16株军团菌全基因组比较及重要毒力因子分析北大核心CSCD

目的运用生物信息学方法,分析军团菌参考菌株全基因组序列,了解军团菌基因组特征,比较不同菌株间的毒力因子、耐药基因以及种系发生,为进一步研究军团菌基因组流行病学、遗传进化提供数据。方法选择NCBI公共数据库中基因组序列完整、背景清楚、不同来源(临床、外环境)和不同种的代表性军团菌16株,运用开源基因组数据分析平台RAST、MAUVE、VFDB、CARD等进行生物信息学分析。结果16株参考菌株基因组大小在(3.13~4.23)Mbp,编码基因(CDSs)3018~3954个,划分为265~387个亚系统。同种军团菌基因组结构基本相同,非嗜肺军团菌(非LP)不同菌株之间基因组结构差异大,同时存在较多非保守区域。嗜肺军团菌血清I型(LP1)和米克戴德军团菌(L.micdadei)各属于1个种系进化主分枝,LP1细分为3个小分枝。临床分离的LP1携带的毒力因子类别和数量最多。菌株YU237缺失Dot/Icm T4BSS分泌系统,其余参考菌株都具有分泌系统的4种毒力因子,临床分离的LP1携带的T4BSS效应蛋白毒力因子数量为31~35个,其它参考菌株3~5个。16株参考菌株都携带有adeF耐药基因,部分菌株携带有LpeA、LpeB、FEZ-1耐药基因。结论不同种的军团菌基因组存在差异,而种内相对保守;相对于临床分离株,外环境非LP不同菌株基因组种间差异大。LP1军团菌存在遗传分化现象。毒力因子种类和数量跟LP1军团菌的致病力相关,特别是T4BSS效应蛋白。全基因组生物信息分析技术,可以对可能的耐药基因进行预测,为临床治疗提供辅助参考,同时可以解析病原菌的遗传和功能特征。

Comparative genemics of 16 Legionella species reference strains and analysis of virulence factors

Several species in the Legionella genus are pathogenic to humans. To compare genomic characterization, virulence genes, antibiotic resistance and phylogenetic relationships within Legionella species, we analyzed the whole genome sequences of 16 reference strains with bioinformatic platforms, including RAST, MAUVE, VFDB and CARD. The genome sizes of the 16 reference strains ranged from 3.13 Mbp to 4.23 Mbp, and contained 3 018 to 3 954 coding sequences that were divided into 265 to 387 subsystems. MAUVE-based multiple genome alignment revealed a similar genome structure within species for L. pneumophila, whereas a distinct genome structure and considerably more non-conserved regions were observed in non-L. pneumophila strains. On the phylogenetic tree, LP1 and L. micdadei strains belonged to two main branches, although LP1 strains consisted of three branches. Environmental non-L. pneumophila strains were divided into two branches. Clinical LP1 strains possessed more virulent factors than environmental LP1 and non-LP isolates. Except for the deletion of Dot/Icm T4BSS in strain YU237, the other strains possessed four virulence factors of the type IV secretion system. Notably, clinical LP1 strains contained 31-35 effectors of T4BSS, whereas effectors in other reference strains contained three to five effectors. The antimicrobial resistance gene adeF was detected in all 16 reference strains, and LpeA, LpeB and FEZ-1 genes were occasionally detectable. Therefore, whole genome analysis indicated that Legionella species differed in genome structure at the interspecies level but showed relative conservation at the intraspecies level. Distinct variations were observed in the genomes of environmental non-LP isolates rather than clinical isolates. Genomic comparison also demonstrated genetic variation within LP1 strains. Virulence factor classes and numbers, especially for T4BSS effector proteins, were associated with the pathogenicity of LP1 strains. In summary, bioinformatic analysis of whole genome sequences can predict potential antimicrobial resistance genes, provide complementary information for clinical treatment, and enable comprehensive genetic and functional characterization of pathogenic Legionella species.