Impact of GeneXpert MTB/RIF on patients and tuberculosis programs in a low-burden setting. a hypothetical trial

Uncertainty in tuberculosis clinical decision-making: An umbrella review with systematic methods and thematic analysis

Tuberculosis is a major infectious disease worldwide, but currently available diagnostics have suboptimal accuracy, particularly in patients unable to expectorate, and are often unavailable at the point-of-care in resource-limited settings. Test/treatment decision are, therefore, often made on clinical grounds. We hypothesized that contextual factors beyond disease probability may influence clinical decisions about when to test and when to treat for tuberculosis. This umbrella review aimed to identify such factors, and to develop a framework for uncertainty in tuberculosis clinical decision-making. Systematic reviews were searched in seven databases (MEDLINE, CINAHL Complete, Embase, Scopus, Cochrane, PROSPERO, Epistemonikos) using predetermined search criteria. Findings were classified as barriers and facilitators for testing or treatment decisions, and thematically analysed based on a multi-level model of uncertainty in health care. We included 27 reviews. Study designs and primary aims were heterogeneous, with seven meta-analyses and three qualitative evidence syntheses. Facilitators for decisions to test included providers' advanced professional qualification and confidence in tests results, availability of automated diagnostics with quick turnaround times. Common barriers for requesting a diagnostic test included: poor provider tuberculosis knowledge, fear of acquiring tuberculosis through respiratory sampling, scarcity of healthcare resources, and complexity of specimen collection. Facilitators for empiric treatment included patients' young age, severe sickness, and test inaccessibility. Main barriers to treatment included communication obstacles, providers' high confidence in negative test results (irrespective of negative predictive value). Multiple sources of uncertainty were identified at the patient, provider, diagnostic test, and healthcare system levels. Complex determinants of uncertainty influenced decision-making. This could result in delayed or missed diagnosis and treatment opportunities. It is important to understand the variability associated with patient-provider clinical encounters and healthcare settings, clinicians' attitudes, and experiences, as well as diagnostic test characteristics, to improve clinical practices, and allow an impactful introduction of novel diagnostics.

The Value of GeneXpert MTB/RIF for Detection in Tuberculosis: A Bibliometrics-Based Analysis and Review

With the continuous development of medical science and technology, especially with the advent of the era of precision diagnosis and treatment, molecular biology detection technology is widely valued and applied as an aid to early diagnosis of tuberculosis. The GeneXpert Mycobacterium tuberculosis Branching (MTB) technology is a suite of semi-nested real-time fluorescent quantitative PCR in vitro diagnostic technologies developed by Cepheid Inc. It targets the rifampicin resistance gene, rpoB, and can detect both MTB and resistance to rifampicin within 2 h. This review analyzed the papers related to GeneXpert using bibliometric software CiteSpace and Bibliometrix. A total of 151 articles were analyzed, spanning from 2011 to 2021. This bibliometrics-based review summarizes the history of the development of GeneXpert in tuberculosis diagnosis and its current status. Contributions of different countries to the topic, journal analysis, key paper analysis, and clustering of keywords were used to analyze this topic.

Evaluation of the use of GeneXpert MTB/RIF in a zone with high burden of tuberculosis in Thailand

GeneXpert MTB/RIF is a reliable molecular diagnostic tool capable of detecting Mycobacterium tuberculosis (MTB) and identifying genetic determinants of rifampicin (RIF) resistance. This study aimed to assess physicians’ diagnostic decision-making processes for TB based on GeneXpert MTB/RIF results and how this affected the initiation of multidrug resistance (MDR) treatment. This study employed a mixed method: data were collected retrospectively from the medical records of TB patients and in-depth interviews were conducted with healthcare workers in areas with a high TB burden in Thailand. A total of 2,030 complete TB records from 2 patient groups were reviewed, including 1443 suspected cases with negative smear results and 587 with high risk of MDR-TB. GeneXpert MTB/RIF was routinely used to assist the physicians in their decision-making for the diagnosis of pulmonary tuberculosis (PTB) and the initiation of MDR-TB treatment. The physicians used it as a “rule-in test” for all patients with negative chest X-rays (CXR) and smear results, to ensure timely treatment. Approximately one-fourth of the patients with negative CXR/smear and GeneXpert MTB/RIF results were diagnosed with PTB by the physicians, who based their decisions on other evidence, such as clinical symptoms, and did not use GeneXpert MTB/RIF as a “rule-out test.” GeneXpert MTB/RIF proved effective in early detection within a day, thereby radically shortening the time required to initiate second-line drug treatment. Despite its high sensitivity for detecting PTB and MDR-TB, GeneXpert MTB/RIF had contradictory results (false positive and/or false negative) for 21.8% of cases among patients with negative smear results and 41.1% of cases among patients with high risk of MDR-TB. Therefore, physicians still used the results of other conventional tests in their decision-making process. It is recommended that GeneXpert MTB/RIF should be established at all points of care and be used as the initial test for PTB and MDR-TB diagnosis.

Nucleic acid amplification tests reduce delayed diagnosis and misdiagnosis of pulmonary tuberculosis

The clinical impact of nucleic acid amplification (NAA) tests on reducing delayed diagnosis and misdiagnosis of pulmonary TB (PTB) has rarely been investigated. PTB patients were classified into a frontline NAA group, an add-on NAA group, and a no NAA group. The outcomes of interest were the proportion of PTB case died before anti-TB treatment, the interval between sputum examination and initiation of treatment, and misdiagnosis of PTB. A total of 2192 PTB patients were enrolled, including 282 with frontline NAA, 717 with add-on NAA, and 1193 with no NAA tests. Patients with NAA tests had a lower death rate before treatment initiation compared to those without NAA tests (1.6% vs. 4.4%, p < 0.001) in all cases. Patients with frontline NAA compared to those with add-on NAA and those without NAA, had a shorter interval between sputum examination and treatment initiation in all cases (3 days vs. 6 days (p < 0.001), vs 18 days (p < 0.001)), and less misdiagnosis in smear-positive cases (1.8% vs. 5.6% (p = 0.039), vs 6.5% (p = 0.026)). In conclusion, NAA tests help prevent death before treatment initiation. Frontline NAA tests perform better than add-on NAA and no NAA in avoiding treatment delay in all cases, and misdiagnosis of PTB in smear-positive cases.

Performance of Nucleic Acid Amplification Tests in Patients with Presumptive Pulmonary Tuberculosis in Taiwan

INTRODUCTION

Several nucleic acid amplification tests (NAATs) for detection of Mycobacterium tuberculosis (TB) complex (MTBC) are available in Taiwan; however, their performances may differ and have not been extensively evaluated. Therefore, we aimed to explore the accuracy of NAATs overall followed by comparison between platforms commonly used in Taiwan.

METHODS

This study enrolled presumptive pulmonary TB patients with NAATs throughout Taiwan. The diagnostic performance of smear microscopy and NAATs was assessed using sputum culture as a reference standard. To investigate the performance of NAATs in excluding non-tuberculous mycobacteria (NTM), we quantified the false-positive proportion of NAATs in patients infected with NTM.

RESULTS

Of the 4126 enrollees, 860 (20.8%) had positive NAATs. The sensitivity and specificity of NAATs were 83.2% and 96.7%, respectively, compared to 81.5% and 55.3% for smear. There was no significant difference in sensitivity between the NAATs and smear; however, the specificity of smear was significantly lower than that of the NAATs [difference 41.4%, 95% confidence interval (CI) 39.6-43.2%]. There was no significant difference in sensitivity among Roche Cobas Amplicor Mycobacterium tuberculosis assay (Amplicor), Xpert MTB/RIF assay (Xpert) and in-house polymerase chain reaction (in-house PCR) (82.2% versus 83.8% versus 82.4%); however, in-house PCR was significantly less specific than Amplicor (difference 5.3%, 95% CI 2.4-8.2%) and Xpert (difference 5.8%, 95% CI 3.1-8.5%). The sensitivity of NAATs among smear-negative cases was 33.1% (95% CI 26.0-40.3%). In-house PCR had a significantly higher false-positive rate among specimens that were culture positive for NTM than Amplicor (7.7% versus 0.3%; difference 7.4%, 95% CI 3.4-11.5%) and Xpert (7.7% versus 0.7%; difference 7.0%, 95% CI 2.9-11.0%).

CONCLUSION

The NAATs overall had a relatively high sensitivity and specificity in detecting MTBC while Amplicor and Xpert performed better than in-house PCR in excluding NTM. Our findings will be useful for the development of national policy.

Needle in a haystack: Looking for tuberculosis in a low-incidence setting

BACKGROUND

Canada is a low-incidence country for tuberculosis (TB). The BC Public Health Laboratory diagnostic algorithm for pulmonary TB includes acid fast bacilli (AFB) smear and mycobacterial culture of all submitted sputa. TB nucleic acid amplification testing (NAT) is routinely performed on AFB-smear-positive (AFB+) sputa only. We assessed the laboratory-associated costs of implementing the international recommendations for TB NAT on AFB-smear-negative (AFB-) sputa.

METHODS

Two data sets were obtained: (1) all AFB- samples for a 3-year period (October 1, 2014-September 30, 2017) and (2) all AFB-, TB-culture-positive samples for the same period. One AFB- sample/patient from each defined diagnostic set of sputa was deemed eligible for TB NAT. To stratify patients by ordering location, a 1-year subset of data (October 1, 2016-September 30, 2017) was examined.

RESULTS

In the 3-year period, 0.7% of all diagnostic sets were AFB- and culture-positive. In the 1-year period, the provincial TB Services clinics submitted 26% of all AFB- samples received, but these constituted 78% of AFB-, culture-positive samples.

CONCLUSIONS

The annual cost of TB NAT on one AFB- sputum sample from each eligible diagnostic set would total approximately $247,000. Targeting only TB Services clinic patients would reduce this cost to approximately $64,000/year while capturing more than 75% of AFB-, culture-positive patients. On the basis of our provincial positivity rate, it would cost approximately $6,000 to provide an early TB diagnosis for an AFB-, culture-positive patient. The cost-effectiveness to public health of this approach in a TB low-incidence setting needs to be carefully evaluated.

Diagnostic performance of GeneXpert in tuberculosis-HIV co-infected patients at Asella Teaching and Referral Hospital, Southeastern Ethiopia: A cross sectional study

BACKGROUND

GeneXpert is a new introduction in the diagnostic modality to fight tuberculosis (TB) among people living with HIV (PLHIV) under the program of intensified TB case finding. This study aimed to evaluate the diagnostic performance of GeneXpert under the program of intensified TB cases finding among PLHIV.

METHODS

Cross-sectional study was conducted by recruiting individuals attending an HIV clinic from February 2018 to January 2019. Data on clinical parameters were collected using a standardized tool. Two-morning sputum samples were collected and processed for smear microscopy and GeneXpert. SPSS 21 used for data analysis. Proportion, percentage, and mean with SD were used to describe variables. Univariate and multivariable logistic regressions were used to assess factors associated with the GeneXpert. Values for which the 95% CI interval not includes 1 and for which P<0.05 were considered significant.

RESULT

A total of 384 presumptive TB-HIV co-infection cases were included, of which 166 (43%) were diagnosed to have TB. Fifty-four (32.5%) TB cases were smear AFB positive while 79 (47.7%) TB cases were GeneXpert positive. The GeneXpert detection rate was almost two-fold of that of smear microscopy and all smear positive TB cases were detected by GeneXpert. Moreover, GeneXpert was able to detect an additional third of TB confirmed cases among smear AFB negative cases. Advanced stage of the disease, high viral load and presence of anemia were significantly associated with TB. The WHO TB screening tool remained least sensitive with the lowest positive predictive value.

CONCLUSION

GeneXpert demonstrated two-fold case detection rate compared to the sputum smear microscopy and additional third TB case detection rate among smear AFB negative cases. Clinical screening tool for evaluation of TB-HIV co-infection showed poor performance in TB case notification.

Use of Xpert Contributes to Accurate Diagnosis, Timely Initiation, and Rational Use of Anti-TB Treatment Among Childhood Tuberculosis Cases in South Central Ethiopia

Background

Childhood tuberculosis (TB) was under-prioritized, and only 15% of childhood TB cases are microbiologically confirmed. Hence, most childhood TB diagnoses are made on a clinical basis and prone to over- or under-treatment. Xpert is a rapid method for the diagnosis of childhood TB with high sensitivity.

Objective

To assess the use of Xpert for accurate diagnosis, timely initiation, and rational use of anti-TB treatment among childhood TB.

Methods

In 2016, the hospital facilitated the installation of the Xpert machine. We reviewed data trends over four consecutive years; two years before the arrival of the machine and two years following the implementation of Xpert. Data were extracted retrospectively from electronically stored databases and medical records and entered to SPSS 21 for analysis.

Results

In the pre-intervention period (2014–2015), 404 cases of children presenting with symptoms or signs suggestive of TB (“presumptive TB”) were evaluated using AFB microscopy. A total of 254 (62.8%) TB diagnoses were made, of which 54 (21.3%) were confirmed by smear AFB while 200 (78.7%) were treated as smear-negative TB cases. The mean waiting time to start anti-TB treatment was 6.95 days [95% CI (3.71–10.90)]. During the intervention period (2016–2017), 371 children with presumptive TB were evaluated using Xpert. A total of 199 (53.6%) childhood TB cases were notified, of which 88 (44.2%) were Xpert positive and 111 (55.8%) were treated as Xpert-negative probable TB cases. The tendency to initiate anti-TB treatment for unconfirmed TB cases was reduced by a third. Compared with smear AFB, Xpert improved accuracy of diagnosing pediatric TB cases two-fold. The average waiting time to start anti-TB treatment was 1.33 days [95% CI (0.95–1.71)]. There was a significant reduction in the waiting time to start anti-TB treatment, with a mean time difference before and during intervention of 5.62 days [95% CI (1.68–9.56)].

Conclusion

Xpert use was associated with a significant increase in the accuracy of identifying confirmed TB cases, reduced unnecessary anti-TB prescription, and shortened the time taken to start TB treatment.

Performance and Utilization of a Laboratory-Developed Nucleic Acid Amplification Test (NAAT) for the Diagnosis of Pulmonary and Extrapulmonary Tuberculosis in a Low-Prevalence Area

OBJECTIVES

Tuberculosis (TB) is a significant global health problem. In low-prevalence areas and low clinical suspicion, nucleic acid amplification tests (NAAT) for direct detection of Mycobacterium tuberculosis complex (MTBC) can speed therapy initiation and infection control. An NAAT assay (TBPCR) targeting MTBC IS6110 is used for detecting MTBC in our low-prevalence population.

METHODS

Fifteen-year review of patient records identified 146 patients with culture-positive pulmonary tuberculosis (PTB) or extrapulmonary tuberculosis (EPTB). Laboratory-developed TBPCR was retrospectively compared with standard stain and cultures for PTB and EPTB diagnoses.

RESULTS

TBPCR assay was used in 57% of patients with PTB and 33% of patients with EPTB. TBPCR detected 88.4% of all TB (smear-positive, 97%; smear-negative, 79%) with 100% specificity. Low bacterial load was indicated in TBPCR-negative PTB (P = .002) and EPTB (P < .008).

CONCLUSIONS

TBPCR performance was optimum but significantly underused. Guidelines are proposed for mandated use of TBPCR that capture patients with clinically suspected PTB. Focused TBPCR use in low prevalence populations will benefit patient care, infection prevention, and public health.

Characteristics Indicative of Tuberculosis/HIV Coinfection in a High-Burden Setting: Lessons from 13,802 Incident Tuberculosis Cases in Harare, Zimbabwe

Country-specific interventions targeting high-risk groups are necessary for a global reduction in Tuberculosis (TB)/HIV burden. We analyzed the data of 13,802 TB cases diagnosed in Harare, Zimbabwe, during 2013-2017. Pearson's chi-square tests and multivariate logistic regression models were used to identify patient characteristics significantly associated with TB/HIV coinfection. Of the 13,802 TB cases analyzed, 9,725 (70.5%) were HIV positive. A significantly higher odds of having TB/HIV coinfection diagnosis was found among females, patients aged 25-64 years, previously treated cases, and acid-fast bacillus sputum smear-negative cases. Compared with nondisseminated pulmonary TB, miliary TB (adjusted odds ratio [aOR]: 1.469, 95% CI: 1.071, 2.015) and TB meningitis (aOR: 1.715, 95% CI: 1.074, 2.736) both had a significantly higher odds for TB/HIV coinfection, whereas pleural TB (aOR 0.420, 95% CI: 0.354, 0.497) and all other extrapulmonary TB (EPTB) (aOR: 0.606, 95% CI: 0.516 0.712) were significantly less likely to have TB/HIV coinfection. The risk for TB/HIV coinfection varied significantly by patients' sociodemographic and clinical characteristics in Harare. Our finding that different forms of EPTB have different relationships with HIV coinfection has extended the knowledge base about clinical markers for TB/HIV coinfection which can lead to a greater public health impact on eliminating TB/HIV infection.

Performances and usefulness of Xpert MTB/RIF assay in low-incidence settings: not that bad?

Xpert MTB/RIF assay, a real-time PCR assay designed to detect Mycobacterium tuberculosis, has proven sensitive and specific when performed on respiratory samples in a high prevalence setting. However, it was suggested as less accurate in a low-incidence environment. We evaluated the accuracy of the Xpert for the diagnosis of tuberculosis (TB) on pulmonary and extrapulmonary samples in Geneva (Switzerland), where the prevalence of active TB is very low. From March 2009 to February 2013, the Xpert was performed on clinical samples. All specimens were also processed using auramine, AFB staining, and mycobacterial culture with both solid and liquid media. The accuracy of both microscopy and Xpert was determined retrospectively using cultures as the reference method. A total of 732 clinical specimens were processed with the Xpert. The Xpert had a high specificity (97.5%; 95% confidence interval (CI), 95.8-98.5%) and revealed much more sensitive (82.7%; 95% CI, 74.1-89.0%) than microscopy (55.5%; 95% CI, 45.7-64.8%) for the diagnosis of TB, with a high negative predictive value (96.8%; 95% CI, 95.0-98.0%). The advantage of PCR over microscopy was even more pronounced for extrapulmonary specimens (sensitivity of 70% (95% CI, 50.4-84.6%) compared with 23.3% (95% CI, 10.6-42.7%)). Despite the low prevalence of TB in Switzerland, results performance for respiratory samples was similar to that reported in high prevalence countries. The high negative predictive value is clinically helpful in our setting, where pulmonary TB needs to be reasonably ruled out. When considering extrapulmonary samples, microscopy performed poorly compared with Xpert. This study shows that the Xpert remains accurate and useful in a low-incidence setting.

Difficulties with the implemented xpert MTB/RIF for determining diagnosis of pulmonary and extrapulmonary tuberculosis in adults and children

Background and aims

Handling of PTB and EPTB patients with adequate standard detection of MTBC and anti-TB drug sensitivity using accurate and rapid methods could provide good TB management and clinical treatment outcomes. The Xpert MTB/RIF assay is an automated, cartridge-based NAAT that can simultaneously detect MTBC and RIF resistance within 2 h. The aim of this study was to evaluate the implementation of Xpert for determining diagnosis of PTB and EPTB in adults and children.

Methods

A descriptive study was performed using e-TB Manager data from the MDR-TB Clinic at Dr. Soetomo Academic Hospital. Suspected TB cases were from the areas of East Java Province from January 2016 to December 2018. Xpert assay was conducted using standardized criteria for clinically suspected TB, and MTBC-positive results with RR were examined by the culture method using MGIT 960 BACTEC System.

Results

A total of 1181 (1181/3009, 39.25%) sputum samples from suspected new MDR-PTB cases tested positive for MTBC with 3.02% RR. Among 3893 sputum samples from previously treated probable MDR-PTB cases tested using Xpert, 1936 (49.73%) were MTBC positive with 13.20% RR. Among 59 new suspected MDR-PTB cases tested using MGIT 960 BACTEC System, 55 tested positive for MTBC, although all RR strains were highly sensitive to amikacin (100%), kanamycin (95%), and ofloxacin (89%). A total of 49 children with suspected PTB were tested using Xpert, revealing low positivity (12%) for MTBC, with all RR strains being rifampicin sensitive (RS). Of the 86 suspected EPTB cases tested using Xpert, very few were MTBC-positive (26%), with 91% RS.

Conclusions

This study revealed that in adults and children with PTB and EPTB, the Xpert assay achieved a low positivity detection rate for MTBC in samples from new or previously treated cases, and this could be the result of many factors.

Impact of nucleic acid amplification test on pulmonary tuberculosis notifications and treatments in Taiwan: a 7-year single-center cohort study

Background

Nucleic acid amplification tests (NAAT) have been used as a diagnostic tool for pulmonary tuberculosis (PTB) in Taiwan for many years. In accordance with Taiwanese legislation, health care personnel are required to notify the Centers for Disease Control and Prevention (CDC) in case of suspected PTB. This study aimed to investigate the impact of NAAT(Gen-Probe) on the notification system for PTB and anti-tuberculosis treatments in Taiwan.

Methods

A retrospective study on the impact of NAAT (Enhanced Amplified Mycobacterium tuberculosis Direct Test [E-MTD], Gen-Probe, San Diego, CA, USA) [NAAT(Gen-Probe)] was carried out at Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation from March 2011 to December 2017. During the study period, microscopic acid-fast-bacilli smears and mycobacterial cultures were available for PTB diagnosis. NAAT(Gen-Probe) was first introduced at the hospital in January 2014 for use as a diagnostic method for PTB. Positive sputum culture was considered as the gold standard for PTB diagnosis. We excluded clinically-diagnosed PTB cases.

Results

When NAAT(Gen-Probe) was applied, the rate of error notification to CDC decreased from 64.3 to 7.0% (P < 0.001), and unnecessary anti-TB treatments administered to suspected cases decreased from 14.9 to 6.5% (P = 0.005). In the non-PTB group, the mean duration of unnecessary anti-TB treatments changed from 38.9 ± 38.3 days to 37.0 ± 37.9 days (P = 0.874). In the PTB group, the mean time from notifying CDC to initiating treatment decreased from 3.05 ± 6.95 days to 1.48 ± 1.99 days (P = 0.004). The sensitivity, specificity, positive predictive value, and negative predictive value of NAAT(Gen-Probe) were 99.0, 92.3, 99.0, and 92.3%, respectively.

Conclusions

Use of NAAT(Gen-Probe) led to decrease in the rate of error notification of suspected PTB cases to the CDC, avoidance of unnecessary use of anti-TB treatments, and accelerated initiation of appropriate treatments.

Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults

BACKGROUND

Xpert MTB/RIF (Xpert MTB/RIF) and Xpert MTB/RIF Ultra (Xpert Ultra), the newest version, are the only World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in persons with signs and symptoms of tuberculosis, at lower health system levels. A previous Cochrane Review found Xpert MTB/RIF sensitive and specific for tuberculosis (Steingart 2014). Since the previous review, new studies have been published. We performed a review update for an upcoming WHO policy review.

OBJECTIVES

To determine diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for tuberculosis in adults with presumptive pulmonary tuberculosis (PTB) and for rifampicin resistance in adults with presumptive rifampicin-resistant tuberculosis.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, to 11 October 2018, without language restriction.

SELECTION CRITERIA

Randomized trials, cross-sectional, and cohort studies using respiratory specimens that evaluated Xpert MTB/RIF, Xpert Ultra, or both against the reference standard, culture for tuberculosis and culture-based drug susceptibility testing or MTBDRplus for rifampicin resistance.

DATA COLLECTION AND ANALYSIS

Four review authors independently extracted data using a standardized form. When possible, we also extracted data by smear and HIV status. We assessed study quality using QUADAS-2 and performed meta-analyses to estimate pooled sensitivity and specificity separately for tuberculosis and rifampicin resistance. We investigated potential sources of heterogeneity. Most analyses used a bivariate random-effects model. For tuberculosis detection, we first estimated accuracy using all included studies and then only the subset of studies where participants were unselected, i.e. not selected based on prior microscopy testing.

MAIN RESULTS

We identified in total 95 studies (77 new studies since the previous review): 86 studies (42,091 participants) evaluated Xpert MTB/RIF for tuberculosis and 57 studies (8287 participants) for rifampicin resistance. One study compared Xpert MTB/RIF and Xpert Ultra on the same participant specimen.Tuberculosis detectionOf the total 86 studies, 45 took place in high tuberculosis burden and 50 in high TB/HIV burden countries. Most studies had low risk of bias.Xpert MTB/RIF pooled sensitivity and specificity (95% credible Interval (CrI)) were 85% (82% to 88%) and 98% (97% to 98%), (70 studies, 37,237 unselected participants; high-certainty evidence). We found similar accuracy when we included all studies.For a population of 1000 people where 100 have tuberculosis on culture, 103 would be Xpert MTB/RIF-positive and 18 (17%) would not have tuberculosis (false-positives); 897 would be Xpert MTB/RIF-negative and 15 (2%) would have tuberculosis (false-negatives).Xpert Ultra sensitivity (95% confidence interval (CI)) was 88% (85% to 91%) versus Xpert MTB/RIF 83% (79% to 86%); Xpert Ultra specificity was 96% (94% to 97%) versus Xpert MTB/RIF 98% (97% to 99%), (1 study, 1439 participants; moderate-certainty evidence).Xpert MTB/RIF pooled sensitivity was 98% (97% to 98%) in smear-positive and 67% (62% to 72%) in smear-negative, culture-positive participants, (45 studies). Xpert MTB/RIF pooled sensitivity was 88% (83% to 92%) in HIV-negative and 81% (75% to 86%) in HIV-positive participants; specificities were similar 98% (97% to 99%), (14 studies).Rifampicin resistance detectionXpert MTB/RIF pooled sensitivity and specificity (95% Crl) were 96% (94% to 97%) and 98% (98% to 99%), (48 studies, 8020 participants; high-certainty evidence).For a population of 1000 people where 100 have rifampicin-resistant tuberculosis, 114 would be positive for rifampicin-resistant tuberculosis and 18 (16%) would not have rifampicin resistance (false-positives); 886 would be would be negative for rifampicin-resistant tuberculosis and four (0.4%) would have rifampicin resistance (false-negatives).Xpert Ultra sensitivity (95% CI) was 95% (90% to 98%) versus Xpert MTB/RIF 95% (91% to 98%); Xpert Ultra specificity was 98% (97% to 99%) versus Xpert MTB/RIF 98% (96% to 99%), (1 study, 551 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

We found Xpert MTB/RIF to be sensitive and specific for diagnosing PTB and rifampicin resistance, consistent with findings reported previously. Xpert MTB/RIF was more sensitive for tuberculosis in smear-positive than smear-negative participants and HIV-negative than HIV-positive participants. Compared with Xpert MTB/RIF, Xpert Ultra had higher sensitivity and lower specificity for tuberculosis and similar sensitivity and specificity for rifampicin resistance (1 study). Xpert MTB/RIF and Xpert Ultra provide accurate results and can allow rapid initiation of treatment for multidrug-resistant tuberculosis.

Design and Implementation of Data Exchange Formats for Molecular Detection of Drug-Resistant Tuberculosis

Drug-resistant tuberculosis (TB) remains a public health threat to the United States and worldwide control of TB. Rapid and reliable drug susceptibility testing (DST) is essential for aiding clinicians in selecting an optimal treatment regimen for TB patients and to prevent ongoing transmission. Growth-based DST results for culture-confirmed cases are routinely reported to the U.S. Centers for Disease Control and Prevention through the National TB Surveillance System (NTSS). However, the NTSS currently lacks the capacity and functionality to accept laboratory results from advanced molecular methods that detect mutations associated with drug resistance. The objective of this study is to design and implement novel comprehensive data exchange formats that utilize the Health Level Seven (HL7) version 2.5.1 messaging hierarchy to capture, store, and monitor molecular DST data, thereby, improving the quality of data, specifications and exchange formats within the NTSS as well as ensuring full reporting of drug-resistant TB.

Evaluation of two tuberculosis PCR assays for routine use in a clinical setting of low population and low tuberculosis prevalence

Today, there are numerous different molecular diagnostic assays for the detection of tuberculosis (TB), allowing the optimization of rapid detection of TB according to the clinical need. In this study, two high-throughput TB PCR assays with combined antimicrobial resistance detection, Anyplex™ II MTB/MDR (Seegene) and RealTime MTB + RealTime MTB RIF/INH Resistance (Abbott Molecular), were evaluated for routine use in a clinical setting of low population and low TB prevalence in Finland. The RealTime MTB assay was 100% concordant (22/22 positive, n = 169) with the reference methods (culture and Xpert MTB/RIF PCR assay, Cepheid). However, with a limitation of four separate PCR cycles per kit, the routine use in a low TB-prevalence setting would easily lead to wasting most of the RIF/INH Resistance reagents. The Anyplex™ II MTB/MDR assay usability was more adaptive to suit the clinical setting but the assay sensitivity was considerably lower (86%, 19/22 positive, n = 76) being closer to the sensitivity of smear microscopy. The findings of this study suggest that the evaluated high-throughput MTB/MDR assays are evidently suboptimal for routine use in a low population, low TB-prevalence setting. In addition, neither of the two assays covers non-tuberculous mycobacteria and could therefore not fully replace acid-fast staining as the initial screening method.

Clinical Impact and Cost-effectiveness of Xpert MTB/RIF Testing in Hospitalized Patients With Presumptive Pulmonary Tuberculosis in the United States

Background

Microscopic examination of acid-fast-stained sputum smears is the current standard of care in the United States to determine airborne infection isolation (AII) of inpatients with presumptive pulmonary tuberculosis (PTB). However, nucleic acid amplification testing (NAAT) with the Xpert MTB/RIF assay (Xpert) may be more efficient and less costly.

Methods

This prospective observational cohort study enrolled a consecutive sample of 318 AII-eligible inpatients from a public hospital in Seattle, Washington, from March 2012 to October 2013. Sputum samples were collected from each inpatient and analyzed using smear microscopy, culture, drug susceptibility testing, and NAAT. The performance, clinical utility (AII duration and survival), and cost-effectiveness from an institutional perspective were compared for 5 testing strategies.

Results

Among the 318 admissions with presumptive PTB, 20 (6.3%) were culture-positive for Mycobacterium tuberculosis. The sensitivity of 1 Xpert, 2 Xperts, 2 smears, or 3 smears compared to culture was 0.85 (95% confidence interval [CI], .61–.96), 0.95 (95% CI, .73–1.0), 0.70 (95% CI, .46–.88), and 0.80 (95% CI, .56–.93), respectively. A cost-effectiveness analysis of the study results demonstrated that an Xpert test on 1 unconcentrated sputum sample (assuming equivalent results for unconcentrated and concentrated sputum samples) is the most cost-effective strategy (99.9% preferred at willingness-to-pay of US$50000) and on average would save 51.5 patient-hours in AII and up to $11466 relative to microscopy without a compromise in sensitivity.

Conclusions

In hospitalized patients with presumptive PTB in a low-burden setting, NAAT can reduce AII and is comparably sensitive, more specific, and more cost-effective than smear microscopy.

Impact of the GeneXpert MTB/RIF Technology on Tuberculosis Control

Molecular technology revolutionized the diagnosis of tuberculosis (TB) with a paradigm shift to faster, more sensitive, clinically relevant patient care. The most recent molecular leader is the GeneXpert MTB/RIF assay (Xpert) (Cepheid, Sunnyvale, CA), which was endorsed by the World Health Organization with unprecedented speed in December 2010 as the initial diagnostic for detection of HIV-associated TB and for where high rates of drug resistance are suspected. South Africa elected to take an aggressive smear replacement approach to facilitate earlier diagnosis and treatment through the decision to implement the Xpert assay nationally in March 2011, against the backdrop of approximately 6.3 million HIV-infected individuals, one of highest global TB and HIV coinfection rates, no available implementation models, uncertainties around field performance and program costs, and lack of guidance on how to operationalize the assay into existing complex clinical algorithms. South Africa's national implementation was conducted as a phased, forecasted, and managed approach (March 2011 to September 2013), through political will and both treasury-funded and donor-funded support. Today there are 314 GeneXperts across 207 microscopy centers; over 8 million assays have been conducted, and South Africa accounts for over half the global test cartridge usage. As with any implementation of new technology, challenges were encountered, both predicted and unexpected. This chapter discusses the challenges and consequences of such large-scale implementation efforts, the opportunities for new innovations, and the need to strengthen health systems, as well as the impact of the Xpert assay on rifampin-sensitive and multidrug-resistant TB patient care that translated into global TB control as we move toward the sustainable development goals.

Use of Nucleic Acid Amplification Tests in Tuberculosis Patients in California, 2010-2013

BACKGROUND

Nucleic acid amplification tests (NAATs) have been used as a diagnostic tool for tuberculosis (TB) in the United States for many years. We sought to assess NAAT use in TB patients in California during a period of time when NAAT availability increased throughout the world.

METHODS

We conducted a retrospective review of surveillance data from 6051 patients with culture-confirmed pulmonary TB who were reported to the California TB registry during 2010-2013.

RESULTS

Only 2336 of 6051 (39%) TB patients had a NAAT for diagnosis before culture results. Although 90% (N = 2101) with NAAT had positive test results, 9% (N = 217) had falsely negative NAAT results, and 0.8% (N = 18) had indeterminate NAAT results. The median time from specimen collection to TB treatment initiation was shorter when NAAT was used (3 vs 14 days, P < .0001), and patients with a positive NAAT result initiated treatment earlier than patients with a falsely negative result (1 vs 11 days from NAAT report, P < .0001). We confirmed the increased sensitivity of NAAT compared with acid-fast bacilli (AFB) smear microscopy in our study population; 92 of 145 AFB smear-negative patients had positive NAATs. Median time from specimen collection to NAAT result report differed by health jurisdiction, from 1 to 11 working days.

CONCLUSIONS

Increased use of NAATs in diagnosis of pulmonary TB could decrease the time-to-treatment initiation and consequently decrease transmission. However, differential use and access to NAAT may prevent full realization of NAAT benefits in California.

Xpert®MTB/RIF for the Diagnosis of Tuberculosis in a Remote Arctic Setting: Impact on Cost and Time to Treatment Initiation

BACKGROUND

Tuberculosis (TB) remains a significant health problem in the Canadian Arctic. Substantial health system delays in TB diagnosis can occur, in part due to the lack of capacity for onsite microbiologic testing. A study recently evaluated the yield and impact of a rapid automated PCR test (Xpert®MTB/RIF) for the diagnosis of TB in Iqaluit (Nunavut). We conducted an economic analysis to evaluate the expected cost relative to the expected reduction in time to treatment initiation, with the addition of Xpert®MTB/RIF to the current diagnostic and treatment algorithms used in this setting.

METHODS

A decision analysis model compared current microbiologic testing to a scenario where Xpert®MTB/RIF was added to the current diagnostic algorithm for active TB, and incorporated costs and clinical endpoints from the Iqaluit study. Several sensitivity analyses that considered alternative use were also considered. We estimated days to TB diagnosis and treatment initiation, health system costs, and the incremental cost per treatment day gained for each individual evaluated for possible TB.

RESULTS

With the addition of Xpert®MTB/RIF, costs increased while days to TB treatment initiation were reduced. The incremental cost per treatment day gained (per individual investigated for TB) was $164 (95% uncertainty range $85, $452). In a sensitivity analysis that considered hospital discharge after a single negative Xpert®MTB/RIF, the Xpert®MTB/RIF scenario was cost saving.

INTERPRETATION

Adding Xpert®MTB/RIF to the current diagnostic algorithm for TB in Nunavut appears to reduce time to diagnosis and treatment at reasonable cost. It may be especially well suited to overcome some of the other logistical barriers that are unique to this and other remote communities.

Impact of Molecular Diagnostics for Tuberculosis on Patient-Important Outcomes: A Systematic Review of Study Methodologies

BACKGROUND

Several reviews on the accuracy of Tuberculosis (TB) Nucleic Acid Amplification Tests (NAATs) have been performed but the evidence on their impact on patient-important outcomes has not been systematically reviewed. Given the recent increase in research evaluating such outcomes and the growing list of TB NAATs that will reach the market over the coming years, there is a need to bring together the existing evidence on impact, rather than accuracy. We aimed to assess the approaches that have been employed to measure the impact of TB NAATs on patient-important outcomes in adults with possible pulmonary TB and/or drug-resistant TB.

METHODS

We first develop a conceptual framework to clarify through which mechanisms the improved technical performance of a novel TB test may lead to improved patient outcomes and outline which designs may be used to measure them. We then systematically review the literature on studies attempting to assess the impact of molecular TB diagnostics on such outcomes and provide a narrative synthesis of designs used, outcomes assessed and risk of bias across different study designs.

RESULTS

We found 25 eligible studies that assessed a wide range of outcomes and utilized a variety of experimental and observational study designs. Many potentially strong design options have never been used. We found that much of the available evidence on patient-important outcomes comes from a small number of settings with particular epidemiological and operational context and that confounding, time trends and incomplete outcome data receive insufficient attention.

CONCLUSIONS

A broader range of designs should be considered when designing studies to assess the impact of TB diagnostics on patient outcomes and more attention needs to be paid to the analysis as concerns about confounding and selection bias become relevant in addition to those on measurement that are of greatest concern in accuracy studies.

Shortening Isolation of Patients With Suspected Tuberculosis by Using Polymerase Chain Reaction Analysis: A Nationwide Cross-sectional Study

BACKGROUND

Isolation of patients suspected for pulmonary tuberculosis is guided by serial sputum smears. This can result in isolation for days for patients with noncontagious tuberculosis. To determine whether a single sample negative for Mycobacterium tuberculosis complex at polymerase chain reaction (PCR) can guide isolation.

METHODS

We retrospectively evaluated sputum samples analyzed for M. tuberculosis complex at the International Reference Laboratory of Mycobacteriology, Copenhagen, Denmark in 2002-2011. We selected culture-confirmed tuberculosis cases with ≥3 samples within 14 days before or after the initial culture-positive sample. We repeated the process for those with ≥2 samples within 28 days. The primary outcome was PCR-negative, smear-positive patients.

RESULTS

We included 53 533 sputum samples from 20 928 individuals; 1636 had culture-confirmed tuberculosis. Of these, 856 had ≥3 sputum samples analyzed within the 28 days, and 482 had ≥1 PCR result. Nine patients (2.5% of smear-positive patients) were smear positive/PCR negative; 8 of the 9 had a smear-positive result in only 1 of 3 samples, and 5 had a low smear grade. Of 722 patients with 2 samples, 7 (1.3% of smear-positive patients) were smear positive/PCR negative. Overall, none were smear positive for the sample that produced the negative PCR result.

CONCLUSIONS

Primary PCR identified >97% of serial smear-positive cases. The majority of the missed cases had low-grade smears. Nevertheless, the occurrence of smear-positive/PCR-negative cases underlines the importance of increasing the quantity and quality of samples. Moreover, it is important that samples analyzed with PCR are cultured, owing to higher-sensitivity drug susceptibility testing, differential diagnosis, and surveillance.

Review of nucleic acid amplification tests and clinical prediction rules for diagnosis of tuberculosis in acute care facilities

Tuberculosis (TB) remains an important cause of hospitalization and mortality in the United States. Prevention of TB transmission in acute care facilities relies on prompt identification and implementation of airborne isolation, rapid diagnosis, and treatment of presumptive pulmonary TB patients. In areas with low TB burden, this strategy may result in inefficient utilization of airborne infection isolation rooms (AIIRs). We reviewed TB epidemiology and diagnostic approaches to inform optimal TB detection in low-burden settings. Published clinical prediction rules for individual studies have a sensitivity ranging from 81% to 100% and specificity ranging from 14% to 63% for detection of culture-positive pulmonary TB patients admitted to acute care facilities. Nucleic acid amplification tests (NAATs) have a specificity of >98%, and the sensitivity of NAATs varies by acid-fast bacilli sputum smear status (positive smear, ≥95%; negative smear, 50%-70%). We propose an infection prevention strategy using a clinical prediction rule to identify patients who warrant diagnostic evaluation for TB in an AIIR with an NAAT. Future studies are needed to evaluate whether use of clinical prediction rules and NAATs results in optimized utilization of AIIRs and improved detection and treatment of presumptive pulmonary TB patients.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.