Genome analysis of blaNDM-5 and blaKPC-2 co-occurrence in ST45-K62 carbapenem-resistant Klebsiella pneumoniae isolate from China

This study aimed to delineate the genomic architecture of a ST45-K62 Klebsiella pneumoniae strain identified as the first global isolate co-carrying bla KPC-2 and bla NDM-5 . Antimicrobial susceptibility was determined using broth microdilution. Whole-genome sequencing was performed using the Illumina HiSeq X-10 and PacBio RS II platforms, and genomic features were analyzed using various bioinformatics tools. HRKP01 showed resistance to most tested antibiotics, being susceptible only to amikacin. It was classified as sequence type (ST) 45 and K-locus type (K) 62. The genome of HRKP01 consisted of a 5,329,093 bp chromosome and three plasmids of 283,811 bp, 122,964 bp and 57,031 bp in length. Comprehensive sequence analysis revealed 12 antimicrobial resistance genes, including bla KPC-2 and bla NDM-5 . Virulence factor screening further demonstrated the presence of numerous virulence-associated genes in this isolate. The bla NDM-5 gene is immediately flanked upstream by IS kox3 -IS 26 - ble MBL at a 2-bp interval, and by Tn3-IS 3000 -IS 5 on the other side at a 14-bp interval. Pan-genome analysis revealed a highly conserved core genome but pronounced accessory genome diversity. To our knowledge, this is the first genomic report of a ST45-K62 K. pneumoniae isolate harboring both bla KPC-2 and bla NDM-5 genes. The pHRKP01-NDM5 harboring blaNDM-5 contains multiple mobile genetic elements (MGEs).