Mycobacterial Infections

Tuberculosis (TB) is one of the world's deadliest diseases.

• In 2024, 10,347 new cases of TB were reported in the United States.¹
• TB diagnostic testing is important; once an infection is detected it is treatable and curable.
• TB drug resistance remains a serious issue. Susceptibility testing helps patients receive the most effective treatment.

Acid-Fast Bacillus (AFB) Culture

ARUP’s AFB Laboratory performs testing seven days a week, isolating, identifying, and performing susceptibility testing on most mycobacteria species. We use a combination of matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF), polymerase chain reaction (PCR), and 16S rRNA sequencing for species-level identification using known quality control databases.

Run Times and Result Reporting

ARUP processes several runs per day, every day of the week, and reports stain results as soon as they are completed.

A preliminary report and AFB stain results are generated within 24 hours. The preliminary report confirms that:

• Testing is in progress.
• Positive culture results will be shared as soon as detected.
• The final report will follow in seven to eight weeks.

Positive stain results are called to clients.

AFB Identification Methods

• Cultures are set up in Mycobacteria Growth Indicator Tube (MGIT) broth and solid media and are continuously monitored.
• Positive results are called and reported as soon as detected.
• MALDI-TOF, PCR, and 16S rRNA sequencing are all performed daily with fresh subcultures.
• M. tuberculosis complex-positive organisms are identified to the species level by PCR.
• Positive culture preliminary reports are updated with the progress of the identification.
• Positive culture results are shared in a final report once the organism has grown on solid media and the organism morphology is consistent with the initial identification.

AFB Susceptibility Testing

Susceptibility testing will be performed for all initial M. tuberculosis complex isolates and rapidly growing mycobacteria. When Acid-Fast Bacillus (AFB) Identification with Reflex to Susceptibility (ARUP test code 0060997) is ordered, susceptibility testing is performed on all primary isolates of M. tuberculosis complex and clinically significant non-TB mycobacteria, regardless of the source. Susceptibility testing is performed automatically when the following organisms are detected:

M. tuberculosis complex, M. kansasii, M. avium-intracellulare, M. abscessus, M. chelonae, M. immunogenum, M. fortuitum complex, and M. mucogenicum

For organisms other than those listed above, the clinician should decide if susceptibility testing is appropriate. ARUP will proceed with susceptibility testing at the clinician’s request for these isolates.

Unless ARUP receives a specific request, susceptibility testing will not be performed on isolates received within 90 days of a previous specimen, even if the isolates are from different sources.

Antimicrobials Tested and Reported

• M. tuberculosis complex: ethambutol, isoniazid (INH), and rifampin. At this time, ARUP does not perform secondary drug susceptibility testing. If susceptibility testing options at ARUP have been exhausted, ARUP can send an isolate to National Jewish Health for secondary drug susceptibility testing.
  • If PZA testing is required, send the isolate to your local health department for pncA sequencing.
• M. kansasii: rifampin and clarithromycin. Rifampin-susceptible isolates are also susceptible to rifabutin. If the isolate is rifampin-resistant, results for the following secondary drugs will also be reported: amikacin, ciprofloxacin, linezolid, moxifloxacin, rifabutin, streptomycin, and trimethoprim/sulfamethoxazole.
• M. avium-intracellulare complex: amikacin, clarithromycin, linezolid, and moxifloxacin. Clarithromycin results predict azithromycin results. Because minimum inhibitory concentration (MIC) results do not predict clinical response and may be misleading, rifampin, rifabutin, and ethambutol MICs are not tested.
• Rapid growers (M. abscessus, M. chelonae, M. immunogenum, M. fortuitum complex, and M. mucogenicum): amikacin, cefoxitin, ciprofloxacin, clarithromycin, clofazimine, doxycycline, imipenem, linezolid, moxifloxacin, tigecycline, and trimethoprim/sulfamethoxazole. Tobramycin is reported on M. chelonae. Extended 14-day incubation is performed on rapidly growing Mycobacteria isolates initially susceptible to clarithromycin to detect erm-dependent inducible macrolide resistance.
• Tests for susceptibility to bedaquiline, omadacycline, and eravacycline can be performed for rapidly growing mycobacteria for an additional charge at the clinician’s request.
• Drug susceptibility testing performed for slow-growing nontuberculous mycobacteria (NTM) includes amikacin, ciprofloxacin, clarithromycin, doxycycline, linezolid, moxifloxacin, rifabutin, rifampin, streptomycin, and trimethoprim/sulfamethoxazole.

Test Information

Additional Resources

• ARUP Consult^® Mycobacterium tuberculosis
• Centers for Disease Control and Prevention. Testing for tuberculosis. Updated Jun 2024; accessed Jul 2025.
• Lewinsohn DM, Leonard MK, LoBue PA, et al. Official American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention clinical practice guidelines: diagnosis of tuberculosis in adults and children. Clin Infect Dis. 2017;64(2):111-115.
• Centers for Disease Control and Prevention. Updated guidelines for using interferon gamma release assays to detect Mycobacterium tuberculosis infection. Morbidity and Mortality Weekly Report. Published Jun 2010; accessed Jul 2025.

References

1. Centers for Disease Control and Prevention. Provisional 2024 tuberculosis data, United States. Published Mar 2025; accessed Jul 2025.