Whole-genome sequencing of 108 CRKP isolates from South China reveals ST11 dominance and emerging hvCRKP

ObjectiveCarbapenem-resistant Klebsiella pneumoniae (CRKP) has become a worldwide public health concern due to its high morbidity and mortality rate. A retrospective study was conducted to explore the molecular epidemiology of antimicrobial resistance and virulence of CRKP in South China.Methods108 CRKP isolates were collected from multiple hospitals in South China. The characteristics of the CRKP strains, including antimicrobial resistance genes, mutations and virulence factors, were analyzed using whole-genome sequencing and the software Kleborate. A phylogenetic tree was constructed to illustrate evolutionary diversification.ResultsThe main Sequence Type (ST) type, capsular serotype, and LPS serotype among CRKP isolates in South China were ST11, KL47, and OL101, respectively. KPC-2 was the most prevalent carbapenemase type. Notably, KPC-12, a recently identified and rarely reported variant of KPC-2, was discovered in four CRKP strains. All ST11 CRKP isolates harbored porin and efflux pump regulator mutations of AcrR-43%, OmpK35-17%, and OmpK36GD as well as fluoroquinolone mutations of GyrA-83I, GyrA-87G, and ParC-80I. All CRKP strains exhibited complex multi-drug resistance (MDR) phenotypes. The most common types of aerobactin (iuc) and yersiniabactin (ybt) were iuc1 and ybt9 ICEKp3, respectively. There were 17 hvCRKP (hypervirulent carbapenem-resistant Klebsiella pneumoniae) strains found in our study, which were mainly ST11-KL64 and ST413-1LV-KL112, harboring the blaKPC-2 gene and blaNDM-1 gene, respectively.ConclusionIn South China, highly virulent and MDR CRKP strains show a trend toward epidemic, underscoring the urgent need for ongoing genomic surveillance and stringent infection control measures. KPC-2 variant KPC-12 and ST413-1LV-KL112 hvCRKP, a novel type of hvCRKP carrying blaNDM-1, require particular attention and further investigation.