title: Antimicrobial resistance surveillance in the genomic age.
abstract: The loss of effective antimicrobials is reducing our ability to protect the global population from infectious disease. However, the field of antibiotic drug discovery and the public health monitoring of antimicrobial resistance (AMR) is beginning to exploit the power of genome and metagenome sequencing. The creation of novel AMR bioinformatics tools and databases and their continued development will advance our understanding of the molecular mechanisms and threat severity of antibiotic resistance, while simultaneously improving our ability to accurately predict and screen for antibiotic resistance genes within environmental, agricultural, and clinical settings. To do so, efforts must be focused toward exploiting the advancements of genome sequencing and information technology. Currently, AMR bioinformatics software and databases reflect different scopes and functions, each with its own strengths and weaknesses. A review of the available tools reveals common approaches and reference data but also reveals gaps in our curated data, models, algorithms, and data-sharing tools that must be addressed to conquer the limitations and areas of unmet need within the AMR research field before DNA sequencing can be fully exploited for AMR surveillance and improved clinical outcomes.
authors.affiliation: M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: McArthur
authors.affiliation: M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada.
authors.forename: Kara K
authors.initials: KK
authors.lastname: Tsang
mesh_terms: D000465:Algorithms; D000818:Animals; D000890:Anti-Infective Agents; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D004351:Drug Resistance / Q000235:genetics*; D016678:Genome; D023281:Genomics / Q000379:methods* / Q000639:trends; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000639:trends; D006801:Humans; D008957:Models, Genetic; D012984:Software
chemical_list: D000890:Anti-Infective Agents
keywords: antimicrobial resistance; biocuration; bioinformatics; genomics