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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. | LitMetric

AI Article Synopsis

  • Next-Generation Sequencing (NGS) technologies are essential for monitoring infectious diseases due to their ability to analyze the genetic basis of virulence and antimicrobial resistance (AMR) in microorganisms.
  • Implementing NGS comes with challenges around standardization, validation, and quality control, largely because it heavily depends on bioinformatics for accurate data interpretation.
  • A workshop held in 2017 highlighted the need for benchmark resources to address these challenges, emphasizing the importance of a "One Health" approach for monitoring AMR across humans, animals, food, and the environment.

Article Abstract

Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms.  In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed.  NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced.  Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process.  This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017.   Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a "One Health" approach.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039958PMC
http://dx.doi.org/10.12688/f1000research.14509.2DOI Listing

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