geneviewer
0.3.11GitHub

Genes of the blaKPC-2 plasmid pQEB1 and four of its variants ​

The genes of five IncN plasmids of the pQEB1 lineage, which carries the carbapenemase gene blaKPC-2, from a hospital outbreak of Enterobacter cloacae and Klebsiella oxytoca. The variants differ from pQEB1 by inversions and transposon insertions. Made by data-raw/pQEB1_plasmids.R from the GenBank files, together with pQEB1_alignment.

Usage ​

r
pQEB1_plasmids

Format ​

A data frame with 401 rows and 10 columns:

  • cluster: Name of the plasmid. A character vector.
  • host: Species and strain the plasmid was found in. A character vector.
  • accession: GenBank accession of the plasmid. A character vector.
  • locus_tag: Locus tag of the gene. A character vector.
  • gene: Gene name, or "" when the gene has none. A character vector.
  • product: Description of the gene product. A character vector.
  • category: Function of the gene from its name and product, e.g. "Carbapenemase (KPC)", "Mobile element" or "Conjugation". A character vector.
  • start: Start position of the gene. A numeric vector.
  • end: End position of the gene. A numeric vector.
  • strand: Strand of the gene, "forward" or "complement". A character vector.

Source ​

GenBank accessions NZ_PQ162285, NZ_PQ162289, NZ_PQ162291, NZ_PQ162292 and NZ_PQ162293.

References ​

Moran RA, Behruznia M, Holden E, Garvey MI, McNally A. pQEB1: a hospital outbreak plasmid lineage carrying blaKPC-2. Microb Genom. 2024;10(9).