genes, and was not necessarily related to the GC content, prophage, and CRISPR sequence in genome.

Key words: porcine-derived pathogenic Escherichia coli, virulence, genome-wide, genotyping, virulence factor genes