Medical College Task Force Workshop on NTEP

1. Establishment and responsibilities of
C&DST laboratory (including NAAT)
in Medical College
Dr. Nishant Kumar
Joint Director (Public Health), CTD
MoHFW, GoI

2. Content
Rationale for
diagnosis
Diagnostic
network
Diagnostic tools
& Tests
Pre- requisites for
establishing
diagnostic facility
Commissioning
the facility
Diagnostic
linkage for
patient services
Quality assured
diagnostic
support
Maintenance of
the facility

3. Rationale for diagnosis
Evidence required to establish etiological relationship between microorganism and
disease
Diagnosis of TB Detection of Drug Resistance Monitoring treatment

4. Diagnosis- The Journey So Far
1882
2020

5. Tools for Diagnosis of TB- Conventional

6. Tools for Diagnosis of TB- Molecular
• Offered for upfront diagnosis of TB among key population and currently being scaled up for all
presumptive TB patients
• Capable of diagnosing TB as well as detection of RIF resistance
Truenat test
Gene Xpert test

7. Tools for detection of Drug Resistant TB
First Line LPA Second Line LPA MGIT 960
Genotypic test- Detect
FQ and SLID resistance
Genotypic test- Detect
RIF and INH resistance
Phenotypic test- Detect
resistance to both 1st & 2nd
line drug

8. Transition of NTEP diagnostic landscape
TB diagnostics landscape in India has been transformed in recent years with the scale up of free rapid TB diagnostics and
treatment all across the country
EQA for ZN
Smear microscopy
Liquid culture
First line FL-LPA
SL-LPA
Universal DST
Extended LCDST
EQA of CBNAAT
LIMS
Truenat testing
Solid Culture and
DST
Liquid culture
SL LCDST
GeneXpert
NABL
Accreditation
Initiation to replace
smear microscopy with
NAAT at 8000 high
workload DMCs
2021
EQA for Truenat
Rifampicin resistance detected
All TB patients
All presumptive TB1 or
key population2 Non-responders
Rifampicin resistance not detected
DS-TB regimen
NAAT3
FL-LPA5 + SL-LPA6 + LC DST7 – Z, Bdq8, Cfz8, Mfx, Lzd, Dlm8
FL-LPA5
H resistance detected4
Reflex testing for SL-LPA 6 +
LC DST7 – Mfx, Z, Lzd, Cfz8
Stop DS-TB
regimen
FIRST SPECIMEN TESTED AT NAAT SITE
SECOND SPECIMEN TESTED AT C&DST LAB
Yes
No
Phased
introduction and
expansion of
diagnostic tools

9. NATIONAL REFERENCE
LABORATORY • Microscopy, NAAT, LPA, Liquid
Culture, LCDST
INTERMEDIATE REFERENCE
LABORATORY (STATE LEVEL)
C&DST LABORATORY
(IN MEDICAL COLLEGES & PRIVATE
SECTOR LABS (N=17)
Microscopy, NAAT, LPA,
Liquid Culture, LCDST
DISTRICT & SUB-
DISTRICT LEVEL
• Microscopy,
• Rapid molecular test
(NAAT) –
• CBNAAT
• TrueNat
PERIPHERAL
LEVEL
6
34
56
4760- NAAT
23038- DMCs
NAAT- Nucleic Acid Amplification Test; LPA- Line Probe Assay; LC DST- Liquid Culture Drug Susceptibility Testing
NTEP Diagnostic Network TESTING MODALITIES

10. Low Risk Facility
• Sputum smear microscopy & NAAT technologies are classified as “Low Risk “
level tests
• Minimal Biosafe requirements are adequate to establish the facility
• However, it is necessary to follow biosafe working practices in the facility

11. Enter Heading Enter Heading
Coverage of diagnostic facilities
Referral laboratories
one per district level
Need based expansion to sub
district level
Decentralised molecular testing at
block level
DMCs- one / Lakh population;
Hilly/
Tribal/Desert/Remote/Difficult
areas - One/ 50,000 population
Med Coll, Corporate & Private
Hospital, ESIC, Railways, NGOs
Designated Microscopy Centre Rapid Molecular tests

12. Structure of NTEP Laboratory network
Central TB Division National Reference Laboratories National Level
State TB Cell Intermediate Reference
Laboratory
State Level
Lab committee
IRL Staff
District TB Centre
TU TU TU
DMC 1 Truenat CBNAAT
Lab Technician
Staff concerned with
DMC ,NAAT & QA
District Level
Direction of Supervision
Direction of Feedback
Annual
Annual
Monthly

13. Pre-requisites for DMC & NAAT facility
Basic requirements
• Dedicated laboratory work area from the public traffic (restricted access);
• Secured to prevent theft or damage
• Ample space for the safe conduct of laboratory work, and for cleaning and maintenance;
• Sturdy, impervious and cluttered free workbench that can be decontaminated easily;
• Smooth floors and walls;
• Adequate storage space/furniture (without any cloth covering);
• Proper illumination in the work area;
• Adequate supply of water and electricity;
• Dedicated sink for hand washing;
• Sample handling & preparation to be done in a naturally or mechanically ventilated
laboratory room ensuring directional airflow i.e air flowing from clean areas to areas
where aerosol may generate and then to outside.

14. Establishing DMC
• To improve Case detection ,
minimise referral loss, States were
directed to expand the DMC facility
in PHIs
Expanding
diagnosis
and linkage

15. Specific requirements for CBNAAT facility
SEPARATE AREA OR ROOM FOR
SPECIMEN PROCESSING.
ADDITIONAL AIR-CONDITIONED
ROOM FOR INSTALLING GENE
XPERT MACHINE , UPS AND
PERIPHERALS.
THE WORK BENCH (PLATFORM)
SHOULD BE STABLE, VIBRATION
FREE, POSITIONED AWAY FROM
DIRECT SUNLIGHT AND WASH
SINK.
THE SIZE OF THE PLATFORM
(WORK BENCH) SHOULD BE AT
LEAST 4 FEET LONG AND 3 FEET
WIDE FOR A 4 MODULE
MACHINE. FOR 8 AND 16
MODULE MACHINES IT SHOULD
BE 5 FEET LONG.
THE HEIGHT OF PLATFORM
SHOULD BE 3 ½ FEET.
GENEXPERT SHOULD BE
INSTALLED AT LEAST 1 FOOT
AWAY FROM WALL.

16. Specific requirements for CBNAAT facility
Room should be air-conditioned, having temperature between 15°C to 25° C. Direct draft
of air from the AC on the GeneXpert system should be avoided. Hence Air Conditioner
should be placed at a side wall from the GeneXpert machine
Electrical connection - 15 Amp- four plugs required with adequate earthing. Power for 110-
220V outlets for the printer.
Double door refrigerator (300 litre) for storing specimen.
Stabilized power for a computer and GeneXpert to be made available. 2 KV online UPS for
a 4 module machine and 5 KV online UPS for 8 / 16 module machine with battery back-up
for 2 hrs.is essential.

17. Network requirement as
the results can be
transmitted using Chip
inbuilt in the machine
Vibration free sturdy table
required
Post testing the
biomedical waste
to be managed
Functions at room
temperature & may
not require AC
Works on both
electricity or
charged batteries
Ease of converting
DMC into NAAT
facility with Truenat
Minimal Infrastructure (near
PoC)
Indigenous molecular tool for diagnosis of TB and detection of Rifampicin resistance
Specific requirements for Truenat facility

18. Coverage of NAAT facilities in NTEP
Present coverage of NAAT facilities
and still expanding to saturate all
blocks (approx.- 8000 nos)
Testing modality 2017 2018 2019 2020 2021 2022 *
CBNAAT 651 1180 1180 1268 1303 1398
Truenat --- --- 367 1879 2457 3362
NAAT 651 1180 1547 3147 3760 4760
*- till 2Q 2022
Mobile medical vans
equipped with X-ray & NAAT
Sites mapped in Ni-kshay 2Q 2022

19. WHO Recommendations- 2021
• Recommendations based on evidence of accuracy in sputum of adults with confirmed
TB
• Extrapolated to adolescents and children and to people with EPTB
• Apply to PLHIV

20. Diagnostic pathway
NAAT
RIF sensitive
RIF resistant
MTB Negative
High risk for mono/poly
INH resistance
Xpert
MTB/XDR
< 80 min
< 90 min
High risk for XDR/ pre-XDR
Same day initiate
Optimal treatment
4-8 weeks
LCDST performed for
additional drugs
Modify treatment
accordingly
Advantages- Operational:
• Diagnosis, RIF resistance and additional drug
resistance detected using single sample and same
time
• TAT for diagnosis and UDST minimized from days
to <3 hours
• Possibility of Extended DST at decentralized level
Proposal: Use of Xpert MTB/XDR test on par with LPA formats for
rapid detection of additional drug resistance and management of
patients at district level
NTEG Recommendations: A sub-committee of experts to be formed by CTD to
develop a white paper on CTD’s proposal and implement to gain local experience
and generate evidence by utilizing Xpert MTB/XDR cartridges in the Xpert
MTB/XDR machines with 10 colour modules available in the programme at limited
sites in India to guide NTEP on further expansion.

21. Establishing C&DST laboratory
Medium & High Risk
Laboratory
BSL 2 – for decontamination
of specimens and processing
for liquid culture
TB Containment Facility for
manipulating MTB positive
cultures and performing
Drug susceptibility testing

22. Scale up of C&DST laboratories
• C&DST laboratory was planned to be
established to aid in
• detection of DRTB
• initiate DST guided treatment
• Initial plan is to establish at least one
C&DST laboratory per a major state,
• Further expansion for one additional IRL
for large states
• Additionally, for augmenting diagnostic
capacity for DRTB testing, C&DST
laboratories were established in medical
colleges
• Infrastructure development was
supported by UNITAID, Global Fund and
GoI
• Presently 96 C&DST laboratories are
available capable of providing
LPA/LC/LCDST services
• 40 Laboratories are functional in
Medical Colleges
• Laboratories are to be quality assured to
initiate patient services
• Structured assessment and certification
plan

23. Infrastructure requirements for C& DST laboratory
• Specimen collection section
• Sterile areas- reagent prep, media room
• Non sterile areas- washing & sterilization
• Molecular facility- Xpert/ Truenat/ LPA (3 rooms)
• Microscopy facility
• Store rooms, Incubator & cold room, instrument
room
• Recording & reporting facility (LIMS)
• Staff room
• BSL 2 facility
• BSL 3 facility- TB containment facility
• AHU area, UPS section
• Training rooms (as per need)
Refer technical specifications
at www.tbcindia.gov.in for
further details
Approx 2000-3000sq.ft area,
preferably in the ground
floor

24. Template- C&DST lab Layout
Layout for C&DST laboratory
Layout for C&DST laboratory to be prepared by officials at identified site, IRL & NRL

25. Performance Indicators & Key Alarms
Indicators Evaluation Range
Percentage of Specimens received within 72 hours of
collection
Time lag-viability, risk of contamination Close to100%
Percentage of specimen rejected Poor training quality in sputum
collection, transportation
Close to 0%
Percentage of Smear-positive diagnostic specimens
reported as culture-positive
Technical proficiency >90%
Contamination Specimen collection, transport
Evaluate processing procedures
LJ - 2-4% ; LC – up to 10% ;
LPA – Clean runs
NTMs Acceptable recovery rate
Troubleshoot contamination
<20% deviation from
reported previously
Reporting results within benchmark TAT Timeliness and Quality of services Close to 100%

26. Scale up of C&DST laboratories
Testing
modality
2017 2018 2019 2020 2021
2022 (Till
2Q)
LPA 56 62 64 64
74-FL
61-SL
79- FL
67-SL
LC DST 45 48 51 50
60- FL
49- SL
64-FL
54-SL
LIN/PZA 47/48
2017 2018 2019 2020 2021 2022
FL- LPA 0.93 Lakhs 2.0 Lakhs 3.5 Lakhs 2.5 Lakhs 3.2 Lakhs 1.3 Lakhs
SL-LPA ---- 0.59 Lakhs 0.72 Lakhs 0.58 Lakhs 0.58 Lakhs 0.23 Lakhs
LC 1.5 Lakhs 2.45 Lakhs 3.53 Lakhs 2.85 Lakhs 3.0 Lakhs 1.4 Lakhs
LC DST
0.26 Lakh 0.18 Lakh 0.19 Lakhs 0.11 Lakhs 0.14 Lakhs 0.20 Lakhs

27. LJ / MGIT for 1st and 2nd line Anti TB drugs
Application by Labs & Pre-assessment visit by NRL/CTD team
C&DST trainings at NRLs for laboratory personnel
NTEP Certification process for C&DST labs
2 Weeks
Lab Design, HR, Equipment & Bio-Safety norms
Action plan for lab accreditation
Developing C&DST skills by the IRL-IQC
1-2 days
Data of 100 DSTs assessed for performance indicators
Proficiency testing –DST (at NRL)-EQA
~3 Months
~ 3 Months Exchange of 20 panel cultures (Blinded to IRL)
Concordance requirement >= 90%
Assessment visit -Evaluation
Full-Conformities
1-2 days
Technical and /Administrative
Non-Conformities
(causes, solutions)
Certification of the Laboratory

28. Phenotypic test
(LC DST)
Genotypic test
(LPA)
Retesting Panel testing
100 LCDST results are
reported by the Laboratory
to the respective NRL
Out of these, 10 are
retested at NRL
Assessment of the
Laboratories in Real time
20 cultures representing different
resistant patterns are sent to the
Laboratory by the NRL
DST is set up by the method
routinely used in the Laboratory
Actual test of performance
Retesting
20 DNA isolates are selected
from the 50 tested
DNA isolates dispatched
from Laboratory to NRL
LPA is set up at NRL
Assessment of the
Laboratories in Real time
50 DNA extracted from
prospective samples
(aliquoted in duplicate)
LPA (FL /SL) is set up as per
SOP by the Laboratory
Results interpreted
Interpretation sheet
submitted to NRL for
performance assessment
and Retesting
Schematic Representation of initial certification process
Post initial certification, quality is assured through
continued annual proficiency testing by NRL

29. Quality Assurance
29
Smear Microscopy:
NRL to State IRLs,
to the district/sub
district level and
then to DMCs
NTEP Certification
Process: NRL to C&
DST Laboratories
(public & private)
NABL
Accreditation:
Completed: 16;
Ongoing: 13
Annual PT for LPA
and LC-DST from
NRL to all certified
C& DST
Laboratories
(Public & Private)
NAAT- Dried Tube
Spots for public
sector and private
sector
Structured Quality Assurance Programme

30. Introduction and coverage of NAAT EQA
Phase I
• Total 41 GeneXpert instrument (21 private and 20 public): Jan – Feb 2018
Phase II
• Total 212 GeneXpert instrument (192 Public + 20 Private): April - June
2018
Phase III
• Total 663 GeneXpert instrument (636 Public + 27 Private): January –
March 2019
Phase IV
Phase V
•Total 1287 GeneXpert instrument second pan country (1213 Public + 74
Private): Dec 21 – March 22
•Total 1187 GeneXpert instrument pan country (1146 Public + 41 Private):
Sep – Nov 2020
Similar activity is
being piloted to
Truenat testing @
750 sites in Phase 1
NAAT EQA is conducted by NRL- NTI, Bangalore

31. Linkage for DRTB testing
Post certification, initiate patient services in linked districts
Initiate certification process with respective NRL
With support of IRL & NRL- capacity building of staff posted
Develop infrastructure and commission the facility
Propose for requirement for new laboratory facility & staff in
State PIP plan for funding
Pre-assessment visit to the selected site
Identify potential sites for establishing C&DST laboratories
Needs assessment -- Demand Vs capacity
For illustration purpose only- adopted from Karnataka State

32. Maintenance of the facility
• It is necessary to ensure proper
functionality of the equipment &
infrastructure
• Maintenance of infrastructure and
equipment are supported by State/
Centre
• Designated laboratory staff to perform
daily/ monthly maintenance as indicated
in SOP
Facility at Pubic
sector
Infrastructure &
Maintenance of
equipment
DMC District/ State Level
NAAT (supplied by
NTEP)
Centre level
C& DST laboratory
Infrastructure
District/ State Level
C& DST laboratory –
proprietary
equipment
Centre level
C& DST laboratory –
Non-proprietary
equipment
District/ State Level
(transition from FIND
support to State level
ongoing)

33. Biomedical waste management
Truenat chips
Used mask / gowns
Infectious liquids
Specimen collection tubes,
sputum cups, CBNAAT cartridges
Infected plastic -Contaminated
tips, Pasteur pipettes, PCR tubes,
MGIT tubes, LJ slants in
disposable tubes
Used gloves
•Glass slide in TrueNat machine
•LJ slants in disposable tubes
33
Annexure 10: Biomedical waste management

34. BMW management at facility
34
All material used for DRT/ DST
to be wrapped in autoclavable
red/ yellow/ blue bag buried in
the pit in isolated area
All BMW to be hand over to
authorized waste collectors
engaged by local bodies within 48
hours
Deposit biomedical waste in color
coded bags at common collection
facility established by site which
should be under lock and key
PHC/CHC/UPHC/sputum collection centre/ NAAT & CDST Facility

35. Operational plan to improve TB diagnosis
• Phased transition from Microscopy to NAAT over a period of time.
• Saturation of blocks with NAAT.
• Microscopy to continue for treatment monitoring.
• Existing Laboratory technicians will be trained and repurposed for performing NAAT
when transitioned.
• Quality assured diagnosis – all technologies
• Extension of support from Private sector