# Plasmid-Driven Resistome Diversity in 9700 Escherichia coli Genomes Across Phylogroups and Sequence Types

## TL;DR

This study shows how plasmids shape the spread of antibiotic resistance in E. coli, highlighting key plasmid types that carry clinically important resistance genes.

## Contribution

The study provides the most extensive plasmid-focused resistome analysis in E. coli, revealing modular plasmid-ARG networks and lineage-specific resistance strategies.

## Key findings

- Plasmids like IncX3, IncX4, IncI, and IncF are strongly associated with clinically important resistance genes such as blaNDM-5 and mcr-1.1.
- Generalist phylogroups maintain diverse plasmid-rich resistomes, while dominant ExPEC clones like ST131 show reduced plasmid dependency and chromosomal resistance integration.
- High-risk plasmid backbones account for the majority of globally relevant ARGs, including 64.6% of blaNDM-5 and 76.4% of mcr-1.1.

## Abstract

Background/Objectives: Plasmids are key vehicles for the dissemination of antimicrobial resistance (AMR), yet their contribution to the global resistome architecture of Escherichia coli remains poorly resolved. This study aimed to quantify how plasmid backbones shape the distribution, mobility, and stabilization of resistance genes across diverse phylogenetic backgrounds. Methods: We analyze 9700 high-quality genomes spanning major phylogroups and sequence types. Plasmidome reconstruction was integrated with lineage-resolved antimicrobial resistance gene (ARG) mapping to characterize plasmid–ARG associations and evolutionary patterns. Results: Although most antimicrobial resistance genes (ARGs) are chromosomal, plasmids disproportionately encode clinically important determinants including blaNDM-5, mcr-1.1, and multiple blaCTX-M alleles that show strong, recurrent associations with a restricted set of backbone families, most notably IncX3, IncX4, IncI, and IncF. These conserved plasmid–gene modules recur across phylogenetic backgrounds and continental scales. We identify a marked divergence in evolutionary strategies: generalist phylogroups (A, B1, D) maintain plasmid-rich and highly diverse resistomes, whereas globally dominant Extraintestinal Pathogenic E. coli (ExPEC) clones such as ST131 and ST410 exhibit reduced plasmid dependency and frequent chromosomal integration of extended-spectrum β-lactamase (ESBL) genes, particularly blaCTX-M-15, consistent with a shift toward vertically stabilized resistomes. By integrating plasmidome reconstruction with lineage-resolved ARG mapping, this study delivers the most extensive plasmid-focused resistome analysis to date, revealing highly modular plasmid–ARG networks structured around a small number of high-risk backbone types. These backbones account for the majority of globally relevant ARGs, including 64.6% of blaNDM-5 and 76.4% of mcr-1.1 detections. Conclusions: Together, our findings establish plasmid lineages rather than individual genes or clones as central units of AMR dissemination and critical targets for future genomic surveillance and intervention strategies.