Identification of molecular markers for meat pathogen detection using advanced genomic approaches
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Date
2025
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UMT, Lahore
Abstract
Foodborne diseases, particularly those caused by meat pathogens, pose a significant health risk to the global population. Therefore, identifying molecular markers for pathogen detection in the food supply chain is crucial for food safety. Advanced genomics approaches, such as comparative genomics, can bridge the application gap in pathogen detection and enhance food safety measures. In a study encompassing 193 pathogens across 37 species and 14 genera, including notable ones like E. coli, Salmonella, and Campylobacter, a comprehensive dataset of over 1 million proteins was analyzed. Among these, beneficial strains comprising 24 isolates from 16 species and nine genera, such as Bifidobacterium and Lactobacillus, were identified, totaling over 46,000 proteins. Phylogenetic analysis revealed a distinct species clustering, with only two particular clusters exhibiting beneficial species, while the remainder were pathogenic species. Evolutionary analysis utilizing maximum likelihood and orthogroup clustering techniques uncovered 29,155ortho-groups, with 22,800 specific to pathogens and 2,773 specific to beneficial species. Despite extensive study, no highly conserved target markers were found across all pathogens. However, particular orthogroups (OGs), such as OGs06613 (Salmonella typhimurium) and OGs03602 (Escherichia coli), were identified, providing potential targets for pathogen-specific detection. Moreover, highly conserved target markers were identified through multiple sequence alignment (MSA), and primers were designed for those conserved regions. Furthermore, pathogenic strains were collected from the Microbial Bank of Punjab University, Lahore, Pakistan, to validate identified markers, and the beneficial bacterial strain, probiotics bacteria, were cultured. Subsequently, total DNA was extracted, and PCR was performed. Results indicated the amplification of only pathogenic bacteria, showing the specificity of identified markers to pathogenic strains. Thus, these novel target regions can be further used in antibody development and guide-RNA design for CRISPR-Cas-based pathogen identification in future applications.