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Feng L, He W, Song Z, Zhao B, Teng C, Liu E, Zhu H, Pei S, Liu L, Song Y, Zheng Y, Liu X, Zhao Y, Ou X. Drug-Resistant Profiles and Genetic Diversity of Mycobacterium Tuberculosis Revealed by Whole-Genome Sequencing in Hinggan League of Inner Mongolia, China. Infect Drug Resist 2024; 17:3089-3100. [PMID: 39050828 PMCID: PMC11268717 DOI: 10.2147/idr.s466197] [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: 02/28/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
Background Tuberculosis remains a major public health concern in China, with varying prevalence and drug resistance profiles across regions. This study explores the genetic diversity and drug-resistant profiles of MTB strains in Hinggan League, a high TB burden in Inner Mongolia, China. Methods This population-based retrospective study, encompassing all culture-positive TB cases from Jun. 2021 to Jun. 2023 in Hinggan League. Drug resistant profiles and genetic diversity of MTB strains were assessed using phenotypic drug susceptibility testing and whole-genome sequencing. Risk factors associated with drug resistance were analyzed using univariate and multivariate logistic regression models. Results A total of 211 MTB strains were recovered successfully and included into final analysis. Lineage 2.2.1 (88.6%, 187/211) was the dominant sub-lineage, followed by lineage 4.5 (7.1%, 15/211) and lineage 4.4 (4.3%, 9/211). MTB strains exhibited the highest resistance rates to isoniazid (16.1%, 34/211), followed by rifampicin (10.0, 21/211). In addition, the MTB strains also showed relatively high rates of resistance against new and repurposed anti-TB drugs, with resistant rates of 2.4% (5/211) to delamanid and 1.9% (4/211) to bedaquiline. Overall, 25.6% (54/211) of MTB strains were DR-TB, and 14 MTB strains met the definition of MDR-TB, including 7 strains of simple-MDR-TB, 5 of pre-XDR-TB, and 2 of XDR-TB. Genetic analysis revealed that the dominant mutations of isoniazid-, rifampin-, ethambutol-, levofloxacin-/moxifloxacin-, and ethionamide- resistance were katG_Ser315Thr(46.4%), rpoB_Ser450Leu (47.4%), embB_Met306Val (25.0%), gyrA_Asp94Ala (40.0%), and fabG1_c15t (42.9%), respectively. Previously treated patients (AOR = 2.015, 95% CI: 1.052-4.210) and male patients (AOR = 3.858, 95% CI: 1.416-10.511) were identified as independent risk factors associated with DR-TB. Conclusion Our study offers crucial insights into the genetic diversity and drug-resistant profiles of TB strains circulating in Hinggan League. These findings are valuable for DR-TB surveillance and for guiding treatment regimens and public health interventions in the region.
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Affiliation(s)
- Liping Feng
- Department of Microbiology, Hinggan League Center for Disease Control and Prevention, Ulanhot, 137499, People’s Republic of China
| | - Wencong He
- Department of Clinical Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, 100176, People’s Republic of China
| | - Zexuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Bing Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Chong Teng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Eryong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Hanfang Zhu
- Department of Microbiology, Hinggan League Center for Disease Control and Prevention, Ulanhot, 137499, People’s Republic of China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, 100191, People’s Republic of China
| | - Lina Liu
- Blood Transfusion Department, Hinggan League People’s Hospital, Ulanhot, 137400, People’s Republic of China
| | - Yuanyuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Yang Zheng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiangyi Liu
- Department of Clinical Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, 100176, People’s Republic of China
| | - Yanlin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xichao Ou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
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2
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Sanchini A, Lanni A, Giannoni F, Mustazzolu A. Exploring diagnostic methods for drug-resistant tuberculosis: A comprehensive overview. Tuberculosis (Edinb) 2024; 148:102522. [PMID: 38850839 DOI: 10.1016/j.tube.2024.102522] [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: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Despite available global efforts and funding, Tuberculosis (TB) continues to affect a considerable number of patients worldwide. Policy makers and stakeholders set clear goals to reduce TB incidence and mortality, but the emergence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) complicate the reach of these goals. Drug-resistance TB needs to be diagnosed rapidly and accurately to effectively treat patients, prevent the transmission of MDR-TB, minimise mortality, reduce treatment costs and avoid unnecessary hospitalisations. In this narrative review, we provide a comprehensive overview of laboratory methods for detecting drug resistance in MTB, focusing on phenotypic, molecular and other drug susceptibility testing (DST) techniques. We found a large variety of methods used, with the BACTEC MGIT 960 being the most common phenotypic DST and the Xpert MTB/RIF being the most common molecular DST. We emphasise the importance of integrating phenotypic and molecular DST to address issues like resistance to new drugs, heteroresistance, mixed infections and low-level resistance mutations. Notably, most of the analysed studies adhered to the outdated definition of XDR-TB and did not consider the pre-XDR definition, thus posing challenges in aligning diagnostic methods with the current landscape of TB resistance.
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Affiliation(s)
| | - Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
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3
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Miotto P, Cirillo DM, Schön T, Köser CU. The exceptions that prove the rule-a historical view of bedaquiline susceptibility. Genome Med 2024; 16:39. [PMID: 38481348 PMCID: PMC10935885 DOI: 10.1186/s13073-024-01311-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 07/08/2024] Open
Abstract
In the accompanying study, Nimmo and colleagues estimated the dates of emergence of mutations in mmpR5 (Rv0678), the most important resistance gene to the anti-tuberculosis drug bedaquiline, in over 3500 geographically diverse Mycobacterium tuberculosis genomes. This provided important insights to improve the design and analysis of clinical trials, as well as the World Health Organization catalogue of resistance mutations, the global reference for interpreting genotypic antimicrobial susceptibility testing results.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Thomas Schön
- Department of Infectious Diseases, Region Östergötland, Linköping University Hospital, Linköping, Sweden
- Division of Infection and Inflammation, Institute of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Kalmar County Hospital, Linköping University, Kalmar, Sweden
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK.
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4
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Xia H, Song Y, Zheng Y, Zhou Y, Ou X, Wang S, Zhao B, Zhao Y. Proficiency testing for drug susceptibility testing of Mycobacterium tuberculosis complex using commercial broth microdilution plate in China in 2021. J Glob Antimicrob Resist 2024; 36:230-236. [PMID: 38072239 DOI: 10.1016/j.jgar.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/31/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVES The characteristic and performance of Broth microdilution (BMD) plates for drug susceptibility of Mycobacterium tuberculosis have not been systematically evaluated in China. This study was designed to review the key information and assess the performance of BMD plates by analysis of proficiency testing results. METHODS We retrospectively analysed the proficiency testing results of phenotypic drug susceptibility testing (PT-DST) of 45 laboratories using BMD plates in China in 2021. Critical information, such as drug layout, concentration range of each drug, plate storage conditions and duration, operating procedures, and interpretation criteria for binary results were compared. The performance was also analysed. RESULTS Eight types of BMD plates produced by four manufactures were reported. The drug layout, number of drugs on plates, and concentration range varied a lot between different plates. The total sensitivity and specificity of BMD plates for drug susceptibility of Mycobacterium tuberculosis to ten drugs (isoniazid (INH), rifampin (RIF), kanamycin (KAM), amikacin (AM), levofloxacin (LFX), moxifloxacin (MFX), bedaquiline (BDQ), linezolid (LZD), clofazimine (CFZ), and delamanid (DLM)) were 93.9% (95% CI 92.-94.9) and 99.1% (95% CI 98.8-99.3), respectively. The lowest sensitivity was 84.8% (95% CI 80.3-88.4) for LFX and 86.4% (95% CI 82.5-89.6) for MFX, or 87.5% (95% CI 84.2-90.2) for Y1 plate and 87.9% (95% CI 83.5-91.1) for T plate. The lowest specificity was 94.4% (95% CI 91.4-96.4) for DLM, or 97.9% (95% CI 96.8-98.7) for B3 plate. CONCLUSION Commercial BMD plates in China showed varied drug layouts and operational procedures, indicating the urgency of standardization. The lower performance for some drugs showed the low quality of the plates utilized or lack of proficiency of lab staffs in operating and interpreting results.
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Affiliation(s)
- Hui Xia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanyuan Song
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zheng
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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5
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Negi A, Perveen S, Gupta R, Singh PP, Sharma R. Unraveling Dilemmas and Lacunae in the Escalating Drug Resistance of Mycobacterium tuberculosis to Bedaquiline, Delamanid, and Pretomanid. J Med Chem 2024; 67:2264-2286. [PMID: 38351709 DOI: 10.1021/acs.jmedchem.3c01892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Delamanid, bedaquiline, and pretomanid have been recently added in the anti-tuberculosis (anti-TB) treatment regimens and have emerged as potential solutions for combating drug-resistant TB. These drugs have proven to be effective in treating drug-resistant TB when used in combination. However, concerns have been raised about the eventual loss of these drugs due to evolving resistance mechanisms and certain adverse effects such as prolonged QT period, gastrointestinal problems, hepatotoxicity, and renal disorders. This Perspective emphasizes the properties of these first-in-class drugs, including their mechanism of action, pharmacokinetics/pharmacodynamics profiles, clinical studies, adverse events, and underlying resistance mechanisms. A brief coverage of efforts toward the generation of best-in-class leads in each class is also provided. The ongoing clinical trials of new combinations of these drugs are discussed, thus providing a better insight into the use of these drugs while designing an effective treatment regimen for resistant TB cases.
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Affiliation(s)
- Anjali Negi
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Summaya Perveen
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ria Gupta
- Natural Products and Medicinal Chemistry, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Parvinder Pal Singh
- Natural Products and Medicinal Chemistry, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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6
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [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: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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7
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Brunner VM, Fowler PW. Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis. Microb Genom 2024; 10:001187. [PMID: 38315172 PMCID: PMC10926696 DOI: 10.1099/mgen.0.001187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase of M. tuberculosis, using over 70 000 M. tuberculosis genomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests more power to investigate the association of putative CMs with resistance-conferring mutations. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higher in vitro growth densities, and hence presumably with higher fitness, in resistant samples in the more virulent M. tuberculosis lineage 2. Our results suggest the association of CM presence with significantly higher in vitro growth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasize the integral role of CMs and lineage affiliation in resistance spread and increases the urgency of antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics for M. tuberculosis infections to not only improve patient outcomes but also prevent the spread of resistant strains.
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Affiliation(s)
| | - Philip W. Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
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8
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Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Fowler PW, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Calisto Matias DVL, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TEA, Pinhata JMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson ER, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Smith G, Kohl TA, Solano W, Spitaleri A, Steyn AJC, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker AS, Walker TM, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. Nat Commun 2024; 15:488. [PMID: 38216576 PMCID: PMC10786857 DOI: 10.1038/s41467-023-44325-5] [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: 03/06/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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9
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [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: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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10
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Grazian C. Clustering minimal inhibitory concentration data through Bayesian mixture models: An application to detect Mycobacterium tuberculosis resistance mutations. Stat Methods Med Res 2023; 32:2423-2439. [PMID: 37920984 PMCID: PMC10710010 DOI: 10.1177/09622802231211010] [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] [Indexed: 11/04/2023]
Abstract
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers are attempting to contrast it by developing both new antibiotics and patient-specific treatments. In the second case, whole-genome sequencing has had a huge impact in two ways: first, it is becoming cheaper and faster to perform whole-genome sequencing, and this makes it competitive with respect to standard phenotypic tests; second, it is possible to statistically associate the phenotypic patterns of resistance to specific mutations in the genome. Therefore, it is now possible to develop catalogues of genomic variants associated with resistance to specific antibiotics, in order to improve prediction of resistance and suggest treatments. It is essential to have robust methods for identifying mutations associated to resistance and continuously updating the available catalogues. This work proposes a general method to study minimal inhibitory concentration distributions and to identify clusters of strains showing different levels of resistance to antimicrobials. Once the clusters are identified and strains allocated to each of them, it is possible to perform regression method to identify with high statistical power the mutations associated with resistance. The method is applied to a new 96-well microtiter plate used for testing Mycobacterium tuberculosis.
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Affiliation(s)
- Clara Grazian
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
- ARC Training Centre in Data Analytics for Resources and Environments (DARE), Australia
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11
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Carter J. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. RESEARCH SQUARE 2023:rs.3.rs-3378915. [PMID: 37886522 PMCID: PMC10602118 DOI: 10.21203/rs.3.rs-3378915/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis; however, molecular diagnostics to date have focused largely on first-line drugs and predicting binary susceptibilities. We used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration in 15,211 Mycobacterium tuberculosis patient isolates from 23 countries across five continents. This identified 492 unique MIC-elevating variants across thirteen drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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12
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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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13
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Nilgiriwala K, Rabodoarivelo MS, Hall MB, Patel G, Mandal A, Mishra S, Andrianomanana FR, Dingle K, Rodger G, George S, Crook DW, Hoosdally S, Mistry N, Rakotosamimanana N, Iqbal Z, Grandjean Lapierre S, Walker TM. Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction. J Clin Microbiol 2023; 61:e0157822. [PMID: 36815861 PMCID: PMC10035339 DOI: 10.1128/jcm.01578-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited, and targeted molecular assays are vulnerable to emerging resistance mutations. Improved protocols for direct-from-sputum Mycobacterium tuberculosis sequencing would accelerate access to comprehensive drug susceptibility testing and molecular typing. We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively analyzed 60 acid-fast bacilli smear-positive clinical sputum samples in India and Madagascar. A diversity of semiquantitative smear positivity-level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms on genomic read depth, drug susceptibility prediction performance, and typing accuracy. M. tuberculosis was identified by direct sputum sequencing in 45/51 samples using Illumina, 34/38 were identified using MinION-monoplex sequencing, and 20/24 were identified using MinION-multiplex sequencing. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ samples on MinION produced higher read depth than Illumina (P < 0.05) and MinION multiplexing (P < 0.01). No significant differences in sensitivity and specificity of drug susceptibility predictions were seen across sequencing modalities or within each technology when stratified by smear grade. Illumina sequencing from sputum accurately identified 1/8 (rifampin) and 6/12 (isoniazid) resistant samples, compared to 2/3 (rifampin) and 3/6 (isoniazid) accurately identified with Nanopore monoplex. Lineage agreement levels between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina), and 100% (MinION-multiplex). M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.
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Affiliation(s)
| | | | - Michael B Hall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Grishma Patel
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | - Ayan Mandal
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | - Shefali Mishra
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | | | - Kate Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Gillian Rodger
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Sophie George
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Sarah Hoosdally
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Nerges Mistry
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | | | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Simon Grandjean Lapierre
- Mycobacteriology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier, Université de Montréal, Montréal, Québec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
| | - Timothy M Walker
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- Oxford University, Clinical Research Unit, Ho Chi Minh City, Vietnam
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14
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Near-field sensor array with 65-GHz CMOS oscillators can rapidly and comprehensively evaluate drug susceptibility of Mycobacterium. Sci Rep 2023; 13:3825. [PMID: 36882499 PMCID: PMC9990582 DOI: 10.1038/s41598-023-30873-9] [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: 09/27/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a major clinical problem. Because Mycobacterium, the causative agent of tuberculosis, are slow-growing bacteria, it takes 6-8 weeks to complete drug susceptibility testing, and this delay contributes to the development of MDR-TB. Real-time drug resistance monitoring technology would be effective for suppressing the development of MDR-TB. In the electromagnetic frequency from GHz to THz regions, the spectrum of the dielectric response of biological samples has a high dielectric constant owing to the relaxation of the orientation of the overwhelmingly contained water molecule network. By measuring the change in dielectric constant in this frequency band in a micro-liquid culture of Mycobacterium, the growth ability can be detected from the quantitative fluctuation of bulk water. The 65-GHz near-field sensor array enables a real-time assessment of the drug susceptibility and growth ability of Mycobacterium bovis (BCG). We propose the application of this technology as a potential new method for MDR-TB testing.
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15
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Wang W, Li S, Ge Q, Guo H, Shang Y, Ren W, Wang Y, Xue Z, Lu J, Pang Y. Determination of critical concentration for drug susceptibility testing of Mycobacterium tuberculosis against para-aminosalicylic acid with clinical isolates with thyA, folC and dfrA mutations. Ann Clin Microbiol Antimicrob 2022; 21:48. [PMCID: PMC9637297 DOI: 10.1186/s12941-022-00537-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Abstract
Background & Objectives
Accurate determination of antimicrobial resistance profiles is of great importance to formulate optimal regimens against multidrug-resistant tuberculosis (MDR-TB). Although para-aminosalicylic acid (PAS) has been widely used clinically, the reliable testing methods for PAS susceptibility were not established. Herein, we aimed to establish critical test concentration for PAS on the Mycobacterial Growth Indicator Tube (MGIT) 960 in our laboratory settings.
Methods
A total of 102 clinical isolates were included in this study, including 82 wild-type and 20 resistotype isolates. Minimum inhibitory concentration (MIC) was determined by MGIT 960. Whole-genome sequencing was used to identify the mutation patterns potentially conferring PAS resistance. Sequence alignment and structure modelling were carried out to analyze potential drug-resistant mechanism of folC mutant.
Results
Overall, the Minimum inhibitory concentration (MIC) distribution demonstrated excellent separation between wild-type and resistotype isolates. The wild-type population were all at least 1 dilution below 4 μg/ml, and the resistotype population were no lower than 4 μg/ml, indicating that 4 μg/ml was appropriate critical concentration to separate these two populations. Of 20 mutant isolates, 12 (60.0%) harbored thyA mutations, 2 (10%) had a mutation on upstream of dfrA, and the remaining isolates had folC mutations. Overall, thyA and folC mutations were scattered throughout the whole gene without any one mutation predominating. All mutations within thyA resulted in high-level resistance to PAS (MIC > 32 μg/ml); whereas the MICs of isolates with folC mutations exhibited great diversity, ranged from 4 to > 32 μg/ml, and sequence and structure analysis partially provided the possible reasons for this diversity.
Conclusions
We propose 4 μg/ml as tentative critical concentration for MGIT 960. The major mechanism of PAS resistance is mutations within thyA and folC in MTB isolations. The whole-gene deletion of thyA locus confers high-level resistance to PAS. The diversity of many distinct mutations scattered throughout the full-length folC gene challenges the PCR-based mutation analysis for PAS susceptibility.
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16
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Transmission and Drug Resistance Genotype of Multidrug-Resistant or Rifampicin-Resistant Mycobacterium tuberculosis in Chongqing, China. Microbiol Spectr 2022; 10:e0240521. [PMID: 36214695 PMCID: PMC9604020 DOI: 10.1128/spectrum.02405-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multidrug-resistant or rifampicin-resistant tuberculosis (MDR/RR-TB) is a global barrier for the Stop TB plan. To identify risk factors for treatment outcome and cluster transmission of MDR/RR-TB, whole-genome sequencing (WGS) data of isolates from patients of the Chongqing Tuberculosis Control Institute were used for phylogenetic classifications, resistance predictions, and cluster analysis. A total of 223 MDR/RR-TB cases were recorded between 1 January 2018 and 31 December 2020. Elderly patients and those with lung cavitation are at increased risk of death due to MDR/RR-TB. A total of 187 MDR/RR strains were obtained from WGS data; 152 were classified as lineage 2 strains. Eighty (42.8%) strains differing by a distance of 12 or fewer single nucleotide polymorphisms were classified as 20 genomic clusters, indicating recent transmission. Patients infected with lineage 2 strains or those with occupations listed as "other" are significantly associated with a transmission cluster of MDR/RR-TB. Analysis of resistant mutations against first-line tuberculosis drugs found that 76 (95.0%) of all 80 strains had the same mutations within each cluster. A total of 55.0% (44 of 80) of the MDR/RR-TB strains accumulated additional drug resistance mutations along the transmission chain, especially against fluoroquinolones (63.6% [28 of 44]). Recent transmission of MDR/RR strains is driving the MDR/RR-TB epidemics, leading to the accumulation of more serious resistance along the transmission chains. IMPORTANCE The drug resistance molecular characteristics of MDR/RR-TB were elucidated by genome-wide analysis, and risk factors for death by MDR/RR-TB were identified in combination with patient information. Cluster characteristics of MDR/RR-TB in the region were analyzed by genome-wide analysis, and risk factors for cluster transmission (recent transmission) were analyzed. These analyses provide reference for the prevention and treatment of MDR/RR-TB in Chongqing.
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17
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Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis. Eur Respir J 2022; 60:2200239. [PMID: 35301246 PMCID: PMC9556810 DOI: 10.1183/13993003.00239-2022] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. While there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, it is necessary to measure the epidemiological cut-off values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-tuberculosis compounds, including bedaquiline and delamanid, derived from 20 637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex, and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression. The proposed ECOFF/ECVs were then validated by comparing with the MIC distributions of high-confidence genetic variants that confer resistance and with qualitative drug susceptibility tests obtained via the Mycobacterial Growth Indicator Tube (MGIT) system or Microscopic-Observation Drug Susceptibility (MODS) assay. These ECOFF/ECVs will inform and encourage the more widespread adoption of broth microdilution: this is a cheap culture-based method that tests the susceptibility of 12-14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.
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Affiliation(s)
- The CRyPTIC Consortium
- For a list of all members of the CRyPTIC Consortium and their affiliations, please see the section at the end of this article
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18
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Puyén ZM, Santos-Lázaro D, Vigo AN, Coronel J, Alarcón MJ, Cotrina VV, Moore DAJ. Evaluation of the broth microdilution plate methodology for susceptibility testing of Mycobacterium tuberculosis in Peru. BMC Infect Dis 2022; 22:705. [PMID: 36002805 PMCID: PMC9399989 DOI: 10.1186/s12879-022-07677-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a communicable, preventable and curable disease caused by the bacterium Mycobacterium tuberculosis (MTB). Peru is amongst the 30 countries with the highest burden of multidrug-resistant tuberculosis (MDR-TB) worldwide. In the fight against drug-resistant tuberculosis, the UKMYC6 microdilution plate was developed and validated by the CRyPTIC project. The objective of the study was to evaluate the use of the broth microdilution (BMD) plate methodology for susceptibility testing of drug-resistant MTB strains in Peru. METHODS MTB strains isolated between 2015 and 2018 in Peru were used. 496 nationally-representative strains determined as drug-resistant by the routine 7H10 Agar Proportion Method (APM) were included in the present study. The Minimum Inhibitory Concentration (MIC) of 13 antituberculosis drugs were determined for each strain using the UKMYC6 microdilution plates. Diagnostic agreement between APM and BMD plate methodology was determined for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. Phenotypes were set using binary (or ternary) classification based on Epidemiological cut-off values (ECOFF/ECV) proposed by the CRyPTIC project. Whole Genome Sequencing (WGS) was performed on strains with discrepant results between both methods. RESULTS MIC distributions were determined for 13 first- and second-line anti-TB drugs, including new (bedaquiline, delamanid) and repurposed (clofazimine, linezolid) agents. MIC results were available for 80% (397/496) of the strains at 14 days and the remainder at 21 days. The comparative analysis determined a good agreement (0.64 ≤ k ≤ 0.79) for the drugs rifampicin, ethambutol, ethionamide and kanamycin, and the best agreement (k > 0.8) for isoniazid and levofloxacin. Overall, 12% of MIC values were above the UKMYC6 plate dilution ranges, most notably for the drugs rifampicin and rifabutin. No strain presented MICs higher than the ECOFF/ECV values for the new or repurposed drugs. Discrepant analysis using genotypic susceptibility testing by WGS supported half of the results obtained by APM (52%, 93/179) and half of those obtained by BMD plate methodology (48%, 86/179). CONCLUSIONS The BMD methodology using the UKMYC6 plate allows the complete susceptibility characterization, through the determination of MICs, of drug-resistant MTB strains in Peru. This methodology shows good diagnostic performances for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. It also allows for the characterization of MICs for other drugs used in previous years against tuberculosis, as well as for new and repurposed drugs recently introduced worldwide.
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Affiliation(s)
- Zully M Puyén
- Instituto Nacional de Salud, Lima, Perú.
- Escuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Perú.
| | | | | | | | | | | | - David A J Moore
- Universidad Peruana Cayetano Heredia, Lima, Perú
- London School of Hygiene & Tropical Medicine, London, UK
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Diagnostic Capacities for Multidrug-Resistant Tuberculosis in the World Health Organization European Region: Action is Needed by all Member States. J Mol Diagn 2022; 24:1189-1194. [PMID: 35964846 DOI: 10.1016/j.jmoldx.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 12/28/2022] Open
Abstract
The World Health Organization (WHO) recently revised its guidelines for rapid diagnosis of drug-resistant tuberculosis (TB). This study aimed to investigate if TB reference diagnostic services are prepared to support these revisions. An online survey was performed among 44 TB National Reference Laboratories (NRLs) in the WHO European Region. Questions addressed the use of WHO-recommended molecular techniques for the diagnosis of drug-resistant TB, the techniques applied to investigate antimicrobial resistance, and questions on quality assurance. Among 35 of 44 (80%) participating NRLs, 29 of 35 (83%) reported using the GeneXpert platform as the initial test to detect Mycobacterium tuberculosis complex and rifampicin resistance. Five laboratories reported using another WHO-recommended, moderate-complexity, automated nucleic acid amplification test for detection of Mycobacterium tuberculosis complex and resistance to rifampicin and isoniazid. Most (32 of 35; 91%) NRLs reported the capacity to test second-line drugs that have been in clinical use for many years (fluoroquinolones, linezolid, and injectable agents). Only 23 of 35 (66%) and 21 of 35 (60%) NRLs reported the capacity to test bedaquiline and clofazimine. Further efforts will be needed to improve the availability of quality-controlled testing against WHO Group A and Group B drugs. Earlier considerations on the scale-up of diagnostic capacities should be enforced as part of future approval processes for new antimycobacterial agents.
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A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics. PLoS Biol 2022; 20:e3001721. [PMID: 35944069 PMCID: PMC9363010 DOI: 10.1371/journal.pbio.3001721] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured in a single assay. It is the largest matched phenotypic and genotypic dataset for M. tuberculosis to date. Here, we provide a summary detailing the breadth of data collected, along with a description of how the isolates were selected, collected, and uniformly processed in CRyPTIC partner laboratories across 23 countries. The compendium contains 6,814 isolates resistant to at least 1 drug, including 2,129 samples that fully satisfy the clinical definitions of rifampicin resistant (RR), multidrug resistant (MDR), pre-extensively drug resistant (pre-XDR), or extensively drug resistant (XDR). The data are enriched for rare resistance-associated variants, and the current limits of genotypic prediction of resistance status (sensitive/resistant) are presented by using a genetic mutation catalogue, along with the presence of suspected resistance-conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid, and linezolid. Finally, a case study of rifampicin monoresistance demonstrates how this compendium could be used to advance our genetic understanding of rare resistance phenotypes. The data compendium is fully open source and it is hoped that it will facilitate and inspire future research for years to come.
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21
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Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. PLoS Biol 2022; 20:e3001755. [PMID: 35944070 PMCID: PMC9363015 DOI: 10.1371/journal.pbio.3001755] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
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22
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Variants in Bedaquiline-Candidate-Resistance Genes: Prevalence in Bedaquiline-Naive Patients, Effect on MIC, and Association with Mycobacterium tuberculosis Lineage. Antimicrob Agents Chemother 2022; 66:e0032222. [PMID: 35758754 PMCID: PMC9295546 DOI: 10.1128/aac.00322-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Studies have shown that variants in bedaquiline-resistance genes can occur in isolates from bedaquiline-naive patients. We assessed the prevalence of variants in all bedaquiline-candidate-resistance genes in bedaquiline-naive patients, investigated the association between these variants and lineage, and the effect on phenotype. We used whole-genome sequencing to identify variants in bedaquiline-resistance genes in isolates from 509 bedaquiline treatment naive South African tuberculosis patients. A phylogenetic tree was constructed to investigate the association with the isolate lineage background. Bedaquiline MIC was determined using the UKMYC6 microtiter assay. Variants were identified in 502 of 509 isolates (98.6%), with the highest (85%) prevalence of variants in the Rv0676c (mmpL5) gene. We identified 36 unique variants, including 19 variants not reported previously. Only four isolates had a bedaquiline MIC equal to or above the epidemiological cut-off value of 0.25 μg/mL. Phylogenetic analysis showed that 14 of the 15 variants observed more than once occurred monophyletically in one Mycobacterium tuberculosis (sub)lineage. The bedaquiline MIC differed between isolates belonging to lineage 2 and 4 (Fisher's exact test, P = 0.0004). The prevalence of variants in bedaquiline-resistance genes in isolates from bedaquiline-naive patients is high, but very few (<2%) isolates were phenotypically resistant. We found an association between variants in bedaquiline resistance genes and Mycobacterium tuberculosis (sub)lineage, resulting in a lineage-dependent difference in bedaquiline phenotype. Future studies should investigate the impact of the presence of variants on bedaquiline-resistance acquisition and treatment outcome.
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Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S, Iqbal Z. Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol 2022; 23:147. [PMID: 35791022 PMCID: PMC9254434 DOI: 10.1186/s13059-022-02714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/20/2022] [Indexed: 12/30/2022] Open
Abstract
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).
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Affiliation(s)
- Martin Hunt
- EMBL-EBI, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Swargam S, Kumari I, Kumar A, Pradhan D, Alam A, Singh H, Jain A, Devi KR, Trivedi V, Sarma J, Hanif M, Narain K, Ehtesham NZ, Hasnain SE, Ahmad S. MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis. FRONTIERS IN BIOINFORMATICS 2022; 1:805338. [PMID: 36303799 PMCID: PMC9580932 DOI: 10.3389/fbinf.2021.805338] [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: 10/30/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequencing (WGS) provides a comprehensive tool to analyze the bacterial genomes for genotype–phenotype correlations, diversity of single-nucleotide variant (SNV), and their evolution and transmission. Several online pipelines and standalone tools are available for WGS analysis of Mycobacterium tuberculosis (Mtb) complex (MTBC). While they facilitate the processing of WGS data with minimal user expertise, they are either too general, providing little insights into bacterium-specific issues such as gene variations, INDEL/synonymous/PE-PPE (IDP family), and drug resistance from sample data, or are limited to specific objectives, such as drug resistance. It is understood that drug resistance and lineage-specific issues require an elaborate prioritization of identified variants to choose the best target for subsequent therapeutic intervention. Mycobacterium variant pipeline (MycoVarP) addresses these specific issues with a flexible battery of user-defined and default filters. It provides an end-to-end solution for WGS analysis of Mtb variants from the raw reads and performs two quality checks, viz, before trimming and after alignments of reads to the reference genome. MycoVarP maps the annotated variants to the drug-susceptible (DS) database and removes the false-positive variants, provides lineage identification, and predicts potential drug resistance. We have re-analyzed the WGS data reported by Advani et al. (2019) using MycoVarP and identified some additional variants not reported so far. We conclude that MycoVarP will help in identifying nonsynonymous, true-positive, drug resistance–associated variants more effectively and comprehensively, including those within the IDP of the PE-PPE/PGRS family, than possible from the currently available pipelines.
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Affiliation(s)
- Sandeep Swargam
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, India
- Department of Molecular Medicine, School of Interdisciplinary Sciences, Jamia Hamdard, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Amit Kumar
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Dibyabhaba Pradhan
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Harpreet Singh
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Vishal Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Jogesh Sarma
- Department of Pulmonary Medicine, Guwahati, India
| | | | - Kanwar Narain
- ICMR-Regional Medical Research Centre, Dibrugarh, India
| | - Nasreen Zafar Ehtesham
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Seyed Ehtesham Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, India
- Department of Life Sciences, Sharda University, Greater NOIDA, India
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Rifampicin-Resistant Mycobacterium tuberculosis in Hunan, China, Revealed by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0154321. [PMID: 35171016 PMCID: PMC8849054 DOI: 10.1128/spectrum.01543-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To gain a deep insight into the additional drug-resistant profiles, genetic diversity, and transmission dynamics of rifampicin-resistant tuberculosis (RR-TB) circulating in Hunan province, drug susceptibility testing and whole-genome-sequencing were performed among RR-TB strains collected from Jan. 2013 to Jun. 2018 in Hunan province. A total of 124 RR-TB strains were recovered successfully and included into the final analysis. Lineage 2.2.1 was the dominant sublineage, accounting for 72.6% (90/124), followed by lineage 4.5 (11.3%, 14/124), lineage 4.4 (8.1%, 10/124), lineage 4.2 (6.5%, 8/124) and lineage 2.2.2 (1.6%, 2/124). Overall, 83.1% (103/124) and 3.2% (4/124) of RR-TB were MDR-TB and XDR-TB, respectively. Nearly 30% of RR-TB isolates were resistant to fluoroquinolones, and 26.6% (33/124) were pre-XDR-TB. Moreover, 30.6% (38/124) of RR-TB strains were identified as phenotypically resistance to pyrazinamide. Totally, 17 clusters containing 48 (38.7%, 48/124) RR-TB strains were identified, ranging in size from 2 to 10 isolates. No significant difference was detected in clustering rate between lineage 2 and lineage 4 (χ2 = 0.027, P = 0.870). Our study revealed the complexity of RR-TB strains circulating in Hunan province with complex additional drug-resistant profile and relatively higher clustering rates. Comprehensive information based on WGS should be used to guide the design of treatment regimens and tailor public interventions. IMPORTANCE Comprehensive information such as genetic background and drug-resistant profile of MTB strains could help to tailor public interventions. However, these data are limited in Hunan province, one of the provinces with high-TB burden in China. So, this study aimed to provide us with deep insight into the molecular epidemiology of RR-TB isolates circulating in Hunan province by combining phenotypic drug susceptibility testing and whole-genome sequencing. To our knowledge, this is the first study to use whole-genome sequencing data of RR-TB strains spanning more than 5 years for molecular epidemiology analysis in Hunan province, which allows us to identify genetic background information and clustered strains more accurately. Our study revealed the complexity of RR-TB strains circulating in Hunan province with complex additional drug-resistant profile and relatively higher clustering rates. Comprehensive information based on WGS should be used to guide the design of treatment regimens and tailor public interventions.
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Mbelele PM, Utpatel C, Sauli E, Mpolya EA, Mutayoba BK, Barilar I, Dreyer V, Merker M, Sariko ML, Swema BM, Mmbaga BT, Gratz J, Addo KK, Pletschette M, Niemann S, Houpt ER, Mpagama SG, Heysell SK. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac042. [PMID: 35465240 PMCID: PMC9021016 DOI: 10.1093/jacamr/dlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background Rifampicin- or multidrug-resistant (RR/MDR) Mycobacterium tuberculosis complex (MTBC) strains account for considerable morbidity and mortality globally. WGS-based prediction of drug resistance may guide clinical decisions, especially for the design of RR/MDR-TB therapies. Methods We compared WGS-based drug resistance-predictive mutations for 42 MTBC isolates from MDR-TB patients in Tanzania with the MICs of 14 antibiotics measured in the Sensititre™ MycoTB assay. An isolate was phenotypically categorized as resistant if it had an MIC above the epidemiological-cut-off (ECOFF) value, or as susceptible if it had an MIC below or equal to the ECOFF. Results Overall, genotypically non-wild-type MTBC isolates with high-level resistance mutations (gNWT-R) correlated with isolates with MIC values above the ECOFF. For instance, the median MIC value (mg/L) for rifampicin-gNWT-R strains was >4.0 (IQR 4.0–4.0) compared with 0.5 (IQR 0.38–0.50) in genotypically wild-type (gWT-S, P < 0.001); isoniazid-gNWT-R >4.0 (IQR 2.0–4.0) compared with 0.25 (IQR 0.12–1.00) among gWT-S (P = 0.001); ethionamide-gNWT-R 15.0 (IQR 10.0–20.0) compared with 2.50 (IQR; 2.50–5.00) among gWT-S (P < 0.001). WGS correctly predicted resistance in 95% (36/38) and 100% (38/38) of the rifampicin-resistant isolates with ECOFFs >0.5 and >0.125 mg/L, respectively. No known resistance-conferring mutations were present in genes associated with resistance to fluoroquinolones, aminoglycosides, capreomycin, bedaquiline, delamanid, linezolid, clofazimine, cycloserine, or p-amino salicylic acid. Conclusions WGS-based drug resistance prediction worked well to rule-in phenotypic drug resistance and the absence of second-line drug resistance-mediating mutations has the potential to guide the design of RR/MDR-TB regimens in the future.
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Affiliation(s)
- Peter M. Mbelele
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Corresponding author. E-mail:
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Elingarami Sauli
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Emmanuel A. Mpolya
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Beatrice K. Mutayoba
- Ministry of Health, National AIDS Control Program, Department of Preventive Services, Dodoma, Tanzania
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | | | | | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Kennedy K. Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Michel Pletschette
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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Bateson A, Ortiz Canseco J, McHugh TD, Witney AA, Feuerriegel S, Merker M, Kohl TA, Utpatel C, Niemann S, Andres S, Kranzer K, Maurer FP, Ghodousi A, Borroni E, Cirillo DM, Wijkander M, Toro JC, Groenheit R, Werngren J, Machado D, Viveiros M, Warren RM, Sirgel F, Dippenaar A, Köser CU, Sun E, Timm J. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1685-1693. [PMID: 35260883 PMCID: PMC9155602 DOI: 10.1093/jac/dkac070] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives To develop a robust phenotypic antimicrobial susceptibility testing (AST) method with a correctly set breakpoint for pretomanid (Pa), the most recently approved anti-tuberculosis drug. Methods The Becton Dickinson Mycobacterial Growth Indicator Tube™ (MGIT) system was used at six laboratories to determine the MICs of a phylogenetically diverse collection of 356 Mycobacterium tuberculosis complex (MTBC) strains to establish the epidemiological cut-off value for pretomanid. MICs were correlated with WGS data to study the genetic basis of differences in the susceptibility to pretomanid. Results We observed ancient differences in the susceptibility to pretomanid among various members of MTBC. Most notably, lineage 1 of M. tuberculosis, which is estimated to account for 28% of tuberculosis cases globally, was less susceptible than lineages 2, 3, 4 and 7 of M. tuberculosis, resulting in a 99th percentile of 2 mg/L for lineage 1 compared with 0.5 mg/L for the remaining M. tuberculosis lineages. Moreover, we observed that higher MICs (≥8 mg/L), which probably confer resistance, had recently evolved independently in six different M. tuberculosis strains. Unlike the aforementioned ancient differences in susceptibility, these recent differences were likely caused by mutations in the known pretomanid resistance genes. Conclusions In light of these findings, the provisional critical concentration of 1 mg/L for MGIT set by EMA must be re-evaluated. More broadly, these findings underline the importance of considering the global diversity of MTBC during clinical development of drugs and when defining breakpoints for AST.
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Affiliation(s)
- Anna Bateson
- Centre for Clinical Microbiology, University College London, Royal Free Campus, London, UK
| | - Julio Ortiz Canseco
- Centre for Clinical Microbiology, University College London, Royal Free Campus, London, UK
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, Royal Free Campus, London, UK
| | - Adam A. Witney
- Institute of Infection and Immunity, St George’s, University of London, London, UK
| | - Silke Feuerriegel
- 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
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Katharina Kranzer
- Department of Clinical Research, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Biomedical Research & Training Institute, Harare, Zimbabwe
- Division of Infectious & Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany
| | - Florian P Maurer
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arash Ghodousi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Daniela Maria Cirillo
- IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Maria Wijkander
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Juan C. Toro
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Ramona Groenheit
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Jim Werngren
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Robin M. Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Frederick Sirgel
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anzaan Dippenaar
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Juliano Timm
- TB Alliance, New York City, NY, USA
- Corresponding author. E-mail:
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Strong Increase in Moxifloxacin Resistance Rate among Multidrug-Resistant Mycobacterium tuberculosis Isolates in China, 2007 to 2013. Microbiol Spectr 2021; 9:e0040921. [PMID: 34851179 PMCID: PMC8635133 DOI: 10.1128/spectrum.00409-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We designed this study to determine the trend of moxifloxacin resistance among multidrug-resistant tuberculosis (MDR-TB) patients from 2007 to 2013 in China to inform the composition of multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB) treatment regimens. We assessed moxifloxacin resistance among MDR-TB isolates collected in national drug resistance surveys in 2007 and 2013 that included 3,634 smear-positive and 7,206 culture-positive pulmonary tuberculosis patients, respectively. Moxifloxacin susceptibility was examined by a Mycobacterium growth indicator tube (MGIT) 960 for the 2007 isolates, and by the minimum inhibitory concentration (MIC) method for the 2013 isolates, at both breakpoints 0.5 and 2.0 μg/mL. Risk factors were explored through multivariable log-binominal regression analysis. Mutations in gyrA and gyrB for part of the isolates were also studied through sequencing. Of 401 MDR strains isolated in 2007, moxifiloxacin resistance could be determined for 319 (79.6%): 41 (12.9%) and 10 (3.1%) were resistant at 0.5 and 2.0 μg/mL, respectively. Of 365 MDR strains isolated in 2013, 338 (92.6%) could be analyzed: 140 (41.4%) and 79 (23.4%) were resistant at 0.5 and 2.0 μg/mL. For patients in 2007, no characteristics were significantly associated with moxifloxacin resistance. For patients in 2013, patients aged ≥60 years (adjusted prevalence ratio [aPR], 1.46; 95% confidence interval [CI], 1.10 to 1.93) were more likely to have resistance at 0.5 μg/mL, whereas those residing in eastern China compared to those in central China had an increased risk of resistance at both 0.5 (aPR, 1.85; 95% CI, 1.38 to 2.48) and 2.0 μg/mL (aPR, 2.14; 95% CI, 1.35 to 3.40). Sequencing results were obtained for 245 and 266 MDR-TB isolates in 2007 and 2013, respectively. In total, 34 of 38 (89.5%) and 89 of 104 (85.6%) of 2007 and 2013 moxifloxacin-resistant (0.5 μg/mL) MDR-TB strains had mutations in the gyrA and gyrB gene, respectively. Asp94Gly was the most common mutation among 2007 (11 of 38, 28.9%) and 2013 isolates (24 of 104, 23.1%) and conferred high-level moxifloxacin resistance. Moxifloxacin resistance among MDR-TB patients in China increased from modest to high from 2007 to 2013. Moxifloxacin should be used carefully as a potentially effective drug for composing MDR/RR-TB regimens especially for elderly patients in China. Individual susceptibility testing especially rapid molecular-based assays should be conducted to confirm the susceptibility to moxifloxacin. IMPORTANCE China is one of the high-burden countries for multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB). Moxifloxacin is one of the critical antituberculosis drugs for MDR/RR-TB treatment. Susceptibility to moxifloxacin is therefore very important to compose effective regimens and to provide protection against development of resistance of companion drugs such as bedaquiline and linezolid. There are, however, no nationally representative data on moxifloxacin resistance among MDR/RR-TB cases in China. Therefore, we assessed the resistance prevalence for moxifloxacin among MDR-TB strains isolated in national drug resistance surveys in 2007 and 2013 that covered 72 sites around the country. We demonstrate that the prevalence of moxifloxacin resistance in MDR-TB isolates increased from modest to high, which should prompt the national tuberculosis program to use moxifloxacin cautiously in second-line regimens to treat MDR/RR-TB unless susceptibility can be laboratory-confirmed.
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Ismail N, Rivière E, Limberis J, Huo S, Metcalfe JZ, Warren RM, Van Rie A. Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis. THE LANCET MICROBE 2021; 2:e604-e616. [PMID: 34796339 PMCID: PMC8597953 DOI: 10.1016/s2666-5247(21)00175-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background Methods Findings Interpretation Funding
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Vargas R, Freschi L, Spitaleri A, Tahseen S, Barilar I, Niemann S, Miotto P, Cirillo DM, Köser CU, Farhat MR. Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex. Antimicrob Agents Chemother 2021; 65:e0116421. [PMID: 34460306 PMCID: PMC8522733 DOI: 10.1128/aac.01164-21] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance among bacterial pathogens poses a major global health threat. Mycobacterium tuberculosis complex (MTBC) is estimated to have the highest resistance rates of any pathogen globally. Given the low growth rate and the need for a biosafety level 3 laboratory, the only realistic avenue to scale up drug susceptibility testing (DST) for this pathogen is to rely on genotypic techniques. This raises the fundamental question of whether a mutation is a reliable surrogate for phenotypic resistance or whether the presence of a second mutation can completely counteract its effect, resulting in major diagnostic errors (i.e., systematic false resistance results). To date, such epistatic interactions have only been reported for streptomycin that is now rarely used. By analyzing more than 31,000 MTBC genomes, we demonstrated that the eis C-14T promoter mutation, which is interrogated by several genotypic DST assays endorsed by the World Health Organization, cannot confer resistance to amikacin and kanamycin if it coincides with loss-of-function (LoF) mutations in the coding region of eis. To our knowledge, this represents the first definitive example of antibiotic reversion in MTBC. Moreover, we raise the possibility that mmpR (Rv0678) mutations are not valid markers of resistance to bedaquiline and clofazimine if these coincide with an LoF mutation in the efflux pump encoded by mmpS5 (Rv0677c) and mmpL5 (Rv0676c).
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Affiliation(s)
- Roger Vargas
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabira Tahseen
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Ivan Barilar
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Maha R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Activity of Pyrazinamide against Mycobacterium tuberculosis at Neutral pH in PZA-S1 Minimal Medium. Antibiotics (Basel) 2021; 10:antibiotics10080909. [PMID: 34438959 PMCID: PMC8388709 DOI: 10.3390/antibiotics10080909] [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: 06/16/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Susceptibility testing of tuberculosis (TB) drugs on Mycobacterium tuberculosis is essential for the rapid detection of strains resistant to the drugs, providing the patient with effective treatment, and preventing the spread of drug-resistant TB strains. Pyrazinamide (PZA) is one of the first-line agents used for the treatment of TB. However, current phenotypic PZA susceptibility testing is unreliable due to its performance in acidic pH conditions. The aims of this study were to develop minimal media to determine the activity of PZA at a neutral pH at 37 °C to avoid problems caused by an acidic pH, which is currently used in PZA susceptibility tests, and to identify PZA-resistant M. tuberculosis in media with reproducibility and accuracy. Different minimal media were used to determine the activity of PZA using the broth microdilution method with M. tuberculosis H37Ra as the reference strain. The PZA-S1 minimal medium was proposed as the most suitable medium. PZA inhibited the growth of M. tuberculosis in PZA-S1 at a neutral pH of 6.8, which is the optimal pH for M. tuberculosis growth. Moreover, PZA showed activity at a neutral pH on a PZA-S1 agar plate when using the disk diffusion method. PZA-resistant M. tuberculosis could be identified at a neutral pH in PZA-S1 minimal medium. This study establishes valuable information regarding the testing of PZA’s susceptibility in relation to M. tuberculosis at a neutral pH of 6.8 with reliability and accuracy in clinical settings.
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He W, Liu C, Liu D, Ma A, Song Y, He P, Bao J, Li Y, Zhao B, Fan J, Cheng Q, Zhao Y. Prevalence of Mycobacterium tuberculosis resistant to bedaquiline and delamanid in China. J Glob Antimicrob Resist 2021; 26:241-248. [PMID: 34214699 DOI: 10.1016/j.jgar.2021.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/06/2021] [Accepted: 06/15/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES The new antituberculous drugs delamanid and bedaquiline form the last line of defence against drug-resistant tuberculosis (TB). Understanding the background prevalence of resistance to new drugs can help predict the lifetime of these drugs' effectiveness and inform regimen design. METHODS Mycobacterium tuberculosis without prior exposure to novel anti-TB drugs were analysed retrospectively. Drug susceptibility testing for bedaquiline, delamanid, linezolid, clofazimine and widely used first- and second-line anti-TB drugs was performed. All TB isolates with resistance to new or repurposed drugs were subjected to whole-genome sequencing to explore the molecular characteristics of resistance and to perform phylogenetic analysis. RESULTS Overall, resistance to delamanid, bedaquiline, linezolid and clofazimine was observed in 0.7% (11/1603), 0.4% (6/1603), 0.4% (7/1603) and 0.4% (6/1603) of TB isolates, respectively. Moreover, 1.0% (1/102), 2.9% (3/102), 3.9% (4/102) and 1.0% (1/102) of multidrug-resistant TB (MDR-TB) were resistant to bedaquiline, delamanid, linezolid and clofazimine, respectively. Whereas 22.2% (2/9) of extensively-drug resistant tuberculosis (XDR-TB) isolates were resistant to both delamanid and linezolid, and none was resistant to bedaquiline or clofazimine. Phylogenetic analysis showed that recent transmission occurred in two XDR-TB with additional resistance to delamanid and linezolid. None known gene mutation associated with delamanid resistance was detected. All four isolates with cross-resistance to bedaquiline and clofazimine had a detected gene mutation in Rv0678. Three of five strains with linezolid resistance had a detected gene mutation in rplC. CONCLUSION Detection of resistance to new anti-TB drugs emphasises the pressing need for intensive surveillance for such resistance before their wide usage.
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Affiliation(s)
- Wencong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dongxin Liu
- Shenzhen Third People's Hospital, Longgang District, Shenzhen City, China
| | - Aijing Ma
- Shenzhen Third People's Hospital, Longgang District, Shenzhen City, China
| | - Yimeng Song
- Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Ping He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jingjing Bao
- Fourth Hospital of Inner Mongolia Autonomous Region, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yuanchun Li
- Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jiale Fan
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qian Cheng
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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33
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Assessment of the GenoType MTBDRsl VER 2.0 compared to the phenotypic drug susceptibility testing and whole genome sequencing for the rapid detection of resistance to fluoroquinolone and second-line injectable drugs among rifampicin-resistant Mycobacterium tuberculosis isolates. Arch Microbiol 2021; 203:3989-3996. [PMID: 34032874 DOI: 10.1007/s00203-021-02387-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 04/23/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Molecular techniques have considerable advantages for rapid detection, a reduction of infectiousness, prevention of further resistance development and surveillance of drug-resistant TB. MTBDRsl VER 2.0 was used to detect resistance to second-line anti-tuberculosis drugs on 35 rifampicin-resistant M. tuberculosis (RR-MTB) isolates compared to the minimum inhibitory concentrations (MICs) and whole genome sequencing (WGS). The MTBDRsl VER 2.0 (Hain Life Science, Nehren, Germany) and WGS (San Diego, CA, USA) were performed for tracing mutations in resistant-related genes involved in resistance to fluoroquinolone (FLQ) and second-line injectable drugs. The broth microdilution method using 7H9 Middlebrook media supplemented with OADC was used to determine the MICs. The MTBDRsl VER 2.0 correctly detected 5/6 (83.3%) of FLQ-resistant strains. The MUT1 A1401G (seven strains) and MUT2 G1484T (one strain) mutations in rrs gene were detected in eight AMK/KAN/CAP-resistant strains. Four low-level KAN-resistant strains with the G-10A/C-12T (three strains) and eis C-14T (one strain) mutations in eis gene was diagnosed using MTBDRsl VER 2.0. Five errors were found in detecting resistance to kanamycin and capreomycin compared to the phenotypic drug susceptibility testing and WGS. Failling wild-type bands without improved mutant bands did not indicate a reliable resistance. WGS could efficiently resolve the discrepancies of the results. MTBDRsl showed better performance in detecting XDR strains than pre-XDR.
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34
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Veziris N, Bonnet I, Morel F, Guglielmetti L, Maitre T, Fournier Le Ray L, Sougakoff W, Robert J, Aubry A. Impact of the revised definition of extensively drug-resistant tuberculosis. Eur Respir J 2021; 58:13993003.00641-2021. [DOI: 10.1183/13993003.00641-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/06/2021] [Indexed: 12/24/2022]
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Nguyen TVA, Anthony RM, Cao TTH, Bañuls AL, Nguyen VAT, Vu DH, Nguyen NV, Alffenaar JWC. Delamanid Resistance: Update and Clinical Management. Clin Infect Dis 2021; 71:3252-3259. [PMID: 32521000 DOI: 10.1093/cid/ciaa755] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/05/2020] [Indexed: 12/29/2022] Open
Abstract
Delamanid, a-first-in-class bicyclic nitroimidazole, was recently approved for multidrug-resistant tuberculosis treatment. Pitted against the hope for improving treatment outcomes is the threat of the rapid resistance emergence. This review provides information on the mechanisms of action, resistance emergence, and drug susceptibility testing (DST) for delamanid. Delamanid resistance has already been reported in both in vitro experiments and clinical settings. Although mutations conferring delamanid resistance have been identified in fbiA, fbiB, fbiC, ddn, and fgd1 genes of Mycobacterium tuberculosis, knowledge about the molecular resistance mechanisms is limited, and there remains no standardized DST method. The rapid acquisition of delamanid resistance emphasizes the need for optimal use of new drugs, the need for drug resistance surveillance, and a comprehensive understanding of drug resistance mechanisms. Further studies are necessary to investigate genetic and phenotypic changes that determine clinically relevant delamanid resistance to help develop a rapid delamanid DST.
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Affiliation(s)
- Thi Van Anh Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, Hanoi, Vietnam
| | - Richard M Anthony
- Tuberculosis reference laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thi Thu Huyen Cao
- The National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Hanoi, Vietnam.,MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Van Anh Thi Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology of Vietnam, Hanoi, Vietnam
| | - Dinh Hoa Vu
- The National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | | | - Jan-Willem C Alffenaar
- University of Sydney, Faculty of Medicine and Health, School of Pharmacy, Sydney, Australia.,Westmead hospital, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
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36
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Grobbel HP, Merker M, Köhler N, Andres S, Hoffmann H, Heyckendorf J, Reimann M, Barilar I, Dreyer V, Hillemann D, Kalsdorf B, Kohl TA, Sanchez-Carballo P, Schaub D, Todt K, Utpatel C, Maurer FP, Lange C, Niemann S. Design of multidrug-resistant tuberculosis treatment regimens based on DNA sequencing. Clin Infect Dis 2021; 73:1194-1202. [PMID: 33900387 DOI: 10.1093/cid/ciab359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Comprehensive and reliable drug susceptibility testing (DST) is urgently needed to provide adequate treatment regimens for patients with multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB). We investigated if next generation sequencing (NGS) analysis of Mycobacterium tuberculosis complex isolates and genes implicated in drug resistance can guide the design of effective MDR/RR-TB treatment regimens. METHODS NGS-based genomic DST predictions of M. tuberculosis complex isolates from MDR/RR-TB patients admitted to a TB reference center in Germany between 01/01/2015 and 04/30/2019 were compared with phenotypic DST results of Mycobacteria growth indicator tubes (MGIT). Standardized treatment algorithms were applied to design individualized therapies based on either genomic or phenotypic DST results, and discrepancies were further evaluated by determination of minimum inhibitory drug concentrations (MIC) using Sensititre MYCOTBI and UKMYC microtiter plates. RESULTS In 70 patients with MDR/RR-TB, agreement among 1048 pairwise comparisons of genomic and phenotypic DST was 86.3%; 76 (7.2%) results were discordant, and 68 (6.5%) could not be evaluated due to presence of polymorphisms with yet unknown implications for drug resistance. Importantly, 549/561 (97.9%) predictions of drug susceptibility were phenotypically confirmed in MGIT, and 27/64 (42.2%) false positive results were linked to previously described mutations mediating a low or moderate MIC increase. Virtually all drugs (99.0%) used in combination therapies that were inferred from genomic DST, were confirmed to be susceptible by pDST. CONCLUSIONS NGS-based genomic DST can reliably guide the design of effective MDR/RR-TB treatment regimens.
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Affiliation(s)
- Hans-Peter Grobbel
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Matthias Merker
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Niklas Köhler
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, IML red GmbH, Gauting, Bavaria, Germany.,SYNLAB Gauting, SYNLAB MVZ of Human Genetics Munich, Bavaria, Germany
| | - Jan Heyckendorf
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Doris Hillemann
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Barbara Kalsdorf
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patricia Sanchez-Carballo
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Dagmar Schaub
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Katharina Todt
- Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, IML red GmbH, Gauting, Bavaria, Germany.,SYNLAB Gauting, SYNLAB MVZ of Human Genetics Munich, Bavaria, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Lange
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany.,Global TB Program, Baylor College of Medicine, Houston, TX, USA
| | - Stefan Niemann
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
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37
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Mishra B, Mohapatra PR. Occult drug resistance in tuberculosis: Emerging issues, upcoming challenges & possible solutions. Indian J Med Res 2021; 151:522-524. [PMID: 32719224 PMCID: PMC7602933 DOI: 10.4103/ijmr.ijmr_316_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Baijayantimala Mishra
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar 751 019, Odisha, India
| | - Prasanta Raghab Mohapatra
- Department of Pulmonary Medicine & Critical Care, All India Institute of Medical Sciences, Bhubaneswar 751 019, Odisha, India
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38
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Alffenaar JWC, Gumbo T, Dooley KE, Peloquin CA, Mcilleron H, Zagorski A, Cirillo DM, Heysell SK, Silva DR, Migliori GB. Integrating Pharmacokinetics and Pharmacodynamics in Operational Research to End Tuberculosis. Clin Infect Dis 2021; 70:1774-1780. [PMID: 31560376 PMCID: PMC7146003 DOI: 10.1093/cid/ciz942] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) elimination requires innovative approaches. The new Global Tuberculosis Network (GTN) aims to conduct research on key unmet therapeutic and diagnostic needs in the field of TB elimination using multidisciplinary, multisectorial approaches. The TB Pharmacology section within the new GTN aims to detect and study the current knowledge gaps, test potential solutions using human pharmacokinetics informed through preclinical infection systems, and return those findings to the bedside. Moreover, this approach would allow prospective identification and validation of optimal shorter therapeutic durations with new regimens. Optimized treatment using available and repurposed drugs may have an increased impact when prioritizing a person-centered approach and acknowledge the importance of age, gender, comorbidities, and both social and programmatic environments. In this viewpoint article, we present an in-depth discussion on how TB pharmacology and the related strategies will contribute to TB elimination.
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Affiliation(s)
- Jan-Willem C Alffenaar
- University of Sydney, Faculty of Medicine and Health, School of Pharmacy, Sydney, Australia.,Westmead Hospital, Sydney, Australia
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, USA
| | - Kelly E Dooley
- Division of Clinical Pharmacology, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Helen Mcilleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Andre Zagorski
- Management Sciences for Health, Arlington, Virginia, USA
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Scott K Heysell
- University of Virginia, Division of Infectious Diseases and International Health, Charlottesville, Virginia, USA
| | - Denise Rossato Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
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39
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Characterization of Genomic Variants Associated with Resistance to Bedaquiline and Delamanid in Naive Mycobacterium tuberculosis Clinical Strains. J Clin Microbiol 2020; 58:JCM.01304-20. [PMID: 32907992 DOI: 10.1128/jcm.01304-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of the genetic variants' role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analyzed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole-genome sequencing (WGS) data set from a collection of 4,795 MTBc clinical isolates from six countries with a high burden of tuberculosis (TB). From WGS analysis, we identified 61 and 163 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to these medicines. To characterize the role of mutations, we calculated the free energy variation upon mutations in the available protein structures of Ddn (DLM), Fgd1 (DLM), and Rv0678 (BDQ) and performed MIC assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural and phenotypic data allowed for cataloguing the mutations clearly associated with resistance to BDQ (n = 4) and DLM (n = 35), only two of which were previously described, as well as about a hundred genetic variants without any correlation with resistance. Significantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance for the development of comprehensive molecular diagnostic tools.
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40
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Tornheim JA, Starks AM, Rodwell TC, Gardy JL, Walker TM, Cirillo DM, Jayashankar L, Miotto P, Zignol M, Schito M. Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex. Clin Infect Dis 2020; 69:1631-1633. [PMID: 30883637 PMCID: PMC6792097 DOI: 10.1093/cid/ciz219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/13/2019] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis is the primary infectious disease killer worldwide, with a growing threat from multidrug-resistant cases. Unfortunately, classic growth-based phenotypic drug susceptibility testing (DST) remains difficult, costly, and time consuming, while current rapid molecular testing options are limited by the diversity of antimicrobial-resistant genotypes that can be detected at once. Next-generation sequencing (NGS) offers the opportunity for rapid, comprehensive DST without the time or cost burden of phenotypic tests and can provide useful information for global surveillance. As access to NGS expands, it will be important to ensure that results are communicated clearly, consistent, comparable between laboratories, and associated with clear guidance on clinical interpretation of results. In this viewpoint article, we summarize 2 expert workshops regarding a standardized report format, focusing on relevant variables, terminology, and required minimal elements for clinical and laboratory reports with a proposed standardized template for clinical reporting NGS results for Mycobacterium tuberculosis.
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Affiliation(s)
- Jeffrey A Tornheim
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angela M Starks
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Timothy C Rodwell
- Foundation for Innovative New Diagnostics, Geneva, Switzerland.,Division of Pulmonary, Critical Care, and Sleep Medicine, University of San Diego, California
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Canada.,Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | | | - Lakshmi Jayashankar
- Columbus Technologies, Inc. Contractor to the National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland
| | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Matteo Zignol
- Global TB Programme, World Health Organization, Geneva, Switzerland
| | - Marco Schito
- Critical Path to Tuberculosis Drug Regimens, Critical Path Institute, Tucson, Arizona
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41
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Farhat MR, Sixsmith J, Calderon R, Hicks ND, Fortune SM, Murray M. Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates. J Antimicrob Chemother 2020; 74:1477-1483. [PMID: 30793747 DOI: 10.1093/jac/dkz048] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES Drug-resistant TB remains a public health challenge. Rifamycins are among the most potent anti-TB drugs. They are known to target the RpoB subunit of RNA polymerase; however, our understanding of how rifamycin resistance is genetically encoded remains incomplete. Here we investigated rpoB genetic diversity and cross-resistance between the two rifamycin drugs rifampicin and rifabutin. METHODS We performed WGS of 1003 Mycobacterium tuberculosis clinical isolates and determined MICs of both rifamycin agents on 7H10 agar using the indirect proportion method. We generated rpoB mutants in a laboratory strain and measured their antibiotic susceptibility using the alamarBlue reduction assay. RESULTS Of the 1003 isolates, 766 were rifampicin resistant and 210 (27%) of these were rifabutin susceptible; 102/210 isolates had the rpoB mutation D435V (Escherichia coli D516V). Isolates with discordant resistance were 17.2 times more likely to harbour a D435V mutation than those resistant to both agents (OR 17.2, 95% CI 10.5-27.9, P value <10-40). Compared with WT, the D435V in vitro mutant had an increased IC50 of both rifamycins; however, in both cases to a lesser degree than the S450L (E. coli S531L) mutation. CONCLUSIONS The observation that the rpoB D435V mutation produces an increase in the IC50 of both drugs contrasts with findings from previous smaller studies that suggested that isolates with the D435V mutation remain rifabutin susceptible despite being rifampicin resistant. Our finding thus suggests that the recommended critical testing concentration for rifabutin should be revised.
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Affiliation(s)
- Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA, USA.,Division of Pulmonary and Critical Care, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, USA
| | - Jaimie Sixsmith
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | | | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA, USA.,Division of Global Health Equity, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA
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Rivière E, Whitfield MG, Nelen J, Heupink TH, Van Rie A. Identifying isoniazid resistance markers to guide inclusion of high-dose isoniazid in tuberculosis treatment regimens. Clin Microbiol Infect 2020; 26:1332-1337. [PMID: 32653663 DOI: 10.1016/j.cmi.2020.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVES Effective use of antibiotics is critical to control the global tuberculosis pandemic. High-dose isoniazid (INH) can be effective in the presence of low-level resistance. We performed a systematic literature review to improve our understanding of the differential impact of genomic Mycobacterium tuberculosis (Mtb) variants on the level of INH resistance. The following online databases were searched: PubMed, Web of Science and Embase. Articles reporting on clinical Mtb isolates with linked genotypic and phenotypic data and reporting INH resistance levels were eligible for inclusion. METHODS All genomic regions reported in the eligible studies were included in the analysis, including: katG, inhA, ahpC, oxyR-ahpC, furA, fabG1, kasA, rv1592c, iniA, iniB, iniC, rv0340, rv2242 and nat. The level of INH resistance was determined by MIC: low-level resistance was defined as 0.1-0.4 μg/mL on liquid and 0.2-1.0 μg/mL on solid media, high-level resistance as >0.4μg/mL on liquid and >1.0 μg/mL on solid media. RESULTS A total of 1212 records were retrieved of which 46 were included. These 46 studies reported 1697 isolates of which 21% (n = 362) were INH susceptible, 17% (n = 287) had low-level, and 62% (n = 1048) high-level INH resistance. Overall, 24% (n = 402) of isolates were reported as wild type and 76% (n = 1295) had ≥1 relevant genetic variant. Among 1295 isolates with ≥1 variant, 78% (n = 1011) had a mutation in the katG gene. Of the 867 isolates with a katG mutation in codon 315, 93% (n = 810) had high-level INH resistance. In contrast, only 50% (n = 72) of the 144 isolates with a katG variant not in the 315-position had high-level resistance. Of the 284 isolates with ≥1 relevant genetic variant and wild type katG gene, 40% (n = 114) had high-level INH resistance. CONCLUSIONS Presence of a variant in the katG gene is a good marker of high-level INH resistance only if located in codon 315.
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Affiliation(s)
- E Rivière
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
| | - M G Whitfield
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - J Nelen
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - T H Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - A Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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Kaniga K, Aono A, Borroni E, Cirillo DM, Desmaretz C, Hasan R, Joseph L, Mitarai S, Shakoor S, Torrea G, Ismail NA, Omar SV. Validation of Bedaquiline Phenotypic Drug Susceptibility Testing Methods and Breakpoints: a Multilaboratory, Multicountry Study. J Clin Microbiol 2020; 58:e01677-19. [PMID: 31969421 PMCID: PMC7098739 DOI: 10.1128/jcm.01677-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/13/2020] [Indexed: 02/08/2023] Open
Abstract
Drug-resistant tuberculosis persists as a major public health concern. Alongside efficacious treatments, validated and standardized drug susceptibility testing (DST) is required to improve patient care. This multicountry, multilaboratory external quality assessment (EQA) study aimed to validate the sensitivity, specificity, and reproducibility of provisional bedaquiline MIC breakpoints and World Health Organization interim critical concentrations (CCs) for categorizing clinical Mycobacterium tuberculosis isolates as susceptible/resistant to the drug. Three methods were used: Middlebrook 7H11 agar proportion (AP) assay, broth microdilution (BMD) assay, and mycobacterial growth indicator tube (MGIT) assay. Each of the five laboratories tested the 40-isolate (20 unique isolates, duplicated) EQA panel at three time points. The study validated the sensitivity and specificity of a bedaquiline MIC susceptibility breakpoint of 0.12 μg/ml for the BMD method and WHO interim CCs of 1 μg/ml for MGIT and 0.25 μg/ml for the 7H11 AP methods. Categorical agreements between observed and expected results and sensitivities/specificities for correctly identifying an isolate as susceptible/resistant were highest at the 0.25, 0.12, and 1 μg/ml bedaquiline concentrations for the AP method, BMD (frozen or dry plates), and MGIT960, respectively. At these concentrations, the very major error rates for erroneously categorizing an isolate as susceptible when it was resistant were the lowest and within CLSI guidelines. The most highly reproducible bedaquiline DST methods were MGIT960 and BMD using dry plates. These findings validate the use of standardized DST methodologies and interpretative criteria to facilitate routine phenotypic bedaquiline DST and to monitor the emergence of bedaquiline resistance.
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Affiliation(s)
- Koné Kaniga
- Johnson & Johnson Global Public Health, Titusville, New Jersey, USA
| | - Akio Aono
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-tuberculosis Association, Kiyose, Japan
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christel Desmaretz
- Department of Biomedical Sciences, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
- Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lavania Joseph
- Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-tuberculosis Association, Kiyose, Japan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Gabriela Torrea
- Department of Biomedical Sciences, Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nazir Ahmed Ismail
- Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Internal Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Shaheed V Omar
- Center for Tuberculosis, National and WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
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Nieto Ramirez LM, Quintero Vargas K, Diaz G. Whole Genome Sequencing for the Analysis of Drug Resistant Strains of Mycobacterium tuberculosis: A Systematic Review for Bedaquiline and Delamanid. Antibiotics (Basel) 2020; 9:antibiotics9030133. [PMID: 32209979 PMCID: PMC7148535 DOI: 10.3390/antibiotics9030133] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 11/24/2022] Open
Abstract
Tuberculosis (TB) remains the deadliest Infectious disease worldwide, partially due to the increasing dissemination of multidrug and extensively drug-resistant (MDR/XDR) strains. Drug regimens containing the new anti-TB drugs bedaquiline (BDQ) and delamanid (DLM) appear as a last resort for the treatment of MDR or XDR-TB. Unfortunately, resistant cases to these drugs emerged just one year after their introduction in clinical practice. Early detection of resistant strains to BDQ and DLM is crucial to preserving the effectiveness of these drugs. Here, we present a systematic review aiming to define all available genotypic variants linked to different levels of resistance to BDQ and DLM that have been described through whole genomic sequencing (WGS) and the available drug susceptibility testing methods. During the review, we performed a thorough analysis of 18 articles. BDQ resistance was associated with genetic variants in Rv0678 and atpE, while mutations in pepQ were linked to a low-level of resistance for BDQ. For DLM, mutations in the genes ddn, fgd1, fbiA, and fbiC were found in phenotypically resistant cases, while all the mutations in fbiB were reported only in DLM-susceptible strains. Additionally, WGS analysis allowed the detection of heteroresistance to both drugs. In conclusion, we present a comprehensive panel of gene mutations linked to different levels of drug resistance to BDQ and DLM.
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Affiliation(s)
| | - Karina Quintero Vargas
- Facultad de Ciencias para la Salud, Departamento de Ciencias Básicas, Universidad de Caldas, Manizales 170002, Colombia;
| | - Gustavo Diaz
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali 760031, Colombia;
- Facultad de Ciencias Naturales, Universidad Icesi, Calle 18 No. 122-135, Cali 760031, Colombia
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Kardan-Yamchi J, Kazemian H, Battaglia S, Abtahi H, Rahimi Foroushani A, Hamzelou G, Cirillo DM, Ghodousi A, Feizabadi MM. Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran. J Clin Med 2020; 9:jcm9020465. [PMID: 32046149 PMCID: PMC7073636 DOI: 10.3390/jcm9020465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Accurate and timely detection of drug resistance can minimize the risk of further resistance development and lead to effective treatment. The aim of this study was to determine the resistance to first/second-line anti-tuberculosis drugs in rifampicin/multidrug-resistant Mycobacterium tuberculosis (RR/MDR-MTB) isolates. Molecular epidemiology of strains was determined using whole genome sequencing (WGS)-based genotyping. A total of 35 RR/MDR-MTB isolates were subjected to drug susceptibility testing against first/second-line drugs using 7H9 Middlebrook in broth microdilution method. Illumina technology was used for paired-end WGS applying a Maxwell 16 Cell DNA Purification kit and the NextSeq platform. Data analysis and single nucleotide polymorphism calling were performed using MTBseq pipeline. The genome-based resistance to each drug among the resistant phenotypes was as follows: rifampicin (97.1%), isoniazid (96.6%), ethambutol (100%), levofloxacin (83.3%), moxifloxacin (83.3%), amikacin (100%), kanamycin (100%), capreomycin (100%), prothionamide (100%), D-cycloserine (11.1%), clofazimine (20%), bedaquiline (0.0%), and delamanid (44.4%). There was no linezolid-resistant phenotype, and a bedaquiline-resistant strain was wild type for related genes. The Beijing, Euro-American, and Delhi-CAS were the most populated lineage/sublineages. Drug resistance-associated mutations were mostly linked to minimum inhibitory concentration results. However, the role of well-known drug-resistant genes for D-cycloserine, clofazimine, bedaquiline, and delamanid was found to be more controversial.
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Affiliation(s)
- Jalil Kardan-Yamchi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Hamidreza Abtahi
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Gholamreza Hamzelou
- Tehran Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
- Correspondence: (A.G.); (M.M.F.)
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Correspondence: (A.G.); (M.M.F.)
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46
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Peretokina IV, Krylova LY, Antonova OV, Kholina MS, Kulagina EV, Nosova EY, Safonova SG, Borisov SE, Zimenkov DV. Reduced susceptibility and resistance to bedaquiline in clinical M. tuberculosis isolates. J Infect 2020; 80:527-535. [PMID: 31981638 DOI: 10.1016/j.jinf.2020.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/18/2019] [Accepted: 01/14/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Bedaquiline is an effective drug used to treat MDR and XDR tuberculosis, providing high cure rates in complex therapy. Mutations in the mmpR (rv0678) and atpE genes are associated with reduced susceptibility to bedaquiline and have been identified in both in vitro selected strains and clinical isolates. However, the phenotypic criteria used to detect bedaquiline resistance have yet to be established due to the collection of few clinical isolates from patients receiving bedaquiline-containing treatment regimens. METHODS One hundred eighty-two clinical isolates from 74 patients receiving bedaquiline and 163 isolates from 107 patients not exposed to bedaquiline were analysed. The bedaquiline MICs were tested using serial dilutions on 7H11 agar plates and the Bactec MGIT 960 system. The mmpR and atpE genes were sequenced by Sanger sequencing. RESULTS The 7H11 agar method allowed for rapid discrimination between mutated and wild-type isolates and between exposed and non-exposed isolates. Seventy-three percent of bedaquiline-exposed isolates, as well as 91% of isolates with mutations, had an elevated bedaquiline MIC (≥ 0.12 mg/L on 7H11 media) compared to the reference isolates (89% had an MIC ≤ 0.03 mg/L). Previously reported in vitro-selected mutants (E61D and A63P) and novel AtpE substitutions (G25S and D28G) were observed in the clinical isolates. Substitutions in codon 63 of AtpE were likely associated with a higher bedaquiline MIC. Five new cases of pre-existing reduced susceptibility to bedaquiline, accompanied by mmpR mutations in most isolates, without a history of bedaquiline treatment were identified. CONCLUSIONS Bedaquiline treatment leads to an elevated bedaquiline MIC and the acquisition of mmpR and atpE gene mutations in tuberculosis strains. The standardisation of bedaquiline phenotypic susceptibility testing is urgently needed based on observed discrepancies between our study and previous studies and differences in solid and liquid media MIC determinations.
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Affiliation(s)
- Irina V Peretokina
- The Moscow Research and Clinical Center for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russia
| | - Ludmila Yu Krylova
- The Moscow Research and Clinical Center for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russia
| | - Olga V Antonova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Margarita S Kholina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena V Kulagina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Yu Nosova
- The Moscow Research and Clinical Center for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russia
| | - Svetlana G Safonova
- The Moscow Research and Clinical Center for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russia
| | - Sergey E Borisov
- The Moscow Research and Clinical Center for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russia
| | - Danila V Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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47
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Advancing the development of new tuberculosis treatment regimens: The essential role of translational and clinical pharmacology and microbiology. PLoS Med 2019; 16:e1002842. [PMID: 31276490 PMCID: PMC6611566 DOI: 10.1371/journal.pmed.1002842] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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48
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Implementation of Semiautomated Antimicrobial Susceptibility Interpretation Hardware for Nontuberculous Mycobacteria May Overestimate Susceptibility. J Clin Microbiol 2019; 57:JCM.01756-18. [PMID: 30760530 DOI: 10.1128/jcm.01756-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/01/2019] [Indexed: 01/14/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) cause severe opportunistic infections and have a rising incidence in most settings. Rising diagnostic need must be met by national reference laboratories, which rely on Clinical and Laboratory Standards Institute (CLSI) guideline-approved manual readout of microtiter plates for antimicrobial susceptibility testing (AST) to determine antibiotic minimum inhibitory concentrations (MICs). Interpretation of these plates leads to different outcomes between laboratories. The SensiTitre Vizion digital MIC viewing system (Vizion) offers a more streamlined approach using semiautomated reading. Here, we conducted a blinded trial comparing the outcome of AST between manual readout and Vizion readout for 132 NTM isolates, amounting to 727 individual tests for antibiotic susceptibility ranging across 13 individual antibiotics with established CLSI breakpoints. From this, we calculated specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV) and the F1 value, as well as assessing major error (ME) and very major error (VME) rates. We find that Vizion-assisted AST produces significantly lower MICs (paired Wilcox signed rank test; P < 0.0001). The Vizion had an accuracy of 89,40%, producing 61 MEs (8.39%) and 16 VMEs (2.20%). The calculated specificity was 0.8370, the sensitivity was 0.9550, the PPV was 0.8460, the NPV was 0.9520, and the F1 score was 0.8970. We show that discrepant readings mostly stem from CLSI guideline breakpoints being close to, or overlapping, the MIC50 values, leading to small discrepancies crossing the breakpoint, contributing to VMEs and MEs. Using the Vizion in standard clinical diagnostics for NTM might lead to an overestimation of antibiotic susceptibility.
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Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.02175-18. [PMID: 30718257 PMCID: PMC6496161 DOI: 10.1128/aac.02175-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/25/2019] [Indexed: 01/10/2023] Open
Abstract
Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinical M. tuberculosis isolates from the Democratic Republic of the Congo, Ivory Coast, Peru, Thailand, and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD Bactec MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.
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50
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Schön T, Matuschek E, Mohamed S, Utukuri M, Heysell S, Alffenaar JW, Shin S, Martinez E, Sintchenko V, Maurer FP, Keller PM, Kahlmeter G, Köser CU. Standards for MIC testing that apply to the majority of bacterial pathogens should also be enforced for Mycobacterium tuberculosis complex. Clin Microbiol Infect 2019; 25:403-405. [PMID: 30771527 DOI: 10.1016/j.cmi.2019.01.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 11/25/2022]
Affiliation(s)
- T Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden; Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - E Matuschek
- EUCAST Development Laboratory, Växjö, Sweden
| | - S Mohamed
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - M Utukuri
- School of Clinical Medicine, University of Cambridge, UK
| | - S Heysell
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - J-W Alffenaar
- Faculty of Medicine and Health, School of Pharmacy and Westmead Hospital, University of Sydney, Sydney, NSW, Australia
| | - S Shin
- Korean Institute of Tuberculosis, Cheongju, Republic of Korea
| | - E Martinez
- Centenary Institute and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia; NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research-Pathology West, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - V Sintchenko
- Centenary Institute and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia; NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research-Pathology West, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - F P Maurer
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
| | - P M Keller
- Institute for Infectious Diseases, University of Berne, Berne, Switzerland
| | - G Kahlmeter
- EUCAST Development Laboratory, Växjö, Sweden
| | - C U Köser
- Department of Genetics, University of Cambridge, UK.
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