Browsing by Subject "WGS"

Carbapenemase-producing Enterobacteriaceae (CPE) resist carbapenem class of antibiotics in addition to the other type of antibiotic resistances they usually carry. The blaKPC-3 gene is one of the genes causing the carbapenemase production in bacteria. The aim of this study was to establish the Oxford Nanopore Technologies MinION sequencing method and integrate it with Illumina sequencing into a hybrid assembly for investigating the location of the blaKPC-3 gene in the bacterial genome. We used 14 isolates suspected of plasmid-mediated gene transfer and prepared three libraries using different DNA extraction methods. The contigs from the hybrid assembly sequences were used to annotate the target genes, which were then included in a phylogenetic tree and distance matrix analysis. DNA extraction method had an impact on the amount of data and the length of reads produced in MinION and the Smart DNA prep extraction kit with InnuPure C16 touch extraction device produced the best results. The blaKPC-3 gene was located on plasmids in each isolate, and the similarity of the plasmid sequences indicated that horizontal plasmid-mediated gene transfer has likely occurred between different species. However, the clonal spread cannot be excluded, and further research is needed to confirm these findings.