A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics
Clostridioides difficile is a major cause of healthcare-associated diarrhea and causes large infection outbreaks. Whole-genome sequencing is increasingly applied for genotyping C. difficile, with the objectives to monitor and curb the pathogen's spread.
We present a publicly accessible database for quality-controlled genome sequences from C. difficile that enables contextual interpretation of newly collected isolates by identifying related strains among published data. It also provides a nomenclature for genomic types to facilitate communication about transmission chains, epidemics and phylogenetic lineages. Finally, we demonstrate that genome-based hierarchical clustering is largely compatible with previously used molecular typing techniques, thus enabling comparisons to earlier surveillance data.
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