On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data

Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks for subtyping pathogens causing foodborne and water-borne disease outbreaks. The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae isolates from WGS data, and enable backward compatibility with traditional MLVA typing methods. The previous development and validation work was done on short (pair-end 300 and 150 nt long) reads from Illumina MiSeq sequencing. In this work, the use of the MLVAType application is validated on long reads generated with Oxford Nanopore Technologies (ONT) sequencing platforms.