Hybrid sequencing of chromosome and plasmids from multidrug-resistant Escherichia coli isolated in Cambodia: Are megaplasmids vectors of antibiotic resistance genes?
Abstract
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 characterize 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 beta-lactamase (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 characterize 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 megasplasmid 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 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.
Related
- Drainage water management reduces nutrient, Escherichia coli, and antibiotic resistance gene export
- Antibiotic resistance profiles of seven genomospecies of Corynebacterium jeikeium analyzed by whole genome sequencing
- Whole-genome sequencing-based characterization of antimicrobial resistance determinants and phenotype–genotype concordance in uropathogenic Escherichia coli isolates from ICU patients in Saudi Arabia
- Shared Resistance, Phage-Receptor, and Biofilm Determinants in Antibiotic-Resistant Pseudomonas aeruginosa, Escherichia coli, and Acinetobacter baumannii: A Bibliometric and Gene-Network Analysis of Phage Cocktail Research.
- Genomic insight into the antibiotic-resistant determinants of Escherichia coli from small ruminants and manure in North West Province, South Africa
BibTeX
@article{marcy2026hybrid,
title = {{Hybrid sequencing of chromosome and plasmids from multidrug-resistant Escherichia coli isolated in Cambodia: Are megaplasmids vectors of antibiotic resistance genes?}},
author = {Ella Marcy and Sivhour Chiek and Mallorie Hidé and Savatey Hak and Chiva Ma and Meymey Lem and Gauthier Delvallez and Anne-Laure Bañuls and Sokleaph Cheng and Juliette Hayer},
journal = {Journal of Global Antimicrobial Resistance},
year = {2026},
month = sep,
doi = {10.1016/j.jgar.2025.09.003},
url = {https://hal.science/hal-05751569v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Hybrid sequencing of chromosome and plasmids from multidrug-resistant Escherichia coli isolated in Cambodia: Are megaplasmids vectors of antibiotic resistance genes?
AU - Ella Marcy
AU - Sivhour Chiek
AU - Mallorie Hidé
AU - Savatey Hak
AU - Chiva Ma
AU - Meymey Lem
AU - Gauthier Delvallez
AU - Anne-Laure Bañuls
AU - Sokleaph Cheng
AU - Juliette Hayer
PY - 2026
DA - 2026/09/16
JO - Journal of Global Antimicrobial Resistance
DO - 10.1016/j.jgar.2025.09.003
UR - https://hal.science/hal-05751569v1
AB - 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 characterize 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 beta-lactamase (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 characterize 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 megasplasmid 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 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.
SN - 2213-7165
SN - 2213-7173
ER -