Genomic and phylogenetic analysis of a multidrug-resistant mcr-1-carrying Klebsiella pneumoniae recovered from a urinary tract infection in China.

Abstract Objectives The emergence and dissemination of colistin resistance Enterobacterales has become a major global public health threat. Here, we investigate the genomic and phylogenetic characteristics of a multidrug-resistant Klebsiella pneumoniae carrying mcr-1 gene recovered from a urinary tract infection in China. Methods The antimicrobial susceptibility of K. pneumoniae KP4823 was determined by broth microdilution method. Whole genomic DNA was extracted and sequenced using Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. Hybrid assembly with long and short reads was performed using Unicycler, and the genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The sequence type (ST), capsular type, antimicrobial resistance and virulence genes were identified from the genome sequence. Core genome multilocus sequence typing (cgMLST) analysis was performed by BacWGSTdb 2.0 server. Results K. pneumoniae KP4823 was resistant to colistin, ceftazidime, cefepime, cefotaxime, fosfomycin and aztreonam. The complete genome sequence of KP4823 consists of five contigs comprising 5,445,519 bp, including one chromosome and four plasmids. The isolate was assigned to ST101 with capsular serotype KL106. Several antimicrobial resistance genes were identified, including the colistin resistance gene mcr-1, which was located in a 34,685 bp IncX4 plasmid. The closest relative of K. pneumoniae KP4823 was another ST101 isolate 08EU827 recovered from Sweden in 2008, which differed by 191 cgMLST loci. Conclusion Our study reports the genome sequence of a multidrug-resistant K. pneumoniae carrying mcr-1 gene in China. These data may help to understand the antimicrobial resistance mechanisms, genomic features and transmission dynamics of colistin resistance in clinical settings.