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

Objectives: The emergence and dissemination of colistin-resistant Enterobacterales has become a ma-jor global public-health threat. Here we investigated the genomic and phylogenetic characteristics of a multidrug-resistant Klebsiella pneumoniae strain (KP4823) carrying the mcr-1 gene recovered from a uri-nary tract infection in China. Methods: Antimicrobial susceptibility of K. pneumoniae KP4823 was determined by broth microdilu-tion. Whole genomic DNA was extracted and sequenced using Oxford Nanopore MinION and Illumina NovaSeq 60 0 0 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 se-quence type (ST), capsular type, and 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: Klebsiella pneumoniae KP4823 was resistant to colistin, ceftazidime, cefepime, cefotaxime, fos-fomycin 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 re-sistance gene mcr-1, which was located on a 34 685-bp IncX4 plasmid. The closest relative of K. pneu-moniae 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 mcr-1-carrying K. pneu-moniae in China. These data may help to understand the antimicrobial resistance mechanisms, genomic features and transmission dynamics of colistin resistance in clinical settings. (c) 2021 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )