1
|
Arbués MD, Rossetti MLR. Evaluation of the GeneXpert MTB/RIF to diagnose tuberculosis in a public health laboratory. Rev Saude Publica 2024; 58:03. [PMID: 38381893 PMCID: PMC10878686 DOI: 10.11606/s1518-8787.2024058005306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/31/2023] [Indexed: 02/23/2024] Open
Abstract
OBJECTIVES To evaluate the performance of geneXpert MTB/Rif versus conventional methods (bacilloscopy and culture) in the diagnosis of tuberculosis in a Central Public Health Laboratory (LACEN, Tocantins), Northern Brazil. METHODS Retrospective study, with information from 1,973 suspected cases of tuberculosis from patients treated from January 2015 to December 2020. RESULTS From the culture (reference standard), the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the geneXpert MTB/Rif were 100%, 97%, 74%, 100%, and 97%, respectively, against 85%, 98%, 80%, 98%, and 97% of bacilloscopy. CONCLUSIONS The geneXpert MTB/Rif performed similarly to culture and better than bacilloscopy. Although positive cases with negative culture should be evaluated with caution, its routine use is important for the early detection of tuberculosis.
Collapse
Affiliation(s)
- Mohanna Damasceno Arbués
- Universidade Luterana do BrasilPrograma de Doutorado em Biologia Molecular e Celular Aplicada à SaúdeCanoasRSBrasilUniversidade Luterana do Brasil. Programa de Doutorado em Biologia Molecular e Celular Aplicada à Saúde. Canoas, RS, Brasil
| | - Maria Lúcia Rosa Rossetti
- Universidade Luterana do BrasilPrograma de Doutorado em Biologia Molecular e Celular Aplicada à SaúdeCanoasRSBrasilUniversidade Luterana do Brasil. Programa de Doutorado em Biologia Molecular e Celular Aplicada à Saúde. Canoas, RS, Brasil
| |
Collapse
|
2
|
Farra A, Koula K, Jolly BL, Gando HG, Ouarandji LM, Mossoro-Kpinde CD, Manirakiza A, Simelo JP, de Dieu Iragena J. Effectiveness of Xpert MTB/RIF and the Line Probe Assay tests for the rapid detection of drug-resistant tuberculosis in the Central African Republic. PLOS Glob Public Health 2023; 3:e0001847. [PMID: 37126485 PMCID: PMC10150968 DOI: 10.1371/journal.pgph.0001847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023]
Abstract
The Xpert MTB/RIF and Line Probe Assay (LPA) tests are more and more frequently used in mycobacteria testing laboratories for the rapid diagnosis of multi-drug resistance (MDR-TB). In this study, we demonstrate the effectiveness of these tests in the Central African Republic. Rifampicin resistance cases detected by the Xpert MTB/RIF during the year 2020 are also underwent first- and second-line LPA, and a first-line of drug susceptibility testing (DST) on solid medium and we compared these results. 101 rifampicin resistance cases based on the Xpert MTB/RIF were detected. Mean age was 34 years [16-81]. The 20-40 years age group represented 73.2% and the male-to-female sex ratio was 1.9:1. Patient profiles were dominated by treatment failure cases (40.6%) followed by relapsed cases (30.7%) and new cases (18.8%). These 101 rifampicin resistance were also detected with the first-line LPA and were confirmed by the DST. Similarly, the isoniazid results obtained with the first-line LPA, were confirmed by the DST, giving a concordance of 100% for these antibiotics. Rifampicin resistance were for the most part due to the absence of the WT8 sequence (56%) and the presence of the Mut3 mutation (53.4%). The majority of the isoniazid resistance (94.2%) were due to the Mut1 mutation in the katG gene and 4.2% of the cases involved both the katG gene and the inhA gene promoter with the Mut1 mutation. The second-line LPA test no resistance to second-line antibiotics. This study demonstrated the effectiveness of the Xpert MTB/RIF and the LPA tests for the rapid diagnosis of MDR-TB in the Central African Republic. However, due to their high cost, these tests have not been extensively deployed in the country. Public authorities and their TB-partners can help make these molecular tests more accessible to fight MDR-TB in the country.
Collapse
Affiliation(s)
- Alain Farra
- National Reference Laboratory for Tuberculosis, Institut Pasteur of Bangui, Bangui, Central African Republic
| | - Karen Koula
- Department of Microbiology, University of Bangui, Bangui, Central African Republic
| | - Boris Lokoti Jolly
- National Reference Laboratory for Tuberculosis, Institut Pasteur of Bangui, Bangui, Central African Republic
| | - Hervé Gildas Gando
- Coordination Unit of the National Tuberculosis Control Program, Ministry of Health, Bangui, Central African Republic
| | - Louis Médart Ouarandji
- Coordination Unit of the National Tuberculosis Control Program, Ministry of Health, Bangui, Central African Republic
| | | | | | | | | |
Collapse
|
3
|
Nguyen HV, de Haas P, Nguyen HB, Nguyen NV, Cobelens FGJ, Mirtskhulava V, Finlay A, Van Nguyen H, Huyen PTT, Tiemersma EW. Discordant results of Xpert MTB/Rif assay and BACTEC MGIT 960 liquid culture to detect Mycobacterium tuberculosis in community screening in Vietnam. BMC Infect Dis 2022; 22:506. [PMID: 35641936 PMCID: PMC9153144 DOI: 10.1186/s12879-022-07481-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Xpert MTB/Rif, a molecular test to detect tuberculosis (TB), has been proven to have high sensitivity and specificity when compared with liquid culture in clinical settings. However, little is known about its performance in community TB screening. METHODS In Vietnam, a national TB prevalence survey was conducted in 2017. Survey participants who screened positive by chest X-ray, cough symptoms and/or recent history of tuberculosis were requested to provide at least two sputum samples that were tested for Mycobacterium tuberculosis by Xpert MTB/Rif G4 (Xpert) and BACTEC MGIT960 culture (MGIT). RESULTS There were 4,649 eligible participants provided both samples for testing. Among them, 236 (5.1%) participants tested positive for TB by Xpert, 244 (5.3%) tested positive by MGIT and 317 tested positive by at least one test; 163 (51.4%) had discordant test results. Of the positive Xpert, 162 (68.6%) showed a low or very low bacterial load. In multivariate logistic regression comparing discordant with Xpert-MGIT concordant positive results, discordant Xpert-positive results occurred more often among participants who had low sputum bacterial load, male sex, a history of TB treatment, or night sweats. The associated factors were male sex, abnormal chest X-ray and having night sweats when the logistic model was against those with both Xpert and MGIT negative. CONCLUSIONS We found high rates of discordance in the performance of Xpert and MGIT for community-based TB case finding. In situations where the majority of TB cases are expected to have a low bacterial load, multiple diagnostic tests and/or multiple samples are required to reach sufficient sensitivity.
Collapse
Affiliation(s)
- Hai Viet Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
- Department of Global Health and Amsterdam Institute of Global Health and Development, Amsterdam University Medical Centres location University of Amsterdam, Amsterdam, the Netherlands
| | - Petra de Haas
- KNCV Tuberculosis Foundation, The Hague, the Netherlands
| | - Hoa Binh Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | - Nhung Viet Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | - Frank G. J. Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Amsterdam University Medical Centres location University of Amsterdam, Amsterdam, the Netherlands
| | - Veriko Mirtskhulava
- KNCV Tuberculosis Foundation, The Hague, the Netherlands
- David Tvildiani Medical University, Tbilisi, Georgia
| | - Alyssa Finlay
- Centers for Disease Control - Vietnam Office, Hanoi, Vietnam
| | - Hung Van Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | - Pham T. T. Huyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | | |
Collapse
|
4
|
Ssengooba W, Komakech K, Namiiro S, Byabajungu H, Nalunjogi J, Katagira W, Kimuli I, Joloba ML, Adakun S, Nakiyingi L, Torrea G, Kirenga BJ. Rifampicin susceptibility discordance between Xpert MTB/RIF G4 and Xpert Ultra before MDRT-TB treatment initiation: A case report from Uganda. J Clin Tuberc Other Mycobact Dis 2021; 25:100286. [PMID: 34816021 PMCID: PMC8592849 DOI: 10.1016/j.jctube.2021.100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis (TB) resistance to rifampicin, the most powerful drug leads to increase in mortality. Globally, half a million new patients develop such resistant TB each year, coupled with both inappropriate diagnosis and treatment initiation. We report a case of rifampicin resistant Mycobacterium tuberculosis whose rifampicin resistance was missed by Xpert MTB/RIF Assay G4 but detected by the Xpert MTB/RIF Ultra assay at different time points leading to increased delays for MDR-TB treatment initiation at Mulago Hospital, Kampala, Uganda. Our case report compels greater urgency in accelerating the transition to the newer assay, Ultra, to benefit from higher sensitivity of rifampicin resistance detection.
Collapse
Affiliation(s)
- Willy Ssengooba
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Kevin Komakech
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Sharon Namiiro
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Henry Byabajungu
- National TB Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Joanitah Nalunjogi
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Winceslaus Katagira
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ivan Kimuli
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Susan Adakun
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- National Tuberculosis Treatment Unit, Mulago Hospital, Kampala, Uganda
| | - Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Gabriela Torrea
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bruce J Kirenga
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| |
Collapse
|
5
|
Van Rie A, Whitfield MG, De Vos E, Scott L, Da Silva P, Hayes C, Heupink TH, Sirgel FA, Stevens W, Warren RM. Discordances between molecular assays for rifampicin resistance in Mycobacterium tuberculosis: frequency, mechanisms and clinical impact. J Antimicrob Chemother 2021; 75:1123-1129. [PMID: 32016320 DOI: 10.1093/jac/dkz564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Molecular assays are endorsed for detection and confirmation of rifampicin-resistant TB. The frequency, causal mechanisms and impact of discordant results between molecular tests are not well understood. METHODS The prevalence of discordant results was determined by pairwise comparison of molecular test results in a cohort of 749 rifampicin-resistant TB patients in three South African provinces. Culture isolates were sent to a research laboratory for WGS and rifampicin MIC determination. Clinical information was collected through medical file review. RESULTS The prevalence of discordances between Xpert MTB/RIF and MTBDRplus was 14.5% (95% CI 10.9%-18.9%), 5.6% (95% CI 2.2%-13.4%) between two consecutive Xpert assays and 4.2% (95% CI 2.2%-7.8%) between two consecutive MTBDRplus assays. Likely mechanisms of discordances were false rifampicin susceptibility on MTBDRplus (due to variants not included in mutant probes or heteroresistance with loss of minor variants in culture), false resistance on molecular assay in rifampicin-susceptible isolates, and human error. The healthcare worker changed the treatment regimen in 33% of patients with discordant results and requested 232 additional molecular tests after a first confirmatory test was performed in 460 patients. A follow-up Xpert assay would give the healthcare worker the 'true' rifampicin-resistant TB diagnosis in at least 73% of discordant cases. CONCLUSIONS The high rate of discordant results between Xpert and MTBDRplus has important implications for the laboratory, clinician and patient. While root causes for discordant result are multiple, a follow-up Xpert assay could guide healthcare workers to the correct treatment in most patients.
Collapse
Affiliation(s)
- Annelies Van Rie
- Department of Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Michael G Whitfield
- Department of Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium.,South African Medical Research Council Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Elise De Vos
- Department of Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pedro Da Silva
- National Health Laboratory Services, Johannesburg, South Africa
| | - Cindy Hayes
- National Health Laboratory Services, Port Elizabeth, South Africa
| | - Tim H Heupink
- Department of Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Frederick A Sirgel
- South African Medical Research Council Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Wendy Stevens
- National Health Laboratory Services, Johannesburg, South Africa.,National Priority Program, National Health Laboratory Service, Johannesburg, South Africa
| | - Robin M Warren
- South African Medical Research Council Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
6
|
Ssengooba W, de Dieu Iragena J, Komakech K, Okello I, Nalunjogi J, Katagira W, Kimuli I, Adakun S, Joloba ML, Torrea G, Kirenga BJ. Discordance of the Repeat GeneXpert MTB/RIF Test for Rifampicin Resistance Detection Among Patients Initiating MDR-TB Treatment in Uganda. Open Forum Infect Dis 2021; 8:ofab173. [PMID: 34189166 PMCID: PMC8223903 DOI: 10.1093/ofid/ofab173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/31/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Global Laboratory Initiative (GLI) guidelines recommend repeat for GeneXpertMTB/RIF (XpertMTB/RIF) in patients with a low pretest probability of rifampicin resistance (RR). METHODS This was a cross-sectional study using results of sputum specimens collected from participants screened for the STREAM 2 trial. We recruited all patients with XpertMTB/RIF RR-TB detected who were referred for RR/multidrug-resistant (MDR) TB treatment initiation at Mulago National Referral Hospital, Kampala, between September 2017 and October 2019. At baseline, smear microscopy, repeat XpertMTB/RIF, Xpert Ultra, and MTBDRplus assays were done on sputum specimens. Culture-based drug susceptibility testing (DST) was performed on discordant specimens. We analyzed the prevalence and factors associated with discordance between initial and repeat XpertMTB/RIF RR and false XpertMTB/RIF RR. False XpertMTB/RIF RR was defined as no RR detected by any of Xpert Ultra, LPA, or culture DST (reference comparator). RESULTS A total of 126/130 patients had repeat XpertMTB/RIF results, of whom 97 (77.0%) had M. tuberculosis detected, 81 (83.5%) had RR detected, and 1 (1.0%) had RR indeterminate. The prevalence of discordant XpertMTB/RIF RR was 15/96 (15.6%), whereas false XpertMTB/RIF RR prevalence was 10/96 (10.4%).Low-bacillary load sputum specimens were more likely to have discordant XpertMTB/RIF RR and false XpertMTB/RIF RR results (adjusted odds ratio [aOR], 0.04; 95% CI, 0.00-0.37; P = .01; aOR, 0.02; 95% CI, 0.01-0.35; P = .01, respectively). CONCLUSIONS Our findings show a high false-positive rifampicin resistance rate in low-TB burden patients, which calls for repeat testing in order to prevent unnecessary prescription of anti-MDR-TB therapy.
Collapse
Affiliation(s)
- Willy Ssengooba
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
- Mycobacteriology (BSL-3) Laboratory, Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Jean de Dieu Iragena
- Communicable Diseases Cluster, HIV/TB and Hepatitis Programme, World Health Organization Regional Office for Africa, Brazzaville, Congo
| | - Kevin Komakech
- Mycobacteriology (BSL-3) Laboratory, Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Iginitius Okello
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Joanitah Nalunjogi
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Winceslaus Katagira
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Ivan Kimuli
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| | - Susan Adakun
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
- National Tuberculosis Treatment Unit, Mulago Hospital, Kampala, Uganda
| | - Moses L Joloba
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
- Mycobacteriology (BSL-3) Laboratory, Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Gabriela Torrea
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bruce J Kirenga
- College of Health Sciences, Makerere University Lung Institute, Kampala, Uganda
| |
Collapse
|
7
|
Abstract
We present a case of a 59-year-old man, who on being evaluated for abdominal pain and headache, was found to have a pancreatic head mass and inflammatory hypophysitis. Xpert MTB/Rif of the pancreatic mass biopsy showed the presence of tuberculosis (TB) with a very low load, and rifampicin resistance was detected with absence of probes A and B. Pyrosequencing (a novel genotypic test for TB) of the Xpert MTB/Rif isolate detected a single, rare, high-confidence mutation (S512T) in the rpoB region (rifampicin resistance determining region in the MTB genome). The TB mycobacteria growth indicator tube (TBMGIT) phenotypic drug susceptibility test (DST), however, showed rifampicin susceptibility. Incidentally, he was unable to tolerate rifampicin and responded well to a non-rifampicin-based regimen. We discuss a possible hypothesis of the Xpert-DST discordance in accordance with a recent literature review on phenotypic DST methods. We also discuss the utility of pyrosequencing in clinical practice for the diagnosis of TB and its resistance patterns.
Collapse
Affiliation(s)
- Umang Agrawal
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Krutarth Kanjiya
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Camilla Rodrigues
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Ayesha Sunavala
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| |
Collapse
|
8
|
Beylis N, Ghebrekristos Y, Nicol M. Management of false-positive rifampicin resistant Xpert MTB/RIF. The Lancet Microbe 2020; 1:e238. [DOI: 10.1016/s2666-5247(20)30123-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022] Open
|
9
|
Mahomed S, Mlisana K, Cele L, Naidoo K. Discordant line probe genotypic testing vs culture-based drug susceptibility phenotypic testing in TB endemic KwaZulu-Natal: Impact on bedside clinical decision making. J Clin Tuberc Other Mycobact Dis 2020; 20:100176. [PMID: 32793816 PMCID: PMC7414011 DOI: 10.1016/j.jctube.2020.100176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The recommendations for Mycobacterium tuberculosis drug susceptibility testing include both phenotypic and genotypic methods. This concurrent use of differing testing platforms has created an emerging challenge of discordant results, creating a diagnostic dilemma for the laboratorians as well as attending clinicians. We undertook a retrospective study to determine the prevalence of discordant results between the MTBDRplus line probe assay and solid culture-based drug susceptibility testing for rifampicin and isoniazid. The analysis was conducted for the period January 2013 and December 2015 at the Inkosi Albert Luthuli Central Hospital. Rifampicin and isoniazid resistance testing data were "paired" on 8273 isolates for culture-based drug susceptibility testing and line probe assay. The latter method showed high sensitivity and specificity of 93% and 95% respectively for isoniazid testing. For rifampicin testing, sensitivity and specificity were 95% and 75%. Overall, discordance was 14.6% for rifampicin and 7.2% for isoniazid. This report is not intended to determine superiority of one method over another. It is merely to show that discordance does exist between different methods of testing. Given the burden of HIV and Tuberculosis in Sub-Saharan Africa, these findings have clinical significance and huge public health implications. Clinicians should understand the limitations of phenotypic testing methods.
Collapse
Affiliation(s)
- Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Lindiwe Cele
- Sefako Makgatho Health Sciences University, Department of Public Health, Epidemiology and Biostatistics Unit, South Africa
| | - Kogieleum Naidoo
- Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
10
|
Kayomo MK, Mbula VN, Aloni M, André E, Rigouts L, Boutachkourt F, de Jong BC, Nkiere NM, Dean AS. Targeted next-generation sequencing of sputum for diagnosis of drug-resistant TB: results of a national survey in Democratic Republic of the Congo. Sci Rep 2020; 10:10786. [PMID: 32612134 DOI: 10.1038/s41598-020-67479-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/02/2020] [Indexed: 11/23/2022] Open
Abstract
The surveillance of drug resistance among tuberculosis (TB) patients is central to preventing the spread of antimicrobial resistance. The Democratic Republic of the Congo (DR Congo) is classified by the World Health Organization (WHO) as a country with a high burden of TB and multidrug-resistant TB (MDR-TB), but there are no nationally representative data on drug resistance. In 2016–2017, a national survey of TB patients was conducted in 108 microscopy centres across all 11 provinces of the country using innovative molecular approaches. Sputum samples were collected from 1,545 new and 163 previously treated patients. These were tested by the Xpert MTB/RIF assay, followed by targeted next-generation sequencing performed directly on sputum. The prevalence of rifampicin resistance was low, at 1.8% (95% CI: 1.0–3.2) among new and 17.3% (95% CI: 11.9–24.4) among previously treated patients. Resistance to pyrazinamide, fluoroquinolones and second-line injectables was also low. The prevalence of resistance to isoniazid among rifampicin-susceptible patients was higher, at 6.6% (95% CI: 4.4–9.8) among new and 8.7% (95% : 3.2–21.2) among previously treated patients. Diagnosing and treating isoniazid-resistant patients remains a challenge, given that many will be missed by the current national diagnostic algorithm that is driven by detecting rifampicin resistance by Xpert MTB/RIF. This is the first nationwide survey incorporating targeted sequencing directly on sputum. It serves as a proof-of-concept for other settings that do yet have rapid specimen transport networks or capacity to conduct culture.
Collapse
|
11
|
Ngabonziza JCS, Decroo T, Migambi P, Habimana YM, Van Deun A, Meehan CJ, Torrea G, Massou F, de Rijk WB, Ushizimpumu B, Niyigena EB, Ivan E, Semahore JM, Mazarati JB, Merle CS, Supply P, Affolabi D, Rigouts L, de Jong BC. Prevalence and drivers of false-positive rifampicin-resistant Xpert MTB/RIF results: a prospective observational study in Rwanda. Lancet Microbe 2020; 1:e74-e83. [PMID: 35544156 DOI: 10.1016/s2666-5247(20)30007-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND The Xpert MTB/RIF (Xpert) assay is used globally to rapidly diagnose tuberculosis and resistance to rifampicin. We investigated the frequency and predictors of false-positive findings of rifampicin resistance with Xpert. METHODS We did a prospective, observational study of individuals who were enrolled in a Rwandan nationwide diagnostic cohort study (DIAMA trial; NCT03303963). We included patients identified to have rifampicin resistance on initial Xpert testing. We did a repeat Xpert assay and used rpoB Sanger and deep sequencing alongside phenotypic drug susceptibility testing (pDST) to ascertain final rifampicin susceptibility status, with any (hetero)resistant result overriding. We used multivariable logistic regression to assess predictors of false rifampicin resistance on initial Xpert testing, adjusted for HIV status, tuberculosis treatment history, initial Xpert semi-quantitative bacillary load, and initial Xpert probe. FINDINGS Between May 4, 2017, and April 30, 2019, 175 people were identified with rifampicin resistance at initial Xpert testing, of whom 154 (88%) underwent repeat Xpert assay. 54 (35%) patients were confirmed as rifampicin resistant on repeat testing and 100 (65%) were not confirmed with resistance. After further testing and sequencing, 121 (79%) of 154 patients had a final confirmed status for rifampicin susceptibility. 57 (47%) of 121 patients were confirmed to have a false rifampicin resistance result and 64 (53%) had true rifampicin resistance. A high pretest probability of rifampicin resistance did not decrease the odds of false rifampicin resistance (adjusted odds ratio [aOR] 6·0, 95% CI 1·0-35·0, for new tuberculosis patients vs patients who needed retreatment). Ten (16%) of the 64 patients with true rifampicin resistance did not have confirmed rifampicin resistance on repeat Xpert testing, of whom four had heteroresistance. Of 63 patients with a very low bacillary load on Xpert testing, 54 (86%) were falsely diagnosed with rifampicin-resistant tuberculosis. Having a very low bacillary load on Xpert testing was strongly associated with false rifampicin resistance at the initial Xpert assay (aOR 63·6, 95% CI 9·9-410·4). INTERPRETATION The Xpert testing algorithm should include an assessment of bacillary load and retesting in case rifampicin resistance is detected on a paucibacillary sputum sample. Only when rifampicin resistance has been confirmed on repeat testing should multidrug-resistant tuberculosis treatment be started. When rifampicin resistance has not been confirmed on repeat testing, we propose that patients should be given first-line anti-tuberculosis drugs and monitored closely during treatment, including by baseline culture, pDST, and further Xpert testing. FUNDING The European & Developing Countries Clinical Trials Partnership 2 programme, and Belgian Directorate General for Development Cooperation.
Collapse
Affiliation(s)
- Jean Claude Semuto Ngabonziza
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Centre, Kigali, Rwanda; Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Research Foundation Flanders, Brussels, Belgium
| | - Patrick Migambi
- Tuberculosis and Other Respiratory Diseases Division, Institute of HIV/AIDS Disease Prevention and Control, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Yves Mucyo Habimana
- Tuberculosis and Other Respiratory Diseases Division, Institute of HIV/AIDS Disease Prevention and Control, Rwanda Biomedical Centre, Kigali, Rwanda
| | | | - Conor J Meehan
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; School of Chemistry and Biosciences, University of Bradford, UK
| | - Gabriela Torrea
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Willem Bram de Rijk
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bertin Ushizimpumu
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Esdras Belamo Niyigena
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Emil Ivan
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Jules Mugabo Semahore
- HIV, STIs, Hepatitis and Tuberculosis Programmes, WHO Country Office, Kigali, Rwanda
| | | | - Corinne Simone Merle
- UNICEF/UNDP/World Bank/WHO Special Programme on Research and Training in Tropical Diseases, Geneva, Switzerland; London School of Hygiene & Tropical Medicine, London, UK
| | - Philip Supply
- University of Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | | | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bouke Catherine de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| |
Collapse
|