Typing Clostridium difficile strains based on tandem repeat sequences

Open Access
Publisher Website
Google Scholar
Abstract
Background: Genotyping of epidemicClostridium difficilestrains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies.Results: This report presents results from a systematic screen for variation in repetitive DNA in the genome ofC. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154C. difficileisolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history.Conclusion: We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing ofC. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains.

This publication has 57 references indexed in Scilit: