Clinical use comparison of a semiautomated PCR with fluorescent ribotyping for typing of Clostridium difficile
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ORIGINAL PAPER
Clinical use comparison of a semiautomated PCR with fluorescent ribotyping for typing of Clostridium difficile Abrar K. Thabit1,2 · M. Jahangir Alam3 · Carey‑Ann D. Burnham4 · David P. Nicolau1,5
Received: 18 December 2015 / Revised: 11 February 2016 / Accepted: 5 October 2016 © Springer-Verlag Berlin Heidelberg 2016
Abstract 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 Communicated by Erko Stackebrandt. * David P. Nicolau [email protected] 1
Center for Anti‑infective Research and Development, Hartford Hospital, 80 Seymour Street, Hartford, CT 06102, USA
2
Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
3
University of Houston College of Pharmacy, Houston, TX, USA
4
Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
5
Division of Infectious Diseases, Hartford Hospital, Hartford, CT, USA
provides important epidemiologic insights, the lack of a common strain library makes interpretation of results using different ribotyping protocols difficult. Keywords Clostridium difficile · PCR · Fluorescent PCR · Ribotype
Introduction Molecular typing for Clostridium difficile strains has been instrumental as a tool to monitor hospitals outbreaks and aid infection control (Knetsch et al. 2013). Although typing using whole genome sequencing is emerging, polymerase chain reaction (PCR) ribotyping and pulsed field gel electrophoresis (PFGE) are the most common methods of C. difficile typing (Burnham and Carroll 2013; Collins et al. 2015). PCR-ribotyping is performed to assess strain relatedness or place strains within an epidemiological context. With many different C. difficile typing systems available (Collins et al. 2015), the correlation of the results between systems is unknown. A more discriminatory test (for example, whole genome sequencing) will identify numerous unique types, while a less discriminatory test (for example, ribotyping) will identify fewer unique types (Knetsch et al. 2013; Mac Aogáin et al. 2015). Ideally, a common referenc
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