Subtype Screening of blaIMP Genes Using Bipartite Primers for DNA Sequencing

Jpn J Infect Dis. 2021 Nov 22;74(6):592-599. doi: 10.7883/yoken.JJID.2020.926. Epub 2021 Mar 31.


Genes conferring carbapenem resistance have spread worldwide among gram-negative bacteria. Subtyping of these genes has epidemiological value due to the global cross-border movement of people. Subtyping of blaIMP genes that frequently detected in Japan appears to be important in public health settings; however, there are few useful tools for this purpose. We developed a subtyping screening tool based on PCR direct sequencing, which targets the internal sequences of almost all blaIMP genes. The tool used bipartite multiplex primers with M13 universal sequences at the 5'-end. According to in silico analysis, among the 78 known IMP-type genes, except for blaIMP-81, 77 detected genes were estimated to be differentiated. In vitro evaluation indicated that sequences of amplicons of IMP-1, IMP-6, IMP-7, and IMP-20 templates were identical to their respective subtypes. Even if the amplicons were small or undetectable through the first PCR, sufficient amplicons for DNA sequencing were obtained through a second PCR using the M13 universal primers. In conclusion, our tool can be possibly used for subtype screening of blaIMP, which is useful for the surveillance of bacteria with blaIMP in clinical and public health settings or environmental fields.

Keywords: 5'-tailed primer; IMP-type carbapenemase gene; direct sequencing; subtyping.

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins* / genetics
  • Bacterial Proteins* / isolation & purification
  • DNA Primers / genetics
  • Drug Resistance, Multiple, Bacterial / genetics
  • Enterobacteriaceae Infections / microbiology
  • Enterobacteriaceae* / drug effects
  • Enterobacteriaceae* / enzymology
  • Enterobacteriaceae* / genetics
  • Enterobacteriaceae* / isolation & purification
  • Genes, Bacterial / genetics
  • Humans
  • Microbial Sensitivity Tests
  • Multiplex Polymerase Chain Reaction* / methods
  • Sequence Analysis, DNA
  • beta-Lactamases* / genetics
  • beta-Lactamases* / isolation & purification


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • beta-Lactamases
  • DNA Primers