February 10, 2020
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Q&A: Sewage represents a viable option for antimicrobial resistance surveillance

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Mark E. J. Woolhouse, OBE, FRSE, MMedSci
Mark E. J. Woolhouse

A pair of researchers recently suggested in Science that sewage could be used for surveillance of antimicrobial resistance because it could be implemented quickly at a low cost. According to the report, such a system would have “substantial and rapid benefits” in many settings, including resource-poor ones.

Healio spoke with Mark E. J. Woolhouse, OBE, FRSE, FMedSci, professor of infectious disease epidemiology at the Usher Institute at the University of Edinburgh and co-author of the paper, to discuss the logistics of implementing a global sewage-based antimicrobial resistance surveillance system. – by Caitlyn Stulpin

Q: Can you elaborate on what prompted the idea to use sewage for surveillance related to antimicrobial resistance?

A: The idea came out of work at the Danish Technical University. Some years ago, it became possible to perform metagenomics analyses on biological material; metagenomics simply means sequencing all the DNA in a sample. Metagenomics is used to study the human microbiome. The microbiome includes a wide range of bacterial species and is now recognized as an important component of human physiology and well-being. Microbiome studies started with fecal samples, so it was a small step to apply the technique to sewage. Using metagenomics, there are many things we can look for in sewage, such as disease-causing enteric bacteria, for example, or viruses. Here, we are using it to look for antimicrobial resistance genes.

Q: How would this be done?

A: Sample collection is straightforward, although we have formal protocols to make sure it is done correctly. Extraction of the DNA is a routine operation; people do it in schools, although not from sewage. The two key steps are metagenomics sequencing, which is also fairly standard these days, and the bioinformatics analysis — the computer algorithms that sort through huge quantities of sequence data and pick out the sequences that correspond to any known antimicrobial resistance (AMR) gene. There are thousands of these in the genome databases.

Q: How could this process improve our surveillance for antimicrobial resistance?

A: Most AMR surveillance takes place in hospitals and clinics. This is very important work, but it only captures a tiny fraction of the population (albeit one for which AMR is very important) and usually just a small number of bacterial species and types of resistance. It is difficult and expensive to perform AMR surveillance in the general population and most countries do little or none of that, despite the fact that most antibiotics are used in the general population and AMR is very common. Sewage offers an easy, effective and cheap route for conducting AMR surveillance in the general population. We see it as a game changer for AMR surveillance worldwide.

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Q: What populations stand to benefit most from an approach like this?

A: We think the approach could be usefully adopted by every country in the world. But it will be especially useful in countries that have limited resources to carry out traditional AMR surveillance. This is so easy and cheap that it can be done anywhere.

Q: What are the next steps for implementing something like this?

A: The next key step is for WHO to endorse the approach as part their portfolio of measures to improve AMR surveillance around the world. We are in discussions with the WHO AMR surveillance team to determine the best way of implementing it.

Disclosure: Woolhouse reports no relevant financial disclosures.