Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge

J Mol Diagn. 2006 Feb;8(1):3-15. doi: 10.2353/jmoldx.2006.050045.


Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Cross Reactions
  • DNA Probes
  • DNA, Bacterial / chemistry
  • Gonorrhea / diagnosis*
  • Gonorrhea / economics
  • Gonorrhea / epidemiology
  • Humans
  • Molecular Diagnostic Techniques*
  • Neisseria gonorrhoeae / genetics*
  • Nucleic Acid Amplification Techniques / methods*
  • Pharyngeal Diseases / diagnosis
  • Pharyngeal Diseases / microbiology
  • Rectal Diseases / diagnosis
  • Rectal Diseases / microbiology
  • Sensitivity and Specificity


  • DNA Probes
  • DNA, Bacterial