I am happy to announce that the opinion/review piece I wrote for Current Opinion in Food Science has been published. The paper (1) extends on some of my thoughts on how high-throughput sequencing and metagenomics can aid in risk assessment of antibiotic resistant bacteria that I outlined in my PhD thesis (2), but specifically focuses on the food supply chain and its role in resistance dissemination and selection.

In the paper, I argue for that the food supply chain is a special type of setting in the resistance puzzle, as it not only serves as a connection between environmental habitats for bacteria and humans, but also sometimes presents a substantial selection for resistance, due to use of antibiotics in agri- and aquaculture. International food standards are clear that both selection and dissemination of foodborne resistance should be considered in the risk analysis of food production (3). However, the current main use of DNA sequencing in food safety is whole genome sequencing to delineate which specific strains that are involved in foodborne disease outbreaks, including the resistance factors they may carry (4,5). Further, I argue that while shotgun metagenomics could be used to screen samples for a large number of genes involved in resistance and virulence in the food supply chain, it would at present be very costly and therefore of doubtful benefit to employ in routine screening programs. Still, metagenomics can contribute knowledge that can be used in quantitative risk assessment of antibiotic resistance in the food supply chain.

The entire paper can be read here.


  1. Bengtsson-Palme J: Antibiotic resistance in the food supply chain: Where can sequencing and metagenomics aid risk assessment? Current Opinion in Food Science, in press (2017). doi: 10.1016/j.cofs.2017.01.010 [Paper link]
  2. Bengtsson-Palme J: Antibiotic resistance in the environment: a contribution from metagenomic studies. Doctoral thesis (medicine), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 2016. [Link]
  3. Codex Alimentarius Commission: Guidelines for risk analysis of foodborne antimicrobial resistance. Food and Agriculture Organization of the United Nations & World Health Organization2011. [Link]
  4. Franz E, Gras LM, Dallman T: Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens. Current Opinion in Food Science, 8, 74-79 (2016). doi: 10.1016/j.cofs.2016.04.004
  5. Stasiewicz MJ, Bakker den HC, Wiedmann M: Genomics tools in microbial food safety. Current Opinion in Food Science, 4, 105-110 (2015). doi: 10.1016/j.cofs.2015.06.002