Dan Lu, Katrina L Kalantar, Victoria T Chu, Abigail L Glascock, Estella S Guerrero, Nina Bernick, Xochitl Butcher, Kirsty Ewing, Elizabeth Fahsbender, Olivia Holmes, Erin Hoops, Ann E Jones, Ryan Lim, Suzette McCanny, Lucia Reynoso, Karyna Rosario, Jennifer Tang, Omar Valenzuela, Peter M Mourani, Amy J Pickering, Amogelang R Raphenya, Brian P Alcock, Andrew G McArthur, Charles R Langelier
Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data...
April 18, 2024: bioRxiv