Comparison of GeneXpert cycle threshold values with smear microscopy and culture as a measure of mycobacterial burden in five regional referral hospitals of Uganda- A cross-sectional study

Correlation of Cyclic Threshold Values Generated by GeneXpert Ultra MTB/RIF and Fluorescence Microscopy to Predict Mycobacterial Burden in Suspected Cases of Pulmonary Tuberculosis

BACKGROUND

Smear microscopy for acid-fast bacilli visualization is important to assess the infectivity rate in patients with pulmonary tuberculosis (PTB), but it has limited sensitivity; hence, it is important to find an alternative strategy. The aim of our study was to compare the fluorescence microscopy grading by Auramine O phenol staining technique of respiratory samples with the cyclic threshold (Ct) values of GeneXpert Ultra (Mycobacterium tuberculosis/rifampicin [MTB/RIF]) and assess the diagnostic efficacy of GeneXpert Ultra (MTB/RIF) compared to microscopy in suspected cases of PTB.

METHODS

The study was conducted in the Mycobacteriology Laboratory, Department of Microbiology, in Kasturba Hospital, Manipal. The study was a prospective, single-centered, cross-sectional study. Four hundred and fifty-two respiratory samples were included in the study. An optimal Ct cutoff value for ruling smear-positivity and smear-negativity and the mean Ct cutoff value were calculated. Clinical and radiological data from the requisition forms were assessed. IBM SPSS statistics software version 22 was used. The correlation between GeneXpert Ultra (MTB/RIF) Ct values and smear status was calculated by polychoric correlation. The extended McNemar's test was used to find the association between the variables.

RESULTS

GeneXpert Ultra (MTB/RIF) yielded a higher positivity rate of 22.2% compared to smear microscopy 17.2%. Ct value and smear grading yielded a positive correlation (P = 0.8681; P < 0.05). GeneXpert Ultra (MTB/RIF) yielded nontuberculous mycobacteria in five undetected cases and speciated as Mycobacterium abscessus complex.

CONCLUSIONS

Our study confirms the GeneXpert Ultra (MTB/RIF) Ct value levels as a predictor of smear positivity.

Xpert MTB/RIF Ultra CT value provides a rapid measure of sputum bacillary burden and predicts smear status in patients with pulmonary tuberculosis

Traditionally, smear microscopy has been used to estimate bacillary burden in order to assess infectiousness in tuberculosis (TB) patients. Since Xpert MTB assays might replace smear microscopy as the first-line diagnostic test for pulmonary tuberculosis, an alternative measure of bacillary load that correlates with smear positivity is needed. This study assessed the correlation between C_T (with and without normalization), smear status, culture time-to-positivity (TTP), and clinical factors in patients with Xpert ultra positive sputum during a four-year period. A cut-off C_T value for smear positivity was also estimated. 204 samples were included. Strong correlation between both Xpert Ultra C_T values (raw and normalized) and smear status was obtained (r = 0.78 and - 0.79, respectively). The association between Raw-C_T and TTP was weaker than normalized-C_T (N-C_T) and TTP (r = 0.50 and r = - 0.70, respectively). A Raw-C_T cut-off value of 21.4 was identified with 85.7% (95% CI 65.4-95) sensitivity and 92.9% (95% CI 84.3-96.9) specificity. A N-C_T cut-off value of 5.2 yielded a sensitivity of 94.3% (95% CI 86.2-97.8) and specificity of 85.7% (95% CI 65.4-95). Our study demonstrates that Xpert Ultra C_T value correlates well with other measures of bacillary load such as smear status or TTP. The correlation with TTP is stronger when the C_T value is normalized using the internal control. The proposed N-C_T cut-off value of 5.2 shows a better sensitivity than the Raw-CT when predicting smear positive status.

Optimizing mycobacteria molecular diagnostics: No decontamination! Human DNA depletion? Greener storage at 4 °C!

Introduction

Tuberculosis (TB) is an infectious disease caused by the group of bacterial pathogens Mycobacterium tuberculosis complex (MTBC) and is one of the leading causes of death worldwide. Timely diagnosis and treatment of drug-resistant TB is a key pillar of WHO's strategy to combat global TB. The time required to carry out drug susceptibility testing (DST) for MTBC via the classic culture method is in the range of weeks and such delays have a detrimental effect on treatment outcomes. Given that molecular testing is in the range of hours to 1 or 2 days its value in treating drug resistant TB cannot be overstated. When developing such tests, one wants to optimize each step so that tests are successful even when confronted with samples that have a low MTBC load or contain large amounts of host DNA. This could improve the performance of the popular rapid molecular tests, especially for samples with mycobacterial loads close to the limits of detection. Where optimizations could have a more significant impact is for tests based on targeted next generation sequencing (tNGS) which typically require higher quantities of DNA. This would be significant as tNGS can provide more comprehensive drug resistance profiles than the relatively limited resistance information provided by rapid tests. In this work we endeavor to optimize pre-treatment and extraction steps for molecular testing.

Methods

We begin by choosing the best DNA extraction device by comparing the amount of DNA extracted by five commonly used devices from identical samples. Following this, the effect that decontamination and human DNA depletion have on extraction efficiency is explored.

Results

The best results were achieved (i.e., the lowest C_t values) when neither decontamination nor human DNA depletion were used. As expected, in all tested scenarios the addition of decontamination to our workflow substantially reduced the yield of DNA extracted. This illustrates that the standard TB laboratory practice of applying decontamination, although being vital for culture-based testing, can negatively impact the performance of molecular testing. As a complement to the above experiments, we also considered the best Mycobacterium tuberculosis DNA storage method to optimize molecular testing carried out in the near- to medium-term. Comparing C_t values following three-month storage at 4 °C and at -20 °C and showed little difference between the two.

Discussion

In summary, for molecular diagnostics aimed at mycobacteria this work highlights the importance of choosing the right DNA extraction device, indicates that decontamination causes significant loss of mycobacterial DNA, and shows that samples preserved for further molecular testing can be stored at 4 °C, just as well at -20 °C. Under our experimental settings, human DNA depletion gave no significant improvement in C_t values for the detection of MTBC.

Discordant results of Xpert MTB/Rif assay and BACTEC MGIT 960 liquid culture to detect Mycobacterium tuberculosis in community screening in Vietnam

BACKGROUND

Xpert MTB/Rif, a molecular test to detect tuberculosis (TB), has been proven to have high sensitivity and specificity when compared with liquid culture in clinical settings. However, little is known about its performance in community TB screening.

METHODS

In Vietnam, a national TB prevalence survey was conducted in 2017. Survey participants who screened positive by chest X-ray, cough symptoms and/or recent history of tuberculosis were requested to provide at least two sputum samples that were tested for Mycobacterium tuberculosis by Xpert MTB/Rif G4 (Xpert) and BACTEC MGIT960 culture (MGIT).

RESULTS

There were 4,649 eligible participants provided both samples for testing. Among them, 236 (5.1%) participants tested positive for TB by Xpert, 244 (5.3%) tested positive by MGIT and 317 tested positive by at least one test; 163 (51.4%) had discordant test results. Of the positive Xpert, 162 (68.6%) showed a low or very low bacterial load. In multivariate logistic regression comparing discordant with Xpert-MGIT concordant positive results, discordant Xpert-positive results occurred more often among participants who had low sputum bacterial load, male sex, a history of TB treatment, or night sweats. The associated factors were male sex, abnormal chest X-ray and having night sweats when the logistic model was against those with both Xpert and MGIT negative.

CONCLUSIONS

We found high rates of discordance in the performance of Xpert and MGIT for community-based TB case finding. In situations where the majority of TB cases are expected to have a low bacterial load, multiple diagnostic tests and/or multiple samples are required to reach sufficient sensitivity.

Status of drug resistant tuberculosis among patients attending a tuberculosis unit of West Bengal: A record based cross-sectional study

Context

Tuberculosis (TB) is one of the main causes of death due to infectious diseases worldwide. Multidrug resistance/rifampicin resistance (MDR/RR) TB remains a public health crisis. India has the highest burden of tuberculosis and multidrug resistant TB (MDR TB) in the world. There is wide geographical variation in the epidemic and its trends that can be updated by regular reporting and sound surveillance systems. The current study tries to fill this gap by analyzing the data of TB patients from a Tuberculosis Unit, studying socio-demographic and clinical profile from December 2017 to November 2019 in Nadia district of West Bengal.

Aims

The aims of this work were to study socio-demographic and clinical profile of TB patients attending Tuberculosis Unit of West Bengal, and to find out factors associated with drug-resistant TB.

Settings and Design

Record-based study from Tuberculosis Unit.

Methods

Records of all patients who undergo CBNAAT in TU are stored as monthly unit. We randomly selected 10 months from a period of December 2017 to November 2019 by using lot method. Data of all patients undergoing CBNAAT at Kalyani - Gayeshpur Tuberculosis Unit during randomly selected 10 months were accessed.

Statistical Analysis Used

Monthly data was entered in Microsoft Excel and descriptive tests of significance, proportions and Chi-square were applied.

Results

There was male preponderance for testing of tuberculosis. Seven percent of the TB suspects were HIV positive. The positivity rate of MTB by CBNAAT was 23%. Four percent of the samples were Rifampicin resistance. Tobacco consumption, contact with TB case and Diabetes were common risk factors of TB. Most of the information was missing in the records.

Conclusions

Most of Rifampicin Resistant cases showed very low Ct value in CBNAAT. Previous history of TB treatment and positive HIV status was significantly associated with RR TB. There is a need to capture complete information on the records of presumptive TB cases.

Epidemiological profile of multidrug-resistant and extensively drug-resistant Mycobacterium Tubrculosis among Congolese patients

BACKGROUND

There is paucity of data on the prevalence and distribution of multidrug- Resistant-Tuberculosis (MDR-TB) in the Republic of Congo. Among the challenges resides the implementation of a robust TB resistance diagnostic program using molecular tools. In resource limited settings there is a need to gather data to enable prioritization of actions. The objective of this study was is to implement molecular tools as a best of diagnosing MDR and XDR-TB among presumptive tuberculosis patients referred to reference hospital of Makelekele in Brazzaville, Republic of the Congo.

METHODS

We have conducted a cross-sectional study, including a total of 92 presumptive pulmonary tuberculosis patients and who had never received treatment recruited at the reference hospital of Makelekele from October 2018 to October 2019. The socio-demographic and clinical data were collected as well as sputum samples. Rifampicin resistance was investigated using Xpert (Cepheid) and second-line TB drugs Susceptibility testing were performed by the Brucker HAIN Line Probe Assay (GenoType MTBDRsl VER 2.0 assay) method.

RESULTS

From the 92 recruited patients, 57 (62%) were found positive for the Mycobacterium tuberculosis complex. The prevalence of rifampicin-resistant tuberculosis (RR-TB) was 9.8% (9/92) and importantly 2.2% were pre-XDR/XDR.

CONCLUSION

This study showed a high rate of rifampicin resistance and the presence of extensively drug-resistant tuberculosis in the study area in new patients. This study highlights the need for further studies of TB drug resistance in the country.

Baseline Xpert MTB/RIF ct values predict sputum conversion during the intensive phase of anti-TB treatment in HIV infected patients in Kampala, Uganda: a retrospective study

Background

In resource-limited settings, sputum smear conversion is used to document treatment response. Many People living with HIV (PLHIV) are smear-negative at baseline. The Xpert MTB/RIF test can indirectly measure bacterial load through cycle threshold (ct) values. This study aimed to determine if baseline Xpert MTB/RIF could predict time to culture negativity in PLHIV with newly diagnosed TB.

Methods

A subset of 138 PLHIV from the ‘SOUTH’ study on outcomes related to TB and antiretroviral drug concentrations were included. Bacterial load was estimated by Mycobacterium Growth Indicator Tubes (MGIT) culture time-to-positivity (TTP) and Lowenstein Jensen (LJ) colony counts. Changes in TTP and colony counts were analyzed with Poisson Generalised Estimating Equations (GEE) and multilevel ordered logistic regression models, respectively, while time to culture negativity analysed with Cox proportional hazard models. ROC curves were used to explore the accuracy of the ct value in predicting culture negativity.

Results

A total of 81 patients (58.7%) were males, median age 34 (IQR 29  – 40) years, median CD4 cell count of 180 (IQR 68  – 345) cells/μL and 77.5% were ART naive. The median baseline ct value was 25.1 (IQR 21.0  – 30.1). A unit Increase in the ct value was associated with a 5% (IRR = 1.05 95% CI 1.04  – 1.06) and 3% (IRR = 1.03 95% CI 1.03  – 1.04) increase in TTP at week 2 and 4 respectively. With LJ culture, a patient’s colony grade was reduced by 0.86 times (0R = 0.86 95% CI 0.74  – 0.97) at week 2 and 0.84 times (OR = 0.84 95% CI 0.79  – 0.95 P = 0.002) at week 4 for every unit increase in the baseline ct value. There was a 3% higher likelihood of earlier conversion to negativity for every unit increase in the ct value. A ct cut point ≥28 best predicted culture negativity at week 4 with a sensitivity of 91. 7% & specificity 53.7% while a cut point ≥23 best predicted culture negativity at week 8.

Conclusion

Baseline Xpert MTB/RIF ct values predict sputum conversion in PLHIV on anti-TB treatment. Surrogate biomarkers for sputum conversion in PLHIV are still a research priority.

The Xpert® MTB/RIF diagnostic test for pulmonary and extrapulmonary tuberculosis in immunocompetent and immunocompromised patients: Benefits and experiences over 2 years in different clinical contexts

Xpert^® MTB/RIF has been widely used for tuberculosis (TB) diagnosis in Brazil, since 2014. This prospective observational study aimed to evaluate the performance of Xpert in different contexts during a two-year period: (i) laboratory and clinical/epidemiological diagnosis; (ii) HIV-positive and -negative populations; (iii) type of specimens: pulmonary and extrapulmonary. Overall, 924 specimens from 743 patients were evaluated. The performance of the assays was evaluated considering culture (Lowenstein Jensen or LJ medium) results and composite reference standard (CRS) classification as gold standard. According to CRS evaluation, 219 cases (29.5%) were classified as positive cases, 157 (21.1%) as ‘possible TB’, and 367 (49.3%) as ‘not TB’. Based on culture, Xpert and AFB smear achieved a sensitivity of 96% and 62%, respectively, while based on CRS, the sensitivities of Xpert, AFB smear, and culture were 40.7%, 20%, and 25%, respectively. The pooled sensitivity and specificity of Xpert were 96% and 94%, respectively. Metric evaluations were similar between pulmonary and extrapulmonary samples against culture, whereas compared to CRS, the sensitivities were 44.6% and 29.3% for the pulmonary and extrapulmonary cases, respectively. The Xpert detected 42/69 (60.9%) patients with confirmed TB and negative culture on LJ medium, and 52/69 (75.4%) patients with negative AFB smear results. There was no significant difference in the diagnostic accuracy based on the types of specimens and population (positive- and negative-HIV). Molecular testing detected 13 cases of TB in culture-negative patients with severe immunosuppression. Resistance to rifampicin was detected in seven samples. Herein, Xpert showed improved detection of pulmonary and extrapulmonary TB cases, both among HIV-positive and -negative patients, even in cases with advanced immunosuppression, thereby performing better than multiple other diagnostic parameters.