Pyrosequencing for the rapid detection of rifampicin resistance in &lt;I&gt;Mycobacterium tuberculosis&lt;/I&gt;: a meta-analysis [Review article]

Q, Guo; Rj, Zheng; Ct, Zhu; Ll, Zou; Jf, Xiu; Li, Jian; Zy, Hu

doi:10.5588/ijtld.12.0519

Cited by 11 publications

(5 citation statements)

References 20 publications

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“…(i) We included a target to identify MTBC, concurrent with drug resistance detection. This has not been done in most published PSQ studies, and it was an improvement over the recommendation for identification of MTBC prior to drug resistance detection made by Guo et al in a meta-analysis publication (32). (ii) Our assay is sensitive enough to test clinical specimens, which significantly shortens the turnaround time for obtaining molecular DST results.…”

Section: Discussionmentioning

confidence: 97%

Pyrosequencing for Rapid Detection of Extensively Drug-Resistant Mycobacterium tuberculosis in Clinical Isolates and Clinical Specimens

et al. 2014

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cTreating extensively drug-resistant (XDR) tuberculosis (TB) is a serious challenge. Culture-based drug susceptibility testing (DST) may take 4 weeks or longer from specimen collection to the availability of results. We developed a pyrosequencing (PSQ) assay including eight subassays for the rapid identification of Mycobacterium tuberculosis complex (MTBC) and concurrent detection of mutations associated with resistance to drugs defining XDR TB. The entire procedure, from DNA extraction to the availability of results, was accomplished within 6 h. The assay was validated for testing clinical isolates and clinical specimens, which improves the turnaround time for molecular DST and maximizes the benefit of using molecular testing. A total of 130 clinical isolates and 129 clinical specimens were studied. The correlations between the PSQ results and the phenotypic DST results were 94.3% for isoniazid, 98.7% for rifampin, 97.6% for quinolones (ofloxacin, levofloxacin, or moxifloxacin), 99.2% for amikacin, 99.2% for capreomycin, and 96.4% for kanamycin. For testing clinical specimens, the PSQ assay yielded a 98.4% sensitivity for detecting MTBC and a 95.8% sensitivity for generating complete sequencing results from all subassays. The PSQ assay was able to rapidly and accurately detect drug resistance mutations with the sequence information provided, which allows further study of the association of drug resistance or susceptibility with each mutation and the accumulation of such knowledge for future interpretation of results. Thus, reporting of false resistance for mutations known not to confer resistance can be prevented, which is a significant benefit of the assay over existing molecular diagnostic methods endorsed by the World Health Organization. Regional increases in the prevalence of tuberculosis (TB) with drug resistance and a broad distribution of multidrug-resistant (MDR) TB and extensively drug-resistant (XDR) TB (1, 2) may reverse recent gains in global TB control (1). Molecular detection of mutations associated with drug resistance has facilitated rapid detection of drug resistance in the Mycobacterium tuberculosis complex (MTBC) (3-7), and the use of such molecular tools has become increasingly important in TB control and TB patient management (5, 7-10). Recognizing the advantages and disadvantages of various molecular methods will help in the selection of optimal methods for improved prediction of drug resistance in MTBC, which is critical in advancing molecular diagnostic approaches for this defined purpose.In 2003, the Microbial Diseases Laboratory (MDL) at the California Department of Public Health developed a real-time, probe-based assay using molecular beacons for screening for MDR TB (11). Remarkable improvements in turnaround times for predicting resistance to isoniazid (INH) and rifampin (RIF) and significant impacts on the management of MDR TB (9) were realized. However, several incidents of detection of rpoB mutations not conferring RIF resistance resulted in erroneous reporting of false RIF resi...

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Section: Discussionmentioning

confidence: 97%

Pyrosequencing for Rapid Detection of Extensively Drug-Resistant Mycobacterium tuberculosis in Clinical Isolates and Clinical Specimens

et al. 2014

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“…Even so, the considerable heterogeneity in the results remained unexplained, which may be caused by variations in the study, patient selection, sample collection method (consecutive or random collection of samples), and/or geographic and genetic variations in the distribution of drug-resistant strains of M . tuberculosis [ 58 , 59 ].…”

Section: Discussionmentioning

confidence: 99%

GenoType MTBDRplus Assay for Rapid Detection of Multidrug Resistance in Mycobacterium tuberculosis: A Meta-Analysis

et al. 2016

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BackgroundThere is an urgent demand for rapid and accurate drug-susceptibility testing for the detection of multidrug-resistant tuberculosis. The GenoType MTBDRplus assay is a promising molecular kit designed for rapid identification of resistance to first-line anti-tuberculosis drugs, isoniazid and rifampicin. The aim of this meta-analysis was to evaluate the diagnostic accuracy of GenoType MTBDRplus in detecting drug resistance to isoniazid and rifampicin in comparison with the conventional drug susceptibility tests.MethodsWe searched PubMed, EMBASE, and Cochrane Library databases to identify studies according to predetermined criteria. A total of 40 studies were included in the meta-analysis. QUADAS-2 was used to assess the quality of included studies with RevMan 5.2. STATA 13.0 software was used to analyze the tests for sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver operating characteristic curves. Heterogeneity in accuracy measures was tested with Spearman correlation coefficient and Chi-square.ResultsPatient selection bias was observed in most studies. The pooled sensitivity (95% confidence intervals were 0.91 (0.88–0.94) for isoniazid, 0.96 (0.95–0.97) for rifampicin, and 0.91(0.86–0.94) for multidrug-resistance. The pooled specificity (95% CI) was 0.99 (0.98–0.99) for isoniazid, 0.98 (0.97–0.99) for rifampicin and 0.99 (0.99–1.00) for multidrug-resistance, respectively. The area under the summary receiver operating characteristic curves ranged from 0.99 to 1.00.ConclusionThis meta-analysis determined that GenoType MTBDRplus had good accuracy for rapid detection of drug resistance to isoniazid and/or rifampicin of M. tuberculosis. MTBDRplus method might be a good alternative to conventional drug susceptibility tests in clinical practice.

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“…While most sensors detailed within this Review focus on detecting the biothreat agent, determining other properties such as the presence of resistance genes is equally as important for the containment and treatment of patients during an outbreak. It is this aspect toward which most sequencing efforts have been directed, particularly with rifampicin and isoniazid resistance in M. tuberculosis − along with resistance to other therapeutics now found in both B. anthracis and Y. pestis . , As the technology and cost of genomic sequencing continues to improve with next generation techniques, use of sequencing in direct biosensing and confirmation of initial screening tests can be expected to increase dramatically.…”

Section: Biochemical Sensorsmentioning

confidence: 99%

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

et al. 2018

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Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

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Pyrosequencing for the rapid detection of rifampicin resistance in <I>Mycobacterium tuberculosis</I>: a meta-analysis [Review article]

Cited by 11 publications

References 20 publications

Pyrosequencing for Rapid Detection of Extensively Drug-Resistant Mycobacterium tuberculosis in Clinical Isolates and Clinical Specimens

Pyrosequencing for Rapid Detection of Extensively Drug-Resistant Mycobacterium tuberculosis in Clinical Isolates and Clinical Specimens

GenoType MTBDRplus Assay for Rapid Detection of Multidrug Resistance in Mycobacterium tuberculosis: A Meta-Analysis

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

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