Time Sensitive

Ordering Recommendation

Comprehensive panel includes acid-fast bacillus culture and stain; positive smears reflex to PCR amplification of M. tuberculosis complex species and rifampin resistance.

New York DOH Approval Status

This test is New York state approved.

Specimen Required

Patient Preparation

Three sputum specimens should be collected at 8-24 hour intervals (24 hours when possible) and at least one first-morning specimen. An individual order must be submitted for each specimen.


Respiratory specimen, pleural fluid, CSF, tissue, gastric aspirate

Specimen Preparation

Transfer (for each collection) 5-10 mL specimen or visible tissue to a sterile container, 50 ml sterile specimen transport tube preferred (Client supply number # 29582). (Min: 1 mL) Place each specimen in an individually sealed bag.

Storage/Transport Temperature


Unacceptable Conditions

Multiple same-site specimens (more than one in 24 hours), dry material, or material collected and transported on a swab.


Specimen source required.


Ambient: 24 hours; Refrigerated: 1 week; Frozen: 2 weeks


Stain/Culture/16S rDNA Sequencing/ Broth Microdilution/Polymerase Chain Reaction/ Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry




1-62 days
Stain reported within 24 hours. Negative cultures reported at 8 weeks. Positive cultures are reported as soon as detected.

Reference Interval

Culture negative for acid-fast bacilli.
Identification ordered and performed on positives.
Susceptibility performed on all initial isolates of M. tuberculosis complex.
Susceptibility performed on Mycobacterium other than M. tuberculosis complex isolates by request only.
Susceptibility testing of M. gordonae is inappropriate.

Interpretive Data

Compliance Category



Respiratory specimens under 5 mL will receive a volume suboptimal disclaimer in the report.

Positive cultures are reported as soon as detected. AFB stain, AFB identification of positives, and susceptibility tests are billed separately from culture. Identification of positive culture is billed by matrix-assisted laser desorption ionization (MALDI) and/or sequencing tests performed.

The laboratory should be notified when the presence of Mycobacterium genavense or Mycobacterium haemophilum is suspected, as these organisms will not grow on media routinely used for Mycobacterium isolation.

The laboratory should be notified when M. xenopii is suspected, as this organism requires a different temperature from routine culture setup.

The laboratory should be notified if the specimen is from a cystic fibrosis patient, as these specimens need additional decontamination from routine culture setup.

Susceptibility will be performed on organisms isolated from a sterile source and isolates of Mycobacterium tuberculosis complex, M. chelonae, M. abscesses, M. fortuitum complex, M. immunogenum, M. mucogenicum. Susceptibility testing will be performed by request only on M. kansasii and M. marinum. Susceptibility testing of M. gordonae is inappropriate.

For AFB susceptibility information, refer to Antimicrobial Susceptibility - AFB Mycobacteria (ARUP test code 0060217).

For AFB culture on blood refer to Culture, Acid-Fast Bacillus, Blood (ARUP test code 0060060).

After a positive result, repeat orders for Mycobacterium tuberculosis Complex Detection and Rifampin Resistance by PCR will continue to yield a positive result and repeat testing is not clinically indicated.

Hotline History


CPT Codes

87116; CPT codes for identification and susceptibility vary based on method; if reflexed, add 87556; 87798


Component Test Code* Component Chart Name LOINC
0060738 Culture, AFB reflex to MTBRIF PCR 539-7
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.


  • AFS, Auramine-rhodamine stain
  • AO stain
  • AR stain
  • GeneXpert
  • MTD
  • Mycobacterium
Acid-Fast Bacillus (AFB) Culture and AFB Stain with Reflex to Mycobacterium tuberculosis Complex Detection and Rifampin Resistance by PCR