Emergence and evolution of rare ST592 blaNDM-1-positive carbapenem-resistant hypervirulent Klebsiella pneumoniae in China

Huan Zhang ¹ Su Dong ² Caiping Mao ¹ Yuejuan Fang ³ Junjie Ying ^4*

• ¹ Zhejiang Cancer Hospital, Hangzhou, China
• ² Shaoxing Hospital of Traditional Chinese Medicine, Shaoxing, Zhejiang Province, China
• ³ Quzhou Maternity and Child Health Care Hospital, Quzhou, Zhejiang, China
• ⁴ Quzhou City People's Hospital, Quzhou, China

Objectives: To characterize the genomes of two rare ST592 Klebsiella pneumoniae isolates and explore their evolution to carbapenem-resistant hypervirulent K. pneumoniae.Methods: Minimum inhibitory concentrations (MICs) were determined using a VITEK 2 compact system. Conjugation experiments were conducted using film matings. Whole genome sequencing (WGS) was performed using Illumina and Nanopore platforms. Antimicrobial resistance determinants were identified using the ABRicate program in the ResFinder database. Insertion sequences were identified using ISFinder. Bacterial virulence factors were identified using virulence factor database (VFDB). The K and O loci were tested using Kleborate. Multilocus sequence typing (MLST) and replicon types were identified by the Center for Genomic Epidemiology. Conjugation-related elements were predicted using oriTfinder. The plasmid structure was visualized using Circos, and a possible evolutionary model was constructed using Biorender.Results: Isolates KPZM6 and KPZM16 were identified as ST592 and KL57, respectively, and were collected from the same department. Antimicrobial susceptibility testing data revealed that KPZM16 possessed an extensively drug-resistant (XDR) profile, whereas KPZM6 was a susceptible K. pneumoniae. The hybrid assembly showed that both KPZM6 and KPZM16 had one pLVPK-like virulence plasmid carrying the rmpA, rmpA2, and iucABCD-iutA gene clusters. However, strain KPZM16 harbored one IncN plasmid carrying the carbapenem resistance genes blaNDM-1, dfrA14, and qnrS1. The results of conjugation experiments demonstrated that the plasmid could be transferred to the recipient strain. It is possible that the NDM-1-producing plasmid was transferred from KPZM6 to KPZM16 via conjugation, leading to the formation of CR-hvKP.Conclusions: This is the first study in which the complete genomic characteristics of the rare NDM-producing ST592 K. pneumoniae clinical isolate was performed. Our study provides a possible evolutionary hypothesis for the of hv-CRKP formation via conjugation. Early detection is recommended to avoid the extensive spread of this clone.