Metagenomic Next-Generation Sequencing of Rectal Swabs for ARO Surveillance

Antimicrobial resistance (AMR) is a public health threat where efficientsurveillance is needed to prevent outbreaks. Existing methods for detection ofgastrointestinal colonization of multidrug-resistant organisms (MDRO) are limited tospecific organisms or resistance mechanisms. Metagenomic next-generationsequencing (mNGS) is a more rapid and agnostic diagnostic approach for microbiomeand resistome investigations. We determined if mNGS can detect MDRO from rectalswabs in concordance with standard microbiology results. Methods: We performed andcompared mNGS performance on short-read Illumina MiSeq (N=10) and long-readNanopore MinION (N=4) platforms directly from peri-rectal swabs to detectvancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negativeorganisms (CRO).