A putative multi-replicon plasmid co-harboring beta-lactamase genes blaKPC-2, blaCTX-M-14 and blaTEM-1 and trimethoprim resistance gene dfrA25 from a Klebsiella pneumoniae sequence type (ST) 11 strain in China

Abstract

The global emergence of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae poses a major public health threat requiring immediate and aggressive action. Some older generation antibiotics, such as trimethoprim, serve as alternatives for treatment of infections. Here, we determined the complete nucleotide sequence of plasmid pHS091147, which co-harbored the carbapenemase (blaKPC-2) and trimethoprim resistance genes (dfrA25) from a Klebsiella pneumoniae sequence type (ST) 11 clone recovered in Shanghai, China. pHS091147 had three replication genes, several plasmid-stability genes and an intact type IV secretion system gene cluster. Besides blaKPC-2 and dfrA25, pHS091147 carried several other resistance genes, including β-lactamase genes blaTEM-1 and blaCTX-M-14, sulphonamide resistance gene sul1, a quinolone resistance gene remnant (ΔqnrB2), and virulence associated gene iroN. Notably, the multidrug-resistance region was a chimeric structure composed of three subregions, which shared strong sequence homology with several plasmids previously assigned in Genbank. To our knowledge, this is the first report of the co-localization of blaKPC-2 and dfrA25 on a novel putative multi-replicon plasmid in a Klebsiella pneumoniae ST11 clone.

Fig 1. Circular map of pHS091147.

Genes are color-coded dependent upon functional annotations as follows: pink, replication; blue, stability; green, propagation; orange, adaptation (the MDR region); grey, other functions and hypothetical proteins. The relaxase gene (traI) is indicated by the red bar. Red text highlights the resistance genes: bla_KPC-2, bla_TEM-1, bla_CTX-M-14, dfrA25, sul1 and ΔqnrB2.

Fig 2. Phylogenetic analysis of plasmid-encoded relaxase homologs.

Plasmid pHS091147 (in bold) and twelve other protein sequences were aligned, and the tree was generated with MEGA5 using the maximum-likelihood method. Solid black arrows point to the prototype plasmids for the MOB_F12 and MOB_F11 subfamilies. Other relaxase sequences of plasmids pKP048 (GenBank accession number FJ628167), pHS082416 (KF724507), pKHS2 (CP003224), pKP09085 (KF719970), pKPN4 (CP000649), pKPX-2 (AP012056), pK1HV (HF545434), F (AP001918), pSLT (AE006471), pED208 (AF411480), pET45 (CU468132) and R388 (BR000038) were obtained from GenBank.

Fig 3. Comparative analysis of the multidrug-resistance region of plasmid pHS091147.

The relevant parts of pKP048, pKPHS2, SGI1-X and pTN48 are shown to highlight the syntenic regions. The horizontal line shown above or below the schematics (with one or both ends demarcated by solid triangles to indicated inverted repeats) represents intact, interrupted or truncated ISs, transposons and integrons as appropriate. Interruptions in the structures above are indicated as dashed lines. Regions with similar sequences are indicated in gray with corresponding percentages between the plasmids.