Sequencing sewage for antimicrobial resistance surveillance

February 06, 2020

In this Policy Forum, Frank Aarestrup and Mark Woolhouse advocate for the immediate establishment of a global antimicrobial resistance surveillance system based on the metagenomic sequencing of human sewage. Most current antimicrobial resistance (AMR) surveillance approaches focus on hospitalized patients in clinical environments. According to the authors, these approaches likely lead to biased understandings and underestimations of AMR spread in healthy humans or for the great majority of commonly used antimicrobial treatments. Raw sewage could provide a potentially powerful tool to accompany clinical AMR surveillance, these authors say. It anonymously combines material from a large and diverse population, which would be unfeasible to monitor otherwise. It has already been used to evaluate the usage of illegal drugs, pharmaceuticals, alcohol, nicotine and caffeine as well as to monitor polio. What's more, recent metagenomic studies have demonstrated the ability to describe the full profile of AMR-genes within human populations by measuring sewage. According to Aarestrup and Woolhouse, sewage-based AMR surveillance would be a valuable addition to the current efforts to combat AMR worldwide. They suggest that such a system could also be useful in identifying and tracking other significant public health concerns, including new and emergent intestinal and food-borne pathogens. The authors estimate that an effective continuous surveillance system could be established globally for less than $1 million USD annually - far cheaper than the annual cost of conventional approaches.

American Association for the Advancement of Science

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