Long-read sequencing for bacterial plasmid analysis: a brief overview

Whole-genome sequencing has transformed microbial genomics since the first bacterial genome was published in 1995. Advances in sequencing technology, together with decreasing costs, now enable high-resolution investigation of bacterial pathogens for epidemiological surveillance, and infection control. A major breakthrough has been the advent of third-generation long-read sequencing (LRS) platforms, such as Pacific Biosciences and Oxford Nanopore Technologies, which overcome the limitations of short-read sequencing by producing long continuous reads. LRS facilitates accurate de novo genome assembly, resolution of repetitive and structurally complex regions, and precise characterization of plasmids and other mobile genetic elements that frequently harbor antimicrobial resistance genes (ARGs). A particular strength of LRS lies in its ability to reveal the complete genomic architecture of ARGs, including their localization, copy number, and surrounding genetic environment. Such contextual information is essential, since e.g. the interpretation of antimicrobial resistance (AMR) depends not only on the presence of specific genes but also on their structural organization, mobility potential, and genomic integration. By contrast, LRS provides a reliable foundation for understanding AMR evolution and dissemination through both clonal expansion and horizontal gene transfer. Recent developments in bioinformatics, including dedicated tools for plasmid reconstruction, typing, and annotation, further enhance the analytical value of LRS and hybrid approaches. Beyond isolate-level analyses, LRS enables plasmid surveillance and the tracing of ARG transmission across strains, hosts, and healthcare settings. This review sets out to give readers a brief overview of LRS technology and its capabilities and outlines current approaches and tools to analyze bacterial plasmids.