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

OBJECTIVES This study aimed to delineate the genomic architecture of a ST45-K62 Klebsiella pneumoniae strain identified as the first global isolate co-carrying blaKPC-2 and blaNDM-5.

METHODS 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.

RESULTS 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 blaKPC-2 and blaNDM-5. Virulence factor screening further demonstrated the presence of numerous virulence-associated genes in this isolate. The blaNDM-5 gene is immediately flanked upstream by ISkox3-IS26-bleMBL at a 2-bp interval, and by Tn3-IS3000-IS5 on the other side at a 14-bp interval. Pan-genome analysis revealed a highly conserved core genome but pronounced accessory genome diversity.

CONCLUSION To our knowledge, this is the first genomic report of a ST45-K62 K. pneumoniae isolate harboring both blaKPC-2 and blaNDM-5 genes. The pHRKP01-NDM5 harboring blaNDM-5 contains multiple mobile genetic elements (MGEs).