Objective: 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 bla_NDM-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 bla_NDM-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 bla_NDM-1 gene was found to be located on the plasmid p2563_NDM (54,035 bp). This plasmid showed remarkable similarity to other bla_NDM-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 bla_NDM-1 gene in China, highlighting the need for ongoing surveillance of this pathogen in clinical settings.
Keywords: whole-genome sequencing, Klebsiella michiganensis , bla_NDM, multidrug-resistant, phylogenetics