Genomic Surveillance for One Health Antimicrobial Resistance: Understanding Human, Animal, and Environmental Reservoirs and Transmission

Springer International Publishing
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Handbook of Environmental Chemistry, 2020, 91, pp. 71-100
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© 2020, Springer Nature Switzerland AG. Whole-genome sequencing (WGS) has significantly improved our ability to understand how, through gene acquisition, bacteria can become resistant to antibiotic therapies and cause an increasingly substantial burden of disease. In this chapter, we take the well-known indicator bacteria and opportunistic pathogen Escherichia coli, predicted to be one of the leading causes of antimicrobial resistance (AMR) infections in the next decades, and demonstrate the potential insights that can be gained using WGS and genomic epidemiology. Specifically, we discuss the mechanisms by which these bacteria acquire, retain, propagate, and disperse gene combinations with a focus on key mobile genetic elements, notably ColV/BM plasmids. Efforts are underway to further standardise and streamline WGS and resistome screening from multiple environments to support the rapidly increasing user base and facilitate regional and global public health monitoring, outbreak tracking, and AMR evolutionary prediction and preparedness. The ability of E. coli to exist in multiple environments as both a pathogen and commensal organism are central to its value for establishing meaningful One Health systems-based AMR monitoring, mitigation, and management.
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