Yuanzhong Fang,1 Juan Jin,1 Minfei Peng,2 Lidong Xu,1 Linyuan Gu,1 Danni Bao,3 Qiuying Zhang,4 Kainan Jin5 

1Department of Clinical Laboratory, Hangzhou Linping District Women & Children Hospital, Hangzhou, Zhejiang, People’s Republic of China; 2Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, People’s Republic of China; 3Department of Clinical Laboratory, Sanmen People’s Hospital, Sanmen Bay Branch of The First Affiliated Hospital, Zhejiang University School of Medicine, Taizhou, Zhejiang, 317100, People’s Republic of China; 4Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, People’s Republic of China; 5Department of Gastroenterology, Linhai First People’s Hospital, Taizhou, Zhejiang, 317000, People’s Republic of China

Correspondence: Qiuying Zhang, Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, People’s Republic of China, Email 26067889@qq.com Kainan Jin, Department of Gastroenterology, Linhai first People’s hospital, Taizhou, Zhejiang, 317000, People’s Republic of China, Email 353803262@qq.com

Background: Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying blaNDM-5, two copies of blaKPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China.
Methods: Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server.
Results: The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including blaNDM-5, blaKPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of blaKPC and blaNDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference.
Conclusion: This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying blaNDM-5, two copies of blaKPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.

Keywords: whole-genome sequencing, K. pneumoniae, multidrug-resistance, blaNDM-5, blaKPC-2, rmpA2, iucABCD-iutA, hvCRKP