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Useful For
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Rapid detection of Mycobacterium tuberculosis complex DNA and Rifampicin Resistance.
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Method name and description
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GeneXpert MTB/RIF Ultra Assay (Real time PCR)
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Clinical information
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Conventional culture methods can generally detect M tuberculosis in 2 to 3 weeks, but in some instances up to 8 weeks of incubation may be required. TB PCR provides faster and more accurate MTB diagnosis, that detects MTB and rifampicin (RIF) resistance simultaneously from respiratory specimens and other specimens without waiting for growth in culture. A mycobacterial culture should always be performed in addition to the PCR assay. The PCR assay is rapid but the culture has increased sensitivity over the PCR assay.
Note: For the diagnosis of active tuberculosis (TB), the National TB Reference Laboratory accepts two consecutive specimens collected 8–24 hours apart sputum specimens. The first specimen is tested for AFB smear, AFB PCR, and AFB culture, while the second specimen undergoes testing for AFB smear and AFB culture only. For other specimen type only one specimen can be accepted and AFB smear, AFB culture and AFB PCR will be performed. The final diagnosis is based on the interpretation of these test results.
Additional reflex tests may be performed by the testing laboratory. These tests are added based on clinical and laboratory findings and are conducted in accordance with guidelines and recommendations from Hamad Medical Corporation (HMC), the World Health Organization(WHO), Clinical and Laboratory Standards Institute (CLSI) and the College of American Pathologists (CAP).
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Aliases
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- TB PCR
- AFB PCR
- Acid Fast Bacilli PCR
- TB PCR Isolation
Note: The test Order TB PCR Isolation should be used for tests performed at the AAH and TCH microbiology laboratories
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Specimen type / Specimen volume / Specimen container
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Specimen Type
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Specimen Volume
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Specimen Container
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Abscesses, aspirates and wound
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5-10 ml.
(Minimum 2 ml)
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50 ml sterile conical tube (leak proof without fixative).
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Body Fluids
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10-15 ml
(Minimum 5ml for adult and 1ml for child
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50 ml sterile conical tube (leak proof without fixative).
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Bone mararrow
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Entire collection
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BD MGIT tube or 10 ml yellow top collectors containing sodium polyanethol sulfonate (SPS).
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Cerebrospinal fluid (CSF)
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2-3 ml
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Sterile leak-proof tubes
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Gastric wash or lavage
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Maximum volume of specimen recommended is 15ml
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50 ml leak proof sterile conical tube
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Sputum (expectorated or induced)
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Collect 5-10 ml (minimum desired volume is 3 ml early morning specimen).
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50 ml sterile conical tube leak proof container.
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Lower Respiratory:
- Bronchoalveolar lavage
- Bronchoalveolar wash
- Endotracheal secretion
- Transtracheal secretion
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Collect 5-10 ml
(minimum desired volume is 3 ml ).
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50 ml sterile conical tube leak proof container without fixative.
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Stool
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5-10 gm (minimum 1gm).
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Sterile leak proof wide mouth container without preservative. (Preferably 50 ml conical tube).
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Tissue / Biopsy.
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5-10 mm
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50 ml sterile conical tube (leak proof without fixative).
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Urine
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15-20 ml (prefer up to 40 ml).
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50 ml sterile conical tube (leak proof without fixative).
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Collection instructions / Special Precautions / Timing of collection
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Specimen Type
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Collection Instructions
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Abscesses, aspirates and wound
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Decontaminate the surface site with 70% alcohol.
Collect purulent material aseptically from an undrained abscess using a sterile needle and syringe. For open abscess (after incision and drainage) collect the expressed material with a needle and syringe.
Transfer 5-10 ml (Minimum 2 ml) of aspirated fluid abscess material or Pus aspirate in 50 ml sterile conical tube (leak proof without fixative).
Pus aspirate is always superior to a swab specimen.
Swab is strongly discouraged unless it is the only specimen available.
Specify anatomic site.
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Body Fluids
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Disinfect site with 70% alcohol if collecting by needle and syringe. Aspirate fluid as much as possible optimal volume (10 ml desirable) in a 50 ml sterile conical tube leak proof container without fixative.
Specify anatomic site (Plural, Pericardial, Peritoneal, Abdominal, Amniotic, Ascites, Bile, Synovial, and OTHERS).
Since many of these fluids may contain fibrinogen, it may be necessary to add anticoagulant (SPS) to collection containers.
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Bone marrow
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Prepare the surgical site as for surgical incision. Use a blood collector tube and mix content of tube after collection in either BD MGIT tube obtained from TB lab.(Discards half of the media and add the sample).
Alternatively, 10 ml yellow top collectors containing sodium polyanethol sulfonate (SPS).
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Cerebrospinal fluid (CSF)
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Lumbar puncture:
CSF must be collected prior to antimicrobial therapy. Place CSF into leak-proof tubes. Submit the most turbid tube to Microbiology section.
Reservoir/shunts:
Disinfect reservoir collection site before collection of CSF.
Submit specimen in sterile tube with appropriate volumes.
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Gastric wash or lavage
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Collect three consecutive days in early morning before patients eat and while are still in bed.
Perform lavage with 25 to 50 mL of chilled, sterile distilled water. Recover sample and place in 50 mL conical sterile tube.
(Comments: The specimen must be processed promptly, since mycobacteria die rapidly in gastric washing, neutralize with 100 mg sodium bicarbonate if transport is delayed more than one hour,)
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Sputum (expectorated or induced)
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Rinse mouth with water to remove food particles, debris, mouthwash, or oral drugs, which may inhibit the growth of Mycobacteria and remove excess oral biota.
Collect sputum (for two consecutive days), have patient breathe deeply and cough several times to achieve a deep lower reparatory specimen (not postnasal fluid).
For induced sputum, use sterile hypertonic saline. Avoid sputum contamination with nebulizer reservoir water. Saprophytic Mycobacteria in tap water may produce false-positive culture or smear results.
Indicate on test order if specimen is induced sputum, as these watery specimens resemble saliva and risk rejection as inadequate.
Induced sputum to be collected by trained staff.
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Lower Respiratory:
- Bronchoalveolar lavage
- Bronchoalveolar wash
- Endotracheal secretion
- Transtracheal secretion
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Lower Respiratory Endo-tracheal, Trans-tracheal secretions, Bronchoalveolar Lavage or Bronchial wash in a 50 ml sterile conical tube leak proof container without fixative.
Collect washing or aspirate in a 50 ml sterile conical tube leak proof container without fixative.
Avoid contaminating bronchoscope with tap water when collecting Bronchoalveolar Lavage or Bronchial washing.
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Stool
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Pass specimen directly into sterile leak-proof 50ml conical tube.
Do not use holding or transport medium or preservatives
Do not submit feces contaminated with urine or toilet water
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Tissue / Biopsy.
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Aseptically collect tissue in 50 ml sterile containers without fixatives or preservatives during surgery or cutaneous biopsy procedure
Tissue collection is an invasive procedure and requires a trained physician. Include material from both the center and the edge of the lesion.
Add 2 to 3 ml of sterile saline for transport.
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Urine
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Collect approximately 40mL of urine in 50 ml sterile containers without fixatives (midstream is never advised). A first morning specimen is preferred
Comments: Organisms accumulate in bladder overnight, so first void morning specimen provides best yield. Specimens collected at other times are dilute and are not optimal.
Collect one specimen per day on three consecutive days.
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| General Collection Instructions |
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1. Collect specimen before administration of antimicrobial agents when possible. Collect sufficient quantity of specimen. Too little may yield false negative results.
2. Collect with as little contamination from normal flora as possible to ensure that the specimen represents the infected site. If collection is through intact skin, cleanse the skin first.
3. Collect specimen at the most active stage of the disease to increase chances of isolation and identification of the causative organisms. Sample the body area, lesion, exudate, or drainage most likely to contain the suspected pathogen (i.e. the leading edge of a skin lesion; depth of a wound, not the surface; sputum, not saliva).
4. Request and encourage the active cooperation of the patient in collection of the specimen. Make sure the patient has adequate instructions and the proper equipment to provide a satisfactory specimen.
5. Use appropriate collection devices, sterile equipment, and aseptic technique. Use only the standard equipment recommended by the laboratory. Do not substitute makeshift containers, bottles, or tubes.
6. Use 50 ml sterile conical tube for all TB specimen collections except for CSF and bone marrow.
7. Minimize transport time; maintain an appropriate environment for specimen transportation.
8. Refrigerate the specimen at 2-8°C (except bone marrow and CSF), if a delay of more than one hour is anticipated.
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| References |
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1.Wilson ML. General principles of specimen collection and transport. Clin Infect Dis 1996; 22:766.
2. James Versalovic , Karen C. Carroll, Guido Funke, James H. Jorgensen, Marie Louise Landry, David W. Warnock. Manual of Clinical Microbiology, 10th edition, American Society for Microbiology, Washington 2010.
3. Forbes BA, Sahm DF, Weissfeld AS (Eds). Specimen Management. In: Bailey & Scott's Diagnostic Microbiology, 12th ed, Mosby, Elsevier, St. Louis, 2007.
4. Baron EJ, Miller JM, Weinstein MP, Richter SS, Gilligan PH, Thomson RB Jr, Bourbeau P, Carroll KC, Kehl SC, Dunne WM, Robinson-Dunn B, Schwartzman JD, Chapin KC, Snyder JW, Forbes BA, Patel R, Rosenblatt JE, Pritt BS. Executive summary: a guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2013 recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM). Clin Infect Dis. 2013 Aug; 57(4):485-8.
5. Lynne S Garcia. Clinical Microbiology Procedure Handbook, 3rd Edition, 2010, ASM. 5. Lynne S Garcia. Clinical Microbiology Procedure Handbook, 3rd Edition, 2010, ASM.
6. UK Standards for Microbiology Investigations (SMIs), Public Health England,
https://www.gov.uk/government/collections/standards-for-microbiology- investigations-smi
7. Atkins, Bridget L., et al. "Prospective evaluation of criteria for microbiological diagnosis of prosthetic-joint infection at revision arthroplasty." Journal of clinical microbiology 36.10 (1998): 2932-2939. |
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Storage and transport instructions
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- Transport as soon as possible.
- Refrigerate the specimen at 2-8 °C
- CSF and bone marrow specimens should not be frozen or refrigerated (transport samples within two hours at room temperature)
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Specimen Rejection Criteria
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- Specimens in leaking containers (unless specimens obtained by invasive procedure eg Biopsy, CSF, FNA, BAL, BW, SPA, Bone marrow etc.).
- Specimen in tube with preservative, fixative, additive or wax (waxed container may produce false-positive smear results.) eg Tissue submitted in formalin Exception: Bone marrow in SPS.
- Unlabeled, mislabeled specimens are unacceptable except for specimens obtained by an invasive procedure. In these situations, lab will call the requesting physician for clarification before rejecting specimen.
- blood specimen
- Specimen submitted in nonsterile containers.
- One specimen for multiple requests, for example, for various organisms (bacteria, AFB Fungi, Virus etc.).
- Multiple specimens with multiple request which is collected from the same anatomical site on the same time will be treated as one and remaining specimen will be rejected
- Frozen specimen (Freezing of specimen may decrease the yield)
- Specimen submitted in insufficient quantity
- Aspirate received in syringe with needle.
- Dry swabs /Swab dipped in fluid/sputum swab
Comment: Swabs are a not optimal specimen for TB diagnosis because they are dry easily and because of the limited amount of material transferred. However, swab collected from pulmonary sites will be rejected, swab collected from extra pulmonary sites can be accepted, but require prior consultation with lab.
- For new patient, initially 2 consecutive sputum specimens will be accepted for AFB smear and culture which is collected at least1hour apart (preferably 8-24 hours early morning), next AFB smear will be done after 2 weeks and ABF culture will be repeated after two months.
- For smear positive(sputum) follow up cases; if previous smear is positive next smear will be done after one week
- If initial sputum TB PCR is negative, next PCR will be repeated after 2 weeks
- If initial sputum TB PCR is positive, next PCR can be accepted only after six months
- Salivary sputum except for patient on therapy in the TB unit and induced sputum.
- Pooled sputum
- Stool sample except immunocompromised and HIV patient
(Comment: Utility of culturing stool for acid-fast bacilli remains
controversial and should be discouraged; however, stool samples
from immunocompromised and HIV patients may be submitted,
mainly to detect MOTT)
- 24 hours pooled Urine collection (They are likely to be diluted and/or contaminated).
- Urine from bag/folly catheter
- Urine received in Boric acid container
Abbreviations:
CSF: Cerebrospinal fluid
FNA: Fine needle aspirate
BAL: Bronchoalveolar lavage
BW: Bronchial wash
SPA: Suprapubic aspiration
SPS: sodium polyanethol sulfonate
AFB: Acid fast bacilli
PCR: Polymerase chain reaction
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Biological reference intervals and clinical decision values
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- Negative: MTB DNA not detected.
- Positive:
- MTB DNA Detected Rif resistance not detected.
- MTB DNA Detected Rif resistance detected.
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Factors affecting test performance and result interpretation
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Factors affecting test performance:
- A negative TB PCR result alone is not enough to rule out TB diagnosis. This test should be run in conjunction with TB Culture.
- GeneXpert Real Time PCR is not approved by FDA for extra pulmonary samples.
- A negative TB PCR does not exclude the Tuberculosis infection
Result interpretation:
- A positive result indicates the presence of Mycobacterium tuberculosis complex DNA, with or without Rifampicin resistance mutations.
- A negative result indicates the absence of detectable M tuberculosis complex DNA.
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Turnaround time / Days and times test performed / Specimen retention time
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Turnaround time
Days and times test performed
*Exceptions:outpatient samples and extra pulmonary specimens received on Thursday and weekends, will be performed on Sunday.
Note: For tests performed at the AAH and TCH microbiology laboratories-24/7
Specimen retention time
- 3 days after results is released.
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