Detection of Mycobacterium tuberculosis and rifampicin resistance by Xpert® MTB/RIF assay among presumptive tuberculosis patients in Addis Ababa, Ethiopia from 2014 to 2021

Efficacy of Xpert MTB/RIF assay in detecting Mycobacterium tuberculosis in samples with different results by smear and culture in a coastal city with high incidence of tuberculosis

BACKGROUND

Tuberculosis (TB) is a global problem that seriously jeopardizes human health. Among them, the diagnosis and treatment of smear- or culture-negative TB patients is a challenge. The Xpert MTB/RIF (Xpert) assay has been reported to be a novel molecular diagnostic tool for rapidly detecting TB. Still, there is limited data on this assay's performance in subgroups of TB patients. This study aimed to evaluate the diagnostic value of the Xpert method in patients with different smear and culture results and to assess its efficacy for rifampicin resistance (RR) detection.

METHODS

We retrospectively collected data from 1,721 patients with a clinical diagnosis of tuberculosis. Smear, Xpert, and traditional solid culture methods were used to detect TB infection and explore the detection rate of Xpert in the grouping of results from different smear and culture methods. Information on RR detected by the Xpert method and proportional method of drug sensitivity test (DST) was also recorded and kappa values, sensitivity, and specificity were calculated.

RESULTS

We observed that among the three methods, the Xpert method had the highest detection rate of 66.8%, followed by the culture method at 56.0% and the smear method had the lowest at 40.0%. The detection rate of Xpert was 98.3% (642/653) when both smear and culture were positive, 85.1% (296/348) when only one of the two methods, smear and culture, was positive, and 29.4% (212/720) when both smear and culture were negative. The Xpert method and DST showed a high agreement (κ = 0.92) for RR detection. The highest mutation rate was observed for probe E (64.7%), and the least number of probe C mutations occurred (1.5%).

CONCLUSION

The Xpert method has high detection efficiency. It has good diagnostic value in detecting MTB and RR, especially in cases where traditional culture and sputum smear results are negative, and significantly reduces the rate of missed diagnosis.

Implementation of the advanced HIV disease package of care using a public health approach: lessons from Nigeria

BACKGROUND

Nigeria adapted the WHO package of care for Advanced HIV Disease (AHD) in 2020. The package includes CD4 + cell count testing to identify People Living with HIV (PLHIV) with AHD, screening and treatment of opportunistic infections, rapid antiretrovirals (ART) initiation, and intensive adherence follow-up. The national program adopted a phased approach in the rollout of the AHD package of care to learn lessons from a few representative health facilities before scaling up across the country. This study describes the process and lessons learned from the first phase of implementation.

METHODS

This was a prospective observational study, and participants were enrolled between February and September 2021. Healthcare-worker (HCW) capacity was built to implement the AHD package of care. The study population included newly diagnosed PLHIV ≥ 10 years presenting to care in 28 selected facilities across 4 states in Nigeria. Eligible participants received CD4 + cell testing at baseline. Those with CD4 + cell count < 200 cells/mm3 were subjected to a blood cryptococcal antigen (CrAg) test and urine TB lateral flow lipoarabinomannan (LF-LAM). Those with positive CrAg tests had a cerebrospinal fluid (CSF) test to confirm cryptococcal meningitis. Those negative for both blood CrAg and TB LF-LAM were rapidly initiated on ART and underwent intensive follow-up. Participants were followed up for 12 months.

RESULTS

A total of 6,781 patients were enrolled; 71% (4,812) received CD4 + cell count test, of which 41% (1,969 of 4812) had a CD4 + count < 200 cells/mm3. Approximately 81% (1,492 of 1,850) of those with CD4 + count < 200 cells/mm3 had TB LF-LAM test results documented; 25% were positive, of which 47% started TB treatment. Blood CrAg screening coverage among those with CD4 + count < 200 cells/mm3 was 88% (1,634 of 1,850), of which 5% (85 of 1,634) were positive. Cotrimoxazole preventive therapy was initiated for 65% (1,198 of 1,850) of the participants with CD4 + count < 200 cells/mm3, and 70% (966 of 1,375) of AHD patients with a negative TB LF-LAM and blood CrAg results were initiated on ART on the day of enrolment. Approximately 91% (421 of 461) of those who received viral load results at month 12 post-enrollment were virally suppressed. The retention rate and the Kaplan Meier survival probability estimate at month 12 were 65% (1,204 of 1,850) and 0.93 (CI, 0.91-0.94), respectively, for the enrolled participants.

CONCLUSION

Implementation of the AHD package of care in Nigeria has improved the diagnosis of TB and CM, and will potentially enhance the quality of care for PLHIV if sustained. Findings from this implementation were used to guide national scale-up.

Trends of Mycobacterium tuberculosis and Rifampicin resistance in Northwest Ethiopia: Xpert® MTB/RIF assay results from 2015 to 2021

BACKGROUND

Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide, particularly in countries with limited resources. The emergence of drug resistance in mycobacterium tuberculosis (MTB), particularly rifampicin (RIF) resistance, hindered TB control efforts. Continuous surveillance and regular monitoring of drug-resistant TB, including rifampicin resistance (RR), are required for effective TB intervention strategies and prevention and control measures.

OBJECTIVE

Determine the trend of TB and RR-TB among presumptive TB patients in Northwest Ethiopia.

METHOD

A retrospective study was conducted at the University of Gondar Comprehensive Specialized Hospital (UoG-CSH). The study included TB registration logbook data from all patients who visited the hospital and were tested for MTB using the Xpert® MTB/RIF assay between 2015 and 2021. The SPSS version 26 software was used to enter, clean, and analyze the laboratory-based data.

RESULTS

A total of 18,787 patient results were included, with 93.8% (17,615/18787) of them being successful, meaning they were not invalid, error, or aborted. About 10.5% (1846/17615) of the 17,615 results were MTB-positive, with 7.42% (137/1846) RIF resistant. Age, anti-TB treatment history, and diagnosis year were associated with the presence of MTB and RR-MTB. Tuberculosis (TB) prevalence was higher in productive age groups, whereas RR-TB prevalence was higher in the elderly. Regarding diagnosis year, the prevalence of TB and RR-TB showed a declining trend as the year progressed. While MTB was detected in 12.8% (471/3669) of new and 22.2% (151/679) of re-treatment presumptive TB patients, RR-MTB was detected in 8.5% (40/471) of new and 18.5% (28/151) of re-treatment TB cases.

CONCLUSION

The prevalence of TB and RR-TB in the study area showed a declining trend over the years. While TB was more prevalent in productive age groups (15 to 45 years), RR-TB was more prevalent in older populations (over 45 years), than others. Moreover, patients with a history of anti-TB drug exposure were more likely to be positive for DR-TB, highlighting the need to strengthen DOT programs for proper management of TB treatment.

Determination of the diagnostic accuracy of nanopore sequencing using bronchoalveolar lavage fluid samples from patients with sputum-scarce pulmonary tuberculosis

PURPOSE

The early and efficient diagnosis of patients suspected of having pulmonary tuberculosis (PTB) remains challenging. This study aimed to evaluate the accuracy of nanopore sequencing for PTB diagnosis using bronchoalveolar lavage fluid (BALF) samples and compared it with other techniques such as acid-fast bacilli smear, culture, Xpert MTB/RIF, and CapitalBio Mycobacterium reverse transcription-polymerase chain reaction (MTB RT-PCR).

METHODS

We retrospectively analyzed the clinical data of 195 patients with suspected PTB who were admitted to our hospital. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) of these assays were calculated and compared.

RESULTS

The overall sensitivity, specificity, PPV, NPV, and AUC of nanopore sequencing were 90.70%, 84.85%, 92.13%, 82.35%, and 0.88; those of acid-fast bacilli smear were 12.40%, 98.48%, 94.12%, 36.52%, and 0.55; those of culture were 36.43%, 100%, 100%, 44.59%, and 0.68; those of Xpert MTB/RIF were 41.09%, 100%, 100%, 46.48%, and 0.71; and those of CapitalBio MTB RT-PCR were 34.88%, 98.48%, 97.83%, 43.62%, and 0.67, respectively.

CONCLUSION

The nanopore sequencing assay using BALF samples showed the best diagnostic accuracy for sputum-scarce PTB. Moreover, it can improve the clinical diagnosis of PTB.