Update on Commonly Used Molecular Typing Methods for Clostridioides difficile

Abstract

This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.

Clostridioides difficile detection and infection in children: are they just small adults?

“…There are a number of different molecular typing techniques utilized to undertake C. difficile surveillance, with the main approaches being split into fragment-based or sequence-based approaches [9]. Commonly utilized fragment-based approaches differ between North America and Europe, with North America predominately utilizing pulse field gel electrophoresis (PFGE) or restriction endonuclease analysis (REA) for typing, whereas Europe maintains a reliance on PCR ribotyping as a primary method [2,9]. PFGE can discriminate some strains better than PCR ribotyping, however ribotyping has the advantage that a harmonized standard method has been validated across North America and Europe, permitting high-quality transferable results.…”

“…PFGE can discriminate some strains better than PCR ribotyping, however ribotyping has the advantage that a harmonized standard method has been validated across North America and Europe, permitting high-quality transferable results. Although PFGE was adopted as the primary typing scheme utilized by the CDCs within Canada and the USA, both have now switched predominantly to sequencing-based approaches utilizing multi-locus sequence typing (MLST) or whole genome sequencing (WGS) [9,24].…”

“…A summary of the molecular characterization of C. difficile strains is shown in Table 3. As homology between sequence types and ribotypes is not exact, with some ribotypes aligning to multiple sequence types and vice versa, it has therefore been suggested that where ribotyping is incapable of detecting strain differences, MLST can be utilized [9]. Caution should also be applied for some sequence types when determining recurrence or treatment failure, as some sequence types may not adequately distinguish between ribotypes leading to clinical interpretation challenges and over-calling relapse rates (Table 3) [9].…”

“…These toxins enter colonic epithelial cells via clathrin-mediated endocytosis and interact with the GTPases Rho, Rac and Cdc42, inducing actin condensation, cell rounding and death [28,29]. A minority of C. difficile strains located in the cryptic clades produce binary toxin (C. difficile transferase -CDT) through the genes cdtA and cdtB on the CDT locus [9,30]. This toxin further disrupts epithelial cell cytoskeletal structures, increasing the permeability of the epithelial cell wall, leading to extensive fluid loss [28].…”

“…Historically, it was believed that the predominant route of spread in healthcare was linked to symptomatic patients; however, new typing methods with higher levels of discrimination now suggest that asymptomatic carriers may have a significant role in transmission. This is an important consideration within paediatric settings as risk of colonization with C. difficile may be linked to the environment in which a child develops [5,9].…”