Paratype

Paratype assigns SNP-based genotypes to Salmonella Paratyphi A isolates to characterize population structure and detect genomic variants including antimicrobial resistance markers and O2-polysaccharide locus mutations.

Key Features:

• Genotyping Scheme: Implements a SNP-based genotyping scheme that categorizes Salmonella Paratyphi A into three primary clades, nine secondary clades, and 18 distinct genotypes defined by alleles on conserved genes.
• Global Database Integration: Leverages a global database built from whole-genome sequencing data of 817 isolates collected from Bangladesh, Nepal, and Pakistan plus 562 publicly available genomes spanning 37 countries from 1917 to 2019.
• Lineage Resolution: Assigns genotypes to isolates that were previously unclassifiable due to non-homologous sub-lineages, improving lineage resolution for genomic surveillance.
• Identification of Genomic Variations and AMR Markers: Detects genomic variation across sampling locations, identifies antimicrobial resistance (AMR) markers, and detects mutations in the O2-polysaccharide synthesis locus.

Scientific Applications:

• Population structure analysis: Enables precise assignment of Salmonella Paratyphi A genotypes to study population structure and lineage relationships.
• Antimicrobial resistance surveillance: Supports detection and monitoring of AMR markers within S. Paratyphi A populations to inform treatment considerations.
• Spatiotemporal tracking and outbreak response: Facilitates analysis of geographic and temporal distribution of genotypes to support surveillance and outbreak investigations.
• Vaccine-target locus evaluation: Allows monitoring of mutations in the O2-polysaccharide synthesis locus relevant to vaccine target assessment.

Methodology:

Uses a SNP-based genotyping scheme defined by alleles on conserved genes and a global whole-genome sequencing database of 1,379 Salmonella Paratyphi A genomes (817 collected isolates and 562 public genomes) to assign genotypes and detect genomic variations including AMR markers and O2-polysaccharide locus mutations.