Genomic analysis of Clostridioides difficile in two regions of the United States reveals a diversity of strains and limited transmission

Background: The epidemic NAP1/027 Clostridioides difficile strain (MLST1, ST1) that emerged in the mid-2000 is on the decline. The current distribution of C. difficile strain types and their transmission dynamics in the United States are poorly defined. We performed whole genome sequencing (WGS) of C. difficile isolates across two regions (New York and Minnesota) to identify the predominant multilocus sequence types (MLSTs) in community and healthcare associated cases and potential transmission between cases using whole genome single nucleotide polymorphisms (SNP) analysis.