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. Author manuscript; available in PMC: 2014 Jun 6.
Published in final edited form as: MMWR Recomm Rep. 2014 Mar 14;63(0):1–19.

TABLE 3.

Chlamydia trachomatis and Neisseria gonorrhoeae Nucleic Acid Amplification Test (NAAT) target sequences and possible false reactions, by test type.

FDA-cleared NAAT Nucleic acid target for C. trachomatis Nucleic acid target for N. gonorrhoeae
Abbott RealTime CT/NG (Abbott Laboratories, Abbott Park, IL) Two distinct specific sequence regions within the 7,500 base pair C. trachomatis cryptic plasmid DNA. 48 base pair sequence within the Opa gene of N. gonorrhoeae.
The test does not detect plasmid free C. trachomatis. No false-positive tests based on analytical specificity testing.
No false-positive tests based on analytical specificity testing.
Aptima COMBO 2 assay Specific region within the 23S rRNA from C. trachomatis (Aptima Combo 2 assay). Specific region within the 16S rRNA from N.gonorrhoeae (Aptima Combo 2 assay).
Aptima CT assay Specific region with the 16S rRNA from C. trachomatis (Aptima CT assay). Specific region with the 16S rRNA from N. gonorrhoeae that is distinct from the Aptima Combo 2 assay target (Aptima GC assay).
Aptima GC assay (Hologic/Gen-Probe Inc., San Diego, CA) The test does not detect plasmid-free C. trachomatis. No false-positive tests based on analytical specificity testing.
No false-positive tests based on analytical specificity testing.
BD ProbeTec ET CT/GC Amplified DNA assay(Becton Dickinson and Company, Sparks, MD) One distinct sequence within the 7,500 base pair C. trachomatis cryptic plasmid DNA. Chromosomal pilin gene-inverting protein homologue.
The test does not detect plasmid-free C. trachomatis. Neisseria cinerea, Neisseria subflava and Neisseria lactamica might result in false-positive test results based on analytical specificity testing.
No false-positive tests based on analytical specificity testing.
BD ProbeTec QX CT Amplified DNA Assay One distinct sequence within the 7,500 base pair C. trachomatis cryptic plasmid DNA. Chromosomal pilin gene-inverting protein homologue.
BD ProbeTec QX GC Amplified DNA Assay (Becton Dickinson and Company, Sparks, MD) The test does not detect plasmid-free C. trachomatis. N. cinerea and N. lactamica might result in false-positive test results based on analytical specificity testing.
No false-positive tests based on analytical specificity testing.
Xpert CT/NG Assay (Cepheid, Sunnyvale, CA) One distinct C. trachomatis chromosomal DNA sequence. Two distinct chromosomal sequences each with a different reporter. Both sequences have to be detected to obtain a positive N. gonorrhoeae result.
No false-positive tests based on analytical specificity testing. No false-positives based on analytical specificity testing
The test detects plasmid-free C. trachomatis.
cobasCT/NG test (Roche Diagnostics, Indianapolis, IN) CT primers CP102 and CP103 to define a sequence of approximately 206 nucleotides within the cryptic plasmid DNA of C. trachomatis. NG primers NG514 and NG519 to define a sequence of approximately 190 nucleotides (DR-9A) from the DR-9 region.
CT primers CTMP101 and CTMP102 to define a sequence of approximately 182 nucleotides within the chromosomal DNA of C. trachomatis. NG primers, NG552 and NG579, to define a second sequence of approximately 215 nucleotides (DR-9B) from the DR-9 region.
No false-positive tests based on analytical specificity testing. No false-positive tests based on analytical specificity testing.
The test detects plasmid-free C. trachomatis.