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Review ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Public Health | doi: 10.3389/fpubh.2019.00242

Using Genomics to Track Global Antimicrobial Resistance

  • 1National Food Institute, Technical University of Denmark, Denmark
  • 2Center for Veterinary Medicine, United States Food and Drug Administration, United States

The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology and microbial surveillance. The availability of bioinformatics tools and online accessible databases has been a prerequisite for this.
We conducted a scientific literature review and here we present a description of examples of available tools and databases for AMR detection and provide future perspectives and recommendations.
At least 47 bioinformatics resources for detection of antimicrobial resistance (AMR) determinants in DNA or amino acid sequence data have been developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder and ResFinder. Bioinformatics resources differ for several parameters including type of accepted input data, presence/absence of software for search within a database of AMR determinants that can be specific to a tool or cloned from other resources, and for the search approach employed, which can be based on mapping or on alignment. As a consequence, each tool has strengths and limitations in sensitivity and specificity of detection of AMR determinants and in application, which for some of the tools have been highlighted in benchmarking exercises and scientific articles. The identified tools are either available at public genome data centers, from GitHub or can be run locally online. NCBI and ENA provide possibilities for online submission of both sequencing and accompanying phenotypic antimicrobial susceptibility data, allowing for other researchers to further analyze data, and develop and test new tools.
The advancement in whole genome sequencing and the application of online tools for real-time detection of AMR determinants is essential for control and prevention strategies to combat the increasing threat of AMR. Accessible tools and DNA sequence data are expanding to establish global pathogen surveillance and AMR tracking based on genomics. There is however, a need for standardization of pipelines and databases as well as phenotypic predictions based on the data.

Keywords: Globaly, Antimicrobial resistance (AMR), surveillance, BioInformatic, Microbiology, Genomic

Received: 18 Jun 2019; Accepted: 13 Aug 2019.

Copyright: © 2019 Hendriksen, Bortolaia, Tate, Tyson, Aarestrup and McDermott. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Rene S. Hendriksen, Technical University of Denmark, National Food Institute, Kongens Lyngby, Denmark, rshe@food.dtu.dk