Development and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile.

Sandra Janezic,Maja Rupnik

doi:10.3389/fpubh.2019.00309

Abstract

Clostridioides difficile is an important nosocomial pathogen increasingly observed in the community and in different non-human reservoirs. The epidemiology and transmissibility of C. difficile has been studied using a variety of typing methods, including more recently developed whole-genome sequence (WGS) analysis that is becoming used routinely for bacterial typing worldwide. Here we review the schemes for WGS-based typing methods available for C. difficile and their applications in the field of human C. difficile infection (CDI). The two main approaches to discover genomic variations are single nucleotide variant (SNV) analysis and methods based on gene-by-gene comparisons (frequently called core genome or whole genome MLST, cgMLST, or wgMLST). SNV analysis currently provides the ultimate resolution, however, typing nomenclature and standardized methodology are missing. On the other hand, gene-by-gene approaches allow portability and standardized nomenclature, and are therefore becoming increasingly popular in bacterial epidemiology and outbreak investigation. Two commercial software packages (BioNumerics and Ridom SeqSphere+) and an open source database (EnteroBase) for allele and sequence type determination for C. difficile are currently available. Proof-of-concept WGS studies have already enabled advances in the investigation of the population structure of C. difficile species, microevolution within the epidemic strains, intercontinental transmission over time and in tracking of transmission events. WGS of clinical C. difficile isolates demonstrated a considerable genetic diversity suggesting diverse reservoirs for CDI. WGS was also shown to aid in resolving relapses and reinfections in recurrent CDI and has potential for use as a tool for assessing hospital infection prevention and control performance.

Highlights

Clostridioides (Clostridium) difficile is currently one of the most important human pathogens [1]
Strain typing based on core genome single nucleotide variant (SNV) is currently considered as a method with very high discriminatory power, since it allows us to distinguish between isolates if their genomes differ in a single nucleotide [7]
Isolates from almost half (45%) the patients were genetically unrelated (≥10 single nucleotide polymorphisms (SNPs)) to any other previous case, meaning that these patients had likely acquired C. difficile from sources other than symptomatic patients. These findings suggest that there are rather diverse reservoirs of C. difficile and that transmissions other that those occurring between symptomatic patients within the hospital settings should be considered [10]

Summary

INTRODUCTION

Clostridioides (Clostridium) difficile is currently one of the most important human pathogens [1]. Strain typing based on core genome SNVs (cgSNVs) is currently considered as a method with very high discriminatory power, since it allows us to distinguish between isolates if their genomes differ in a single nucleotide [7] In this approach, short reads (data generated from sequencing of short genomic fragments) or assembled contigs (longer contiguous sequences of overlapping reads) are mapped against the genome of a reference strain to identify differences in coding and non-coding regions. Similar estimations of C. difficile evolutionary rates were obtained in other studies, either by using serial samples from the patients with recurrent or on-going CDI and/or in in vitro gut models [9, 10, 13] By using this prediction of evolutionary rate, the guideline for two isolates being clonal, or genetically related (are most probably a result of direct transmission), is that there are ≤2 SNVs between their sequenced genomes. All studies that explored the source of recurrent infection demonstrated

Aim

Findings

CONCLUSION