Whole-genome sequencing of clinical isolates of Klebsiella michiganensi in China carrying blaIPM-4 and blaNDM-1

Abstract

AimThis study aimed to analyze the prevalence, phenotypes, and carriage of resistance genes of carbapenem-resistant Klebsiella michiganensis strains isolated in our hospital. Methodology: Four K. michiganensis strains were collected from January 2015 to December 2023. Antimicrobial susceptibility was tested using 21 antibiotics with the BD Phoenix™ M50 System. Whole-genome sequencing of the four strains was performed on an Illumina NovaSeq 6000 platform. Species identification was performed using Kleborate software, sequence type (ST) was performed using MLST, and prediction of antibiotic resistance genes and virulence genes were performed using ABRicate. PlasmidFinder was used to search for plasmids. Whole genome data from 211 strains of carbapenem-resistant K. michiganensis were downloaded from the NCBI database; together with the strains in this study, these data were used to construct an phylogenetic tree using genome single nucleotide polymorphisms (SNP). ResultsAntimicrobial susceptibility showed that K. michiganensis was highly resistant to β-lactams. For the three carbapenems, strain WF0046 was only resistant to ertapenem, while WF0047, WF0052, and WF0053 were resistant to all three carbapenems tested. The four strains of K. michiganensis only showed complete sensitivity to polymyxin E and tigecycline. The four K. michiganensis strains were found to have 43 resistance genes, and all carried carbapenem resistance genes; WF0046 carried the carbapenem resistance gene blaIMP-4, while the other three strains carried blaNDM-1. Among the other resistance genes, β-lactam resistance genes were predicted most (11 types), followed by eight types of aminoglycoside resistance genes. Of the strains characterized in this study, WF0046 belonged to ST158, WF0047 belonged to ST40, WF0052 belonged to ST533, and WF0053 belonged to ST13. These four strains, along with 211 carbapenem-resistant K. michiganensis strains downloaded from NCBI, were divided into five clades; WF0052 belonged to clade A, WF0046 belonged to clade C, and WF0047 and WF0053 both belonged to clade D. The four strains had relatively distant genetic relationships; WF0046, WF0047, and WF0053 were closely related to strains of human origin from other regions of China, while WF0052 was genetically close with a strain of K. michiganensis isolated in the United States. ConclusionThe strains of K. michiganensis from our hospital were resistant to multiple antibiotics, and all strains carried carbapenem resistance genes along with multiple other antibiotic resistance genes. The phylogenetic results showed that these four strains had distant genetic relationships and different ST types, indicating that they came from different sources and the possibility of polyclonal transmission.