Current application and future perspectives of molecular typing methods to study Clostridium difficile infections

Abstract

Molecular typing is an essential tool to monitor Clostridium difficile infections and outbreaks within healthcare facilities. Molecular typing also plays a key role in defining the regional and global changes in circulating C. difficile types. The patterns of C. difficile types circulating within Europe (and globally) remain poorly understood, although international efforts are under way to understand the spatial and temporal patterns of C. difficile types. A complete picture is essential to properly investigate type-specific risk factors for C. difficile infections (CDI) and track longrange transmission. Currently, conventional agarose gel-based polymerase chain reaction (PCR) ribotyping is the most common typing method used in Europe to type C. difficile. Although this method has proved to be useful to study epidemiology on local, national and European level, efforts are made to replace it with capillary electrophoresis PCR ribotyping to increase pattern recognition, reproducibility and interpretation. However, this method lacks sufficient discriminatory power to study outbreaks and therefore multilocus variable-number tandem repeat analysis (MLVA) has been developed to study transmission between humans, animals and food. Sequence-based methods are increasingly being used for C. difficile fingerprinting/ typing because of their ability to discriminate between highly related strains, the ease of data interpretation and transferability of data. The first studies using whole-genome single nucleotide polymorphism typing of healthcare-associated C. difficile within a clinically relevant timeframe are very promising and, although limited to select facilities because of complex data interpretation and high costs, these approaches will likely become commonly used over the coming years.

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

“…CE combined with other favorable factors (polymerases, sequencing gels, etc.) to develop next-generation sequencing-based diagnostic technology [147,[162][163][164][165]. 4.…”

“…Third, the waste from these techniques causes severe pollution. Fourth, these methods are limited by the difficulties of accurate size estimation, digital-based data preparation, and data interpretation and transferability [147]. These issues are increasingly urgent when considering future applications in infectious disease diagnosis where speed, safety, and effectiveness are compulsory for clinical needs.…”

“…Although the equipment for CE may be relatively expensive, the operational costs are not because the consumed reagents are mainly water, inorganic salt, and a small amount of gel. Thus, after the investment of fixed assets, CE becomes cost-effective and has a great potential for use in clinical diagnostics (Tables 1 and 2) [147].…”

Molecular characterisation of Czech Clostridium difficile isolates collected in 2013–2015

“…Molecular typing of clinically significant C. difficile isolates is a crucial tool for surveillance and spread control of C. difficile infections (CDI). The typing approaches are focused on conserved parts, repetitive regions or entire genomes (Knetsch et al, 2013). They include PCR-ribotyping (Bidet et al, 1999, Stubbs et al, 1999Indra et al, 2008;Fawley et al, 2015), multi-locus sequence typing (MLST) (Griffiths et al, 2010), and toxinotyping (Rupnik, 2010).…”

Bioinformatics Challenges and Potentialities in Studying Extreme Environments

“…Result showed that among the isolations there was a predominant C. difficile lineage spreading in the hospital, with 5 out 14 identical ribotyping patterns. PCR RT has rapidly become the most widely used, straightforward and affordable typing method to detect diversities among the same microorganism species [18].…”