On the ability to extract MLVA profiles ofVibrio choleraeisolates from WGS data generated with Oxford Nanopore Technologies

AbstractMultiple-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. TheMLVAType shinyapplication was previously designed to extract MLVA profiles ofVibrio choleraeisolates 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 and Hiseq sequencing. In this work, the use of theMLVATypeapplication was validated on long reads generated with Oxford Nanopore Technologies (ONT) sequencing platforms. Accordingly, the MLVA profiles ofV. choleraeisolates (n=9) from the Democratic Republic of the Congo were obtained using theMLVATypeapplication on WGS data. The WGS-derived MLVA profiles were extracted from canu (v.2.2) assemblies obtained after the MinION and GridION, ONT, sequencing. The results were compared to those obtained from SPAdes assemblies (v3.13.0; k-mer 175) generated from short-read (pair-end 300-bp) data obtained by MiSeq sequencing, Illumina, taken as a reference. For each isolate, the MLVA profiles were concordant for all three sequencing methods, demonstrating that theMLVATypeapplication can accurately predict the MLVA profiles from assembled genomes generated with long-reads ONT sequencers.