Diagnostic performance of Xpert MTB/RIF ultra in detecting Mycobacterium tuberculosis and Rifampicin Resistance in AFB Smear-negative Pulmonary and Extrapulmonary Tuberculosis samples in Malaysia

Rapid and highly accurate diagnostic tools are critically needed to diagnose Mycobacterium tuberculosis and rifampicin resistance in AFB smear-negative samples. In this study, we evaluated the diagnostic performance of Xpert MTB/RIF Ultra (Ultra) as a rapid test to diagnose tuberculosis in smear-negative cases in Malaysia. A retrospective study of 1960 smear-negative pulmonary and extrapulmonary samples obtained from patients was conducted. Culture was used as the reference standard for the study. The overall sensitivity and specificity of Ultra on the tested samples were 88.7 % and 77.2 %, respectively, while the PPV was 32.3 % and the NPV was 98.2 %. Ultra showed slightly higher sensitivity in pulmonary (89.9 %) compared to extrapulmonary samples (86.1 %). The overall accuracy of Ultra was 78.5 % (kappa=0.37; 95 %CI: 0.32,0.42). Ultra showed good diagnostic accuracy for detecting MTB and rifampicin resistance in various AFB smear-negative samples. Ultra also had excellent capability in rifampicin resistance detection.

The diagnostic performance of endobronchial ultrasound with Xpert MTB/RIF Ultra in smear-negative pulmonary tuberculosis

OBJECTIVE

This study investigated the diagnostic performance of endobronchial ultrasound with Xpert MTB/RIF Ultra (Ultra) for detecting smear-negative pulmonary tuberculosis (TB).

METHODS

143 patients suspected of sputum smear-negative pulmonary tuberculosis were enrolled in this study in Shanghai Pulmonary Hospital, China. These patients underwent endobronchial ultrasound with a guide sheath (EBUS-GS) or endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) based on their chest CT manifestations. We assessed the sensitivity and specificity of tissue specimens with Ultra in the TB group and non-TB group. Culture and clinical diagnosis were used as gold-standard for TB.

RESULTS

Among these 143 patients, 11 patients were culture-positive TB, 85 patients were diagnosed with culture-negative TB and 47 were with the non-TB diseases. Direct testing with microscopy (Acid-Fast Bacilli smear, AFB), liquid culture, pathology, Xpert MTB/RIF(Xpert) test and Ultra had a sensitivity of 8.3%, 11.5%, 42.7%, 64.6%, and 78.1% individually among all the TB patients. Ultra had a higher sensitivity than Xpert (P = 0.011). But Ultra had a specificity of 59.6% (95% CI 44.3-73.3), lower than that of Xpert (89.4%, 95% CI 76.1-96.0, P = 0.001). Ultra had the same sensitivity on specimens from EBUS-TBNA and EBUS-GS (P = 0.975). Ultra's positive predictive value and negative predictive value were 79.8% and 57.1% respectively.

CONCLUSIONS

Tissue specimens from interventional bronchoscopy combined with Ultra provide a sensitive method for diagnosing smear-negative pulmonary tuberculosis, but its specificity was lower than Xpert.

Detection of Leishmania donovani using ITS1-RFLP from positive and negative smear samples among clinically reported patients visiting University of Gondar Comprehensive Specialized Hospital

BACKGROUND

Visceral leishmaniasis is caused by the Leishmania donovani species complex that can spread to internal organs and leading to death if not treated on time. Diagnosis of leishmaniasis is based on clinical signs and symptoms, microscopy, serological and molecular techniques. Because of a broad spectrum of diverse clinical manifestations and similarities of the responses to different species, identification to the species level is often difficult for the proper patient treatment and management. Therefore, the objective of this study was to evaluate the PCR- RFLP assay of the ITS1 region for identification of L. donovani species from clinical smear slide patient samples.

METHOD

DNA extraction was performed on a total of 90 smear slide samples using phenol-chloroform method. The PCR detection limit was determined by L. donovani reference strain DNA. The ITS1 region was amplified at 320 bp using LITSR/L5.8S genus specific primers and then the ITS1-PCR products were subjected to RFLP assay for confirmation of L. donovani species using HaeIII restriction enzyme.

RESULTS

Of the total samples ITS1-PCR revealed the true positive, false positive, true negative, and false negative results of 42 (46.7%), 6 (6.7%), 37 (41.1%) and 5 (5.6%), respectively. Considering microscopy as the gold standard, the sensitivity, specificity, positive predictive values, and negative predictive values of the ITS1- PCR technique was 89.4%, 86.0%, 87.5%, and 88.1% respectively. All ITS1-PCR positive clinical samples were confirmed as L. donovani species by PCR-RFLP patterns.

CONCLUSION

In conclusion, the ITS1- RFLP method is highly sensitive and more specific for identification of L. donovani species in the smear negative clinical samples of visceral leishmaniasis patients. There is also significant association and degree of agreement between the two methods. For direct identification of L. donovani species from clinical samples, irrespective of genus and species level, PCR-RFLP is more recommendable than a microscope.

The value of Xpert MTB/RIF assay of urine samples in the early diagnosis of smear-negative urinary tuberculosis

BACKGROUND

According to reports, between 30 and 40 percent of extrapulmonary tuberculosis (EPTB) cases are caused by urinary tract tuberculosis (UTB). It is critical to identify UTB quickly since it frequently precedes delayed medical attention, which can have detrimental effects. This study examined the use of Xpert MTB/RIF, a PCR test that can detect MTB as well as resistance to an important drug, rifampicin (RIF), in UTB particularly, for the early identification of UTB.

METHODS

180 participants with clinically presumptive UTB whose urine samples were chosen for urine sediment smear, culture, Xpert MTB/RIF, and TB-DNA testing at Henan Chest Hospital between January 2019 and July 2022. Evaluation of test performance using Composite Reference Standards (CRSs). We studied and compared the positivity rate for various tests using the t-test. The effectiveness of smear, culture, Xpert MTB/RIF, and TB-DNA was assessed using McNemar test.

RESULTS

In this subject, a total of 108 participants were diagnosed with UTB, and the positivity rate was 67.1%. Compared with CRS, the positivity rate of Xpert MTB/RIF, smear, culture, and TB-DNA was 29.69% (19/64, P < 0.001), 7.56% (9/119, P < 0.1), 12.12% (4/33, P > 0.05), and 18.75% (6/32, P < 0.1), respectively. The sensitivity of Xpert MTB/RIF assay was significantly better than that of smear and culture tests (78.9% vs. 77.8%, P < 0.05; 78.9% vs. 75%, P < 0.05). Under CRS, the positivity rate for Xpert, culture, and TB-DNA was 31.6% (6/19, P < 0.1), 6.2% (1/16, P > 0.05), and 26.7% (4/15, P > 0.05) for TB-DNA, respectively, compared to smear negative. Xpert MTB/RIF assay specificity was significant for culture and TB-DNA (53.6% vs. 25%, P < 0.01; 53.6% vs. 38.9%, P < 0.05), and Xpert MTB/RIF assay FPV was significant for culture and TB-DNA (53.6% vs. 0%, P < 0.001; 53.6% vs. 0%, P < 0.001).

CONCLUSION

Xpert MTB/RIF outperforms smear, cultures, and TB-DNA in detecting UTB, plus Xpert MTB/RIF is better suited for early diagnosis in smear-negative UTB.

Diagnostic performance of GeneXpert MTB/RIF in detecting MTB in smear-negative presumptive TB patients

BACKGROUND

Tuberculosis (TB) is a leading cause of morbidity and mortality worldwide. Control of TB is lingering by the lack of diagnostic tests that are simple, rapid, yet accurate. Thus, smear-negative pulmonary TB often misses the diagnosis. The study evaluated the performance of GeneXpert MTB/RIF assay for the detection of Mycobacterium tuberculosis (MTB).

METHODS

The study was carried out from June to December 2016 in Nepal Tuberculosis Center, Bhaktapur, Nepal. A total of 173 sputum samples were collected and processed by microscopy [Auramine-O staining and Ziehl-Neelsen (ZN) staining], followed by GeneXpert MTB/RIF assay and culture in Lowenstein-Jensen (LJ) medium.

RESULTS

Of 173 sputum samples, 162 (93.6%) were smear-negative. Of 162 smear-negative sputum samples, 35 (21.6%) were confirmed to have MTB by culture, and 31 (19.1%) by GeneXpert MTB/RIF assay. Of 31 GeneXpert-positive samples, 25 (80.6%) were susceptible, 4 (12.9%) were resistant, and 2 (6.45%) were intermediate to rifampicin. The sensitivity, specificity, positive predictive value, and negative predictive value of GeneXpert MTB/RIF assay for smear-negative sputum samples were 74.3%, 96.6%, 86.7%, and 92%, respectively. The GeneXpert MTB/RIF has a substantial diagnostic agreement of 90.91% with culture (Cohen's Kappa coefficient = 0.73).

CONCLUSION

The diagnostic performance of GeneXpert MTB/RIF assay was almost on par with culture, and thus can be relied upon for MTB detection in smear-negative sputum samples.

Treatment outcomes of patients with multidrug and extensively drug-resistant tuberculosis in Zhejiang, China

Background

The aim of this study was to assess the treatment outcomes of multidrug and extensively drug-resistant tuberculosis (M/XDR-TB) in Zhejiang, China and to evaluate possible risk factors associated with poor outcomes of M/XDR-TB.

Methods

Two-hundred-and-sixty-two patients having M/XDR-TB who received the diagnosis and treatment at nine referral hospitals from 1 January 2016 to 31 December 2016 in Zhejiang, China were included. All patients received second-line regimens recommended by WHO under the DOTS-Plus strategy.

Results

Among the 262 patients, the treatment success rate was 55.34% (n = 145) with 53.44% (n = 140) cured and 1.91% (n = 5) who completed treatment, 62 (23.66%) failed, 27 (10.31%) died, 16 (6.11%) defaulted and 12 (4.58%) transferred out. Forty (64.52%) of the 62 M/XDR-TB patients who failed treatment were due to adverse effects in the first 10 months of treatment. Eighteen patients (6.37%) had XDR-TB. Treatment failure was significantly higher among patients with XDR-TB at 50% than that among patients with non-XDR-TB at 21.72% (P = 0.006). Failure outcomes were associated with a baseline weight less than 50 kg (OR, 8.668; 95% CI 1.679–44.756; P = 0.010), age older than 60 years (OR, 9.053; 95% CI 1.606–51.027; P = 0.013), hemoptysis (OR, 8.928; 95% CI 1.048–76.923; P = 0.045), presence of cavitary diseases (OR, 10.204; 95% CI 2.032–52.631; P = 0.005), or treatment irregularity (OR, 47.619; 95% CI 5.025–500; P = 0.001).

Conclusion

Treatment outcomes for M/XDR-TB under the DOTS-Plus strategy in Zhejiang, China were favorable but still not ideal. Low body weight (< 50 kg), old age (> 60 years), severe symptoms of TB including cavitary disease, hemoptysis and irregular treatment were independent prognostic factors for failure outcomes in patients with M/XDR-TB.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40001-021-00502-0.

Comparison of Xpert MTB/RIF (G4) and Xpert Ultra, including trace readouts, for the diagnosis of pulmonary tuberculosis in a TB and HIV endemic setting

BACKGROUND

There are limited data about Xpert-Ultra performance in different settings, in HIV-infected persons, in those with a history of previous TB, and with trace readouts.

METHODS

We evaluated the relative accuracy of Xpert-MTB/RIF and Xpert-Ultra in 272 selected but well-characterized archived sputum samples. Of these, 168 were culture-positive (64/168 smear-positive and 104/168 smear-negative), and 104 were culture-negative (102/104 from patients with previous TB and 2/104 from patients without a TB history). Assay-specific limit-of-detection (LOD) experiments were conducted using serial dilutions of Mycobacterium tuberculosis H37Rv.

RESULTS

Overall sensitivity (95%CI) in smear-negative culture-positive samples for Xpert-MTB/RIF and Xpert-Ultra were 71.2% (62.5-79.9) and 77% (68.9-85.1), respectively (and in HIV-infected persons: 63.5% (50-76.1) and 73.1% (61.1-85.2), respectively). The LOD for Xpert-Ultra was lower (9 versus 184 CFU/ml). There were a total of 9/272 (3.3%) Xpert Ultra trace readouts (6/104 [5.8%]) in smear-negative culture-positive persons, and 3/102 (3%) in culture-negative non-TB persons with a history of previous TB).

CONCLUSIONS

Xpert-Ultra had a lower LOD compared to Xpert-MTB/RIF. A small proportion of samples (<5%) from culture-negative patients but with a history of previous TB had a likely false-positive trace readout. These data inform the management of patients with suspected TB in endemic settings.

Diagnosis of tuberculosis from smear-negative presumptive TB cases using Xpert MTB/Rif assay: a cross-sectional study from Nepal

BACKGROUND

In most developing countries, smear-negative pulmonary TB (SNPT) often gets missed from the diagnosis of consideration, though it accounts 30-65% of total PTB cases, due to deficient or inaccessible molecular diagnostic modalities.

METHODS

The cross-sectional study enrolled 360 patients with clinical-radiological suspicion of SNPT in Tribhuvan University Teaching Hospital (TUTH). The patient selection was done as per the algorithm of Nepal's National Tuberculosis Program (NTP) for Xpert MTB/RIF testing. Participants' demographic and clinical information were collected using a pre-tested questionnaire. The specimens were collected, processed directly for Xpert MTB/RIF test according to the manufacturer's protocol. The same samples were stained using the Ziehl-Neelsen technique then observed microscopically. Both findings were interpreted; rifampicin-resistant, if obtained, on Xpert testing was confirmed with a Line Probe Assay.

RESULT

Of 360 smear-negative sputum samples analyzed, 85(23.61%) found positive while 3(0.8%) of them were rifampicin resistance. The infection was higher in males, i.e. 60(25.3%) compared to female 25(20.3%). The age group, > 45(nearly 33%) with median age 42 ± 21.5, were prone to the infection. During the study period, 4.6% (515/11048) sputum samples were reported as smear-positive in TUTH. Consequently, with Xpert MTB/RIF assay, the additional case 16.5% (n = 85/515) from smear-negative presumptive TB cases were detected. Among the most occurring clinical presentations, cough and chest pain were positively associated with SNPT. While upper lobe infiltrates (36.4%) and pleural effusion (40.4%) were the most peculiar radiological impression noted in PTB patient. 94 multi-drug resistant(MDR) suspected cases were enrolled; of total suspects, 29(30.8%) samples were rifampicin sensitive, 1(1.06%) indeterminate, 3(3.19%) rifampicin-resistant while remaining of them were negative. 2(2.2%) MDR cases were recovered from the patient with a previous history of ATT, of total 89 previously treated cases enrolled However, a single rifampicin-resistant from the new suspects.

CONCLUSION

With an application of the assay, the additional cases, missed with smear microscopy, could be sought and exact incidence of the diseases could be revealed.

Xpert MTB/RIF Ultra improved the diagnosis of paucibacillary tuberculosis: A prospective cohort study

OBJECTIVES

We assessed the diagnostic performance of Xpert MTB/RIF Ultra (Xpert Ultra) in comparison to Xpert MTB/RIF (Xpert) for the detection of paucibacillary tuberculosis (TB).

METHODS

Smear-negative sputum, pleural fluid and cerebrospinal fluid (CSF) were collected from TB suspects at Beijing Chest Hospital (Beijing, China) and were examined using smear, Xpert and culture. Xpert Ultra was tested using specimens stored at -80 °C. Drug susceptibility testing (DST) was conducted for all of the isolates recovered. The performances of Xpert Ultra and Xpert were evaluated using composite reference standard (CRS) as gold standard, which included clinical, laboratory, histopathological, radiological and follow-up features.

RESULTS

Totally 689 cases were included. The direct head-to-head diagnostic performance comparison showed higher sensitivity of Xpert Ultra in contrast with Xpert among 292 smear-negative pulmonary TB (PTB) (70.89% vs 57.88%, P = 0.001), 108 tuberculous pleurisy (61.11% vs 34.26%, P<0.001), and 43 tuberculous meningitis (44.19% vs 18.60%, P = 0.011). The percentage of definite PTB, tuberculous pleurisy and tuberculous meningitis increased from 67.12% to 78.77%, 61.11% to 69.44% and 23.26% to 51.16%, respectively after integrating Xpert Ultra outcomes. The specificity of Xpert Ultra and Xpert was 96.75% (238/246) and 98.37% (242/246), respectively. Xpert Ultra and Xpert performed similarly in detecting rifampicin resistance.

CONCLUSION

Xpert Ultra has higher sensitivity but relatively reduced specificity compared with Xpert in diagnosis of paucibacillary TB. Performing Xpert Ultra would improve the definite diagnosis of smear-negative pulmonary tuberculosis, tuberculous pleurisy and tuberculous meningitis.

Evaluation of GeneXpert MTB/RIF for detection of pulmonary tuberculosis at peripheral tuberculosis clinics

Tuberculosis is one of the most common infectious diseases in China, while delayed patient finding obstructed disease control, especially for smear-negative patients. The current study was undertaken to evaluate the diagnostic accuracy of GeneXpert MTB/RIF compared with conventional methods in the detection of pulmonary tuberculosis patients. A total of 295 spot sputum samples from confirmed pulmonary tuberculosis patients were evaluated from September 2014 to June 2015. Each sample was examined by acid-fast bacillus smear microscopy, culture and GeneXpert MTB/RIF. The sputum culture on Löwenstein-Jensen (L-J) was considered as the gold-standard. After testing by smear, 68.81% (203/295) was negative and 31.19% (92/295) was positive. As the gold-standard, L-J culture detected 37.97% (112/295) positive of all specimens, while the positivity for GeneXpert MTB/RIF was 46.44% (137/295). Compared with L-J culture, the combined sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for GeneXpert MTB/RIF were 94.64%, 82.97%, 77.37% and 96.18% respectively. For smear-negative specimens, the sensitivity, specificity, PPV and NPV for GeneXpert MTB/RIF were 96.00%, 83.05%, 44.44% and 99.32%; while for smear-positive specimens, the corresponding accuracy values were 94.25%, 80.00%, 98.80% and 44.44%. The findings of study indicated that GeneXpert MTB/RIF assay demonstrated a high sensitivity in detecting Mycobacterium tuberculosis compared to smear method and a high NPV among smear negative patients.

Comparison of the Xpert MTB/RIF Assay and Real-time PCR for the Detection of Mycobacterium tuberculosis

INTRODUCTION

We compared the Xpert MTB/RIF assay with a real-time PCR assay using samples from culture-positive patients with TB. In addition, drug susceptibility test results were compared to evaluate the usefulness of these methods.

MATERIALS AND METHODS

Fifty-two clinical specimens were analyzed by standard smear-microscopy, mycobacterial growth indicator tube (MGIT) culture, solid culture, MGIT drug-susceptibility testing, TB real-time PCR, and the Xpert MTB/RIF assay.

RESULTS

Diagnostic sensitivity of AdvanSure TB/NTM real-time PCR was 80.0%. As shown from smear positive and negative specimens, sensitivities were 87.5% and 75.9%, respectively. The diagnostic sensitivity of Xpert MTB/RIF assay was 75.5%, and from smear positive and negative specimens, sensitivities were 93.8% and 65.5%, respectively. There were 10 cases with discrepant results between two methods. 2 cases were found resistant to rifampin, although Xpert MTB/RIF assay was able to detect rifampin resistance in only one specimen.

DISCUSSION

Xpert MTB/RIF assay is an easier method to conduct and while its ability to detect rifampin resistance simultaneously is a benefit, its sensitivity from smear negative-culture positive specimens was lower than Advansure TB/NTM real-time PCR. Further investigation to increase the sensitivity and detect other drug resistances by kit-based assays is required for the rapid and accurate diagnosis of tuberculosis.