Multi-omics Approaches to Understand the Evolution and Adaptation of High-Risk Bacterial Lineages

The remarkable success of a limited number of bacterial lineages in causing disease across human, animal, food, and environmental settings represents one of the major challenges in contemporary microbiology. High-risk bacterial lineages are characterized not only by their capacity to disseminate globally, but also by their extraordinary adaptability, ecological versatility, and ability to acquire traits that enhance persistence, virulence, transmission, and, in many cases, antimicrobial resistance. Examples of these globally successful populations include Escherichia coli ST131, Klebsiella pneumoniae ST258, ST11, and ST15, Pseudomonas aeruginosa ST235, ST111, and ST175, Acinetobacter baumannii International Clone 2 (IC2), Enterococcus faecium Clonal Complex 17 (CC17), epidemic methicillin-resistant Staphylococcus aureus (MRSA) lineages, pandemic Salmonella clones and Vibrio cholerae O1 7PET. While whole-genome sequencing has revolutionized our understanding of bacterial evolution, the increasing availability of complementary multi-omics technologies now provides unprecedented opportunities to uncover the complex molecular mechanisms underlying the emergence, persistence, and global success of these bacterial clones.A central, unifying challenge in modern microbial evolutionary biology is understanding how resistance, virulence, and persistence traits co-evolve within these high-risk lineages to drive their success. This Research Topic aims to move beyond descriptive genomic epidemiology toward a system-level, predictive understanding of these interconnected adaptive traits. Recent advances in culturomics, population genomics, pangenomics, transcriptomics, proteomics, metabolomics, epigenomics, mobilomics, and other high-throughput approaches are transforming our view of bacterial adaptation across diverse ecological niches from a One Health perspective.This Research Topic welcomes multidisciplinary studies that apply integrated omics approaches to investigate the evolutionary biology, ecological adaptation, dissemination, and persistence of clinically relevant, veterinary, foodborne, and environmental bacterial species and lineages. Submissions must be framed around bacterial evolution or adaptation, including antimicrobial resistance, to fit the scope of the section and journal. We particularly encourage submissions bridging multiple disciplines, including microbiology, genomics, evolutionary biology, systems biology, computational biology, epidemiology, bioinformatics, artificial intelligence and machine learning, aiming to clarify how resistance, virulence and persistence co-evolve in successful clones.The sub-topics may include, but are not limited to:• Population genomics, phylogenomics, and pangenomics of emerging and high-risk bacterial lineages across human, animal, food, and environmental interfaces.• Multi-omics integration for understanding bacterial evolution, adaptation, heteroresistance, tolerance and persistence. • Transcriptomic, proteomic, metabolomic, epigenomic, and single-cell approaches to bacterial adaptation, pathogenesis, and host-pathogen interactions.• Mobilomics, plasmidomics, phageomics, and the contribution of mobile genetic elements to bacterial evolution. • Antibiotic-driven adaptive evolution and compensatory or fitness-cost mutations as well as collateral sensitivity and resistance trade-offs• Computational frameworks, artificial intelligence, machine learning, pipelines, and databases for integrating large-scale microbial omics datasets.• Multi-omics approaches supporting One Health surveillance of bacterial pathogens. • Co-evolution of virulence, persistence, transmission, and antimicrobial resistance, and systems biology approaches to decipher the molecular basis of globally successful bacterial clones.This collection aims to foster interdisciplinary collaborations among microbiologists, genomic epidemiologists, evolutionary biologists, bioinformaticians, computational scientists, veterinarians, clinicians, and environmental researchers. By promoting the integration of complementary omics technologies, this Research Topic seeks to advance a holistic understanding of the biological processes driving the emergence and worldwide dissemination of high-risk bacterial lineages across interconnected One Health ecosystems.We welcome submissions in the following article types: FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, Technology and Code. Topic editors: William Calero-Cáceres, João Pedro Rueda Furlan, Pramod Kumar Source: https://www.frontiersin.org/research-topics/85691/multi-omics-approaches-to-understand-the-evolution-and-adaptation-of-high-risk-bacterial-lineages