Laboratory Hierarchy and Network
ContentNTEP laboratory network is comprising of National Reference Laboratories (NRLs), state level Intermediate reference laboratories (IRLs), Culture & Drug Susceptibility Testing (C & DST) laboratories and peripheral level laboratories. Peripheral level laboratories consist of designated microscopy centres (DMCs) and NAAT labs.
NTEP has a quality assured laboratory network for bacteriological examination of sputum in a 3-tiered system.
Figure: Laboratory network of NTEP
Resources:
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Roles of NRLs
Content- National Reference Laboratories (NRLs) conducts annual on-site evaluation/supervisory visits to laboratories for assessing the quality of microscopy, culture and drug susceptibility test (C&DST), and for improvement of the overall laboratory quality.
- NRLs also assist Central TB Division (CTD), in developing laboratory guidelines, standard operating procedures (SOPs), and conduct training to state-level Intermediate reference laboratories (IRLs) and other technical issues.
- NRLs conduct C&DST training to the IRLs, and develop SOPs for the technical procedures, equipment maintenance, infection control and recording and reporting.
- NRLs are also responsible for offering second-line drug susceptibility tests (DST) for multi-drug resistant TB (MDR-TB) treatment failures.
- NRLs are responsible for the accreditation of the mycobacteriology laboratory for culture and drug sensitivity testing under the National Tuberculosis Elimination Program (NTEP).
- In addition, NRLs are also responsible for the conduct of research for the programme and evaluation of newer tools for the diagnosis of TB.
- The National Institute for Research in Tuberculosis (NIRT) Chennai, the Supranational Reference Laboratory (SRL) of the region is responsible for the external quality assurance of the other 5 NRLs. NIRT is in turn quality-assured through the SRL coordinating laboratory at Antwerp, Belgium.
Assessment Questions
Question
Answer 1
Answer 2
Answer3
Answer 4
Correct Answer
Correct explanation
Part of pre-test
Part of post-test
What are the functions of National Reference Laboratories?
Providing Culture and DST training to the IRLs
Developing SOPs for the technical procedures
Offering second-line DST
All of the above
4
All the functions stated are performed by the National Reference Laboratories.
Yes
Yes
Which institute is responsible for the external quality assurance of NRLs?
SRL
CTD
National Institute for Research in Tuberculosis, Chennai
National Tuberculosis Institute, Bangalore
3
The National Institute for Research in Tuberculosis (NIRT) Chennai, the Supranational Reference Laboratory (SRL) of the region is responsible for the external quality assurance of the other 5 NRLs. NIRT is in turn quality-assured through the SRL coordinating laboratory at Antwerp, Belgium.
Yes
Yes
Roles of IRLs
ContentThe Intermediate Reference Laboratories (IRLs) function as a culture and drug susceptibility testing (C&DST) facility for the state level.
In addition to performing CDST, IRL is also responsible for:
- Undertaking training on laboratory technologies for district and field level staffs
- Conducting on-site evaluation visits to districts for sputum microscopy at least once a year
- Undertaking panel testing of Senior TB Laboratory Supervisors (STLS) at each district linked to it
- Ensuring the proficiency of staff performing National Tuberculosis Elimination Programme (NTEP) smear microscopy activities by providing training to laboratory technicians and STLS
Resources
- Guidelines for Programmatic Management of Drug-resistant TB in India, 2021.
- NTEP Laboratory Network.
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CDST labs and their role
ContentUnder the National Tuberculosis Elimination Programme (NTEP), many labs are established at the regional level within states for providing Culture and Drug Susceptibility Testing (C&DST) facilities for presumptive TB/DRTB and for TB/DRTB patients.
- C&DST laboratories are mostly located in intermediate reference laboratories (IRLs) or medical colleges.
- There are 42 C&DST laboratories established under the programme in different geographies.
- Dedicated human resources are provided for the laboratories under the programme.
- Districts are linked with laboratories for providing facilities for Culture and DST using:
- Phenotypic Methods (Solid – Lowenstein Jensen (LJ), and Liquid Culture – Mycobacteria Growth Indicator Tube (MGIT))
- Genotypic technology (Line Probe Assay (LPA) and Cartridge Based Nucleic Acid Amplification Test (CBNAAT))

Figure: Culture and Drug Susceptibility Testing (C&DST) facility,
Source: The Foundation For Innovative New Diagnostics (FIND)Resources
- Guidelines for Programmatic Management of Drug Resistant TB in India, 2021
- Training Modules (1-4) for Programme Managers and Medical Officers; New Delhi, India: Central TB Division, July 2020
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NAAT Labs and their role
ContentThe National Tuberculosis (TB) Elimination Program (NTEP) has a network of Nucleic Acid Amplification Tests (NAAT) laboratories coupled with Designated Microscopy Centers (DMCs) to form the backbone of the diagnostic component of TB services.
Nucleic Acid Amplification Tests (NAAT) laboratories includes Cartridge-based NAAT (CBNAAT) and TrueNat tests. These tests detect tuberculosis as well as rifampicin resistance and are more sensitive than smear microscopy.
Functions of Nucleic Acid Amplification Test (NAAT) Laboratories:
- Acting as a hub for collection of samples from public and private health facilities (spokes)
- Universal Drug Susceptibility Testing (UDST) to rule out rifampicin resistance among confirmed TB patients
- Timely provision of NAAT test result to the TB patient, medical officer of the concerned health facility and NTEP staff for related actions
- Acting as a sample dispatch center for the Culture DST laboratory for subsequent processing of samples for first-line line probe assay (LPA) and second-line drug resistance testing utilizing second line LPA and liquid culture DST
- Recording and reporting including digitization of diagnostic process from collection to test result in NTEP Nikshay portal and Laboratory Information Management System
- Management of supplies and logistic associated with laboratory logistic (CBNAAT cartridges and TrueNAT chips) and reporting any additional requirement thereof
- Supporting the quality assurance activities undertaken by District or Intermediate Reference Laboratory under NTEP
- Support health system in carrying out special drives for vulnerable and at-risk population and their testing directly by CBNAAT (slum population, diabetic population, smoker, malnourished people, patients of silicosis and kidney dialysis etc.)
Resources
- RNTCP Technical and Operational Guidelines for TB Control in India, 2016.
- Guidelines for Programmatic Management of Drug Resistant Tuberculosis in India, 2021.
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Functions of a Designated Microscopy Centres [DMC]
ContentFunctions and Integrated Services of the DMC
- Testing of Sputum samples by Microscopy.
- Request/ referral for microscopy or Nucleic Acid Amplification Test (NAAT) or Culture and Drug Susceptibility Test (C&DST) or Chest X-ray (CXR) or Tuberculin Skin Test (TST) is generated at the PHI-DMC, as well as follow-up tests.
- Maintain consumables and logistics required for testing/ packaging and transport.
- Maintain TB laboratory registers for recording and reporting.
- Notify every TB patient in Nikshay at the earliest and update information of patients on comorbidity, treatment adherence, treatment outcome, contact investigation and TB Preventive Treatment (TPT).
- Biomedical waste management for the waste generated at DMCs.
- A DMC is required to participate in the External Quality Assurance system(EQA) of NTEP to ensure standardized quality diagnostic testing.
Resources
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Sputum Collection centres
ContentTo increase access to diagnostic services, NTEP has a provision for sputum collection centres in areas where the health facility is not equipped with key requirements to conduct sputum microscopy, molecular tests, drug susceptibility testing or follow up examinations.
Sputum collection centres are dedicated locations where sputum samples are collected, packaged and then transported to nearby TB diagnostic centres. It could be attached to any near-by health-facility as well.
Requirements of a Sputum Collection Centre
To function as sputum collection centres, the following is essential:
- Linkage/ mapping (time and distance) to testing laboratory
- Availability of adequate number of sputum cups and falcon tubes, logistics for sample packaging and transport
- Identification of open areas for sputum collection
- Staff trained in NTEP guidelines on sputum collection, sample packaging and transport, complete and correct documentation of laboratory request form, and infection control practices
- Feasibility and financial measures required for sample transport
- Inclusion of local volunteers, courier services, sample transportation under National Health Mission Free Diagnostic Services or other mechanisms as decided by the state/district
- Availability of Information, Education and Communication (IEC) material, training modules, and job-aids
Sputum collection centres are established in:
- Ayushman Bharat Health and Wellness Centres/Sub-centres
- Urban primary health centres
- Tribal, hilly, desert and difficult-to-reach areas of the country
Resources
- Training Modules for Programme Managers and Medical Officers
- Operational Guidelines for TB Services at Ayushman Bharat Health and Wellness Centres
- Mycobacteriology Laboratory Manual, GLI Initiative, 2014
Assessment:
Question Answer 1 Answer 2 Answer 3 Answer 4 Correct answer Correct explanation Page id Part of Pre-test Part of Post-test Under NTEP, where are sputum collection centres established to increase access to diagnostic services? Tribal areas Ayushman Bharat health and wellness centres Difficult-to-reach areas All of the above 4 To increase access to diagnostic services, sputum collection centres are established in Ayushman Bharat health and wellness centres, Urban health centres, tribal, hilly, desert and difficult-to-reach areas of the country. Yes Yes
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