Recent updates in diagnosis of abdominal tuberculosis with emphasis on nucleic acid amplification tests

Diagnosis of abdominal tuberculosis: Detection of mycobacterial CFP-10 and HspX proteins by gold nanoparticle-PCR amplified immunoassay

Attempts were made to improve the efficacy of PCR amplified immunoassay (I-PCR) for diagnosing abdominal TB cases by utilizing the gold nanoparticle (AuNP)-based I-PCR, where AuNPs were functionalized with detection antibodies/oligonucleotides that exhibited 84.3% sensitivity and 95.1% specificity. This assay would improve the ongoing algorithms used in abdominal TB diagnosis.

Diagnosis of extrapulmonary tuberculosis by GeneXpert MTB/RIF Ultra assay

INTRODUCTION

Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS6110, IS1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R).

AREA COVERED

We described the assay chemistry/work design of Xpert Ultra and evaluated its performance in several EPTB types, that is, TB lymphadenitis, TB pleuritis, TB meningitis, and so on, against the microbiological reference standard or composite reference standard. Notably, Xpert Ultra exhibited better sensitivities than Xpert, but mostly at the compensation of specificity values. Moreover, Xpert Ultra exhibited low false-negative and false-positive RIF-R results, compared with Xpert. We also detailed other molecular tests, that is, Truenat MTBTM/TruPlus, commercial real-time PCR, line probe assay, and so on, for EPTB diagnosis.

EXPERT OPINION

A combination of clinical features, imaging, histopathological findings, and Xpert Ultra are adequate for definite EPTB diagnosis so as to initiate an early anti-tubercular therapy.

Diagnosis of abdominal tuberculosis by multi-targeted (mpt64 and IS6110) loop-mediated isothermal amplification assay

BACKGROUND AND AIM

Diagnosis of abdominal TB is an exigent task due to variable anatomical sites and non-specific clinical manifestations that closely resemble other diseases. Most of the available diagnostic modalities yield low sensitivities and need expertise to handle the specialized equipment. Hence, there is an urgent need to develop a rapid and reliable diagnostic test, so as to reduce the unnecessary morbidity. Therefore, we designed a multi-targeted loop-mediated isothermal amplification (MT-LAMP) for diagnosing abdominal TB.

METHODS

We evaluated an MT-LAMP (using mpt64 and IS6110) to diagnose abdominal TB within ascitic fluids and intestinal/peritoneal biopsies and compared these results with multiplex-PCR (M-PCR) using the same targets. MT-LAMP products were analyzed by gel electrophoresis and visual detection methods, that is, hydroxy naphthol blue and SYBR Green I reaction.

RESULTS

Sensitivities of 80.9% and 84.6% were obtained in suspected (n = 42) and total abdominal TB (n = 52) cases, respectively by gel-based MT-LAMP, with 97.3% (n = 37) specificity in non-TB controls. Notably, sensitivities attained by gel-based/SYBR Green I MT-LAMP in both clinically suspected and total abdominal TB cases were significantly higher (P < 0.05) than M-PCR. Furthermore, sensitivity obtained with SYBR Green I was equivalent to that of gel-based MT-LAMP, while somewhat lesser specificity (94.6%) was attained with SYBR Green I, compared with gel-based MT-LAMP.

CONCLUSION

Both gel-based and SYBR Green MT-LAMP exhibited equivalent sensitivities to diagnose abdominal TB. Because SYBR Green LAMP is easier to perform than a gel-based assay, we are currently focused on improving the specificity of this assay so as to develop a diagnostic kit.

Current role of endoscopic ultrasound for gastrointestinal and abdominal tuberculosis

A high incidence of tuberculosis (TB), especially in endemic countries, makes this infectious disease a concern. Abdominal TB contributes to 10% of extrapulmonary TB. Due to nonspecific clinical, radiological, and endoscopic findings, diagnosing abdominal TB continues to be a challenge. Hence, a precise diagnosis is needed. The diagnosis of gastrointestinal disease using endoscopic ultrasound (EUS) is often performed due to its high resolution and ability to provide a real‐time visual representation of the gastrointestinal tract and extramural structures. EUS‐guided fine‐needle aspiration (FNA) and fine‐needle biopsy (FNB) have helped diagnose TB as they offer an adequate specimen for cytology or histopathological examination. This method is considered safer, more effective, and more efficient. The capacity of EUS to diagnose abdominal TB based on the affected organs was examined via a literature search. We reviewed the role of EUS in diagnosing esophageal, gastric, pancreatic, peripancreatic, hepatosplenic, peritoneal, and intestinal TB. Generally, EUS aids in diagnosing abdominal TB. In some organs, it is superior to other diagnostic modalities. However, further examinations, such as cytology or histopathology and microbial, are still needed. We also studied the roles of EUS‐FNA and EUS‐FNB. EUS‐FNA has shown a high diagnostic yield in esophageal (94.3–100%), pancreatic and peripancreatic (76.2%), and intestinal TB (84.1%). As minimally invasive methods, EUS‐FNA and EUS‐FNB can successfully provide sufficient samples. EUS is a functional diagnostic modality for abdominal TB. EUS‐FNA and EUS‐FNB provide sufficient samples safely and efficiently for further cytology, histopathology, and microbial examinations.

Acid fast bacillus smear, mycobacterial culture and Xpert MTB/RIF assay for the diagnosis of tuberculous peritonitis in patients with and without end stage renal failure

Introduction.

Diagnosis of tuberculous peritonitis (TBP) requires a high index of suspicion.

Hypothesis /gap statement.

Information about the diagnostic features of TBP among patients with end-stage renal failure (ESRF) from India is limited.

Aim.

To assess the utility of the Gene Xpert MTB/RIF assay in the diagnosis of TBP in patients with end-stage renal failure (ESRF), compared with those without ESRF.

Methodology.

This prospective observational single centre cohort study was performed at a tertiary care centre in Northern India. Ascitic fluid and/or whole continuous ambulatory peritoneal dialysis (CAPD) bag with effluent from 300 clinically suspected cases of TBP were included in the study. Diagnosis was based on detection of Mycobacteria on smear, Xpert MTB/RIF assay and/or culture. Cell counting was done in a Neubauer chamber. Cell predominance was seen by Giemsa stain. Line probe assay (LPA) for drug susceptibility testing was performed on all positive cultures.

Results.

TBP was diagnosed in 168 cases. Diabetes mellitus was a significant risk factor for developing TBP in patients with ESRF (P value<0.01). Lymphocytic predominance was seen in 21 patients without ESRF (P value 0.033) while majority of the patients in both groups had neutrophils in their ascitic and peritoneal fluids (138/168; P value 0.033). We recovered 15 cases of laboratory diagnosed TBP (11 without ESRF and four with ESRF). Microscopy was positive in two cases while ten isolates were recovered on culture. The Xpert MTB/RIF assay was positive in seven ascitic fluid samples out of which three were rifampicin resistant. All these were patients without renal failure (P value 0.010). Eight culture positive samples tested by the line probe assay did not detect any resistance to either rifampicin or isoniazid.

Conclusion.

The GeneXpert MTB/RIF assay has a limited value in the diagnosis of TBP in patients with ESRF.

Diagnosis of genitourinary tuberculosis by loop-mediated isothermal amplification based on SYBR Green I dye reaction

A multitargeted loop-mediated isothermal amplification (MT-LAMP) assay targeting mpt64 (Rv1980c) and IS6110 was designed to diagnose genitourinary tuberculosis (GUTB) cases. While assessing gel-based, hydroxynaphthol blue (HNB) and SYBR Green I MT-LAMP assays on GUTB specimens (n = 28) in a pilot study, both gel-based/SYBR Green I assays exhibited better sensitivity than HNB LAMP. Since SYBR Green MT-LAMP is easier to perform compared with a gel-based assay, a higher number of GUTB specimens (n = 55) were evaluated by SYBR Green MT-LAMP, wherein 85.5% sensitivity and 94.4% specificity (n = 36) were obtained. Moreover, the sensitivity attained by MT-LAMP was significantly higher (p < 0.05) than with multiplex-PCR (mpt64 + IS6110). After further validating these MT-LAMP data in different epidemiological settings, this assay may be developed as a diagnostic kit.

Insight into diagnosis of pleural tuberculosis with special focus on nucleic acid amplification tests

INTRODUCTION

Pleural tuberculosis (TB) is the archetype of extrapulmonary TB (EPTB), which mainly affects the pleural space and leads to exudative pleural effusion. Diagnosis of pleural TB is a difficult task predominantly due to atypical clinical presentations and sparse bacillary load in clinical specimens.

AREA COVERED

We reviewed the current literature on the globally existing conventional/latest modalities for diagnosing pleural TB. Bacteriological examination (smear/culture), tuberculin skin testing/interferon-γ release assays, biochemical testing, imaging and histopathological/cytological examination are the main modalities. Moreover, nucleic acid amplification tests (NAATs), i.e. loop-mediated isothermal amplification, PCR/multiplex-PCR, nested-PCR, real-time PCR and GeneXpert® MTB/RIF are being utilized. Currently, GeneXpert Ultra, Truenat MTB^TM, detection of circulating Mycobacterium tuberculosis (Mtb) cell-free DNA by NAATs, aptamer-linked immobilized sorbent assay and immuno-PCR (I-PCR) have also been exploited.

EXPERT OPINION

Routine tests are not adequate for effective pleural TB diagnosis. The latest molecular/immunological tests as discussed above, and the other tools, i.e. real-time I-PCR/nanoparticle-based I-PCR and identification of Mtb biomarkers within urinary/serum extracellular vesicles being utilized for pulmonary TB and other EPTB types may also be exploited to diagnose pleural TB. Reliable diagnosis and early therapy would reduce the serious complications associated with pleural TB, i.e. TB empyema, pleural fibrosis, etc.

Identification of mycobacterial MPT-64 and ESAT-6 proteins in urogenital tuberculosis patients by real-time immuno-PCR

Aim: Diagnosis of urogenital tuberculosis (UGTB) is difficult and there is an immediate need to develop a reliable diagnostic test. Methods: A real-time immuno-PCR (RT-I-PCR) was developed to identify a cocktail of MPT-64 + ESAT-6 in both male/female UGTB patients comprising five confirmed cases, 40 clinically suspected cases and 37 non-TB controls, from whom mid-stream urine specimens were collected, while endometrial biopsies of female patients were obtained on day 1 of their menstrual cycle. Results obtained by RT-I-PCR were compared with I-PCR/ELISA and GeneXpert. Results: A wide range (500 fg/ml-10 ng/ml) of MPT-64 + ESAT-6 was detected in UGTB specimens by RT-I-PCR, although ELISA showed a narrow range (2.5-11 ng/ml). Sensitivities of 80% and 82.2% were obtained by RT-I-PCR in clinically suspected and total UGTB cases, respectively, whereas 94.6% specificity was obtained. Concurrently, RT-I-PCR revealed significantly higher (p < 0.05-0.001) sensitivity than I-PCR/ELISA and GeneXpert. Conclusion: After improving the specificity, the authors may develop RT-I-PCR into a diagnostic kit.

Diagnosis of peritoneal tuberculosis by real-time immuno-PCR assay based on detection of a cocktail of Mycobacterium tuberculosis CFP-10 and HspX proteins

BACKGROUND

Diagnosis of peritoneal TB is difficult owing to unusual clinical manifestations and low sensitivities obtained with most of the available diagnostic modalities. Hence, there is an urgent need to design a reliable diagnostic test so that an early therapy is initiated.

RESEARCH DESIGN AND METHODS

We designed a quantitative real-time immuno-PCR (RT-I-PCR) assay to detect a cocktail of Mycobacterium tuberculosis CFP-10 (Rv3874) and HspX (Rv2031c) proteins in clinical samples (ascitic fluids and peritoneal biopsies) of peritoneal TB patients, and results were compared with I-PCR/ELISA.

RESULTS

A wide range of CFP-10+ HspX (0.6 pg/mL to 9.9 ng/mL) was detected in clinical samples of peritoneal TB patients by RT-I-PCR, whereas ELISA exhibited a narrow range (3 ng/mL to 11.5 ng/mL). Sensitivities of 81.5% and 65.7% and specificities of 92.5% and 90% were obtained in a total of 78 cases (comprising 38 peritoneal TB and 40 non-TB controls) by RT-I-PCR and I-PCR, respectively. Markedly, sensitivity obtained by RT-I-PCR was significantly higher than I-PCR (p = 0.0143) and ELISA (p = 0.0005).

CONCLUSIONS

Our RT-I-PCR revealed good accuracy for the rapid diagnosis of peritoneal TB cases. After further improving the specificity and reducing the cost, this assay may develop into a diagnostic kit.