咸阳市市售食品中单核细胞增生李斯特菌基因组特征及耐药和致病基因分析

Analysis of genomic characteristics,antimicrobial and pathogenic genes of Listeria monocytogens in commercial food in Xianyang City

目的采用全基因组测序技术对从咸阳市市售食品中分离的64株单核细胞增生李斯特菌(单增李斯特菌)的基因组特征,耐药和致病性基因进行分析。方法收集咸阳市市售食品中分离的64株单增李斯特菌,利用微量肉汤法进行药敏测定,同时进行全基因组测序,原始序列经拼接后利用生物信息学软件进行基因组注释、系统发育树构建及基因组特征和遗传原件分析。结果64株分离株对于氨苄西林、青霉素、美罗培南、复方新诺明、万古霉素5种抗生素结果均为敏感。其中2株分离株对2种抗生素产生抗性,分别为四环素和红霉素。全基因组测序分析表明,64株分离株分属3个谱系,分为15个克隆群(CC),以谱系Ⅰ和谱系Ⅱ为主;2株耐药株基因型与表型一致,耐药基因上下游遗传环境分析表明,这些基因的可能来源为猪丹毒杆菌、肠球菌和外源质粒。所有分离株均携带致病基因岛LIPI-1和LIPI-2,部分谱系Ⅰ菌株携带LIPI-3或LIPI-4,具有潜在致病风险。携带质粒和抗性相关基因的主要为谱系Ⅱ菌株。inl A基因提前终止突变均发生在谱系Ⅱ,可能降低菌株毒力。结论咸阳市市售食品中单增李斯特菌基因组结构相对稳定,菌株存在获得性耐药,且因携带更多毒力基因而产生潜在的高致病性菌株。谱系Ⅰ和谱系Ⅱ菌株在毒力基因、抗性相关基因和质粒携带方面均具有差异,显示不同CC型菌株的毒力和环境适应性存在差异,为咸阳市单增李斯特菌的监测和防控提供了参考数据。

Objective To use whole genome sequencing(WGS)to analysis the genomic characteristics,the antimicrobial resistance and virulence genotypes of 64 Listeria monocytogenes strains isolated from commercial food in Xianyang City.Methods Sixty four Listeria monocytogenes were isolated and the susceptibilities were determined by broth microdilution.After the whole genome sequencing,using bioinformatics software for genome annotation,phylogenetic tree construction,genome features and genetic components analysis.Results All isolates were found to be susceptible to ampicillin,Penicillin,meropenem,trimethoprim-sulfamethoxazole,vancomycin.2 isolates were resistant to tetracycline and erythromycin at the same time.All isotates were categorized into three different lineages and 15 CCs,LineageⅠandⅡwere the predominant types.The genotypes of 2 resistant isolates correlated well with its resistant phenotype.Up and down stream analysis of the genetic context,in which these resistant genes were found,suggested that they may have been acquired from Erysipelothrix rhusiopathiae,Enterococcus and plasmid.All the isolates harboured the LIPI-1 and LIPI-2,subset of lineageⅠisotates harboured LIPI-3 or LIPI-4 with potential pathogenicity.LineageⅡisotates harboured more plasmids and genes linked to stress adaptation.The premature stop codon(PMSC)mutation in inl A more frequently happened in lineageⅡand may reduce virulence.Conclusion The genome of Listeria monocytogenes in commercial food in Xianyang City is stable.Acquires resistance existed in this bacterium,and can be a potential public health risk due to its high harboring rate of virulence genes.LineageⅠand LineageⅡisolates were differ in virulence genes,stress adaptation genes and plasmids harboring,indicating differences among subtypes.This findings would be helpful to the surveillance and control of this foodborne pathogen in Xianyang City.