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Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164

Jeroen Corver14*, Dennis Bakker1, Michael S M Brouwer2, Céline Harmanus1, Marjolein P Hensgens1, Adam P Roberts2, Len J A Lipman3, Ed J Kuijper1 and Hans C van Leeuwen1

Author Affiliations

1 Department of Medical Microbiology, Section Experimental Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands

2 Division of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK

3 Division of Veterinary Public Health, Faculty of Veterinary Medicine, Institute of Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands

4 LUMC, Medical Microbiology, E4P, Postbus 9600, 2300 RC Leiden, The Netherlands

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BMC Microbiology 2012, 12:130  doi:10.1186/1471-2180-12-130

Published: 2 July 2012



Clostridium difficile is the main cause of antibiotic associated diarrhea. In the past decade, the number of C. difficile patients has increased dramatically, coinciding with the emergence of two PCR ribotypes 027 and 078. PCR ribotype 078 is also frequently found during C. difficile outbreaks in pigfarms. Previously, the genome of the PCR ribotype 078 strain M120, a human isolate, was described to contain a unique insert of 100 kilobases.


Analysis of this insert revealed over 90 open reading frames, encoding proteins originating from transposons, phages and plasmids. The insert was shown to be a transposon (Tn6164), as evidenced by the presence of an excised and circularised molecule, containing the ligated 5’and 3’ends of the insert. Transfer of the element could not be shown through filter-mating experiments. Whole genome sequencing of PCR ribotype 078 strain 31618, isolated from a diarrheic piglet, showed that Tn6164 was not present in this strain. To test the prevalence of Tn6164, a collection of 231 Clostridium difficile PCR ribotype 078 isolates from human (n = 173) and porcine (n = 58) origin was tested for the presence of this element by PCR. The transposon was present in 9 human, tetracycline resistant isolates, originating from various countries in Europe, and none of the pig strains. Nine other strains, also tetracycline resistant human isolates, contained half of the transposon, suggesting multiple insertion steps yielding the full Tn6164. Other PCR ribotypes (n = 66) were all negative for the presence of the transposon. Multi locus variable tandem repeat analysis revealed genetic relatedness among transposon containing isolates. Although the element contained several potential antibiotic resistance genes, it did not yield a readily distinguishable phenotype.


Tn6164 is a newly described transposon, occurring sporadically in C. difficile PCR ribotype 078 strains. Although no transfer of the element could be shown, we hypothesize that the element could serve as a reservoir of antibiotic resistance genes for other bacteria. Further research is needed to investigate the transfer capabilities of the element and to substantiate the possible role of Tn6164 as a source of antibiotic resistance genes for other gut pathogens.

Clostridium difficile; Transposable element; Phage; Antimicrobial resistance; Virulence