Cartridge – Based Nucleic

Acid Amplification Test (CBNAAT) Dr.M.P. Samrat Abhishek M.B.B.S.,FICM

District TB Control

Medical officer (RNTCP)

Born Robert Heinrich Herman Koch11 December 1843Clausthal, Kingdom of Hanover

Died 27 May 1910 (aged 66)Baden-Baden, Grand Duchy of Baden

Nationality German

Fields Microbiology

•Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis and, less commonly, by other organisms of the ‘tuberculosis complex’. It is estimated that 3 million people die from TB each year—the majority of them in developing countries.

• The annual incidence of New cases of all forms of TB (pulmonary and extra-pulmonary) worldwide is estimated to be approximately 8 million, of which about 95% occur in developing countries. Many TB cases in developing countries remain undiscovered. Of the discovered smear-positive cases, less than half complete treatment.

• Consequently, the estimated prevalence (the total number of tuberculosis cases at a given time) worldwide is 16 to 20 million, of whom about 8 to 10 million are sputum smear-positive and highly infectious.

•The number of persons infected with the tuberculosis bacillus is estimated to be 1.7 billion, of which 1.3 billion live in developing countries. In India, more than 40% of adults are infected with TB, and approximately 1.5 million cases are put on treatment every year. An estimated 5 lakh deaths from TB occur every year.

INCIDENCE OF TB IN INDIA

o Tuberculosis is one of the deadliest public health threats today, but there remains a lack of effective diagnostic tools.

o untreated tb patients remain a source of infection for other members of community & results in considerable morbidity & mortality , especially in PLHIV group.

Screening methods for tuberculosis:

The most widely used method to detect TB is sputum smear microscopy test, which has a number of drawbacks including……

• low sensitivity (especially in HIV-positive individuals and children)

• inability to determine drug-susceptibility• variable performance that depends on

operator training.

X-Ray especially the digital version serves as the most sensitive tool but only shows opacities which is further depends upon the x-ray reader(inter & intra reader variations of reporting).

Conventional diagnosis of drug resistant TB relies on mycobacterial culture and drug susceptibility testing (DST), a slow and cumbersome process requiring sequential procedures for isolation of mycobacteria from clinical specimens.

Identification of Mycobacterium tuberculosis complex, and in vitro testing of strain susceptibility to anti-TB drugs.

During this time patients may be inappropriately treated, drug-resistant strains may continue to spread, and amplification of resistance may occur.

The CBNAAT/ Xpert MTB/Rif test is a cartridge-based fully automated NAAT (nucleic acid amplification test) for TB case detection and Rifampicin resistance testing.

Purifies, concentrates, amplifies (by rapid, real-time PCR) and identifies targeted nucleic acid It sequences in the TB genome (rpo b), and provides results from unprocessed sputum samples in less than 2 hours, with minimal hands-on technical time.

Diagnosis of TB, TBHIV, MDR-TB and XDR-TB WITH CBNAAT :

Sputum smear microscopy has a particularly low sensitivity for detecting TB among PLHIV.

This is because people in later stages of HIV infection and with compromised immune systems often release fewer organisms into their sputum, at concentrations below the threshold for visual detection under a microscope.

For PLHIV with a negative smear microscopy result but who are still presumed to have TB, bacterial culture has been the other option.

culture can only be undertaken at central level laboratories, and results are normally only available after a number of weeks or months.

Culture is therefore not good enough for people living with HIV, who need a speedy TB diagnosis and prompt treatment.

CBNAAT allows for the rapid detection of TB and resistance to rifampicin in a single test.

It has a sensitivity superior to that of conventional microscopy or culture on solid media, and is therefore useful in the diagnosis of TB in HIV co-infected persons where the sensitivity of microscopy alone is low.

o The system simultaneously detects resistance to rifampicin, which is a good and reliable proxy for MDR TB.

who guide line:

WHO recommends the use of Xpert MTB/RIF as a primary diagnostic test for all people living with HIV who have signs and symptoms of TB.

For people with unknown HIV status presenting with strong clinical evidence of HIV infection.

For people who are seriously ill and suspected of having TB regardless of HIV status and those at high risk of MDR-TB.

WHO has issued policy recommendations for the use of Xpert MTB/RIF in thediagnosis of extrapulmonary TB and rifampicin resistance detection

• Xpert MTB/RIF should be used in preference to conventional microscopy andculture as the initial diagnostic test in testing cerebrospinal fluid specimensfrom patients presumed to have TB meningitis (strong recommendation given the urgency of rapid diagnosis, very low quality of evidence);

• Xpert MTB/RIF may be used as a replacement test for usual practice (including conventional microscopy, culture, and/or histopathology) for testing of specific non-respiratory specimens (lymph nodes and other tissues) from patients presumed to have extrapulmonary TB (conditional recommendation, very low quality of evidence).

•For CSF specimens, Xpert MTB/RIF should be preferentially used over culture if thesample volume is low or additional specimens cannot be obtained, in order to reachquick diagnosis. If sufficient volume of material is available, concentration methodsshould be used to increase yield;

•Individuals presumed to have extrapulmonary TB but with a single Xpert MTB/RIF -negative result should undergo further diagnostic testing and hence processing oftissue samples (lymph nodes and other tissues) for Xpert MTB/RIF should include adecontamination step to enable samples to be concurrently cultures

•Pleural fluid is a suboptimal sample for the bacterial confirmation of pleural TB, usingany method. A pleural biopsy is the preferred sample.

•These recommendations do not apply to stool, urine or blood, given the lack ofdata on the utility of Xpert MTB/RIF on these specimens.

CBNAAT SUSPECTS CRITERIA:

A. All PLHIV cases.B. All MDR close contacts .C. All retreatment smear negative cases &

extra pulmonary cases.D. All Peadiatric TB suspect cases.E. Referral cases from public private

partnership.

Samples that are recommended for CBNAAT are…

Sputum- BAL , Gastric lavage (with out food particles).

Pleural fluid.Ascitic fluid.CSF.FNAC / BIOPSY material.Mid stream urine.Stool & blood are not recommended.

Lymph nodes / biopsy: Tissue sample pieces grinded in a sterile container (tissue grinder).

CSF sample of 0.1 ml to 1 ml is recommended for cbnaat. Less than 0.1 ml is insufficient sample.

Pleural fluid & asitic fluid of 5 ml is recommended for cbnaat.

Blood stained & xanthochromic samples may cause false negative.

All specimens should be transferred to the DTC as early as possible preferred in a stored condition at 2 – 8 degree centigrade.

Specimen processing

The Xpert MTB/RIF assay can be used directly for CSF specimens and homogenised extrapulmonary samples (lymph node biopsies and other tissues) or on decontaminated specimens if culture is performed concurrently.

Whenever possible, specimens should be transported and stored at 2 to 8°C prior toprocessing (a maximum of 7 days).

conclusionLPAs are currently limited to detecting

resistance to rifampicin and isoniazid and are suitable only on smear positive Specimens.

Conventional DST is needed to detect resistance to anti-TB agents other than rifampicin and isoniazid & to detect XDR-TB.

conclusionOverall the LPA test is a reliable, rapid and

easy to perform for the simultaneous detection of RMP and INH resistance in M.tuberculosis

It is recommend that the LPA should serve as an early guidance of therapy, which should be followed by a phenotypic DST confirmation for all suspected MDR-TB patients.

conclusionAlthough Xpert MTB/RIF is suitable for use at all

levels of the health system & does not require additional laboratory equipment, it requires care in handling, a stable and uninterrupted electrical supply, security against theft, adequate storage space & bio-safety measures.

Xpert MTB/RIF does not eliminate the need for capacity for conventional TB microscopy, culture and DST.

conclusionThe Xpert MTB/RIF assay is suitable for

diagnosing TB and detecting RR-TB.

A negative result accurately excludes the possibility of rifampicin resistance and no further testing is needed to confirm the negative results. (NPV>99%)

conclusionMicroscopy or culture, or both, remain

essential for monitoring treatment since molecular tests based on DNA detection have not been shown to be suitable.

Liquid culture, molecular LPAs and the Xpert MTB/RIF assay should be phased in to programmes in a way that ensures that the existing capacity for solid culture and DST is maintained.

Cartridge preparation

Xpert MTB-RIF Cartridge preparation.mp4

Sample in cartidge

Cartridge-ROBAL.mov

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