Clostridioides difficile is a One Health pathogen found in humans, animals, and environment, with food representing a potential transmission route. One Health studies are often limited to single country or selected reservoirs and ribotypes. This study provides a varied and accessible collection of C. difficile isolates and sequencing data derived from human, animal, and food sources across thirteen European countries. A total of 441 strains (human hospital and community associated cases n = 280, animal n = 96, food n = 65) were analysed by ribotyping, toxinotyping and whole genome sequencing (WGS). We detected 83 sequence types (STs), with ST11 (n = 80 isolates) and ST1 (n = 54 isolates) being the most represented. Several STs included strains originating from all source combinations. Further genomic analysis confirmed close genetic relatedness in some of the STs. Additionally, genomic analysis identified ten strains from cryptic clades (C-I to C-III) and four of them were mono-toxigenic possessing only a variant form of tcdA gene. Amongst 106 ribotypes, ten were shared between all three sources and 68 were source specific. Some ribotypes were only found at intersection of human and food source (RT023, RT027), or between human and animal source (RT009, RT045, RT046). C. difficile ribotypes and STs in Europe were diverse. In this collection some ribotypes showed potential association with food or animal transmission routes. C. difficile strains from divergent clades CI-III, currently emerging in human population, were rare and mostly food associated.

中文翻译：

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艰难梭菌核糖型和序列类型在 13 个欧洲国家中在人类、动物和食物中的分布。


艰难梭菌是一种在人类、动物和环境中发现的 One Health 病原体，食物是一种潜在的传播途径。One Health 研究通常仅限于单个国家或选定的储库和核糖型。本研究提供了来自 13 个欧洲国家的人类、动物和食物来源的艰难梭菌分离株和测序数据。通过核糖分型、毒素分型和全基因组测序 （WGS） 分析了总共 441 种菌株 （人类医院和社区相关病例 n = 280，动物 n = 96，食物 n = 65）。我们检测到 83 种序列类型 （STs），其中 ST11 （n = 80 个分离株） 和 ST1 （n = 54 个分离株） 代表性最强。几个 STs 包括来自所有来源组合的菌株。进一步的基因组分析证实了一些 ST 的密切遗传相关性。此外，基因组分析确定了来自隐蔽分支 （C-I 至 C-III） 的 10 个菌株，其中 4 个是单毒的，仅具有 tcdA 基因的变体形式。在 106 种核糖型中，10 种在所有三个来源之间共享，68 种是来源特异性的。一些核糖型仅在人类和食物来源的交集处 （RT023， RT027） 或人与动物来源之间 （RT009， RT045， RT046） 发现。欧洲的艰难梭菌核糖型和 STs 是多种多样的。在这个集合中，一些核糖型显示出与食物或动物传播途径的潜在关联。目前在人类中出现的不同分支 CI-III 的艰难梭菌菌株很少见，并且主要与食物有关。