Developing a novel approach to complex evolution of antimicrobial resistance via mobile genetic elements from a persistent environmental biofilm

Mobile genetic elements are key to the global emergence of antibiotic resistance. We successfully reconstructed the complete bacterial genome and plasmid assemblies of isolates sharing the same blaKPC carbapenemase gene to understand evolution over time in six confined hospital drain biofilms over five years. From 82 isolates we identified 14 unique strains from 10 species with 113 blaKPC-carrying plasmids across 16 distinct replicon types. To assess dynamic gene movement, we introduced the 'Composite-Sample Complex', a novel mathematical approach to using probability to capture the directional movement of antimicrobial resistance genes accounting for the co-occurrence of both plasmids and chromosomes within an isolate, and highlighting likely donors and recipients. From the validated model, we demonstrate frequent transposition events of blaKPC from plasmids to other plasmids, as well as integration into the bacterial chromosome within specific drain biofilms. We present a novel approach to estimate the directional movement of antimicrobial resistance via gene mobilization.