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The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex microbiomes presents a significant global health challenge. This review examines recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescence-based techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.

Original publication

DOI

10.1016/j.tim.2024.12.013

Type

Journal article

Journal

Trends Microbiol

Publication Date

05/2025

Volume

33

Pages

496 - 509

Keywords

antibiotic resistance genes (ARGs), antimicrobial resistance (AMR), horizontal gene transfer, mobile genetic elements, plasmid–host interaction, Plasmids, Bacteria, Bacteriophages, Humans, Single-Cell Analysis, Gene Transfer, Horizontal, Drug Resistance, Bacterial