Diagnostic microbiology and infectious disease · 2026
Investigation in genomic signatures of helicobacter pylori through a microbial-genome wide association study exploring virulence variation.
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Ghareeb Abdulameer M
Аннотация
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.
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.