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Comparison of Whole-Genome Sequence-Based Methods and PCR Ribotyping for Subtyping of Clostridioides difficile.

A Baktash¹, J Corver¹, C Harmanus^1,2

¹Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Centergrid.10419.3d, Leiden, The Netherlands.

Journal of Clinical Microbiology

|December 16, 2021

Summary

Core genome multilocus sequence typing (cgMLST) shows promise for Clostridioides difficile typing, offering improved discrimination over traditional methods. However, specific thresholds are needed for accurate outbreak detection in certain C. difficile strains.

Keywords:

Clostridioides difficile core-genome MLST typing methods whole-genome MLST whole-genome sequencing

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Area of Science:

Microbiology
Infectious Diseases
Molecular Epidemiology

Background:

Clostridioides difficile infections are a leading cause of antibiotic-associated gastrointestinal illness.
Current gold standard typing (CE-PCR ribotyping) lacks sufficient discriminatory power for detailed outbreak investigations.
Emerging molecular methods offer enhanced differentiation and standardized data exchange.

Purpose of the Study:

To compare the discriminatory power of core genome multilocus sequence typing (cgMLST), whole-genome MLST (wgMLST), and single-nucleotide polymorphism (SNP) analysis for C. difficile typing.
To evaluate the utility of these methods in distinguishing strains during specific outbreak scenarios.
To assess the potential of cgMLST as a successor to CE-PCR ribotyping.

Main Methods:

Utilized a collection of 630 C. difficile strains representing 100 unique ribotypes.
Compared cgMLST (SeqSphere, EnteroBase), wgMLST (EnteroBase), and SNP analysis.
Applied methods to two outbreak settings involving RT078 and RT181.

Main Results:

cgMLST distinguished 82 out of 100 ribotypes, demonstrating high but not absolute discriminatory power.
cgMLST failed to differentiate outbreak from non-outbreak strains for RT078 and RT181, unlike wgMLST and SNP analysis.
A proposed allelic threshold of three for cgMLST could aid in outbreak identification.

Conclusions:

cgMLST is a reproducible and easily standardized method with higher discrimination than CE-PCR ribotyping.
cgMLST shows potential as an alternative typing method for C. difficile.
Adjusted thresholds and epidemiological data are crucial for recognizing outbreaks of specific C. difficile ribotypes using cgMLST.