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

Diverse plasmid clustering tools reveal different notions of relatedness, complicating antimicrobial resistance surveillance in the era of complete genomic sequencing.

• Why it matters: Understanding plasmid relatedness is crucial for tracking the spread of antimicrobial resistance, yet current methods lack standardization, hindering effective surveillance and comparison across studies.
• What they did: The authors reviewed and organized existing plasmid clustering tools into conceptual families, analyzing how their assumptions influence surveillance outcomes, and proposed hierarchical, multitool strategies for better comparison.
• The result: Implementing these strategies and clearer models of plasmid evolution can enable scalable, interpretable, and more accurate plasmid-based antimicrobial resistance surveillance.