铜绿假单胞菌前噬菌体的生物信息学分析

Bioinformatic Analysis of Prophages Carried by Pseudomonas aeruginosa

目的预测分析83株铜绿假单胞菌中前噬菌体携带情况和分布特征,以及鉴定前噬菌体编码的抗生素耐药基因和毒力因子。方法采用Phaster在线工具对菌株基因组序列进行前噬菌体预测,采用Cadr数据库和Vfdb数据库进行耐药基因和毒力基因注释分析。结果83株铜绿假单胞菌中共检测出601条前噬菌体序列,其中完整型304条,不完整型161条,可疑型136条,平均每株铜绿假单胞菌中至少存在3条完整的前噬菌体。平均每株铜绿假单胞菌中携带的所有前噬菌体占其基因组长度比例约为2%~4%。61条前噬菌体预测到125个耐药基因,分别来自23个不同家族,产生7种耐药机制。356条前噬菌体共编码545个毒力基因,归类为119种毒力基因,编码78种相关毒力因子,平均每个前噬菌体携带1~2个毒力因子编码基因,少数前噬菌体携带3条及以上。毒力因子的宿主来源除了铜绿假单胞菌外,百日咳杆菌、微黄分枝杆菌、鸟分枝杆菌及其亚种、肺炎克雷伯菌及其亚种也占有较高来源比例。结论前噬菌体在铜绿假单胞菌中分布广泛且携带多种耐药和毒力基因,对铜绿假单胞菌耐药性获得、传播和致病性演变具有重要影响。

Objective To determine the virulence factors and antibiotic resistance genes encoded by prophage,as well as to predict and assess the prophage carrier and distribution properties in 83 strains of Pseudomonas aeruginosa.Methods Phaster network database was used to compare and predict phage gene sequences,Cadr database and Vfdb database were used to compare drug resistance genes and virulence genes,respectively.Results A total of 601 prophage sequences were detected in 83 strains of Pseudomonas aeruginosa,of which 304 were intact,161 were incomplete and 136 were questionable.On average,there were at least 3 complete prophage sequences in each strain of Pseudomonas aeruginosa.On average,the proportion of all prophages carried by each Pseudomonas aeruginosa strain in its genome is about 2%to 4%.Sixty-one prophages predicted 125 resistance genes,each from 23 different families,resulting in seven resistance mechanisms.356 prophages encode a total of 545 virulence genes,which are classified as 119 virulence genes encoding 78 related virulence factors.Each prophage typically carries one to two virulence factors,although some prophages carry three or more.Apart from Pseudomonas aeruginosa,other host sources of virulence factors included Bacillus pertussis,Mycobacterium flavum,Mycobacterium avium,and its subspecies,as well as Klebsiella pneumoniae and its subspecies.Conclusion Prophages are widely distributed in Pseudomonas aeruginosa and carry drug resistance and virulence genes,which have asignificant impact on the acquisition,transmission,and pathogenicity evolution of resistance in Pseudomonas aeruginosa.