On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies

Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks to subtype 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 provide 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 the initial phase of this work, the MLVAType application was validated on long reads generated by Oxford Nanopore Technologies (ONT) sequencing platforms. The MLVA profiles of V. cholerae isolates (n=9) from the Democratic Republic of the Congo were produced using the MLVAType application on WGS data. The WGS-derived MLVA profiles were extracted from canu (v.2.2) assemblies obtained through MinION and GridION sequencing by ONT. 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 the MLVAType application can accurately predict the MLVA profiles from assembled genomes generated with long-reads ONT sequencers. In the final phase of this study, we conducted phylogenomic analysis on data generated by both sequencing technologies, highlighting the superior resolution of Illumina short-read sequencing compared to the ONT-based approach. However, there was a remarkable concordance between isolate clusters identified using ONT-based MLVA profiles and those derived from the short-read-based phylogenomic analysis. This striking agreement enabled us to identify specific benefits and drawbacks of both technologies.