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Investigating the differences between diseased and healthy states using differentially expressed genes aids in understanding disease pathophysiology and enables the exploration of protein-drug interactions. This study aimed to find the most common genes in diarrhea-causing bacteria such as<jats:italic>Salmonella enterica<\/jats:italic>serovar Typhimurium,<jats:italic>Campylobacter jejuni<\/jats:italic>,<jats:italic>Escherichia coli<\/jats:italic>,<jats:italic>Shigella dysenteriae<\/jats:italic>(CESS) to find new drugs. Thus, differential gene expression datasets of CESS were screened through computational algorithms and programming. Subsequently, hub and common genes were prioritized from the analysis of extensive protein\u2013protein interactions. Binding predictions were performed to identify the common potential therapeutic targets of CESS. We identified a total of 827 dysregulated genes that are highly linked to CESS. Notably, no common gene interaction was found among all CESS bacteria, but we identified 3 common genes in both<jats:italic>Salmonella-Escherichia<\/jats:italic>and<jats:italic>Escherichia-Campylobacter<\/jats:italic>infections. Later, out of 73 protein complexes, molecular simulations confirmed 5 therapeutic candidates from the CESS. We have developed a new pipeline for identifying therapeutic targets for a common medication strategy against CESS. 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