Global emergence of carbapenem-resistant Klebsiella pneumoniae co-carrying multiple carbapenemases

Hao Guo; Yuye Wu; Lirong Li; Jianfeng Wang; Juan Xu; Fang He

doi:10.1016/j.csbj.2023.07.013

Global emergence of carbapenem-resistant Klebsiella pneumoniae co-carrying multiple carbapenemases

Comput Struct Biotechnol J. 2023 Jul 13:21:3557-3563. doi: 10.1016/j.csbj.2023.07.013. eCollection 2023.

Authors

Hao Guo¹, Yuye Wu², Lirong Li¹, Jianfeng Wang³, Juan Xu⁴, Fang He¹

Affiliations

¹ Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
² Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
³ Department of Respiratory and Critical Care Medicine, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, Zhejiang 310003, China.
⁴ School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China.

Abstract

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) co-carrying multiple carbapenemases is complicating clinical treatment. This study aimed to investigate the global dissemination trends of CRKP strains that co-carry multiple carbapenemases. The CRKP isolate KP424 co-carrying bla_NDM-1 and bla_KPC-2, recovered from a stool specimen, was identified by the NG-Test Carba 5 test, and the genome sequence was further determined by using Nanopore MinION and Illumina NovaSeq 6000 technologies. The genome sequences of the CRKP strains carrying multiple carbapenemase genes were further retrieved from the NCBI GenBank database. Thirteen antimicrobial resistance genes, including bla_NDM-1 and bla_KPC-2, have been identified in KP424, with bla_NDM-1 and bla_KPC-2 located on different plasmids. In total, 832 genome sequences of CRKP strains co-carrying two carbapenemase genes were retrieved from the NCBI database. Strains carrying both bla_NDM and bla_OXA-48-like accounted for 665 (79.9 %) of the total strains, ranking first, and those carrying both bla_KPC and bla_NDM accounted for 103 (12.4 %), ranking second. The prevalence of CRKP strains co-carrying two carbapenemase genes increased significantly over time, from 0.40 % in 2010 to 9.67 % in 2021. The proportion of strains carrying both bla_KPC and bla_NDM has also increased, from 0.00 % in 2010 to 4.40 % in 2021. The strains carrying both bla_KPC and bla_NDM had the highest prevalence (66.7 %, 52/78) in China, while those carrying both bla_NDM and bla_OXA-48-like had the highest prevalence worldwide. Multiple-carbapenemase producers pose a great threat to public health; further research on the mechanisms underlying multiple carbapenemase gene occurrence is required to prevent their global dissemination.

Keywords: Carbapenemase; KPC; Klebsiella pneumoniae; NDM; Whole-genome sequencing.