In our research, we analyzed well-defined strains of Enterobacteriaceae with carbapenemases (CPE) from various species, isolated from individual patients. We used whole-genome sequencing to further characterize plasmid-encoded carbapenemases. Sequencing was performed using short-read platforms (Illumina, United States) and long-read platforms (Oxford Nanopore Technologies, United Kingdom). We applied bioinformatics tools to identify possible plasmid transfers between different CPE species and compared the suitability of both platforms for determining plasmid transfers. We demonstrated the presence of plasmids with carbapenemase genes blaOXA-48, blaOXA-181 and blaVIM-1 in Enterobacteriaceae isolates, including Escherichia coli, Citrobacter spp., Klebsiella pneumoniae and K. quasipneumoniae. Long-read sequencing proved more reliable for plasmid detection, as it enabled the assembly of complete circular plasmids in a single contig. In some cases, short-read sequencing had difficulty determinig the location of the carbapenemase gene and resulted in sequence fragmentation, leading to incorrect plasmid assembly. In patients, from whom we had sufficient quality data to study plasmid transfers, we found, based on long-read sequencing data, that horizontal transfer of plasmids with carbapenemase genes between different species of Enterobacteriaceae most likely occurred. No transmission was observed in the case of two isolates obtained from two different patients.
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