From Animal Colonization to Food-Chain Persistence: Functional Genomics of Zoonotic Pathogen Transmission

Zoonotic pathogens persist across interconnected animal, environmental, and food-production systems, creating complex routes of transmission to humans. Understanding this process requires moving beyond conventional surveillance towards functional genomics, which examines how specific genes and regulatory pathways support colonization, survival, adaptation, and spread. Pathogens must first establish themselves within animal hosts, evade immune defences, compete with resident microbiota, and respond to physiological stress. They may then enter food-production environments, where traits such as biofilm formation, antimicrobial resistance, stress tolerance, and metabolic flexibility promote persistence during processing, storage, and distribution. Functional genomic approaches, including comparative genomics, transcriptomics, mutational screening, and genome-wide association studies, can identify the molecular determinants underlying these stages. Integrating genomic findings with epidemiological and food-chain data can clarify transmission pathways, improve risk assessment, and support targeted interventions that reduce pathogen persistence and protect public health. This integrated perspective is essential for developing more resilient, evidence-based One Health strategies globally.This research aims to elucidate the functional genomic mechanisms that enable zoonotic pathogens to transition from animal colonization to sustained persistence within food chains and subsequent transmission to humans. By integrating comparative genomics, transcriptomics, metagenomics, and targeted functional assays, the study will identify genes, regulatory networks, and adaptive traits associated with host colonization, environmental survival, antimicrobial resistance, biofilm formation, stress tolerance, and cross-species transmission. It will examine how pathogen populations evolve across livestock, wildlife, processing environments, retail products, and human exposure points, with particular attention to genomic changes that promote persistence under production and food-processing pressures. The project will also distinguish core transmission determinants from strain-specific or niche-dependent adaptations, supporting the development of robust molecular markers for surveillance and source attribution. Experimental validation of priority genes will clarify their causal roles in pathogen fitness and transmission. Ultimately, the research seeks to generate a mechanistic framework linking genomic variation to epidemiological behaviour, thereby improving early detection, risk assessment, outbreak investigation, and evidence-based interventions. The findings will inform targeted control strategies at critical points across the farm-to-fork continuum, reducing zoonotic exposure, strengthening food safety, and supporting One Health approaches to prevent pathogen emergence and protect animal, environmental, and public health systems.This topic welcomes original research, reviews, and methodological studies examining the functional genomics of zoonotic pathogens across the animal-to-food-to-human transmission continuum. Contributions should investigate genetic determinants of animal colonization, host adaptation, environmental survival, biofilm formation, stress tolerance, antimicrobial resistance, virulence, and persistence in food production or processing environments. Studies integrating comparative genomics, transcriptomics, metagenomics, proteomics, genome-wide association analyses, gene editing, mutagenesis, or functional validation are particularly encouraged. Authors may address bacterial, viral, fungal, or parasitic pathogens relevant to livestock, wildlife, aquaculture, fresh produce, processing facilities, retail foods, or human exposure. Manuscripts should clearly define the transmission context, sampling framework, analytical methods, and biological significance of identified genomic features. Authors should provide appropriate metadata, quality-control procedures, statistical validation, and accession numbers for deposited sequence data. Submissions linking genomic findings to surveillance, source attribution, risk assessment, intervention design, or One Health policy are strongly encouraged. Ethical approvals and data-sharing statements are required. Topic editors: Nicolae Corcionivoschi, Kálmán Imre Source: https://www.frontiersin.org/research-topics/86939/from-animal-colonization-to-food-chain-persistence-functional-genomics-of-zoonotic-pathogen-transmission