title: Macro and micro diversity of Clostridium difficile isolates from diverse sources and geographical locations.
abstract: Clostridium difficile has emerged rapidly as the leading cause of antibiotic-associated diarrheal disease, with the temporal and geographical appearance of dominant PCR ribotypes such as 017, 027 and 078. Despite this continued threat, we have a poor understanding of how or why particular variants emerge and the sources of strains that dominate different human populations. We have undertaken a breadth genotyping study using multilocus sequence typing (MLST) analysis of 385 C. difficile strains from diverse sources by host (human, animal and food), geographical locations (North America, Europe and Australia) and PCR ribotypes. Results identified 18 novel sequence types (STs) and 3 new allele sequences and confirmed the presence of five distinct clonal lineages generally associated with outbreaks of C. difficile infection in humans. Strains of animal and food origin were found of both ST-1 and ST-11 that are frequently associated with human disease. An in depth MLST analysis of the evolutionary distant ST-11/PCR ribotype 078 clonal lineage revealed that ST-11 can be found in alternative but closely related PCR ribotypes and PCR ribotype 078 alleles contain mutations generating novel STs. PCR ribotype 027 and 017 lineages may consist of two divergent subclades. Furthermore evidence of microdiversity was present within the heterogeneous clade 1. This study helps to define the evolutionary origin of dominant C. difficile lineages and demonstrates that C. difficile is continuing to evolve in concert with human activity.
authors.affiliation: Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Stabler
authors.forename: Lisa F
authors.initials: LF
authors.lastname: Dawson
authors.forename: Esmeralda
authors.initials: E
authors.lastname: Valiente
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Cairns
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Martin
authors.forename: Elizabeth H
authors.initials: EH
authors.lastname: Donahue
authors.forename: Thomas V
authors.initials: TV
authors.lastname: Riley
authors.forename: J Glenn
authors.initials: JG
authors.lastname: Songer
authors.forename: Ed J
authors.initials: EJ
authors.lastname: Kuijper
authors.forename: Kate E
authors.initials: KE
authors.lastname: Dingle
authors.forename: Brendan W
authors.initials: BW
authors.lastname: Wren
mesh_terms: D000483:Alleles; D000818:Animals; D015373:Bacterial Typing Techniques; D044822:Biodiversity; D019070:Cell Lineage; D016360:Clostridioides difficile / Q000235:genetics* / Q000502:physiology*; D016000:Cluster Analysis; D004285:Dogs; D019143:Evolution, Molecular; D014644:Genetic Variation; D023281:Genomics; D005843:Geography; D006736:Horses; D006801:Humans; D051379:Mice; D009154:Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013552:Swine