Genomic Characteristics of a Carbapenem-Resistant Co-Carrying and Capsular Type KL25 Recovered from a County Level Hospital in China.

BACKGROUND

Hypervirulent carbapenem-resistant (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 isolate SM117 with capsular serotype KL25, co-carrying , two copies of and multiple plasmid-borne virulence genes from a county level hospital in China.

METHODS

Antimicrobial susceptibility of SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then 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 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 , and multiple plasmid-borne virulence genes including and aerobactin genes . The coexistence of and in 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 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 with capsular serotype KL25, co-carrying , two copies of 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 .