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.

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

“…NB: Where ribotypes are associated with multiple sequence types, the most common sequence types is given (Dingle et al, 2011;Stabler et al, 2012). …”

The host immune response to Clostridium difficile infection

“…Although a degree of cross reactivity has been observed for particular vaccine candidates , future therapies may have to take into account the continual evolution of the C. difficile species and emergence of new genetically distinct clades [Cairns et al 2012;Stabler et al 2006Stabler et al , 2012He et al 2010]. Monitoring both the genetic diversity and epidemiology of circulating C. difficile strains may enable a prediction of newly emerging genetically distinct strain types that are able to cause severe disease or epidemics.…”

Community-acquired Clostridium difficile infection and Australian food animals

“…Three toxigenic RTs predominate (77%) in veal calves in Australia: RT127, RT033 and RT126. Along with RT 078, these genotypes form part of the genetically divergent clade 5 39 . These RTs have been isolated from humans with CDI in Australia although RT033 may be underreported as it is poorly detected by commonly used molecular tests 40 .…”