Lociq: A Loci-Seeking Approach for Enhanced Plasmid Subtyping and Structural Characterization

Abstract Antimicrobial resistance (AMR) monitoring for public health is relying more on whole genome sequencing to characterize and compare resistant strains. This requires new approaches to describe and track AMR that take full advantage of the detailed data provided by genomic technologies. Tracking the plasmid-mediated spread of AMR genes is a primary concern for AMR monitoring. Sequence rearrangements can integrate new AMR genes into the plasmid backbone or promote hybridization of multiple plasmids. To better monitor plasmid evolution and dissemination, we developed a subtyping method to classify plasmids by variations in the sequence and arrangement of core plasmid genetic elements. This method generates multiple typing schema that both cluster related plasmids and characterize individual plasmids. This method provides an alpha-numeric nomenclature for plasmid subtyping to denominate plasmid diversity across multiple plasmid families. The Lociq method generates typing schema to track and characterize the origin, evolution and epidemiology of multidrug resistant plasmids.