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 more 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 bla_KPC gene in 2.5 minutes and provided genetic context (bla_KPC harbored on pKPC_Kp46 IncF plasmid).

Illumina sequencing provided accurate allelic variant determination (i.e., bla_KPC-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.