Navigating TB eradication in Africa by fighting drug resistance with Genomics

By Belinda Ngongo

Despite the advancements in tuberculosis (TB) surveillance and genomic sequencing technologies, the disease continues to be a global health crisis, with an excess of 10.6 million people contracting the bacterial infection in 2022. Within the same year, over 3 million people suffering from TB died. According to the Africa World Health Organisation (WHO) 2023 report, Africa alone accounted for 23 percent of all new cases, with 31 percent of TB-related deaths, despite only constituting 15 percent of the world’s population.

Read also: One Nigerian dies of tuberculosis every 5 minutes — NTBLCP

TB mainly affects the lungs and is caused by Mycobacterium tuberculosis. The illness thrives in tight and poorly ventilated spaces where it enters through the respiratory system, usually with no noticeable symptoms. It can develop quickly within months or slowly over years. This sometimes-slow onset of symptoms, coupled with a lack of knowledge of the disease, has accelerated the development of drug-resistant strains of TB, resulting in severe barriers to successful treatment. Many patients across the continent lack access to crucial healthcare services, and they often have little to no knowledge about TB’s symptoms and treatment options. In poor communities, where access to services and good nutrition is especially lacking, people living with TB are unlikely to seek and finish treatments.

Although TB is treatable, according to the WHO, the biggest public health threat is drug-resistant TB (DR-TB), meaning mutations in the bacteria are becoming increasingly resistant to the two most powerful anti-TB antibiotics, rifampicin and isoniazid.

Treatment of multi-resistant TB requires treatment courses that are longer, less effective, and far more expensive than those for non-resistant TB. Globally, on average, less than 60 percent of those treated are successfully cured. WHO estimates in 2022 that there were 410 000 cases with resistance to rifampicin at the global level and 62 000 in the African region.

To help combat this trend, the WHO has included in its recommendation to fight TB the use of targeted Next Generation Sequencing (NGS), which promises greater accuracy and speed in identifying drug-resistant TB. This is beneficial to national TB programmes in Africa as it can ultimately reduce the risk of transmission and give information on which strains of bacteria are circulating.

The landscape and prevalence in Africa: Nigeria, Kenya, and South Africa

The prevalence of TB is relatively high on the continent, with Nigeria, Kenya, and South Africa being the most heavily impacted by the disease. In 2021, Nigeria ranked first on the African continent and sixth in the world in terms of TB prevalence. In 2023, the country had 300 000 diagnosed cases of TB, which was an improvement from the 467 000 incidents in 2021, wherein 125 000 people died from the disease.

According to the WHO, Kenya had a 32 percent decline in TB-related incidents during 2020, which saw the country reach its WHO “End TB Strategy” milestone for 2020, evidence that the strategy to reduce the number of TB cases is in fact working.

Although TB cases in South Africa have also decreased by 53 percent between 2015 (552 000) and 2022 (280 000), according to a study conducted by The Lancet, the country’s TB burden has been listed in the top 30 by the WHO, with one of the highest incident rates of reported cases in the world.

These numbers indicate that interventions are being implemented to lower infections in these three countries specifically. The challenges that the continent is facing to combat TB present opportunities to seek alternative methods of detection, surveillance, treatment, and multi-drug-resistant options, such as Next Generation Sequencing. NGS has been shown to enable accurate and high-throughput decoding of TB genetic information. It is a fast, sensitive, scalable, and culture-free drug susceptibility testing method that provides a comprehensive anti-TB drug resistance profile.

Routine TB drug resistance surveillance and drug-susceptibility testing (DST) are critical to combating the global TB epidemic. DST helps determine appropriate TB treatment regimens. Previous methods, such as culturing the mycobacteria that cause TB, can be slow and take about a month to see what treatments are effective against the disease. With NGS, this can be done within days.

Read also: Delta demands collective efforts against tuberculosis

Crucial statistical information provides medical researchers and healthcare workers with critical data that can help address gaps in the management and treatment of this disease. By stressing detection in underserved communities, improving patient support through the development of personalised medicines through genomic sequencing, helping to increase adherence to treatments, and most importantly, by closing the disease knowledge gap by creating awareness in previously hard-to-reach areas to foster understanding and impact of the disease, countries can further reduce the impact of this disease on their populations.

In the quest to eradicate TB and its various drug-resistant strains, scientists across the globe need to be equipped with cutting-edge technologies such as NGS. This means that innovations need to have the capacity to accurately detect, analyse, and characterise TB strains across the board.

Through NGS, genomic-based TB surveillance is possible and empowers medical scientists with the ability to not only detect TB and characterise anti-TB drug resistance, but equally enhance the monitoring of the evolution and subsequent mutation of DR-TB to develop new treatments, which are critical for elimination.

A future-fit solution: Genomics sequencing and NGS for TB eradication

Innovations such as NGS, a technology used for DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) sequencing to track genetic mutations, boast the capacity to isolate genetic materials associated with the presence of multi-drug-resistant TB (MTB) and anti-drug TB resistance, advancing the field of research.

NGS involves the sequencing of large amounts of small DNA fragments simultaneously while improving workflows for precisely detecting TB for drug resistance profiling. Subsequently, the applications of NGS towards the eradication of the disease are infinite and provide a crucial solution for the surveillance of TB within public health.

By harnessing the power of genomics, the medical industry can usher in a new era of precision medicine, where treatment decisions are informed by the unique genetic profiles of patients and their infecting strains. However, realising the full potential of NGS necessitates sustained investments in research, capacity-building, and equitable access to technology, particularly in regions hardest hit by the disease.

In the quest to successfully roll out sequencing technologies and help fight the eradication of TB, it is prudent to have technological partners that are at the pioneering end of scientific discovery. Illumina, whose technology, together with scientific partners on genomic sequencing and TB surveillance, has helped accurately assess drug-resistant markers for and beyond the scope of TB.

Belinda Ngongo- Director, Global Health External Affairs, Illumina