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Whole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission ofClostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a singleC. difficile colony is selected from culture for WGS, significant within-host genetic diversity could preclude identification of transmission events.

Clostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric Cohort