Antimicrobial resistance and the microbiome

Microbiome, Environmental Microbiome and Animal Microbiome are coming together to launch a special series inviting authors to submit their research pertaining to antimicrobial resistance (AMR) and the microbiome. © Image by Arek Socha from Pixabay The emergence and spread of AMR can only be described as a catastrophic problem for human and animal health. It is projected that there would be more deaths due to AMR than cancer by 2050. During the last decade a large number of studies have reported the emergence and spread of antimicrobial resistance genes (ARG) and defined in detail how these are mobilized between pathogens and also within communities of bacteria. The impact of antibiotics on microbiomes particularly those of humans and animals is a cause for concern and can alter physiology quite dramatically. In addition the spread of ARG to these microbiomes has been reported and occurs on a global scale clearly indicated in studies of sewage and waste water treatment plants. Further spread may occur under selective conditions in the presence of antibiotics in sewage and other biocides such as detergents both of which could cause significant changes in diversity. We need to understand the impacts of ingression of ARG into microbiomes and consider the wider issue of AMR spread into the environment. The importance of human microbiomes is indisputable now as many new aspects of their roles have emerged in the past few years and continue to build a complex picture of metabolic interactions with their hosts. Similarly, animal and plant microbiomes studies have provided an exciting view into the potential benefits of healthy, diverse and stable microbiomes for sustainable agriculture. Understanding the persistence and spread of ARG in agricultural and other food production systems such as aquaculture will be critical for food safety and production. We are just beginning to reveal the importance of microbial assemblages in the environment for both bioremediation and biodegradation in addition to the vital roles played in nutrient cycles. Antimicrobial agents can have impact on all these activities in addition to spreading new gene combinations due to the rapid mobilization of ARGs due to the highly selective effects of antibiotic therapy. Whilst some antibiotics are natural products others are xenobiotics and remain and persist in the environment and mobile ARG will spread as a result of selection. Most naturally occurring resistance genes are chromosomal and further work is needed to investigate these impacts. Microbiomes may work syntrophically to degrade recalcitrant compounds and recent research has demonstrated the emergence of antibiotic biodegraders within the environment and these bacteria may provide the answer to reduce the persistence of antibiotics and their detrimental effects in nature. By understanding the natural role of antibiotics produced in nature we may find the clues to avoiding the arms race of ever increasing resistance in the face of novel drugs, streptomycin production gene clusters are still found in soil streptomycetes and were dated thought to have emerged several million years ago yet they are still apparently useful in nature today. Further research will inform new ways to administer antibiotics, new types of drugs and new ways to combat resistance.