MLVAType

MLVAType extracts Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) profiles for Vibrio cholerae directly from whole genome sequencing (WGS) data to enable backward-compatible MLVA typing.

Key Features:

• Backward compatibility: Produces MLVA profiles from WGS that are comparable to profiles obtained by in silico PCR and Sanger sequencing.
• Algorithm validation: Validated on 19 Vibrio cholerae isolates (Democratic Republic of the Congo n=9; Uganda n=10) by comparing WGS-derived MLVA profiles to in silico PCR and Sanger sequencing, showing total concordance with Sanger sequencing.
• Censored estimation management: Identifies and quantifies censored VNTR copy-number estimations arising during genome assembly, with censored rates inversely proportional to the assembly k-mer size.
• K-mer parameter optimization: Reports that a k-mer of 127 yields less than 15% censored estimations for V. cholerae VNTRs and recommends longer k-mers (e.g., 175) to prevent censored estimations while noting SPAdes v.3.13.0 does not support such larger k-mers.
• Sequencing dependence: Notes that increases in read length and quality from next-generation sequencing will enable use of larger k-mers and reduce censored estimations.

Scientific Applications:

• Surveillance of Vibrio cholerae outbreaks: Enables integration of WGS-derived MLVA profiles into laboratory-based surveillance networks monitoring foodborne and water-borne disease outbreaks.
• Epidemiological investigations: Supports outbreak investigations by providing MLVA profiles that are compatible with historical typing data.
• Data harmonization: Facilitates backward compatibility between traditional MLVA typing methods and WGS-based pathogen subtyping to integrate new genomic data with existing MLVA datasets.

Methodology:

MLVA profiles are extracted from assembled WGS data; genome assembly was performed with SPAdes v.3.13.0 using variable k-mer sizes, outputs were compared to in silico PCR and Sanger sequencing references, and censored VNTR estimations were quantified relative to k-mer size.