HPTT

HPTT performs whole-genome SNP profiling of Helicobacter pylori to enable high-resolution genomic typing and geographic surveillance using whole-genome sequencing (WGS) data.

Key Features:

• Genomic typing based on SNP profiling: Uses single nucleotide polymorphism (SNP) profiles derived from WGS and a compiled database of 1,211 publicly available Helicobacter pylori genomes to enable high-resolution typing and population structure analysis.
• Geographic surveillance at continental and country scales: Provides geographic distribution insights of H. pylori isolates, identifying Asia as a primary source with notable contributions from Europe and Oceania, including Switzerland and Australia.
• Validation and accuracy assessment: Demonstrates accuracy by placing ten newly assembled genomes within expected genomic branches.

Scientific Applications:

• Genetic population structure analysis: Facilitates analysis of genetic diversity and population structure of Helicobacter pylori.
• Epidemiological surveillance: Supports mapping and tracking of geographic distribution patterns of H. pylori isolates for epidemiological studies.
• Clinical outcome correlation: Enables investigation of associations between specific genomic profiles and clinical outcomes of H. pylori-related disease.

Methodology:

SNP profiling derived from whole-genome sequencing (WGS), construction of a database from 1,211 publicly available H. pylori genomes, and placement of query genomes into established genomic branches for validation.