Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
National Institute for Biological Standards and Controls (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK.
Sci Rep. 2019 Oct 25;9(1):15330. doi: 10.1038/s41598-019-51628-5.
The major global pathogen Clostridium difficile (recently renamed Clostridioides difficile) has large genetic diversity including multiple mobile genetic elements. In this study, whole genome sequencing of 86 strains from the poorly characterised clade 3, predominantly PCR ribotype (RT)023, of C. difficile revealed distinctive surface architecture characteristics and a large mobile genetic island. These strains have a unique sortase substrate phenotype compared with well-characterised strains of C. difficile, and loss of the phage protection protein CwpV. A large genetic insertion (023_CTnT) comprised of three smaller elements (023_CTn1-3) is present in 80/86 strains analysed in this study, with genes common among other bacterial strains in the gut microbiome. Novel cargo regions of 023_CTnT include genes encoding a sortase, putative sortase substrates, lantibiotic ABC transporters and a putative siderophore biosynthetic cluster. We demonstrate the excision of 023_CTnT and sub-elements 023_CTn2 and 023_CTn3 from the genome of RT023 reference strain CD305 and the transfer of 023_CTn3 to a non-toxigenic C. difficile strain, which may have implications for the use of non-toxigenic C. difficile strains as live attenuated vaccines. Finally, we show that the genes within the island are expressed in a regulated manner in C. difficile RT023 strains conferring a distinct "niche adaptation".
主要的全球病原体艰难梭菌（最近更名为艰难梭菌）具有包括多个移动遗传元件在内的巨大遗传多样性。在这项研究中，对 86 株来自特征不明显的 3 型分支、主要为 PCR 核糖体型（RT）023 的艰难梭菌进行了全基因组测序，揭示了独特的表面结构特征和一个大型移动遗传岛。与特征明确的艰难梭菌菌株相比，这些菌株具有独特的分选酶底物表型，并且缺失噬菌体保护蛋白 CwpV。在本研究分析的 86 株菌株中，有 80/86 株存在一个由三个较小元件（023_CTn1-3）组成的大型遗传插入（023_CTnT），其中包含与肠道微生物组中其他细菌菌株共同的基因。023_CTnT 的新型货物区域包括编码分选酶、假定的分选酶底物、类细菌素 ABC 转运蛋白和假定的铁载体生物合成簇的基因。我们证明了 RT023 参考菌株 CD305 基因组中 023_CTnT 及其亚元件 023_CTn2 和 023_CTn3 的切除，以及 023_CTn3 向非产毒艰难梭菌菌株的转移，这可能对非产毒艰难梭菌菌株作为活减毒疫苗的应用产生影响。最后，我们表明，该岛上的基因在艰难梭菌 RT023 菌株中以受调控的方式表达，赋予其独特的“生态位适应”。
