Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group
Kate S. Baker, Elita Jauneikaite, J Nunn, Janet Midega, Rifat Atun, Kathryn E. Holt, Kāmini Walia, Benjamin P. Howden, Heather Tate, Iruka N. Okeke, Alessandra Carattoli, Li Yang Hsu, Katie L. Hopkins, Dishon Muloi, Nicole E. Wheeler, David M. Aanensen, Lewis C. E. Mason, Jonah Rodgus, René S. Hendriksen, Sabiha Y. Essack, Beverly Egyir, Alison Laufer Halpin, Duncan MacCannell, Josefina Campos, Padmini Srikantiah, Nicholas Feasey, Sharon J. Peacock
Abstract
Nearly a century after the beginning of the antibiotic era, which has been associated with unparalleled improvements in human health and reductions in mortality associated with infection, the dwindling pipeline for new antibiotic classes coupled with the inevitable spread of antimicrobial resistance (AMR) poses a major global challenge. Historically, surveillance of bacteria with AMR typically relied on phenotypic analysis of isolates taken from infected individuals, which provides only a low-resolution view of the epidemiology behind an individual infection or wider outbreak. Recent years have seen increasing adoption of powerful new genomic technologies with the potential to revolutionise AMR surveillance by providing a high-resolution picture of the AMR profile of the bacteria causing infections and providing real-time actionable information for treating and preventing infection. However, many barriers remain to be overcome before genomic technologies can be adopted as a standard part of routine AMR surveillance around the world. Accordingly, the Surveillance and Epidemiology of Drug-resistant Infections Consortium convened an expert working group to assess the benefits and challenges of using genomics for AMR surveillance. In this Series, we detail these discussions and provide recommendations from the working group that can help to realise the massive potential benefits for genomics in surveillance of AMR.