Current scenario of TB diagnosis and what the future holds?

‘So much done; yet, so much to achieve!,’ Tuberculosis (TB) is still looming as a major global concern, being the 2nd leading infectious killer after COVID-19 (above HIV/AIDS). Almost 1.5 million people lost their lives to TB in 2020 and an estimated 10 million fell ill worldwide; including 5.6 million men, 3.3 million women and 1.1 million children. Individuals infected with TB bacteria, have a 5-10% lifetime risk of falling ill with TB, and immunocompromised individuals (people with HIV, malnutrition, diabetes, or using tobacco) have greater risk of contracting the disease [1].

More than 95% of the cases and higher mortality are witnessed in developing countries, affecting people of all age, reducing the productivity of the nation. India leads amongst the countries accounting for 2/3rd of the global TB cases, followed by China, Indonesia, the Philippines, Pakistan, Nigeria, Bangladesh and South Africa. Growing Multidrug-resistant TB (MDR-TB) cases have only increased the disease burden worldwide [1]. These patients do not respond to isoniazid and rifampicin (the 2 most-effective first-line anti-TB drugs). Treating MDR-TB is complex and quite expensive, primarily due to its association with important adverse events in patients. The success rate of treatment lowers from 83% in patients having newly diagnosed or relapse non-DR-TB receiving first-line therapy to 54% in MDR-TB patients, to 30% in extensively DR-TB (XDR-TB- showing resistance to at least one fluoroquinolone and one second-line injectable agent) patients [2]. 

Early and comprehensive detection of TB and MDR-TB is the call of the hour and over the recent decades, many techniques have been devised to tackle this issue. The gold standard for TB diagnosis is culture –drug sensitivity test (CDST); however, due to its time-consuming nature, several major alternatives were devised like line-probe assays, real-time PCRs, GenXpert (Xpert) [2]. The line-probe assays, although simple, quick and easy-to-perform, requires expensive equipment, whereas real-time PCRs despite of lesser contamination chances and rapid results, require specific equipment and skilled technicians [2]. Xpert MTB/RIF, which is a rapid molecular-based test endorsed by WHO, based on cartridge-based assay has revolutionized the TB diagnosis and can detect MTB complex and RIF resistance, using semi-quantitative nested real-time PCR for amplifying hotspot region of the rpoB gene. It has remarkable sensitivity (100%) and specificity (99%) for smear-positive samples and 67% sensitivity and 99% specificity for smear-negative samples, as compared to CDST. Xpert has been very valuable in tackling TB burden in low- and middle-income countries, with turnaround time (TAT) being <2hours [2] , with Xpert Ultra, adding more value, thereby increasing the sensitivity, especially in paucibacillary TB including tuberculous pleurisy, tuberculous meningitis and paediatric TB [3] as well as in pulmonary and extra-pulmonary TB [4]. XpertUltra is a 10-channel upgradation of classic Xpert MTB/RIF, with information regarding second-line injectable drugs (SLIDs) and 98-100% specificity[5] however most of the SLIDs are not recommended in the current treatment protocols longer. Despite these advantages, mutations linked with isoniazid resistance could be missed by Xpert and thus warrants other tests CDST for confirming. The higher cost also makes it unaffordable in many high-burden countries, along with need for constant electric supply and sensitivity to heat and dust adding to the challenges [2].

Some of these issues can be effectively addressed by using sequencing technology, especially next generation sequencing (NGS), which can rapidly analyze the entire genome, allow species identification, screen all mutations, detecting drug resistance and predicting evolution of organism. Whole Genome Sequencing (WGS) screens the entire genome using high-end sequencing technique, spanning entire genome, to trace the culprit gene/mutation causing TB or drug resistance. It is more advantageous, as it gives greater genome coverage (not only the target region),  increased epidemiological information and understanding of new resistance mechanism for both existing and novel drugs [2]. WGS can assist in efficient prediction of treatment outcomes and resistance profiles of all anti-TB drugs in a single run with rapid results [6]. Poly-microbial infections (mixed and co-infections) can cause misidentification of strains and underestimation of disease transmission, resulting in poor treatment outcomes [7]. Susceptibility profile of drugs like pyrazinamide can be achieved with WGS, which can help in shortening the treatment regimen. WGS can provide high resolution in investigating disease transmission outbreaks, influence early decision of optimum drug therapy and improve patient outcomes [8]. WGS was found to be 7% more cost-effective and consistent in performance as compared to DST [9, 10].  

With the advent of WGS, there has been a revolutionary change in TB diagnosis, which can facilitate rapid and timely diagnosis and thereby appropriate treatment for the patients. Disruption in the transmission outbreaks can speed-up the path towards TB elimination, a goal definitely nurtured by all!

Reference:

1. W.H.O. Tuberculosis. 2021.[Internet]. https://www.who.int/news-room/fact-sheets/detail/tuberculosis. 
2. Nyugen TNA, Anton-Le Berre V, Bañuls AL, Nguyen TVA. Molecular Diagnosis of Drug-Resistant Tuberculosis; A Literature Review. Front Microbiol. 2019 Apr; 10: 794.  201. doi: 10.3389/fmicb.2019.00794.
3. Jiang J, Yang J, Shi Y, Jin Y, Tang S, Zhang N, et al. Head-to-head comparison of the diagnostic accuracy of Xpert MTB/RIF and Xpert MTB/RIF Ultra for tuberculosis: a meta-analysis. Infectious Diseases. 2020;52(11): 763-775. http://doi.org/10.1080/23744235.2020.1788222. 
4. Zhang M, Xue M, He J. Diagnostic accuracy of the new Xpert MTB/RIF Ultra for tuberculosis disease: A preliminary systematic review and meta-analysis. Int J Infect Dis. 2020; 90:35-45. doi: 10.1016/j.ijid.2019.09.016.
5. Penn-Nicholson A, Georghiou SB, Ciobanu N, Kazi M, Bhalla M, David A, et al. Detection of isoniazid, fluoroquinolone, ethionamide, amikacin, kanamycin, and capreomycin resistance by the Xpert MTB/XDR assay: a cross-sectional multicentre diagnostic accuracy study. Lancet Infect Dis. 2021; S1473-3099(21)00452-7. doi: 10.1016/S1473-3099(21)00452-7.
6. He G, Chen X, Chen J, Zhang W. Prediction of treatment outcomes for multidrug-resistant tuberculosis by whole-genome sequencing. Int J Infect Dis. 2020 Jul; 96:68-72. doi: 10.1016/j.ijid.2020.04.043.
7. Advani J, Verma R, Chatterjee O, et al. Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates From India Reveals Genetic Heterogeneity and Region-Specific Variations That Might Affect Drug Susceptibility. Front Microbiol. 2019 Feb 26; 10:309. doi: 10.3389/fmicb.2019.00309.  
8. Katale BZ, Mbelele PM, Lema NA, Campino S, Mshana SE, Rweyemamu MM, et al. Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania. BMC Genomics (2020) 21:174 https://doi.org/10.1186/s12864-020-6577-1. 
9. World Health Organization. Meeting report of the WHO expert consultation on the definition of extensively drug-resistant tuberculosis. 2020.
10. CRyPTIC Consortium and the 100,000 Genomes Project, et al. Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing. N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474.