Kuley Runa, Kuijt Eric, Smits Mari A, Roest Hendrik I J, Smith Hilde E, Bossers Alex
Department of Infection Biology, Wageningen Bioveterinary ResearchLelystad, Netherlands.
Host Microbe Interactomics, Wageningen University and Research CentreWageningen, Netherlands.
Front Microbiol. 2017 Aug 10;8:1526. doi: 10.3389/fmicb.2017.01526. eCollection 2017.
is an obligate intracellular bacterium and the etiological agent of Q fever. During 2007-2010 the largest Q fever outbreak ever reported occurred in The Netherlands. It is anticipated that strains from this outbreak demonstrated an increased zoonotic potential as more than 40,000 individuals were assumed to be infected. The acquisition of novel genetic factors by these outbreak strains, such as virulence-related genes, has frequently been proposed and discussed, but is not proved yet. In the present study, the whole genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few additionally selected strains from different geographical locations and publicly available genome sequences were used for a comparative bioinformatics approach. The study focuses on the identification of specific genetic differences in the outbreak related CbNL01 strains compared to other strains. In this approach we investigated the phylogenetic relationship and genomic aspects of virulence and host-specificity. Phylogenetic clustering of whole genome sequences showed a genotype-specific clustering that correlated with the clustering observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA). Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP) analysis of complete genome sequences demonstrated the presence of genotype-specific gene contents and SNP variations in strains. It also demonstrated that the currently used MLVA genotyping methods are highly discriminatory for the investigated outbreak strains. In the fully reconstructed genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a relatively large number of transposon-linked genes were identified as compared to the other published complete genome sequences of . Additionally, large numbers of SNPs in its membrane proteins and predicted virulence-associated genes were identified in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.
是一种专性胞内细菌，也是Q热的病原体。在2007年至2010年期间，荷兰发生了有史以来报告的最大规模的Q热疫情。据推测，由于假定有超过40000人被感染，此次疫情中的菌株显示出更高的人畜共患病潜力。这些疫情菌株获得新的遗传因子，如毒力相关基因，这一点经常被提出和讨论，但尚未得到证实。在本研究中，使用了几株荷兰菌株（CbNL01和CbNL12基因型）的全基因组序列、另外从不同地理位置选择的一些菌株以及公开可用的基因组序列进行比较生物信息学分析。该研究的重点是确定与其他菌株相比，与疫情相关的CbNL01菌株中的特定遗传差异。在这种方法中，我们研究了毒力和宿主特异性的系统发育关系及基因组方面。全基因组序列的系统发育聚类显示出基因型特异性聚类，这与使用多位点可变数目串联重复分析（MLVA）观察到的聚类相关。对预测基因的直系同源分析和完整基因组序列的单核苷酸多态性（SNP）分析表明，菌株中存在基因型特异性基因内容和SNP变异。这也表明，目前使用的MLVA基因分型方法对所研究的疫情菌株具有高度鉴别力。在CbNL01基因型的荷兰疫情NL3262菌株的完全重建基因组序列中，与其他已发表的该菌完整基因组序列相比，鉴定出相对大量的转座子相关基因。此外，与NM参考菌株和CbNL12基因型的其他菌株相比，在所有荷兰疫情菌株中其膜蛋白和预测的毒力相关基因中鉴定出大量SNP。大量转座元件和突变基因的存在，很可能导致了疫情菌株高水平的基因组重排和基因型特异性致病性。因此，荷兰疫情菌株的流行潜力可能与基因组可塑性增加以及毒力和逃避宿主免疫系统相关关键基因的突变有关。
