Developing Protocols for multiplex PCR based Screening and Computational Models for Virulence Factors Associated with H. pylori and colibactin (genotoxin) producing E. coli
This project focuses on the development of molecular and computational approaches for investigating virulence determinants in Helicobacter pylori and colibactin-producing Escherichia coli. H. pylori is a major human pathogen associated with gastritis, peptic ulcers, and gastric cancer, while certain E. coli strains carry the pks genomic island encoding colibactin, a genotoxin implicated in colorectal carcinogenesis.To address these important pathogens, we designed and optimized multiplex PCR protocols for the rapid screening of key virulence genes in H. pylori. These molecular assays enable the simultaneous detection of multiple virulence-associated factors, supporting efficient characterization of clinical isolates.In parallel, we performed whole genome sequencing of E. coli strains to investigate the genetic basis of colibactin production. Comprehensive genome analysis allowed the identification and annotation of the colibactin gene cluster and associated virulence markers. Comparative genomic approaches were also applied to assess variability among isolates, providing insights into the distribution and potential evolutionary dynamics of the pks island.The data generated from this project contribute to a deeper understanding of bacterial virulence mechanisms relevant to gastrointestinal disease and cancer risk. By integrating PCR-based screening with genome-wide analysis, our study aims to provide both rapid diagnostic strategies and genomic resources that can be leveraged for future research, surveillance, and the development of targeted interventions.