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Review Article
162 (
1
); 15-27
doi:
10.25259/IJMR_527_2025

Reliable, accessible, cost-effective, & easy (RACE) diagnostic modality: A key for elimination of tuberculosis

Aarupadai Veedu Medical College, Vinayaka Mission’s Research Foundation (Deemed University), Puducherry, India
Advanced Centre for Chronic and Rare Diseases, New Delhi, India
Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
Department of Biological Sciences, Indian Institute Science Education and Research, Bhopal, Madhya Pradesh, India

For correspondence: Prof Sarman Singh, Advanced Centre for Chronic and Rare Diseases, New Delhi 110 068 & Former Director, All India Institute of Medical Sciences, Bhopal 462 020, Madhya Pradesh, India e-mail: sarman_singh@yahoo.com

Licence
This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-Share Alike 4.0 License, which allows others to remix, transform, and build upon the work non-commercially, as long as the author is credited and the new creations are licensed under the identical terms.

Abstract

Tuberculosis (TB) is still a major health concern. However, each year more than one-third of all global TB cases remain undetected and unreported. On top of that, emergence of drug-resistant TB poses a major challenge. Therefore, a Reliable, Accessible, Cost-Effective, and Easy (RACE) diagnostic modality is crucial for starting suitable treatment of TB and curtailing its transmission. In the last two decades, several advances have been made for improved diagnosis, which include liquid culture and drug susceptibility testing (DST), line probe assay (LPA) for drug resistance detection at the molecular level, and cartridge-based nucleic acid amplification tests (CBNAAT) for rapid diagnosis of TB and rifampicin resistance detection. Newer drugs and treatment regimens have been introduced and vaccines are in the pipeline. Despite these advances and opportunities, a precise, affordable, and accessible diagnostic model is yet to be evolved, especially in rural and difficult-to-reach areas, where the most desirable test would be a test that is easy to perform, accessible to masses, is cost-effective, besides being reliable. Only a point-of-care triage test can meet these requirements, which can be used by an unskilled or minimally trained healthcare worker or even by the patient (self-testing). This test should be able to detect all forms of tuberculosis and latent TB infection. Currently, no such test is available. In this narrative review, we will discuss how such a diagnostic modality can help eliminate TB.

Keywords

CBNAAT
PCR
point-of-care test
serology
TB elimination

Tuberculosis (TB) is a chronic infectious disease of humans, caused by an aerobic gram-positive acid-fast bacillus known as Mycobacterium tuberculosis (MTB). According to the Houben et al1, approximately 26 per cent of the world’s population is estimated to be infected with MTB, however, it remains dormant under the host defence system in majority of the exposed individuals2,3. Every year more than 10 million incidental cases of TB with approximately three million deaths are occurring world-wide4. In India, almost every three minutes two deaths are occurring due to TB. It is also imposing a financial burden on our economy and future developmental goals.

The World Health Organization (WHO) is committed to end tuberculosis by 20304 while some countries like India have proactively advanced this goal to end tuberculosis by this yearend. Though ending tuberculosis from India by this year-end and from the world in next five years seem herculean tasks, various Government organs are working on various fronts5. Early diagnosis using portable chest x-rays and molecular tests with shortest turnaround time (TAT), early and accessible drug susceptibility testing and free medication with nutritional supplementation are some of these efforts being made by the Government in this direction. Furthermore, recent endorsement of WHO for shorter duration all oral drug treatment for multi-drug resistant TB is another global effort to control this highly infectious disease6. An effective anti-TB vaccine is extremely important, considering that a century old BCG is still the only available and effective vaccine even though more than 32 vaccines are in developmental pipeline7,8.

It is felt that no single approach, how advanced it could be, will be able to end TB at least by 20305,9,10. In this article, we would like to invite attention of readers towards the role of early and rapid diagnostic tests preferably in a triage module and how this approach can help early elimination of TB. We shall put forth this argument that if the timely detection of TB infection at affordable cost, with reliable accuracy is not made available to the population, especially those living in high TB burden countries, people will continue to spread the infection, and prophylactic measures may not be of much help.

Therefore, financial support for research to develop novel cost-effective tests for early diagnosis cannot be undermined. A number of new advances in the diagnostics are being made and implemented by respective national TB elimination programme implementing agencies are reviewed elsewhere11-18, hence this review will remain restricted to highlighting the recent advancements made international and nationally. Many of these are not yet approved or rolled out in the national programme. This update also emphasizes on futuristic screening and diagnostic tests including the clinical examination, imaging analyses, smear-microscopy, mycobacterial culture, molecular and immunological tests. All these diagnostic modalities must adhere to the standards like high yield, turn-around-time, sensitivity, specificity, predictive values, reproducibility, cost-effectiveness, safety, non-cumbersomeness, robustness, and easy roll out for wider use18.

Conventional methods of diagnosis

In the recent past, several advancements have been made in the field of diagnostic methods, including the artificial-intelligence and machine-learning (AI-ML) in recording, storing and transporting the patient data from one place to another. The AI-ML has become major components of digital-health and carry a great future in resolving several limitations.

Radio-imaging modalities

The conventional age-old X-ray chest examination still remains the most commonly used method for screening and preliminary diagnosis as well as for follow up of the pulmonary tuberculosis (PTB patients on anti-tuberculous treatment (ATT). In many forms of extra pulmonary tuberculosis (EPTB) such as Bone TB, role of X-ray cannot be undermined. However, technology has limited specificity. Newer radiographic tools including the use of digital plates and digital radiography obviating the need of dark rooms and more recently the computer-aided diagnosis (CAD) have revolutionized the TB diagnosis and management13,14. In a recent study, newer versions of five commercial AI algorithms: the ‘qXR’’ ‘CAD4TB’, ‘L unit INSIGHT CXR’, ‘JF CXR-1’, and ‘InferRead DR’, were compared to find their sensitivity and specificity. These advances helped precise and early identification of parenchymal lesions or enlargement of mediastinal lymph nodes (LN) and to determine the disease activity. All the five AI algorithms, as mentioned above, reduced the need of Xpert/MTB-Rif tests by 50 per cent while the sensitivity of more than 90 per cent was maintained. However, AI algorithms performed poorly among the older age groups and people with a past history of TB19. Qin et al20 further evaluated 12 CAD products available in the market of South Africa and found that ‘Lunit’, ‘Nexus’, ‘JF CXR-2’, and ‘qXR’ maintained high sensitivity of >90 per cent for pulmonary TB requiring confirmatory diagnostic testing in only a few cases. However, all products including the WHO endorsed products showed poor performance in older individuals, people with previous TB, and people living with HIV (PLWH)20.

Recently, sequential pulmonary ‘18F-2-fluoro-deoxy-D-glucose (18F-FDG) positron emission tomography (PET)’ was compared with the ‘high-resolution-computed-tomography (HRCT)’ and the results were encouraging. This non-invasive method was found useful in monitoring the disease activity and responses to ATT. It is well known that F-FDG accumulates in the metabolically active cells, including the inflammatory cells including macrophages, neutrophils, and lymphocytes, are typically involved in active lesions of TB. Combining ‘18F-FDG positron emission tomography (PET)’ with CT imaging (PET/CT) has a bright future in TB treatment monitoring. Although expensive, this technique could be useful for the management of patients with dreaded form of TB such as MDR and XDR-TB. Data from multiple cohorts have demonstrated that PET glycolytic activity decreases in response to effective TB treatment which means that it can predict the treatment outcome with high precision21.

India has made several breakthroughs in the field of TB, and a software developed by Qure.ai®22 is another breakthrough which India can boast. An Artificial Intelligence (AI) solution disrupting the conventional methods of radiodiagnosis has been developed by enhancing the image accuracy and thereby improving the health outcomes. With ever improving machine-learning tools, accuracy is expected to increase further. Qure.ai uses ‘deep-learning’ technology to provide automated interpretation of radio-imaging platforms like X-rays, CTs and ultrasounds scans enabling faster diagnosis and speedy treatment22. Efforts are underway by Indian Council of Medical Research (ICMR), FIND and Stop TB Partnership to compile a database of paediatric X-rays to develop CAD algorithms for children and to validate the accuracy of CAD. ‘Artificial intelligence and Machine Learning (AI and ML)’ tools have been developed jointly by ICMR, Department of Health Research and Department of Atomic Energy, Government of India for screening of pulmonary TB and other lung diseases using CxR images, with high accuracy in differentiating pulmonary TB and other diseases (personal communication). Once these tools and software are validated on patients of TB and other diseases, added with portable X-ray machines, can be the game changer. The literature suggests that CAD systems could be highly useful tools for TB screening programmes in difficult-to-reach areas where physical access to expert radiologists may be a limiting factor. However, more large-scale prospective studies, preferably random clinical trials (RCTS) are needed to address long awaited questions especially the operational feasibility of the CAD systems. The WHO, in the year 2021 recommended the use of CAD tools for TB screening among adults but did not include children in this recommendation due to low evidence of diagnostic accuracy among children.

Sample collection, processing and smear microscopy

Collection, storage and transportation of clinical samples is of paramount importance. In the previous decade various solid substrate such as glass slides, FTA cards, and Geno Cards have been evaluated for preserving the morphology and /or nucleic acids for molecular testing with similar detection rates as from fresh samples23.The molecular testing has also been found highly useful in archived samples, if stored at sub-zero temperature, where detection of MTB using conventional phenotypic methods was not possible when the sample was collected24.The morphological demonstration of the Mycobacteria has been possible with microscopic aids and even after a century, microscopy remains a rapid, cost-effective and easy method for diagnosing TB. However, there are two major concerns. One that microscopy cannot differentiate between the MTB from other non-tuberculous mycobacteria (NTM) and second that it lacks sensitivity (requiring 5000-10000 bacilli /mL of sample to get the positive results), giving false negative results, with low diagnostic yield, in paucibacillary situations11,12. The sensitivity of the smear-microscopy for the detection of acid-fast-bacilli (AFB) has marginally improved with fluorochromes like Auramine-rhodamine11.

Artificial-intelligence and machine-learning (AI and ML) in smear microscopy

AI-ML technologies are now being tried in the field of medicine with exponential number of applications particularly the image analysis or in the microscopy. In recent years, the ‘operator independent sputum smear-microscopy based on the ZEISS AxioScan®’ and other AI-ML based systems have been evaluated to detect and count the AFB automatically with 97 per cent sensitivity and 86 per cent specificity25.The scope is increasing every day and neural network software are being developed to develop algorithms for diagnosis and treatment prescription based on signs and symptoms entered in the system. However, such developments may not be very useful for resource limited countries and settings due to low literacy rate and inaccurate data entry, which may lead to wrong algorithmic output.

Culture and phenotypic drug susceptibility testing (pDST)

The culture isolation of MTB remains a highly sensitive diagnostic method, that permits practically 10 colony forming units (CFU) or live mycobacteria to grow to a visible colony on solid medium. In liquid cultures theoretically as low as single Mycobacterium can grow to give a positive signal, albeit with longer incubation period. The positive mycobacterial growth means almost 100 per cent specificity. Mycobacteria were first cultivated by Lowenstein in 1931 on egg base with malachite green along with other nutritional supplements and one year later Jensen made some modification in the medium after which the medium is renamed as Lowenstein-Jensen (L-J) medium. A few more modifications have been made in the composition of the medium, but the base still remains the whole egg or its yolk. The cultivation of Mycobacteria and doing anti-mycobacterial drug susceptibility on solid culture medium remained backbone of TB diagnosis for almost a century, but the process is time-consuming taking as long as six wk thus providing limited clinical value.

In 2007, WHO endorsed liquid cultures for the mycobacterial culture and drug susceptibility. Though there are a number of commercial liquid culture systems but BACTEC-MGIT960 system remains the gold-standard for the diagnosis of TB and drug susceptibility testing (DST)4,15,18,19,21,24.The MGIT 960 is also endorsed by the WHO. However, the culture based diagnosis has limitations of improved yet undesirably long turn-around-time (TAT) for 11-42 days, requirement of trained personnel, and level 3 biosafety laboratory environment15,18,19,21. A number of non-commercialized culture based methods have reported for drug susceptibility testing. These tests are useful in the early stages of mass screening and testing of new drugs, when the WHO endorsed culture based or molecular tests are yet endorsed by the WHO. However, these tests require biosafety precaution and cannot be used in peripheral laboratories. Some of the well-studied and reported tests in this category are ‘Microscopic Observation of Drug Susceptibility (MODS)’, ‘Nitrate Reductase Assay (NRA)’, ‘Calorimetric Redox Indicator (CRI)’, Fast-Flaque and thin-layer agar (TLA). Except the last two, these tests have been recommended by WHO provided stringent quality control, and only in reference laboratories9.

Molecular tools for TB diagnosis

Early diagnosis of TB was based on capturing and multiplying the nucleic acid and simultaneously detecting the mutations in drug-resistance genes of MTB with high sensitivity and specificity. These advancements have reduced the TAT significantly and thereby allowing the treating physician to initiate the treatment/preventive services within few days. Several molecular tests have now been endorsed by the WHO for early diagnosis of TB, which we will discuss in following sections.

Polymerase chain reaction (PCR)

This technology has been used for the diagnosis of TB since early 1990s26. In recent years various forms of PCR have been developed including multiplex PCR, that can detect genus and species specific amplicons, thereby differentiating MTB and NTM, in a single tube5,27. The conventional PCR requires agarose gel for detection of amplified products, and this limitation has been overcome by the development of real time PCR, in which the DNA amplification reaction could be monitored on the LED screen as the PCR runs on a real-time basis15,19,28. The quantitative real-time PCR (qRT-PCR) could be used for amplifying the DNA, but also for the RNA using the reverse-transcription technology. The technology provides quantification of the pathogen load in the given sample. There are several commercially available PCR kits, such as Cobas-TaqMan-based PCR, and these PCR platforms have shown high sensitivity and specificity for TB detection, and additionally detection of various other species of the mycobacteria, which is not possible by GeneXpert/MTB-Rif29.The details of these PCR systems are published extensively elsewhere.

GeneXpert®/MTB-RIF or Xpert®/MTB-RIF

During the terror threats in USA, the envelopes containing suspected anthrax, required identification of the pathogen with minimal manipulation of the samples. For this ‘Cepheid™ Inc. (USA)’ developed a new technology known as ‘cartridge-based-nucleic-acid-amplification test (CBNAAT)’ or GeneXpert29. These systems were deployed by the United States Postal Service in postal sorting facilities to detect anthrax in postal envelops. Because of possibility of bioterrorism, the application had to be an integrated, self-contained, and automated that could be operated with minimal technical expertise. Sputum samples from PTB patients also require separate processing of each sample for mycobacterial DNA extraction. The sample processing remains a major challenge for all types of PCRs. To overcome this challenge M/s Cepheid Inc. (USA) and Foundation for Innovative New Diagnostics (FIND), with financial support from the ‘National Institutes of Health (NIH), USA’, modified the technology and first time applied and evaluated for the diagnosis of TB on clinical samples in 201030.The unique features of this system include sample processing and DNA amplification in a single closed cartridge. The results are reported in 90 min, In addition, the system not only detects the MTB DNA in the sample with high accuracy, it also detects rifampicin resistance simultaneously. Here onward, Xpert/MTB-Rif would be used instead of GeneXpert/MTB-Rif, for convenience purposes.

The Xpert MTB/RIF was endorsed by WHO in 2010 for the diagnosis of TB and simultaneous rifampicin resistance detection16. After this endorsement the Xpert-MTB /Rif was rolled out by various national TB control programmes. The Indian Government rolled in the national TB control programme in 2013. Since than more than 4000 systems have been installed in Government and private sector laboratories with exceptional performance in PTB17 albeit low to very low (11%) in the paediatric PTB and in adult EPTB samples, especially in plural fluid31 the ascitic fluid32, CSF from suspected cases of TB menigitis33. The ‘lower limit of detection (LOD)’ of Xpert-MTB /Rif is estimated to be 113 ‘CFU/mL’ of the sample.

GeneXpert®/MTB-Rif Ultra or Xpert®/MTB-Rif Ultra

After thousands of clinical samples were processed in Xpert/MTB-Rif, some reports of its suboptimal performance and discordance with line probe assay and MGIT-960 culture DST started coming. Considering these reports, in 2017 Cepheid™ Inc. (USA) included probes for some additional genetic mutations and two new primers. The new system is named as Xpert/MTB-Rif Ultra which is claimed to have lower 16 CFU/mL LOD for MTB as compared to Xpert/MTB-Rif34. Both Xpert/MTB-Rif and Xpert/MTB-Rif Ultra are recommended by the WHO for TB diagnosis4. Several comparative studies have been conducted. In one study, the sensitivity of Xpert/MTB-Rif Ultra was found to be superior to that of Xpert/MTB-Rif (63 vs. 46%). However, this increased sensitivity came by compromising the specificity (93 vs. 98%) for patients with a past history of TB. But the performance of Xpert Ultra and the Xpert/MTB-Rif was similar in detecting the rifampicin resistance35. However, in a later study, Xpert/MTB-Rif Ultra was not found statistically superior to Xpert/MTB-Riff or the diagnosis of TB meningitis. The sensitivity of Xpert/MTB-Rif Ultra was reported to be only 38.9 per cent in HIV-uninfected adults versus 22.9 per cent by Xpert/MTB-Rif; while in HIV co-infected patients, the sensitivity rates were 64.3 per cent for Xpert/MTB-Rif Ultra and 76.9 per cent for Xpert/MTB-Rif36. In another study, while comparing the Xpert MTB/RIF Ultra with standard GeneXpert MTB/Rif and Truenat MTB on 211 extrapulmonary tuberculosis (EPTB) samples, the Xpert MTB/RIF Ultra exhibited the highest overall sensitivity (50%) for EPTB detection, outperforming the standard GeneXpert MTB/RIF (29.4%) and Truenat MTB (35.3%), with comparable specificity (96.2-87.8%) across all three assays. However, in comparison to composite reference standard the sensitivity of these tests was 98.2, 98.2 and 95.4 per cent, respectively37.

GeneXpert® MTB/XDR or Xpert® MTB/XDR

The WHO has considered rifampicin resistance a surrogate of multidrug resistant tuberculosis (MDR-TB). However, there are several report where rifampicin monoresistance (RR) is found and the isolate is susceptible to all remaining drugs. Along with increasing demand from users, the manufacturers considered it prudent to include genetic mutations for other drugs in the cartridge. This version of GeneXpert10 colour multiplexing GeneXpert® technology. The GeneXpert MTB/XDR was launched in 2020 for clinical use, allowing faster drug resistance testing. As the name indicates, it included mutations conferring resistance not only for rifampicin (RIF) and isoniazid (INH) but also for second line drugs, fluoroquinolones (FLQ), injectable drugs (amikacin, kanamycin, capreomycin) and ethionamide (ETH), in a single test run. In a recent study done at two sites with 100 sputum samples and 214 clinical isolates, its performance was found to be high with sensitivity of 94 per cent to 100 per cent and specificity of 100 per cent as compared to sequencing, for all drugs except for ETH38. Its sensitivity and specificity for drug resistance detection in comparison to phenotypic DST was 94.2 per cent and 98.5 per cent for INH, 93.2 per cent and 98 per cent for fluoroquinolones, 98 per cent and 99.7 per cent for ethionamide and 86.1 per cent and 98.9 per cent for amikacin resistance. While applying the test on clinical samples with RR/MDR, in a recent Indian study, resistance to fluroquinolone, amikacin, kanamycin, and capreomycin was 78.7, 88.3, 83 and 89.3 per cent, respectively39,40.

GeneXpert edge

Whether Xpert/MTB-Rifisa point-of-care test or not, may be a debatable question because it requires some laboratory infrastructure (at least BSL-2 level), including electric supply. To overcome these limitations, in 2018 the Cepheid launched the GeneXpert® Edge (GX-Edge), which is a new generation molecular test platform. This system is developed for health services with limited infrastructure, as it is run on re-chargeable battery. However, the GX-Edge is a single-slot platform, allowing a single sample run per cycle, thus limiting its use in programmatic management of TB. It can be run on electricity too. There is very limited data on its feasibility and acceptability in the field39.

“Cepheid GeneXpert® MTB-HR”

For the diagnosis of all forms of TB, an ideal test which is a non-sputum-based, fast and accurate, remains an urgent need. Several stakeholders are working on various platforms, however, Cepheid™ Inc. (USA) remains in leadership position. Recently, they have developed a new finger prick blood test which is named as Xpert MTB Host Response (MTB-HR). This system generates a TB score based on messenger RNA (mRNA) expression of three genes. Several studies have been carried out in clinical settings, where its sensitivity and specificity, are reported to be 87 per cent and 94 per cent, respectively. Considering this as low sensitivity triage test, the scoring system was adjusted to raise its sensitivity to 90 per cent, but the specificity decreased to 86 per cent41.

In a later study, Seifert et al42 found that when the diagnostic threshold of this test was set to achieve the overall sensitivity of >90 per cent, specificity dropped down to 32 per cent when compared to Xpert MTB/RIF Ultra, and only 29 per cent when compared to a bacteriological confirmation. It further dropped down to 22 per cent when compared to a composite reference standard (CRS). Recently, a multicentre multination study was published, which included adult patients from India, Philippines, South Africa, Vietnam and Uganda. Its sensitivity was similar across countries, and gender of patients, although its specificity was lower in people living with HIV (45.1%) than in HIV negative subjects (65.9%). Though it showed high negative predictive value of 95.8 per cent, the positive predictive value was only 40.1 per cent43. Olbrich et al44 while including a large cohort of eligible children, concluded that the Xpert-MTB-HR does not meet WHO minimum criteria in the general population. They reported its sensitivity of 59.8 per cent in culture confirmed cases. If culture plus Xpert MTB/Rif Ultra confirmed cases were taken for comparison, its sensitivity was 41.6 per cent, but it went down to only 29.6 per cent if only clinical reference standard was taken for comparison. For the diagnosis of paediatric TB, the mRNA expression score using the Xpert-MTB-HR was used in the culture-confirmed TB vis-à-vis with unlikely TB cases it could differentiate the two but with an accuracy of only 59.8 per cent. Further in microbiologically confirmed cases its sensitivity decreased to 41.6 per cent but 90 per cent specificity. The sensitivity was even lower in children with HIV44.

Truenat®

India has developed a cartridge based test for the diagnosis of PTB. The manufacturers of this product (M/s Molbio Diagnostics, Goa, India) started with one basic test and later it has developed three improved versions called Truenat MTB, MTB-Plus and MTB-RIF Dx. These tests are intended to be used in the health system as suggested for Xpert MTB/RIF. The WHO, 2020 recommended the Truenat MTB and Truenat MTB Plus assays as the initial diagnostic tests for TB. The WHO also recommended these tests “to be run along with the Truenat MTB-RIF-Dx for detection of rifampicin resistance on sample that are found positive in Truenat-MTB or TruenatMTB-Plus results. After its endorsement by WHO, the test has undergone extensive evaluation, nationally and globally. The sensitivity of Truenat MTB-Plus is found to be 91 per cent as compared to Xpert/MTB-Rif (90%). In HIV-TB coinfected patients its reported sensitivity was 85 per cent compared to 81 per cent for Xpert/MTB-Rif. The specificity of Truenat MTB Plus was, however, slightly lower (96%) than GeneXpert(99%)45. However, the older versions had a limitation that for drug resistance detection another module has to be used. The manufacturers have developed a fourth version, called Truenat MTB Ultima. Abdulgader et al46 compared Truenat MTB Ultima, Truenat MTB Plus, and Xpert MTB-Rif Ultra and showed that Truenat MTB Ultima, Truenat MTB Plus, and Xpert MTB Ultra had sensitivities of 90, 84, and 92 per cent, respectively and specificities of 85, 95, and 95 per cent, respectively.

Line probe assays

In last three decades when more emphasis was given on TB and its control, several innovations took place, including liquid cultures and development of molecular tests. In the early years of this century two crucial molecular tests were developed, one was real-time PCR based technology, the Xpert/MTB-Rif and the other was reverse hybridization of mycobacterial DNA on the strips, known as line probe assay (LPA). The origin and other details of this technology are covered by us elsewhere39.The earlier versions were developed only for detecting the mutations which confer resistance to first line (FL) drugs i.e. Rifampicin (Rif) and isoniazid (INH) resistance. The new-generation LPAs have been developed with improved sensitivity, and cover more genetic mutations that confer resistance to second line (SL) drugs. These include Genotype MTBDRsl version 2.0 (Hain Lifesciences-Bruker) for second line drugs. Genotype MTBDRsl V2.0 showed higher sensitivity for detection of fluoroquinolones (FQ) and XDR-TB isolates over Genotype MTBDRsl V1.047,48. Emerging novel mutations conferring drug resistance in MTB isolates have limited the use of this assay because it does not include the probes corresponding to mutations that are associated with MDR and XDR- TB. In addition, longer turnaround time (TAT), high cost, biosafe laboratory environment and tedious nature of the west remains an issue.

LAMP (loop-mediated isothermal amplification)

Loop-mediated isothermal amplification (LAMP) is based on isothermal PCR amplification method that can be performed in a standard-BSL-2 level molecular biology setting. The LAMP-based TB test has been recommended by WHO since 2016, as a potential replacement for smear microscopy. Its average sensitivity (89.6%) and specificity (94%) are reported to be lower than GeneXpert/MTB-Rif. However, its analytical sensitivity has been reported as 5 fg of mycobacterial DNA, which is equivalent to one mycobacterial cell49. The test has been developed for various applications including to detect and differentiate MTB and NTM in single tube39,50. Moreover, the test is cumbersome, involving multiple steps and BSL-2 or higher laboratory infrastructure.

Next-generation sequencing

In 1998 the whole genome of MTB was sequenced. After the availability of whole genome sequence (WGS) data targeted next-generation sequencing (tNGS) or Sanger’s sequencing method can allow us to sequence millions of fragments in each run simultaneously and undertake profiling of the MTB for drug resistance, lineages detection and also to detect novel mutations39. In 2023, WHO issued an advisory encouraging tNGS for the detection of DR-TB. The tNGS allows us to test new drugs and novel molecules against MTB. The traditional sequencing of MTB was dependent on bacterial culture but newer tNGS platforms provide opportunity to carry out directly onthe clinical samples obviating the process of bacterial culture11,51. There are at least three platforms, the Illumina, Ion Torrent and Oxford Nanopore. However, the technology requires skilled manpower with experience in bioinformatics, beside the comparatively high cost for resource constrained regions. Hence this technology can best be utilized by pooling the human and laboratory resources in a centralised place. In a recent study conducted in Bangladesh, tNGS results show higher sensitivities for rifampicin (99.3%), isoniazid (96.3%), fluoroquinolones (94.4%), and very high to aminoglycosides (100%) but comparatively lower for ethambutol (76.6%), streptomycin (68.7%), ethionamide (56.0%) and pyrazinamide (50.7%) when compared with pDST50.While the tNGS primarily has clinical application, for deeper insight of the pathogen whole genome sequence (WGS) has to be carried, which can unravel new information on the genomic data and regional or lineage specific genetic variations. The WGS can also help understand the new mechanisms of survival, fitness, and DNA repair mechanisms adopted by the pathogen under specific conditions51,52.

With the rapid development in the field of molecular biology detection technologies, CRISPR/Cas system is more widely being used in clinical practice for pathogen detection51. Recent studies show that if the trans cleavage ability of CRISPR-Cas12a against the single-stranded DNA is combined with hybridization steps and chemiluminescence to establish an imaging sensor for the supersensitive detection of MTBDNA, this technology can be a game changer. Qiao et al53 reported a linear relationships between the concentration of MTBDNA and the output signal in the ranges of 10 to 200 pM and 200 to 800 pMDNA. The lowest limit of detection (LOD) was as low as 0.83 pM of MTB genomic DNA, and a plasmid containing MTB-specific sequence was detected at one copy per μL, which is a very high analytical sensitivity. A detection sensitivity of 100 per cent was achieved by analysing the MTB-DNA isolated from sputum samples of TB patients. This study shows new hopes for TB detection and broadens the application of CRISPR-Cas12a based sensors in clinical diagnosis.

Immunological methods of diagnosis

Immunological tests used for TB diagnosis can be of two types. One which are done in vivo or ex vivo and the other type are in vitro tests. Typical examples of in-vivo tests are skin tests, while T-spot and QuantiFERON-TB gold (QFT) are ex-vivo tests. These are primarily used to screen and for the purpose of ruling out the disease. These tests are not advised for diagnosing the clinical disease. Beside these there are a number of surrogate markers including C-reactive protein (CRP), various cytokines, antibodies, low serum albumin level and even subsets of CD cells that are not being covered in this article, because these are only supportive investigations with very low specificity for the diagnosis of TB1,11,19,21.

Tuberculin skin test

Tuberculin skin test (TST), also known as Mantoux test or PPD (purified protein derivative) test evaluates the cell mediated (Type IV) immunity. It was developed more than 104 years back and is still used as an initial screening test in some of the industrialized countries, which are TB non-endemic, to detect MTB exposure. It has several limitations specially its poor specificity. The TST has low sensitivity especially in immunocompromised individuals. There are also variations in the composition of purified protein which is the basis of this test. Therefore, in recent years several advances have been made to prepare a more standardized protein substrate. In early years of this century Staten’s Serum Institute, Copenhagen, Denmark prepared an ovel Skin Test (C-Tb) which consists of recombinant antigens–ESAT-6 and CFP-10, that are included in the IGRAs also. The C-Tb test has been reported to be highly specific skin test for the detection of LTBI and it also addresses some of the drawbacks of TST and IGRAs. C-Tb is done in the same manner as the TST. In a recently published study sensitivity of C-Tb, TST and QuantiFERON-TB-Gold-In-Tube (QFT) were found to be 72 per cent vs. 75 per cent vs. 73 per cent, respectively. Although, all the three tests showed similar sensitivity in HIV-TB co-infected participants, but the positivity rates were found low when CD4 counts were <100 cells/μL. Among the asymptomatic paediatric contacts, 32 per cent tested positive with C-Tb and 32 per cent (28/87) with TST with a concordance rate of 89 per cent. Overall, the C-Tb and TST showed a similar safety profile54. Now the Staten’s Serum Institute has collaborated with Serum Institute of India and other manufacturing units globally to market these antigens to replace the PPD based TST.

QuantiFERON-TB /IGRA tests

The QuantiFERON-TB-Gold-In-Tube (QFT) or IGRA is an interferon gamma (IFN-γ) release assay is used to replace the TST. The use of IGRA is recommended in individuals who cannot come for the reading of the TST on 3rd day, or who are known to have had exposure to MTB, HIV infection, or other immunocompromised conditions. There are a number of variants of the test, viz QuantiFERON, QuantiFERON-Gold and QuantiFERON GoldPlus55. It has several advantages over the TST including its non-reactivity with non-tuberculous mycobacteria, high specificity, but high cost is the major limitation of its wider use in resource constrained settings. The QFT is reported to be more specific than TST, as the QFT has ESAT-6 and CFP-10, which are specific only to MTB complex and does not cross react with NTM exposure11,19,21. Despite clear instructions from all manufactures, QFT gold is often misused to diagnose the active TB while its best utility is for latent TB and past exposure to TB.

Serological diagnostic methods

Serological tests refer to blood based in-vitro tests which detect humoral immune responses, antibodies to MTB antigens. These tests offer several advantages such as: (i) rapid results (within minutes), (ii) easy to perform (iii) can be truly point of care tests and (iv) in cases of extrapulmonary tuberculosis (EPTB), paucibacillary TB and where the appropriate samples is difficult to obtain or the site of pathology is not identifiable, a blood test may be more practical; because immune response is not site-specific but systemic.

The International Standards for TB Care do not recommend the use of serological tests in routine practice. After finding the performance of the tests which were in the market before 2010, very poor, in 2011 WHO banned these test kits. Subsequently Government of India also banned antibody detection kits marketed at thattime56. Although the intention behind the ban was validated and desired to avoid false positive as well as false negative results, the nuanced language in WHO policy statement regarding new research has become a point of confusion for various researchers, kit developers as well as for funding bodies. The WHO guidelines do mention that further research to identify new/alternative point-of-care tests for TB diagnosis and/or serological tests with improved accuracy is strongly encouraged. The document also mentions that “such research should be based on adequate study design including quality principles such as representative suspected populations, prospective follow up and adequate and explicit blinding. The report strongly recommended that proof of-principle studies be followed by evidence produced from prospectively implemented and well-designed evaluation and demonstration studies, including assessment of patient impact. Unfortunately, the report was misunderstood as complete ban on commercialized as well as on developing new serological tests, specially by the administrative ministries and local policy makers, rather than encouraging innovating novel antigens and point of care triage tests. After this ban the research on finding novel serological tests has completely stopped and only rarely such studies are being published in recent years57-64. Even though these guidelines did not ban any future research, a wrong message is gone in, which needs to clarification from WHO and national TB Elimination programme managers, so that funding for innovative research can be encouraged. In another review article several proteomics platforms, developed for the detection of host immune responses, have been covered. These include timeline of proteomic technologies and protein database development, such as mass spectrometry (MS); two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), matrix-assisted laser desorption/ionization (MALDI), electrospray ionization (ESI), peptide mass fingerprinting (PMF), isotope-coded affinity tag (ICAT), difference-gel 2D-electrophoresis (DIGE), surface-enhanced laser desorption/ionization time of flight (SELDI-TOF), Human Proteome Organization (HUPO), and Human Protein Atlas (HPA)59.There are several antigens which have been evaluated for the diagnosis of pulmonary and other forms of TB. After WHO ban on TB serology in 2011, between January 2012 to till May 2025, more than 634 articles are published in PubMed. Of these 354 were on humans, and only 37 were on antibody-based diagnostic tests, averaging less than four articles per year. Further, only 12 studies were based in vitro diagnostic tests, of which 10 studies analysed the antibodies against various antigen in the plasma or serum while in two studies novel monoclonal antibodies were used to detect circulating antigens. The researchers used various test platforms and various antigens. Baumann et al60, used antigen Apa, HSP 16.3, HSP20, PE35 and lipoarabinomannan (LAM) to stimulate the host cells. They found sensitivity of 71 per cent and specificity of 86 per cent. In 2015, Chen et al61 from China in a multicentric study used MTB-specific antigens Ag14-16kDa, Ag32kDa, Ag38kDa and Ag85B in protein array system but found very low sensitivity ranging from 28 per cent to 55 per cent and specificity ranging from 93 per cent to 100 per cent, of various antigens singly or even in combination. In 2017, Zhao et al62 from Japan evaluated the utility of 11 antigens in differentiating MTB infection, caused by Beijing and non-Beijing lineages. They used Rv0679c142Asn, Rv0679c142Lys, Ag85B, Ag85A, ARC, TDM-M, TDM-K, HBHA, MDP-1, LAM, and TBGL antigens in an ELISA platform, but the results were not encouraging. In 2019, two studies were published: one from Thailand and the other from China63-64.These authors used several antigens including B: I-TAC, I-309, MIG, Granulysin, FAP, MEP1B, Furin and LYVE-1and multiple platforms. Yang et al63 used a protein array and by using the combination algorithm of these eight antigens, reported a sensitivity of 74-100 per cent and specificity of 71-100 per cent. Recently Mahmood et al64 from Pakistan used chimera of two antigens Rv3874 and Rv3875 in ELISA platform and concluded that chimera of these antigens gave better results than individual antigen assays. Nonetheless, for the first time, Singh et al10 demonstrated that novel antigens they have developed could be used as a point of care test using the immunochromatographic flow through assay in 10 min. Gupta et al57 advanced the previous study and developed novel monoclonal antibodies to detect MTB specific antigens in the clinical samples. The monoclonal antibodies can be used in various platform like direct fluorescence test on biopsies and fine needle aspiration cytology samples, ELISA, or in a ICT based rapid POC tests.

Recent studies show high potential of novel antigens to develop flow-through or lateral flow immunochromatography based rapid tests, that can be used in remotest areas requiring no equipment, no electricity and no skilled manpower. We hope that if emphasis is given on innovative research and developing novelantigens10 or monoclonal antibodies54 using recombinant DNA technology, as is given on developing molecular technologies or vaccine development by the funding and licencing authorities, the innovative technologies will help TB elimination mission possible. Nevertheless, the point of care tests should be used with care and preferably as triage tests, and an algorithmic combination of serological triage tests and confirmatory molecular with or without standard microbiological tests (Figure) should be developed for elimination of TB.

A proposed algorithm for diagnostic approach using triage strategy. The antibody detection based lateral flow or flow through immunochromatographic point of care tests (IC-POCT) can revolutionize the management strategy of Tuberculosis and may help in timely elimination of Tuberculosis. These POCs can be applied for mass population screening as well as for the symptomatic cases. A triage test with very high sensitivity can rule out any form of tuberculosis and test negative subjects, will not be require further investigations. Those who are found POC test positive will be required to get investigated further using standard microbiological, molecular, histopathological or radio-imaging investigation depending on the suspected site of infection and the clinical criteria.
Figure.
A proposed algorithm for diagnostic approach using triage strategy. The antibody detection based lateral flow or flow through immunochromatographic point of care tests (IC-POCT) can revolutionize the management strategy of Tuberculosis and may help in timely elimination of Tuberculosis. These POCs can be applied for mass population screening as well as for the symptomatic cases. A triage test with very high sensitivity can rule out any form of tuberculosis and test negative subjects, will not be require further investigations. Those who are found POC test positive will be required to get investigated further using standard microbiological, molecular, histopathological or radio-imaging investigation depending on the suspected site of infection and the clinical criteria.

Other biomarkers

There is plethora of information and research findings in the field of TB diagnosis, including the discovery of various proteins and circulating linear and circular rRNA biomarkers, and host and pathogen metabolites, combinedly known as metabolomics. Profiling of volatile biomarkers provides a new diagnostic pathway enabling a non-invasive, faster, and accurate way of detecting TB. This platform relies on TB‐specific volatile organic compounds (VOCs) that are detected from the skin of the patient. A specifically designed nano material‐based sensors array translates to a sensitivity of above 90 per cent65. Interest in the VOCs is increasing and differential quantities of specific VOCs have been found correlated with various diseases of lungs, liver and gastrointestinal tracts including TB66. However, these VOCs have poor specificity and background noise of atmospheric gases and pollutants make these non-feasible, like we saw when we compared these parameters between India and South Africa65.

It is well known that cell wall of MTB has chains of mycolic acid (MA) linked to middle layer of arabinogalactan (AG) covalently attached to the inner layer of “peptidoglycan (PPG)”. The cell wall also contains major lipids, lipomannan (LM), phosphatidylinositol (PIM), and lipoarabinomannan (LAM) which are being estimated by various workers and it is proposed that these could be good markers of Mycobacterial multiplication inside the body of patient. However, like many other studies, a recent study from India shows that LAM is not very useful biomarker for extrapulmonary TB. The authors compared its sensitivity as compared to microbiological standard and composite reference standard were only 61.5 per cent and 45.8 per cent and positive predictive value 57.1 per cent and 78.6 per cent, respectively in pleural TB. However, the specificity was good (91.7% and 95%) with a negative predictive value of 93 per cent and 81.7 per cent. The urinary LAM-Lateral flow assay performed even worse than pleural LAM-Lateral flow assay67.

Need for triage tests

The triage strategy could be best approach to optimally utilise the resources and thereby in the elimination of the disease. The triage tests are intended to identify who, in a pool of at-risk people, may be having disease and requires further investigations to confirm the TB diagnosis (Figure). In a mass application of these tests, while several individuals who may not be symptomatic, can be identified. On the other hand, many individuals who are presenting with similar symptoms, these tests can rule out the specific disease, or start TB prophylactic treatment (TPT)68 so that resources are optimally utilised to reach final diagnosis. Triage-negative patients should typically not require further investigation for TB, and therefore, these tests are ought to be highly sensitive, even if specificity may be slightly low. The advanced investigations and resources can be allocated to those patients who need confirmatory tests, including the culture and molecular methods, as discussed above. Triage is also important because confirmatory test capacity is often unevenly distributed, require skilled manpower and often very costly. Hence, triage tests would not only increase the efficiency but, if applied appropriately, will also reduce the volume and variety of referrals for confirmatory testing69.

Conclusion

Several developments in the field of TB diagnosis, therapeutics and treatment monitoring have taken place in the last two decades. These developments provide us best opportunity to control and end TB in coming years. However, the task is challenging. Most of these newer developments are restricted to centralized laboratories. The aim should be to reach the unreachable to detect, track and treat the infected person requiring more emphasis on detecting the MTB infection at the earliest. To achieve this goal can be met only by use of point of care test with very high sensitivity. A diagnostic algorithm is required to be developed, where easy to perform and cost-effective rapid test using drop of blood can detect every infected person, including symptomatic and asymptomatic. The test should be primary screening test in the triage. There are several scientific groups and test device manufacturers who are eager to come forward. However, the progress has been hindered due to WHO’s ban on serological tests for the diagnosis of TB. Although the intention of WHO 14 years ago was validated and needed at that time, the nuanced language and meanings between the lines are not understood correctly by the researchers, the programme manager, the local governments and the manufacturers who always avoid any confrontation with Government. Therefore, the nuances in the policy statement of WHO, need to be reframed, to encourage innovation and development of point-of-care serological tests. It is reemphasized that no single approach will succeed in TB elimination, but only a combined multipronged approach to screen the infected, track the laboratory confirmed index cases and their contacts, offering supervised, appropriate and uninterrupted treatment. It is also emphasised that vigorous efforts be made by all nations in the area of vaccine development and vaccination of at-risk population can eliminate the TB.

Acknowledgment

Authors acknowledge Ms. A. Pradhinila, MBA, Office of the Director Medical Research, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission’s Research Foundation (Deemed University), Puducherry, for her technical support.

Declaration

Authors declare all the images, including the X-ray and the pictorial diagram of the granuloma are taken from the authors’ own collection and that no external source of these images, info graphics or diagrams has been used in the figure provided in this review.

Financial support & sponsorship

None.

Conflicts of Interest

None.

Use of Artificial Intelligence (AI)-Assisted Technology for manuscript preparation

The authors confirm that there was no use of AI-assisted technology for assisting in the writing of the manuscript and no images were manipulated using AI.

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