Haplo-ST

Haplo-ST performs standardized whole-genome multi-locus sequence typing (wgMLST) of Listeria monocytogenes from whole-genome sequencing (WGS) reads to enable strain-level subtyping and comparative genomic analyses.

Key Features:

• Standardization and nomenclature: Assigns allelic profiles using a centralized nomenclature from the BIGSdb-Lm database to ensure consistent wgMLST typing.
• Input processing and assembly: Accepts raw WGS reads, performs read cleaning, maps reads to reference genes, and assembles loci to generate wgMLST profiles.
• Sensitivity and coverage: Demonstrated 97.5% sensitivity on simulated Lm reads from reference strains and effective profiling at coverage depths of ≥ 20×.
• Phylogenetics and paralog detection: Identifies paralogous genes and supports phylogenetic tree reconstruction from wgMLST data.
• Genetic differentiation analyses: Enables detection of loci associated with adaptation and persistence, supporting comparisons such as isolates from natural environments versus poultry processing plants.
• Flexibility and scalability: Adaptable to characterize any haploid organism by installing an organism-specific gene database and scalable by adjusting the number of reference genes for low- or high-resolution typing.

Scientific Applications:

• Surveillance and outbreak investigation: Provides standardized wgMLST-based subtyping for routine surveillance and outbreak detection of Listeria monocytogenes.
• Source tracking and attribution: Enables source tracking and attribution through allelic profile comparison and lineage clustering.
• Phylogenetic and population analyses: Supports phylogenetic reconstruction and lineage assignment using wgMLST profiles and paralog identification.
• Detection of adaptation and persistence loci: Facilitates genetic differentiation analyses to identify loci linked to adaptation and persistence in food processing and natural environments.
• Comparative genomics of haploid organisms: Can be applied to comparative genomic studies of other haploid organisms via organism-specific gene databases.

Methodology:

Haplo-ST cleans raw WGS reads, maps them to reference genes, assembles loci to produce wgMLST profiles, assigns allelic profiles using BIGSdb-Lm, identifies paralogous genes, reconstructs phylogenetic trees, and performs genetic differentiation analyses, with validation reported using simulated Lm reads (97.5% sensitivity) and a recommended coverage of ≥ 20×.