Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease
Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease
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DOI：
10.1038/s41598-018-20135-4
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发表时间：
2018-01-30
影响因子：
4.6
通讯作者：
Nielsen, Henrik
中科院分区：
文献类型：
--
作者：
Kirk, Karina Frahm;Meric, Guillaume;Nielsen, Henrik
密集弯曲杆菌是一种与炎症性肠病（IBD）相关的新型病原体，但对该菌的遗传多样性知之甚少。concisus关系到主机的壁龛和疾病。我们分离出104 C.从来自41个个体（26个IBD，3个胃肠炎（GE），12个健康对照（HC））的唾液、粘膜活检和粪便样品中分离浓缩物。全基因组测序和数据集泛基因组检查，基因组信息用于分型使用多位点序列分型（MLST）。C. concisus分离物聚成两个主要组/基因种（GS），代表71个不同的序列类型（ST）。取样地点（p < 0.001）而不是疾病表型（p = 1.00）与特定GS相关。我们确定了97个候选基因与增加或减少的患病率在解剖下降过程中，从口腔粘膜活检粪便。与细胞壁/膜生物合成相关的基因在口腔分离株中更常见，而与细胞运输、代谢和分泌途径相关的基因在肠道分离株中更普遍。此外，个体遗传多样性与临床表型之间没有相关性。本研究证实了C. concisus，并提供证据表明，基因组变异与分离的来源，而不是临床表型。
Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated 104 C. concisus isolates from saliva, mucosal biopsies and faecal samples from 41 individuals (26 IBD, 3 Gastroenteritis (GE), 12 Healthy controls (HC)). Whole genomes were sequenced and the dataset pan-genome examined, and genomic information was used for typing using multi-locus-sequence typing (MLST). C. concisus isolates clustered into two main groups/genomospecies (GS) with 71 distinct sequence types (STs) represented. Sampling site (p < 0.001), rather than disease phenotype (p = 1.00) was associated with particular GS. We identified 97 candidate genes associated with increase or decrease in prevalence during the anatomical descent from the oral cavity to mucosal biopsies to faeces. Genes related to cell wall/membrane biogenesis were more common in oral isolates, whereas genes involved in cell transport, metabolism and secretory pathways were more prevalent in enteric isolates. Furthermore, there was no correlation between individual genetic diversity and clinical phenotype. This study confirms the genetic heterogeneity of C. concisus and provides evidence that genomic variation is related to the source of isolation, but not clinical phenotype.