Plasmid typing challenges in the era of genomic antimicrobial resistance surveillance.

Authors

Gijs Teunis, Louise Roer, Anita C Schürch, Lapo Mughini-Gras, Antoni P A Hendrickx

Published in

Trends in microbiology. Sep 24, 2026. Epub Sep 24, 2026.

Abstract

Plasmids are central drivers of antimicrobial resistance (AMR) dissemination, yet their modular, recombinogenic genomes defy concepts of relatedness derived from bacterial chromosomes. Long-read sequencing now routinely yields complete plasmid sequences, exposing a key gap: we can reconstruct plasmids but lack agreed principles for comparing them. In response, diverse clustering tools have emerged that emphasise different signals, such as marker genes, whole-sequence similarity, gene content, backbone structure, or explicit rearrangement events. Each encodes a distinct notion of plasmid distance. This review organises these tools into conceptual families, highlights how their assumptions shape surveillance outputs, and proposes hierarchical, multitool strategies and clearer models of plasmid evolution as the basis for scalable and interpretable plasmid-based AMR surveillance.

PMID:
42786073
Bibliographic data and abstract were imported from PubMed on 25 Sep 2026.

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