Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations

Plasmids are self-replicating, extrachromosomal genetic elements that serve as vehicles for antimicrobial resistance (AMR) genes. In bacteria, plasmids frequently carry critical AMR genes such as extended spectrum beta-lactamases (bla_CTX-M) in gram-negative and glycopeptide resistance gene (vanA) in gram-positive species. Plasmid sequences are genetically diverse within and across taxa, with the PLSDB database recording up to 72,360 non-redundant sequences in May 2024. Horizontal transfer of plasmids continues to threaten the effectiveness of last-resort antibiotics, especially as plasmids can disseminate horizontally crossing taxonomic boundaries. Whole-genome sequencing is a powerful approach for investigating AMR plasmids, yet there are several challenges facing bioinformatic tools and databases. Here, we review those challenges and their implications for AMR plasmid research as well as summarizing key bioinformatic analyses and tools used in AMR plasmid investigations. The review highlights how genomics has revolutionized AMR plasmid studies in drug-resistant pathogens and provides insights on the current limitations and future challenges to leverage plasmid genomics in public health research.