Antimicrobial Use, Antimicrobial Resistance, and the Microbiome in Animals, volume II

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Background

Antimicrobials contributed to the prevention of millions of deaths and they remain the primary treatment option for potentially fatal bacterial infections in both humans and animals. Antibiotics have been widely used, which has promoted the emergence and spread of AMR in all ecosystems (One Health). Now, AMR constitutes a significant global threat to humans, animals, and the environment. However, accurate estimates of the amount of antimicrobials used in animals, including pet animals, are still lacking in many countries. The emergence, spread and transmission of AMR is a complex issue and can be influenced by several factors including AMU and biosecurity practices (access, cleaning, disinfection, etc.). The origin and fate of the antimicrobial resistant pathogenic bacteria of animals still needs to be established by large and should be addressed in a “One Health” perspective. To understand and mitigate the global health crisis of AMR, it is important be able to link the observed resistance phenotypes with their underlying genomic mechanisms (genome determinants) as well as the genetic supports (chromosomal or extrachromosomal) on which these resistance genes are located.

The animal gut microbiome plays an important role in maintaining the overall health and the development of the immune system, energy homeostasis, digestion and protection against pathogens. However, the environment and nutritional factors (feed, water, bedding and litter, etc.), animal rearing practices (biosecurity and sanitation) and host factors (line, sex and age and disease conditions) can significantly influence the composition of the microbiome in an animal’s body. Therefore, it is important to study the molecular epidemiology and ecology of AMR and related genes (resistome) in relation to the microbiomes. In addition, there is a need to further investigate the role of direct cross-infection or horizontal gene transfer of AMR among bacteria, as well as host factors including immunity, which could influence the microbiome and resistome of importance to animal and human health.

This Research Topic will be open for Reviews, Brief Research Reports and Original Research articles dealing with, but not limited to:
• Antimicrobial use in animals, with or without focus on the microbiome in a “One Health” concept.
• Ecology of AMR in relation to the microbiome of animals (both food animals and pet animals) and their environment.
• Molecular mechanisms of evolution and survival of pathogenic and resistant bacteria associated with animals.
• Artificial intelligence/machine learning for the AMR phenotype prediction from genomic data, phenotype-genotype relationships and detection of AMR bacteria associated with food animals.
• Risk factors and mitigation of dissemination, transmission, distribution of AMR in relation to veterinary practices and environmental factors.
• Pharmacodynamics and pharmacokinetic of traditional antimicrobials and alternative products used in animals.

The emphasis will be on the relationship between microbiome function, antimicrobial (resistome) and virulence (virulome) determinants as well as on host immunity and their precise role in the survival and maintenance of animal pathogens. Research on the impact of environmental factors and climate change, lessons learned across the world, and best practices and antimicrobial stewardship including alternative production methods and transformational adaptive management for healthy animal microbiota/microbiome is also particularly welcomed.

Keywords: antimicrobial use, pathogens, production animals, antimicrobial resistance, microbiome

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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