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Genome-Based Phylogeny of Clostridioides difficile

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David W. Ussery, Se-Ran Jun, Duah Alkam, Joyce J Johnsrud, Visanu Wanchai, and Trudy Wassenaar

Background: Clostridioides difficile infections are a major problem in hospitals. Some strains of C. difficile can spread as community acquired infections, whilst other strains are unique to individuals. Genome sequences from clinical samples can be used for epidemiological monitoring of C. difficile infections.

Results: Using Average Amino acid Identity (AAI) of more than 500 Clostridioides difficile genomes, we find several distinct clusters, some of which reflect known nosocomial infections from hospitals. Further, we find additional genomes in GenBank that are likely to be in the C. difficile group, but have different names, and some of the C. difficile genomes are likely to belong to different genera.

Conclusion: Our analysis of all the currently available C. difficile genomes allows a framework to place newly sequenced clinical isolates, quickly determining novel strains, as well as potential community-outbreak strains. This work is funded in part from the Arkansas Research Alliance and the Helen Adams & Arkansas Research Alliance Professor & Chair.

Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205

Department of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205

Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, D-55576 Zotzenheim, Germany