鲍曼不动杆菌携带前噬菌体的生物信息学分析

Bioinformatic analysis of prophages carried by Acinetobacter baumannii

摘要:

[目的] 预测并分析82株全基因组测序的鲍曼不动杆菌前噬菌体的携带情况，鉴定前噬菌体编码的抗生素耐药基因和毒力因子。[方法] 利用PHASTER （Phage Search Tool Enhanced Release）软件预测鲍曼不动杆菌携带的前噬菌体，采用CARD （The Comprehensive Antibiotic Research Database）和VFDB （Virulence Factors Database）在线分析软件预测前噬菌体编码的抗生素耐药基因和毒力因子。[结果] 预测到472条鲍曼不动杆菌前噬菌体，其中完整型前噬菌体201条，疑似型前噬菌体91条，缺陷型前噬菌体180条。平均每株鲍曼不动杆菌基因组中可携带至少2条完整型前噬菌体。每株鲍曼不动杆菌所携带的全部前噬菌体占其基因组比例约为4%-6%。29条前噬菌体携带77个耐药基因，耐药表型共有14种，分别来自15个不同的家族，涵盖6种抗生素耐药的作用机制。132条前噬菌体编码毒力基因，归类为38种毒力基因和34种毒力因子。不同类型的前噬菌体普遍携带1-2种毒力因子，少数前噬菌体携带3种及以上毒力因子。分析毒力因子可能的宿主来源构成比发现，除鲍曼不动杆菌外，脑膜炎奈瑟菌、痢疾志贺氏菌、嗜肺军团菌及其亚种等也有较高的结构比例，是可能的宿主来源。[结论] 鲍曼不动杆菌普遍携带前噬菌体，但前噬菌体基因在鲍曼不动杆菌基因组中所占比例不高。部分前噬菌体携带抗生素耐药基因，以氨基糖苷类、磺胺类及β-内酰胺类耐药为主。约30%的前噬菌体携带毒力基因。前噬菌体可能在鲍曼不动杆菌抗生素耐药性的获得、传播及致病性演变中发挥重要作用。

Abstract:

[Objective] To analyze the prophages carried by 82 strains of Acinetobacter baumannii with completely sequenced genomes, then identify antibiotic resistance genes and virulence factors encoded by prophages. [Methods] Phage Search Tool Enhanced Release (PHASTER) software was used to predict the prophages carried by A. baumannii. The Comprehensive Antibiotic Research Database (CARD) and Virulence Factors Database (VFDB) online analysis software were used to predict the antibiotic resistance genes and virulence factors encoded by the prophages, respectively. [Results] A total 472 prophages were found, of which 201 were "intact", 91 were "questionable", and 180 were "incomplete". On average, at least two intact prophages were carried per A. baumannii genome. The percentage of the prophage genome ranged between 4% and 6% in each A. baumannii genome. Twenty-nine out of the 472 prophages carried 77 resistance genes, which belong to 14 different antimicrobial types, could be grouped into 15 different drug families, and could be classified into six antibiotic resistance mechanisms. One hundred and thirty-two out of the 472 prophages encode putative virulence genes, grouped into 38 virulence gene and 34 virulence factor classes. Most of these prophages encode one or two virulence factors, and a few of them encode three or more virulence factors. Analysis of component ratios of possible virulence factor host sources indicated Neisseria meningitidis, Shigella dysenteriae, and Legionella pneumophila, as well as A. baumannii, as host sources.[Conclusion] A. baumannii generally carries prophages, but the proportion of prophage genes in the genome of A. baumannii is not high. Some prophages carry antibiotic resistance genes, mainly aminoglycosides, sulfonamides, and beta-lactams. Nearly 30% of the prophages carry virulence genes. Prophages may play an important role in the acquisition and spread of antibiotic resistance, and evolution of pathogenicity in A. baumannii.