Clostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo

Helen Alexandra Shaw,Jeroen Corver,Ladan Khodadoost,Mark D Preston,Brendan W Wren,Peter Mullany

doi:10.1038/s41598-019-51628-5

Abstract

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”.

Highlights

Have a modified cell surface and contain a large transposable island with novel cargo Helen Alexandra Shaw 1,2*, Ladan Khodadoost[3], Mark D
Clade 3 strains contain a truncated protease PPEP-1 resulting in permanent association of cell wall protein CD2831
There is a 2 bp deletion in the reference strain CD305 PPEP-1 homologue (CD305_03825) introducing an in frame stop codon (Fig. 1a) that was consistent between all strains in this clade (Supplementary Table S1)

Summary

Introduction

Have a modified cell surface and contain a large transposable island with novel cargo Helen Alexandra Shaw 1,2*, Ladan Khodadoost[3], Mark D. 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. Acquisition of loci could be related to outbreaks, such as observed in an RT017 outbreak in a London hospital where strains harboured a transposon newly observed in C. difficile strains[17] These occurrences add to the genome plasticity of the C. difficile species

Methods

Results

Conclusion