Combining metagenomics and metatranscriptomics to study human, animal and environmental resistomes

Antibiotic resistance (AR) is a grim and very common phenomenon around the world, posing a significant threat to public health and food safety. The emergence of multi-drug and even pan-resistant strains carrying novel antibiotic resistance genes (ARGs) and insufficient development of new antibiotics are the major reasons that limit the choice of antibiotics for treating bacterial infections. Because of the heavy use of antibiotics in human medicine and animal husbandry, human and animal guts and farm environments now constitute reservoirs for antibiotic-resistant pathogens and ARGs. ARGs can circulate in humans, animals, and their associated environments in many ways, leading to a wide dissemination and spread of AR. Characterizing the collective ARGs (resistome) in host-associated and natural environments will deepen our understanding of the origin, evolution and transmission of ARGs. As many microbes cannot be cultivated in the laboratory, culture-independent strategies are urgent needed to explore the resistomes in living and nonliving environments. With the development of high-throughput sequencing technologies, metagenomics and metatranscriptomics are becoming important tools for characterizing microbiomes as well as resistomes. Here, we summarize the research progress and future directions for combining metagenomics and metatranscriptomics to study human, animal and environmental resistomes.