Typing Clostridium difficile strains based on tandem repeat sequences

N Henning Zaiß,Celine Harmanus,Ed J Kuijper,Maja Rupnik,Koen Janssens,Ulrich Nübel,Dolf Michielsen

doi:10.1186/1471-2180-9-6

Abstract

BackgroundGenotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies.ResultsThis report presents results from a systematic screen for variation in repetitive DNA in the genome of C. 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 154 C. difficile isolates 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.ConclusionWe conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. 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.

Highlights

Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread
The two most variable loci were designated TR6 and TR10 (Table 1). They are located at positions 0.7 Mb and 3.7 Mb of the C. difficile 630 chromosome, respectively, and exhibited both, sequence and length polymorphisms
TR10 is located within a predicted non-coding region

Summary

Introduction

Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Clostridium difficile is a Gram-positive, spore-forming, obligately anaerobic bacterium. It is the leading cause of nosocomial diarrhoea among patients undergoing antibiotic treatment [1,2]. The severity of C. difficile-associated disease (CDAD) ranges from mild diarrhoea to pseudomembranous colitis, toxic megacolon, and intestinal perforation [3,4,5,6]. In the USA and Canada, this increase has been associated with the emergence of a novel, hypervirulent strain designated NAP1/ 027 [11,15]. Strains with the same genotype and associated outbreaks have been reported from several European countries [14,16,17,18]

Methods

Results

Conclusion