Hybrid sequencing of ESBL and carbapenemase-producing E. coli isolated from patients in Cambodia

In Cambodia, factors as weak monitoring and control systems of antibiotic usage have exacerbated the spread of AMR, particularly Extended Spectrum Betalactamase (ESBL) and Carpapenemase Producing (CP) Escherichia coli (E. coli), highlighting the urgent need for comprehensive data and improved control measures. Our study aims at understanding the spread of the genetic determinants of AMR from ESBL and CP strains isolated from patients in Battambang Province, Cambodia. We collected and analyzed six Escherichia coli isolates from hospitalized patients in Battambang, Cambodia, characterizing them by combining short and long read sequencing technologies to understand antibiotic resistance gene spread. The study involved detailed bacteriological and genomics analyses to identify plasmids, resistance mechanisms, and phylogenetic relationships among the strains. The hybrid assembly successfully recovered the chromosome and multiple plasmids for each strain. Five sequence types (ST1193, ST131, ST205, ST405 and ST4204) were detected among the 6 strains. In each strain we observed a megaplasmid and one or several regular plasmids. Each strain carried carbapenemase and/or ESBL-coding genes on these megaplasmid sequences. The pairwise comparison of plasmid sequences revealed that several strains share identical or nearly-identical megaplasmids and plasmids. This study highlights the importance of combining short and long reads sequencing technologies for studying plasmid structure. It confirmed the circulation of multi-drug resistant clones ST131 and ST1193 in Battambang province, Cambodia. Megaplasmids carrying antibiotic resistance genes were identified in all strains, and some were identical between different strains, highlighting their role in antimicrobial resistance spread.