大肠杆菌J2_5的全基因组测序及比较基因组分析

Whole genome sequencing and comparative genomics analysis of Escherichia coli J2_5

目的:分析多耐药大肠杆菌J2_5的进化分群、耐药基因及毒力基因,为临床诊断及用药提供理论依据。方法:采用高通量测序法对J2_5进行全基因组测序,并使用多种生物信息学工具和数据库进行数据比对分析。结果:该菌的全基因组总长度为4.7 Mb,GC含量为50.78%。多位点序列分型(MLST)分析发现其ST型为ST2491,和大肠杆菌野生株MG1655分型ST10不同。系统发育树进一步分析表明J2_5与MG1655的亲缘关系较近。抗生素耐药性综合数据库(CARD)分析发现该菌有65个耐药基因,主要通过4类耐药机制(抗生素外排泵、抗生素失活、抗生素靶点改变、降低对抗生素的渗透性)产生耐药性。毒力因子数据库(VFDB)分析发现该菌有7类40个毒力基因,编码黏附素、侵袭、自主转运蛋白等毒素蛋白。使用Prophage Hunter网上工具发现J2_5基因组存在3个前噬菌体,并且前噬菌体上带有1个毒力基因。结论:全基因组测序结果表明J2_5携带更多的毒力基因及耐药基因,是其致病性强和具有多种抗生素耐药性的原因。

Objective:A novel multidrug resistant(MDR)Escherichia coli(E.coli)strain J2_5 was isolated from a patient’s midstream urine sample.According to the genome sequence of J2_5,we analyzed its evolutionary classification,drug resistance genes and virulence genes,providing theoretical basis for clinical diagnosis and drug selection for drug resistant bacterial infection.Methods:Genome DNA of J2_5 was isolated and sequenced by high-throughput sequencing technology,after analyzed the high-throughput sequencing data and compared it with known databases by a variety of bioinformatics tools,a high integrity genome of J2_5 was obtained.Results:The total length of the whole genome of J2_5 was 4.7Mb and GC content was 50.78%.Phylogenetic tree analysis showed that J2_5’genome was closely related to that of wild type E.coli strain MG1655.But Multilocus sequence typing(MLST)analysis revealed ST type of J2_5 was ST2491,which was different from that of MG1655(ST10).Furthermore,CARD database analysis showed that the genome of J2_5 encodes 65 drug resistance genes,which make the strain obtain drug-resistant ability through four different mechanisms(antibiotic efflux pump,antibiotic inactivation,antibiotic target change,reduced permeability to antibiotics).VFDB database analysis showed that there were 40 virulence genes in 7 categories,encoding adhesive proteins,invasion proteins,autonomic transporters and other toxin proteins.After analyzing the whole genome of J2_5 through the Prophage Hunter online tool,we found that there were three prophages in the genome of J2_5,and a virulence gene was carried by one of the prophages.Conclusion:The whole genome sequencing results showed that J2_5 carries some virulence genes and drug resistance genes,which makes the strain obtain strong pathogenicity and resistance ability to a variety of antibiotics.