Research progress on phage-mediated dissemination of antibiotic resistance genes

The emergence and spread of antibiotic resistance are threatening environmental and public health worldwide, challenging the efficient treatment and prevention of infectious diseases. Bacteria acquire antibiotic resistance through horizontal gene transfer, occurring both within and across bacterial species, facilitated by mobile genetic elements such as plasmids, integrons, insertion sequences and bacteriophages. Bacteriophages, the most abundant biological entities on Earth, play a crucial role in accelerating the rapid dissemination of antibiotic resistance genes (ARGs) among bacterial pathogens, thereby driving the emergence of multidrug-resistant “superbugs.” Bacteriophages transfer ARGs through transduction, driving their evolution and dissemination across various ecosystems, including soils, aquatic environments, animal guts, wastewater treatment systems and clinical settings. Despite growing evidence of their role, the mechanisms underlying the bacteriophage-mediated ARG transmission, the co-evolutionary dynamics of bacteriophages and bacteria, as well as the interaction between active bacteriophages and their hosts, remain poorly understood. This review systematically examines bacteriophage-mediated dissemination of ARGs, the ecological co-evolution between bacteriophages and their bacterial hosts, and the contribution of active bacteriophages to ARG transmission. First, we elaborated on the diversity and ecological functions of bacteriophages as carriers of ARGs, including the classification of bacteriophages, the ecological roles of their auxiliary metabolic genes in the biogeochemical cycling, and the horizontal gene transfer mediated by bacteriophages. Secondly, we examined the role of bacteriophages in ARGs dissemination, addressing the types of ARGs carried by bacteriophages, their distribution across diverse habitats, the driving factors influencing the bacteriophage-mediated ARGs transmission, and the main methodologies for studying these processes. Furthermore, we summarized the co-evolutionary dynamics between bacteriophages and their hosts, emphasizing how shifts in bacteriophage life cycles regulate the microbial community dynamics, and how the ongoing “arms race” between bacterial defense systems and bacteriophage counter-defense systems influences the transfer of ARGs. Finally, we reviewed the methodologies for studying active bacteriophages and the association between active bacteriophages (i.e., those in the replication, infection, and dissemination states) and ARGs. Given the limitations of current research, we propose several key directions for future studies: (1) constructing multi-scale networks for phage-host interaction for exploring the association between auxiliary metabolic genes and ARGs, alongside in-depth analysis of how bacteriophage-host dynamics at the community level shape ARGs distribution and dissemination; (2) advancing and integrating multi-omics techniques, including metagenomics, metatranscriptomics, single-virus sequencing, and DNA-SIP, to achieve more precise monitoring of bacteriophage activity, clarify the role of active phages in ARG transfer, and support the establishment of an active bacteriophage-ARG database; and (3) integration of viral ecology into a broader ecosystem food web framework to explore the environmental dissemination of phage-mediated ARGs among different trophic levels (such as microorganisms, protists, plants, and animals) and their profound impacts on biodiversity, biogeochemical cycles, and human health. In conclusion, this systematic review advances understanding of the mechanisms underlying bacteriophage-mediated ARGs dissemination, providing a scientific basis for understanding the interaction between bacteriophages and ARGs, and guiding the development of innovative strategies for the prevention and control of ARGs contamination, including bacteriophage-based therapy. From the macroscopic perspective of “One Health”, it further underscores the importance of interdisciplinary research and global collaboration in addressing bacteriophage-host interactions and their implications for antibiotic resistance.