Metagenomic Next-Generation Sequencing of Rectal Swabs for the Surveillance of Antimicrobial Resistant Organisms on the Illumina Miseq and Oxford MinION Platforms

Purpose: Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multidrug-resistant organisms (MDRO) are limited to specific organisms or resistance mechanisms. Metagenomic next-generation sequencing (mNGS) is a rapid and agnostic diagnostic approach for microbiome and resistome investigations. We determined if mNGS can detect MDRO from rectal swabs in concordance with standard microbiology results. Methods: We performed and compared mNGS performance on short-read Illumina MiSeq (N=10) and long-read Nanopore MinION (N=4) platforms directly from peri-rectal swabs to detect vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative organisms (CRO). Results: We detected E. faecium (N=8) and E. faecalis (N=2) with associated van genes (9/10) in concordance with VRE culture-based results. We studied the microbiome and identified CRO organisms, P. aeruginosa (N=1), E. cloacae (N=1), and KPC-producing K. pneumoniae (N=1). Nanopore real-time detection detected the blaKPC gene in 2.5 minutes and provided genetic context (blaKPC harbored on pKPC_Kp46 IncF plasmid). Illumina sequencing provided accurate allelic variant determination (i.e., blaKPC-2) and strain typing of the K. pneumoniae (ST-15). Conclusions: We demonstrated an agnostic approach for surveillance of MDRO, examining advantages of both short and long-read mNGS methods for AMR detection.