Long-Read Sequencing-Based Characterization of Plasmid Architecture and Resistance Gene Mobility in Carbapenem-Resistant Enterobacteriaceae from Community and Hospital Sources in Benue State

The architecture of plasmids carrying carbapenem resistance genes determines their conjugal transfer potential, host range, and capacity for rapid dissemination across community-hospital interfaces, yet these structural features remain uncharacterized in Nigerian carbapenem-resistant Enterobacteriaceae (CRE). This study employed Oxford Nanopore Technologies long-read sequencing to resolve complete plasmid architectures and characterize resistance gene mobility in CRE from community and hospital sources in Makurdi, Benue State, in the North Central geopolitical zone of Nigeria. Sixty CRE isolates (30 community-derived from stool of healthy volunteers and outpatients, 30 hospital-derived from clinical cultures) underwent short-read Illumina and long-read Nanopore hybrid assembly using Unicycler to achieve complete chromosomal and plasmid resolution. Plasmid incompatibility typing, conjugation assays, transposon mapping, and IS element characterization were performed. NDM-1-carrying IncF plasmids averaging 220 kb were identified in 42.9 percent of hospital isolates and 20 percent of community isolates. Three structurally identical plasmid architectures were shared between community and hospital isolates, providing direct evidence of bidirectional community-hospital CRE exchange. IS26-mediated composite transposons flanking blaNDM-1 were identified in 76.9 percent of NDM plasmids, facilitating chromosomal integration. Conjugation efficiency to E. coli J53 was high for IncF plasmids (transfer frequency 10 to the power of minus 3). These findings advance understanding of plasmid-driven CRE dissemination in Benue State and establish long-read sequencing as an essential tool for plasmid epidemiology and AMR transmission investigation in Nigeria. Keywords: carbapenem resistance, plasmid architecture, long-read sequencing, NDM-1, Benue State.