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Learn how to use metagenomics for antimicrobial resistance surveillance

22 April 2020

How can metagenomics be used to survey antimicrobial resistance (AMR) globally and what are its challenges? A SAFOSO team has contributed to building a blended learning course (e-learning and a hands-on workshop) on the use of metagenomics to tackle antimicrobial resistance (AMR). In their recent publication in Frontiers in Public Health, co-authored by SAFOSO, provides an overview over the course structure, its contents and as well as participants’ insights. The course is now freely available as a Massive Open Online Course (MOOC).

Antimicrobial resistance (AMR) is a One Health problem and a global challenge. Effective surveillance of AMR depends on collaboration between the public health, veterinary and food systems. A harmonized method that can be used between regions and sectors is needed for surveillance of AMR. Shot-gun metagenomics is considered a good candidate method. It is the culture-independent, untargeted sequencing of all DNA present in a sample, and it therefore offers the possibility to investigate taxonomic composition, to predict AMR, and to recover whole genome sequences. There are, however, shortcomings and bias factors that need to be considered when applying metagenomics. For the method to be used effectively, dissemination of knowledge on this topic is needed.

To this end, a blended learning course (e-learning and a hands-on workshop) on the use metagenomics in surveillance of AMR was created. The face-to-face workshop organized by SAFOSO was essential to understand the expectations of the participants about the transition to metagenomics-based surveillance.

The entire training is now also released as a Massive Open Online Course (MOOC) and is available online. Over 20 sessions of the course have been conducted, more than 3,000 learners enrolled from over 120 countries. The paper, published in Frontiers in Public Health, provides an overview of the course structure and content as well as insights of participants’ expectations on the application of metagenomics-based surveillance. The main challenges identified by participants included the lack of harmonized protocols and the uncertainty of metagenomics data and its linkage to risk factors.

The e-learning project is  part of the EFFORT project (Ecology from Farm to Fork Of microbial drug Resistance and Transmission).

Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance. Duarte ASR, Stärk KDC, Munk P, Leekitcharoenphon P, Bossers A, Luiken R, Sarrazin S, Lukjancenko O, Pamp SJ, Bortolaia V, Nissen JN, Kirstahler P, Van Gompel L, Poulsen CS, Kaas RS, Hellmér M, Hansen RB, Muñoz-Gomez V, Hald T. Front Public Health. 2020 Feb 25;8:38. Article

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