National Tuberculosis Reference Laboratory (NTRL)2018-11-07T10:29:09+00:00

The National Tuberculosis Reference Laboratory (NTRL)

About Us

The National Tuberculosis Reference Laboratory (NTRL) is a unit under the division of National Public Health Laboratory (NPHL). It is the third reference laboratory in the division to be approved for ISO 15189:2012 accreditation by Kenya National Accreditation Systems (KENAS) after National HIV Reference Laboratory (NHRL) and National Microbiology Reference Laboratory (NMRL).

Key Functions

The NTRL’s mandate is to perform surveillance for both drug susceptible and drug resistant TB by conducting culture and drug susceptibility testing (DST) for 1st and 2nd line TB drugs.

In addition, NTRL plays the following roles:

  • NTRL coordinates microscopy support supervision for County referral hospitals
  • Conducts gene-xpert external quality assurance (EQA) in collaboration with CDC Atlanta
  • Performs cultures on both solid and liquid media
  • Performs both phenotypic and genotypic first line and second line DST. This includes Line probe assays (LPA Hain) – MTBDRplus and MTBDRsl.

Key Sections

The NTRL has 6 key sections as follows:

  1. BSL 2-This entails sample reception, accessioning, decontamination, smear microscopy
  2. BSL 3– This entails culture offloading, identification tests, and drug susceptibility testing
  3. Molecular section – This entails running of gene Xpert assays and line probe assays
  4. Media Preparation –All reagents and media are prepared here
  5. Data Section – Results entry into an online Laboratory Information Management System (LIMS) for review of results, reporting and releasing of results.
  6. Commodities/Stores – Ensures forecasting and quantification for laboratory commodities is done and the laboratory does not run out of stock.

Classification of TB

TB is classified as pulmonary TB (affecting the lungs) and extra pulmonary TB (affecting other parts of the body except hair, teeth)

TB drug resistance types are:

  1. Rifampicin-resistant TB (RR-TB) – TB with resistance to rifampicin, which is detected using phenotypic or genotypic methods, with or without resistance to other anti-TB agents.
  2. Mono-resistance TB – refers to TB resistance to a single first-line drug.
  3. Poly-resistance TB – refer to resistance to two or more first-line drugs but not to both isoniazid and rifampicin i.e. not MDR–TB.
  4. Multidrug-resistant TB (MDR-TB) is TB with resistance to at least isoniazid and rifampicin.
  5. Extensively drug resistant TB (XDR-TB) is MDR-TB plus resistance to a flouroquinolone and at least one of three injectable second-line agents (amikacin,capreomycin or kanamycin)

Specimens/Samples

The samples used for TB testing include:

  • Sputum
  • Cerebral spinal fluid (CSF)
  • Ascetic fluids
  • Swabs
  • Biopsies
  • Urine
  • Stool
  • Bone marrow
  • Gastric Lavage

Tests Done

The National Tuberculosis Reference laboratory has the capacity to perform the following test procedures or assays.

Test menu Type of container & transport conditions Turnaround time (TAT) Comments
Acid First Bacilli (AFB) Microscopy Sterile 50 mls centrifuge tubes or universal bottles. Environment temperature within 12hrs

2-80c up to 72 hours

24-48 hours All specimens
TB culture-

Solid culture

Sterile 50 mls centrifuge tubes or universal bottles. Environment temperature within 12hrs

2-80c up to 72 hours

68days  All specimens
TB culture-

Liquid Culture

Sterile 50 mls Centrifuge tubes or universal bottles. Environment temperature within 12hrs

2-80c up to 72 hours

50 Days All specimens
TB drug susceptibility testing(1st line and 2nd line) Sterile 50 mls centrifuge tubes or universal bottles. Environment temperature within 12hrs

2-80c up to 72 hours

21 Days MGIT DST
Molecular Drug Susceptibility Testing – Line Probe assay Testing (DST – LPA)

(1st line and 2nd line)

Sterile 50 mls centrifuge tubes or universal bottles. Environment temperature within 12hrs

2-80c up to 72 hours

5 working Days Smear Positives

Rifampicin Resistant

Molecular DST -Gene Xpert Sterile 50 mls centrifuge tubes or universal bottles. Environment temperature within 12hrs

2-80c up to 72 hours

1  working day Smear Negatives/ On request

NTRL Sample Flow and Return of Results Feedback

NTRL samples analysed between 2014 – 2017

There has been gradual increase in the samples analysed in the NTRL over the years with the most increase recorded between 2016 and 2017. This can be attributed to the intensified sensitization on active case finding and improved turnaround times for samples sent for culture and DST.

The number of previously treated cases in the country in 2017 was 5,630 while those who were smear positive at month 2 were 1359. This gives 6,989 number of patients as eligible for DRTB surveillance. 6731 (96%) samples were received for culture.

Distribution of MDR TB cases diagnosed at NTRL in 2017 by phenotypic and genotypic DST

The case detection of DR TB cases has been increasing over the years. The trend is expected to rise with increasing access to drug sensitivity testing following the scale up of gene Xpert machines and the increased capacity for 1st and 2nd line probe assay (LPA) in the country.

Key achievements/milestones

  • NTRL took lead in the Kenya National TB prevalence survey in 2015-16.
  • NTRL monitors treatment of patients on short term DRTB (Drug resistant TB) regimen through second line DST.
  • Increased capacity to strengthen DST for short term regimen; – Four staff were trained in second line DST at the Supra Reference Laboratory in Brisbane, Australia.
  • Increased coverage of sites participating in Gene-Xpert PT, from 93 sites in 2016 to 153 Sites in 2017.
  • Developed a dash board where by County TB and Leprosy Coordinators (CTLC’s) can monitor the progress and status of samples sent to NTRL.
  • Laboratory recommended for ISO 15189:2012 Accreditation

Role of NTRL in the devolved system

  • NTRL coordinates and communicates with National TB, Leprosy and Lung Diseases Program (NTLD-P) and development partners to facilitate implementation of TB laboratory activities
  • Provision of regular TA’s (Technical Assistance) to peripheral laboratories
  • Provision of training on different TB diagnostics
  • Conducts Corrective Action Preventive Action (CAPA) trainings to xpert sites.
  • Provides, distributes and coordinates EQA to peripheral laboratories performing smear microscopy and gene Xpert MTB/RIF.

Future Direction

  • The laboratory is focusing on improving its services by enhancing sample referral systems, reduce Turn Around Time and additional testing like genome sequencing and other rapid test (TB LAM, Quantiferon, Gene Xpert Ultra).The laboratory is implementing remote logging to reduce pre-analytical errors.