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Friesen I, Dreyer V, Klingmüller A, Zuber S, Hoffmann AM, Suárez I, Schütz B, Preßel T, Andres S, Niemann S, Rybniker J. First detection of a Mycobacterium tuberculosis XDR clinical isolate harbouring an RpoB I491F mutation in a Ukrainian patient treated in Germany, October 2023. Euro Surveill 2024; 29:2400420. [PMID: 38994601 PMCID: PMC11241856 DOI: 10.2807/1560-7917.es.2024.29.28.2400420] [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: 06/27/2024] [Accepted: 07/11/2024] [Indexed: 07/13/2024] Open
Abstract
This report documents the case of a Ukrainian patient infected with an extensively drug-resistant (XDR) lineage 2 Mycobacterium tuberculosis strain harbouring the rifampicin resistance mutation RpoB I491F. This mutation is not detected by routine molecular WHO-recommended rapid diagnostics, complicating the detection and treatment of these strains. The occurrence of such mutations underscores the need for enhanced diagnostic techniques and tailored treatment regimens, especially in eastern Europe where lineage 2 strains and XDR-tuberculosis are prevalent.
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Affiliation(s)
- Inna Friesen
- Research Center Borstel, Leibniz Lung Center, Supranational and National Reference Center for Mycobacteria, Borstel, Germany
| | - Viola Dreyer
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Research Center Borstel, Leibniz Lung Center, Molecular and Experimental Mycobacteriology, Borstel, Germany
| | - Angela Klingmüller
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sylvia Zuber
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Ada M Hoffmann
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Isabelle Suárez
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Beatrice Schütz
- Klinikum Dorsten, St. Elisabeth-Krankenhaus, Dorsten, Germany
| | - Tim Preßel
- Eurofins MVZ Medizinisches Labor Gelsenkirchen GmbH, Eurofins GeLaMed, Gelsenkirchen, Germany
| | - Sönke Andres
- Research Center Borstel, Leibniz Lung Center, Supranational and National Reference Center for Mycobacteria, Borstel, Germany
| | - Stefan Niemann
- These authors contributed equally to this work and share last authorship
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Research Center Borstel, Leibniz Lung Center, Molecular and Experimental Mycobacteriology, Borstel, Germany
| | - Jan Rybniker
- These authors contributed equally to this work and share last authorship
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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2
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Köser CU, Miotto P, Ismail N, Anthony RM, Utpatel C, Merker M, Niemann S, Tahseen S, Rigouts L, Rodrigues C, Omar SV, Farhat MR, Antonenka U, Hoffmann H, Cirillo DM, Schön T. A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for Mycobacterium tuberculosis complex. Eur Respir J 2024; 64:2400391. [PMID: 38991722 PMCID: PMC11237371 DOI: 10.1183/13993003.00391-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/06/2024] [Indexed: 07/13/2024]
Abstract
We echo the latest calls that have been made to increase the capacity for antimicrobial susceptibility testing (AST) for bedaquiline for the Mycobacterium tuberculosis complex [1, 2]. However, we would like to highlight the limitations of using insufficiently standardised or validated phenotypic AST methods and breakpoints as the reference standard for bedaquiline AST. Moreover, we advocate for adoption of a composite reference standard that considers genotypic AST results to minimise false-susceptible results for borderline/low-level resistance mechanisms and avoid confusion during clinical decision-making. A composite reference standard minimises false-susceptible AST results for bedaquiline https://bit.ly/3wAVvFm
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Affiliation(s)
- Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
- Both authors contributed equally
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Both authors contributed equally
| | - Nabila Ismail
- South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Richard M Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Matthias Merker
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Sabira Tahseen
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - Shaheed V Omar
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Uladzimir Antonenka
- Institute of Microbiology and Laboratory Medicine, Department IML red GmbH, WHO, Supranational Tuberculosis Reference Laboratory, Gauting, Germany
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, Department IML red GmbH, WHO, Supranational Tuberculosis Reference Laboratory, Gauting, Germany
- SYNLAB Gauting, SYNLAB MVZ Dachau GmbH, Munich, Germany
| | - 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
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Friesen I, Saluzzo F, Groenheit R, Aubry A, Anthony R, Niemann S, Mathys V, Cirillo DM. Re: 'Availability of drugs and resistance testing for BPaLM regimen for rifampicin-resistant tuberculosis in Europe' by Lange et al. Clin Microbiol Infect 2024:S1198-743X(24)00277-5. [PMID: 38851424 DOI: 10.1016/j.cmi.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Affiliation(s)
- Inna Friesen
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - Ramona Groenheit
- National and WHO Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Alexandra Aubry
- Sorbonne Université, Inserm, U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France; AP-HP, Sorbonne-Université, Hôpital Pitié-Salpêtrière, Laboratoire de Bactériologie-Hygiène, Centre National de Référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, Paris, France
| | - Richard Anthony
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Stefan Niemann
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Vanessa Mathys
- Human Bacterial Diseases Service, NRC Mycobacterium, Sciensano, Brussels, Belgium
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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Roberts LW, Malone KM, Hunt M, Joseph L, Wintringer P, Knaggs J, Crook D, Farhat MR, Iqbal Z, Omar SV. MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis. THE LANCET. MICROBE 2024:S2666-5247(24)00053-3. [PMID: 38851206 DOI: 10.1016/s2666-5247(24)00053-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND The antibiotic bedaquiline is a key component of new WHO regimens for drug-resistant tuberculosis; however, predicting bedaquiline resistance from bacterial genotypes remains challenging. We aimed to understand the genetic mechanisms of bedaquiline resistance by analysing Mycobacterium tuberculosis isolates from South Africa. METHODS For this genomic analysis, we conducted whole-genome sequencing of Mycobacterium tuberculosis samples collected at two referral laboratories in Cape Town and Johannesburg, covering regions of South Africa with a high prevalence of tuberculosis. We used the tool ARIBA to measure the status of predefined genes that are associated with bedaquiline resistance. To produce a broad genetic landscape of M tuberculosis in South Africa, we extended our analysis to include all publicly available isolates from the European Nucleotide Archive, including isolates obtained by the CRyPTIC consortium, for which minimum inhibitory concentrations of bedaquiline were available. FINDINGS Between Jan 10, 2019, and July, 22, 2020, we sequenced 505 M tuberculosis isolates from 461 patients. Of the 64 isolates with mutations within the mmpR5 regulatory gene, we found 53 (83%) had independent acquisition of 31 different mutations, with a particular enrichment of truncated MmpR5 in bedaquiline-resistant isolates resulting from either frameshift mutations or the introduction of an insertion element. Truncation occurred across three M tuberculosis lineages, and were present in 66% of bedaquiline-resistant isolates. Although the distributions overlapped, the median minimum inhibitory concentration of bedaquiline was 0·25 mg/L (IQR 0·12-0·25) in mmpR5-disrupted isolates, compared with 0·06 mg/L (0·03-0·06) in wild-type M tuberculosis. INTERPRETATION Reduction in the susceptibility of M tuberculosis to bedaquiline has evolved repeatedly across the phylogeny. In our data, we see no evidence that this reduction has led to the spread of a successful strain in South Africa. Binary phenotyping based on the bedaquiline breakpoint might be inappropriate to monitor resistance to this drug. We recommend the use of minimum inhibitory concentrations in addition to MmpR5 truncation screening to identify moderate increases in resistance to bedaquiline. FUNDING US Centers for Disease Control and Prevention.
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Affiliation(s)
- Leah W Roberts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kerri M Malone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lavania Joseph
- Centre for Tuberculosis, National and Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Penelope Wintringer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Jeff Knaggs
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK; The Milner Centre for Evolution, University of Bath, Bath, UK.
| | - Shaheed V Omar
- Centre for Tuberculosis, National and Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
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5
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Umpeleva T, Chetverikova E, Belyaev D, Eremeeva N, Boteva T, Golubeva L, Vakhrusheva D, Vasilieva I. Identification of genetic determinants of bedaquiline resistance in Mycobacterium tuberculosis in Ural region, Russia. Microbiol Spectr 2024; 12:e0374923. [PMID: 38345388 PMCID: PMC10913728 DOI: 10.1128/spectrum.03749-23] [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: 11/01/2023] [Accepted: 01/24/2024] [Indexed: 03/06/2024] Open
Abstract
Collecting data on rare Mycobacterium tuberculosis (Mtb) clinical isolates with resistance to the new anti-tuberculosis drug bedaquiline is an important task for improving antimicrobial susceptibility testing methods. Nanopore whole genome sequencing, the proportion method on Middlebrook 7H11 medium, and BACTEC MGIT 960 assays were used to analyze genotypic and phenotypic resistance to bedaquiline. We found four mutations: atpE I66M, atpE А63Р, Rv0678 А36Т, and Rv0678 S53P in five isolates with different levels of phenotypic bedaquiline resistance. IMPORTANCE Bedaquiline (BDQ) is a new anti-tuberculosis drug. The phenotypic and genotypic data describing the mechanism of drug resistance are critical for the design of rapid and accurate diagnostic tests. We consider that our work, which describes genotypic and phenotypic resistance to BDQ, can contribute to the standardization of drug susceptibility testing.
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Affiliation(s)
- Tatiana Umpeleva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Elena Chetverikova
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Danila Belyaev
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
- Laboratory of Medical Chemistry, Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Natalya Eremeeva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Tatiana Boteva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Ludmila Golubeva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Diana Vakhrusheva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Irina Vasilieva
- Administration, National Medical Research Center of Phthisiopulmonology and Infection Disease, Moscow, Russia
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Barilar I, Fernando T, Utpatel C, Abujate C, Madeira CM, José B, Mutaquiha C, Kranzer K, Niemann T, Ismael N, de Araujo L, Wirth T, Niemann S, Viegas S. Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study. THE LANCET. INFECTIOUS DISEASES 2024; 24:297-307. [PMID: 37956677 DOI: 10.1016/s1473-3099(23)00498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND In 2021, an estimated 4800 people developed rifampicin-resistant tuberculosis in Mozambique, 75% of which went undiagnosed. Detailed molecular data on rifampicin-resistant and multidrug-resistant (MDR) tuberculosis are not available. Here, we aimed at gaining precise data on the determinants of rifampicin-resistant and MDR tuberculosis in Mozambique. METHODS In this retrospective observational study, we performed whole-genome sequencing of 704 rifampicin-resistant Mycobacterium tuberculosis complex (Mtbc) strains submitted to the National Tuberculosis Reference Laboratory (NTRL) in Maputo, Mozambique, between 2015 and 2021. Phylogenetic strain classification, genomic resistance prediction, and cluster analysis were performed. FINDINGS Between Jan 1, 2015, and July 31, 2021, 2606 Mtbc isolates with an isoniazid or rifampicin resistance were identified in the NTRL biobank, of which, 1483 (56·9%) were from men, 1114 (42·7%) from women, and nine (0·4%) were unknown. Genome-based drug-resistant prediction classified 704 Mtbc strains as rifampicin resistant. 628 (89%) of the 704 Mtbc strains were classified MDR; of those, 146 (23%) were pre-extensively drug resistant (pre-XDR; additional fluoroquinolone resistance), and 24 (4%) extensively drug resistant (XDR; combined fluoroquinolone and bedaquiline resistance). Overall, 61 (9%) of 704 strains revealed resistance to bedaquiline: five (7%) of 76 rifampicin resistant plus bedaquiline resistant, 32 (7%) of 458 MDR plus bedaquiline resistant, and 24 (100%) of 24 XDR. Prevalence of bedaquiline resistance increased from 3% in 2016 to 14% in 2021. The cluster rate (12 single-nucleotide polymorphism threshold) was 42% for rifampicin-resistant strains, 78% for MDR strains, 94% for pre-XDR strains, and 96% for XDR Mtbc strains. 31 (4%) of 704 Mtbc strains, belonging to a diagnostic escape outbreak strain previously described in Eswatini (group_56), had an rpoB Ile491Phe mutation which is not detected by Xpert MTB/RIF (no other rpoB mutation). Of these, 23 (74%) showed additional resistance to bedaquiline, 13 (42%) had bedaquiline and fluoroquinolone resistance, and two (6%) were bedaquiline, fluoroquinolone, and delamanid resistant. INTERPRETATION Pre-XDR resistance is highly prevalent among MDR Mtbc strains in Mozambique and so is bedaquiline resistance; and the frequency of bedaquiline resistance quadrupled over time and was found even in Mtbc strains without fluoroquinolone resistance. Importantly, strains with Ile491Phe mutation were frequent, accounting for 31% (n=10) of MDR plus bedaquiline-resistant strains and 54% (n=13) of XDR Mtbc strains. Given the current diagnostic algorithms and treatment regimens, both the emergence of rifampicin resistance due to Ile491Phe and bedaquiline resistance might jeopardise MDR tuberculosis prevention and care unless sequencing-based technology is rolled out. The potential cross border spread of diagnostic escape strains needs further investigation. FUNDING The German Ministry of Health through the Seq_MDRTB-Net project, the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy Precision Medicine in Inflammation and the Research Training Group 2501 TransEvo, the Leibniz Science Campus Evolutionary Medicine of the Lung, and the German Ministry of Education and Research via the German Center for Infection Research.
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Affiliation(s)
- Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | | | - Benedita José
- National Tuberculosis Control Program, Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - Claudia Mutaquiha
- National Tuberculosis Control Program, Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - Katharina Kranzer
- Biomedical Research and Training Institute, Harare, Zimbabwe; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität, Munich, Munich, Germany
| | - Tanja Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Nalia Ismael
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Leonardo de Araujo
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thierry Wirth
- Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres University, Paris, France; Institut de Systématique, Evolution, Biodiversite, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France; Ecole Pratique des Hautes Etudes, Université des Antilles, Paris, France
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia.
| | - Sofia Viegas
- Instituto Nacional de Saúde, Marracuene, Mozambique
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7
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Utpatel C, Zavaleta M, Rojas-Bolivar D, Mühlbach A, Picoy J, Portugal W, Esteve-Solé A, Alsina L, Miotto P, Bartholomeu DC, Sanchez J, Cuadros DF, Alarcon JO, Niemann S, Huaman MA. Prison as a driver of recent transmissions of multidrug-resistant tuberculosis in Callao, Peru: a cross-sectional study. LANCET REGIONAL HEALTH. AMERICAS 2024; 31:100674. [PMID: 38500964 PMCID: PMC10945431 DOI: 10.1016/j.lana.2024.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 03/20/2024]
Abstract
Background We sought to identify resistance patterns and key drivers of recent multidrug-resistant tuberculosis (MDR-TB) transmission in a TB-prevalent area in Peru. Methods Cross-sectional study including MDR Mycobacterium tuberculosis complex (Mtbc) strains identified in Callao-Peru between April 2017 and February 2019. Mtbc DNA was extracted for whole genome sequencing which was used for phylogenetic inference, clustering, and resistance mutation analyses. Clusters indicative of recent transmission were defined based on a strain-to-strain distance of ≤5 (D5) single nucleotide polymorphisms (SNPs). Epidemiologic factors linked to MDR-TB clustering were analyzed using Poisson regression. Findings 171 unique MDR-Mtbc strains were included; 22 (13%) had additional fluoroquinolone resistance and were classified as pre-XDR. Six strains (3.5%) harboured bedaquiline (BDQ) resistance mutations and were classified as MDR + BDQ. 158 (92%) Mtbc strains belonged to lineage 4 and 13 (8%) to lineage 2. Using a cluster threshold of ≤5 SNPs, 98 (57%) strains were grouped in one of the 17 D5 clusters indicative of recent transmission, ranging in size from 2 to the largest cluster formed by 53 4.3.3 strains (group_1). Lineage 4.3.3 strains showed the overall highest cluster rate (43%). In multivariate analyses, current or previous imprisonment was independently associated with being part of any MDR-TB transmission clusters (adjusted prevalence ratio [aPR], 1.45; 95% CI, 1.09-1.92). Interpretation Pre-XDR-TB emerged in more than 10% of the MDR-TB strains investigated. Transmission of 4.3.3 Mtbc strains especially of the dominant group_1 clone is a major driver of the MDR-TB epidemic in Callao. Current or previous imprisonment was linked to recent MDR-TB transmissions, indicating an important role of prisons in driving the MDR-TB epidemic. Funding This work was supported in part by the ERANet-LAC Network of the European Union, Latin America and the Caribbean Countries on Joint Innovation and Research Activities, and FONDECYT. Additional support was received from Leibniz Science Campus Evolutionary Medicine of the Lung, the Deutsche Forschungsgemeinschaft (German Research Foundation, under Germany's Excellence Strategy-EXC 2167 Precision Medicine in Inflammation), and the Research Training Group 2501 TransEvo.
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Affiliation(s)
- Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Milagros Zavaleta
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Daniel Rojas-Bolivar
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Andreas Mühlbach
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Janet Picoy
- Direccion Regional de Salud del Callao, Callao, Peru
| | | | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu Institut de Recerca Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu Institut de Recerca Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniella C. Bartholomeu
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Diego F. Cuadros
- Department of Geography and GIS, Health Geography and Disease Modeling Laboratory, University of Cincinnati, Cincinnati, USA
| | - Jorge O. Alarcon
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
- Epidemiology Section, Instituto de Medicina Tropical, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Moises A. Huaman
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
- Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati, Cincinnati, USA
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8
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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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9
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Brown TS, Tang L, Omar SV, Joseph L, Meintjes G, Maartens G, Wasserman S, Shah NS, Farhat MR, Gandhi NR, Ismail N, Brust JCM, Mathema B. Genotype-Phenotype Characterization of Serial Mycobacterium tuberculosis Isolates in Bedaquiline-Resistant Tuberculosis. Clin Infect Dis 2024; 78:269-276. [PMID: 37874928 DOI: 10.1093/cid/ciad596] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Emerging resistance to bedaquiline (BDQ) threatens to undermine advances in the treatment of drug-resistant tuberculosis (DRTB). Characterizing serial Mycobacterium tuberculosis (Mtb) isolates collected during BDQ-based treatment can provide insights into the etiologies of BDQ resistance in this important group of DRTB patients. METHODS We measured mycobacteria growth indicator tube (MGIT)-based BDQ minimum inhibitory concentrations (MICs) of Mtb isolates collected from 195 individuals with no prior BDQ exposure who were receiving BDQ-based treatment for DRTB. We conducted whole-genome sequencing on serial Mtb isolates from all participants who had any isolate with a BDQ MIC >1 collected before or after starting treatment (95 total Mtb isolates from 24 participants). RESULTS Sixteen of 24 participants had BDQ-resistant TB (MGIT MIC ≥4 µg/mL) and 8 had BDQ-intermediate infections (MGIT MIC = 2 µg/mL). Participants with pre-existing resistance outnumbered those with resistance acquired during treatment, and 8 of 24 participants had polyclonal infections. BDQ resistance was observed across multiple Mtb strain types and involved a diverse catalog of mmpR5 (Rv0678) mutations, but no mutations in atpE or pepQ. Nine pairs of participants shared genetically similar isolates separated by <5 single nucleotide polymorphisms, concerning for potential transmitted BDQ resistance. CONCLUSIONS BDQ-resistant TB can arise via multiple, overlapping processes, including transmission of strains with pre-existing resistance. Capturing the within-host diversity of these infections could potentially improve clinical diagnosis, population-level surveillance, and molecular diagnostic test development.
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Affiliation(s)
- Tyler S Brown
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Linrui Tang
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Molecular Medicine & Hematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lavania Joseph
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gary Maartens
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - N Sarita Shah
- Departments of Epidemiology and Global Health and Medicine, Rollins School of Public Health and Emory School of Medicine, Atlanta, Georgia, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Neel R Gandhi
- Departments of Epidemiology and Global Health and Medicine, Rollins School of Public Health and Emory School of Medicine, Atlanta, Georgia, USA
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - James C M Brust
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
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10
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Bhattarai SK, Du M, Zeamer AL, Morzfeld BM, Kellogg TD, Firat K, Benjamin A, Bean JM, Zimmerman M, Mardi G, Vilbrun SC, Walsh KF, Fitzgerald DW, Glickman MS, Bucci V. Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption. Sci Transl Med 2024; 16:eadi9711. [PMID: 38232140 PMCID: PMC11017772 DOI: 10.1126/scitranslmed.adi9711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
Despite their therapeutic benefits, antibiotics exert collateral damage on the microbiome and promote antimicrobial resistance. However, the mechanisms governing microbiome recovery from antibiotics are poorly understood. Treatment of Mycobacterium tuberculosis, the world's most common infection, represents the longest antimicrobial exposure in humans. Here, we investigate gut microbiome dynamics over 20 months of multidrug-resistant tuberculosis (TB) and 6 months of drug-sensitive TB treatment in humans. We find that gut microbiome dynamics and TB clearance are shared predictive cofactors of the resolution of TB-driven inflammation. The initial severe taxonomic and functional microbiome disruption, pathobiont domination, and enhancement of antibiotic resistance that initially accompanied long-term antibiotics were countered by later recovery of commensals. This resilience was driven by the competing evolution of antimicrobial resistance mutations in pathobionts and commensals, with commensal strains with resistance mutations reestablishing dominance. Fecal-microbiota transplantation of the antibiotic-resistant commensal microbiome in mice recapitulated resistance to further antibiotic disruption. These findings demonstrate that antimicrobial resistance mutations in commensals can have paradoxically beneficial effects by promoting microbiome resilience to antimicrobials and identify microbiome dynamics as a predictor of disease resolution in antibiotic therapy of a chronic infection.
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Affiliation(s)
- Shakti K Bhattarai
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Muxue Du
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Abigail L Zeamer
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Benedikt M Morzfeld
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Tasia D Kellogg
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kaya Firat
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Anna Benjamin
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James M Bean
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Gertrude Mardi
- Haitian Study Group for Kaposi’s Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Stalz Charles Vilbrun
- Haitian Study Group for Kaposi’s Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Kathleen F Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY 10065, USA
- Division of General Internal Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01605, USA
- Immunology and Microbiology Program, UMass Chan Medical School, Worcester, MA 01605, USA
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11
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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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12
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Islam MM, Alam MS, Liu Z, Khatun MS, Yusuf B, Hameed HMA, Tian X, Chhotaray C, Basnet R, Abraha H, Zhang X, Khan SA, Fang C, Li C, Hasan S, Tan S, Zhong N, Hu J, Zhang T. Molecular mechanisms of resistance and treatment efficacy of clofazimine and bedaquiline against Mycobacterium tuberculosis. Front Med (Lausanne) 2024; 10:1304857. [PMID: 38274444 PMCID: PMC10809401 DOI: 10.3389/fmed.2023.1304857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/21/2023] [Indexed: 01/27/2024] Open
Abstract
Clofazimine (CFZ) and bedaquiline (BDQ) are currently used for the treatment of multidrug-resistant (MDR) Mycobacterium tuberculosis (Mtb) strains. In recent years, adding CFZ and BDQ to tuberculosis (TB) drug regimens against MDR Mtb strains has significantly improved treatment results, but these improvements are threatened by the emergence of MDR and extensively drug-resistant (XDR) Mtb strains. Recently, CFZ and BDQ have attracted much attention for their strong clinical efficacy, although very little is known about the mechanisms of action, drug susceptibility test (DST), resistance mechanisms, cross-resistance, and pharmacokinetics of these two drugs. In this current review, we provide recent updates on the mechanisms of action, DST, associated mutations with individual resistance and cross-resistance, clinical efficacy, and pharmacokinetics of CFZ and BDQ against Mtb strains. Presently, known mechanisms of resistance for CFZ and/or BDQ include mutations within the Rv0678, pepQ, Rv1979c, and atpE genes. The cross-resistance between CFZ and BDQ may reduce available MDR-/XDR-TB treatment options. The use of CFZ and BDQ for treatment in the setting of limited DST could allow further spread of drug resistance. The DST and resistance knowledge are urgently needed where CFZ and BDQ resistance do emerge. Therefore, an in-depth understanding of clinical efficacy, DST, cross-resistance, and pharmacokinetics for CFZ and BDQ against Mtb can provide new ideas for improving treatment outcomes, reducing mortality, preventing drug resistance, and TB transmission. Along with this, it will also help to develop rapid molecular diagnostic tools as well as novel therapeutic drugs for TB.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Department of Microbiology, Shaheed Shamsuzzoha Institute of Biosciences, Affiliated with University of Rajshahi, Rajshahi, Bangladesh
| | - Md Shah Alam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou Medical University, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Mst Sumaia Khatun
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Buhari Yusuf
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - H. M. Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chiranjibi Chhotaray
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, NJ, United States
| | - Rajesh Basnet
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haftay Abraha
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaofan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shahzad Akbar Khan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Laboratory of Pathology, Department of Pathobiology, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chunyu Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Sohel Hasan
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shouyong Tan
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jinxing Hu
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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13
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Dreyer V, Sonnenkalb L, Diricks M, Utpatel C, Barilar I, Mohr V, Niemann S, Kohl TA, Merker M. Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing: From Sequence Data to Resistance Profiles. Methods Mol Biol 2024; 2833:195-210. [PMID: 38949712 DOI: 10.1007/978-1-0716-3981-8_18] [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] [Indexed: 07/02/2024]
Abstract
Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) isolates has been shown to provide accurate predictions for resistance and susceptibility for many first- and second-line anti-tuberculosis drugs. However, bioinformatic pipelines and mutation catalogs to predict antimicrobial resistances in MTBC isolates are often customized and detailed protocols are difficult to access. Here, we provide a step-by-step workflow for the processing and interpretation of short-read sequencing data and give an overview of available analysis pipelines.
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Affiliation(s)
- Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Lindsay Sonnenkalb
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Vanessa Mohr
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Matthias Merker
- Evolution of the Resistome, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
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14
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Kong Y, Geng Z, Jiang G, Jia J, Wang F, Jiang X, Gu Y, Qi Z, Chu N, Huang H, Yu X. Comparison of the in vitro antibacterial activity of ofloxacin, levofloxacin, moxifloxacin, sitafloxacin, finafloxacin, and delafloxacin against Mycobacterium tuberculosis strains isolated in China. Heliyon 2023; 9:e21216. [PMID: 37954372 PMCID: PMC10637932 DOI: 10.1016/j.heliyon.2023.e21216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/14/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
Objective The resistance of Mycobacterium tuberculosis (Mtb) to currently available fluoroquinolones (FQs), namely ofloxacin (OFX), levofloxacin (LFX), and moxifloxacin (MFX), renders the treatment of TB infections less successful. In this study, we aimed to evaluate the susceptibility and intracellular killing assay of Mtb to next-generation FQs in vitro and determine the correlation of FQs resistance and newly detected mutations in gyrB by molecular docking. Methods Antimicrobial susceptibility test was performed to determine the minimum inhibitory concentrations (MICs) of six FQs, including currently available FQs (OFX, LFX, and MFX) and next-generation FQs, i.e., sitafloxacin (SFX), finafloxacin (FIN) and delafloxacin (DFX) against Mtb clinical isolates obtained in 2015 and 2022, respectively. Quinolone-resistance-determining regions of gyrA and gyrB were subjected to DNA sequencing and the correlation of FQs resistance and new mutations in gyrB were determined by molecular docking. Furthermore, the intracellular antibacterial activity of the six FQs against Mtb H37Rv in THP-1 cells was evaluated. Results SFX exhibited the highest antibacterial activity against Mtb isolates (MIC90 = 0.25 μg/mL), whereas DFX and OFX exhibited comparable activity (MIC90 = 8 μg/mL). A statistically significant difference was observed among the MICs of the new generation FQs (SFX, P = 0.002; DFX, P = 0.008). Additionally, a marked increase in MICs was found in strains isolated in 2022 compared with those isolated in 2015. There might be correlation between FQs resistance and mutations in gyrB G520T and G520A. Cross-resistance rate between SFX and MFX was 40.6 % (26/64). At a concentration of 1 μg/mL, SFX exhibited high intracellular antibacterial activity (96.6 % ± 1.5 %) against the Mtb H37Rv, comparable with that of MFX at a concentration of 2 μg/mL. Conclusion SFX exhibits the highest inhibitory activity against Mtb in vitro and THP-1 cell lines, which exhibits partial-cross resistance with MFX. There might be correlation between FQs resistance and mutations in gyrB G520T and G520A.Our findings provide crucial insights into the potential clinical application of SFX and DFX in the treatment of Mtb infections.
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Affiliation(s)
- Yaoyao Kong
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, Beijing, China
| | - Zhi Geng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Junnan Jia
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Fen Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Xiaoyi Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Yuzhen Gu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Zhenyan Qi
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, Beijing, China
| | - Naihui Chu
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
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15
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Auganova D, Atavliyeva S, Amirgazin A, Akisheva A, Tsepke A, Tarlykov P. Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan. Antibiotics (Basel) 2023; 12:1523. [PMID: 37887224 PMCID: PMC10604462 DOI: 10.3390/antibiotics12101523] [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] [Received: 09/06/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the "aggressive" Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.
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Affiliation(s)
- Dana Auganova
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
| | | | | | - Akmaral Akisheva
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Anna Tsepke
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
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16
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Köser CU, Maurer FP. Minimum inhibitory concentrations and sequencing data have to be analysed in more detail to set provisional epidemiological cut-off values for Mycobacterium tuberculosis complex. Eur Respir J 2023; 61:61/5/2202397. [PMID: 37147011 DOI: 10.1183/13993003.02397-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 05/07/2023]
Affiliation(s)
- Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Florian P Maurer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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