一株红霉素耐药百日咳鲍特菌的完整基因组分析

Complete genomic analysis of a erythromycin resistant Bordetella pertussisIsolate

目的明确国内一株红霉素耐药百日咳鲍特菌P2013109的全基因组序列,了解其基因特征。方法对一株抗原基因型为ptxA1/ptxC1/ptxP1/prn1/fim2⁃1/fim3⁃1/tcfA2的临床分离红霉素耐药百日咳鲍特菌P2013109采用了二代和三代高通量测序技术进行了全基因组测序,对基因组进行组装、基因预测和功能注释,并与包含我国疫苗株CS、国外疫苗株Tohama I,以及国外发表临床分离的共15株菌的完整基因组序列进行全基因组比较分析。结果P2013109的完整基因组序列总长度4126010 bp,GC含量为67.72%,预测基因有4085个。该基因组的所有拷贝23s rRNA基因均显示A2047G突变。相比P2013109,其他15株菌主要存在3个比较大的缺失区域。另外,将P2013109与其他16株进行系统发育树分析,显示全部菌株分成3个遗传分支。Tohama I和CS这两个疫苗株归类为Ⅰ型,它们与其他2个型别相比较呈现76个SNPs。P2013109独立为Ⅱ型,与其他菌株的进化关系相对较远,相比较其他菌株呈现25个SNPs。国外菌株为Ⅲ型,与其他菌株相比呈现21个SNPs。结论国内当前流行的红霉素耐药百日咳鲍特菌具有独特的系统发育分支,其遗传进化与疫苗株和国外流行菌株不同。

Objective To determine the entire genome sequence of a domestic erythromycin resistant Bordetella pertussis P2013109 and understand its genetic characteristics.Methods The strain P2013109 with antigen type ptxA1/ptxC1/ptxP1/prn1/fim2⁃1/fim3⁃1/tcfA2 was sequenced using the Illumina Hiseq 2000 and Pacbio platforms.After complete genome assembly,gene prediction and function annotation were processed for further analysis.15 other strains containing China vaccine strain CS and Tohama I were then adopted to perform comparison analysis.Results The whole genome of P2013109 is 4126010 bp with GC content of 67.72%,and 4085 predicted ORFs encoded.All of the 23s rRNA gene locus display the A2047G mutation.Comparing with P2013109,3 long fragments are missing from the genomes ofthe 15 other strains.The phylogenetic tree analysis showed that all strains exhibited 3 lineages,of which the two vaccine strains CS and Tohama I belonged to lineage I,displaying 76 SNPs in comparison to the other two lineages.However,lineageⅡincluded only P2013109,which was divergent from the others by 25 SNPs.The remaining strains were grouped into lineageⅢby 21 lineage⁃specific SNPs.Conclusion The endemic erythromycin resistant Bordetella pertussis in China showed a specific phylogenetic lineage,which was different from the vaccine strains and foreign endemic strains in its genetic evolution.