Infection and Drug Resistance (May 2023)
Genomic and Phylogenetic Analysis of a Multidrug-Resistant blaNDM-carrying Klebsiella michiganensis in China
Abstract
Tian Jiang,1,* Guoli Li,2,* Linyao Huang,1 Ding Ding,1 Zhi Ruan,2 Jianxin Yan1 1Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China; 2Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China*These authors contributed equally to this workCorrespondence: Zhi Ruan; Jianxin Yan, Email [email protected]; [email protected]: Klebsiella michiganensis is an emerging hospital-acquired bacterial pathogen. However, there is a dearth of knowledge on the antimicrobial resistance and transmission of K. michiganensis. Here, we characterized the microbiological and genomic features of a carbapenem-resistant K. michiganensis strain harboring the blaNDM-1 gene in China.Methods: K. michiganensis strain 2563 was recovered from the sputum sample of a hospitalized patient with pulmonary infection. Whole-genome sequencing of K. michiganensis strain 2563 was conducted using both the short-read Illumina and long-read MinION platforms to thoroughly characterize the genetic context of blaNDM-carrying plasmid in K. michiganensis 2563. Furthermore, BacWGSTdb server was utilized to perform in silico multilocus sequence typing (MLST), identify antimicrobial resistance genes, and conduct genomic epidemiological analyses of the closely related isolates deposited in the public database.Results: K. michiganensis 2563 was resistant to piperacillin, aztreonam, meropenem, imipenem, amoxicillin-clavulanic acid, ampicillin, cefotaxime, cefazolin, ampicillin/sulbactam, cefepime, piperacillin-tazobactam, and ceftazidime. It belonged to sequence type (ST) 43, and the blaNDM-1 gene was found to be located on the plasmid p2563_NDM (54,035 bp). This plasmid showed remarkable similarity to other blaNDM-1-encoding plasmids found in various Enterobacterium species in the public database. The occurrence of global ST43 K. michiganensis was primarily sporadic, and the closest relative of K. michiganensis 2563 was another ST43 isolate 12,084 recovered from China in 2013, which differed by 171 SNPs.Conclusion: Our study reports the genome characteristics of a carbapenem-resistant K. michiganensis strain carrying the blaNDM-1 gene in China, highlighting the need for ongoing surveillance of this pathogen in clinical settings.Keywords: whole-genome sequencing, Klebsiella michiganensis, blaNDM, multidrug-resistant, phylogenetics
