Stellenbosch University Study Aims to Expedite Drug-Resistant TB Diagnosis

Drug-resistant tuberculosis (DR-TB) is a global health threat due to high mortality, cost of treatment and risk of transmission. In 2021, there were an estimated 450 000 cases of DR-TB worldwide and 191 000 deaths. South Africa has one of the highest numbers of drug-resistant patients globally, but shockingly only 50% of these patients are started on treatment.

“Drug-resistant TB threatens to derail the World Health Organisation’s (WHO) END-TB strategy that aims to eradicate the disease globally by 2035. We therefore need new and improved methods for diagnosing DR-TB in the shortest possible time to curb transmission, improve treatment and save lives,” says Dr Brigitta Derendinger from the Clinical Mycobacteriology and Epidemiology (CLIME) Group in the Division of Molecular Biology and Human Genetics at Stellenbosch University’s (SU’s) Faculty of Medicine and Health Sciences.

Derendinger, who recently obtained her doctorate at SU, examined ways in which existing tests to diagnose DR-TB could be improved. She also characterised the programmatic emergence (non-clinical trial patients) of bedaquiline resistance – the first new TB drug in almost 40 years –​ in high-risk patients. Bedaquiline is part of injectable-free treatment regimens for drug-resistant TB.

Derendinger points out that Xpert MTB and RIF Ultra are some of the most widely used tests for the diagnosis of TB and drug resistance, but a second sputum is still needed to verify resistance to rifampicin, which is frequently prescribed to treat TB, and to diagnose second-line resistance. In addition, two WHO-endorsed molecular tests (MTBDRplus and MTBDRsl) are done routinely to confirm a drug-resistant diagnosis and to further diagnose resistance to other drugs.

“Since the roll-out of Xpert, Ultra and MTBDRplus in South Africa, the time from the initial diagnosis of multi-drug-resistant TB to when the patient starts to receive treatment has shortened, but this process is still long.

​“Furthermore, many countries with a high TB burden lack the biosafety and infrastructure for the extraction of DNA and additional molecular testing. There is, therefore, an urgent need to reduce these diagnostic delays and develop or improve rapid molecular methods to help minimise the reliance on the collection of a second sputum sample.”

To help address these shortcomings, Derendinger extracted DNA of Mycobacterium tuberculosis (the bacterium that causes TB) from used Xpert cartridges (cartridge extract – CE) that would otherwise be discarded by laboratories. She showed this by doing first (MTBDRplus)- and second-line (MTBDRsl) TB drug testing from the CE collected from this one cartridge, thus allowing a quicker diagnosis of DR-TB and negating the need to collect a second specimen.

“We* have identified ways to reduce the need for collection of a second sputum sample, thereby potentially reducing the time it takes to make a diagnosis from weeks to a few days. A quicker diagnosis will mean that patients can be placed on treatment sooner.

“We have identified thresholds to implement to ensure that no test needs to be wasted on CE likely to give an invalid result. This has profound implications, especially in countries like South Africa where patients often do not return to give a second sputum or simply cannot produce one to confirm the diagnosis of drug-resistant TB.

“We also found that by correcting a parameter used in the MTBDRplus and MTBDRsl tests, we can diagnose more patients with DR-TB and place them on effective treatment,” adds Derendinger.

Regarding bedaquiline, she says it is being scaled up rapidly but largely in the absence of TB drug testing.

“The WHO recommends TB drug testing to be done on all patients receiving bedaquiline and to monitor their treatment, but this is not done regularly in South Africa and only a few centralised laboratories have the capacity to do so which causes diagnostic delays.

“Clinical bedaquiline resistance is emerging but the data is scarce, especially in settings where patients are more likely to experience delays and drug shortages, receive less support, and are monitored even less than patients on clinical trials.

“Consequently, these patients can be non-adherent and failing treatment regimens are less likely to be detected, therefore resistance is more likely to be acquired and later transmitted in these settings.”

Derendinger emphasises the need to optimise established molecular drug-resistant TB tests and development of new drug-resistant TB tests to monitor resistance to new drugs like bedaquiline to curb the delayed diagnosis and ongoing transmission.

She says the findings of her study have informed WHO course training material and been incorporated into global laboratory performance and quality assessments.