Hybrid Sequencing of Chromosome and Plasmids from Multidrug Resistant Escherichia coli Isolated in Cambodia: Are Megaplasmids Vectors of Antibiotic Resistance Genes?

Objectives: The prevalence of Antimicrobial Resistance (AMR) in Escherichia coli infections in Cambodia is high and increasing, yet data distinguishing plasmid- and chromosome-mediated AMR-spread remain limited. The aim of this study was to characterise chromosomal and plasmid structures in clinically relevant E. coli resistant strains to investigate mechanisms driving the spread of Antibiotic Resistance Genes (ARGs) in Battambang Province, Cambodia.

Methods: Hybrid genome assembly was performed using short- and long-read sequencing of six Extended Spectrum Betalactamase (ESBL)- and Carbapenemase Producing (CP) E. coli isolates collected from patients at Battambang Provincial Hospital, Cambodia. Detailed bacteriological analyses were conducted, as well as comprehensive genomic investigations to characterise Sequence Types (STs), plasmids, resistance mechanisms, and phylogenetic relationships among the strains, and to perform pairwise comparisons of plasmid sequences.

Results: Chromosome and plasmid sequences were successfully recovered for each strain. Five STs were identified: ST1193 (two strains), ST131, ST205, ST405 and ST4204. All strains displayed a megaplasmid carrying ARGs, and one to five regular-sized plasmids without ARGs. Four distinct megasplasmids sequences were identified, including one shared by two ST1193 strains and one shared by ST131 and ST205 strains.

Conclusions: The identification of megaplasmids carrying ARGs and shared by different strains highlights their potential role in the spread of antimicrobial resistance through horizontal gene transfer (HGT) in Cambodia. This study also confirms the circulation of the high-risk multidrug-resistant (MDR) clones ST131 and ST1193 in Battambang province, Cambodia, and underscores the importance of hybrid genome assembly to study plasmid structure and identify their role in AMR spread.