Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027)Clostridioides difficile

Abstract

Clostridioides difficile (C. difficile), a leading cause of nosocomial infection, produces toxins that damage the colonic epithelium and results in colitis that varies from mild to fulminant. Variation in disease severity is poorly understood and has been attributed to host factors (age, immune competence and intestinal microbiome composition) and/or virulence differences between C. difficile strains, with some, such as the epidemic BI/NAP1/027 (MLST1) strain, being associated with greater virulence. We tested 23 MLST1(ST1) C. difficile clinical isolates for virulence in antibiotic-treated C57BL/6 mice. All isolates encoded a complete Tcd pathogenicity locus and achieved similar colonization densities in mice. Disease severity varied, however, with 5 isolates causing lethal infections, 16 isolates causing a range of moderate infections and 2 isolates resulting in no detectable disease. The avirulent ST1 isolates did not cause disease in highly susceptible Myd88-/- or germ-free mice. Genomic analysis of the avirulent isolates revealed a 69 base-pair deletion in the N-terminus of the cdtR gene, which encodes a response regulator for binary toxin (CDT) expression. Genetic deletion of the 69 base-pair cdtR sequence in the highly virulent ST1 R20291 C. difficile strain rendered it avirulent and reduced toxin gene transcription in cecal contents. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile strain without reducing colonization and persistence in the gut. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.

Genomic surveillance ofClostridioides difficiletransmission and virulence in a healthcare setting

“…Importantly 4a). The latter finding supports previous data indicating that clade 2 isolates are hypervirulent, often attributed to the presence of the binary toxin operon or increased expression from the PaLoc 19,56,57 . Meanwhile, some clade 1 isolates contain no toxin genes, indicating a diversity of colonization strategies in this lineage.…”

Protection againstClostridioides difficiledisease by a naturally avirulentC. difficilestrain

“…Protection by the avirulent ST1-75 is not due to differences in the lysogenic phages between strains. ST1-75 harbors two unique prophages in its genome, namely phiCD75-2 and phiCD75-3, which can become infectious upon induction (27). Prophages can determine the susceptibility of the bacterial host to phage infections via superinfection exclusion or other anti-phage defense systems (30)(31)(32).…”

Unique growth and morphology properties of Clade 5Clostridioides difficilestrains revealed by single-cell time-lapse microscopy

“…Thus, analyzing more strains within a clade may reveal fewer differences between clades. A caveat to our analyses is that C. difficile strains exhibit considerable genetic diversity even within a ribotype (20,22), so our conclusions may only reflect the behavior of RT078 Clade 5 strains. It is also possible that analyzing more strains within this ribotype will reveal a broader spectrum of phenotypes than the somewhat bimodal ones we have reported with respect to cell length and chaining propensity (Figures 2, 3).…”

“…Notably, RT027 (ST1), RT017 (ST45), and RT078 (ST11) strains are from ribotypes/ multilocus sequencing types that are frequently isolated from patients with C. difficile infection (CDI) (12,19,22,25).…”

“…These epidemic strains can also cause severe disease symptoms in part due to their production of three toxins: TcdA, TcdB, and CDT (binary toxin) (6). Although RT027 strains have frequently been associated with "hypervirulence," there is considerable phenotypic diversity within this lineage with respect to virulence, toxin production levels, and sporulation (20)(21)(22).…”