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

• DOI: 10.1016/j.cmi.2019.09.004
• Publication Date: 2019-09-13T23:11:56Z
• Authors: H.A. Shaw; M.D. Preston; K.E.W. Vendrik; M.D. Cairns; H.P. Browne; R.A. Stabler; M.J.T. Crobach; J. Corver; H. Pituch; A. Ingebretsen; M. Pirmohamed; A. Faulds-Pain; E. Valiente; T.D. Lawley; N.F. Fairweather; E.J. Kuijper; B.W. Wren
• Keywords: Adult; Diarrhea; Male; 0301 basic medicine; Adolescent; Clade 3; Article; S-layer; Cohort Studies; 03 medical and health sciences; Clostridium difficile infection; Humans; Child; RT023; Aged; Netherlands; Aged, 80 and over; Clostridioides difficile; Trehalose; High-Throughput Nucleotide Sequencing; Infant; Clostridium difficile; Middle Aged; Hospitals; Bacterial Typing Techniques; 3. Good health; Child, Preschool; Next-generation sequencing; Clostridium Infections; Female; Multilocus Sequence Typing

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.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.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.Given their recent emergence, virulence and genomic characteristics, the surveillance of clade 3 strains should be more highly prioritized.