Yes! We Can End TB!

Led by Countries. Powered by People.

KEMRI CGHR’s Frontline Contributions to Kenya’s TB Elimination Agenda

By Dr. Steve Wandiga | Head of Tuberculosis Division, KEMRI Centre for Global Health Research

600/100K TB prevalence at study launch (Kisumu area)

700/100K TB notification rate in Kisumu urban peak

~52-57% TB–HIV co-infection rate in Nyanza region

2,500+ MDR-TB specimens tested annually (Nyanza)

Two Decades of Partnership Against TB in Western Kenya

Every year on March 24 the world observes World TB Day, remembering that, globally tuberculosis still claims more than 1.25 million lives annually — remaining the world’s leading infectious disease killer. This year’s global theme, Yes! We Can End TB! Led by Countries. Powered by People, is a clarion call for national ownership, devolved-government action, and science deployed in service of communities. At the KEMRI Centre for Global Health Research (CGHR), this call has been our guiding mandate since we established the TB Division in 2006 in collaboration with the U.S. Centers for Disease Control and Prevention (CDC).

Based at the Kisian Campus in Kisumu, KEMRI CGHR’s TB Division — formerly known as the TB Branch — grew to a team of approximately 100 staff drawn across four core sections: Program Research and Strengthening (PRS), Drug and Vaccine Trials, Laboratory Science, and cross-cutting Data and Quality Assurance functions. Every member of this team trained in Good Clinical Practice (GCP) and Good Clinical and Laboratory Practices (GCLP). Together, we have spent nearly two decades generating the evidence that shapes national TB policy and, crucially, delivering that evidence back to the communities that need it most.

The TB Burden in Western Kenya: Why This Region Demands Attention

Kenya is one of the 30 high-burden TB countries that collectively account for over 87% of the global TB caseload. Within Kenya, the western counties — Nyanza and its neighbours — carry a disproportionate weight. Kisumu County records annual TB case notification rates of approximately 300 per 100,000 population, with Kisumu town reaching as high as 700 per 100,000 — a rate more than 230 times that of the United States (3/100,000). The situation is compounded by an exceptionally high HIV burden: in Nyanza, approximately 52-57 of TB patients are co-infected with HIV, compared to 25% nationally, and Kisumu County’s HIV prevalence stands at 17.6%.

It was precisely because of this concentrated burden that KEMRI CGHR and CDC chose western Kenya as the base for what has become one of Africa’s most productive TB research programmes. Our early cross-sectional prevalence survey (2006–2008) — the first of its kind in rural western Kenya — confirmed a TB prevalence of 600 per 100,000 population in the Asembo and Gem areas of the HDSS catchment. Subsequent epidemiological cohort studies among infants (2,900 enrolled) and adolescents (5,004 enrolled) revealed even higher rates: An all TB incidence of 2 per 100 person years of observation among infants and a TB prevalence of 700 per 100,000 among adolescents — a sobering reminder that TB is not only a disease of adults.

Supporting Counties: Retreatment Cases in Nyanza/Western and South Rift

Among the most clinically complex patients in any TB programme are retreatment cases — individuals who have experienced treatment failure, relapse, or interrupted therapy. These patients carry an elevated risk of drug resistance and require enhanced clinical and laboratory support that county health systems, particularly in resource-constrained settings, often struggle to provide alone.

KEMRI CGHR’s TB Division has worked directly with the National TB Programme (NTP) and targeted county governments across Nyanza, Western, and South Rift Kenya to strengthen retreatment case management. This collaboration takes the form of diagnostic support, specimen transport and testing, data feedback to facility-level clinicians, and capacity building for county laboratory and clinical staff. The CGHR TB Laboratory has been processing and reporting on approximately 2,500 MDR-TB specimens per year from across the Nyanza and western region alone — a volume that reflects the programme’s reach and the confidence that county health systems place in our laboratory.

This model of engagement embodies the 2026 World TB Day theme in practice: country-owned strategy, delivered through a collaborative, people-centred approach. By operating within devolved health structures rather than parallel to them, KEMRI CGHR amplifies county capacity and ensures that laboratory science translates directly into improved patient outcomes.

A World-Class TB Laboratory in Kisumu: Kenya’s National Back-Up

The scientific backbone of KEMRI CGHR’s TB programme is our dedicated TB Laboratory — a facility of exceptional accreditation and capability, purpose-built for the complexity of TB diagnostics in a high-burden, high-HIV setting.

The Laboratory is organized into four sections: sample reception, two BSL-II laboratories (immunology and molecular testing), and the BSL-III containment suite for high-risk work. Its testing menu encompasses the full complexity spectrum of TB diagnostics: AFB microscopy (Ziehl-Neelsen and fluorescence methods), liquid (MGIT 960) and solid (Löwenstein-Jensen) mycobacterial culture, first- and second-line phenotypic and genotypic drug susceptibility testing (DST), line probe assays (Hain LifeScience), GeneXpert-based molecular testing, and genetic sequencing of resistance-determining genes (rpoB, inhA, and katG). The immunology section offers IGRA testing (QuantiFERON Gold 4th Generation, T-SPOT), plasma processing for cell mediated immunity (CMI) and humoral immunity (HI) and PBMC separation.

As the only designated back-up to the National TB Reference Laboratory in Nairobi, the KEMRI CGHR TB Laboratory provides an irreplaceable surge capacity for Kenya’s national TB response. During periods of high demand, system disruption, or public health emergencies, this designation ensures that no diagnostic gap emerges in the country’s ability to confirm drug-resistant TB — a function that protects not just patients in western Kenya, but the integrity of the entire national programme.

Validating the Diagnostics Kenya Depends On

A diagnostic test reaches patients only when it has been rigorously validated. KEMRI CGHR’s TB Laboratory has served as a primary or co-investigator site for the validation of several diagnostic platforms now integral to Kenya’s testing algorithm:

• GeneXpert MTB/RIF: The molecular cornerstone of Kenya’s rapid TB diagnosis, detecting both M. tuberculosis and rifampicin resistance within two hours. CGHR was among the pioneering sites deploying GeneXpert as the primary test for retreatment specimens across Nyanza.
• GeneXpert MTB/RIF Ultra: In 2016, KEMRI CGHR participated in a landmark multi-country evaluation of this next-generation assay. Published in The Lancet, the study demonstrated that Ultra had superior sensitivity to the original GeneXpert — particularly in patients with lower bacillary burden and people living with HIV — while specificity was slightly reduced. These findings directly supported the WHO recommendation to adopt Ultra as the preferred replacement for GeneXpert MTB/RIF.
• QuantiFERON Gold 4th Generation: Recently validated at the CGHR TB Laboratory’s immunology section, expanding latent TB infection testing capacity.
• Bioneer: A molecular diagnostic system validated at CGHR as a high-throughput alternative for TB and respiratory pathogen testing, offering additional capacity options for high-volume settings. As well as demonstrating the Bioneer test’s ability to diagnose both first- and second-line drug susceptibility resistances on raw sputum simultaneously.
• PlusLife: A point-of-care molecular platform validated to extend TB diagnosis beyond centralised laboratories, bringing accurate testing closer to patients in decentralised and community settings.

Through this body of validation work, KEMRI CGHR provides the evidence base that enables Kenya’s Ministry of Health to make informed, data-driven decisions about which diagnostics to adopt, scale, or retire — a concrete expression of country-led TB control.

Science That Saves Resources and Reaches More Patients

Sputum Pooling: Up to 75% Cartridge Savings Without Sacrificing Accuracy

GeneXpert cartridges are expensive, supply chain-constrained commodities — a real structural barrier to scale-up in Kenya and across Africa. Responding to this challenge, KEMRI CGHR’s TB Laboratory developed and evaluated sputum pooling strategies, combining multiple samples for batch molecular testing. The results were striking: pooling could reduce GeneXpert cartridge consumption by up to 75% — without materially compromising diagnostic sensitivity.

Saving 75% of cartridges in a high-burden county programme translates directly into more patients tested, more TB cases found, and more lives saved — with the same budget.

This finding has direct policy implications for Kenya’s National TB Programme and for global TB diagnostic stewardship. It is a powerful demonstration of how KEMRI CGHR’s laboratory science is oriented not just toward publishing results, but toward solving the practical constraints that health systems face on the ground.

Paediatric TB Diagnosis: Non-Invasive Samples That Perform as Well as Invasive Ones

Tuberculosis in children remains one of the most difficult diagnostic challenges in medicine. The standard approaches — induced sputum under sedation or gastric lavage — are invasive, distressing for the child and family, technically demanding, and logistically burdensome for health facilities. As a result, TB in children is chronically under-diagnosed: globally, an estimated two-thirds of children with TB are never diagnosed.

KEMRI CGHR’s TB Division conducted a paediatric diagnostic study — later referenced in a WHO Best Practices guidance document (2018) — with the primary objective of determining the most feasible combination of specimens and tests to diagnose TB in children five years of age and younger. The study enrolled children and compared non-invasive sample types against the invasive gold standard.

Key Finding: The combination of one nasopharyngeal aspirate and one stool specimen showed a comparable diagnostic yield to that of gastric aspirates — the previous gold standard. This means clinicians can obtain equivalent diagnostic information through less invasive, more child-friendly, more feasible collection procedures.

The implications are transformational for paediatric TB programmes in Kenya and beyond: if non-invasive sample types replace invasive collection as standard practice, thousands more children can be tested earlier, with less suffering, in a far wider range of health facility settings. This study exemplifies KEMRI CGHR’s commitment to generating science that serves real patients in real health systems.

TB Impact Studies: Demonstrating What Active Case Finding Can Achieve

KEMRI CGHR has led Kenya’s most ambitious community-level TB incidence reduction programmes through a series of TB Impact studies conducted in partnership with the Ministry of Health and the County Government of Kisumu. The overarching aim: to measure whether a best-practice package of active case-finding and prevention interventions — implemented at county scale — could achieve a measurable, sustained decline in TB incidence.

The results from TB Impact 1 and 2 (2016–2019) were compelling. Over the intervention period, CGHR teams approached 1,156,042 persons entering 204 health facilities in Kisumu County, screening all for TB symptoms. A total of 104,042 (9%) were found to be symptomatic; 84,274 (81%) of these had sputum tested by GeneXpert. Bacteriologically confirmed and clinical TB cases detected numbered 4,251 and 2,804 respectively, with 6,985 (99%) initiated on treatment. In addition, the programme identified 1,038 previously undiagnosed HIV cases — patients who would otherwise have entered the health system only when severely ill.

This integrated, systematic approach to active case finding — linking TB screening with HIV testing and treatment initiation — is the model that Kenya’s National TB Programme piloted for rollout across 10 counties following KEMRI CGHR’s evidence. TB Impact 3, proposed for 2020–2025, builds on these foundations, adding isoniazid preventive therapy (IPT) initiation and 3HP treatment for latent TB infection as active components of a comprehensive elimination strategy.

Clinical Trials: Generating the Drug Evidence That Will Shorten TB Treatment

Alongside its diagnostic and programmatic work, KEMRI CGHR’s TB Division is an active site for international clinical drug trials conducted through the TB Clinical Trials Consortium (TBTC) — which the Division joined in 2010 — and the AIDS Clinical Trials Group (ACTG). Key contributions include:

• Study 29X: A randomised, partially blinded dose-ranging study of rifapentine for pulmonary TB treatment. Results showed that high rifapentine exposures were associated with high levels of sputum sterilization at the end of the intensive phase — an important finding for treatment shortening research.
• TBTC Study 31 / A5349: A Phase III randomised controlled trial evaluating rifapentine-containing treatment shortening regimens for pulmonary TB. KEMRI CGHR enrolled participants and contributed to the multisite evidence base for this pivotal study.
• A5279 (ACTG): A landmark Phase III trial of ultra-short-course rifapentine/isoniazid for prevention of active TB in HIV-infected individuals with latent TB infection. The study’s landmark finding — that 4 weeks of isoniazid and rifapentine worked as well as 9 months of isoniazid — was a major breakthrough for TB preventive therapy.
• Brief Bactericidal Activity (BBA) studies: Designed to inform management of MDR-TB patients by assessing the antimicrobial activity of anti-TB drugs, with the aim of informing regimen selection based on timely drug susceptibility testing.

These trial participations position KEMRI through CGHR as a direct contributor to the global evidence base for new TB drugs and regimens — work that ultimately benefits Kenyan patients as new treatment guidelines incorporate trial findings.

The NTM Challenge: Addressing TB’s Shadow Epidemic

As Kenya’s TB response matures, a parallel and significantly under-recognised challenge has come into the clinical foreground: the rising burden of Non-Tuberculous Mycobacteria (NTM). These are environmental mycobacteria — organisms distinct from Mycobacterium tuberculosis — that can cause pulmonary disease clinically indistinguishable from TB. They are increasingly prevalent in immunocompromised individuals, particularly people living with HIV, and in persons with structural lung disease.

NTM infections are not TB. Treating them with standard anti-TB drugs is not only ineffective — it is potentially harmful, causing drug toxicity without therapeutic benefit, and consuming medicines that should reach true TB patients.

KEMRI CGHR’s TB Laboratory has established a robust quality management system that includes routine monitoring of both M. tuberculosis and NTM culture positivity rates. Building on this surveillance infrastructure, the Laboratory has conducted targeted NTM research to characterise the true burden of NTM disease in western Kenya and — critically — to perform mycobacterial speciation: the precise species-level identification of NTM isolates.

Speciation transforms the clinical picture. Rather than a generic “mycobacterium detected” result that could trigger empirical anti-TB therapy, the clinician receives a specific species identification — for example, Mycobacterium avium complex, Mycobacterium kansasii, or Mycobacterium abscessus — enabling selection of the appropriate targeted antibiotic regimen for that species. This precision approach prevents misdiagnosis, avoids unnecessary anti-TB drug exposure, optimises treatment, and preserves TB programme resources for patients with true tuberculosis.

KEMRI CGHR’s NTM speciation work is a direct clinical service to Kenya’s health system — identifying a problem that is growing but remains poorly measured, and providing the diagnostic tools that clinicians need to manage it correctly.

Looking Forward: Science, Systems, and the People We Serve

The 2026 World TB Day theme — Yes! We Can End TB! Led by Countries. Powered by People — is not an aspiration for the distant future. It is a description of what is already happening in western Kenya.

Countries are leading. Kenya’s National TB Programme and the county governments in Nyanza, Western, and South Rift are making data-driven decisions about retreatment protocols, diagnostic rollouts, and active case-finding strategies — decisions informed in no small part by KEMRI CGHR’s TB research evidence.

People are powering the response. The community health workers who conduct household contact investigations. The laboratory technicians who process 2,500 MDR-TB specimens a year. The clinicians who now reach for a nasopharyngeal swab rather than subjecting a five-year-old to gastric lavage. The patients who complete treatment under community-based directly observed therapy. Each of these is an expression of the theme in action.

And the science continues. From sputum pooling that stretches every cartridge budget, to GeneXpert Ultra validation that reaches HIV-positive patients with lower bacillary load, to NTM speciation that prevents costly misdiagnosis — KEMRI CGHR’s TB Division remains committed to generating research that serves people where they live.

Yes, we can end TB.

And at KEMRI CGHR, the work of ending it, is already underway.

ABOUT THE AUTHOR

Dr. Steve Wandiga is the Head of the Tuberculosis Division and a Principal Research Scientist at the KEMRI Centre for Global Health Research (CGHR), and acting Deputy Director of Infectious and Parasitic Diseases Research Programme at KEMRI. He has been the KEMRI Principal Investigator for US CDC, US NIH, EDCTP, UNITAID/LSTM-funded TB research collaborations and leads the TB Division’s programmatic and scientific agenda across diagnostic development, clinical trials, active case-finding, and laboratory systems strengthening.

Acknowledgements: The KEMRI CGHR TB Division gratefully acknowledges the support of the study participants, communities, U.S. Centers for Disease Control and Prevention (CDC/DGHT), the U.S. National Institutes of Health (NIH/DAIDS), the European and Developing Countries Clinical Trial Partnerships (EDCTP), UNITAID/Liverpool School of Tropical Medicine (LSTM), AMREF, HJFMRI, the Ministry of Health, National TB Programme, and the County Governments of Kisumu, Siaya, and partner counties in Nyanza, Western, and South Rift. We recognise our TB Division colleagues — Albert Okumu, Janet Agaya, Benard Owuor, Irene Omondi, Josephine Awino, laboratory, clinic and community teams — without whom none of this work would be possible.