title: Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile.
abstract: Clostridium difficile is a common cause of infectious diarrhea in hospitalized patients. A severe and increased incidence of C. difficile infection (CDI) is associated predominantly with the NAP1 strain; however, the existence of other severe-disease-associated (SDA) strains and the extensive genetic diversity across C. difficile complicate reliable detection and diagnosis. Comparative genome analysis of 14 sequenced genomes, including those of a subset of NAP1 isolates, allowed the assessment of genetic diversity within and between strain types to identify DNA markers that are associated with severe disease. Comparative genome analysis of 14 isolates, including five publicly available strains, revealed that C. difficile has a core genome of 3.4 Mb, comprising ∼ 3,000 genes. Analysis of the core genome identified candidate DNA markers that were subsequently evaluated using a multistrain panel of 177 isolates, representing more than 50 pulsovars and 8 toxinotypes. A subset of 117 isolates from the panel had associated patient data that allowed assessment of an association between the DNA markers and severe CDI. We identified 20 candidate DNA markers for species-wide detection and 10,683 single nucleotide polymorphisms (SNPs) associated with the predominant SDA strain (NAP1). A species-wide detection candidate marker, the sspA gene, was found to be the same across 177 sequenced isolates and lacked significant similarity to those of other species. Candidate SNPs in genes CD1269 and CD1265 were found to associate more closely with disease severity than currently used diagnostic markers, as they were also present in the toxin A-negative and B-positive (A-B+) strain types. The genetic markers identified illustrate the potential of comparative genomics for the discovery of diagnostic DNA-based targets that are species specific or associated with multiple SDA strains.
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Canada.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Forgetta
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Oughton
authors.forename: Pascale
authors.initials: P
authors.lastname: Marquis
authors.forename: Ivan
authors.initials: I
authors.lastname: Brukner
authors.forename: Ruth
authors.initials: R
authors.lastname: Blanchette
authors.forename: Kevin
authors.initials: K
authors.lastname: Haub
authors.forename: Vince
authors.initials: V
authors.lastname: Magrini
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Dale N
authors.initials: DN
authors.lastname: Gerding
authors.forename: Vivian G
authors.initials: VG
authors.lastname: Loo
authors.forename: Mark A
authors.initials: MA
authors.lastname: Miller
authors.forename: Michael R
authors.initials: MR
authors.lastname: Mulvey
authors.forename: Maja
authors.initials: M
authors.lastname: Rupnik
authors.forename: Andre
authors.initials: A
authors.lastname: Dascal
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
mesh_terms: D000328:Adult; D000368:Aged; D015373:Bacterial Typing Techniques; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics / Q000472:pathogenicity*; D003015:Clostridium Infections / Q000382:microbiology* / Q000473:pathology; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D005819:Genetic Markers; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D012720:Severity of Illness Index; D014774:Virulence
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers