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Svensson E, Ketelsen H, Andres S, Folkvardsen DB, Hillemann D, Conteh O, Norman A, Niemann S, Lillebaek T, Kuhns M. Dual-centre evaluation of the FluoroType MTBDR version 2 assay for detection of Mycobacterium tuberculosis complex and resistance-conferring mutations in pulmonary and extrapulmonary samples from Denmark, Germany and Sierra Leone. Clin Microbiol Infect 2024:S1198-743X(24)00192-7. [PMID: 38621623 DOI: 10.1016/j.cmi.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVES We evaluated the ability of FluoroType MTBDR version 2 (FTv2; Hain Lifescience), a second-step real-time PCR assay, to simultaneously detect Mycobacterium tuberculosis complex (MTBC) DNA and mutations conferring resistance to rifampicin (RIF) and isoniazid (INH), in pulmonary and extrapulmonary samples from patients and compared them with corresponding cultures. METHODS FTv2 MTBC was evaluated on 1815 and 432 samples from Denmark (DK) and Germany (DE), respectively. RIF and INH resistance mutations were assessed in the German samples and 110 samples from Sierra Leone and subsequently compared to phenotypic antimicrobial susceptibility testing and a composite reference DNA (CRD) based on the GenoType MTBDR line-probe assay and Sanger sequencing or whole-genome sequencing. RESULTS Of the 584 (557 smear-negative) Danish and 277 (85 smear-negative) German sputum samples, 42 (16) and 246 (54) were culture positive, and 44 (18) and 222 (35) were FTv2 positive, providing an FTv2 sensitivity and specificity of 0.86 (0.63) and 0.98 (DK), 0.90 (0.65) and 1.00 (DE), respectively. The count, sensitivities, and specificities for all pulmonary samples were 1434, 0.79, and 0.99 (DK) and 347, 0.86, and 1.00 (DE), respectively; for extrapulmonary samples, 381, 0.33, 0.99 (DK) and 83, 0.50, and 1.00 (DE). The valid count, sensitivity, and specificity compared with CRD for detecting resistance mutations were RIF 355, 0.99, 0.96, and INH 340, 1.00, and 0.98, respectively. DISCUSSION FTv2 reliably detects MTBC DNA in pulmonary and extrapulmonary samples and detects resistance mutations for INH and RIF resistance in inhA promoter, katG, and rpoB genes.
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Affiliation(s)
- Erik Svensson
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark.
| | - Hannah Ketelsen
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Dorte Bek Folkvardsen
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark
| | - Doris Hillemann
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Ousman Conteh
- National Tuberculosis Reference Laboratory, Lakka Government Hospital, Freetown, Sierra Leone
| | - Anders Norman
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Troels Lillebaek
- Statens Serum Institut, International Reference Laboratory of Mycobacteriology, WHO Supranational Reference Laboratory, Copenhagen, Denmark; Department of Public Health, University of Copenhagen, Denmark
| | - Martin Kuhns
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
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Cannas A, Butera O, Mazzarelli A, Messina F, Vulcano A, Parracino MP, Gualano G, Palmieri F, Di Caro A, Nisii C, Fontana C, Girardi E. Implementation of Whole Genome Sequencing of Tuberculosis Isolates in a Referral Center in Rome: Six Years' Experience in Characterizing Drug-Resistant TB and Disease Transmission. Antibiotics (Basel) 2024; 13:134. [PMID: 38391520 PMCID: PMC10885968 DOI: 10.3390/antibiotics13020134] [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: 11/24/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
Over the past years, Tuberculosis (TB) control strategies have been effective in reducing drug-resistant (DR) TB globally; however, a wider implementation of new diagnostic strategies, such as Whole genome sequencing (WGS), would be critical for further improvement. The aim of this study, based on WGS of Mycobacterium tuberculosis (MTB) strains isolated in a TB referral center over 6 years, was to evaluate the efficacy of this methodology in improving therapy guidance for clinicians and in improving the understanding of the epidemiology of TB transmission. WGS was performed in addition to pDST on 1001 strains consecutively isolated between January 2016 and December 2021; the results allowed us to improve the quality of data on resistance and to identify possible clusters of transmission. Prediction of rifampicin-resistant (RR) or multi-drug-resistant TB strains (MDR-TB, defined as resistance to at least rifampicin and isoniazid) was obtained for 50 strains (5%). Mutations predictive of an MDR isolate were further characterized, and Ser450Leu and Ser315Thr were found to be the most frequent mutations in rpoB and katG genes, respectively. Discordances between WGS and phenotypic drug susceptibility testing (pDST) were found in few strains, and their impact on clinical decisions and outcome was addressed. The introduction of WGS in our Institute improved our diagnostic routine, allowing accurate patient management, and was a valid instrument for epidemiological investigations and infection control.
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Affiliation(s)
- Angela Cannas
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Ornella Butera
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Antonio Mazzarelli
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Francesco Messina
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Antonella Vulcano
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | | | - Gina Gualano
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Fabrizio Palmieri
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Antonino Di Caro
- Department of Medicine, UniCamillus International University, 00131 Rome, Italy
| | - Carla Nisii
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Carla Fontana
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
| | - Enrico Girardi
- National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, 00149 Rome, Italy
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Qadir M, Faryal R, Khan MT, Khan SA, Zhang S, Li W, Wei DQ, Tahseen S, McHugh TD. Phenotype versus genotype discordant rifampicin susceptibility testing in tuberculosis: implications for a diagnostic accuracy. Microbiol Spectr 2024; 12:e0163123. [PMID: 37982632 PMCID: PMC10783056 DOI: 10.1128/spectrum.01631-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE An accurate diagnosis of drug resistance in clinical isolates is an important step for better treatment outcomes. The current study observed a higher discordance rate of rifampicin resistance on Mycobacteria Growth Indicator Tube (MGIT) drug susceptibility testing (DST) than Lowenstein-Jenson (LJ) DST when compared with the rpoB sequencing. We detected a few novel mutations and their combination in rifampicin resistance isolates that were missed by MGIT DST and may be useful for the better management of tuberculosis (TB) treatment outcomes. Few novel deletions in clinical isolates necessitate the importance of rpoB sequencing in large data sets in geographic-specific locations, especially high-burden countries. We explored the discordance rate on MGIT and LJ, which is important for the clinical management of rifampicin resistance to avoid the mistreatment of drug-resistant TB. Furthermore, MGIT-sensitive isolates may be subjected to molecular methods of diagnosis for further confirmation and treatment options.
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Affiliation(s)
- Mehmood Qadir
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rani Faryal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Sajjad Ahmed Khan
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Shulin Zhang
- School of Medicine, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Weimin Li
- National Tuberculosis Clinical Lab of China, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dong Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - Sabira Tahseen
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
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Li K, Hu Q, Liu J, Liu S, He Y. Effects of sputum bacillary load and age on GeneXpert and traditional methods in pulmonary tuberculosis: a 4-year retrospective comparative study. BMC Infect Dis 2023; 23:831. [PMID: 38012541 PMCID: PMC10680317 DOI: 10.1186/s12879-023-08832-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The purpose of this study was to evaluate the diagnostic value of the GeneXpert® MTB/RIF (Xpert®), Auramine O staining method, and Lowenstein-Jensen medium for bacteriologically confirmed pulmonary tuberculosis and explore the effects of the sputum bacillary load (SBL) and qRT‒PCR threshold cycle (Ct) value on the detection methods. METHODS We retrospectively analysed the results in the Department of Infectious Disease for 49 months. The χ2 test was used to compare the performances of each method, receiver operating characteristic curve analysis was used to determine the optimal cut-off values, and the factors associated with a false-negative result from Xpert® were analysed by logistic regression. RESULTS Simultaneous analysis of 980 sputum specimens showed that the positive detection rate of Xpert® did not increase with increasing SBL, and there were differences between the three when SBL ≤ 1 + (all P < 0.05). There was a good negative correlation between the Ct value and the SBL (P < 0.0001). Age was an independent risk factor for false-negative Xpert® results (P = 0.029), and when Ct < 16, the diagnostic sensitivity and specificity were both 100.00%. The optimal cut-off Ct values for resegmentation based on the drug resistance classification were < 18.6, 18.6-34.1, and > 34.1 cycles. CONCLUSIONS Xpert® was not affected by SBL but it was by age, and it is more advantageous when SBL ≤ 1 + . The results regarding rifampicin resistance were reliable, and the novel Ct segmentation was a practical and more clinically meaningful classification method for diagnosing rifampicin resistance. These findings will help improve physicians' ability to accurately diagnose TB.
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Affiliation(s)
- Kui Li
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West YantaRoad, Xi'an, Shaanxi Province, 710061, China
- Department of Infectious Diseases, Ankang Central Hospital, 85 South Jinzhou Road, Ankang, Shaanxi Province, 725000, China
| | - Qianqian Hu
- Laboratory of Molecular Pathology and Tuberculosis Diseases, Ankang Central Hospital, 85 South Jinzhou Road, Ankang, Shaanxi Province, 725000, China
| | - Jun Liu
- Laboratory of Molecular Pathology and Tuberculosis Diseases, Ankang Central Hospital, 85 South Jinzhou Road, Ankang, Shaanxi Province, 725000, China
| | - Siyi Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West YantaRoad, Xi'an, Shaanxi Province, 710061, China
| | - Yingli He
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West YantaRoad, Xi'an, Shaanxi Province, 710061, China.
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Shi T, Shou F, He Y, Zhou K, Gao W, Nie X, Han M, Liao C, Li T. Whole genome sequencing of drug resistance Mycobacterium tuberculosis from extra-pulmonary sites. Life Sci Alliance 2023; 6:e202302076. [PMID: 37591723 PMCID: PMC10435967 DOI: 10.26508/lsa.202302076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
This study aimed to determinate characteristics of drug resistance Mycobacterium tuberculosis from patients with extra-pulmonary tuberculosis (EPTB). Patients were retrospectively studied from January 2020 to December 2021. All the isolates were cultured, tested drug susceptibility, and detected the gene mutation using whole genome sequencing. The correlations of whole genome sequencing, pattern of DR, patients' distribution, and transmission were analyzed. 111 DR-EPTB isolates included pre-XDR-TB (53.2%), MDR-TB (29.7%), and poly-DR-TB (12.6%). The resistant drugs were INH followed by RFP and SM. The genotypes of 111 strains were lineage 2 and lineage 4. KatG_p.Ser315Thr was main gene mutation for resistance to INH; rpsL_p.Lys43Arg for SM, rpoB_p.Ser450Leu for rifampicin, embB_p.Met306Val for ethambutol, gyrA_p.Asp94Gly for FQs, and pncA_p.Thr76Pro for PZA. The residence was a significant risk factor for cluster transmission by patients and phenotypic DR types of strains for lineage 2 transmission. In the local area of southwest China INH, rifampicin and SM were main drugs in patients with DR-EPTB. KatG_p.Ser315, rpoB_p.Ser450Leu, and rpsL_p.Lys43Arg were main gene mutations. Phenotypic DR types and residence were main risk of transmission.
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Affiliation(s)
- Tao Shi
- Department of Orthopedics, Tianjin First Central Hospital, Tianjin, China
| | - Fenyong Shou
- Department of Orthopedics, Tianjin First Central Hospital, Tianjin, China
| | - Ying He
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Kan Zhou
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Wenwan Gao
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Xiaoping Nie
- Medical Department, Chongqing Public Health Medical Center, Chongqing, China
| | - Mei Han
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Chuanyu Liao
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Tongxin Li
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
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Dohál M, Dvořáková V, Šperková M, Pinková M, Spitaleri A, Rasmussen EM, Škereňová M, Krivošová M, Gondáš E, Porvazník I, Solovič I, Cirillo DM, Mokrý J. Resistance patterns and transmission of mono- and polyresistant TB: clinical impact of WGS. JAC Antimicrob Resist 2023; 5:dlad108. [PMID: 37799267 PMCID: PMC10549209 DOI: 10.1093/jacamr/dlad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023] Open
Abstract
Objectives Rapidly diagnosing drug-resistant TB is crucial for improving treatment and transmission control. WGS is becoming increasingly accessible and has added value to the diagnosis and treatment of TB. The aim of the study was to perform WGS to determine the rate of false-positive results of phenotypic drug susceptibility testing (pDST) and characterize the molecular mechanisms of resistance and transmission of mono- and polyresistant Mycobacterium (M.) tuberculosis. Methods WGS was performed on 53 monoresistant and 25 polyresistant M. tuberculosis isolates characterized by pDST. Sequencing data were bioinformatically processed to infer mutations encoding resistance and determine the origin of resistance and phylogenetic relationship between isolates studied. Results The data showed the variable sensitivity and specificity of WGS in comparison with pDST as the gold standard: isoniazid 92.7% and 92.3%; streptomycin 41.9% and 100.0%; pyrazinamide 15% and 94.8%; and ethambutol 75.0% and 98.6%, respectively. We found novel mutations encoding resistance to streptomycin (in gidB) and pyrazinamide (in kefB). Most isolates belonged to lineage 4 (80.1%) and the overall clustering rate was 11.5%. We observed lineage-specific gene variations encoding resistance to streptomycin and pyrazinamide. Conclusions This study highlights the clinical potential of WGS in ruling out false-positive drug resistance following phenotypic or genetic drug testing, and recommend this technology together with the WHO catalogue in designing an optimal individualized treatment regimen and preventing the development of MDR TB. Our results suggest that resistance is primarily developed through spontaneous mutations or selective pressure.
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Affiliation(s)
- Matúš Dohál
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
| | - Věra Dvořáková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Prague, Czech Republic
| | - Miluše Šperková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Prague, Czech Republic
| | - Martina Pinková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Prague, Czech Republic
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Mária Škereňová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
- Department of Molecular Medicine, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
| | - Michaela Krivošová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
| | - Eduard Gondáš
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
| | - Igor Porvazník
- Department of Clinical Microbiology and Department of Pneumophthiology, National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Ivan Solovič
- Department of Clinical Microbiology and Department of Pneumophthiology, National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Juraj Mokrý
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
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Rao M, Wollenberg K, Harris M, Kulavalli S, Thomas L, Chawla K, Shenoy VP, Varma M, Saravu K, Hande HM, Shanthigrama Vasudeva CS, Jeffrey B, Gabrielian A, Rosenthal A. Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India. Microbiol Spectr 2023; 11:e0453122. [PMID: 37671895 PMCID: PMC10580826 DOI: 10.1128/spectrum.04531-22] [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: 11/13/2022] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
Whole-genome sequencing has created a revolution in tuberculosis management by providing a comprehensive picture of the various genetic polymorphisms with unprecedented accuracy. Studies mapping genomic heterogeneity in clinical isolates of Mycobacterium tuberculosis using a whole-genome sequencing approach from high tuberculosis burden countries are underrepresented. We report whole-genome sequencing results of 242 clinical isolates of culture-confirmed M. tuberculosis isolates from tuberculosis patients referred to a tertiary care hospital in Southern India. Phylogenetic analysis revealed that the isolates in our study belonged to five different lineages, with Indo-Oceanic (lineage 1, n = 122) and East-African Indian (lineage 3, n = 80) being the most prevalent. We report several mutations in genes conferring resistance to first and second line antitubercular drugs including the genes rpoB, katG, ahpC, inhA, fabG1, embB, pncA, rpsL, rrs, and gyrA. The majority of these mutations were identified in relatively high proportions in lineage 1. Our study highlights the utility of whole-genome sequencing as a potential supplemental tool to the existing genotypic and phenotypic methods, in providing expedited comprehensive surveillance of mutations that may be associated with antitubercular drug resistance as well as lineage characterization of M. tuberculosis isolates. Further larger-scale whole-genome datasets with linked minimum inhibition concentration testing are imperative for resolving the discrepancies between whole-genome sequencing and phenotypic drug sensitivity testing results and quantifying the level of the resistance associated with the mutations for optimization of antitubercular drug and precise dose selection in clinics. IMPORTANCE Studies mapping genetic heterogeneity of clinical isolates of M. tuberculosis for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242 M. tuberculosis isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of M. tuberculosis in Southern India. We report several genetic variations in M. tuberculosis that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize M. tuberculosis genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.
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Affiliation(s)
- Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kurt Wollenberg
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Harris
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shrivathsa Kulavalli
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavitha Saravu
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - H. Manjunatha Hande
- Department of Medicine, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Brendan Jeffrey
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei Gabrielian
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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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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Anthony R, Groenheit R, Mansjö M, de Zwaan R, Werngren J. The Relative Positioning of Genotyping and Phenotyping for Tuberculosis Resistance Screening in Two EU National Reference Laboratories in 2023. Microorganisms 2023; 11:1809. [PMID: 37512981 PMCID: PMC10383358 DOI: 10.3390/microorganisms11071809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The routine use of whole genome sequencing (WGS) as a reference typing technique for Mycobacterium tuberculosis epidemiology combined with the catalogued and extensive knowledge base of resistance-associated mutations means an initial susceptibility prediction can be derived from all cultured isolates in our laboratories based on WGS data alone. Preliminary work has confirmed, in our low-burden settings, these predictions are for first-line drugs, reproducible, robust with an accuracy similar to phenotypic drug susceptibility testing (pDST) and in many cases able to also predict the level of resistance (MIC). Routine screening for drug resistance by WGS results in approximately 80% of the isolates received being predicted as fully susceptible to the first-line drugs. Parallel testing with both WGS and pDST has demonstrated that routine pDST of genotypically fully susceptible isolates yields minimal additional information. Thus, rather than re-confirming all fully sensitive WGS-based predictions, we suggest that a more efficient use of available mycobacterial culture capacity in our setting is the development of a more extensive and detailed pDST targeted at any mono or multi-drug-resistant isolates identified by WGS screening. Phenotypic susceptibility retains a key role in the determination of an extended susceptibility profile for mono/multi-drugresistant isolates identified by WGS screening. The pDST information collected is also needed to support the development of future catalogues of resistance-associated mutations.
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Affiliation(s)
- Richard Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721BA Bilthoven, The Netherlands
| | - Ramona Groenheit
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, 171 82 Solna, Sweden
| | - Mikael Mansjö
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, 171 82 Solna, Sweden
| | - Rina de Zwaan
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721BA Bilthoven, The Netherlands
| | - Jim Werngren
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, 171 82 Solna, Sweden
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Sailo CV, Lalremruata R, Sanga Z, Fela V, Kharkongor F, Chhakchhuak Z, Chhakchhuak L, Nemi L, Zothanzama J, Kumar NS. Distribution and frequency of common mutations in rpoB gene of Mycobacterium tuberculosis detected by Xpert MTB/RIF and identification of residential areas of Rifampicin Resistant-TB cases: A first retrospective study from Mizoram, Northeast India. J Clin Tuberc Other Mycobact Dis 2022; 29:100342. [DOI: 10.1016/j.jctube.2022.100342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Singh K, Sharma S, Banerjee T, Gupta A, Anupurba S. Mutation detection and minimum inhibitory concentration determination against linezolid and clofazimine in confirmed XDR-TB clinical isolates. BMC Microbiol 2022; 22:236. [PMID: 36192704 PMCID: PMC9531458 DOI: 10.1186/s12866-022-02622-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of multidrug-resistant tuberculosis (MDR-TB) has complicated the situation due to the decline in potency of second-line anti-tubercular drugs. This limits the treatment option for extensively drug-resistant tuberculosis (XDR-TB). The aim of this study was to determine and compare the minimum inhibitory concentration (MIC) by agar dilution and resazurin microtiter assay (REMA) along with the detection of mutations against linezolid and clofazimine in confirmed XDR-TB clinical isolates. RESULTS A total of 169 isolates were found positive for Mycobacterium tuberculosis complex (MTBC). The MIC was determined by agar dilution and REMA methods. The isolates which showed non-susceptibility were further subjected to mutation detection by targeting rplC gene (linezolid) and Rv0678 gene (clofazimine). The MIC for linezolid ranged from 0.125 µg/ml to > 2 µg/ml and for clofazimine from 0.25 µg/ml to > 4 µg/ml. The MIC50 and MIC90 for linezolid were 0.5 µg/ml and 1 µg/ml respectively while for clofazimine both were 1 µg/ml. The essential and categorical agreement for linezolid was 97.63% and 95.26% and for clofazimine, both were 100%. The sequencing result of the rplC gene revealed a point mutation at position 460 bp, where thymine (T) was substituted for cytosine (C) while seven mutations were noted between 46 to 220 bp in Rv0678 gene. CONCLUSION REMA method has been found to be more suitable in comparison to the agar dilution method due to lesser turnaround time. Mutations in rplC and Rv0678 genes were reasons for drug resistance against linezolid and clofazimine respectively.
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Affiliation(s)
- Kamal Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Swati Sharma
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Tuhina Banerjee
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ankush Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
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Mvelase NR, Singh R, Swe Swe-Han K, Mlisana KP. Pyrazinamide resistance in rifampicin discordant tuberculosis. PLoS One 2022; 17:e0274688. [PMID: 36129921 PMCID: PMC9491533 DOI: 10.1371/journal.pone.0274688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Mycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported. Materials and methods We evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid. Results Pyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates. Conclusion Given the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.
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Affiliation(s)
- Nomonde Ritta Mvelase
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
- * E-mail:
| | - Ravesh Singh
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
| | - Khine Swe Swe-Han
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
| | - Koleka Patience Mlisana
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, Durban, South Africa
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13
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Getahun M, Blumberg HM, Ameni G, Beyene D, Kempker RR. Minimum inhibitory concentrations of rifampin and isoniazid among multidrug and isoniazid resistant Mycobacterium tuberculosis in Ethiopia. PLoS One 2022; 17:e0274426. [PMID: 36099255 PMCID: PMC9469996 DOI: 10.1371/journal.pone.0274426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Traditionally, single critical concentrations of drugs are utilized for Mycobacterium tuberculosis (Mtb) drug susceptibility testing (DST); however, the level of drug resistance can impact treatment choices and outcomes. Mutations at the katG gene are the major genetic mutations in multidrug resistant (MDR) Mtb and usually associated with high level resistance. We assessed the minimum inhibitory concentrations (MICs) of MDR or rifampin resistant (RR) and isoniazid (INH) resistant Mtb isolates to determine the quantification of drug resistance among key anti-tuberculosis drugs. Methods The study was conducted on stored Mtb isolates collected as part of a national drug resistance survey in Ethiopia. MIC values were determined using Sensititre™ MYCOTB plates. A line probe assay (MTBDRplus) was also performed to identify genetic determinants of resistance for all isolates. Results MIC testing was performed on 74 Mtb isolates including 46 MDR, 2 RR and 26 INH phenotypically resistant isolates as determined by the Löwenstein Jensen (LJ) method. Four (15%) INH resistant Mtb isolates were detected as borderline rifampin resistance (MIC = 1 μg/ml) using MYCOTB MIC plates and no rifampin resistance mutations were detected by LPA. Among the 48 MDR/RR TB cases, 9 (19%) were rifabutin susceptible (MIC was between ≤0.25 and 0.5μg/ml). Additionally, the MIC for isoniazid was between 2–4 μg/ml (moderate resistance) for 58% of MDR TB isolates and 95.6% (n = 25) of the isolates had mutations at the katG gene. Conclusion Our findings suggest a role for rifabutin treatment in a subset of RR TB patients, thus potentially preserving an important drug class. The high proportion of moderate level INH resistant among MDR Mtb isolates indicates the potential benefit of high dose isoniazid treatment in a high proportion of katG gene harboring MDR Mtb isolates.
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Affiliation(s)
- Muluwork Getahun
- TB and HIV Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
| | - Henry M. Blumberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
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Finci I, Albertini A, Merker M, Andres S, Bablishvili N, Barilar I, Cáceres T, Crudu V, Gotuzzo E, Hapeela N, Hoffmann H, Hoogland C, Kohl TA, Kranzer K, Mantsoki A, Maurer FP, Nicol MP, Noroc E, Plesnik S, Rodwell T, Ruhwald M, Savidge T, Salfinger M, Streicher E, Tukvadze N, Warren R, Zemanay W, Zurek A, Niemann S, Denkinger CM. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study. THE LANCET. MICROBE 2022; 3:e672-e682. [PMID: 35907429 PMCID: PMC9436784 DOI: 10.1016/s2666-5247(22)00116-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce. METHODS In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS. FINDINGS Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations. INTERPRETATION The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background). FUNDING Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.
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Affiliation(s)
- Iris Finci
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; Evolution of the Resistome, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Nino Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Tatiana Cáceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeriu Crudu
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Nchimunya Hapeela
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Harald Hoffmann
- SYNLAB Gauting, SYNLAB MVZ Dachau, Gauting, Germany; Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | | | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Katharina Kranzer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Biomedical Research and Training Institute, Harare, Zimbabwe
| | | | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark P Nicol
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Ecaterina Noroc
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Sara Plesnik
- Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | - Timothy Rodwell
- FIND, Geneva, Switzerland; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Theresa Savidge
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA; Alaska State Public Health Laboratories, Anchorage, AK, USA
| | - Max Salfinger
- College of Public Health, University of South Florida, Tampa, FL, USA; Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elizabeth Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nestani Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna Zurek
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland; German Center for Infection Research, Heidelberg, Germany; Division of Clinical Tropical Medicine and German Centre for Infection Research, Heidelberg University Hospital, Heidelberg, Germany.
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Patterns of Presentation of Drug-Resistant Tuberculosis in Nigeria: A Retrospective File Review. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13030043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: An understanding of the patterns of drug-resistant tuberculosis (DR-TB) is needed to develop the best diagnostic tools and decide on optimal treatment combination therapies for the management of DR-TB in Nigeria. Objective: We aimed to investigate patterns of DR-TB for the five first-line anti-TB drugs over a period of seven years (2010–2016) and the associated clinical and socio-demographic factors. Methods: A retrospective study recruited 2555 DR-TB patients between 2010 and 2016 across the six geopolitical treatment zones in Nigeria. We determined DR-TB patterns based on standard case definition and their association with demographic and clinical information. Data were analyzed using Statistical Package for Social Sciences (SPSS) software. Independent predictors of DR-TB patterns/types were determined using bivariate and multivariate analyses with a statistical significance of p < 0.05 and a 95% confidence interval. Results: The majority of the participants were males, 66.93% (1710), 31–40 years old, 35.19% (899), previously treated, 77.10% (1909), had received at least two treatments, 411 (49.94%) and were multi-drug resistant, 61.41% (1165). The Southwest zone had the highest number of DR-TB cases, 36.92%. We found an upward trend in the prevalence of DR-TB from 2010 to 2016. Participants who had received one previous treatment showed statistically significant higher rifampicin resistance (59.68%), those with two previous treatments reported a statistically significant higher polydrug resistance (78.57%), and those with three or more previous treatments had a statistically significant higher multidrug resistance (19.83%) (χ2 = 36.39; p = 0.001). Mono-drug resistance and rifampicin resistance were statistically significantly higher in the southwest zone (29.48% and 34.12% respectively), polydrug resistance in the northcentral (20.69%) and south-south zones (20.69%), and multidrug resistance in the southwest (30.03%) and northcentral zones (19.18%) (χ2 = 98.26; p = 0.001). Conclusions: We present patterns of DR-TB across the six geopolitical zones in Nigeria. Clinicians should weigh in on these patterns while deciding on the best first-line drug combinations to optimize treatment outcomes for DR-TB patients. A national scale-up plan for DST services should focus on patients with previous multiple exposures to anti-TB treatments and on those in the Northeastern zone of the country.
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Diriba G, Kebede A, Tola HH, Alemu A, Yenew B, Moga S, Addise D, Mohammed Z, Getahun M, Fantahun M, Tadesse M, Dagne B, Amare M, Assefa G, Abera D, Desta K. Utility of line probe assay in detecting drug resistance and the associated mutations in patients with extrapulmonary tuberculosis in Addis Ababa, Ethiopia. SAGE Open Med 2022; 10:20503121221098241. [PMID: 35646363 PMCID: PMC9130810 DOI: 10.1177/20503121221098241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Molecular tests allow rapid detection of Mycobacterium tuberculosis and drug resistance in a few days. Identifying the mutations in genes associated with drug resistance may contribute to the development of appropriate interventions to improve tuberculosis control. So far, there is little information in Ethiopia about the diagnostic performance of line probe assay (LPA) and the M. tuberculosis common gene mutations associated with drug resistance in extrapulmonary tuberculosis. Thus, this study aimed to assess the frequency of drug resistance-associated mutations in patients with extrapulmonary tuberculosis (EPTB) and to compare the agreement and determine the utility of the genotypic in the detection of drug resistance in Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted on stored M. tuberculosis isolates. The genotypic and phenotypic drug susceptibility tests were performed using LPA and BACTEC-MGIT-960, respectively. The common mutations were noted, and the agreement and the utility of the LPA were determined using the BACTEC-MGIT-960 as a gold standard. Results Of the 151 isolates, the sensitivity and specificity of MTBDRplus in detecting isoniazid resistance were 90.9% and 100%, respectively. While for rifampicin, it was 100% and 99.3% for sensitivity and specificity, respectively. The katG S315Tl was the most common mutation observed in 85.7% of the isoniazid-resistant isolates. In the case of rifampicin, the most common mutation (61.9%) was observed at position rpoB S531L. Mutations in the gyrA promoter region were strongly associated with Levofloxacin and Moxifloxacin resistance. Conclusion Line probe assay has high test performance in detecting resistance to anti-TB drugs in EPTB isolates. The MTBDRplus test was slightly less sensitive for the detection of isoniazid resistance as compared to the detection of rifampicin. The most prevalent mutations associated with isoniazid and rifampicin resistance were observed at katG S315Tl and rpoB S531L respectively. Besides, all the fluoroquinolone-resistant cases were associated with gyrA gene. Finally, a validation study with DNA sequencing is recommended.
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Affiliation(s)
- Getu Diriba
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Department of Microbial, Cellular and
Molecular Biology, College of Natural and Computational Sciences, Addis Ababa
University, Addis Ababa, Ethiopia
| | | | - Ayinalem Alemu
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology,
Addis Ababa University, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | | | | | | | - Mengistu Fantahun
- St. Paul’s Hospital Millennium Medical
College, Addis Ababa, Ethiopia
| | | | - Biniyam Dagne
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | | | - Dessie Abera
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
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17
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Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing. Genome Med 2022; 14:52. [PMID: 35585607 PMCID: PMC9118838 DOI: 10.1186/s13073-022-01054-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background Stool is an important diagnostic specimen for tuberculosis in populations who struggle to provide sputum, such as children or people living with HIV. However, the culture of Mycobacterium tuberculosis (M. tuberculosis) complex strains from stool perform poorly. This limits the opportunity for phenotypic drug resistance testing with this specimen. Therefore, reliable molecular methods are urgently needed for comprehensive drug resistance testing on stool specimens. Methods We evaluated the performance of targeted next-generation sequencing (tNGS, Deeplex® Myc-TB) for the detection of mutations associated with M. tuberculosis complex drug resistance on DNA isolated from stool specimens provided by participants from a prospective cohort of patients treated for tuberculosis in Eswatini (n = 66; 56 with and 10 participants without M. tuberculosis complex DNA detected in stool by real-time quantitative PCR), and an independent German validation cohort of participants with culture-confirmed tuberculosis (n = 21). Results The tNGS assay detected M. tuberculosis complex DNA in 38 of 56 (68%) samples; for 28 of 38 (74%) samples, a full M. tuberculosis complex drug resistance prediction report was obtained. There was a high degree of concordance with sputum phenotypic drug susceptibility results (κ = 0.82). The ability to predict resistance was concentration-dependent and successful in 7/10 (70%), 18/25 (72%), and 3/21 (14%) of samples with stool PCR concentration thresholds of > 100 femtogram per microliter (fg/μl), 1 to 100 fg/μl, and < 1 fg/μl, respectively (p = 0.0004). The German cohort confirmed these results and demonstrated a similarly high concordance between stool tNGS and sputum phenotypic drug susceptibility results (κ = 0.84). Conclusions tNGS can identify drug resistance from stool provided by tuberculosis patients. This affords the opportunity to obtain critical diagnostic information for tuberculosis patients who struggle to provide respiratory specimens. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01054-6.
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Xia H, Song Y, Zheng Y, Wang S, Zhao B, He W, Liu D, Ou X, Zhou Y, Zhao Y. Detection of Mycobacterium tuberculosis Rifampicin Resistance Conferred by Borderline rpoB Mutations: Xpert MTB/RIF is Superior to Phenotypic Drug Susceptibility Testing. Infect Drug Resist 2022; 15:1345-1352. [PMID: 35378895 PMCID: PMC8976515 DOI: 10.2147/idr.s358301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Wencong He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Dongxin Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Correspondence: Yanlin Zhao, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, People’s Republic of China, Tel +86 10-58900517, Email
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Reevaluating Rifampicin Breakpoint Concentrations for Mycobacterium tuberculosis Isolates with Disputed rpoB Mutations and Discordant Susceptibility Phenotypes. Microbiol Spectr 2022; 10:e0208721. [PMID: 35107324 PMCID: PMC8809345 DOI: 10.1128/spectrum.02087-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, rifampicin resistance breakpoints based on MICs of disrupted rpoB mutants of Mycobacterium tuberculosis (MTB) were explored using the Mycobacteria Growth Indicator Tube (MGIT) system and microplate alamarBlue assay (MABA). Sixty-one MTB isolates with disputed low-level rifampicin resistance-associated rpoB mutations and 40 RIF-susceptible wild-type isolates were included. Among the 61 resistant isolates, 25 (41.0%) had MICs ≥2.0 mg/L via MABA, while 16 (26.2%) were identified as RIF resistant via MGIT. Epidemiological cut-off (ECOFF) values obtained using MABA and MGIT were 0.25 and 0.125 mg/L, respectively. Based on 0.125 mg/L as a tentative critical concentration (CC), MABA RIF resistance-detection sensitivity was 93.4%, prompting the reduction of the MGIT CC to 0.125 mg/L, given that only a single isolate (1.6%) with the borderline mutation would be misclassified as susceptible to RIF based on this CC. Based on DNA sequencing of RRDR as the gold standard, the diagnostic accuracy of MGIT (99.0%) was significantly higher than that of MABA (91.1%). MICs of Leu511Pro mutant isolates were negatively correlated with time to liquid culture positivity (TTP) in our analysis (R = 0.957, P < 0.01). In conclusion, our results demonstrated missed detection of a high proportion of rifampicin-resistant isolates based on the WHO-endorsed CC. Such missed detections would be avoided by reducing the optimal MGIT RIF CC to 0.125 mg/L. In addition, MGIT based on reduced CC outperformed MABA in detecting borderline RIF resistance, with MABA MIC results obtained for isolates with the same mutation correlating with MTB growth rate. IMPORTANCE Tuberculosis (TB) is still one of the world's leading infectious disease killers. The early and accurate diagnosis of RIF resistance is necessary to deliver timely and appropriate treatment for TB patients and improve their clinical outcome. Actually, a proportion of MTB isolates with disputed rpoB mutations present a diagnostic dilemma between Xpert and phenotypical drug susceptibility testing (pDST). Recently, WHO reported a pragmatic approach by lowering critical concentration (CC) to boost sensitivity of resistance detection of pDST. Therefore, a detailed analysis of the association between RIF susceptibility and disrupted mutations within rpoB gene would lay a foundation to assess the diagnostic accuracy of pDST with lowering RIF CC. In this study, we aim to determine the MICs of MTB isolates with disrupted mutations by MGIT and microplate alamarBlue assay (MABA). We also aimed to determine the optimal breakpoints for MTB isolates with these mutations.
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20
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Rafael LL, Raquel MS, Rogelio FA, Miroslava FP, Alejandra-Isabel JG, Paola RTS. Discordant results between genotypic and phenotypic assays (Xpert MTB/RIF vs. BACTEC MGIT 960 system) for detection of RIF-resistant Mycobacterium tuberculosis isolates in a high burden region. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105142. [PMID: 34800711 DOI: 10.1016/j.meegid.2021.105142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/31/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Clinical isolates with discordant phenotypic and genotypic results were submitted to DNA sequencing to identify which were genuinely resistant to rifampin and determine the frequency of silent and disputed mutations in our region. We present the retrospective analysis of all the culture-proven TB cases tested with the Xpert®MTB/RIF assay at the Tuberculosis Clinic and Laboratory of the Tijuana General Hospital, Mexico. Clinical isolates showing a discrepancy between phenotypic and molecular tests were analyzed by DNA sequencing. Thirteen isolates tested as rifampin susceptible on the MGIT system were rifampin-resistant according to Xpert®MTB/RIF assay. DNA sequencing showed that seven (53.8%) isolates had a silent (P514P) mutation; three isolates showed different missense (L511P, D516Y, and S531L) mutations. Three isolates showed no mutations. The existence of heteroresistance and silent or disputed mutations warrants that all rifampin-resistance cases diagnosed with the Xpert®MTB/RIF should be referred to specialized centers for DNA sequencing.
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Affiliation(s)
- Laniado-Laborín Rafael
- Clínica y Laboratorio de Tuberculosis Hospital General Tijuana, ISESALUD, Tijuana, Baja California, Mexico; Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Baja California, Mexico; Regional Green Light Committee for the Americas (rGLC), World Health Organization, United States of America.
| | - Muñiz-Salazar Raquel
- Laboratorio de Epidemiología y Ecología Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Flores-Acosta Rogelio
- Clínica y Laboratorio de Tuberculosis Hospital General Tijuana, ISESALUD, Tijuana, Baja California, Mexico; Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Baja California, Mexico
| | - Félix-Ponce Miroslava
- Clínica y Laboratorio de Tuberculosis Hospital General Tijuana, ISESALUD, Tijuana, Baja California, Mexico; Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Baja California, Mexico
| | - Jiménez-Gracia Alejandra-Isabel
- Clínica y Laboratorio de Tuberculosis Hospital General Tijuana, ISESALUD, Tijuana, Baja California, Mexico; Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Baja California, Mexico
| | - Ruiz-Tamayo Saritzia Paola
- Laboratorio de Epidemiología y Ecología Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
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21
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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] [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.
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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
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22
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Li MC, Lu J, Lu Y, Xiao TY, Liu HC, Lin SQ, Xu D, Li GL, Zhao XQ, Liu ZG, Zhao LL, Wan KL. rpoB Mutations and Effects on Rifampin Resistance in Mycobacterium tuberculosis. Infect Drug Resist 2021; 14:4119-4128. [PMID: 34675557 PMCID: PMC8502021 DOI: 10.2147/idr.s333433] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Objective To investigate the mutations within the whole rpoB gene of Mycobacterium tuberculosis and analyze their effects on rifampin (RIF) resistance based on crystal structure. Methods We sequenced the entire rpoB gene in 175 tuberculosis isolates and quantified their minimum inhibitory concentrations using microplate-based assays. Additionally, the structural interactions between wild-type/mutant RpoB and RIF were also analyzed. Results Results revealed that a total of 34 mutations distributed across 17 different sites within the whole rpoB gene were identified. Of the 34 mutations, 25 could alter the structural interaction between RpoB and RIF and contribute to RIF resistance. Statistical analysis showed that S450L, H445D, H445Y and H445R mutations were associated with high-level RIF resistance, while D435V was associated with moderate-level RIF resistance. Conclusion Some mutations within the rpoB gene could affect the interaction between RpoB and RIF and thus are associated with RIF resistance. These findings could be helpful to design new antibiotics and develop novel diagnostic tools for drug resistance in TB.
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Affiliation(s)
- Ma-Chao Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Yao Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Tong-Yang Xiao
- Guangdong Key Laboratory for Diagnosis & Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Hai-Can Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shi-Qiang Lin
- Department of Bioinformatics, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, People's Republic of China
| | - Da Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Gui-Lian Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xiu-Qin Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhi-Guang Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Li-Li Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Kang-Lin Wan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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23
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Rifampicin-Monoresistant Tuberculosis Is Not the Same as Multidrug-Resistant Tuberculosis: a Descriptive Study from Khayelitsha, South Africa. Antimicrob Agents Chemother 2021; 65:e0036421. [PMID: 34460307 PMCID: PMC8522772 DOI: 10.1128/aac.00364-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Rifampin monoresistance (RMR; rifampin resistance and isoniazid susceptibility) accounts for 38% of all rifampin-resistant tuberculosis (RR-TB) in South Africa and is increasing. We aimed to compare RMR-TB with multidrug-resistant TB (MDR-TB) in a setting with high TB, RR-TB, and HIV burdens. Patient-level clinical data and stored RR Mycobacterium tuberculosis isolates from 2008 to 2017 with available whole-genome sequencing (WGS) data were used to describe risk factors associated with RMR-TB and to compare RR-conferring mutations between RMR-TB and MDR-TB. A subset of isolates with particular RR-conferring mutations were subjected to semiquantitative rifampin phenotypic drug susceptibility testing. Among 2,041 routinely diagnosed RR-TB patients, 463 (22.7%) had RMR-TB. HIV-positive individuals (adjusted odds ratio [aOR], 1.4; 95% confidence interval [CI], 1.1 to 1.9) and diagnosis between 2013 and 2017 versus between 2008 and 2012 (aOR, 1.3; 95% CI, 1.1 to 1.7) were associated with RMR-TB. Among 1,119 (54.8%) patients with available WGS data showing RR-TB, significant differences in the distribution of rpoB RR-conferring mutations between RMR and MDR isolates were observed. Mutations associated with high-level RR were more commonly found among MDR isolates (811/889 [90.2%] versus 162/230 [70.4%] among RMR isolates; P < 0.0001). In particular, the rpoB L430P mutation, conferring low-level RR, was identified in 32/230 (13.9%) RMR isolates versus 10/889 (1.1%) in MDR isolates (P < 0.0001). Among 10 isolates with an rpoB L430P mutation, 7 were phenotypically susceptible using the critical concentration of 0.5 μg/ml (range, 0.125 to 1 μg/ml). The majority (215/230 [93.5%]) of RMR isolates showed susceptibility to all other TB drugs, highlighting the potential benefits of WGS for simplified treatment. These data suggest that the evolution of RMR-TB differs from MDR-TB with a potential contribution from HIV infection.
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24
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Rando-Segura A, Aznar ML, Moreno MM, Espasa Soley M, Sulleiro Igual E, Bocanegra Garcia C, Gil Olivas E, Nindia Eugénio A, Escartin Huesca C, Zacarias A, Vegue Collado J, Katimba D, Vivas Cano MC, Gabriel E, López García MT, Pumarola Suñe T, Molina Romero I, Tórtola Fernández MT. Molecular characterization of rpoB gene mutations in isolates from tuberculosis patients in Cubal, Republic of Angola. BMC Infect Dis 2021; 21:1056. [PMID: 34641802 PMCID: PMC8507306 DOI: 10.1186/s12879-021-06763-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
Background The importance of Mycobacterium tuberculosis strains with disputed rpoB mutations remains to be defined. This study aimed to assess the frequency and types of rpoB mutations in M. tuberculosis isolates from Cubal, Angola, a country with a high incidence of tuberculosis. Methods All isolates included (n = 308) were analyzed using phenotypic drug susceptibility testing and GenoType MTBDRplus assay. DNA sequencing of the rpoB gene and determination of rifampicin MIC by macrodilution method were additionally performed on isolates yielding discordant results (n = 12) and those in which the mutation detected was not characterized (n = 8). Results In total, 85.1% (74/87) of rifampicin-resistant strains had undisputed rpoB mutations -S450L (49), D435V (15), H445D (3), H445Y (2), Q432ins (1), L449M plus S450F (1), S450F (1), S450W (1) and S450Y (1)-; 10.3% (9/87) had disputed rpoB mutations—L430P plus S493L (1), N437del (1), H445L (3), D435Y (2), L452P (2)-, 2.3% (2.3%) showed no rpoB mutations and 2.3% (2/87) showed heteroresistance—D435Y plus L452P and L430P plus S493L-. Conclusion Disputed rpoB mutations were common, occurring in 10.3% of rifampicin resistant isolates. Current phenotyping techniques may be unable to detect this resistance pattern. To increase their sensitivity, a lower concentration of RIF could be used in these tests or alternatively, rpoB mutations could be screened and characterized in all M. tuberculosis strains.
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Affiliation(s)
- Ariadna Rando-Segura
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain.
| | - María Luisa Aznar
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain.,Hospital Nossa Senhora da Paz, Cubal, Angola
| | | | - Mateu Espasa Soley
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | - Elena Sulleiro Igual
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | - Cristina Bocanegra Garcia
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain.,Hospital Nossa Senhora da Paz, Cubal, Angola
| | - Eva Gil Olivas
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain.,Hospital Nossa Senhora da Paz, Cubal, Angola
| | | | - Carlos Escartin Huesca
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | | | - Josep Vegue Collado
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | | | - Maria Carmen Vivas Cano
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | | | | | - Tomas Pumarola Suñe
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
| | - Israel Molina Romero
- Infectious Disease Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Teresa Tórtola Fernández
- Microbiology Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119 - 129, 08035, Barcelona, Spain
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GeneXpert on patients with human immunodeficiency virus and smear-negative pulmonary tuberculosis. PLoS One 2021; 16:e0253961. [PMID: 34228759 PMCID: PMC8259960 DOI: 10.1371/journal.pone.0253961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/17/2021] [Indexed: 11/25/2022] Open
Abstract
Objectives Vietnam is a high-prevalence country for tuberculosis (TB). Xpert MTB/RIF is a novel PCR-based diagnostic test that is substantially more sensitive for detecting M. tuberculosis than traditional smear-based techniques. However, locally-derived evidence of Xpert MTB/RIF in HIV-infected people is limited. This study evaluates the performance of the Xpert MTB/RIF in HIV-infected patients with smear-negative pulmonary TB (SNTB). Methods This was a cross-sectional study in 3 hospitals. The performance of Xpert MTB/RIF was compared with the reference standard of liquid culture and phenotypic drug-susceptibility testing for rifampicin (RIF) resistance. Results Out of 123 patients, the median age was 37.0 (IQR: 32.0–41.0) and 81.3% were male. The area under the receiver operating characteristic curve, sensitivity (Se) and specificity (Sp) of Xpert MTB/RIF for pulmonary TB diagnosis were 0.72 (95% confidence interval [CI]: 0.63–0.81), 66.7% (95%CI: 54.8–77.1) and 77.1% (95%CI: 62.7–88.0), respectively, while Se and Sp of Xpert MTB/RIF in detecting RIF resistance were 50.0 (11.8–88.2) and 86.4% (95%CI: 72.7–94.8). Conclusion The performance of Xpert MTB/RIF in HIV-infected patients with SNTB for the diagnosis of TB and RIF-resistance was low. Further studies are required to evaluate the results of Xpert MTB/RIF assay in HIV-infected patients with SNTB and the role of Xpert repetition on the same specimens.
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26
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Qadir M, Tahseen S, McHugh TD, Hussain A, Masood F, Ahmed N, Faryal R. Profiling and identification of novel rpoB mutations in rifampicin-resistant Mycobacterium tuberculosis clinical isolates from Pakistan. J Infect Chemother 2021; 27:1578-1583. [PMID: 34244055 DOI: 10.1016/j.jiac.2021.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/07/2021] [Accepted: 06/27/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Rifampicin (RIF) is one of the most effective anti-tuberculosis first-line drugs prescribed along with isoniazid. However, the emergence of RIF resistance Mycobacterium tuberculosis (MTB) isolates is a major issue towards tuberculosis (TB) control program in high MDR TB-burdened countries including Pakistan. Molecular data behind phenotypic resistance is essential for better management of RIF resistance which has been linked with mutations in rpoB gene. Since molecular studies on RIF resistance is limited in Pakistan, the current study was aimed to investigate the molecular data of mutations in rpoB gene behind phenotypic RIF resistance isolates in Pakistan. METHOD A total of 322 phenotypically RIF-resistant isolates were randomly selected from National TB Reference Laboratory, Pakistan for sequencing while 380 RIF resistance whole-genome sequencing (WGS) of Pakistani isolates (BioProject PRJEB25972), were also analyzed for rpoB mutations. RESULT Among the 702 RIF resistance samples, 675 (96.1%) isolates harbored mutations in rpoB in which 663 (94.4%) were detected within the Rifampicin Resistance Determining Region (RRDR) also known as a mutation hot spot region, including three novel. Among these mutations, 657 (97.3%) were substitutions including 603 (89.3%) single nucleotide polymorphism, 49 (7.25%) double and five (0.8%) triple. About 94.4% of Phenotypic RIF resistance strains, exhibited mutations in RRDR, which were also detectable by GeneXpert. CONCLUSION Mutations in the RRDR region of rpoB is a major mechanism of RIF resistance in MTB circulating isolates in Pakistan. Molecular detection of drug resistance is a faster and better approach than phenotypic drug susceptibility testing to reduce the time for transmission of RIF resistance strains in population. Such insights will inform the deployment of anti-TB drug regimens and disease control tools and strategies in high burden settings, such as Pakistan.
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Affiliation(s)
- Mehmood Qadir
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sabira Tahseen
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Alamdar Hussain
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Faisal Masood
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Niaz Ahmed
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Rani Faryal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Disputed rpoB Mutations in Mycobacterium tuberculosis and Tuberculosis Treatment Outcomes. Antimicrob Agents Chemother 2021; 65:e0157320. [PMID: 33846134 DOI: 10.1128/aac.01573-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discordant results between genotypic drug susceptibility testing (gDST) and phenotypic DST (pDST) for Mycobacterium tuberculosis isolates with disputed (discordance between gDST and pDST results) mutations affect rifampin (RIF)-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) treatments due to a lack of practical clinical guidelines. To investigate the role of disputed rpoB mutations in M. tuberculosis and TB treatment outcomes, initial isolates of 837 clinical RR- or MDR-TB cases confirmed during 2014 to 2018 were retested using agar-based RIF pDST and rpoB gene sequencing. MICs were determined for isolates with disputed rpoB mutations. Disputed rpoB mutations were identified in 77 (9.2%) M. tuberculosis isolates, including 50 (64.9%) and 14 (18.2%) phenotypically RIF- and rifabutin (RFB)-resistant isolates, respectively. The predominant single mutations were those encoding L533P (a change of L to P at position 533) (44.2%) and L511P (20.8%). Most of the isolates harboring mutations encoding L511P (87.5%), H526N (100%), D516Y (70.0%), and L533P (63.6%) had MICs of ≤1 mg/liter, whereas isolates harboring the mutation encoding H526L (75%) had a MIC of >1 mg/liter. Of the 63 cases with treatment outcomes available, 11 (17.5%) cases died, 1 (1.6%) case transferred out, and 51 (81%) cases had favorable outcomes, including 8 and 20 cases treated with standard-dose RIF- and RFB-containing regimens, respectively. Excluding cases that transferred out or received no or 1-day treatment, we observed statistically significant differences between the outcomes using active and inactive fluoroquinolones (FQs) (P = 0.008, odds ratio = 0.05 [95% confidence interval, 0.01 to 0.38]) in 57 cases (where active means a case susceptible to the drug and inactive means a case resistant to the drug or drug not used). We concluded that disputed rpoB mutations are not rare. Depending on the resources available, sequencing and/or MIC testing is recommended for better management of RR- and MDR-TB cases.
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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] [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.
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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
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Thin-Layer-Agar-Based Direct Phenotypic Drug Susceptibility Testing on Sputum in Eswatini Rapidly Detects Mycobacterium tuberculosis Growth and Rifampicin Resistance Otherwise Missed by WHO-Endorsed Diagnostic Tests. Antimicrob Agents Chemother 2021; 65:AAC.02263-20. [PMID: 33722892 PMCID: PMC8315964 DOI: 10.1128/aac.02263-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/02/2021] [Indexed: 11/20/2022] Open
Abstract
Xpert MTB/RIF rapidly detects resistance to rifampicin (RR); however, this test misses I491F-RR conferring rpoB mutation, common in southern Africa. In addition, Xpert MTB/RIF does not distinguish between viable and dead Mycobacterium tuberculosis (MTB). We aimed to investigate the ability of thin-layer agar (TLA) direct drug-susceptibility testing (DST) to detect MTB and its drug-resistance profiles in field conditions in Eswatini. Consecutive samples were tested in parallel with Xpert MTB/RIF and TLA for rifampicin (1.0 μg/ml) and ofloxacin (2.0 μg/ml). TLA results were compared at the Reference Laboratory in Antwerp with indirect-DST on Löwenstein-Jensen or 7H11 solid media and additional phenotypic and genotypic testing to resolve discordance. TLA showed a positivity rate for MTB detection of 7.1% versus 10.0% for Xpert MTB/RIF. Of a total of 4,547 samples included in the study, 200 isolates were available for comparison to the composite reference. Within a median of 18.4 days, TLA detected RR with 93.0% sensitivity (95% confidence interval [CI], 77.4 to 98.0) and 99.4% specificity (95% CI, 96.7 to 99.9) versus 62.5% (95% CI, 42.7 to 78.8) and 99.3% (95% CI, 96.2 to 99.9) for Xpert MTB/RIF. Eight isolates, 28.6% of all RR-confirmed isolates, carried the I491F mutation, all detected by TLA. TLA also correctly identified 183 of the 184 ofloxacin-susceptible isolates (99.5% specificity; 95% CI, 97.0 to 99.9). In field conditions, TLA rapidly detects RR, and in this specific setting, it contributed to detection of additional RR patients over Xpert MTB/RIF, mainly but not exclusively due to I491F. TLA also accurately excluded fluoroquinolone resistance.
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Chiposi L, Cele LP, Mokgatle M. Prevalence of delay in seeking tuberculosis care and the health care seeking behaviour profile of tuberculous patients in a rural district of KwaZulu Natal, South Africa. Pan Afr Med J 2021; 39:27. [PMID: 34394818 PMCID: PMC8348261 DOI: 10.11604/pamj.2021.39.27.26717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/19/2021] [Indexed: 12/05/2022] Open
Abstract
Introduction patient delay in seeking TB (tuberculosis) care is reported as one of the major hurdles undermining the efforts of controlling TB by many TB control programmes of the world. The main aim of this study was to determine the prevalence of this phenomenon and to profile the TB patients that delayed seeking TB care in a rural area of KwaZulu Natal province of South Africa. Methods this was a cross-sectional study, conducted among 200 TB patients attending primary health care facilities in Ugu District. Patient data were collected by a self-administered questionnaire, entered into an Excel file and imported into the EpiInfo 7 statistical software for analysis. Frequency tables were used to display the data and the p value was used for statistical significance. Results about 40% of the participants delayed seeking TB care in this study, and these were mostly individuals who were married, the employed and those who walked to the clinic. Delay was also prevalent among those that self-medicated, bought medication from the pharmacy and sought TB care from a private doctor. The reasons included the great distances, long queues waiting at the facilities, and not feeling ill. Conclusion the 4 weeks cut-off in seeking TB care in this study far exceeds the recommended 2 weeks. This study recommends periodic active TB case finding and active engagement between the public and the private health sectors.
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Affiliation(s)
- Linda Chiposi
- Epidemiology and Biostatistics Unit, Department of Public Health, Sefako Makgatho Health Sciences University, Ga-Rankuwa, South Africa
| | - Lindiwe Priscilla Cele
- Epidemiology and Biostatistics Unit, Department of Public Health, Sefako Makgatho Health Sciences University, Ga-Rankuwa, South Africa
| | - Mathildah Mokgatle
- Epidemiology and Biostatistics Unit, Department of Public Health, Sefako Makgatho Health Sciences University, Ga-Rankuwa, South Africa
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Should treatment of low-level rifampicin mono-resistant tuberculosis be different? J Clin Tuberc Other Mycobact Dis 2021; 23:100240. [PMID: 34095546 PMCID: PMC8167426 DOI: 10.1016/j.jctube.2021.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Che Y, Yang T, Lin L, Xiao Y, Jiang F, Chen Y, Chen T, Zhou J. Comparative Utility of Genetic Determinants of Drug Resistance and Phenotypic Drug Susceptibility Profiling in Predicting Clinical Outcomes in Patients With Multidrug-Resistant Mycobacterium tuberculosis. Front Public Health 2021; 9:663974. [PMID: 33968888 PMCID: PMC8100237 DOI: 10.3389/fpubh.2021.663974] [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: 02/04/2021] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Setting: Programmatic management of drug-resistant tuberculosis in Ningbo, China. Objective: To assess whether data-driven genetic determinants of drug resistance patterns could outperform phenotypic drug susceptibility testing in predicting clinical meaningful outcomes among patients with multidrug-resistant tuberculosis (MDR-TB). Design: We conducted a prospective cohort study of 104 MDR-TB patients. All MDR-TB isolates underwent drug susceptibility testing and genotyping for mutations that could cause drug resistance. Study outcomes were time to sputum smear conversion and probability of treatment success, as well as time to culture conversion within 6 months. Data were analyzed using latent class analysis, Kaplan–Meier curves, and Cox regression models. Results: We report that latent class analysis of data identified two latent classes that predicted sputum smear conversion with P = 0.001 and area under receiver-operating characteristic curve of 0.73. The predicted latent class memberships were associated with superior capability in predicting sputum culture conversion at 6 months and overall treatment success compared to phenotypic drug susceptibility profiling using boosted logistic regression models. Conclusion: These results suggest that genetic determinants of drug resistance in combination with phenotypic drug-resistant tests could serve as useful biomarkers in predicting treatment prognosis in MDR-TB.
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Affiliation(s)
- Yang Che
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Tianchi Yang
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Lv Lin
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Yue Xiao
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
| | - Feng Jiang
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
| | - Yanfei Chen
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
| | - Tong Chen
- Ningbo Municipal Center for Disease Control and Prevention, Institute of Tuberculosis Prevention and Control, Ningbo, China
| | - Jifang Zhou
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, China
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Florou Z, Mavroidi A, Vatidis G, Daniil Z, Gourgoulianis K, Petinaki E. Molecular Basis of Resistance to First-Line Drugs of Mycobacterium tuberculosis/canettii Strains in Greece. Microb Drug Resist 2021; 27:1389-1396. [PMID: 33877884 DOI: 10.1089/mdr.2020.0396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine the rate and the mutations of genes involved to the first-line antituberculous drugs' resistance of M. tuberculosis/canettii isolated in Central Greece from 2010 to 2019. During the study period, the rate of resistance to isoniazid, rifampicin, ethambutol, and pyrazinamide was 5.4%, 0.4%, 1.1%, and 1.1%, respectively. All phenotypically resistant isolates (14 to isoniazid, 3 to ethambutol, 3 to pyrazinamide, and 1 to rifampicin) and 17 susceptible isolates (control group) were tested for the presence of mutations/alterations/polymorphisms by PCR followed by sequencing analysis. The molecular typing of isolates was based on multispacer sequence typing. Despite the phenotypic resistance, mutations were detected in 13 of 21 isolates (11 isoniazid resistant, 1 rifampicin, and 1 pyrazinamide resistant). Four isoniazid-resistant strains carried the most common mutations S315T and C-15T, whereas the remaining seven isolates carried either less known (E399, A162, W477STOP, S94A, G-48A, C-54T, C-17T, L203, A196, S124, and K367) or novel (D74N, G691S, Ains-85, and D171G); none of the susceptible strains was found to be positive for any novel mutation. The two single rifampicin- and pyrazinamide-resistant strains carried the known mutations S450L (also referred as S531L) and L182W, respectively. The presence of uncommon or novel mutations conferring resistance to isoniazid (INH) creates a diagnostic problem in the routine microbiological laboratory, since commercial methods are focused on the detection of the most common mechanisms of resistance (S315T, C-15T, A-16G, T-8C, and T-8A), therefore, fail to detect such strains. The regional differences in the frequencies of mutations associated with resistance to the first-line drugs provide hints for the development of better molecular-based diagnostic tests.
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Affiliation(s)
- Zoi Florou
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Aggeliki Mavroidi
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - George Vatidis
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Zoi Daniil
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, Greece
| | - Konstantinos Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, Greece
| | - Efi Petinaki
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
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Al-Mutairi NM, Ahmad S, Mokaddas E. Increasing prevalence of resistance to second-line drugs among multidrug-resistant Mycobacterium tuberculosis isolates in Kuwait. Sci Rep 2021; 11:7765. [PMID: 33833390 PMCID: PMC8032671 DOI: 10.1038/s41598-021-87516-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular methods detect genetic mutations associated with drug resistance. This study detected resistance-conferring mutations in gyrA/gyrB for fluoroquinolones and rrs/eis genes for second-line injectable drugs (SLIDs) among multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates in Kuwait. Fifty pansusceptible M. tuberculosis and 102 MDR-TB strains were tested. Phenotypic susceptibility testing was performed by MGIT 960 system using SIRE drug kit. GenoType MTBDRsl version 1 (gMTBDRslv1) and GenoType MTBDRsl version 2 (gMTBDRslv2) tests were used for mutation detection. Results were validated by PCR-sequencing of respective genes. Fingerprinting was performed by spoligotyping. No mutations were detected in pansusceptible isolates. gMTBDRslv1 detected gyrA mutations in 12 and rrs mutations in 8 MDR-TB isolates. gMTBDRsl2 additionally detected gyrB mutations in 2 and eis mutation in 1 isolate. Mutations in both gyrA/gyrB and rrs/eis were not detected. gMTBDRslv1 also detected ethambutol resistance-conferring embB mutations in 59 isolates. Although XDR-TB was not detected, frequency of resistance-conferring mutations for fluoroquinolones or SLIDs was significantly higher among isolates collected during 2013–2019 versus 2006–2012. Application of both tests is warranted for proper management of MDR-TB patients in Kuwait as gMTBDRslv2 detected resistance to fluoroquinolones and/or SLIDs in 3 additional isolates while gMTBDRslv1 additionally detected resistance to ethambutol in 58% of MDR-TB isolates.
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Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
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Tuberculosis Drug Susceptibility, Treatment, and Outcomes for Belarusian HIV-Positive Patients with Tuberculosis: Results from a National and International Laboratory. Tuberc Res Treat 2021; 2021:6646239. [PMID: 33868727 PMCID: PMC8035031 DOI: 10.1155/2021/6646239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background To cure drug-resistant (DR) tuberculosis (TB), the antituberculous treatment should be guided by Mycobacterium tuberculosis drug-susceptibility testing (DST). In this study, we compared conventional DST performed in Minsk, Belarus, a TB DR high-burden country, with extensive geno- and phenotypic analyses performed at the WHO TB Supranational Reference Laboratory in Copenhagen, Denmark, for TB/HIV coinfected patients. Subsequently, DST results were related to treatment regimen and outcome. Methods Thirty TB/HIV coinfected patients from Minsk were included and descriptive statistics applied. Results Based on results from Minsk, 10 (33%) TB/HIV patients had drug-sensitive TB. Two (7%) had isoniazid monoresistant TB, 8 (27%) had multidrug-resistant (MDR) TB, 5 (17%) preextensive drug-resistant (preXDR) TB, and 5 (17%) had extensive drug-resistant (XDR) TB. For the first-line drugs rifampicin and isoniazid, there was DST agreement between Minsk and Copenhagen for 90% patients. For the second-line anti-TB drugs, discrepancies were more pronounced. For 14 (47%) patients, there were disagreements for at least one drug, and 4 (13%) patients were classified as having MDR-TB in Minsk but were classified as having preXDR-TB based on DST results in Copenhagen. Initially, all patients received standard anti-TB treatment with rifampicin, isoniazid, pyrazinamide, and ethambutol. However, this was only suitable for 40% of the patients based on DST. On average, DR-TB patients were changed to 4 (IQR 3-5) active drugs after 1.5 months (IQR 1-2). After treatment adjustment, the treatment duration was 8 months (IQR 2-11). Four (22%) patients with DR-TB received treatment for >18 months. In total, sixteen (53%) patients died during 24 months of follow-up. Conclusions We found high concordance for rifampicin and isoniazid DST between the Minsk and Copenhagen laboratories, whereas discrepancies for second-line drugs were more pronounced. For patients with DR-TB, treatment was often insufficient and relevant adjustments delayed. This example from Minsk, Belarus, underlines two crucial points in the management of DR-TB: the urgent need for implementation of rapid molecular DSTs and availability of second-line drugs in all DR-TB high-burden settings. Carefully designed individualized treatment regimens in accordance with DST patterns will likely improve patients' outcome and reduce transmission with drug-resistant Mycobacterium tuberculosis strains.
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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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Cheng S, Hide M, Pheng SH, Kerléguer A, Delvallez G, Sam S, Mao TE, Nguyen TVA, Bañuls AL. Resistance to Second-Line Anti-TB Drugs in Cambodia: A Phenotypic and Genetic Study. Infect Drug Resist 2021; 14:1089-1104. [PMID: 33762833 PMCID: PMC7982564 DOI: 10.2147/idr.s289907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/06/2021] [Indexed: 12/25/2022] Open
Abstract
Background Due to the emergence of Mycobacterium tuberculosis (M.tb) clinical isolates resistant to most potent first-line drugs (FLD), second-line drugs (SLD) are being prescribed more frequently. We explore the genetic characteristics and molecular mechanisms of M.tb isolates phenotypically resistant to SLD, including pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) isolates. Methods Drug-resistant (DR) M.tb isolates collected from 2012 to 2017 were tested using sequencing and phenotypic drug susceptibility testing. Genotypes were determined to explore their links with SLD resistance patterns. Results Of the 272 DR M.tb isolates, 6 non-multidrug resistant (non-MDR) isolates were fluoroquinolones (FQ)-resistant, 3 were XDR and 16 were pre-XDR (14 resistant to FQ and 2 to second-line injectable drugs). The most frequent mutations in FQ-resistant and second-line injectable drugs resistant isolates were gyrA D94G (15/23) and rrs a1401g (3/5), respectively. Seventy-five percent of pre-XDR isolates and 100% of XDR isolates harbored mutations conferring resistance to pyrazinamide. All XDR isolates belonged to the Beijing genotype, of which one, named XDR+, was resistant to all drugs tested. One cluster including pre-XDR and XDR isolates was observed. Conclusion This is the first description of SLD resistance in Cambodia. The data suggest that the proportion of XDR and pre-XDR isolates remains low but is on the rise compared to previous reports. The characterization of the XDR+ isolate in a patient who refused treatment underlines the risk of transmission in the population. In addition, genotypic results show, as expected, that the Beijing family is the main involved in pre-XDR and XDR isolates and that the spread of the Beijing pre-XDR strain is capable of evolving into XDR strain. This study strongly indicates the need for rapid interventions in terms of diagnostic and treatment to prevent the spread of the pre-XDR and XDR strains and the emergence of more resistant ones.
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Affiliation(s)
- Sokleaph Cheng
- Institut Pasteur du Cambodge and Ministry of Health, Phnom Penh, Cambodia.,Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Mallorie Hide
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
| | - Sok Heng Pheng
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Alexandra Kerléguer
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Gauthier Delvallez
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophan Sam
- Cambodian Health Committee, Phnom Penh, Cambodia
| | - Tan Eang Mao
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Thi Van Anh Nguyen
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Martinique, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
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Shi J, Tao B, Li Z, Song H, Wu J, Qiu B, Wang J. Diagnostic Performance of GeneChip for the Rapid Detection of Drug-Resistant Tuberculosis in Different Subgroups of Patients. Infect Drug Resist 2021; 14:597-608. [PMID: 33633456 PMCID: PMC7900445 DOI: 10.2147/idr.s297725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Objective Drug-resistant tuberculosis (DR-TB) is a growing problem worldwide. The rapid drug susceptibility test (DST) of DR-TB enables the timely administration of a chemotherapy regimen that effectively treats DR-TB. GeneChip has been reported as a novel molecular diagnostic tool for rapid diagnosis but has limited data on the performance of subgroup patients with DR-TB. This study aims to assess the diagnostic value of GeneChip in patients with different sexes, ages, treatment histories, treatment outcomes, and places of residence. Methods We recruited newly registered sputum smear-positive pulmonary TB patients from January 2011 to September 2020 in Lianyungang City, Jiangsu Province, China. We applied both GeneChip and DST to measure drug resistance to rifampin (RIF) and isoniazid (INH). The kappa value, sensitivity, specificity, and agreement rate (AR) were calculated. We also applied a Classification and Regression Tree to explore factors related to the performance of GeneChip. Results We observed that sex, age, treatment history, treatment outcomes, and drug resistance type were significantly associated with the performance of GeneChip. For RIF resistance, there was significant accordance in young patients (kappa: 0.79) and cases with the treatment failure outcome (kappa: 0.92). For multidrug resistance (MDR), there was significant accordance in young cases (kappa: 0.77). Compared with previously treated patients, the newly treated patients had a significantly higher AR in detecting RIF resistance (0.97 vs 0.92), INH resistance (0.95 vs 0.89), and MDR (0.98 vs 0.92). The overall sensitivity, specificity, AR and kappa value for the diagnosis of MDR-TB were 0.70 (95% CI: 0.63–0.70), 0.99 (95% CI: 0.98–0.99), 0.98 (95% CI: 0.97–0.98), and 0.72 (95% CI: 0.67–0.78), respectively. Conclusion We observed a high concordance between GeneChip and DST among TB patients with different characteristics, indicating that GeneChip can be a potential alternative tool for rapid MDR-TB detection.
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Affiliation(s)
- Jinyan Shi
- Department of Clinical Laboratory, The Fourth People's Hospital of Lianyungang, Lianyungang, Jiangsu, People's Republic of China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
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Gopie F, Commiesie E, Baldi S, Kamst M, Kaur D, de Lange W, Pinas P, Stijnberg D, Wongsokarijo M, Zijlmans C, de Zwaan R, van Soolingen D, Vreden S, de Vries G. Should treatment of low-level rifampicin mono-resistant tuberculosis be different? J Clin Tuberc Other Mycobact Dis 2021; 23:100222. [PMID: 33598570 PMCID: PMC7869001 DOI: 10.1016/j.jctube.2021.100222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Rifampicin resistant tuberculosis (RR-TB) was frequently detected in Suriname after the introduction of Xpert MTB/RIF in 2012. Subsequent phenotypic drug-susceptibility testing (DST) was not conclusive at that moment, while RR-TB patients treated with first-line tuberculostatics had good treatment outcome. In our study, we analysed this interesting observation. Methods We collected demographic and clinical characteristics and treatment outcome of TB patients from May 2012-December 2018 and performed a univariate and multivariate analysis to assess possible associations with resistance to rifampicin. Secondly, we conducted whole genome sequencing on all available Mycobacterium tuberculosis isolates that had a rifampicin resistance in the Xpert MTB/RIF test and performed phenotypic DST on selected isolates. Findings RR-TB was detected in 59 (9.6%) patients confirmed by Xpert. These patients were treated with rifampicin-containing regimens in most (88%) of the cases. In all 32 samples examined, a D435Y mutation in the rpoB gene was identified; only one isolate revealed an additional isoniazid mutation. Phenotypic DST indicated low-level rifampicin resistance. In multivariate analysis, the Creole ethnicity was a factor associated with rifampicin resistance (aOR 3.5; 95%CI 1.9–6.4). The treatment success rate for patients with RR-TB (78.0%) was comparable to the treatment outcome in non-RR-TB patients 77.8%. Interpretation This study confirms a low-level rifampicin mono-resistance in TB patients of Suriname. These patients could benefit from a first-line regimen with high dose rifampicin (or rifabutin), rather than from the lengthy treatment regimens for rifampicin-resistant and multi-drug resistant TB, a concept of stratified medicine also advocated for the treatment of TB. Funding None.
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Affiliation(s)
- F.A. Gopie
- Academic Hospital Paramaribo, Paramaribo, Suriname
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
- Corresponding author at: Academic Hospital Paramaribo, Paramaribo, Suriname.
| | - E. Commiesie
- National Tuberculosis Program, Paramaribo, Suriname
| | - S. Baldi
- Central Laboratory, Paramaribo, Suriname
| | - M. Kamst
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. Kaur
- Massachusetts Supranational TB Reference Laboratory, University of Massachusetts Medical School, Jamaica Plane, MA, USA
| | - W.C.M. de Lange
- Department Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, the Netherlands
| | - P.S. Pinas
- Central Laboratory, Paramaribo, Suriname
| | - D. Stijnberg
- National Tuberculosis Program, Paramaribo, Suriname
| | | | - C.W.R. Zijlmans
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - R. de Zwaan
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - G. de Vries
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Guo Y, Cao X, Yang J, Wu X, Liu Y, Wan B, Hu L, Wang H, Yu F. Rifampin-resistance-associated mutations in the rifampin-resistance-determining region of the rpoB gene of Mycobacterium tuberculosis clinical isolates in Shanghai, PR China. J Med Microbiol 2021; 70. [PMID: 33507146 DOI: 10.1099/jmm.0.001317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Resistance to rifampin (RIF) in Mycobacterium tuberculosis infection is associated with mutations in the rpoB gene coding for the β-subunit of RNA polymerase. The contribution of various rpoB mutations to the development and level of RIF resistance remains elusive.Hypothesis/Gap Statement. Various rpoB mutations may be associated with differential levels of RIF resistance.Aim. This study aimed to investigate the relationship between specific rpoB mutations and the MICs of RIF and rifabutin (RFB) against M. tuberculosis.Methodology. Of the 195 clinical isolates, 105 and 90 isolates were randomly selected from isolates resistant to RIF and sensitive to RIF, respectively. The MICs of 12 agents for M. tuberculosis isolates were determined using commercial Sensititre M. tuberculosis MIC plates and the broth microdilution method. Strains were screened for rpoB mutations by DNA extraction, rpoB gene amplification and DNA sequence analysis.Results. One hundred isolates (95.24 %) were found to have mutations in the RIF-resistance-determining region (RRDR) of the rpoB gene. Three rpoB mutations were identified in 90 RIF-susceptible isolates. Out of 105 isolates, 86 (81.90 %) were cross-resistant to both RIF and RFB. The most frequent mutation occurred at codons 450 and 445. We also found a novel nine-nucleotide (ATCATGCAT) deletion (between positions 1543 and 1551) in the rpoB gene in two strains (1.90 %) with resistance to RIF, but susceptibility to RFB. In addition, the mutation frequency at codon 450 was significantly higher in RIF-resistant/RFB-resistant (RIFR/RFBR) strains than in RIFR/RFBS strains (75.58 % versus 21.05 %, P<0.01), whereas the mutation frequency at codon 435 was significantly lower in RIFR/RFBR strains than in RIFR/RFBS strains (1.16 % versus 26.32 %, P<0.01).Conclusion. Our data support previous findings, which reported that various rpoB mutations are associated with differential levels of RIF resistance. The specific mutations in the rpoB gene in RIFR/RFBR isolates differed from those in the RIFR/RFBS isolates. A novel deletion mutation in the RRDR might be associated with resistance to RIF, but not to RFB. Further clinical studies are required to investigate the efficacy of RFB in the treatment of infections caused by M. tuberculosis strains harbouring these mutations.
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Affiliation(s)
- Yinjuan Guo
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China.,Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Xingwei Cao
- Jiangxi Provincial Key laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, 330000, PR China
| | - Jinghui Yang
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Xiaocui Wu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Yin Liu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Baoshan Wan
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Longhua Hu
- Jiangxi Provincial Key laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, 330000, PR China
| | - Hongxiu Wang
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, PR China
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Gil H, Margaryan H, Azamat I, Ziba B, Bayram H, Nazirov P, Gomez D, Singh J, Zayniddin S, Parpieva N, Achar J. Accuracy of molecular drug susceptibility testing amongst tuberculosis patients in Karakalpakstan, Uzbekistan. Trop Med Int Health 2021; 26:421-427. [PMID: 33406316 DOI: 10.1111/tmi.13543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES In this retrospective study, we evaluated the diagnostic accuracy of molecular tests (MT) for the detection of DR-TB, compared to the gold standard liquid-based drug susceptibility testing (DST) in Karakalpakstan. METHODS A total of 6670 specimens received in the Republican TB No 1 Hospital Laboratory of Karakalpakstan between January and July 2017 from new and retreatment patients were analysed. Samples were tested using Xpert MTB/RIF and line probe assays (LPA) for the detection of mutations associated with resistance. The sensitivity and specificity of MTs were calculated relative to results based on DST. RESULTS The accuracy of MT for detection of rifampicin resistance was high, with sensitivity and specificity over 98%. However, we observed reduced sensitivity of LPA for detection of resistance; 86% for isoniazid (95% CI 82-90%), 86% for fluoroquinolones (95% CI 68-96%), 70% for capreomycin (95% CI 46-88%) and 23% for kanamycin (95% CI 13-35%). CONCLUSIONS We show that MTs are a useful tool for rapid and safe diagnosis of DR-TB; however, clinicians should be aware of their limitations. Although detection of rifampicin resistance was highly accurate, our data suggest that resistance mutations circulating in the Republic of Karakalpakstan for other drugs were not detected by the methods used here. This merits further investigation.
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Affiliation(s)
- Horacio Gil
- Médecins Sans Frontières (MSF), Nukus, Uzbekistan
| | | | | | | | - Halmuratov Bayram
- Republican TB No 1 Hospital Laboratory of Karakalpakstan, Nukus, Uzbekistan
| | - Pirimqul Nazirov
- Republican TB No 1 Hospital of Karakalpakstan, Nukus, Uzbekistan
| | | | | | | | - Nargiza Parpieva
- National Tuberculosis Reference Laboratory, Tashkent, Uzbekistan
| | - Jay Achar
- MSF, London, UK.,Karolinska Institutet, Stockholm, Sweden
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Ajbani K, Kazi M, Agrawal U, Jatale R, Soman R, Sunavala A, Shetty A, Rodrigues C. Evaluation of CSF pyrosequencing to diagnose tuberculous meningitis: A retrospective diagnostic accuracy study. Tuberculosis (Edinb) 2021; 126:102048. [PMID: 33421910 DOI: 10.1016/j.tube.2020.102048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/23/2020] [Accepted: 12/27/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND We evaluated the performance of pyrosequencing, a genotypic test which detects TB and XDR-defining mutations within 6 h, directly on CSF samples for diagnosing TB meningitis(TBM). METHODS This retrospective, diagnostic accuracy study was conducted in Hinduja hospital, Mumbai from May-2017 to May-2019. 107 consecutive patients with physician-suspected TBM for whom CSF pyrosequencing was requested were screened. Seven patients with incomplete data were excluded. Diagnostic accuracy of pyrosequencing was compared with Xpert MTB/Rif and TBMGIT (TB Mycobacterial Growth Indicator Tube) culture against the uniform case definition of definite or probable TBM. Susceptibility concordance rate of pyrosequencing with TBMGIT culture and Xpert MTB/Rif was determined. RESULTS The study cohort comprised of 100 patients[Definite(n = 33), Probable(n = 20), Possible(n = 30), Alternative(n = 17)] with 50% males[median age(years):38(Range:2-87)]. Against the uniform case definition, pyrosequencing had 98·11%(95%CI 89·93-99·95; n = 52/53) sensitivity and 97·79%(86·31-99·67; n = 44/45) negative predictive value(NPV) compared with 43.39%(29·83-57·72; n = 23/53,p < 0.0001) sensitivity and 61.04%(55·31-66·48; n = 47/77) NPV for Xpert MTB/Rif and 45·28%(31·56-59·55; n = 24/53,p < 0.0001) sensitivity and 61·84%(55·92-67·43; n = 47/76) NPV for TBMGIT culture. Susceptibility concordance rate of pyrosequencing with phenotypic Drug Susceptibility Testing was 91.3%(n = 21/23) and with Xpert MTB/Rif was 95·45%(n = 21/22). CONCLUSION CSF pyrosequencing is significantly more sensitive than Xpert MTB/Rif and TBMGIT culture for diagnosing TBM. Additionally, it facilitates early therapeutic decision-making by providing information on XDR-defining mutations.
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Affiliation(s)
- Kanchan Ajbani
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Mubin Kazi
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Umang Agrawal
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Raj Jatale
- Department of Research, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Rajeev Soman
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Ayesha Sunavala
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Anjali Shetty
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
| | - Camilla Rodrigues
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Veer Savarkar Marg, Mahim (West), Mumbai, 400016, India.
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Chiang CY, Lin CJ. Principles of chemotherapy for tuberculosis in national tuberculosis programmes of low- and middle-income countries. Indian J Tuberc 2020; 67:S16-S22. [PMID: 33308663 DOI: 10.1016/j.ijtb.2020.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
National tuberculosis programmes (NTPs) should aim for achieving a very high proportion of cure of all tuberculosis (TB) cases. Ineffective chemotherapy of TB that keeps a substantial proportion of patients alive without cure may amplify resistance during treatment and promote transmission of TB. In 2017, the World Health Organization (WHO) recommended that in patients who require TB retreatment, the retreatment regimen that comprised 8 months of isoniazid, rifampicin and ethambutol supplemented by streptomycin for the initial 2 months, and pyrazinamide for the initial 3 months (2SHRZE/HRZE/5HRE) should no longer be prescribed and drug susceptibility testing (DST) should be conducted to inform the choice of treatment regimen. While GeneXpert MTB/RIF assay may detect rifampicin resistance, it does not detect isoniazid resistance. A 6-month regimen consisting of rifampicin, isoniazid, pyrazinamide and ethambutol may be used for the treatment of previously treated cases in whom rifampicin resistance has been excluded but DST of isoniazid is not available. WHO recommended to treat isoniazid-resistant, rifampicin-susceptible TB (Hr-TB) with rifampicin, ethambutol, pyrazinamide and levofloxacin for a duration of 6 months. In several low- and middle-income countries, the majority of Hr-TB cases are detected after the initiation of treatment with first-line regimens. If patients have an unsatisfactory response to first-line treatment with persistent positive sputum, modification of regimens needs to be done very carefully. Adding a fluoroquinolone in cases with undetected rifampicin resistance runs the risk of acquired fluoroquinolone resistance. Recently, WHO advises NTPs to phase out the injectable-containing short regimen for multidrug-resistant and rifampicin-resistant TB (MDR-/RR-TB) and recommends that the preferred treatment option is a shorter, all-oral, bedaquiline-containing regimen. WHO emphasizes that access to rapid DST, especially for ruling out fluoroquinolone resistance, is required before starting the bedaquiline-containing shorter regimen. The problem is that access to rapid DST for ruling out fluoroquinolone resistance is limited in low- and middle-income countries. The use of WHO-recommended bedaquiline-containing regimens in the treatment of MDR-/RR-TB patients with undetected resistance to fluoroquinolones runs a high risk of acquired bedaquiline resistance, especially in settings with a high prevalence of fluoroquinolone resistance. It is crucial to mitigate the risks of both primary and acquired resistance of rifampicin, fluoroquinolone and bedaquiline by rational design of regimens and effective management of TB patients.
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Affiliation(s)
- Chen-Yuan Chiang
- International Union Against Tuberculosis and Lung Disease, Paris, France; Division of Pulmonary Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Chou-Jui Lin
- Division of Pulmonary Medicine, Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
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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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Huo F, Ma Y, Li S, Xue Y, Shang Y, Dong L, Li Y, Pang Y. Specific gyrA Gene Mutations Correlate with High Prevalence of Discordant Levofloxacin Resistance in Mycobacterium tuberculosis Isolates from Beijing, China. J Mol Diagn 2020; 22:1199-1204. [DOI: 10.1016/j.jmoldx.2020.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/25/2020] [Accepted: 06/18/2020] [Indexed: 11/26/2022] Open
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Feuerriegel S, Kohl TA, Utpatel C, Andres S, Maurer FP, Heyckendorf J, Jouet A, Badalato N, Foray L, Fouad Kamara R, Conteh OS, Supply P, Niemann S. Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB. Eur Respir J 2020; 57:13993003.01796-2020. [DOI: 10.1183/13993003.01796-2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/25/2020] [Indexed: 11/05/2022]
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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] [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.
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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
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Van Deun A, Decroo T, Kya Jai Maug A, Hossain MA, Gumusboga M, Mulders W, Ortuño-Gutiérrez N, Lynen L, de Jong BC, Rieder HL. The perceived impact of isoniazid resistance on outcome of first-line rifampicin-throughout regimens is largely due to missed rifampicin resistance. PLoS One 2020; 15:e0233500. [PMID: 32421749 PMCID: PMC7233532 DOI: 10.1371/journal.pone.0233500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/06/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Meta-analyses on impact of isoniazid-resistant tuberculosis informed the World Health Organization recommendation of a levofloxacin-strengthened rifampicin-based regimen. We estimated the effect of initial rifampicin resistance (Rr) and/or isoniazid resistance (Hr) on treatment failure or relapse. We also determined the frequency of missed initial and acquired Rr to estimate the impact of true Hr. METHODS Retrospective analysis of 7291 treatment episodes with known initial isoniazid and rifampicin status obtained from individual patient databases maintained by the Damien Foundation Bangladesh over 20 years. Drug susceptibility test results were confirmed by the programme's designated supra-national tuberculosis laboratory. To detect missed Rr among isolates routinely classified as Hr, rpoB gene sequencing was done randomly and on a sample selected for suspected missed Rr. RESULTS Initial Hr caused a large recurrence excess after the 8-month regimen for new cases (rifampicin for two months), but had little impact on rifampicin-throughout regimens: (6 months, new cases; 3.8%; OR 0.8, 95%CI:0.3,2.8; 8 months, retreatment cases: 7.3%, OR 1.8; 95%CI:1.3,2.6). Rr was missed in 7.6% of randomly selected "Hr" strains. Acquired Rr was frequent among recurrences on rifampicin-throughout regimens, particularly after the retreatment regimen (31.9%). It was higher in mono-Hr (29.3%; aOR 3.5, 95%CI:1.5,8.5) and poly-Hr (53.3%; aOR 10.2, 95%CI 4.4,23.7) than in susceptible tuberculosis, but virtually absent after the 8-month new case regimen. Comparing Bangladesh (low Rr prevalence) with a high Rr prevalence setting,true Hr corrected for missed Rr caused only 2-3 treatment failures per 1000 TB cases (of whom 27% were retreatments) in both. CONCLUSIONS Our analysis reveals a non-negligible extent of misclassifying as isoniazid resistance of what is actually missed multidrug-resistant tuberculosis. Recommending for such cases a "strengthened" regimen containing a fluoroquinolone provokes a direct route to extensive resistance while offering little benefit against the minor role of true Hr tuberculosis in rifampicin-throughout first-line regimen.
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Affiliation(s)
- Armand Van Deun
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Research Foundation Flanders, Brussels, Belgium
| | | | | | - Murid Gumusboga
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wim Mulders
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Lutgarde Lynen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C. de Jong
- Biomedical Department, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hans L. Rieder
- Tuberculosis Consultant Services, Kirchlindach, Switzerland
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Systematic Review of Whole-Genome Sequencing Data To Predict Phenotypic Drug Resistance and Susceptibility in Swedish Mycobacterium tuberculosis Isolates, 2016 to 2018. Antimicrob Agents Chemother 2020; 64:AAC.02550-19. [PMID: 32122893 DOI: 10.1128/aac.02550-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/21/2020] [Indexed: 11/20/2022] Open
Abstract
In this retrospective study, whole-genome sequencing (WGS) data generated on an Ion Torrent platform was used to predict phenotypic drug resistance profiles for first- and second-line drugs among Swedish clinical Mycobacterium tuberculosis isolates from 2016 to 2018. The accuracy was ∼99% for all first-line drugs and 100% for four second-line drugs. Our analysis supports the introduction of WGS into routine diagnostics, which might, at least in Sweden, replace phenotypic drug susceptibility testing in the future.
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50
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A pilot study: VereMTB detection kit for rapid detection of multidrug-resistant mycobcterium tuberculosis in clinical sputum samples. PLoS One 2020; 15:e0228312. [PMID: 32150745 PMCID: PMC7062499 DOI: 10.1371/journal.pone.0228312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/31/2019] [Indexed: 11/19/2022] Open
Abstract
The performance of VereMTBTM Detection Kit for detection of multidrug-resistant tuberculosis (MDR-TB) was validated by using 124 sputum samples. Comparing with MGIT culture, the sensitivity and specificity of VereMTB Detection Kit for MTBC detection were 97.0% and 98.3%, respectively. Compared with MGIT DST, the sensitivity and specificity of VereMTB Detection Kit for RIF resistance detection were 85.7% and 93.9%, respectively, and the sensitivity and specificity of VereMTB Detection Kit for INH resistance detection were 75.0% and 95.7%, respectively. 6 NTM samples were also detected and identified correctly. The VereMTB Detection Kit can detect MDR-TB rapidly and accurately in sputum samples from TB suspects.
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