A novel peptide nucleic acid- and loop-mediated isothermal amplification assay for the detection of mutations in the 23S rRNA gene of Treponema pallidum

J Med Microbiol. 2020 Dec;69(12):1339-1345. doi: 10.1099/jmm.0.001275. Epub 2020 Nov 9.


Introduction. Macrolides could be a potential alternative treatment for Treponema pallidum infections in patients; however, macrolide-resistant T. pallidum is spreading rapidly worldwide.Hypothesis/Gap Statement. There are presently no alternatives to serological tests for syphilis that can be used to evaluate therapeutic effects due to the fact that T. pallidum cannot be cultured in vitro.Aim. In this study, we constructed a method for rapidly identifying T. pallidum and confirming macrolide resistance by using loop-mediated isothermal amplification (LAMP) with peptide nucleic acids (PNAs).Methodology. A set of LAMP primers was designed to span nucleotide positions 2058 and 2059 in 23S rRNA. A PNA clamping probe was also designed to be complementary to the wild-type sequence (A2058/A2059) and positioned to interfere with both the annealing of the 3' end of the backward inner primer and the concomitant extension. Prior to the LAMP assay, swab samples from suspected syphilitic lesions were boiled for DNA extraction.Results. The assay had an equivalent detection limit of 1.0×101 copies/reaction and showed specificity against 38 pathogens. In the presence of a 4 µM PNA probe, LAMP amplified up to 1.0×101 copies/reaction using plasmids harbouring the complementary mutant sequences (A2058G or A2059G), whereas amplification was completely blocked for the wild-type sequence up to a concentration of 1.0×103 copies/reaction. For the 66 PCR-positive clinical specimens, the overall detection rate via LAMP was 93.9 % (62/66). Amplification was successful for all 53 mutant samples and was incomplete for all nine WT samples by the PNA-mediated LAMP assays.Conclusion. We developed a PNA-mediated LAMP method that enabled us to rapidly identify T. pallidum and determine its macrolide susceptibility via a culture-independent protocol.

Keywords: 23S rRNA; Treponema pallidum; loop-mediated isothermal amplification; macrolide; peptide nucleic acid.

Publication types

  • Evaluation Study

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Drug Resistance, Bacterial / genetics
  • Humans
  • Macrolides / pharmacology
  • Molecular Diagnostic Techniques / methods*
  • Mutation*
  • Nucleic Acid Amplification Techniques / methods*
  • Peptide Nucleic Acids
  • Point-of-Care Testing
  • RNA, Bacterial / genetics*
  • RNA, Ribosomal, 23S / genetics*
  • Sensitivity and Specificity
  • Syphilis / diagnosis
  • Syphilis / microbiology
  • Treponema pallidum / drug effects
  • Treponema pallidum / genetics*


  • Anti-Bacterial Agents
  • Macrolides
  • Peptide Nucleic Acids
  • RNA, Bacterial
  • RNA, Ribosomal, 23S

Supplementary concepts

  • LAMP assay