Investigation in genomic signatures of helicobacter pylori through a microbial-genome wide association study exploring virulence variation.

BACKGROUND

Helicobacter (H.) pylori is characterized by a high degree of genomic diversity, with regional differences in virulence determinants. This study aims to explore genomic composition, phylogeography and accessory-gene relationships of Iraqi H. pylori isolates in a global contextualized dataset.

METHODS

A total of 198 H. Pylori genomes were reviewed, including 41 isolates sequenced from gastric samples of patients undergoing diagnostic endoscopy at Al-Yarmouk Teaching Hospital, Baghdad from June 2024 to February 2025. Illumina MiSeq was used to sequence genomes, which were quality-filtered and assembled using SPAdes. Prokka was used to perform annotation and Roary to infer pan-genome structure. FastTree was used to reconstruct core-genome phylogeny. Anatomical micro-niche (corpus vs. other gastric sites) were explored with pan-genome-wide association study (pan-GWAS) with Pyseer (linear mixed model, kinship based on the core alignment).

RESULTS

The H. Pylori pan-genome showed 955 core gene families and 9,400 accessory genes. Isolates from Iraq were polyphyletic, mixing with European and Middle Eastern lineages. In the primary Pyseer linear mixed-model analysis, Benjamini-Hochberg correction across 3,259 valid lrt-pvalue tests identified 151 FDR-significant associations; after excluding rows with problematic Pyseer diagnostic notes, 70 unflagged loci remained significant. The strongest unflagged positive association was group_2036, whereas a co-occurring block including cagS, cagT, and virB4_1 was strongly depleted in corpus-derived isolates. These signals implicate accessory-genome variation in gastric micro-niche adaptation while also underscoring the need to interpret flagged Pyseer rows cautiously.

CONCLUSIONS

The genomic variation of squamous H. Pylori isolates in Iraq corresponds to the global recombination trends and to the regional admixture. The corpus sampling-related accessory-gene cluster implies possible micro-niche adaptation. These preliminary results highlight the necessity of large, stratified Middle Eastern cohorts and long-read sequencing to dispel functional genetic constructions of tissue tropism and virulence.