致病性大肠杆菌携带原噬菌体的预测及耐药性与毒力研究

doi:10.16431/j.cnki.1671-7236.2022.03.035

摘要/Abstract

摘要： 【目的】研究致病性大肠杆菌携带原噬菌体的比例、原噬菌体携带毒力基因及耐药基因的情况，了解致病性大肠杆菌中原噬菌体对菌株的耐药性与毒力的影响，保证噬菌体生产菌的生物安全性，为大肠杆菌噬菌体的基础研究与应用提供借鉴。【方法】从NCBI中下载大肠杆菌全基因组信息，通过在线网站预测大肠杆菌中携带的原噬菌体数目，并分析原噬菌体的GC含量、基因组大小、占细菌基因组比例等基因组特征及完整型原噬菌体的类型，对原噬菌体做初步分类，统计分析完整型原噬菌体中携带耐药基因数目、耐药表型、耐药机制与毒力基因数目、毒力基因家族分布等。【结果】 112株大肠杆菌携带完整型原噬菌体1 024个，疑似型原噬菌体287个，缺陷型原噬菌体505个。1 024个完整型原噬菌体中，多数与长尾噬菌体相似，占70.21%（719/1 024）；共有63种噬菌体类型，其中BP4795（登录号：NC_004813.1）类型的占比最高，达到19.24%（197/1 024），其次是DE3（登录号：NC_042057.1），占比11.72%（120/1 024）。大肠杆菌携带原噬菌体的GC含量在38%~57%之间，基因组大小为3.1~152.6 kb，其中80 kb以内的原噬菌体占97.03%（1 762/1 816）。1 024个完整型原噬菌体中携带耐药基因占比为6.35%（65/1 024），共携带耐药基因253个，分别来自11个抗生素耐药基因家族；携带一个或多个毒力基因的完整性原噬菌体占42.78%（438/1 024），共携带毒力基因1 274个，分别来自9个不同毒力因子家族，平均每个完整型原噬菌体携带毒力基因2.9个。【结论】大肠杆菌普遍携带原噬菌体，原噬菌体中部分携带耐药基因与毒力基因，在实际应用中应充分评估其风险，防止原噬菌体造成的耐药基因与毒力基因在菌株之间的转移。

关键词: 大肠杆菌; 原噬菌体; 耐药基因; 毒力基因

Abstract: 【Objective】 This study was aimed to study the proportion of prophages carried by Escherichia coli (E.coli) and the virulence genes as well as drug resistance genes carried by prophages, understand the effect of prophages in pathogenic E.coli on drug resistance and virulence of strains, ensure the biosafety of phage-producing bacteria, and provide a reference for the basic research and application of E.coli phages.【Method】 In this study, the whole genome information of E.coli was downloaded from NCBI, the number of prophages carried in E.coli through the online website was predicted, the genomic characteristics such as GC content, genome size, and proportion of bacterial genome of prophages and the type of intact prophages were analyzed, a preliminary classification of prophages was made, and the intact prophages carrying drug resistance genes, the number of drug resistance genes, drug resistance phenotypes, drug resistance mechanisms and virulence genes, and the distribution of virulence gene families were also statistically analyzed.【Result】 112 strains of E.coli carried 1 024 intact prophages, 287 questionable prophages, and 505 incomplete prophages.Most of the 1 024 intact prophages were similar to long tailed phages, accounting for 70.21% (719/1 024).There were 63 phage types in 1 024 complete type prophages, among which the phage BP4795 (accession No.:NC_004813.1) type accounted for the highest proportion, reaching 19.24%(197/1 024), followed by the phage DE3(accession No.:NC_042057.1), accounting for 11.72%(120/1 024).The GC content of E.coli carrying prophage was 38%-57%, E.coli prophage genomes vary in size was 3.1-152.6 kb, prophages within 80 kb accounted for 97.03%(1 762/1 816).65 of 1 024 complete prophages carried resistance genes, and a total of 253 carried resistance genes, which were from 11 antibiotic resistance gene families, respectively, and the complete prophage resistance gene carriage rate was 6.35%;Out of 1 024 prophages, 438 of the prophages carrying one or more virulence genes, with a high carriage rate of 42.78%, carried a total of 1 274 virulence genes, and on average each complete type prophage carried 2.9 virulence genes, from 9 different virulence factor families, respectively.【Conclusion】 E.coli usually carried prophages, and parts of the prophages carried drug resistance genes and virulence genes.The risk should be fully evaluated in practical application, attention should be paid to prevent the transfer of drug resistance genes and virulence genes caused by prophages between the strains.

Key words: Escherichia coli; prophage; resistance gene; virulence gene

中图分类号:

Q939.48

祝希辉, 庞喆羽, 王志伟, 裴兰英, 曹胜亮, 薛希娟, 李玉保. 致病性大肠杆菌携带原噬菌体的预测及耐药性与毒力研究[J]. 中国畜牧兽医, 2022, 49(3): 1126-1134.

ZHU Xihui, PANG Zheyu, WANG Zhiwei, PEI Lanying, CAO Shengliang, XUE Xijuan, LI Yubao. Prediction of Prophage Carrying by Pathogenic Escherichia coli and Its Drug Resistance and Virulence[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(3): 1126-1134.

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