Antibiotic resistance in Helicobacter pylori shows a significant discrepancy between in vitro and in vivo profiles. Laboratory studies often identify specific patterns of multi-drug resistance, while clinical isolates reveal a more complex resistance landscape influenced by the host environment. Understanding the genetic determinants of these differences, particularly regarding biofilm formation, is essential for addressing treatment failures. The aim of this study is to investigate the genetic determinants that influence biofilm formation in Helicobacter pylori strains within the Iranian population.

In this study, 30 Helicobacter pylori strains were isolated from Iranian patients with previous eradication failure. The isolated strains were subjected to whole-genome sequencing. In the conducting of in silico analyses, no distinct resistance genes were identified. The genomic sequences were processed and aligned against known databases of biofilm genes to assess the distribution and variation of these genes among the isolated strains. An automated alignment tool utilizing Python and Structured Query Language (SQL), along with BLAST+ was developed for sequence alignment. This custom tool facilitated the investigation of the presence and novelty of 103 biofilm-related genes within the collected whole genomes.

The prevalence of 103 biofilm-related genes varied among different strains, with the range of identified genes spanning from 43 to 83 per strain. Blast analysis totally reported 800 novels alleles. These variations may indicate genetic diversity in the biofilm-forming capabilities of these strains and highlight the need for further investigation into the impact of these genes on biofilm behavior and resistance to treatments.

The identification of a wide range of biofilm-related genes, with variations between strains, reflects significant genetic diversity that may contribute to treatment failures. The detection of 800 novel alleles further emphasizes the potential for undiscovered genetic factors influencing both biofilm formation and antibiotic resistance. Understanding these genetic determinants is crucial for developing more effective therapeutic strategies against H. pylori infections.