The role of whole genome sequencing in reducing the risk of AMR spread

As we reach the end of World AMR Awareness Week, Microbiome Services Manager Julie MacKinnon reflects on the role of whole genome sequencing in assessing strains intentionally used in the food chain to ensure they do not add to the pool of antimicrobial resistance genes in the gut.

Antimicrobial resistance (AMR) is one of the top global public health threats, with bacterial AMR estimated to have been directly responsible for 1.27 million global deaths in 2019.

Antimicrobial Resistance (AMR) occurs when bacteria, viruses, fungi and parasites no longer respond to antimicrobial agents. As a result of drug resistance, antibiotics and other antimicrobial agents become ineffective and infections become difficult or impossible to treat. World AMR Awareness Week is a global campaign to raise awareness and understanding of AMR and promote best practices. The theme, “preventing antimicrobial resistance together” calls for cross-sectoral collaboration to preserve the effectiveness of antimicrobials. To effectively reduce AMR, all sectors must use antimicrobials prudently and appropriately, take preventative measures to decrease the incidence of infections and follow good practices in the disposal of antimicrobial contaminated waste.

The increase in AMR is primarily driven by the misuse and overuse of antimicrobials. However, it is important to also remember the importance of assessing microbial strains intentionally used in the food chain in order to minimise the risk of adding to the pool of antimicrobial resistance genes already present in the gut bacterial population, or otherwise increasing the risk of transferring drug resistance. 

Recent research has led to a much better understanding of the beneficial role that microorganisms can play in human health as well as in agriculture, and viable bacteria are increasingly being used in products such as probiotics and animal feed additives. Another very active area of research and development at the moment is live biotherapeutics.

Its an exciting time for microbiology, with so much potential benefit for mankind, but it is critical that bacterial strains are selected carefully and used responsibly.

To this end, within Europe, authorisation processes, guidance documents and regulations are in place. For example, for animal feed additives, the European Food Safety Authority (EFSA) states that viable micro-organisms used as active agents should not add to the pool of antimicrobial resistance genes already present in the gut bacterial population, or otherwise increase the risk of transferring drug resistance. One of the ways that this is achieved is through establishing the susceptibility of strains used to a range of antimicrobials of human and veterinary importance. Strains can be tested for minimum inhibitory concentrations of these antimicrobials and candidate strains can be categorized as susceptible or resistant.

Another important tool is whole genome sequencing, and analysis of the data generated can provide not only information on the taxonomic identification of the strains, but also on the characterisation of their potential functional traits of concern which may include resistance to antimicrobials of clinical relevance for humans and animals.

NCIMB has worked closely with probiotic and biotherapeutics companies to provide data for these kinds of assessments.  Our whole genome sequencing and analysis service includes genome sequencing, assembly and screening for antimicrobial resistance genes and virulence factors using the Qiagen CLC Genomics Workbench. Once sequenced, the whole genome data is available for any future analysis required, and we can undertake analysis of existing datasets.

Julie MacKinnon, Microbiome Services Manager