Impact of the GeneXpert MTB/RIF Technology on Tuberculosis Control

Towards the development of cost-effective point-of-care diagnostic tools for poverty-related infectious diseases in sub-Saharan Africa

In this review, we examine the current landscape of point-of-care testing (POCT) diagnostic tools designed for poverty-related infectious diseases (PRIDs) in sub-Saharan Africa (sSA) while delineating key avenues for future advancements. Our analysis encompasses both established and emerging diagnostic methods for PRIDs, addressing the persistent challenges in POCT tool development and deployment, such as cost, accessibility, and reliability. We emphasize recent advancements in POCT diagnostic tools as well as platforms poised to enhance diagnostic testing in sSA. Recognizing the urgency for affordable and widely accessible POCT diagnostic tools to detect PRIDs in sSA, we advocate for a multidisciplinary approach. This approach integrates current and emerging diagnostic methods, explicitly addressing challenges hindering point-of-care (POC) tool development. Furthermore, it recognizes the profound impact of misdiagnosis on public and global health, emphasizing the need for effective tools. To facilitate the successful development and implementation of POCT diagnostic tools in sSA, we propose strategies including the creation of multi-analyte detection POCT tools, the implementation of education and training programs, community engagement initiatives, fostering public-private collaborations, and the establishment of reliable supply chains. Through these concerted efforts, we aim to accelerate the development of POCT in the sSA region, ensuring its effectiveness and accessibility in addressing the diagnostic challenges associated with PRIDs.

Acquired rifamycin resistance among patients with tuberculosis and HIV in new York City, 2001-2023

Introduction

Acquired rifamycin resistance (ARR) in tuberculosis (TB) has been associated with HIV infection and can necessitate complicated TB treatment regimens, particularly in people living with HIV (PLWH). This work examines clinical characteristics and treatment outcomes of PLWH who developed ARR from 2001 to 2023 in New York City (NYC) to inform best practices for treating these patients.

Methods

PLWH who developed ARR 2001-2023 were identified from the NYC TB registry.

Results

Sixteen PLWH developed ARR; 15 were diagnosed 2001-2009 and the 16th was diagnosed in 2017. Median CD4 count was 48/mm3. On initial presentation, 14 had positive sputum cultures; of these, 12 culture-converted prior to developing ARR. Ten patients completed a course of TB treatment but subsequently relapsed; in six of these cases, ARR was discovered upon relapse, triggering treatment with a non-rifamycin-containing regimen, while in the other four, ARR was discovered during a second round of rifamycin-containing treatment. Three patients were lost to follow-up during their initial course of TB treatment and later returned to care; after being restarted on a rifamycin-containing regimen, ARR was discovered. Finally, three patients culture-converted during their first course of treatment but subsequently had cultures that grew rifamycin-resistant Mycobacterium tuberculosis prior to treatment completion, leading to changes in their treatment regimens. Among the 16 patients, eight died before being cured of TB, seven successfully completed treatment, and one was lost to follow-up.

Conclusions

PLWH should be monitored closely for the development of ARR during treatment for TB, and sputum culture conversion should be interpreted cautiously in this group. Collecting a final sputum sample may be especially important for PLWH, as treatment failure and relapse were common in this population. The decrease in the number of cases of ARR among PLWH during the study period may reflect the decrease in the total number of PLWH diagnosed with TB in NYC in recent years, improved immune status of PLWH due to increased uptake of antiretroviral drugs, and improvements in the way anti-TB regimens are designed for PLWH (such as recommending daily rather than intermittent rifamycin dosing).

How has the municipal availability of the GeneXpert®MTB/RIF system affected the detection of drug-resistant tuberculosis in Brazil?

OBJECTIVE

To evaluate the association between the availability of GeneXpert®MTB/RIF in municipalities and the proportion of people who have access to this diagnostic technology for tuberculosis (TB), as well as the resistance detected by the surveillance system in Brazil.

METHODS

We analysed 4998 Brazilian municipalities that reported 432,937 new TB cases between 2015 and 2020. We compared municipalities with and without the availability of GeneXpert®MTB/RIF regarding the effective access to GeneXpert®MTB/RIF diagnosis and the prevalence of detected resistance.

RESULTS

Municipalities with at least one GeneXpert®MTB/RIF system had three times (95% CI 2.9-3.0) the access to diagnostic tests and 80.4% (95% CI 70.6%-90.2%) higher detection of resistance, compared with municipalities without this technology. We estimated that there have been 1890 cases of undetected resistance during this period in the country.

CONCLUSIONS

The availability of GeneXpert®MTB/RIF system in the municipality increased the sensitivity of the surveillance for detecting TB resistance.

PUBLIC HEALTH IMPLICATIONS

It is a priority to strengthen laboratory networks and narrow the gap in access to rapid diagnosis in remote areas to improve the detection and control of drug-resistant tuberculosis.

Rifampin Mono-Resistant Tuberculosis in New York City, 2010-2021: A Retrospective Case Series

Background

Although relatively rare, rifampin mono-resistant tuberculosis (RMR TB) poses important challenges to effective TB treatment and control. Information on the burden of RMR TB and treatment outcomes is needed to inform diagnosis and management.

Methods

Standardized variables were collected from the New York City (NYC) tuberculosis surveillance system for patients treated for RMR TB in NYC during 2010-2021.

Results

Of 7097 TB cases reported in 2010-2021, 31 (<1%) were treated clinically as RMR TB. Five (16%) of these patients had HIV. Seventeen patients (55%) had TB that was rifampin-resistant by both molecular and phenotypic drug susceptibility testing; 2 (6%) had rifampin resistance by phenotypic tests, and molecular tests were not done; and 12 (39%) were identified based only on molecular tests. Among these 12, 7 were rifampin-sensitive by phenotypic tests, and phenotypic testing could not be done for the other 5. Ten of the 31 (32%) were diagnosed in 2010-2015; the other 21 (including 10/12 diagnosed by molecular tests alone) were diagnosed in 2016-2021. Of the 31 patients, 21 (68%) completed treatment (median treatment duration of 18 months). Although the interval between tuberculosis treatment initiation and change to a non-rifamycin-containing regimen decreased significantly during the study period, the overall duration of treatment did not decrease significantly between 2010 and 2021.

Conclusions

Molecular drug susceptibility tests identified cases of RMR TB that were not detected by phenotypic testing and helped enable timely adjustment of tuberculosis treatment regimens. Short-course regimens are needed to reduce duration of treatment for RMR TB.

How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality

The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays' gene targets. This continuous quality monitoring rapidly identified delayed hybridization of RdRp in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; S-gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently E-gene delayed hybridization in the Xpert® Xpress SARS-CoV-2 due to XBB.1.5. This near "real-time" monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.

Analysis of Xpert MTB/RIF results in retested patients with very low initial bacterial loads: A retrospective study in China

BACKGROUND

The Xpert MTB/RIF (Xpert) assay has been widely used to diagnose suspected active tuberculosis (TB) and rifampicin-resistant TB cases. Despite its excellent performance record, false-positive Xpert rifampicin (RIF) resistance results are obtained for specimens with extremely low bacterial loads.

OBJECTIVE

We aimed to study the feasibility of repeat Xpert testing as a strategy for reducing the odds of obtaining false-positive results when testing paucibacillary TB patients.

METHODS

We enrolled previously tested TB patients with very low initial bacterial loads from May 2016 to February 2022 for Xpert retesting. A total of 251 TB patients were retested using the Xpert assay.

RESULTS

RIF resistance was noted in 65 (25.9 %) patients when tested by Xpert at initial diagnosis. Only 107 (42.6 %) of 251 patients tested positive for MTB when retested via Xpert. The majority (98.6 %) of RIF-susceptible cases were still susceptible to RIF when retested. Initial Xpert testing yielded 35 positive results for MTB in the RIF-resistant group, of whom 25 (71.4 %) still exhibited RIF resistance when retested. All culture-positive MTB isolates in the RIF-susceptible group were also RIF-susceptible by phenotypic DST. In the RIF-resistant group, 10 of 14 culture-positive MTB isolates exhibited RIF resistance, of which 4 isolates were deemed RIF-susceptible by phenotypic DST. The proportion of double mutations within the MTB rpoB RRDR sequence, as detected by hybridization of Xpert D and E probes, was significantly higher in the RIF-susceptible group than in the RIF-susceptible group.

CONCLUSIONS

Our results demonstrated that initial RIF-susceptible results were more accurate than RIF-resistant results. Additionally, patients with double mutations that delayed probe D/E hybridization were more likely to have false-positive Xpert results. Our findings emphasize that repeat Xpert MTB/RIF testing is necessary for TB patients with extremely low bacterial loads who are at high risk for RIF-resistant TB.

Rapid Evaluation of the Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus Tests

The Xpert^® Xpress SARS-CoV-2 and Xpert^® Xpress SARS-CoV-2/Flu/RSV tests were rapidly developed and widely used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. In response to emerging genetic variability, a new SARS-CoV-2 target (RNA-dependent RNA-polymerase) has been added to both tests: Xpert^® Xpress CoV-2 plus and Xpert^® Xpress CoV-2/Flu/RSV plus test. A rapid evaluation of both tests was performed in South Africa, using residual respiratory specimens. Residual respiratory specimens (n = 125) were used to evaluate the Xpert^® Xpress CoV-2 plus test and included 50 genotyped specimens. The Xpert^® Xpress CoV-2/Flu/RSV plus test was assessed using 45 genotyped SARS-CoV-2 specimens, 10 influenza A, 10 influenza B and 20 respiratory syncytial virus specimens. Results were compared to in-country standard-of-care tests. Genotyped specimens tested the performance of the test under pressure from circulating SARS-CoV-2 variants of concern. Reference material was included to assess the test limits and linearity. The Xpert^® Xpress CoV-2 plus test performance compared to reference results across residual respiratory specimens was good (positive percentage agreement (PPA) = 95.2%, negative percentage agreement (NPA) = 95.0%) The Xpert^® Xpress CoV-2/Flu/RSV plus test showed good performance across all residual respiratory specimens (PPA = 100%, NPA = 98.3%). All genotyped variants of concern were detected by both tests. The Xpert^® Xpress CoV-2 plus and Xpert^® Xpress CoV-2/Flu/RSV plus tests can be used to diagnose SARS-CoV-2, and to diagnose and differentiate SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus, respectively. The NPA was lower than the recommended 99%, but was influenced by the low number of negative specimens tested. The variants of concern assessed did not affect test performance. It is recommended that sites perform their own assessments compared to in-country standard-of-care tests.

Bhesania Hodiwala A, Wagh S, Patil MS. Evaluation of Rpoβ Gene and Its Various Mutants in Multidrug-Resistant Tuberculosis Cases by GeneXpert Method

INTRODUCTION

India is one of the countries in the world which contribute to the global burden of multidrug-resistant tuberculosis (MDR-TB). GeneXpert is a method recommended by the World Health Organization (WHO) that uses five overlapping probes (Probe A to E) to detect mutation in the beta subunit of ribonucleic acid (RNA) polymerase gene (Rpoβ) responsible for rifampicin resistance in Mycobacterium tuberculosis (MTB).

METHOD

All the pulmonary and extrapulmonary samples received in tuberculosis (TB) laboratory for testing of MTB from January 2018 to December 2020 were analyzed for bacillary load and rifampicin resistance was identified by analyzing the number of missing probes.

RESULTS

During the study period, a total of 10,021 samples were tested for MDR-TB. Out of those samples, 2674 samples were positive for MTB of which 2321 were pulmonary samples and 353 were extra-pulmonary samples. Rifampicin resistance was detected in 385 pulmonary samples and 63 extrapulmonary samples. These samples were further differentiated according to the bacillary load. The highest number of mutations was observed in Probe E followed by Probe B, Probe A, and Probe D, and the lowest was observed in Probe C. Also, mutations were associated when all probes were present or a few combinations of probes were missing.

CONCLUSION

GeneXpert assay is a rapid molecular method that detected MTB and rifampicin resistance with a two-hour turnaround. It uses molecular beacons to detect mutation in the Rpoβ gene. This study can be useful in analyzing the prevalence and epidemiology of MTB in a particular demographic area and also the addition of a few more probes can enhance the identification of the mutation in other codons and therefore better therapeutic interventions can be developed accordingly.

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.

Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review

Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.

The evolving biology of Mycobacterium tuberculosis drug resistance

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.

GeneXpert rollout in three high-burden tuberculosis countries in Africa: A review of pulmonary tuberculosis diagnosis and outcomes from 2001 to 2019

Background

The rollout of GeneXpert aimed at increasing early diagnosis of tuberculosis to improve treatment outcomes and global tuberculosis targets.

Objective

This study evaluated trends in tuberculosis diagnosis and outcomes pre- and post-introduction of GeneXpert in three African countries – the Democratic Republic of the Congo (DRC), Nigeria and South Africa.

Methods

Data from 2001 to 2019 were extracted from the World Health Organization’s data repository. Descriptive analysis, paired t-tests and interrupted time series models were used.

Results

Estimated tuberculosis incidence decreased from 327/100 000 to 324/100 000 in the DRC, and from 1220/100 000 to 988/100 000 in South Africa. Incidence remained at 219/100 000 in Nigeria. The tuberculosis case notification rate did not change significantly. Increases in the new case treatment success rates were statistically significant (DRC: p = 0.0201; Nigeria: p = 0.0001; South Africa: p = 0.0017); decreases in mortality were also statistically significant (DRC: p = 0.0264; Nigeria: p = 0.0001; South Africa: p < 0.0001). Time series models showed insignificant increases in new tuberculosis cases in DRC (n = 1856, p = 0.085) and Nigeria (n = 785, p = 0.555) from 2011 to 2019; and a statistically significant decrease in South Africa (n = 15 269, p = 0.006).

Conclusion

Improvements in tuberculosis treatment outcomes were achieved, but little progress has been made in new case notification due to varied implementation and scale-up of GeneXpert across the three countries. Implementation barriers need to be addressed to achieve the required tuberculosis targets.

Rapid molecular tests for tuberculosis and tuberculosis drug resistance: a qualitative evidence synthesis of recipient and provider views

BACKGROUND

Programmes that introduce rapid molecular tests for tuberculosis and tuberculosis drug resistance aim to bring tests closer to the community, and thereby cut delay in diagnosis, ensure early treatment, and improve health outcomes, as well as overcome problems with poor laboratory infrastructure and inadequately trained personnel. Yet, diagnostic technologies only have an impact if they are put to use in a correct and timely manner. Views of the intended beneficiaries are important in uptake of diagnostics, and their effective use also depends on those implementing testing programmes, including providers, laboratory professionals, and staff in health ministries. Otherwise, there is a risk these technologies will not fit their intended use and setting, cannot be made to work and scale up, and are not used by, or not accessible to, those in need.

OBJECTIVES

To synthesize end-user and professional user perspectives and experiences with low-complexity nucleic acid amplification tests (NAATs) for detection of tuberculosis and tuberculosis drug resistance; and to identify implications for effective implementation and health equity.

SEARCH METHODS

We searched MEDLINE, Embase, CINAHL, PsycInfo and Science Citation Index Expanded databases for eligible studies from 1 January 2007 up to 20 October 2021. We limited all searches to 2007 onward because the development of Xpert MTB/RIF, the first rapid molecular test in this review, was completed in 2009.

SELECTION CRITERIA

We included studies that used qualitative methods for data collection and analysis, and were focused on perspectives and experiences of users and potential users of low-complexity NAATs to diagnose tuberculosis and drug-resistant tuberculosis. NAATs included Xpert MTB/RIF, Xpert MTB/RIF Ultra, Xpert MTB/XDR, and the Truenat assays. Users were people with presumptive or confirmed tuberculosis and drug-resistant tuberculosis (including multidrug-resistant (MDR-TB)) and their caregivers, healthcare providers, laboratory technicians and managers, and programme officers and staff; and were from any type of health facility and setting globally. MDR-TB is tuberculosis caused by resistance to at least rifampicin and isoniazid, the two most effective first-line drugs used to treat tuberculosis.

DATA COLLECTION AND ANALYSIS

We used a thematic analysis approach for data extraction and synthesis, and assessed confidence in the findings using GRADE CERQual approach. We developed a conceptual framework to illustrate how the findings relate.

MAIN RESULTS

We found 32 studies. All studies were conducted in low- and middle-income countries. Twenty-seven studies were conducted in high-tuberculosis burden countries and 21 studies in high-MDR-TB burden countries. Only one study was from an Eastern European country. While the studies covered a diverse use of low-complexity NAATs, in only a minority of studies was it used as the initial diagnostic test for all people with presumptive tuberculosis. We identified 18 review findings and grouped them into three overarching categories. Critical aspects users value People with tuberculosis valued reaching diagnostic closure with an accurate diagnosis, avoiding diagnostic delays, and keeping diagnostic-associated cost low. Similarly, healthcare providers valued aspects of accuracy and the resulting confidence in low-complexity NAAT results, rapid turnaround times, and keeping cost to people seeking a diagnosis low. In addition, providers valued diversity of sample types (for example, gastric aspirate specimens and stool in children) and drug resistance information. Laboratory professionals appreciated the improved ease of use, ergonomics, and biosafety of low-complexity NAATs compared to sputum microscopy, and increased staff satisfaction. Challenges reported to realizing those values People with tuberculosis and healthcare workers were reluctant to test for tuberculosis (including MDR-TB) due to fears, stigma, or cost concerns. Thus, low-complexity NAAT testing is not implemented with sufficient support or discretion to overcome barriers that are common to other approaches to testing for tuberculosis. Delays were reported at many steps of the diagnostic pathway owing to poor sample quality; difficulties with transporting specimens; lack of sufficient resources; maintenance of low-complexity NAATs; increased workload; inefficient work and patient flows; over-reliance on low-complexity NAAT results in lieu of clinical judgement; and lack of data-driven and inclusive implementation processes. These challenges were reported to lead to underutilization.  Concerns for access and equity The reported concerns included sustainable funding and maintenance and equitable use of resources to access low-complexity NAATs, as well as conflicts of interest between donors and people implementing the tests. Also, lengthy diagnostic delays, underutilization of low-complexity NAATs, lack of tuberculosis diagnostic facilities in the community, and too many eligibility restrictions hampered access to prompt and accurate testing and treatment. This was particularly the case for vulnerable groups, such as children, people with MDR-TB, or people with limited ability to pay. We had high confidence in most of our findings.

AUTHORS' CONCLUSIONS

Low-complexity diagnostics have been presented as a solution to overcome deficiencies in laboratory infrastructure and lack of skilled professionals. This review indicates this is misleading. The lack of infrastructure and human resources undermine the added value new diagnostics of low complexity have for recipients and providers. We had high confidence in the evidence contributing to these review findings. Implementation of new diagnostic technologies, like those considered in this review, will need to tackle the challenges identified in this review including weak infrastructure and systems, and insufficient data on ground level realities prior and during implementation, as well as problems of conflicts of interest in order to ensure equitable use of resources.

Nucleic Acids Analytical Methods for Viral Infection Diagnosis: State-of-the-Art and Future Perspectives

The analysis of viral nucleic acids (NA), DNA or RNA, is a crucial issue in the diagnosis of infections and the treatment and prevention of related human diseases. Conventional nucleic acid tests (NATs) require multistep approaches starting from the purification of the pathogen genetic material in biological samples to the end of its detection, basically performed by the consolidated polymerase chain reaction (PCR), by the use of specialized instruments and dedicated laboratories. However, since the current NATs are too constraining and time and cost consuming, the research is evolving towards more integrated, decentralized, user-friendly, and low-cost methods. These will allow the implementation of massive diagnoses addressing the growing demand of fast and accurate viral analysis facing such global alerts as the pandemic of coronavirus disease of the recent period. Silicon-based technology and microfluidics, in this sense, brought an important step up, leading to the introduction of the genetic point-of-care (PoC) systems. This review goes through the evolution of the analytical methods for the viral NA diagnosis of infection diseases, highlighting both advantages and drawbacks of the innovative emerging technologies versus the conventional approaches.

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.

Point-of-care testing for sexually transmitted infections in low-resource settings

BACKGROUND

Both the global incidence and prevalence of sexually transmitted infections continue to increase, affecting hundreds of millions of individuals, particularly in low-to middle-income countries. While a definitive diagnosis is desirable to inform STI treatment, syndromic management is the most widely used strategy in resource-limited settings. With the development of point-of-care (POC) tests, it is important to discuss how laboratories will need to adapt to new training and supervisory roles in support of testing which will largely be performed by peripheral clinical staff.

OBJECTIVES

To discuss potential applications of STI POC tests, how they could improve existing STI control strategies and the role of clinical and reference laboratories in support of initiatives to improve STI management and control activities.

SOURCES

Narrative literature review and expert opinion.

CONTENT

The paper outlines the current status of the STI epidemic worldwide and discusses the problems associated with current approaches to control these infections, particularly in low resource settings. The roles of clinical and reference laboratories will need to change in order to provide support for POC and near-patient STI testing as these technologies are introduced into clinical as well as laboratory settings.

IMPLICATIONS

Laboratories will be expected to play a leading role in the introduction and implementation of POC and near-patient STI testing. They will be required to facilitate training and provide technical and supervisory support to clinical staff on the use of these technologies to augment existing STI management and surveillance programs. In order to provide quality service, they will need to develop, introduce and maintain sustainable local QC and EQA systems. Evidence from implementation research for introduction and scale up of STI POCTs in different STI epidemic and laboratory infrastructure settings is required.

Point-of-care diagnostics for infectious diseases: From methods to devices

The current widespread of COVID-19 all over the world, which is caused by SARS-CoV-2 virus, has again emphasized the importance of development of point-of-care (POC) diagnostics for timely prevention and control of the pandemic. Compared with labor- and time-consuming traditional diagnostic methods, POC diagnostics exhibit several advantages such as faster diagnostic speed, better sensitivity and specificity, lower cost, higher efficiency and ability of on-site detection. To achieve POC diagnostics, developing POC detection methods and correlated POC devices is the key and should be given top priority. The fast development of microfluidics, micro electro-mechanical systems (MEMS) technology, nanotechnology and materials science, have benefited the production of a series of portable, miniaturized, low cost and highly integrated POC devices for POC diagnostics of various infectious diseases. In this review, various POC detection methods for the diagnosis of infectious diseases, including electrochemical biosensors, fluorescence biosensors, surface-enhanced Raman scattering (SERS)-based biosensors, colorimetric biosensors, chemiluminiscence biosensors, surface plasmon resonance (SPR)-based biosensors, and magnetic biosensors, were first summarized. Then, recent progresses in the development of POC devices including lab-on-a-chip (LOC) devices, lab-on-a-disc (LOAD) devices, microfluidic paper-based analytical devices (μPADs), lateral flow devices, miniaturized PCR devices, and isothermal nucleic acid amplification (INAA) devices, were systematically discussed. Finally, the challenges and future perspectives for the design and development of POC detection methods and correlated devices were presented. The ultimate goal of this review is to provide new insights and directions for the future development of POC diagnostics for the management of infectious diseases and contribute to the prevention and control of infectious pandemics like COVID-19.

Burden of Antimicrobial Resistance: Compared to What?

The increased focus on the public health burden of antimicrobial resistance (AMR) raises conceptual challenges, such as determining how much harm multidrug-resistant organisms do compared to what, or how to establish the burden. Here, we present a counterfactual framework and provide guidance to harmonize methodologies and optimize study quality. In AMR-burden studies, 2 counterfactual approaches have been applied: the harm of drug-resistant infections relative to the harm of the same drug-susceptible infections (the susceptible-infection counterfactual); and the total harm of drug-resistant infections relative to a situation where such infections were prevented (the no-infection counterfactual). We propose to use an intervention-based causal approach to determine the most appropriate counterfactual. We show that intervention scenarios, species of interest, and types of infections influence the choice of counterfactual. We recommend using purpose-designed cohort studies to apply this counterfactual framework, whereby the selection of cohorts (patients with drug-resistant, drug-susceptible infections, and those with no infection) should be based on matching on time to infection through exposure density sampling to avoid biased estimates. Application of survival methods is preferred, considering competing events. We conclude by advocating estimation of the burden of AMR by using the no-infection and susceptible-infection counterfactuals. The resulting numbers will provide policy-relevant information about the upper and lower bound of future interventions designed to control AMR. The counterfactuals should be applied in cohort studies, whereby selection of the unexposed cohorts should be based on exposure density sampling, applying methods avoiding time-dependent bias and confounding.

Analysis of the gap in PCR monitoring availability for patients with chronic myeloid leukemia in 60 low- and middle-income countries

Purpose

To estimate the resource gap in the polymerase chain reaction (PCR) monitoring for patients with chronic myeloid leukemia (CML) in low- and middle-income countries (LMICs).

Methods

We developed a model of demand and supply of PCR monitoring of CML patients in 60 LMICs. PCR testing was assumed to use Cepheid’s GeneXpert® ^IV system. We included costs of GeneXpert® instruments, uninterrupted power supplies, warranties, calibration kits, test cartridges, and shipping. We calculated the country-specific monetary gap in PCR monitoring, stratified by country priority defined as the availability of tyrosine kinase inhibitors (TKIs) through The Max Foundation initiatives.

Results

The 5-year gap in PCR monitoring was $29.1 million across all countries, 22% ($6.4 million) in countries with all five TKIs available, 20% ($5.7 million) in countries with four TKIs available, 50% ($14.5 million) in countries with three TKIs available, 8% ($2.2 million) in countries with two TKIs available, and 1% ($0.3 million) in countries with one TKI available. The gap was highest in South Asia (52%; $15.1 million) and lowest in Latin America (6%; $1.9 million). Excluding labor costs, the bulk of the resource needs (86%; $25.2 million) were for procurement of BCR-ABL cartridges.

Conclusion

Removing the 5-year gap in PCR monitoring capacity for CML in LMICs will require the mobilization of significant resources and will likely lead to better treatment outcomes and reduced treatment costs through optimization of treatment, discontinuation of therapy in appropriate patients, and facilitation of clinical research. Development of streamlined monitoring guidelines for resource-limited countries should be considered.

Comparing the impact of genotypic based diagnostic algorithm on time to treatment initiation and treatment outcomes among drug-resistant tuberculosis patients in Amhara region, Ethiopia

Background

To end Tuberculosis (TB) by 2030, early detection and timely treatment of Drug-Resistant Tuberculosis (DR-TB) is vital. The role of rapid, accurate, and sensitive DR-TB diagnostic tool is indispensable to accelerate the TB control program. There are evidence breaks in the time difference and its effect on treatment outcomes among different DR-TB diagnostic tools in Ethiopia. This article aimed to compare the different DR-TB diagnostic tools with time pointers and evaluate their effect on the treatment outcomes.

Method

We performed a retrospective chart review of 574 DR-TB patients from September 2010 to December 2017 to compare the impact of molecular DR-TB diagnostic tests (Xpert MTB/RIF, Line Probe Assay (LPA), and solid culture-based Drug Susceptibility Testing (DST)) on time to diagnosis, treatment initiation, and treatment Outcomes. Kruskual-Wallis test was employed to assess the presence of a significant difference in median time among the DR-TB diagnostic tests. Chi-Square and Fisher exact tests were used to test the presence of relations between treatment outcome and diagnostic tests.

Result

The data of 574 DR-TB patients were included in the analysis. From these, 321, 173, and 80 patients were diagnosed using Xpert MTB/RIF, Line Probe Assay (LPA), and solid culture-based DST, respectively. The median time in a day with (Interquartile range (IQR)) for Xpert MTB/RIF, LPA, and solid culture-based DST was from a first care-seeking visit to diagnosis: 2(0, 9), 4(1, 55), and 70(18, 182), from diagnosis to treatment initiation: 3(1, 8), 33(4, 76), and 44(9, 145), and from a first care-seeking visit to treatment initiation: 4(1, 11), 3(1, 12) and 76(3.75, 191) respectively. The shorter median time was observed in the Xpert MTB/RIF followed by the LPA, and this was statistically significant with a p-value <0.001. There was no statistically significant difference concerning treatment outcomes among the three DST tests.

Conclusion

Xpert MTB/RIF can mitigate the transmission of DR-TB significantly via quick diagnosis and treatment initiation followed by LPA as equating to the solid culture base DST, particularly in smear-positive patients. However, we didn’t see a statistically significant impact in terms of treatment outcomes. Xpert MTB/RIF can be used as the first test to diagnose DR-TB by further complimenting solid culture base DST to grasp the drug-resistance profile.

Turnaround times - the Achilles' heel of community screening and testing in Cape Town, South Africa: A short report

Early in the course of the coronavirus infection disease 2019 (COVID-19) pandemic in South Africa, the Department of Health implemented a policy of community screening and testing (CST). This was based on a community-orientated primary care approach and was a key strategy in limiting the spread of the pandemic, but it struggled with long turnaround times (TATs) for the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) reverse transcriptase polymerase chain reaction test. The local experience at Symphony Way Community Day Centre (Delft, Cape Town), highlighted these challenges. The first positive tests had a median TAT of 4.5 days, peaking at 29 days in mid-May 2020. Issues that contributed to long TATs were unavailability of viral transport medium, sample delivery and storage difficulties, staffing problems, scarcity of testing supplies and other samples prioritised over CST samples. At Symphony Way, many patients who tested COVID-19 positive had abandoned their self-isolation because of the delay in results. Employers were unhappy with prolonged sick leave whilst waiting for results and patients were concerned about not getting paid or job loss. The CST policy relies on a rapid TAT to be successful. Once the TAT is delayed, the process of contacting patients, and tracing and quarantining contacts becomes ineffective. With hindsight, other countries’ difficulties in upscaling testing should have served as warning. Community screening and testing was scaled back from 18 May 2020, and testing policy was changed to only include high-risk patients from 29 May 2020. The delayed TATs meant that the CST policy had no beneficial impact at local level.

Performance of the Xpert® MTB/RIF assay in the rapid diagnosis of tracheobronchial tuberculosis using bronchial washing fluid

Objective

To assess the diagnostic value of the Xpert® MTB/RIF (GeneXpert) assay for tracheobronchial tuberculosis (TBTB) using bronchial washing fluid (BWF).

Methods

This retrospective study enrolled patients suspected of having TBTB and patients with non-TB pulmonary disease as controls. BWF were used to undertake acid-fast bacillus (AFB) smears, the GeneXpert assay and the Lӧwenstein–Jensen (LJ) culture method. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were compared among BWF AFB smears, BWF GeneXpert and the BWF LJ culture method.

Results

A total of 130 patients with TBTB and 102 patients with non-TB pulmonary disease were enrolled in the study. Sputum AFB smears were positive in 62 of 130 patients (47.7%) with TBTB. Using the clinical diagnosis of TBTB as the gold standard, the sensitivity, specificity, PPV and NPV of the three methods using BWF were as follows: 93.1%, 99.0%, 99.2% and 91.8% for BWF GeneXpert; 73.1%, 100.0%, 100.0% and 74.5% for BWF LJ cultures; 53.8%, 99.0%, 98.6% and 62.7% for BWF AFB smears. The diagnostic yield of BWF GeneXpert was significantly higher compared with BWF cultures for type III and IV TBTB.

Conclusion

The Xpert® MTB/RIF assay using BWF exhibited higher sensitivity than bacteriological diagnostic methods and was particularly useful for the early diagnosis of smear-negative TBTB.

Immunology of Mycobacterium tuberculosis Infections

Tuberculosis (TB) is a serious global public health challenge that results in significant morbidity and mortality worldwide. TB is caused by infection with the bacilli Mycobacterium tuberculosis (M. tuberculosis), which has evolved a wide variety of strategies in order to thrive within its host. Understanding the complex interactions between M. tuberculosis and host immunity can inform the rational design of better TB vaccines and therapeutics. This chapter covers innate and adaptive immunity against M. tuberculosis infection, including insights on bacterial immune evasion and subversion garnered from animal models of infection and human studies. In addition, this chapter discusses the immunology of the TB granuloma, TB diagnostics, and TB comorbidities. Finally, this chapter provides a broad overview of the current TB vaccine pipeline.

Use of Digital Technology to Enhance Tuberculosis Control: Scoping Review

Background

Tuberculosis (TB) is the leading cause of death from a single infectious agent, with around 1.5 million deaths reported in 2018, and is a major contributor to suffering worldwide, with an estimated 10 million new cases every year. In the context of the World Health Organization’s End TB strategy and the quest for digital innovations, there is a need to understand what is happening around the world regarding research into the use of digital technology for better TB care and control.

Objective

The purpose of this scoping review was to summarize the state of research on the use of digital technology to enhance TB care and control. This study provides an overview of publications covering this subject and answers 3 main questions: (1) to what extent has the issue been addressed in the scientific literature between January 2016 and March 2019, (2) which countries have been investing in research in this field, and (3) what digital technologies were used?

Methods

A Web-based search was conducted on PubMed and Web of Science. Studies that describe the use of digital technology with specific reference to keywords such as TB, digital health, eHealth, and mHealth were included. Data from selected studies were synthesized into 4 functions using narrative and graphical methods. Such digital health interventions were categorized based on 2 classifications, one by function and the other by targeted user.

Results

A total of 145 relevant studies were identified out of the 1005 published between January 2016 and March 2019. Overall, 72.4% (105/145) of the research focused on patient care and 20.7% (30/145) on surveillance and monitoring. Other programmatic functions 4.8% (7/145) and electronic learning 2.1% (3/145) were less frequently studied. Most digital health technologies used for patient care included primarily diagnostic 59.4% (63/106) and treatment adherence tools 40.6% (43/106). On the basis of the second type of classification, 107 studies targeted health care providers (107/145, 73.8%), 20 studies targeted clients (20/145, 13.8%), 17 dealt with data services (17/145, 11.7%), and 1 study was on the health system or resource management. The first authors’ affiliations were mainly from 3 countries: the United States (30/145 studies, 20.7%), China (20/145 studies, 13.8%), and India (17/145 studies, 11.7%). The researchers from the United States conducted their research both domestically and abroad, whereas researchers from China and India conducted all studies domestically.

Conclusions

The majority of research conducted between January 2016 and March 2019 on digital interventions for TB focused on diagnostic tools and treatment adherence technologies, such as video-observed therapy and SMS. Only a few studies addressed interventions for data services and health system or resource management.

A fieldable electrostatic air sampler enabling tuberculosis detection in bioaerosols

Tuberculosis (TB) infects about 25% of the world population and claims more human lives than any other infectious disease. TB is spread by inhalation of aerosols containing viable Mycobacterium tuberculosis expectorated or exhaled by patients with active pulmonary disease. Air-sampling technology could play an important role in TB control by enabling the detection of airborne M. tuberculosis, but tools that are easy to use and scalable in TB hotspots are lacking. We developed an electrostatic air sampler termed the TB Hotspot DetectOR (THOR) and investigated its performance in laboratory aerosol experiments and in a prison hotspot of TB transmission. We show that THOR collects aerosols carrying microspheres, Bacillus globigii spores and M. bovis BCG, concentrating these microparticles onto a collector piece designed for subsequent detection analysis. The unit was also successfully operated in the complex setting of a prison hotspot, enabling detection of a molecular signature for M. tuberculosis in the cough of inmates. Future deployment of this device may lead to a measurable impact on TB case-finding by screening individuals through the aerosols they generate.

Realizing the "40 by 2022" Commitment from the United Nations High-Level Meeting on the Fight to End Tuberculosis: What Will It Take to Meet Rapid Diagnostic Testing Needs?

Existing rapid diagnostics offer faster and more sensitive diagnosis of tuberculosis (TB) and simultaneous detection of multidrug-resistant TB. A 5-fold increase in investment in these tools is needed to meet the needs of the TB community and the United Nations’ ambitious 40 million by 2022 diagnosis and treatment target.

The potential gains from full adoption of World Health Organization (WHO)-recommended rapid diagnostics (WRDs) for tuberculosis (TB) are significant, but there is no current analysis of the additional investment needed to reach this goal. We sought to estimate the necessary investment in instruments, tests, and money, using Xpert MTB/RIF (Xpert), which detects Mycobacterium tuberculosis (MTB) and tests for resistance to rifampicin (RIF), as an example. An existing calculator for TB diagnostic needs was adapted to estimate the Xpert needs for a group of 24 countries with high TB burdens. This analysis assumed that countries will achieve the case-finding commitments agreed to at the recent United Nations High-Level Meeting on the Fight to End Tuberculosis, and that countries would adopt the WHO-recommended algorithm in which all people with signs and symptoms of TB receive an Xpert test. When compared to the current investments in these countries, this baseline model revealed that countries would require a 4-fold increase in the number of Xpert modules and a 6-fold increase in the number of Xpert test cartridges per year to meet their full testing needs. The incremental cost of the additional instruments for these countries would total approximately US$474 million, plus an incremental cost each year of cartridges of approximately $586 million, or a 5-fold increase over current investments. A sensitivity analysis revealed a variety of possible changes under alternative scenarios, but most of these changes either do not meet the global goals, are unrealistic, or would result in even greater investment needs. These findings suggest that a major investment is needed in WRD capacity to implement the recommended diagnostic algorithm for TB and reach the case-finding commitments by 2022.

Fluorescent Double-Stranded DNA-Templated Copper Nanoprobes for Rapid Diagnosis of Tuberculosis

In this work, we investigate highly sensitive fluorescent Cu nanoparticles for use as rapid and specific nucleic acid amplification nanoprobes (NPs) for the diagnosis of tuberculosis. After applying polymerase chain reaction (PCR) to a tuberculosis (TB) sample, we demonstrate that the presence of the targeted IS6110 DNA sequence of TB can be easily and directly detected through the in situ formation of DNA-templated fluorescent Cu NPs and subsequently quantified using only a smartphone. Compared to traditional DNA analysis, this sensing platform does not require purification steps and eliminates the need for electrophoresis to confirm the PCR results. After optimization, this dsDNA-Cu NP-PCR method has the ability to analyze clinical TB nucleic acid samples at a detection limit of 5 fg/μL, and the fluorescent signal can be distinguished in only ∼3 min after the DNA has been amplified. Moreover, with the combination of smartphone-assisted imaging analysis, we can further reduce the instrument size/cost and enhance the portability. In this manner, we are able to eliminate the need for a fluorescent spectrophotometer to measure the clinical sample. These results demonstrate this platform's practical applicability, combining a smartphone and on-site analysis while retaining the detection performance, making it suitable for clinical DNA applications in resource-limited regions of the world.

Tuberculosis, HIV, and viral hepatitis diagnostics in eastern Europe and central Asia: high time for integrated and people-centred services

Globally, high rates (and in the WHO European region an increasing prevalence) of co-infection with tuberculosis and HIV and HIV and hepatitis C virus exist. In eastern European and central Asian countries, the tuberculosis, HIV, and viral hepatitis programmes, including diagnostic services, are separate vertical structures. In this Personal View, we consider underlying reasons for the poor integration for these diseases, particularly in the WHO European region, and how to address this with an initial focus on diagnostic services. In part, this low integration has reflected different diagnostic development histories, global funding sources, and sample types used for diagnosis (eg, typically sputum for tuberculosis and blood for HIV and hepatitis C). Cooperation between services improved as patients with tuberculosis needed routine testing for HIV and vice versa, but financial, infection control, and logistical barriers remain. Multidisease diagnostic platforms exist, but to be used optimally, appropriate staff training and sensible understanding of different laboratory and infection control risks needs rapid implementation. Technically these ideas are all feasible. Poor coordination between these vertical systems remains unhelpful. There is a need to increase political and operational integration of diagnostic and treatment services and bring them closer to patients.

Detecting tuberculosis: rapid tools but slow progress

The World Health Organization (WHO) currently recommends Xpert^® MTB/RIF as the initial test for all people with presumptive tuberculosis (TB). A number of challenges have been reported, however, in using this technology, particularly in low-resource settings. Here we examine these challenges, and provide our perspective of the barriers to Xpert scale-up as assessed through a survey in 16 TB burden countries in which the Médecins Sans Frontières is present. We observed that the key barriers to scale-up include a lack of policy adoption and implementation of WHO recommendations for the use of Xpert, resulting from high costs, poor sensitisation of clinical staff and a high turnover of trained laboratory staff; insufficient service and maintenance provision provided by the manufacturer; and inadequate resources for sustainability and expansion. Funding is a critical issue as countries begin to transition out of support from the Global Fund. While it is clear that there is still an urgent need for research into and development of a rapid, affordable point-of-care test for TB that is truly adapted for use in low-resource settings, countries in the meantime need to develop functional and sustainable Xpert networks in order to close the existing diagnostic gap.

Factors associated with delays in pulmonary tuberculosis diagnosis and treatment initiation in Cali, Colombia

Objective.

To determine factors associated with delays in pulmonary tuberculosis diagnosis and treatment initiation in the city of Cali, Colombia.

Methods.

This was a retrospective cohort study of cases of tuberculosis (TB) reported in the TB control program of Cali between January and December 2016. The information was collected from the databases of the TB control program, individual treatment cards, and clinical histories. The variables considered were sociodemographic factors, clinical factors, substance use, and performance of the health service.

Results.

A total of 623 cases were identified, of which 57.0% were male. The median age was 42 years (interquartile range (IQR): 27–60). The median time from onset of symptoms to TB diagnosis was 57 days (IQR: 21–117), and from onset of symptoms to TB treatment initiation was 72 days (IQR: 35–145). A factor associated with longer time from the onset of symptoms to TB treatment was being a previously treated TB patient (coefficient: 123.8 days, 95% confidence interval (CI): 48.3 to 199.3). In contrast, being incarcerated was a protective factor for earlier TB treatment initiation (coefficient: -57.3 days; 95% CI: -92.4 to -22.3).

Conclusions.

Our results provide important information concerning risk factors that are associated with delays in the diagnosis and treatment of tuberculosis, and that are subject to future interventions. Health insurance program managers must work together with health care providers on issues that include patient care, health promotion, and updating TB protocols and standards.

Management of co-existent tuberculosis and lung cancer

Tuberculosis (TB) and lung cancer are important global health threats, each accounting for 1.6 million deaths yearly. The incidence of both conditions remains high in many developing countries, especially in East Asia. There is now epidemiologic evidence that pre-existing TB poses an increased lung cancer risk. The clinical diagnosis of co-existent TB and lung cancer relies on symptoms of infection, typical radiological features and microbiological confirmation, and remains a challenge in both early and late stage lung cancer. The presence of histological granulomatous inflammation in resected lung specimens is not exclusively indicative of TB. The widely accepted systemic chemotherapy and immunotherapy for treating lung cancer are highly relevant to the occurrence of TB and its management. This review addresses the clinical approach to the diagnosis and treatment of TB that co-exists with lung cancer.

Current Status of Point-of-Care Testing for Human Immunodeficiency Virus Drug Resistance

Healthcare delivery has advanced due to the implementation of point-of-care testing, which is often performed within minutes to hours in minimally equipped laboratories or at home. Technologic advances are leading to point-of-care kits that incorporate nucleic acid-based assays, including polymerase chain reaction, isothermal amplification, ligation, and hybridization reactions. As a limited number of single-nucleotide polymorphisms are associated with clinically significant human immunodeficiency virus (HIV) drug resistance, assays to detect these mutations have been developed. Early versions of these assays have been used in research. This review summarizes the principles underlying each assay and discusses strategic needs for their incorporation into the management of HIV infection.

Genetic Mimetics of Mycobacterium tuberculosis and Methicillin-Resistant Staphylococcus aureus as Verification Standards for Molecular Diagnostics

Molecular diagnostics have revolutionized the management of health care through enhanced detection of disease or infection and effective enrollment into treatment. In recognition of this, the World Health Organization approved the rollout of nucleic acid amplification technologies for identification of Mycobacterium tuberculosis using platforms such as GeneXpert MTB/RIF, the GenoType MTBDRplus line probe assay, and, more recently, GeneXpert MTB/RIF Ultra. These assays can simultaneously detect tuberculosis infection and assess rifampin resistance. However, their widespread use in health systems requires verification and quality assurance programs. To enable development of these, we report the construction of genetically modified strains of Mycobacterium smegmatis that mimic the profile of Mycobacterium tuberculosis on both the GeneXpert MTB/RIF and the MTBDRplus line probe diagnostic tests. Using site-specific gene editing, we also created derivatives that faithfully mimic the diagnostic result of rifampin-resistant M. tuberculosis, with mutations at positions 513, 516, 526, 531, and 533 in the rifampin resistance-determining region of the rpoB gene. Next, we extended this approach to other diseases and demonstrated that a Staphylococcus aureus gene sequence can be introduced into M. smegmatis to generate a positive response for the SCCmec probe in the GeneXpert SA Nasal Complete molecular diagnostic cartridge, designed for identification of methicillin-resistant S. aureus These biomimetic strains are cost-effective, have low biohazard content, accurately mimic drug resistance, and can be produced with relative ease, thus illustrating their potential for widespread use as verification standards for diagnosis of a variety of diseases.

Performance of the Abbott RealTime MTB and MTB RIF/INH Assays in a Setting of High Tuberculosis and HIV Coinfection in South Africa

South Africa is a country with a high incidence of tuberculosis (TB), complicated by coinfection with human immunodeficiency virus (HIV). The Xpert MTB/RIF (Cepheid, Sunnyvale, CA, USA) is used in South Africa as the test for the initial diagnosis of TB, and other molecular platforms such as the m2000 (Abbott Molecular, Des Plaines, IL, USA) are widely used for molecular monitoring of HIV load. The latter platform is now also equipped with the RealTime (RT) MTB and RealTime MTB RIF/INH assays for TB and first-line drug resistance screening but has not been evaluated in settings of HIV and TB coinfection. A prospective clinical validation study was conducted at a community health center in Johannesburg, South Africa, and consenting individuals with presumptive pulmonary TB were enrolled. The performance of the Abbott assays was compared with those of the Xpert MTB/RIF, liquid culture, drug susceptibility testing, and clinical case definitions. A statistical analysis was performed on 206 individuals (73% were HIV positive). The sensitivity and specificity of the RT MTB were 82.5% (confidence interval [CI], 67.2 to 92.7) and 93.1% (CI, 86.2 to 97.2) on raw sputum and 77.5% (CI, 61.5 to 89.2) and 95.1% (CI, 88.9 to 98.4) on concentrated sputum, respectively, compared with those from liquid culture. The RT MTB correctly identified 17/35 more smear-negative culture-positive specimens than the Xpert MTB/RIF. Both the RT MTB and the Xpert MTB/RIF displayed sensitivities >70% and specificities >90% in HIV-positive individuals. The available drug resistance results concurred with MTBDRplus and drug susceptibility profiles. The RT MTB assay has similar diagnostic performance to the Xpert MTB/RIF and is suited to testing presumptive TB patients coinfected with HIV. The existing laboratory information system connectivity, training, and technical support make this a viable polyvalent option to scale up TB alongside HIV laboratory testing services in South Africa.