Comparative analysis of homology of carbapenem-resistant Klebsiella pneumoniae based on pulsed-field gel electrophoresis and whole genome sequencing

This study was conducted to compare the homology of carbapenem- resistant Klebsiella pneumoniae (CRKP) obtained based on different methods. Methods A total of 44 CRKP strains were collected from a Class A tertiary hospital in China from 2017 to 2023. The homology of these CRKP strains was analyzed based on pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Besides, the sequence types (STs), drug resistance genes, genome islands, and prophages of different clonal strains were comparatively analyzed. Moreover, the homology of these CRKP strains was comparatively analyzed using the average nucleotide identity (ANI), BLAST score ratio (BSR) scatter plots, homologous gene heatmaps, phylogenetic trees based on 16S rRNA gene sequences, phylogenetic trees based on core genes, phylogenetic trees based on whole-genome single nucleotide polymorphism (SNP), SNP distance heatmaps, and minimum spanning trees based on SNP and STs. Results The ANI between two homologous strains was greater than 99.99 %, and the BSR scores of homologous strains were close to the center line. The results of phylogenetic trees based on 16S rRNA gene sequences were significantly different from those of PFGE. In contrast, the results of phylogenetic trees based on core genes and whole-genome SNP were similar to those of PFGE. There were significant differences in the SNP between the homologous strains of ST11. Conclusion The ST11CRKP strain demonstrates polymorphism. Furthermore, WGS can be employed to distinguish between the genetic variations of clonal strains and analyze the homology of CRKP strains via various comparative genomic methods from multiple perspectives.