来自临床,动物,植物和环境来源的Clostridium butyricum菌株的基于全基因组测序的分型方法
Nadim Cassir1,2,3,4, Victoria Mesa1, Laurent Ferraris1
1Université Paris Cité, Inserm, U1139, FPRM, Paris, France.
Microbiology spectrum
|December 12, 2025
概括
使用cgMLST和cgSNP方案进行Clostridium butyricum的高分辨率基因定型,有助于追踪这种机会性病原体. 这些方法改善了监测和疫情调查,特别是与新生儿死性肠球炎 (NEC) 相关的菌株.
科学领域:
- 微生物学和分子流行病学
- 基因组学和生物信息学
- 传染病监测 传染病监测 传染病
背景情况:
- Clostridium butyricum具有双重作用,作为一种有益的益生菌和一种机会性病原体,涉及新生儿死性肠球炎 (NEC) 和婴儿肉毒症.
- 准确的分子类型确定对于有效监测和对C. butyricum疫情的调查至关重要,特别是在新生儿重症监护病房.
研究的目的:
- 开发和验证高分辨率的基因型化框架,特别是核心基因组多部位序列类型化 (cgMLST) 和核心基因组单核酸多态化 (cgSNP) 分析,用于C. butyricum.
- 加强对C.butyricum的分子监测和疫情调查能力,重点关注新生儿环境中的临床分离物.
主要方法:
- 对297个C.butyricum基因组的分析,包括20年来来自法国新生儿重症监护室的200个分离物和97个公共基因组.
- 使用chewBBACA开发cgMLST方案,定义2621个位点,并应用于高位点存在的基因组.
- 补充cgSNP分析以获得更好的分辨率,特别是与NEC相关的菌株.
主要成果:
- 遗传学cgMLST将分离物分为9个分类;特定的分类被确定为与植物相关的和产生E型肉毒神经毒素的菌株.
- 与NEC相关的分离物体表现出地理和时间的聚类,但没有单一的类单独与NEC联系在一起.
- cgSNP分析显示了比cgMLST更高的歧视力,为NEC菌株之间的相关性提供了更好的分辨率.
结论:
- 开发的cgMLST和cgSNP方案为C. butyricum提供了强大的,高分辨率的基因型鉴定.
- 这些基因组工具对于改善流行病学监测和促进新生儿群体中C.butyricum爆发调查至关重要.
- 虽然NEC菌株显示集群,但没有特定的遗传基因单元与该病症独特相关,这突显了其病因学的复杂性.
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