Countrywide roll-out of Xpert(®) MTB/RIF in Swaziland: the first three years of implementation

Analysis of unsuccessful tests and the effect of prolonged clinical sample preprocessing in the GeneXpert MTB/RIF assay

BACKGROUND

The GeneXpert MTB/RIF (Xpert) assay is a widely used technology for detecting Mycobacterium tuberculosis (MTB) in clinical samples. However, the study on the failure of the Xpert assay during routine implementation and its potential solutions is limited.

METHODS

We retrospectively analyzed the records of unsuccessful tests in the Xpert and the GeneXpert MTB/RIF Ultra (Ultra) assays between April 2017 and April 2021 at the Shanghai Public Health Clinical Center. To further investigate the effect of prolonged preprocessing on clinical sputum, an additional 120 sputum samples were collected for Xpert testing after 15 min, 3 h, and 6 h preprocessing. The analysis was performed by SPSS version 19.0 software.

RESULTS

A total of 11,314 test records were analyzed, of which 268 (2.37%) had unsuccessful test results. Among these, 221 (1.95%) were reported as "Error", 43 (0.38%) as "Invalid", and 4 (0.04%) as "No result". The most common clinical specimen for Xpert tests was sputum, accounting for 114 (2.17%) unsuccessful tests. The failure rate of urine specimens was lower than that of sputum (OR = 0.12, 95% CI: 0.02-0.88, χ2 = 6.22, p = 0.021). In contrast, the failure rate of stool specimens was approximately twice as high as that of sputum (OR = 1.93, 95% CI: 1.09-3.40, χ2 = 5.35, p = 0.014). In the prolonged preprocessing experiment, 102 cases (85%) yielded consistent results in Xpert tests. Furthermore, 7 cases (5.83%) detected an increase in MTB load, 8 cases (6.67%) detected a decrease in MTB load, and 3 cases (2.5%) yielded incongruent results in MTB and rifampicin resistance detection.

CONCLUSIONS

The primary cause of unsuccessful tests in the Xpert assay was reported as "Error". Despite varying failure rates depending on the samples, the Xpert assay can be applied to extrapulmonary samples. For paucibacillary specimens, retesting the remaining preprocessed mixture should be carefully considered.

Challenges with the use of Xpert HPV as a screening tool for oral HPV among people living with HIV (PLHIV): experiences from Pune, India

BACKGROUND

People living with HIV (PLHIV) are at higher risk for human papillomavirus (HPV)-related oropharyngeal cancers compared to the general population. Xpert HPV test is a polymerase chain reaction (PCR) assay capable of rapid HPV detection. Performing the assay requires minimal intervention by laboratory personnel. Its use could improve oropharyngeal cancer screening among PLHIV living in low-and middle-income countries (LMICs) with limited diagnostic capacities. However, Xpert HPV performance for oral samples has not been evaluated. Here, we describe our experience with Xpert HPV and compare its results with traditional PCR, for oral samples.

METHODS

Oral samples from 429 PLHIV receiving care at a tertiary care hospital affiliated antiretroviral therapy center in Pune, India were used. Samples were collected either after a 30s oral rinse and gargle (n = 335) or in combination with cytobrush scraping of the oral mucosa (n = 91). Unsuccessful tests were those that generated an invalid or error result on Xpert HPV. Successful tests were those that generated a positive or negative result. Kappa statistic was used to compare concordance between Xpert HPV and traditional real-time PCR results.

RESULTS

There were 29.8% (n = 127) unsuccessful tests, of which 78.7% (n = 100) were invalid and 21.3% (n = 27) were error results. Adding cytobrush scraping to oral rinse as a collection procedure did not significantly reduce the proportion of unsuccessful tests (p = 0.9). For successful tests, HPV positivity on Xpert was 0.3% (n = 1/299). Kappa statistic was 0.11, indicating poor agreement between Xpert HPV and traditional PCR results.

CONCLUSIONS

Presently, Xpert HPV appears to have limited use for oral HPV detection among PLHIV using oral samples. More research to improve the diagnostic capabilities of Xpert HPV for oral samples among PLHIV is needed.

Evolution of Mycobacterium tuberculosis drug resistance in the genomic era

Mycobacterium tuberculosis has acquired drug resistance to all drugs that have been used against it, including those only recently introduced into clinical practice. Compared to other bacteria, it has a well conserved genome due to its role as an obligate human pathogen that has adapted to a niche over five to ten thousand years. These features facilitate reconstruction and dating of M. tuberculosis phylogenies, giving key insights into how resistance has been acquired and spread globally. Resistance to each new drug has occurred within five to ten years of clinical use and has occurred even more rapidly with recently introduced drugs. In most cases, resistance-conferring mutations come with a fitness cost, but this can be overcome by compensatory mutations which restore fitness to that of wild-type bacteria. It is likely that M. tuberculosis acquires drug resistance while maintaining limited genomic variability due the generation of low frequency within-host variation, combined with ongoing purifying selection causing loss of variants without a clear fitness advantage. However, variants that do confer an advantage, such as drug resistance, can increase in prevalence amongst all bacteria within a host and become the dominant clone. These resistant strains can then be transmitted leading to primary drug resistant infection in a new host. As many countries move towards genomic methods for diagnosis of M. tuberculosis infection and drug resistance, it is important to be aware of the implications for the evolution of resistance. Currently, understanding of resistance-conferring mutations is incomplete, and some targeted genetic diagnostics create their own selective pressures. We discuss an example where a rifampicin resistance-conferring mutation which was not routinely covered by standard testing became dominant. Finally, resistance to new drugs such as bedaquiline and delamanid is caused by individually rare mutations occurring across a large mutational genomic target that have been detected over a short time, and do not provide statistical power for genotype-phenotype correlation – in contrast to longer-established drugs that form the backbone of drug-sensitive antituberculosis therapy. Therefore, we need a different approach to identify resistance-conferring mutations of new drugs before their resistance becomes widespread, abrogating their usefulness.

Implementation of GeneXpert for TB Testing in Low- and Middle-Income Countries: A Systematic Review

This review highlights a commonality of implementation barriers across geographically dispersed GeneXpert interventions for TB testing. This indicates the importance of using implementation frameworks to report findings that can improve public health outcomes across low- and middle-income countries.

Introduction:

Current evidence indicates that the impact of GeneXpert for diagnosing TB in low- and middle-income countries (LMICs) has not demonstrated equivalent outcomes when compared to Xpert evaluations in upper-middle-income countries. Challenges associated with implementation are possible contributing factors preventing this innovative diagnostic technology from achieving more significant public health outcomes. This review aimed to assess the use of implementation science frameworks when reporting the enablers and barriers for the implementation of GeneXpert for diagnosing TB in LMICs.

Methods:

We conducted a qualitative systematic review of the peer-reviewed literature using PubMed, Medline, and Scopus. Eligible articles were those published between January 2010 and March 2020 that identified enablers and barriers to GeneXpert implementation, as well as the implementation approach delivered in an LMIC.

Results:

Eleven studies were included in the review. Implementation barriers were found to be relatively consistent across studies and included patient-level factors, human resources, material resources, service implementation, service coordination, and technical operations. Few studies (n=5) identified enabling factors in the implementation of Xpert for TB testing. Identified enablers included strategies such as active case finding, expanding diagnostic algorithms, and daily transport of samples. The public health impact of Xpert TB testing interventions was commonly influenced by implementation barriers (n=4). Of the 11 studies, only 3 reported against an implementation framework.

Conclusion:

This review identified a commonality in implementation barriers and enablers that influenced the overall public health impact of GeneXpert. With greater transparency of these barriers and enablers, program planners can promote a more collaborative approach and adapt interventions. It is recommended that program planners use implementation science frameworks when conducting research and publishing. This will build an evidence base focused on implementation and thereby support programs to address implementation barriers and include enabling factors in program design.

Scaling Up Molecular Diagnostic Tests for Drug-Resistant Tuberculosis in Uzbekistan from 2012-2019: Are We on the Right Track?

Uzbekistan has a large burden of drug-resistant tuberculosis (TB). To deal with this public health threat, the National TB Program introduced rapid molecular diagnostic tests such as Xpert MTB/RIF (Xpert) and line probe assays (LPAs) for first-line and second-line drugs. We documented the scale-up of Xpert and LPAs from 2012–2019 and assessed whether this led to an increase in patients with laboratory-confirmed multidrug-resistant/rifampicin-resistant TB (MDR/RR-TB) and extensively drug-resistant TB (XDR-TB). This was a descriptive study using secondary program data. The numbers of GeneXpert instruments cumulatively increased from six to sixty-seven, resulting in annual assays increasing from 5574 to 107,330. A broader use of the technology resulted in a lower proportion of tests detecting Mycobacterium tuberculosis with half of the positive results showing rifampicin resistance. LPA instruments cumulatively increased from two to thirteen; the annual first-line assays for MDR-TB increased from 2582 to 6607 while second-line assays increased from 1435 in 2016 to 6815 in 2019 with about one quarter to one third of diagnosed patients showing second-line drug resistance. Patient numbers with laboratory-confirmed MDR-TB remained stable (from 1728 to 2060) but there was a large increase in patients with laboratory-confirmed XDR-TB (from 31 to 696). Programmatic implications and ways forward are discussed.

Coverage and fidelity of the Xpert MTB/RIF™ implementation in a high-burden area for pulmonary tuberculosis in Colombia

Introducción.

La prueba Xpert MTB/RIF™ es una prueba molecular rápida para el diagnóstico de la tuberculosis y la resistencia a la rifampicina. Desde el 2010 es la recomendada por la Organización Mundial de la Salud (OMS) y, aunque fue introducida en Colombia en el 2012, se desconocen los resultados de su uso.

Objetivo.

Describir la cobertura y la fidelidad en el uso de la prueba Xpert MTB/RIF™ en pacientes con tuberculosis pulmonar en una ciudad con alta carga de la enfermedad en Colombia.

Materiales y métodos.

Se hizo un estudio retrospectivo descriptivo de casos del programa de tuberculosis en Cali entre el 2013 y el 2019. La cobertura se estimó como el total de pruebas empleadas en los casos registrados en el programa. La fidelidad se midió con base en los protocolos internacionales de uso de la Xpert MTB/RIF™. Además, se hizo un análisis de correspondencias múltiples entre la prueba y las variables sociodemográficas.

Resultados.

Se incluyeron 6.328 pacientes con tuberculosis pulmonar, de los cuales 181 eran resistentes a los fármacos. La cobertura total de la Xpert MTB/RIF™ durante el periodo de estudio fue de 10,3 % (n=655), con una variación anual entre 0,2 y 23 %. La fidelidad fue de 46,8 % para los grupos de mayor riesgo de tuberculosis multirresistente (TB-MDR). El uso de la prueba se relacionó con la condición de ser hombre, afrocolombiano, y tener entre 41 y 60 años de edad.

Conclusiones.

La cobertura de la prueba Xpert MTB/RIF™ en Cali es baja y su uso no responde a la priorización recomendada para su implementación. Se requieren estrategias para promover su uso adecuado, de manera que contribuya a la meta de poner fin a la tuberculosis.

MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era

Background

Multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains not detected by commercial molecular drug susceptibility testing (mDST) assays due to the RpoB I491F resistance mutation are threatening the control of MDR tuberculosis (MDR-TB) in Eswatini.

Methods

We investigate the evolution and spread of MDR strains in Eswatini with a focus on bedaquiline (BDQ) and clofazimine (CFZ) resistance using whole-genome sequencing in two collections ((1) national drug resistance survey, 2009–2010; (2) MDR strains from the Nhlangano region, 2014–2017).

Results

MDR strains in collection 1 had a high cluster rate (95%, 117/123 MDR strains) with 55% grouped into the two largest clusters (gCL3, n = 28; gCL10, n = 40). All gCL10 isolates, which likely emerged around 1993 (95% highest posterior density 1987–1998), carried the mutation RpoB I491F that is missed by commercial mDST assays. In addition, 21 (53%) gCL10 isolates shared a Rv0678 M146T mutation that correlated with elevated minimum inhibitory concentrations (MICs) to BDQ and CFZ compared to wild type isolates. gCL10 isolates with the Rv0678 M146T mutation were also detected in collection 2.

Conclusion

The high clustering rate suggests that transmission has been driving the MDR-TB epidemic in Eswatini for three decades. The presence of MDR strains in Eswatini that are not detected by commercial mDST assays and have elevated MICs to BDQ and CFZ potentially jeopardizes the successful implementation of new MDR-TB treatment guidelines. Measures to limit the spread of these outbreak isolates need to be implemented urgently.

Situating trade-offs: Stakeholder perspectives on overtreatment versus missed diagnosis in transition to Xpert MTB/RIF Ultra in Kenya and Swaziland

Implementing new diagnostics in public health programs can involve difficult trade-off decisions between individual patient benefits and public health considerations. Such decision-making processes are often not documented and may not include engagement of affected communities. This paper examines the perspectives of stakeholders on the trade-off between over-treatment and missed diagnosis captured during decision-making workshops on the transition from use of Xpert MTB/RIF to diagnose tuberculosis to Xpert MTB/RIF Ultra in Kenya and Swaziland. Xpert MTB/RIF Ultra has an overall increase in sensitivity but a decrease in specificity when compared to its predecessor. We conducted a qualitative study using four focus group discussions with a total of 47 participants and non-participant observation. The analysis reveals how participants deemed Xpert MTB/RIF Ultra’s reduced specificity vis-à-vis its increased sensitivity to be an acceptable trade-off. The way participants assessed this trade-off was shaped by their experiences with the general uncertainty of all diagnostic tests, alternative testing options, historical evolution of diagnostic practices, epidemiological factors and resource constraints. In assessing the trade-off community and individual benefit and harm was frequently discussed together. Qualitative research on stakeholder engagement activities for diagnostic development and implementation can identify everyday experiences and situate assessments and perspectives of key stakeholders and as such aid in decision-making, improving implementation as well as patient outcomes. Further research is needed on the intended and unintended consequences of such engagement activities, how findings are being incorporated by decision-makers, and the impact on programmatic implementation.

Impact of External Quality Assurance on the Quality of Xpert MTB/RIF Testing in Viet Nam

Following the endorsement of the Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA, USA) by the World Health Organization (WHO) in 2010, Viet Nam's National Tuberculosis Control Program (NTP) began using GeneXpert instruments in NTP laboratories. In 2013, Viet Nam's NTP implemented an Xpert MTB/RIF external quality assurance (EQA) program in collaboration with the U.S. Centers for Disease Control and Prevention (CDC) and the Foundation for Innovative New Diagnostics (FIND). Proficiency-testing (PT) panels comprising five dried tube specimens (DTS) were sent to participating sites approximately twice a year from October 2013 to July 2016. The number of enrolled laboratories increased from 22 to 39 during the study period. Testing accuracy was assessed by comparing reported and expected results; percentage scores were assigned; and feedback reports were provided to sites. On-site evaluation (OSE) was conducted for underperforming laboratories. The results from the first five rounds demonstrate the positive impact of PT and targeted OSE visits on testing quality. On average, for every additional round of feedback, the odds of achieving PT scores of ≥80% increased 2.04-fold (95% confidence interval, 1.39- to 3.00-fold). Future work will include scaling up PT to all sites and maintaining the performance of participating laboratories while developing local panel production capacity.

Challenges and Progress with Diagnosing Pulmonary Tuberculosis in Low- and Middle-Income Countries

Case finding and the diagnosis of tuberculosis (TB) are key activities to reach the World Health Organization's End TB targets by 2030. This paper focuses on the diagnosis of pulmonary TB (PTB) in low- and middle-income countries. Sputum smear microscopy, despite its many limitations, remains the primary diagnostic tool in peripheral health facilities; however, this is being replaced by molecular diagnostic techniques, particularly Xpert MTB/RIF, which allows a bacteriologically confirmed diagnosis of TB along with information about whether or not the organism is resistant to rifampicin within two hours. Other useful diagnostic tools at peripheral facilities include chest radiography, urine lipoarabinomannan (TB-LAM) in HIV-infected patients with advanced immunodeficiency, and the loop-mediated isothermal amplification (TB-LAMP) test which may be superior to smear microscopy. National Reference Laboratories work at a higher level, largely performing culture and phenotypic drug susceptibility testing which is complemented by genotypic methods such as line probe assays for detecting resistance to isoniazid, rifampicin, and second-line drugs. Tuberculin skin testing, interferon gamma release assays, and commercial serological tests are not recommended for the diagnosis of active TB. Linking diagnosis to treatment and care is often poor, and this aspect of TB management needs far more attention than it currently receives.

Has the utilisation of Xpert® MTB/RIF in Manicaland Province, Zimbabwe, improved with new guidance on whom to test?

Setting: Manicaland Province, Zimbabwe. Objectives: To compare the utilisation and results of deploying Xpert^® MTB/RIF in 13 (one provincial, six district and six rural) hospitals between January and June 2016, when Xpert was recommended only for those with presumptive multidrug-resistant tuberculosis (MDR-TB) and coinfection with human immunodeficiency virus (HIV), and between January and June 2017, when Xpert was recommended for all presumptive TB patients. Design: This was a cross-sectional study. Results: Xpert assays averaged 759 monthly in 2016 and 1430 monthly in 2017 (88% increase). Utilisation of Xpert averaged 22% monthly in 2016 and 42% in 2017 (88% increase). In 2017, utilisation of Xpert was significantly higher in provincial (82%) than in district (51%) and rural (26%) hospitals (P < 0.001). The proportion of successful assays that detected TB decreased significantly from 13% in 2016 to 7% in 2017 (a 46% decrease, P < 0.001); this phenomenon was observed in all types of hospital. The proportion of persons detected with rifampicin-resistant TB was similar between hospitals (4% in 2016 and 3% in 2017). The proportion of registered TB cases with bacteriological confirmation increased from 48% in 2016 to 53% in 2017 (P = 0.04). Conclusion: Xpert use in all presumptive TB patients led to a significant increase in assay numbers and utilisation of Xpert instruments, resulting in more bacteriological confirmation of cases.

Smear Microscopy for Diagnosis of Pulmonary Tuberculosis in Eastern Sudan

Background

In Sudan, tuberculosis diagnosis largely relies on clinical symptoms and smear microscopy as in many other low- and middle-income countries. The aim of this study was to investigate the positive predictive value of a positive sputum smear in patients investigated for pulmonary tuberculosis in Eastern Sudan.

Methods

Two sputum samples from patients presenting with symptoms suggestive of tuberculosis were investigated using direct Ziehl-Neelsen (ZN) staining and light microscopy between June to October 2014 and January to July 2016. If one of the samples was smear positive, both samples were pooled, stored at −20°C, and sent to the National Reference Laboratory (NRL), Germany. Following decontamination, samples underwent repeat microscopy and culture. Culture negative/contaminated samples were investigated using polymerase chain reaction (PCR).

Results

A total of 383 samples were investigated. Repeat microscopy categorized 123 (32.1%) as negative, among which 31 were culture positive. This increased to 80 when PCR and culture results were considered together. A total of 196 samples were culture positive, of which 171 (87.3%), 14 (7.1%), and 11 (5.6%) were M. tuberculosis, M. intracellulare, and mixed species. Overall, 15.6% (57/365) of the samples had no evidence of M. tuberculosis, resulting in a positive predictive value of 84.4%.

Conclusions

There was a discordance between the results of smear microscopy performed at local laboratories in the Sudan and at the NRL, Germany; besides, a considerable number of samples had no evidence of M. tuberculosis. Improved quality control for smear microscopy and more specific diagnostics are crucial to avoid possible overtreatment.

How has the Zimbabwe mycobacterial culture and drug sensitivity testing system among re-treatment tuberculosis patients functioned during the scale-up of the Xpert MTB/RIF assay?

Background

In Zimbabwe, while the Xpert MTB/RIF assay is being used for diagnosing tuberculosis and rifampicin-resistance, re-treatment tuberculosis (TB) patients are still expected to have culture and drug sensitivity testing (CDST) performed at national reference laboratories for confirmation. The study aim was to document the Xpert MTB/RIF assay scale-up and assess how the CDST system functioned for re-treatment TB patients.

Methods

We performed an ecologic study using national aggregate data.

Results

Use of the Xpert MTB/RIF assay increased from 11 829 to 68 153 between 2012 and 2016. Xpert assays worked well, with successful tests in more than 90% of cases, TB detection rates at 15–17% and rifampicin resistance in <10%. During Xpert scale-up, the number of sputum specimens from re-treatment TB patients reaching national reference laboratories for CDST increased from 12% to 51%. In terms of laboratory performance, culture contamination increased from 3% to 17%, positive cultures from 13% to 17% and successful CDST from 6% to 14%: the proportion of CDST showing any resistance to rifampicin averaged 44%. From 2009 to 2016, the proportion of notified re-treatment TB patients with successful CDST increased from <1% to 7%.

Conclusions

While components of Zimbabwe’s CDST system for re-treatment TB patients showed some changes during the scale-up of the Xpert MTB/RIF assay, overall performance was poor. The country must either invest in improving CDST performance or in advanced molecular diagnostic technology.

Impact of Laboratory Practice Changes on the Diagnosis of Tuberculosis with the Introduction of Xpert MTB/RIF in Kiribati

The Republic of Kiribati, Central Pacific, has the largest tuberculosis epidemic in the region. There is a national tuberculosis control program, which has used smear microscopy for acid-fast bacilli as the main diagnostic tool for many years. In 2015, an Xpert MTB/RIF machine was procured and became functional within the tuberculosis hospital. The aim of this cross-sectional study, using routinely collected data, was to determine the effects of introducing Xpert MTB/RIF on laboratory smear microscopy practices and the pattern of registered tuberculosis cases. Between February 2015 and January 2016, there were 220 Xpert MTB/RIF assays performed with 6.4% errors and 15% detection of Mycobacterium tuberculosis: one patient showed rifampicin-resistance. One year before and after introducing Xpert MTB/RIF, the number of presumptive tuberculosis patients increased by 9% from 2,138 to 2,322. There were no changes in demographic characteristics, smear-positive results, or acid-fast bacilli grade between the two periods. The number of specimens cultured for Mycobacterium tuberculosis significantly declined from 638 to zero, with 76 positive MTB cultures before and none after introducing Xpert MTB/RIF. There was a significant change in the profile of registered tuberculosis cases with more children (34% versus 21%) and fewer bacteriologically-confirmed cases (29% versus 43%) - P < .001. Since the deployment of Xpert MTB/RIF in Kiribati, there have been a small number of assays performed and this has been associated with no adverse effects on smear microscopy, a stoppage in mycobacterial cultures, and a change in the types and categories of diagnosed tuberculosis.

Adherence, tolerability, and outcome after 36 months of isoniazid-preventive therapy in 2 rural clinics of Swaziland: A prospective observational feasibility study

Although efficacy of 36 months isoniazid preventive therapy (IPT) among HIV-positive individuals has been proven in trial settings, outcome, tolerance, and adherence have rarely been evaluated in real-life settings.This is a prospective observational cohort study conducted in 2 primary care rural clinics in Swaziland.After negative tuberculosis symptom screening, patients either with the positive tuberculin skin test (TST) or after tuberculosis treatment were initiated on IPT for 144 weeks. In addition to routine clinic visits, adherence was assessed every semester.Of 288 eligible patients, 2 patients never started IPT (1 refusal, 1 contraindication), and 253 (87.8%), 234 (81.3%), and 228 (79.2%) were still on IPT after 48, 96, and 144 weeks, respectively (chiP = .01). Of 41 patients who interrupted IPT before 144 weeks, 21 defaulted (of which 17 also defaulted HIV care); 16 stopped because of adverse drug reactions; 2 were discontinued by clinicians' mistake and 1 because of TB symptoms. Five patients (1.7%) died of causes not related to IPT, 5 (1.7%) developed TB of which 2 were isoniazid-resistant, and 9 (3.1%) were transferred to another clinic. As an indicator of adherence, isoniazid could be detected in the urine during 86.3% (302/350) and 73.6% (248/337) of patient visits in the 2 clinics, respectively (chiP < .001).The routine implementation of IPT 36 months was feasible and good patient outcomes were achieved, with low TB incidence, good tolerance, and sustained adherence.

Treatment decisions and mortality in HIV-positive presumptive smear-negative TB in the Xpert™ MTB/RIF era: a cohort study

BACKGROUND

The Xpert™ MTB/RIF (XP) has a higher sensitivity than sputum smear microscopy (70% versus 35%) for TB diagnosis and has been endorsed by the WHO for TB high burden countries to increase case finding among HIV co-infected presumptive TB patients. Its impact on the diagnosis of smear-negative TB in a routine care setting is unclear. We determined the change in diagnosis, treatment and mortality of smear-negative presumptive TB with routine use of Xpert MTB/RIF (XP).

METHODS

Prospective cohort study of HIV-positive smear-negative presumptive TB patients during a 12-month period after XP implementation in a well-staffed and trained integrated TB/HIV clinic in Kampala, Uganda. Prior to testing clinicians were asked to decide whether they would treat empirically prior to Xpert result; actual treatment was decided upon receipt of the XP result. We compared empirical and XP-informed treatment decisions and all-cause mortality in the first year.

RESULTS

Of 411 smear-negative presumptive TB patients, 175 (43%) received an XP; their baseline characteristics did not differ. XP positivity was similar in patients with a pre-XP empirical diagnosis and those without (9/29 [17%] versus 14/142 [10%], P = 0.23). Despite XP testing high levels of empirical treatment prevailed (18%), although XP results did change who ultimately was treated for TB. When adjusted for CD4 count, empirical treatment was not associated with higher mortality compared to no or microbiologically confirmed treatment.

CONCLUSIONS

XP usage was lower than expected. The lower sensitivity of XP in smear-negative HIV-positive patients led experienced clinicians to use XP as a "rule-in" rather than "rule-out" test, with the majority of patients still treated empirically.

The impact of the roll-out of rapid molecular diagnostic testing for tuberculosis on empirical treatment in Cape Town, South Africa

OBJECTIVE

To investigate the impact of introducing a rapid test as the first-line diagnostic test for drug-sensitive tuberculosis in Cape Town, South Africa.

METHODS

Xpert® MTB/RIF (Xpert®), an automated polymerase-chain-reaction-based assay, was rolled out between 2011 and 2013. Data were available on 102 007 adults treated for pulmonary tuberculosis between 2010 and 2014. Tuberculosis notification rates per 100 000 population were calculated for each calendar year and for each year relative to the test roll-out locally, overall and by bacteriological confirmation. Empirical treatment was defined as treatment given without bacteriological confirmation by Xpert®, sputum smear microscopy or sputum culture.

FINDINGS

Between 2010 and 2014, the proportion of human immunodeficiency virus (HIV)-negative patients treated empirically for tuberculosis declined from 23% (2445/10 643) to 11% (1149/10 089); in HIV-positive patients, it declined from 42% (4229/9985) to 27% (2364/8823). The overall tuberculosis notification rate decreased by 12% and 19% among HIV-negative and HIV-positive patients, respectively; the rate of bacteriologically confirmed cases increased by 1% and 3%, respectively; and the rate of empirical treatment decreased by 56% and 49%, respectively. These changes occurred gradually following the test's introduction and stabilized after 3 years.

CONCLUSION

Roll-out of the rapid test in a setting with a high prevalence of pulmonary tuberculosis and HIV infection was associated with a halving of empirical treatment that occurred gradually after the test's introduction, possibly reflecting the time needed for full implementation. More than a quarter of HIV-positive patients with tuberculosis were still treated empirically, highlighting the diagnostic challenge in these patients.

Diagnosis and treatment of TB patients with rifampicin resistance detected using Xpert(®) MTB/RIF in Zimbabwe

SETTING

In Zimbabwe, there are concerns about the management of tuberculosis (TB) patients with rifampicin (RMP) resistance diagnosed using Xpert(®) MTB/RIF.

OBJECTIVE

To assess linkages between diagnosis and treatment for these patients in Harare and Manicaland provinces in 2014.

DESIGN

A retrospective cohort study.

RESULTS

Of 20 329 Xpert assays conducted, 90% were successful, 11% detected Mycobacterium tuberculosis and 4.5% showed RMP resistance. Of 77 patients with RMP-resistant TB diagnosed by Xpert, 70% had samples sent to the reference laboratory for culture and drug susceptibility testing (CDST); 53% of the samples arrived. In 21% the samples showed M. tuberculosis growth, and in 17% the DST results were recorded, all of which confirmed RMP resistance. Of the 77 patients, 34 (44%) never started treatment for multidrug-resistant (MDR) TB, with documented reasons being death, loss to follow-up and incorrect treatment. Of the 43 patients who started MDR-TB treatment, 12 (71%) in Harare and 17 (65%) in Manicaland started within 2 weeks of diagnosis.

CONCLUSION

Xpert has been rolled out successfully in two Zimbabwe provinces. However, the process of confirming CDST for Xpert-diagnosed RMP-resistant TB works poorly, and many patients are either delayed or never initiate MDR-TB treatment. These shortfalls must be addressed at the programmatic level.

Implementation of Xpert MTB/RIF in Uganda: Missed Opportunities to Improve Diagnosis of Tuberculosis

Background.  The effect of Xpert MTB/RIF (Xpert) scale-up on patient outcomes in low-income settings with a high tuberculosis (TB) burden has not been established. We sought to characterize the effectiveness of Xpert as implemented across different levels of the healthcare system in Uganda. Methods.  We reviewed laboratory records from 2012 to 2014 at 18 health facilities throughout Uganda. In 8 facilities, Xpert had been implemented onsite since 2012, and in 10 sites Xpert was available as an offsite referral test from another facility. We describe Xpert testing volumes by facility, Xpert and smear microscopy results, and downtime due to malfunction and cartridge stockouts. We compare TB treatment initiation as well as time to treatment between facilities implementing Xpert and those that did not. Results.  The median number of Xpert assays run at implementing facilities was 25/month (interquartile range [IQR], 10-63), amounting to 8% of total capacity. Among 1251 assays run for a new TB diagnosis, 19% were positive. Among 1899 patients with smear-negative presumptive TB, the proportion starting TB treatment was similar between Xpert facilities (11%; 95% confidence interval [CI], 9%-13%) and non-Xpert facilities (9%; 95% CI, 8%-11%; P = .325). In Xpert facilities, a positive Xpert preceded TB treatment initiation in only 12 of 70 (17%) smear-negative patients initiated on treatment. Conclusions.  Xpert was underutilized in Uganda and did not significantly increase the number of patients starting treatment for TB. Greater attention must be paid to appropriate implementation of novel diagnostic tests for TB if these new tools are to impact patient important outcomes.