The recent emergence of a highly related virulent Clostridium difficile clade with unique characteristics

Abstract

Objectives: Clostridium difficile is a major global human pathogen divided into five clades, of which clade 3 is the least characterized and consists predominantly of PCR ribotype (RT) 023 strains. Our aim was to analyse and characterize this clade. Methods: In this cohort study the clinical presentation of C. difficile RT023 infections was analysed in comparison with known 'hypervirulent' and non-hypervirulent strains, using data from the Netherlands national C. difficile surveillance programme. European RT023 strains of diverse origin were collected and whole-genome sequenced to determine the genetic similarity between isolates. Distinctive features were investigated and characterized. Results: Clinical presentation of C. difficile RT023 infections show severe infections akin to those seen with 'hypervirulent' strains from clades 2 (RT027) and 5 (RT078) (35%, 29% and 27% severe CDI, respectively), particularly with significantly more bloody diarrhoea than RT078 and non-hypervirulent strains (RT023 8%, other RTs 4%, p 0.036). The full genome sequence of strain CD305 is presented as a robust reference. Phylogenetic comparison of CD305 and a further 79 previously uncharacterized European RT023 strains of diverse origin revealed minor genetic divergence with >99.8% pairwise identity between strains. Analyses revealed distinctive features among clade 3 strains, including conserved pathogenicity locus, binary toxin and phage insertion toxin genotypes, glycosylation of S-layer proteins, presence of the RT078 four-gene trehalose cluster and an esculinase-negative genotype. Conclusions: Given their recent emergence, virulence and genomic characteristics, the surveillance of clade 3 strains should be more highly prioritized.

Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents

“…Minor clone strains of C. difficile are well-known to often remain susceptible to fluoroquinolones (Wiuff et al, 2011;Knight et al, 2015;Seugendo et al, 2018) or evolve various mutations in the gyrB gene and display reduced resistance to this group of antibiotics (Lee et al, 2014;Wasels et al, 2015;Shaw et al, 2019;Vernon et al, 2019). Though some of the genetic alterations in gyrB will confer some fitness gain onto the isolates (Wasels et al, 2015;Vernon et al, 2019), it is also well-established that these mutations will accord just a low-level resistance to moxifloxacin rendering the isolates "vulnerable" to exposure (Wasels et al, 2015;Vernon et al, 2019).…”

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

“…Several highly virulent CDT-producing strains, including ST1 (PCR ribotype [RT] 027), a lineage associated with major hospital outbreaks in North America, Europe, and Latin America ( He et al, 2013 ), are found in clade 2 (C2). Comparatively little is known about clade 3 (C3), although it contains ST5 (RT 023), a toxigenic CDT-producing strain with characteristics that may make laboratory detection difficult ( Shaw et al, 2020 ). C. difficile ST37 (RT 017) is found in clade 4 (C4) and, despite the absence of a toxin A gene, is responsible for much of the endemic CDI burden in Asia ( Imwattana et al, 2019 ).…”

Molecular characterization of pathogenicity locus (PaLoc) and tcdC genetic diversity among tcdAB Clostridioides difficile clinical isolates in Tehran, Iran

“…It is assumed that the different RTs within a certain toxinotype may have evolved from a common ancestral strain. This event could be due to independent mutations or horizontal gene transfer (HGT) that occurred in the PaLoc of an ancestral strain [4]. In a previous study, a sequence analysis of the 16S rRNA gene revealed that the strains with toxinotypes V, VI, and XI had a single base change when compared to the VPI 10463 strain [30].…”