Genomic Surveillance for One Health Antimicrobial Resistance: Understanding Human, Animal, and Environmental Reservoirs
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 w
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Genomic Surveillance for One Health AMR Genomic Workflow for the Detection of Antimicrobial Resistance Genes (ARGs) Using WGS for One Health AMR Surveillance Enterobacteriaceae and AMR Escherichia coli E. coli: Intestinal and Extraintestinal Pathogens 6.1 Intestinal Pathogenic E. coli (IPEC) 6.2 Extraintestinal Pathogenic E. coli (ExPEC) 7 ExPEC Virulence Factors and AMR 7.1 ColV/BM Plasmids 7.2 ST131:H22 Lineages Carrying ColV Plasmids 7.3 Hybrid Plasmids 8 WGS One Health Insights: ExPEC, APEC, and Zoonoses 9 WGS One Health Insights: The Case of blaIMP-4 Metallo-Beta-Lactamase (MBL)-Producing Enterobacteriaceae in Eastern Australia
S. P. Djordjevic (*) and V. M. Jarocki The University of Technology Sydney, Sydney, NSW, Australia Australian Centre for Genomic Epidemiological Microbiology (AusGEM), University of Technology Sydney, Broadway, NSW, Australia e-mail: [email protected] B. Morgan The University of Technology Sydney, Sydney, NSW, Australia Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia E. Donner Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia Celia M. Manaia, Erica Donner, Ivone Vaz-Moreira, and Peiying Hong (eds.), Antibiotic Resistance in the Environment: A Worldwide Overview, Hdb Env Chem, DOI 10.1007/698_2020_626, © Springer Nature Switzerland AG 2020
S. P. Djordjevic et al. 10 WGS One Health Insights: The Role of Environmental AMR 11 Outlook References
Abstract 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 systemsbased AMR monitoring, mitigation, and management. Keywords APEC, Escherichia coli, ExPEC, One Health, Whole-genome sequencing, Zooanthroponoses, Zoonoses
1 Genomic Surveillance for One Health AMR The development of rapid and affordable whole-genome sequencing (WGS) technology has given scientists a bacterial subtyping tool of unprecedented precision and discrimination th
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