食源性单增李斯特菌与英诺克李斯特菌基因组特征比较

Comparative genomic analysis of foodborne Listeria monocytogenes and Listeria innocua

目的通过全基因组测序对甘肃省市售食品中分离的单增李斯特菌和英诺克李斯特菌基因组特征进行比较分析。方法收集2021—2022年甘肃省市售食品中分离的25株单增李斯特菌和7株英诺克李斯特菌作为研究对象,对菌株进行全基因组测序,分析其系统发育谱系、克隆复合群(CC)、序列型(ST)、毒力基因、抗性基因及泛基因组。结果32株李斯特菌分属单增李斯特菌谱系Ⅰ和Ⅱ及英诺克李斯特菌3个群,单增李斯特菌分为10个亚群,英诺克李斯特菌分为5个亚群,与CC型保持一致,核心基因组多位点序列分型能将各谱系中不同CC型的菌株明显分开,谱系Ⅰ与英诺克李斯特菌的进化关系更近。25株单增李斯特菌均携带李斯特菌毒力岛LIPI-1和内化素基因,不携带LIPI-3,有2株ST87型菌株携带LIPI-4;7株英诺克李斯特菌均不携带LIPI-1和内化素基因,均携带LIPI-4,有5株菌携带LIPI-3。单增李斯特菌有16株携带SSI-1、3株携带SSI-2,7株英诺克李斯特菌均不携带SSI-1,有6株携带SSI-2。李斯特菌的泛基因组大小随着测序基因组数目的增加呈现线性增多,25株单增李斯特菌当菌株数量达到15后核心基因数目稳定在2272个,占泛基因组基因数目的46.2%,25株单增李斯特菌和7株英诺克李斯特菌共同的核心基因1487个,当菌株数量达到10后数目趋于稳定。结论核心基因组多位点序列分型可将不同谱系不同克隆复合群的李斯特菌进行区分,英诺克李斯特菌与单增李斯特菌生化特性相似与其亲缘关系相近有关,致病性差异与英诺克李斯特菌缺失单增李斯特菌特有的毒力基因相关。

Objective To utilize whole genome sequencing to comprehensively compare and analyze the genomic characteristics of Listeria monocytogenes(L.monocytogenes)and Listeria innocua(L.innocua)isolated from commercially available foods in Gansu Province.Methods During 2021 and 2022,25 strains of L.monocytogenes and 7 strains of L.innocua were isolated from commercially available food sources within Gansu Province and subjected to whole genome sequencing for phylogenetic lineage,clonal complex(CC),sequence type(ST),virulence gene,resistance gene,and pan-genome analyses.Results The 32 Listeria strains examined could be classified into three distinct groups:L.monocytogenes lineagesⅠandⅡand L.innocua.Considering their CC types,further subdivision into 10 subgroups was observed for L.monocytogenes,whereas L.innocua had 5 subgroups.Core genome multi-locus sequence typing effectively differentiated strains with different CC types within each lineage,with lineageⅠshowing a closer evolutionary relationship with L.innocua.All 25 L.monocytogenes strains carried Listeria pathogenicity island 1(LIPI-1)and internalin genes;none carried LIPI-3,and 2 strains of ST87 carried LIPI-4.Conversely,none of the seven strains of L.innocua carried LIPI-1 or internalin genes;however,they all carried LIPI-4,and 5 carried LIPI-3.Among the L.monocytogenes strains,16 carried surface sensory island 1(SSI-1),and 3 carried SSI-2;all 7 L.innocua strains did not carry SSI-1,but 6 of them carried SSI-2.The pan-genome size of L.monocytogenes increased linearly with the number of sequenced genomes.Upon reaching 15 strains,the number of core genes stabilized at 2272,accounting for 46.2%of the pan-genome genes.Furthermore,1487 common core genes were shared between the 25 L.monocytogenes strains and 7 L.innocua strains,with the count tending to stabilize when the strain count reached 10.Conclusion Multi-locus sequence typing of the core genome can effectively distinguish among Listeria strains originating from different lineages and CCs.The similarity in the biochemical characteristics of L.monocytogenes and L.innocua is due to their close genetic relationship,while the differences in their pathogenicity can be attributed to the presence of certain virulence genes in L.monocytogenes.