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Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
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Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
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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 GLOBAL 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] [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.
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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
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Che Y, Lin Y, Yang T, Chen T, Sang G, Chen Q, He T. Evaluation of whole-genome sequence to predict drug resistance of nine anti- tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China. Front Public Health 2022; 10:956171. [PMID: 36062095 PMCID: PMC9433565 DOI: 10.3389/fpubh.2022.956171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/28/2022] [Indexed: 01/24/2023] Open
Abstract
Setting Controlling drug-resistant tuberculosis in Ningbo, China. Objective Whole-genome sequencing (WGS) has not been employed to comprehensively study Mycobacterium tuberculosis isolates, especially rifampicin-resistant tuberculosis, in Ningbo, China. Here, we aim to characterize genes involved in drug resistance in RR-TB and create a prognostic tool for successfully predicting drug resistance in patients with TB. Design Drug resistance was predicted by WGS in a "TB-Profiler" web service after phenotypic drug susceptibility tests (DSTs) against nine anti-TB drugs among 59 clinical isolates. A comparison of consistency, sensitivity, specificity, and positive and negative predictive values between WGS and DST were carried out for each drug. Results The sensitivities and specificities for WGS were 95.92 and 90% for isoniazid (INH), 100 and 64.1% for ethambutol (EMB), 97.37 and 100% for streptomycin (SM), 75 and 100% for amikacin (AM), 80 and 96.3%for capreomycin (CAP), 100 and 97.22% for levofloxacin (LFX), 93.33 and 90.91% for prothionamide (PTO), and 70 and 97.96% for para-aminosalicylic acid (PAS). Around 53 (89.83%) and 6 (10.17%) of the isolates belonged to lineage two (East-Asian) and lineage four (Euro-American), respectively. Conclusion Whole-genome sequencing is a reliable method for predicting resistance to INH, RIF, EMB, SM, AM, CAP, LFX, PTO, and PAS with high consistency, sensitivity, and specificity. There was no transmission that occurred among the patients with RR-TB in Ningbo, China.
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Affiliation(s)
- Yang Che
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yi Lin
- Center for Health Economics, Faculty of Humanities and Social Sciences, University of Nottingham, Ningbo, China
| | - Tianchi Yang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Tong Chen
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Guoxin Sang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Qin Chen
- Department of Disease Prevention and Health Promotion, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China,*Correspondence: Qin Chen
| | - Tianfeng He
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China,Tianfeng He
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Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol 2021; 59:JCM.01885-20. [PMID: 32999007 DOI: 10.1128/jcm.01885-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 μg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.
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Brandao AP, Pinhata JMW, Simonsen V, Oliveira RS, Ghisi KT, Rabello MCS, Fukasava S, Ferrazoli L. Transmission of Mycobacterium tuberculosis presenting unusually high discordance between genotypic and phenotypic resistance to rifampicin in an endemic tuberculosis setting. Tuberculosis (Edinb) 2020; 125:102004. [PMID: 33017720 DOI: 10.1016/j.tube.2020.102004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND Since the implementation of the Xpert MTB/RIF in Sao Paulo, Brazil, numerous Mycobacterium tuberculosis isolates presenting "rifampicin-resistant genotype with rifampicin-susceptible phenotype" were observed. OBJECTIVE To evaluate the prevalence, rpoB mutations and transmission of M. tuberculosis resistant to rifampicin on Xpert MTB/RIF but susceptible on BACTEC MGIT system, in Sao Paulo state. METHODS Patients' isolates with this pattern of rifampicin discordance, collected from 2014 to 2017, had their rpoB predominant rifampicin-resistance-determining region sequenced and were genotyped by IS6110 restriction fragment-length polymorphism. FINDINGS The prevalence of rifampicin-discordant M. tuberculosis with genotypic resistance was 55.1% (156/283). Among the sequenced and genotyped isolates, 75.5% (111/147) were in clusters, largely associated with the type of rpoB mutation. Most isolates (98.6%; 72/73) harbouring the predominant mutation, His445Asn, were pooled into the two largest clusters, SP2ga (42/72; 58.3%) and SP5o (12/72; 16.7%). Ranking second, isolates carrying the silent mutation Phe433Phe were mostly (92.3%; 24/26) gathered into four groups of the family SP25. CONCLUSION These findings suggest that this unusual high rifampicin discrepancy proportion was greatly influenced by few actively circulating clusters. Further studies on many of the rpoB mutations identified in our setting are needed to elucidate their association with phenotypic rifampicin resistance.
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Affiliation(s)
- Angela Pires Brandao
- Instituto Adolfo Lutz, São Paulo, SP, Brazil; IOC/FIOCRUZ, Rio de Janeiro, RJ, Brazil.
| | | | | | | | | | | | - Suely Fukasava
- Centro de Vigilância Epidemiológica do Estado de São Paulo, São Paulo, SP, Brazil
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Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China. Int J Infect Dis 2020; 96:48-53. [DOI: 10.1016/j.ijid.2020.04.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 11/19/2022] Open
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Gaude G, Vishwanath S. Molecular diagnosis of tuberculosis with emphasis on Xpert Mycobacterium tuberculosis assay – Clinical review. JOURNAL OF CLINICAL SCIENCES 2020. [DOI: 10.4103/jcls.jcls_52_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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Nachappa SA, Neelambike SM, Amruthavalli C, Ramachandra NB. Detection of First-Line Drug Resistance Mutations and Drug–Protein Interaction Dynamics from Tuberculosis Patients in South India. Microb Drug Resist 2018; 24:377-385. [DOI: 10.1089/mdr.2017.0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Somanna Ajjamada Nachappa
- Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Mysuru, India
| | | | - Chokkanna Amruthavalli
- The Centre for Information Science and Technology (CIST), University of Mysore, Mysuru, India
| | - Nallur B. Ramachandra
- Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Mysuru, India
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Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria. Clin Microbiol Rev 2018; 31:31/2/e00038-17. [PMID: 29386234 DOI: 10.1128/cmr.00038-17] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.
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Nurwidya F, Handayani D, Burhan E, Yunus F. Molecular Diagnosis of Tuberculosis. Chonnam Med J 2018; 54:1-9. [PMID: 29399559 PMCID: PMC5794472 DOI: 10.4068/cmj.2018.54.1.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks. New advances in the molecular detection of TB, including the faster and simpler nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have resulted in a shorter time for diagnosis and, therefore, faster TB treatments. In this review, we explored the current findings on molecular diagnosis of TB and drug-resistant TB to see how this advancement could be integrated into public health systems in order to control TB.
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Affiliation(s)
- Fariz Nurwidya
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Diah Handayani
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Erlina Burhan
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
| | - Faisal Yunus
- Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Persahabatan Hospital, Jakarta, Indonesia
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Rice JP, Seifert M, Moser KS, Rodwell TC. Performance of the Xpert MTB/RIF assay for the diagnosis of pulmonary tuberculosis and rifampin resistance in a low-incidence, high-resource setting. PLoS One 2017; 12:e0186139. [PMID: 29016684 PMCID: PMC5633176 DOI: 10.1371/journal.pone.0186139] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/26/2017] [Indexed: 02/07/2023] Open
Abstract
Performance of the Xpert MTB/RIF assay, designed to simultaneously detect Mycobacterium tuberculosis complex (MTBC) and rifampin (RIF) resistance, has been well documented in low-resource settings with high TB-incidence. However, few studies have assessed its accuracy in low TB incidence settings. We evaluated the performance of Xpert MTB/RIF using clinical sputum specimens routinely collected from suspect pulmonary TB patients over a 4-year time period in San Diego County, California. Xpert MTB/RIF results were compared to acid-fast bacilli (AFB) smear microscopy, mycobacterial culture, and phenotypic drug susceptibility testing (DST). Of 751 sputum specimens, 134 (17.8%) were MTBC culture-positive and 2 (1.5%) were multidrug-resistant (MDR). For the detection of MTBC, Xpert MTB/RIF sensitivity was 89.6% (97.7% and 74.5% in smear-positive and -negative sputa, respectively) and specificity was 97.2%; while AFB smear sensitivity and specificity were 64.9% and 77.8%, respectively. Xpert MTB/RIF detected 35 of 47 smear-negative culture-positive specimens, and excluded 124 of 137 smear-positive culture-negative specimens. Xpert MTB/RIF also correctly excluded 99.2% (121/122) of nontuberculous mycobacteria (NTM) specimens, including all 33 NTM false-positives by smear microscopy. For the detection of RIF resistance, Xpert MTB/RIF sensitivity and specificity were 100% and 98.3%, respectively. Our findings demonstrate that Xpert MTB/RIF is able to accurately detect MTBC and RIF resistance in routinely collected respiratory specimens in a low TB-incidence setting, with comparable performance to that achieved in high-incidence settings; and suggest that under these conditions the assay has particular utility in detecting smear-negative TB cases, excluding smear-positive patients without MTBC disease, and differentiating MTBC from NTM.
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Affiliation(s)
- Jason P. Rice
- Division of Preventive Medicine, University of California, San Diego, California, United States of America
- * E-mail:
| | - Marva Seifert
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, California, United States of America
| | - Kathleen S. Moser
- Tuberculosis Control and Refugee Health Program, County of San Diego Health and Human Services Agency, San Diego, California, United States of America
| | - Timothy C. Rodwell
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, California, United States of America
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Banu S, Pholwat S, Foongladda S, Chinli R, Boonlert D, Ferdous SS, Rahman SMM, Rahman A, Ahmed S, Houpt ER. Performance of TaqMan array card to detect TB drug resistance on direct specimens. PLoS One 2017; 12:e0177167. [PMID: 28472124 PMCID: PMC5417650 DOI: 10.1371/journal.pone.0177167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 12/31/2022] Open
Abstract
Culture based phenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis (TB) is time consuming therefore rapid genotypic methods are increasingly being utilized. We previously developed and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC) that detects mutations in several resistance-associated genes using dozens of primer pairs, probes, and high resolution melt analysis, with >96% accuracy versus Sanger sequencing. In this study we examined the performance of TAC on sputum, comparing results between 71 paired sputum and TB isolates of which 62 were MDR-TB. We also adapted the TAC to include wild-type probes and broadened coverage for rpoB and gyrA mutations. TAC was 89% successful at detecting wild-type or mutations within inhA, katG, rpoB, eis, gyrA, rplC, and pncA on smear positive sputa and 33% successful on smear negative sputa. The overall accuracy of these detections as compared to the TAC results of the paired isolate was 95% ± 7 (average sensitivity 98% ± 3; specificity 92% ± 14). Accuracy of sputum TAC results versus phenotypic DST for isoniazid, rifampin, ofloxacin/moxifloxacin, and pyrazinamide was 85% ± 12. This was similar to that of the isolate TAC results (accuracy 88% ± 13), thus inaccuracies primarily reflected intrinsic genotypic-phenotypic discordance. The TAC is a rapid, modular, comprehensive, and accurate TB DST for the major first and second line TB drugs and could be used for supplemental testing of GeneXpert resistant smear positive sputum.
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Affiliation(s)
- Sayera Banu
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Suporn Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rattapha Chinli
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Duangjai Boonlert
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sara Sabrina Ferdous
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - S. M. Mazidur Rahman
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Arfatur Rahman
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Shahriar Ahmed
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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Direct Detection of Rifampin and Isoniazid Resistance in Sputum Samples from Tuberculosis Patients by High-Resolution Melt Curve Analysis. J Clin Microbiol 2017; 55:1755-1766. [PMID: 28330890 DOI: 10.1128/jcm.02104-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/17/2017] [Indexed: 01/22/2023] Open
Abstract
Drug-resistant tuberculosis (TB) is a major threat to TB control worldwide. Globally, only 40% of the 340,000 notified TB patients estimated to have multidrug-resistant-TB (MDR-TB) were detected in 2015. This study was carried out to evaluate the utility of high-resolution melt curve analysis (HRM) for the rapid and direct detection of MDR-TB in Mycobacterium tuberculosis in sputum samples. A reference plasmid library was first generated of the most frequently observed mutations in the resistance-determining regions of rpoB, katG, and an inhA promoter and used as positive controls in HRM. The assay was first validated in 25 MDR M. tuberculosis clinical isolates. The assay was evaluated on DNA isolated from 99 M. tuberculosis culture-positive sputum samples that included 84 smear-negative sputum samples, using DNA sequencing as gold standard. Mutants were discriminated from the wild type by comparing melting-curve patterns with those of control plasmids using HRM software. Rifampin (RIF) and isoniazid (INH) monoresistance were detected in 11 and 21 specimens, respectively, by HRM. Six samples were classified as MDR-TB by sequencing, one of which was missed by HRM. The HRM-RIF, INH-katG, and INH-inhA assays had 89% (95% confidence interval [CI], 52, 100%), 85% (95% CI, 62, 97%), and 100% (95% CI, 74, 100%) sensitivity, respectively, in smear-negative samples, while all assays had 100% sensitivity in smear-positive samples. All assays had 100% specificity. Concordance of 97% to 100% (κ value, 0.9 to 1) was noted between sequencing and HRM. Heteroresistance was observed in 5 of 99 samples by sequencing. In conclusion, the HRM assay was a cost-effective (Indian rupee [INR]400/US$6), rapid, and closed-tube method for the direct detection of MDR-TB in sputum, especially for direct smear-negative cases.
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Spinato J, Boivin É, Bélanger-Trudelle É, Fauchon H, Tremblay C, Soualhine H. Genotypic characterization of drug resistant Mycobacterium tuberculosis in Quebec, 2002-2012. BMC Microbiol 2016; 16:164. [PMID: 27459848 PMCID: PMC4962473 DOI: 10.1186/s12866-016-0786-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/22/2016] [Indexed: 11/30/2022] Open
Abstract
Background The increasing emergence of drug-resistant tuberculosis presents a threat to the effective control of tuberculosis (TB). Rapid detection of drug-resistance is more important than ever to address this scourge. The purpose of this study was to genotypically characterize the first-line antitubercular drug-resistant isolates collected over 11 years in Quebec. Results The main mutations found in our resistant strains collection (n = 225) include: the S315T substitution in katG (50.2 %), the -15 C/T mutation in the inhA promoter (29 %); the S531L substitution in rpoB (43 %); the deletion 8 bp 446 / + R140S in pncA (72.9 %); the M306I (35.7 %) and M306V (21.4 %) substitutions in embB. Ten of the mutations in katG and 4 mutations identified in pncA were previously undescribed. Conclusion Screening of mutations conferring resistance to first-line antituberculous drugs using DNA-sequencing approach seems to be feasible and would drastically shorten the time to determine the resistance profile compared to the proportion method.
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Affiliation(s)
- Joanna Spinato
- McGill University, Montreal, Quebec, Canada.,Present address: Public Health Ontario Laboratory, Toronto, Ontario, M5G 1 M1, Canada
| | - Élyse Boivin
- Laboratoire de santé publique du Quebec, 20045 chemin Sainte-Marie, Sainte-Anne de Bellevue, Quebec, H9X 3R5, Canada
| | - Émilie Bélanger-Trudelle
- Laboratoire de santé publique du Quebec, 20045 chemin Sainte-Marie, Sainte-Anne de Bellevue, Quebec, H9X 3R5, Canada
| | - Huguette Fauchon
- Laboratoire de santé publique du Quebec, 20045 chemin Sainte-Marie, Sainte-Anne de Bellevue, Quebec, H9X 3R5, Canada
| | | | - Hafid Soualhine
- Laboratoire de santé publique du Quebec, 20045 chemin Sainte-Marie, Sainte-Anne de Bellevue, Quebec, H9X 3R5, Canada.
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Banerjee R, Starke JR. What tuberculosis can teach us about combating multidrug-resistant Gram negative bacilli. J Clin Tuberc Other Mycobact Dis 2016; 3:28-34. [PMID: 31723682 PMCID: PMC6850263 DOI: 10.1016/j.jctube.2016.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 12/03/2022] Open
Abstract
There are striking similarities between the dual pandemics of multidrug-resistant tuberculosis (MDR TB) and multidrug-resistant Gram negative bacilli (MDR GNB) despite fundamental differences in the pathogenesis and epidemiology of these pathogens. In this perspective, we highlight several strategies that have been used by the global TB community to address the MDR TB problem, including approaches to: encourage appropriate use of anti-TB medications, enhance appropriate utilization of molecular diagnostic testing, facilitate development of new antimicrobial agents, and strengthen surveillance systems and infection control practices. Understanding the successes and challenges of these strategies for MDR TB control will be instructive for efforts to curb emergence and spread of MDR GNB.
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Affiliation(s)
- Ritu Banerjee
- Division of Pediatric Infectious Diseases, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States
| | - Jeffrey R. Starke
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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