NTM Culture and qPCR

Legionella qPCR



NTM Culture and qPCR FAQs


What is the test code for NTM culture?

What is the test code for NTM qPCR?

What is the TAT for NTM culture?
6 – 8 weeks

What is the TAT for NTM qPCR?
2-4 days

Should I order both NTM qPCR and NTM culture?
That depends on the goals of your testing. Culture will provide you with speciation and the ability to
save organisms isolated while qPCR can determine if NTM is present but not define the species.

Example Scenarios

  • Need quick results and don’t need to know species present – NTM qPCR.
  • In no rush and want to know all species present – NTM culture.
  • Need results quickly for remediation and need species for case investigation/comparison to
  • past problem species – Both NTM qPCR and Culture.

If I want NTM Culture and NTM qPCR on the same sample, what volume sample is needed?
Order a 500mL bottle to have enough for both tests.

Are there any discounts available for NTM qPCR?
Contact your account manager or the lab directly. Volume discounts may apply.

I just got my final report.  There is Mycobacterium X in my water sample.  What should I do?
Please see our NTM fact sheet.  If you have additional questions, please reach out to our consulting department by emailing clientservices@specialpathogenslab.com.

Does qPCR differentiate individual species of NTM?
No.  The assay is designed to detect all NTM species as a single group.  This detection method is the most affordable way to use qPCR to detect the growing list of NTM.  If individual species of interest were to be identified using qPCR, a specifically designed assay for each individual species would be needed.

However, when combined with culture, qPCR provides the rapid detection desired for slow growing NTM while culture provides the speciation and organism isolation.

How does qPCR handle live, dead and viable but not culturable organisms?
Currently we are extracting all DNA which would include live, dead and viable-but-not-culturable.
At this point we are still researching the best option for performing viability manipulations for qPCR testing and will not implement a method until we find one that meets our high standards of excellence.

Does qPCR provide quantification?
Our NTM test reports the presence or absence of NTM.  If NTM is detected, we provide an approximate quantification range of low, medium, and high representing specific ranges of genomic unit concentrations per mL of sample.

Range LevelsGU/mL of Sample*
Low1 - 200
Medium200 -1000

*Concentrations are based on standard 100mL samples.  GU = Genomic Unit

While exact quantification is not possible due to the variability in amplification efficiency between different species, we chose to provide approximate quantity levels to give more information on the severity of NTM contamination.  The ranges are determined by using a standard curve prepared from M.avium DNA.

I just got my final report.  How do NTM qPCR results compare to NTM culture?
Comparing culture to qPCR is like comparing apples to oranges.  Any concentration determined by qPCR cannot and should not be directly correlated to CFU/mL.  This is because culture and qPCR are optimized to perform differently with each having its own limitations that impact final concentrations.


  • Only able to detect organisms that are culturable. Does not detect viable but not culturable (VBNC) organisms.
  • Selective culture media can be optimized for specific species of organisms over others.
  • Overgrowth of non-intended organisms competes for resources and hinders growth of NTM.
  • Weakened NTM can have hindered growth due to inhibitors/acid treatments intended to combat non-specific organism overgrowth.

Standard qPCR

  • Utilizes all extracted DNA from living, dead and VBNC organisms.
  • Quantification ability is influenced by the quality and target of the assay design.
    • Broader targets such as those detecting all species in a genus require broader designs that will have species to species variability.
    • Broader targets cannot differentiate what species are present and in what concentration.
  • Not impacted by non-NTM organisms in sample. There is no chance for overgrowth as immediate DNA extraction does not give the non-NTM organisms time to grow.