M. tuberculosis PCR with AFB Culture and Stain, respiratory (rifampin resistance detection)

Test Mnemonic


CPT Codes

  • 87556 - QTY (1)
  • 87798 - QTY (1)
  • 87015 - QTY (1)
  • 87116 - QTY (1)
  • 87206 - QTY (1)

Performing Laboratory

Cleveland Clinic Laboratories

Specimen Requirements

Volume Type Container Collect Temperature Transport Temperature Special Instructions
5 mLSputumClean, leakproof container RefrigeratedSputum may be expectorated or induced. PCR testing of 2 high quality sputum samples is recommended prior to removal from airborne precautions. Culture of 3 sputum specimens at least 8 hours apart with at least one first morning specimen is recommended. To rule-out M. tuberculosis order MTBRIF x2 and AFC x1. Refrigeration is preferred if transport is delayed longer than 2 hours. Volume: 5 mL (preferred); 1 mL minimum.
10 mLBronchoscopy specimenClean, leakproof container  Larger volumes improve recovery. Collect BAL, wash, or aspirate into sputum trap or sterile cup. Volume: at least 10 mL (preferred). Place bronchial brush in sterile, leak-proof tube or cup with enough non-bacteriostatic sterile saline to cover the brush (1-10 ml). Transfer temperature is ambient. Refrigeration is preferred if transport is delayed longer than 2 hours.


Environmental Condition Description
RefrigeratedRespiratory samples can be stored at 2-8C for up to seven days. Sputum concentrates can be stored at 2-8C for up to seven days.
AmbientRespiratory specimens can be stored at a maximum of 35C for up to three days.

Days Performed

7 days a week

Turnaround Time

8 weeks


Name Description
Probe and Pyrosequencing for Identification 
Real-Time Polymerase Chain Reaction (RT-PCR) 

Reference Range

Special Info

Species and subspecies within the M. tuberculosis complex are not distinguished. If positive for M. tuberculosis complex a result for rifampin resistance is reported. Although 95% of mutations conferring rifampin resistance will be detected, other resistance mutations are possible. In vitro susceptibility testing is required. Similarly, false positive rifampin resistance may occur due to mutations that do not confer resistance. Culture is always performed when PCR is requested because culture is more sensitive. Additionally, culture provides organisms for susceptibility testing and optimizes detection of non-tuberculous mycobacteria. CPT codes billed as applicable: MALDI-TOF 87118, DNA Probe 87149, Sequencing 87153, and Susceptibility 87186.

Clinical Info

This order code includes 6 week acid fast culture and stain as well as Cepheid GeneXpert MTB/RIF assay testing performed on original sample within 1-2 days of submission. The Xpert MTB/RIF assay should be performed on specimens from patients for whom there is clinical suspicion of tuberculosis and who have received less than 3 days of anti-tuberculosis therapy. Since M. tuberculosis typically takes 2 to 3 weeks to grow in conventional culture, PCR is recommended for rapid detection of M. tuberculosis in sputum specimens. PCR is 98% sensitive for detection of smear positive/culture positive pulmonary infection. M. tuberculosis may also be detected in smear-negative sputum samples because of the greater sensitivity of the MTB/RIF assay compared to acid fast microscopy. A positive result may occur in the presence of non-viable M. tuberculosis. A negative result does not rule-out infection. The predictive value for the absence of smear positive/culture positive tuberculosis is 99.7% for one negative Xpert PCR assay and 100% for two negative Xpert PCR assays. Therefore, the Xpert assay can be used to help determine if continued isolation is warranted in patients with suspected pulmonary tuberculosis. (Steingart Cochran Rev 2013; Luetkemeyer CID 2016)