Nucleic acid amplification testing

What it is

Nucleic acid amplification, that is PCR, is one of the assays that answer whether mycobacteria are present in a clinical specimen. The others are culture on solid media, that is Lowenstein Jensen egg-based or Middlebrook agar-based media, culture in liquid broth, the acid-fast stain, and urinary antigen detection such as ELISA for LAM. Nucleic acid amplification with GeneXpert MTB/RIF is listed as an assay of its own.

How it is diagnosed

Its advantages are same-day results, a sensitivity intermediate between the acid-fast stain and culture, and that it identifies organisms as members of the M. tuberculosis complex. With GeneXpert MTB/RIF the sensitivity nearly approximates culture, the test requires 100 minutes, and it detects rifampin resistance mutations.

Four uses are given for it:

• Rapid identification of MTB.
• Differentiating between MTB and non-tuberculosis mycobacteria (NTM).
• Identifying TB in smear-negative sputum specimens.
• Detecting the presence of rifampicin resistance. Genetic mutations in bacterial DNA conferring rifampicin resistance are highly predictive of multi-drug resistance, which makes it the test of first choice in those with MDR. Molecular testing for drug resistance has also become possible using PCR.

Outside tuberculosis, nucleic acid amplification (NAAT) is one of the investigations for trichomoniasis, with wet microscopy and culture.

Where that intermediate sensitivity sits is best held by the limit of detection of the three assays placed side by side. Smear microscopy needs 10,000 cfu/ml and its sensitivity is low; nucleic acid amplification needs 100 cfu/ml and its sensitivity is medium; culture needs 1-10 cfu/ml and its sensitivity is high. So the answer to a question that asks how it compares is that it is more sensitive than smear microscopy and still below culture. It is also the named test in the genital tract. For Chlamydia a NAAT should be used, and it can be the same swab as the gonorrhoea NAAT. For gonorrhoea the culture route is an endocervical swab, a charcoal transport swab, and alternatively a NAAT; a vulvo-vaginal swab, which can be self-taken, may also be used to detect gonorrhoea and Chlamydia. In pelvic inflammatory disease the investigations include a cervical swab for N. gonorrhoeae and Chlamydia by nucleic acid amplification test.