Molecular Epidemiology of Rifampicin Resistance in Using the GeneXpert MTB/RIF Assay from a Rural Setting in India

Overview

Journal J Pathog

Publisher Wiley

Date 2017 Dec 12

PMID 29225973

Citations 18

Authors

Raghuprakash Reddy

Gerardo Alvarez-Uria

Affiliations

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Abstract

The Xpert MTB/RIF assay can detect mutations in gene that confer rifampicin resistance (RR) using five overlapping probes (A, B, C, D, and E). In this study, we described our experience with the Xpert assay in a rural setting in India. During the study period, 3250 samples were processed. The result was unsuccessful in 5.7% of cases. For extrapulmonary specimens, the risk of unsuccessful result was higher in tissue biopsy and stool samples. Among samples positive for , rifampicin resistance was indeterminate in 1.2% of them. Our results and a review of the literature showed that the most frequent mutations conferring RR were located in the region of Probe E (63.6%; 95% confidence interval [CI] 56.26-70.94), followed by Probe B (15.02%; 95% CI 11.94-18.10), Probe D (13.35%; 95% CI 10.01-16.69), Probe A (4.73%; 95% CI 1.92-7.54), and Probe C (1.61%; 95% CI 0.67-2.54). Although the high cost of the cartridges precluded using the Xpert assay for routine diagnosis of tuberculosis, our results demonstrate that the assay can be used to diagnose RR-tuberculosis in rural areas with limited laboratory infrastructure and could be a convenient tool to investigate the molecular epidemiology of RR in resource-limited settings.

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References

Rahman A, Sahrin M, Afrin S, Earley K, Ahmed S, Rahman S . Comparison of Xpert MTB/RIF Assay and GenoType MTBDRplus DNA Probes for Detection of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis. PLoS One. 2016; 11(4):e0152694. PMC: 4824420. DOI: 10.1371/journal.pone.0152694. View

Agizew T, Boyd R, Ndwapi N, Auld A, Basotli J, Nyirenda S . Peripheral clinic versus centralized laboratory-based Xpert MTB/RIF performance: Experience gained from a pragmatic, stepped-wedge trial in Botswana. PLoS One. 2017; 12(8):e0183237. PMC: 5560557. DOI: 10.1371/journal.pone.0183237. View

Bodmer T, Strohle A . Diagnosing pulmonary tuberculosis with the Xpert MTB/RIF test. J Vis Exp. 2012; (62):e3547. PMC: 3598386. DOI: 10.3791/3547. View

Kaur R, Jindal N, Arora S, Kataria S . Epidemiology of Rifampicin Resistant Tuberculosis and Common Mutations in rpoB Gene of Mycobacterium tuberculosis: A Retrospective Study from Six Districts of Punjab (India) Using Xpert MTB/RIF Assay. J Lab Physicians. 2016; 8(2):96-100. PMC: 4866391. DOI: 10.4103/0974-2727.180789. View

Mboowa G, Namaganda C, Ssengooba W . Rifampicin resistance mutations in the 81 bp RRDR of rpoB gene in Mycobacterium tuberculosis clinical isolates using Xpert® MTB/RIF in Kampala, Uganda: a retrospective study. BMC Infect Dis. 2014; 14:481. PMC: 4164707. DOI: 10.1186/1471-2334-14-481. View

Alvarez-Uria G, Azcona J, Midde M, Naik P, Reddy S, Reddy R . Rapid Diagnosis of Pulmonary and Extrapulmonary Tuberculosis in HIV-Infected Patients. Comparison of LED Fluorescent Microscopy and the GeneXpert MTB/RIF Assay in a District Hospital in India. Tuberc Res Treat. 2012; 2012:932862. PMC: 3433122. DOI: 10.1155/2012/932862. View

Thirumurugan R, Kathirvel M, Vallayyachari K, Surendar K, Samrot A, Muthaiah M . Molecular analysis of rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis isolates by multiple allele specific polymerase chain reaction in Puducherry, South India. J Infect Public Health. 2015; 8(6):619-25. DOI: 10.1016/j.jiph.2015.05.003. View

Suresh N, Singh U, Arora J, Pant H, Seth P, Sola C . rpoB gene sequencing and spoligotyping of multidrug-resistant Mycobacterium tuberculosis isolates from India. Infect Genet Evol. 2006; 6(6):474-83. DOI: 10.1016/j.meegid.2006.03.001. View

Lawn S, Nicol M . Xpert® MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance. Future Microbiol. 2011; 6(9):1067-82. PMC: 3252681. DOI: 10.2217/fmb.11.84. View

10.

Metcalfe J, Makumbirofa S, Makamure B, Sandy C, Bara W, Mason P . Xpert(®) MTB/RIF detection of rifampin resistance and time to treatment initiation in Harare, Zimbabwe. Int J Tuberc Lung Dis. 2016; 20(7):882-9. PMC: 4961684. DOI: 10.5588/ijtld.15.0696. View

11.

Ochang E, Udoh U, Emanghe U, Tiku G, Offor J, Odo M . Evaluation of rifampicin resistance and 81-bp rifampicin resistant determinant region of rpoB gene mutations of Mycobacterium tuberculosis detected with XpertMTB/Rif in Cross River State, Nigeria. Int J Mycobacteriol. 2017; 5 Suppl 1:S145-S146. DOI: 10.1016/j.ijmyco.2016.09.007. View

12.

Creswell J, Codlin A, Andre E, Micek M, Bedru A, Carter E . Results from early programmatic implementation of Xpert MTB/RIF testing in nine countries. BMC Infect Dis. 2014; 14:2. PMC: 3898850. DOI: 10.1186/1471-2334-14-2. View

13.

Theron G, Zijenah L, Chanda D, Clowes P, Rachow A, Lesosky M . Feasibility, accuracy, and clinical effect of point-of-care Xpert MTB/RIF testing for tuberculosis in primary-care settings in Africa: a multicentre, randomised, controlled trial. Lancet. 2013; 383(9915):424-35. DOI: 10.1016/S0140-6736(13)62073-5. View

14.

Ullah I, Shah A, Basit A, Ali M, Khan A, Ullah U . Rifampicin resistance mutations in the 81 bp RRDR of rpoB gene in Mycobacterium tuberculosis clinical isolates using Xpert MTB/RIF in Khyber Pakhtunkhwa, Pakistan: a retrospective study. BMC Infect Dis. 2016; 16:413. PMC: 4983047. DOI: 10.1186/s12879-016-1745-2. View

15.

Singh U, Pandey P, Mehta G, Bhatnagar A, Mohan A, Goyal V . Genotypic, Phenotypic and Clinical Validation of GeneXpert in Extra-Pulmonary and Pulmonary Tuberculosis in India. PLoS One. 2016; 11(2):e0149258. PMC: 4760939. DOI: 10.1371/journal.pone.0149258. View

16.

Raizada N, Sachdeva K, Sreenivas A, Vadera B, Gupta R, Parmar M . Feasibility of decentralised deployment of Xpert MTB/RIF test at lower level of health system in India. PLoS One. 2014; 9(2):e89301. PMC: 3935858. DOI: 10.1371/journal.pone.0089301. View