Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infectionsPaula Hayakawa Serpa, Xianding Deng, Mazin Abdelghany, Emily Crawford, Katherine Malcolm, Saharai Caldera, Monica Fung, Aaron McGeever, Katrina L. Kalantar, Amy Lyden, Rajani Ghale, Thomas Deiss, Norma Neff, Steven A. Miller, Sarah B. Doernberg, Charles Y. Chiu, Joseph L. DeRisi, Carolyn S. Calfee & Charles R. Langelier
BMC, 2022Abstract: Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing.
