New genomic test reveals hidden drug-resistant tuberculosis in Eswatini
Targeted sequencing identifies dangerous tuberculosis strains missed by routine diagnostic tests and informs life-saving treatment decisions.
Electron micrograph of Mycobacterium tuberculosis.
Researchers in Eswatini, in collaboration with an international consortium, have made a significant breakthrough in tuberculosis (TB) diagnostics. Using targeted genome sequencing, they detected drug-resistant strains of TB that had previously been overlooked by conventional tests. Their findings, published in the journal Nature Communications, reveal an underestimated gap in tuberculosis control in southern Africa and open up new possibilities for better treatment of affected patients.
The study examined the use of “targeted next-generation sequencing” (tNGS) as part of routine tuberculosis care in Eswatini, a country with a high burden of multidrug-resistant tuberculosis (MDR-TB). This method enables a detailed analysis of the genetic characteristics of pathogens directly from patient samples, thereby providing significantly more comprehensive information on drug resistance than standard tests.
The results show that a particularly problematic form of rifampicin-resistant tuberculosis, caused by the rpoB I491F mutation, is often not detected by routine diagnostic tests. This leads to a significant underestimation of drug resistance and poses a major risk of inadequate treatment.
“Accurate resistance testing is the foundation of any successful TB treatment,” says project coordinator Prof. Stefan Niemann, director of the Infections program area at the Borstel Research Center, Leibniz Lung Center, and deputy coordinator of the Tuberculosis research area at the German Center for Infection Research (DZIF). “Our results show that many patients who were initially classified as having lower levels of resistance actually harbored multidrug-resistant strains that were not detected by conventional diagnostic methods.”
Hidden resistance revealed
Between June 2021 and December 2024, researchers analysed 234 patient samples from individuals with suspected drug-resistant TB or treatment failure. Using tNGS, the team identified rifampicin resistance in 159 TB strains. Remarkably, nearly two-thirds of these strains carried the rpoB I491F rifampicin resistance mutation, a well-known “diagnostic escape” mutation that is poorly detected by several widely used diagnostic assays.
Even more concerning, the study found high levels of resistance to bedaquiline, one of the most important drugs used in modern MDR-TB treatment regimens. Genetic markers associated with bedaquiline resistance were detected in more than half of all rifampicin-resistant strains and in 85 percent of strains carrying the rpoB I491F mutation.
“These findings suggest that a substantial proportion of patients may be receiving treatment regimens that include drugs to which their infecting strain is already resistant,” said Debrah Vambe of the Baylor College of Medicine Children’s Foundation Eswatini, the study’s first author and principal investigator in Eswatini.
Graphical overview of the study design, key findings, and clinical implications of targeted next-generation sequencing (tNGS) for tuberculosis drug resistance detection in Eswatini.
Direct impact on patient care
The introduction of tNGS had an immediate clinical impact. Sequencing results prompted treatment modifications in more than half of the patients for whom detailed clinical information was available. Despite the complexity of the resistance patterns observed, treatment success was achieved in 88 percent of these patients, demonstrating the value of comprehensive resistance testing for guiding individualized therapy.
Implications for global TB control
The study raises important questions about current approaches to diagnosing and classifying drug-resistant TB. Because routine diagnostic tools may fail to identify rpoB I491F-associated rifampicin resistance, patients can be incorrectly classified and treated. The frequent co-occurrence of rifampicin and bedaquiline resistance also challenges the effectiveness of standardized treatment regimens such as BPaLM in settings where these strains are prevalent.
The researchers argue that broader implementation of sequencing-based diagnostics could significantly improve the detection of drug resistance and help prevent treatment failure, ongoing transmission, and the further emergence of resistance.
As countries increasingly adopt genomic technologies for infectious disease surveillance, the experience from Eswatini demonstrates how targeted sequencing can close critical diagnostic gaps and support more effective, personalized TB care.
Key findings
- Targeted next-generation sequencing identified rifampicin resistance in 159 TB strains.
- Sixty-four percent of rifampicin-resistant strains carried the diagnostic escape mutation rpoB I491F.
- Bedaquiline resistance-associated mutations were detected in 55 percent of rifampicin-resistant strains.
- Routine diagnostic tests substantially underestimated the burden of multidrug-resistant TB.
- Sequencing results led to treatment changes in 53 percent of patients.
- Treatment success was achieved in 88 percent of patients with available outcome data.
The findings underscore the growing importance of genomic technologies for tuberculosis diagnosis, surveillance, and treatment, particularly in regions where highly drug-resistant strains continue to emerge and spread.
Participating organisations
The study was conducted through an international collaboration involving researchers from the Baylor College of Medicine Children’s Foundation Eswatini (Mbabane, Eswatini), the Global TB Program at Baylor College of Medicine (Houston, USA), the National Tuberculosis Reference Laboratory, Eswatini Health Laboratory Services, Ministry of Health (Mbabane, Eswatini), the National TB Control Program (Manzini, Eswatini), the Research Center Borstel, Leibniz Lung Center (Germany) and German Center for Infection Research (DZIF, Germany), as well as partner institutions from Eswatini, Europe, and the United States.
Source: Press release of Research Center Borstel, Leibniz Lung Center
