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Omar SV, Louw G, Ismail F, Liu X, Ngcamu D, Gwala T, van der Meulen M, Joseph L. Performance evaluation of the Xpert MTB/XDR test for the detection of drug resistance to Mycobacterium tuberculosis among people diagnosed with tuberculosis in South Africa. J Clin Microbiol 2024; 62:e0022924. [PMID: 39058018 PMCID: PMC11323472 DOI: 10.1128/jcm.00229-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/24/2024] [Indexed: 07/28/2024] Open
Abstract
Drug-resistant tuberculosis (TB) poses a significant public health concern in South Africa due to its complexity in diagnosis, treatment, and management. This study assessed the diagnostic performance of the Xpert MTB/XDR test for detecting drug resistance in patients with TB by using archived sputum sediments. This study analyzed 322 samples collected from patients diagnosed with TB between 2016 and 2019 across South Africa, previously characterized by phenotypic and genotypic methods. The Xpert MTB/XDR test was evaluated for its ability to detect resistance to isoniazid (INH), ethionamide (ETH), fluoroquinolones (FLQ), and second-line injectable drugs (SLIDs) compared with phenotypic drug susceptibility testing (pDST) and whole-genome sequencing (WGS). Culture, Xpert MTB/RIF Ultra, and Xpert MTB/RIF (G4) tests were performed to determine sensitivity and agreement with this test for TB detection. The sensitivities using a composite reference standard, pDST, and sequencing were >90% for INH, FLQ, amikacin (AMK), kanamycin (KAN), and capreomycin (CAP) resistance, meeting the WHO target product profile criteria for this class. A lower sensitivity of 65.9% (95% CI: 57.1-73.6) for ETH resistance was observed. The Xpert MTB/XDR showed a sensitivity of 98.3% (95% CI: 96.1-99.3) and specificity of 100% (95% CI: 86.7-100) compared with culture, a positive percent agreement (PPA) of 98.8% (95% CI: 93.7-99.8) and negative percent agreement (NPA) of 100.0% (95% CI: 78.5-100.0) compared with G4, and a PPA of 99.5% (95% CI: 97.3-99.9) and NPA of 100.0% (95% CI: 78.5-100.0) compared with Xpert MTB/RIF Ultra for detecting Mycobacterium tuberculosis. The test offers a promising solution for the rapid detection of drug-resistant TB and could significantly enhance control efforts in this setting.
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Affiliation(s)
- Shaheed Vally Omar
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Gail Louw
- Cepheid (PTY) LTD, Johannesburg, South Africa
- Cepheid, Sunnyvale, California, USA
| | - Farzana Ismail
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Dumsani Ngcamu
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Minty van der Meulen
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Lavania Joseph
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
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Shanmugam SK, Kumar N, Sembulingam T, Ramalingam SB, Selvaraj A, Rajendhiran U, Solaiyappan S, Tripathy SP, Natrajan M, Chandrasekaran P, Swaminathan S, Parkhill J, Peacock SJ, Ranganathan UDK. Mycobacterium tuberculosis Lineages Associated with Mutations and Drug Resistance in Isolates from India. Microbiol Spectr 2022; 10:e0159421. [PMID: 35442078 PMCID: PMC9241780 DOI: 10.1128/spectrum.01594-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Current knowledge on resistance-conferring determinants in Mycobacterium tuberculosis is biased toward globally dominant lineages 2 and 4. In contrast, lineages 1 and 3 are predominant in India. In this study, we performed whole-genome sequencing of 498 MDR M. tuberculosis isolates from India to determine the prevalence of drug resistance mutations and to understand the genomic diversity. A retrospective collection of 498 M. tuberculosis isolates submitted to the National Institute for Research in Tuberculosis for phenotypic susceptibility testing between 2014 to 2016 were sequenced. Genotypic resistance prediction was performed using known resistance-conferring determinants. Genotypic and phenotypic results for 12 antituberculosis drugs were compared, and sequence data were explored to characterize lineages and their association with drug resistance. Four lineages were identified although lineage 1 predominated (43%). The sensitivity of prediction for isoniazid and rifampicin was 92% and 98%, respectively. We observed lineage-specific variations in the proportion of isolates with resistance-conferring mutations, with drug resistance more common in lineages 2 and 3. Disputed mutations (codons 430, 435, 445, and 452) in the rpoB gene were more common in isolates other than lineage 2. Phylogenetic analysis and pairwise SNP difference revealed high genetic relatedness of lineage 2 isolates. WGS based resistance prediction has huge potential, but knowledge of regional and national diversity is essential to achieve high accuracy for resistance prediction. IMPORTANCE Current knowledge on resistance-conferring determinants in Mycobacterium tuberculosis is biased toward globally dominant lineages 2 and 4. In contrast, lineages 1 and 3 are predominant in India. We performed whole-genome sequencing of 498 MDR M. tuberculosis isolates from India to determine the prevalence of drug resistance mutations and to understand genomic diversity. Four lineages were identified although lineage 1 predominated (43%). The sensitivity of prediction for isoniazid and rifampicin was 92% and 98%, respectively. We observed lineage-specific variations in the proportion of isolates with resistance-conferring mutations, with drug resistance more common in lineages 2 and 3. Disputed mutations (codons 430, 435, 445, and 452) in the rpoB gene were more common in isolates other than lineage 2. Phylogenetic analysis and pairwise SNP difference revealed high genetic relatedness of lineage 2 isolates. WGS based resistance prediction has huge potential, but knowledge of regional and national diversity is essential to achieve high accuracy for resistance prediction.
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Affiliation(s)
- Siva Kumar Shanmugam
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Narender Kumar
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Tamilzhalagan Sembulingam
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Suresh Babu Ramalingam
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Ashok Selvaraj
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Udhayakumar Rajendhiran
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Sudha Solaiyappan
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Srikanth P. Tripathy
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | - Mohan Natrajan
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
| | | | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Uma Devi K. Ranganathan
- Indian Council of Medical Research (ICMR)-National Institute for Research in Tuberculosis, Chennai, India
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