Archives of Microbiology

, Volume 199, Issue 2, pp 317–323 | Cite as

Clinical use comparison of a semiautomated PCR with fluorescent ribotyping for typing of Clostridium difficile

  • Abrar K. Thabit
  • M. Jahangir Alam
  • Carey-Ann D. Burnham
  • David P. NicolauEmail author
Original Paper


Molecular typing of Clostridium difficile is performed to assess strain relatedness or place strains within an epidemiological context. Different C. difficile ribotyping systems are available. However, a common strain library does not exist. We aimed to compare ribotyping results of 29 clinical C. difficile isolates by two methods: semiautomated PCR-ribotyping and fluorescent PCR-ribotyping. For certain ribotypes (n = 16/29; 55.2 %), the inter-laboratory reproducibility was consistent among multiple samples from individual subjects, while 54.8 % (n = 14/29) were discordant. Additionally, 11/29 ribotypes (38 %) and 12/29 ribotypes (41 %) did not match with known reference strains in the semiautomated PCR-fluorescent ribotyping systems’ libraries, respectively. The identification of 027 ribotype by both systems was consistent for 75 % of the isolates. Discriminatory indices for the semiautomated PCR-ribotyping and fluorescent PCR-ribotyping systems are 0.906 and 0.886, respectively. Although ribotyping provides important epidemiologic insights, the lack of a common strain library makes interpretation of results using different ribotyping protocols difficult.


Clostridium difficile PCR Fluorescent PCR Ribotype 



We acknowledge Kevin W. Garey, PharmD, MS from the University of Houston, Houston, TX, for his efforts in ribotyping the C. difficile isolates. We also acknowledge Lucinda Lamb, Mary Anne Banevicius, and the staff and fellows of the Center for Anti-Infective Research and Development (CAIRD), Hartford Hospital, Hartford, CT and Megan Wallace from Washington University, St. Louis, MO for assistance with the collection, processing, and ribotyping of the recovered isolates. The authors also acknowledge the funding support of Cubist Pharmaceuticals (Lexington, MA) for the conduct of the randomized trial comparing the microbiologic outcomes of fidaxomicin and vancomycin from which isolates were collected. Funding support for the additional studies described herein was provided by the CAIRD.


  1. Aitken SL et al (2015) In the endemic setting, Clostridium difficile Ribotype 027 is virulent but not hypervirulent. Infect Control Hosp Epidemiol. doi: 10.1017/ice.2015.187 PubMedPubMedCentralGoogle Scholar
  2. Burnham CA, Carroll KC (2013) Diagnosis of Clostridium difficile infection: an ongoing conundrum for clinicians and for clinical laboratories. Clin Microbiol Rev 26:604–630. doi: 10.1128/cmr.00016-13 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Collins DA, Elliott B, Riley TV (2015) Molecular methods for detecting and typing of Clostridium difficile. Pathology 47:211–218. doi: 10.1097/pat.0000000000000238 CrossRefPubMedGoogle Scholar
  4. Eckert C et al (2011) Comparison of a commercially available repetitive-element PCR system (DiversiLab) with PCR ribotyping for typing of Clostridium difficile strains. J Clin Microbiol 49:3352–3354. doi: 10.1128/jcm.00324-11 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Fawley WN et al (2015) Development and validation of an internationally-standardized, high-resolution capillary gel-based electrophoresis PCR-ribotyping protocol for Clostridium difficile. PLoS One 10:e0118150. doi: 10.1371/journal.pone.0118150 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Housman ST, Thabit AK, Kuti JL, Quintiliani R, Nicolau DP (2016) Assessment of Clostridium difficile burden in patients over time with first episode infection following fidaxomicin or vancomycin. Infect Control Hosp Epidemiol 37:215–218. doi: 10.1017/ice.2015.270 CrossRefPubMedGoogle Scholar
  7. Hunter PR, Gaston MA (1988) Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity. J Clin Microbiol 26:2465–2466PubMedPubMedCentralGoogle Scholar
  8. Knetsch CW et al (2012) Comparative analysis of an expanded Clostridium difficile reference strain collection reveals genetic diversity and evolution through six lineages. Infect Genet Evol 12:1577–1585. doi: 10.1016/j.meegid.2012.06.003 CrossRefPubMedGoogle Scholar
  9. Knetsch CW, Lawley TD, Hensgens MP, Corver J, Wilcox MW, Kuijper EJ (2013) Current application and future perspectives of molecular typing methods to study Clostridium difficile infections. Euro Surveill 18:20381PubMedGoogle Scholar
  10. Kurka H et al (2014) Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation. PLoS One 9:e86535. doi: 10.1371/journal.pone.0086535 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Mac Aogáin M et al (2015) Whole-genome sequencing improves discrimination of relapse from reinfection and identifies transmission events among patients with recurrent Clostridium difficile infections. J Hosp Infect 90:108–116. doi: 10.1016/j.jhin.2015.01.021 CrossRefPubMedGoogle Scholar
  12. Magurran A (2004) Measuring Biological Diversity. Blackwell Science Ltd, OxfordGoogle Scholar
  13. Martinson JN et al (2015) Evaluation of portability and cost of a fluorescent PCR ribotyping protocol for Clostridium difficile epidemiology. J Clin Microbiol 53:1192–1197. doi: 10.1128/jcm.03591-14 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Pépin J et al (2005) Increasing risk of relapse after treatment of Clostridium difficile colitis in Quebec, Canada. Clin Infect Dis 40:1591–1597. doi: 10.1086/430315 CrossRefPubMedGoogle Scholar
  15. Valiente E, Dawson LF, Cairns MD, Stabler RA, Wren BW (2012) Emergence of new PCR ribotypes from the hypervirulent Clostridium difficile 027 lineage. J Med Microbiol 61:49–56. doi: 10.1099/jmm.0.036194-0 CrossRefPubMedGoogle Scholar
  16. Westblade LF et al (2013) Development and evaluation of a novel, semiautomated Clostridium difficile typing platform. J Clin Microbiol 51:621–624. doi: 10.1128/jcm.02627-12 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Abrar K. Thabit
    • 1
    • 2
  • M. Jahangir Alam
    • 3
  • Carey-Ann D. Burnham
    • 4
  • David P. Nicolau
    • 1
    • 5
    Email author
  1. 1.Center for Anti-infective Research and DevelopmentHartford HospitalHartfordUSA
  2. 2.Faculty of PharmacyKing Abdulaziz UniversityJeddahSaudi Arabia
  3. 3.University of Houston College of PharmacyHoustonUSA
  4. 4.Department of Pathology and ImmunologyWashington University School of Medicine in St. LouisSt. LouisUSA
  5. 5.Division of Infectious DiseasesHartford HospitalHartfordUSA

Personalised recommendations