101
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Tukvadze N, Bablishvili N, Apsindzelashvili R, Blumberg HM, Kempker RR. Performance of the MTBDRsl assay in Georgia. Int J Tuberc Lung Dis 2014; 18:233-9. [PMID: 24429319 DOI: 10.5588/ijtld.13.0468] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SETTING The country of Georgia has a high burden of multi- (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). OBJECTIVE To assess the performance of the GenoType® MTBDRsl assay in the detection of resistance to kanamycin (KM), capreomycin (CPM) and ofloxacin (OFX), and of XDR-TB. DESIGN Consecutive acid-fast bacilli smear-positive sputum specimens identified as MDR-TB using the MTBDRplus test were evaluated with the MTBDRsl assay and conventional second-line drug susceptibility testing (DST). RESULTS Among 159 specimens, amplification was adequate in 154 (97%), including 9 of 9 culture-negative and 2 of 3 contaminated specimens. Second-line DST revealed that 17 (12%) Mycobacterium tuberculosis isolates were XDR-TB. Compared to DST, the MTBDRsl had 41% sensitivity and 98% specificity in detecting XDR-TB and 81% sensitivity and 99% specificity in detecting OFX resistance. Sensitivity was low in detecting resistance to KM (29%) and CPM (57%), while specificity was respectively 99% and 94%. Median times from sputum collection to second-line DST and MTBDRsl results were 70-104 vs. 10 days. CONCLUSION Although the MTBDRsl assay had a rapid turnaround time, detection of second-line drug resistance was poor compared to DST. Further genetic mutations associated with resistance to second-line drugs should be included in the assay to improve test performance and clinical utility.
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Affiliation(s)
- N Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - N Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | | | - H M Blumberg
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - R R Kempker
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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102
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Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med 2014; 4:a021188. [PMID: 25190252 DOI: 10.1101/cshperspect.a021188] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools.
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103
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Shekar S, Yeo ZX, Wong JCL, Chan MKL, Ong DCT, Tongyoo P, Wong SY, Lee ASG. Detecting novel genetic variants associated with isoniazid-resistant Mycobacterium tuberculosis. PLoS One 2014; 9:e102383. [PMID: 25025225 PMCID: PMC4099304 DOI: 10.1371/journal.pone.0102383] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 06/18/2014] [Indexed: 12/30/2022] Open
Abstract
Background Isoniazid (INH) is a highly effective antibiotic central for the treatment of Mycobacterium tuberculosis (MTB). INH-resistant MTB clinical isolates are frequently mutated in the katG gene and the inhA promoter region, but 10 to 37% of INH-resistant clinical isolates have no detectable alterations in currently known gene targets associated with INH-resistance. We aimed to identify novel genes associated with INH-resistance in these latter isolates. Methodology/Principal Findings INH-resistant clinical isolates of MTB were pre-screened for mutations in the katG, inhA, kasA and ndh genes and the regulatory regions of inhA and ahpC. Twelve INH-resistant isolates with no mutations, and 17 INH-susceptible MTB isolates were subjected to whole genome sequencing. Phylogenetically related variants and synonymous mutations were excluded and further analysis revealed mutations in 60 genes and 4 intergenic regions associated with INH-resistance. Sanger sequencing verification of 45 genes confirmed that mutations in 40 genes were observed only in INH-resistant isolates and not in INH-susceptible isolates. The ratios of non-synonymous to synonymous mutations (dN/dS ratio) for the INH-resistance associated mutations identified in this study were 1.234 for INH-resistant and 0.654 for INH-susceptible isolates, strongly suggesting that these mutations are indeed associated with INH-resistance. Conclusion The discovery of novel targets associated with INH-resistance described in this study may potentially be important for the development of improved molecular detection strategies.
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Affiliation(s)
- Sandhya Shekar
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Zhen Xuan Yeo
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Joshua C. L. Wong
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Maurice K. L. Chan
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Danny C. T. Ong
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Pumipat Tongyoo
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
| | - Sin-Yew Wong
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Ann S. G. Lee
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
- Office of Clinical & Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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104
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de Keijzer J, de Haas PE, de Ru AH, van Veelen PA, van Soolingen D. Disclosure of selective advantages in the "modern" sublineage of the Mycobacterium tuberculosis Beijing genotype family by quantitative proteomics. Mol Cell Proteomics 2014; 13:2632-45. [PMID: 25022876 DOI: 10.1074/mcp.m114.038380] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mycobacterium tuberculosis Beijing genotype, consisting of the more ancient (atypical) and modern (typical) emerging sublineage, is one of the most prevalent and genetically conserved genotype families and has often been associated with multidrug resistance. In this study, we employed a 2D-LC-FTICR MS approach, combined with dimethylation of tryptic peptides, to systematically compare protein abundance levels of ancient and modern Beijing strains and identify differences that could be associated with successful spread of the modern sublineage. The data is available via ProteomeXchange using the identifier PXD000931. Despite the highly uniform protein abundance ratios in both sublineages, we identified four proteins as differentially regulated between both sublineages, which could explain the apparent increased adaptation of the modern Beijing strains. These proteins are; Rv0450c/MmpL4, Rv1269c, Rv3137, and Rv3283/sseA. Transcriptional and functional analysis of these proteins in a large cohort of 29 Beijing strains showed that the mRNA levels of Rv0450c/MmpL4 are significantly higher in modern Beijing strains, whereas we also provide evidence that Rv3283/sseA is less abundant in the modern Beijing sublineage. Our findings provide a possible explanation for the increased virulence and success of the modern Beijing sublineage. In addition, in the established dataset of 1817 proteins, we demonstrate the pre-existence of several, possibly unique, antibiotic efflux pumps in the proteome of the Beijing strains. This may reflect an increased ability of Beijing strains to escape exposure to antituberculosis drugs.
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Affiliation(s)
- Jeroen de Keijzer
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands;
| | - Petra E de Haas
- §Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, The Netherlands
| | - Arnoud H de Ru
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands
| | - Peter A van Veelen
- From the ‡Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre (LUMC), Leiden, 2300 RC, The Netherlands
| | - Dick van Soolingen
- §Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, The Netherlands; ¶Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Centre, Nijmegen, 6500 HB, The Netherlands
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105
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Trauner A, Borrell S, Reither K, Gagneux S. Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy. Drugs 2014; 74:1063-72. [PMID: 24962424 PMCID: PMC4078235 DOI: 10.1007/s40265-014-0248-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-resistant tuberculosis is a growing threat to global public health. Recent efforts to understand the evolution of drug resistance have shown that changes in drug-target interactions are only the first step in a longer adaptive process. The emergence of transmissible drug-resistant Mycobacterium tuberculosis is the result of a multitude of additional genetic mutations, many of which interact, a phenomenon known as epistasis. The varied effects of these epistatic interactions include compensating for the reduction of the biological cost associated with the development of drug resistance, increasing the level of resistance, and possibly accommodating broader changes in the physiology of resistant bacteria. Knowledge of these processes and our ability to detect them as they happen informs the development of diagnostic tools and better control strategies. In particular, the use of whole genome sequencing combined with surveillance efforts in the field could provide a powerful instrument to prevent future epidemics of drug-resistant tuberculosis.
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Affiliation(s)
- Andrej Trauner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
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106
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Hughes D. Selection and evolution of resistance to antimicrobial drugs. IUBMB Life 2014; 66:521-9. [PMID: 24933583 DOI: 10.1002/iub.1278] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 05/21/2014] [Indexed: 01/22/2023]
Abstract
The overuse and misuse of antibiotics over many years has selected a high frequency of resistance among medically important bacterial pathogens. The evolution of resistance is complex, frequently involving multiple genetic alterations that minimize biological fitness costs and/or increase the resistance level. Resistance is selected at very low drug concentrations, such as found widely distributed in the environment, and this selects for resistant mutants with a high fitness. Once resistance with high fitness is established in a community it is very difficult to reduce its frequency. Addressing the problem of resistance is essential if we are to ensure a future where we can continue to enjoy effective medical control of bacterial infections. This will require several actions including the discovery and development of novel antibiotics, the creation of a continuous pipeline of drug discovery, and the implementation of effective global antibiotic stewardship to reduce the misuse of antibiotics and their release into the environment.
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Affiliation(s)
- Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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107
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Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG. PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb) 2014; 94:346-54. [PMID: 24637013 PMCID: PMC4066953 DOI: 10.1016/j.tube.2014.02.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/08/2014] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.
| | - Mark Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Grant Hill-Cawthorn
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney, NSW 2006, Australia
| | - David Harris
- Pathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Francis Drobniewski
- Centre for Immunology and Infectious Disease, Queen Mary University of London, E1 2AT London, UK
| | | | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julian Parkhill
- Pathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Nigel Martin
- School of Computer Science and Information Systems, Birkbeck College, WC1E 7HX London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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108
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Chernyaeva EN, Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, Govorun VM, Zhuravlev VY, Manicheva OA, Yablonsky PK, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Lapidus AL, O'Brien SJ. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics 2014; 15:308. [PMID: 24767249 PMCID: PMC4234438 DOI: 10.1186/1471-2164-15-308] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 04/15/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains.
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Affiliation(s)
- Ekaterina N Chernyaeva
- St, Petersburg State University, Theodosius Dobzhansky Center for Genome Bioinformatics, 41 Sredniy prospect, St, Petersburg, Russia.
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109
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Köser CU, Comas I, Feuerriegel S, Niemann S, Gagneux S, Peacock SJ. Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay. Tuberculosis (Edinb) 2014; 94:451-3. [PMID: 24870943 PMCID: PMC4075347 DOI: 10.1016/j.tube.2014.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/09/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
| | - Iñaki Comas
- Genomics and Health Unit, FISABIO, Valencia, Spain; CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Spain
| | - Silke Feuerriegel
- Molecular Mycobacteriology, Borstel, Germany; German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular Mycobacteriology, Borstel, Germany; German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
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110
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Köser CU, Bryant JM, Comas I, Feuerriegel S, Niemann S, Gagneux S, Parkhill J, Peacock SJ. Comment on: characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array. J Antimicrob Chemother 2014; 69:2298-9. [PMID: 24752956 PMCID: PMC4100706 DOI: 10.1093/jac/dku101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Iñaki Comas
- Genomics and Health Unit, FISABIO, Valencia, Spain CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Barcelona, Spain
| | - Silke Feuerriegel
- Molecular Mycobacteriology, Borstel, Germany German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular Mycobacteriology, Borstel, Germany German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Hinxton, UK Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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111
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New antituberculosis drugs, regimens, and adjunct therapies: needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:327-40. [DOI: 10.1016/s1473-3099(13)70328-1] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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113
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114
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Koch A, Mizrahi V, Warner DF. The impact of drug resistance on Mycobacterium tuberculosis physiology: what can we learn from rifampicin? Emerg Microbes Infect 2014; 3:e17. [PMID: 26038512 PMCID: PMC3975073 DOI: 10.1038/emi.2014.17] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/12/2013] [Accepted: 12/30/2013] [Indexed: 01/08/2023]
Abstract
The emergence of drug-resistant pathogens poses a major threat to public health. Although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. The fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. Rifampicin (RIF) is a frontline anti-tuberculosis agent that targets the rpoB-encoded β subunit of the DNA-dependent RNA polymerase (RNAP). In Mycobacterium tuberculosis (Mtb), RIF resistance (RIF(R)) maps to mutations in rpoB that are likely to impact RNAP function and, therefore, the ability of the organism to cause disease. However, while numerous studies have assessed the impact of RIF(R) on key Mtb fitness indicators in vitro, the consequences of rpoB mutations for pathogenesis remain poorly understood. Here, we examine evidence from diverse bacterial systems indicating very specific effects of rpoB polymorphisms on cellular physiology, and consider these observations in the context of Mtb. In addition, we discuss the implications of these findings for the propagation of clinically relevant RIF(R) mutations. While our focus is on RIF, we also highlight results which suggest that drug-independent effects might apply to a broad range of resistance-associated mutations, especially in an obligate pathogen increasingly linked with multidrug resistance.
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Affiliation(s)
- Anastasia Koch
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
| | - Valerie Mizrahi
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
| | - Digby F Warner
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
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115
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Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, Corander J, Bryant J, Parkhill J, Nejentsev S, Horstmann RD, Brown T, Drobniewski F. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet 2014; 46:279-86. [PMID: 24464101 PMCID: PMC3939361 DOI: 10.1038/ng.2878] [Citation(s) in RCA: 347] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/02/2014] [Indexed: 12/30/2022]
Abstract
The molecular mechanisms determining the transmissibility and prevalence of drug-resistant tuberculosis in a population were investigated through whole-genome sequencing of 1,000 prospectively obtained patient isolates from Russia. Two-thirds belonged to the Beijing lineage, which was dominated by two homogeneous clades. Multidrug-resistant (MDR) genotypes were found in 48% of isolates overall and in 87% of the major clades. The most common rpoB mutation was associated with fitness-compensatory mutations in rpoA or rpoC, and a new intragenic compensatory substitution was identified. The proportion of MDR cases with extensively drug-resistant (XDR) tuberculosis was 16% overall, with 65% of MDR isolates harboring eis mutations, selected by kanamycin therapy, which may drive the expansion of strains with enhanced virulence. The combination of drug resistance and compensatory mutations displayed by the major clades confers clinical resistance without compromising fitness and transmissibility, showing that, in addition to weaknesses in the tuberculosis control program, biological factors drive the persistence and spread of MDR and XDR tuberculosis in Russia and beyond.
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Affiliation(s)
- Nicola Casali
- PHE National Mycobacterium Reference Laboratory, Clinical TB and HIV Group, Blizard Institute, Queen Mary University of London, 2 Newark Street, London E1 2AT, UK
| | - Vladyslav Nikolayevskyy
- PHE National Mycobacterium Reference Laboratory, Clinical TB and HIV Group, Blizard Institute, Queen Mary University of London, 2 Newark Street, London E1 2AT, UK
| | - Yanina Balabanova
- PHE National Mycobacterium Reference Laboratory, Clinical TB and HIV Group, Blizard Institute, Queen Mary University of London, 2 Newark Street, London E1 2AT, UK
| | - Simon R Harris
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Olga Ignatyeva
- Samara Oblast Tuberculosis Dispensary, 154 Novosadovaya Street, 443068 Samara, Russian Federation
| | - Irina Kontsevaya
- Samara Oblast Tuberculosis Dispensary, 154 Novosadovaya Street, 443068 Samara, Russian Federation
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Josephine Bryant
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Rolf D Horstmann
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Timothy Brown
- PHE National Mycobacterium Reference Laboratory, Clinical TB and HIV Group, Blizard Institute, Queen Mary University of London, 2 Newark Street, London E1 2AT, UK
| | - Francis Drobniewski
- PHE National Mycobacterium Reference Laboratory, Clinical TB and HIV Group, Blizard Institute, Queen Mary University of London, 2 Newark Street, London E1 2AT, UK
- Department of Infectious Diseases, Imperial College, London, UK
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Song T, Park Y, Shamputa IC, Seo S, Lee SY, Jeon HS, Choi H, Lee M, Glynne RJ, Barnes SW, Walker JR, Batalov S, Yusim K, Feng S, Tung CS, Theiler J, Via LE, Boshoff HIM, Murakami KS, Korber B, Barry CE, Cho SN. Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the β' subunit of RNA polymerase. Mol Microbiol 2014; 91:1106-19. [PMID: 24417450 DOI: 10.1111/mmi.12520] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2014] [Indexed: 12/31/2022]
Abstract
Rifampicin resistance, a defining attribute of multidrug-resistant tuberculosis, is conferred by mutations in the β subunit of RNA polymerase. Sequencing of rifampicin-resistant (RIF-R) clinical isolates of Mycobacterium tuberculosis revealed, in addition to RIF-R mutations, enrichment of potential compensatory mutations around the double-psi β-barrel domain of the β' subunit comprising the catalytic site and the exit tunnel for newly synthesized RNA. Sequential introduction of the resistance allele followed by the compensatory allele in isogenic Mycobacterium smegmatis showed that these mutations respectively caused and compensated a starvation enhanced growth defect by altering RNA polymerase activity. While specific combinations of resistance and compensatory alleles converged in divergent lineages, other combinations recurred among related isolates suggesting transmission of compensated RIF-R strains. These findings suggest nutrient poor growth conditions impose larger selective pressure on RIF-R organisms that results in the selection of compensatory mutations in a domain involved in catalysis and starvation control of RNA polymerase transcription.
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Affiliation(s)
- Taeksun Song
- International Tuberculosis Research Center, Changwon, South Korea
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117
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Liu B, Zhang X, Huang H, Zhang Y, Zhou F, Wang G. A novel molecular typing method of Mycobacteria based on DNA barcoding visualization. J Clin Bioinforma 2014; 4:4. [PMID: 24555538 PMCID: PMC3931916 DOI: 10.1186/2043-9113-4-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 02/10/2014] [Indexed: 11/10/2022] Open
Abstract
Different subtypes of Mycobacterium tuberculosis (MTB) may induce diverse severe human infections, and some of their symptoms are similar to other pathogenes, e.g. Nontuberculosis mycobacteria (NTM). So determination of mycobacterium subtypes facilitates the effective control of MTB infection and proliferation. This study exploits a novel DNA barcoding visualization method for molecular typing of 17 mycobacteria genomes published in the NCBI prokaryotic genome database. Three mycobacterium genes (Rv0279c, Rv3508 and Rv3514) from the PE/PPE family of MT Band were detected to best represent the inter-strain pathogenetic variations. An accurate and fast MTB substrain typing method was proposed based on the combination of the aforementioned three biomarker genes and the 16S rRNA gene. The protocol of establishing a bacterial substrain typing system used in this study may also be applied to the other pathogenes.
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Affiliation(s)
| | | | | | | | - Fengfeng Zhou
- Department of Pathogenobiology, Basic Medical College of Jilin University, Changchun, Jilin, China.
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118
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Strategies to overcome the action of aminoglycoside-modifying enzymes for treating resistant bacterial infections. Future Med Chem 2014; 5:1285-309. [PMID: 23859208 DOI: 10.4155/fmc.13.80] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Shortly after the discovery of the first antibiotics, bacterial resistance began to emerge. Many mechanisms give rise to resistance; the most prevalent mechanism of resistance to the aminoglycoside (AG) family of antibiotics is the action of aminoglycoside-modifying enzymes (AMEs). Since the identification of these modifying enzymes, many efforts have been put forth to prevent their damaging alterations of AGs. These diverse strategies are discussed within this review, including: creating new AGs that are unaffected by AMEs; developing inhibitors of AMEs to be co-delivered with AGs; or regulating AME expression. Modern high-throughput methods as well as drug combinations and repurposing are highlighted as recent drug-discovery efforts towards fighting the increasing antibiotic resistance crisis.
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119
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Ågren J, Finn M, Bengtsson B, Segerman B. Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance. PLoS One 2014; 9:e89112. [PMID: 24551231 PMCID: PMC3923885 DOI: 10.1371/journal.pone.0089112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/18/2014] [Indexed: 12/22/2022] Open
Abstract
Anthrax is a bacterial disease primarily affecting grazing animals but it can also cause severe disease in humans. We have used genomic epidemiology to study microevolution of the bacterium in a confined outbreak in cattle which involved emergence of an antibiotic-resistant phenotype. At the time of death, the animals contained a heterogeneous population of Single Nucleotide Variants (SNVs), some being clonal but most being subclonal. We found that independent isolates from the same carcass had similar levels of SNV differences as isolates from different animals. Furthermore the relative levels of subclonal populations were different in different locations in the same carcass. The heterogeneity appeared to be derived in part from heterogeneity in the infectious dose. The resistance phenotype was linked to clonal mutations in an anti-sigma factor gene and in one case was preceded by an acquisition of a hypermutator phenotype. In another animal, small subclonal populations were observed with counteracting mutations that had turned off the resistance genes. In summary, this study shows the importance of accounting for both acquired and inherited heterogeneity when doing high-resolution infection tracing and when estimating the risks associated with penicillin treatment.
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Affiliation(s)
- Joakim Ågren
- Department of Bacteriology, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Maria Finn
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Björn Bengtsson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Bo Segerman
- Department of Bacteriology, National Veterinary Institute (SVA), Uppsala, Sweden
- * E-mail:
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120
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Shitikov EA, Bespyatykh JA, Ischenko DS, Alexeev DG, Karpova IY, Kostryukova ES, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Vishnevsky BI, Otten TF, Zhuravlev VY, Yablonsky PK, Ilina EN, Govorun VM. Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates. PLoS One 2014; 9:e84971. [PMID: 24416324 PMCID: PMC3885621 DOI: 10.1371/journal.pone.0084971] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/28/2013] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis (MTB) Beijing family isolates are geographically widespread, and there are examples of Beijing isolates that are hypervirulent and associated with drug resistance. One-fourth of Beijing genotype isolates found in Russia belong to the B0/W148 group. The aim of the present study was to investigate features of these endemic strains on a genomic level. Four Russian clinical isolates of this group were sequenced, and the data obtained was compared with published sequences of various MTB strain genomes, including genome of strain W-148 of the same B0/W148 group. The comparison of the W-148 and H37Rv genomes revealed two independent inversions of large segments of the chromosome. The same inversions were found in one of the studied strains after deep sequencing using both the fragment and mate-paired libraries. Additionally, inversions were confirmed by RFLP hybridization analysis. The discovered rearrangements were verified by PCR in all four newly sequenced strains in the study and in four additional strains of the same Beijing B0/W148 group. The other 32 MTB strains from different phylogenetic lineages were tested and revealed no inversions. We suggest that the initial largest inversion changed the orientation of the three megabase (Mb) segment of the chromosome, and the second one occurred in the previously inverted region and partly restored the orientation of the 2.1 Mb inner segment of the region. This is another remarkable example of genomic rearrangements in the MTB in addition to the recently published of large-scale duplications. The described cases suggest that large-scale genomic rearrangements in the currently circulating MTB isolates may occur more frequently than previously considered, and we hope that further studies will help to determine the exact mechanism of such events.
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MESH Headings
- Antitubercular Agents/therapeutic use
- China/epidemiology
- Chromosome Inversion
- Chromosome Mapping
- Chromosomes, Bacterial
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genome, Bacterial
- High-Throughput Nucleotide Sequencing
- Humans
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Phylogeny
- Russia/epidemiology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Egor A. Shitikov
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- * E-mail:
| | - Julia A. Bespyatykh
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitry G. Alexeev
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Irina Y. Karpova
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | | | - Yulia D. Isaeva
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Elena Y. Nosova
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Igor V. Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Anna A. Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Olga V. Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Boris I. Vishnevsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Tatiana F. Otten
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Valery Y. Zhuravlev
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Peter K. Yablonsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Elena N. Ilina
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Vadim M. Govorun
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
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121
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Consequences of whiB7 (Rv3197A) mutations in Beijing genotype isolates of the Mycobacterium tuberculosis complex. Antimicrob Agents Chemother 2013; 57:3461. [PMID: 23761426 DOI: 10.1128/aac.00626-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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122
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Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, Rüsch-Gerdes S, Fattorini L, Oggioni MR, Cox H, Varaine F, Niemann S. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients. PLoS One 2013; 8:e82551. [PMID: 24324807 PMCID: PMC3855793 DOI: 10.1371/journal.pone.0082551] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/29/2013] [Indexed: 12/13/2022] Open
Abstract
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains represent a major threat for tuberculosis (TB) control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR) variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS) to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A) and nine (Patient B) polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and molecular drug resistance tests. Furthermore, high resolution WGS analysis is necessary to accurately detect exogenous re-infection as classical genotyping lacks discriminatory power in high incidence settings.
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Affiliation(s)
- Matthias Merker
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A. Kohl
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Andreas Roetzer
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
- Biomedizinische ForschungsgmbH, Vienna, Austria
| | - Leona Truebe
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
- Department of Medical Microbiology, Virology and Hygiene, Universitätsklinikum Eppendorf, Hamburg, Germany
| | - Elvira Richter
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Lanfranco Fattorini
- Dipartimento di Malattie Infettive, Parassitarie e Immunomediate, Istituto Superiore di Sanità, Rome, Italy
| | - Marco R. Oggioni
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Helen Cox
- Médecins sans Frontières, Cape Town, South Africa
- Centre of Infectious Disease Epidemiology & Research, University of Cape Town, Cape Town, South Africa
| | | | - Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
- * E-mail:
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123
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Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH, van Helden P, Pym A, Mahayiddin AA, Chuchottaworn C, Sanne IM, Louw C, Boeree MJ, Hoelscher M, McHugh TD, Bateson ALC, Hunt RD, Mwaigwisya S, Wright L, Gillespie SH, Bentley SD. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. THE LANCET RESPIRATORY MEDICINE 2013; 1:786-92. [PMID: 24461758 PMCID: PMC3861685 DOI: 10.1016/s2213-2600(13)70231-5] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Recurrence of tuberculosis after treatment makes management difficult and is a key factor for determining treatment efficacy. Two processes can cause recurrence: relapse of the primary infection or re-infection with an exogenous strain. Although re-infection can and does occur, its importance to tuberculosis epidemiology and its biological basis is still debated. We used whole-genome sequencing-which is more accurate than conventional typing used to date-to assess the frequency of recurrence and to gain insight into the biological basis of re-infection. METHODS We assessed patients from the REMoxTB trial-a randomised controlled trial of tuberculosis treatment that enrolled previously untreated participants with Mycobacterium tuberculosis infection from Malaysia, South Africa, and Thailand. We did whole-genome sequencing and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing of pairs of isolates taken by sputum sampling: one from before treatment and another from either the end of failed treatment at 17 weeks or later or from a recurrent infection. We compared the number and location of SNPs between isolates collected at baseline and recurrence. FINDINGS We assessed 47 pairs of isolates. Whole-genome sequencing identified 33 cases with little genetic distance (0-6 SNPs) between strains, deemed relapses, and three cases for which the genetic distance ranged from 1306 to 1419 SNPs, deemed re-infections. Six cases of relapse and six cases of mixed infection were classified differently by whole-genome sequencing and MIRU-VNTR. We detected five single positive isolates (positive culture followed by at least two negative cultures) without clinical evidence of disease. INTERPRETATION Whole-genome sequencing enables the differentiation of relapse and re-infection cases with greater resolution than do genotyping methods used at present, such as MIRU-VNTR, and provides insights into the biology of recurrence. The additional clarity provided by whole-genome sequencing might have a role in defining endpoints for clinical trials. FUNDING Wellcome Trust, European Union, Medical Research Council, Global Alliance for TB Drug Development, European and Developing Country Clinical Trials Partnership.
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Affiliation(s)
| | | | | | - Rodney Dawson
- Division of Pulmonology, University of Cape Town, Cape Town, South Africa
| | - Andreas H Diacon
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Paul van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Alex Pym
- South African Medical Research Council and KwaZulu Research Institute for TB and HIV, Durban, South Africa
| | | | | | - Ian M Sanne
- Clinical HIV Research Unit, Helen Joseph Hospital, Westdene, Johannesburg, South Africa
| | - Cheryl Louw
- Madibeng Centre for Research, Brits, South Africa
| | - Martin J Boeree
- Radboud MD University Nijmegen Medical Centre/UCCZ Dekkerswald, Nijmegen, Netherlands
| | - Michael Hoelscher
- Department of Infectious Diseases and Tropical Medicine, Klinikum, Ludwig-Maximilians-University, Munich, Germany; DZIF German Centre for Infection Research, Munich, Germany
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London, UK
| | - Anna L C Bateson
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London, UK
| | - Robert D Hunt
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London, UK
| | - Solomon Mwaigwisya
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London, UK
| | - Laura Wright
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London, UK
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124
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Current status and future trends in the diagnosis and treatment of drug-susceptible and multidrug-resistant tuberculosis. J Infect Public Health 2013; 7:75-91. [PMID: 24216518 DOI: 10.1016/j.jiph.2013.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 08/29/2013] [Accepted: 09/18/2013] [Indexed: 11/21/2022] Open
Abstract
The global burden of tuberculosis (TB) is still large. The increasing incidence of drug-resistant, multidrug-resistant (MDR) (resistant to at least rifampicin and isoniazid), and extensively drug-resistant (XDR) (additionally resistant to a fluoroquinolone and kanamycin/amikacin/capreomycin) strains of Mycobacterium tuberculosis and the association of active disease with human immunodeficiency virus coinfection pose a major threat to TB control efforts. The rapid detection of M. tuberculosis strains and drug susceptibility testing (DST) for anti-TB drugs ensure the provision of effective treatment. Rapid molecular diagnostic and DST methods have been developed recently. Treatment of drug-susceptible TB is effective in ≥95% of disease cases; however, supervised therapy for ≥6 months is challenging. Non-adherence to treatment often results in the evolution of drug-resistant strains of M. tuberculosis due to mutations in the genes encoding drug targets. Sequential accumulation of mutations results in the evolution of MDR and XDR strains of M. tuberculosis. Effective treatment of MDR-TB involves therapy with 5-7 less effective, expensive, and toxic second-line and third-line drugs for ≥24 months and is difficult in most developing countries. XDR-TB is generally an untreatable disease in developing countries. Some currently existing drugs and several new drugs with novel modes of action are in various stages of development to shorten the treatment duration of drug-susceptible TB and to improve the outcome of MDR-TB and XDR-TB.
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125
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Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PKC, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet 2013; 45:1183-9. [PMID: 23995135 PMCID: PMC3887553 DOI: 10.1038/ng.2747] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 08/08/2013] [Indexed: 11/09/2022]
Abstract
M. tuberculosis is evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including genetic changes favored by selection in resistant isolates, are incompletely understood. Using 116 newly sequenced and 7 previously sequenced M. tuberculosis whole genomes, we identified genome-wide signatures of positive selection specific to the 47 drug-resistant strains. By searching for convergent evolution--the independent fixation of mutations in the same nucleotide position or gene--we recovered 100% of a set of known resistance markers. We also found evidence of positive selection in an additional 39 genomic regions in resistant isolates. These regions encode components in cell wall biosynthesis, transcriptional regulation and DNA repair pathways. Mutations in these regions could directly confer resistance or compensate for fitness costs associated with resistance. Functional genetic analysis of mutations in one gene, ponA1, demonstrated an in vitro growth advantage in the presence of the drug rifampicin.
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Affiliation(s)
- Maha R Farhat
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114
| | - B Jesse Shapiro
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA 02115
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Karen J Kieser
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Razvan Sultana
- Dana Farber Cancer Institute, Department of Bioinformatics and Computational Biology, Boston, MA, 02115
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA 02118
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Thomas C Victor
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Elizabeth M Streicher
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Alistair Calver
- Anglogold Ashanti Health West Vaal Hospital, Orkney, North West, South Africa
| | - Alex Sloutsky
- University of Massachusetts Medical School, Massachusetts Supranational TB Reference Laboratory, 305 South St., Boston MA 01230
| | - Devinder Kaur
- University of Massachusetts Medical School, Massachusetts Supranational TB Reference Laboratory, 305 South St., Boston MA 01230
| | - Jamie E Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333
| | - Bonnie Plikaytis
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333
| | - Marco R Oggioni
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Jennifer L Gardy
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver V5Z 4R4, Canada
| | - James C Johnston
- Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver V5Z 4R4, Canada
| | - Mabel Rodrigues
- Mycobacteriology/TB Laboratory, BCCDC Public Health Microbiology and Reference Laboratory, Provincial Health Services Authority Laboratories, Vancouver V5Z 4R4, Canada
| | - Patrick K C Tang
- Mycobacteriology/TB Laboratory, BCCDC Public Health Microbiology and Reference Laboratory, Provincial Health Services Authority Laboratories, Vancouver V5Z 4R4, Canada
| | - Midori Kato-Maeda
- Division of Pulmonary and Critical Care, University of California, San Francisco, San Francisco CA 94043
| | - Mark L Borowsky
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Harvard University, Boston MA 02115
| | - Bhavana Muddukrishna
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Harvard University, Boston MA 02115
| | - Barry N Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers, The State University of NJ, Newark, NJ 07103
| | - Natalia Kurepina
- Public Health Research Institute Tuberculosis Center, Rutgers, The State University of NJ, Newark, NJ 07103
| | - James Galagan
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
- Departments of Biomedical Engineering, Boston University, Boston, MA 02215
- Department of Microbiology, Boston University, Boston, MA 02215
- Bioinformatics Program, Boston University, Boston, MA 02215
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Bruce Birren
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Eric S Lander
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
| | - Pardis C Sabeti
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA 02115
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA 02115
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115
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126
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Zhang H, Li D, Zhao L, Fleming J, Lin N, Wang T, Liu Z, Li C, Galwey N, Deng J, Zhou Y, Zhu Y, Gao Y, Wang T, Wang S, Huang Y, Wang M, Zhong Q, Zhou L, Chen T, Zhou J, Yang R, Zhu G, Hang H, Zhang J, Li F, Wan K, Wang J, Zhang XE, Bi L. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet 2013; 45:1255-60. [DOI: 10.1038/ng.2735] [Citation(s) in RCA: 348] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 07/30/2013] [Indexed: 12/29/2022]
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Multidrug-resistant tuberculosis in panama is driven by clonal expansion of a multidrug-resistant Mycobacterium tuberculosis strain related to the KZN extensively drug-resistant M. tuberculosis strain from South Africa. J Clin Microbiol 2013; 51:3277-85. [PMID: 23884993 DOI: 10.1128/jcm.01122-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a significant health problem in Panama. The extent to which such cases are the result of primary or acquired resistance and the strain families involved are unknown. We performed whole-genome sequencing of a collection of 66 clinical MDR isolates, along with 31 drug-susceptible isolates, that were isolated in Panama between 2001 and 2010; 78% of the MDR isolates belong to the Latin American-Mediterranean (LAM) family. Drug resistance mutations correlated well with drug susceptibility profiles. To determine the relationships among these strains and to better understand the acquisition of resistance mutations, a phylogenetic tree was constructed based on a genome-wide single-nucleotide polymorphism analysis. The phylogenetic tree shows that the isolates are highly clustered, with a single strain (LAM9-c1) accounting for nearly one-half of the MDR isolates (29/66 isolates). The LAM9-c1 strain was most prevalent among male patients of working age and was associated with high mortality rates. Members of this cluster all share identical mutations conferring resistance to isoniazid (KatG S315T mutation), rifampin (RpoB S531L mutation), and streptomycin (rrs C517T mutation). This evidence of primary resistance supports a model in which MDR-TB in Panama is driven by clonal expansion and ongoing transmission of several strains in the LAM family, including the highly successful MDR strain LAM9-c1. The phylogenetic analysis also shows that the LAM9-c1 strain is closely related to the KwaZulu-Natal (KZN) extensively drug-resistant TB strain identified in KwaZulu-Natal, South Africa. The LAM9-c1 and KZN strains likely arose from a recent common ancestor that was transmitted between Panama and South Africa and had the capacity to tolerate an accumulation of multiple resistance mutations.
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128
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U. Köser C, M. Bryant J, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med 2013; 369:290-2. [PMID: 23863072 PMCID: PMC3836233 DOI: 10.1056/nejmc1215305] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | | | - Jennifer Becq
- Illumina (Cambridge), Little Chesterford, United Kingdom
| | | | | | | | - Andrew J. Carmichael
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
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Brandis G, Hughes D. Genetic characterization of compensatory evolution in strains carrying rpoB Ser531Leu, the rifampicin resistance mutation most frequently found in clinical isolates. J Antimicrob Chemother 2013; 68:2493-7. [PMID: 23759506 DOI: 10.1093/jac/dkt224] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES The evolution of rifampicin resistance in Mycobacterium tuberculosis is a major threat to effective tuberculosis therapy. Much is known about the initial emergence of rifampicin resistance, but the further evolution of these resistant strains has only lately been subject to investigation. Although resistance can be caused by many different mutations in rpoB, among clinical M. tuberculosis isolates the mutation rpoB S531L is overwhelmingly the most frequently found. Clinical isolates with rpoB S531L frequently carry additional mutations in genes for RNA polymerase subunits, and it has been speculated that these are fitness-compensatory mutations, ameliorating the fitness cost of the primary resistance mutation. We tested this hypothesis using Salmonella as a model organism. METHODS We created the rpoB S531L mutation in Salmonella and then evolved independent lineages with selection for mutants with increased relative fitness. Relative fitness associated with putative compensatory mutations was measured after genetic reconstruction in isogenic strains. RESULTS Compensatory mutations were identified in genes coding for different subunits of RNA polymerase: rpoA, rpoB and rpoC. Genetic reconstructions demonstrated that each of these secondary mutations reduced the fitness cost of the rpoB S531L resistance mutation. CONCLUSIONS The compensatory mutations identified in Salmonella cluster in similar locations to the additional mutations found in M. tuberculosis isolates. These new data strongly support the idea that many of the previously identified rpoA, rpoB and rpoC mutations in rifampicin-resistant M. tuberculosis (rpoB S531L) are indeed fitness-compensatory mutations.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
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130
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Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet 2013; 45:784-90. [PMID: 23749189 PMCID: PMC3777616 DOI: 10.1038/ng.2656] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 05/06/2013] [Indexed: 11/30/2022]
Abstract
A critical question in tuberculosis control is why some strains of Mycobacterium tuberculosis are preferentially associated with multiple drug resistances. We demonstrate that M. tuberculosis strains from Lineage 2 (East Asian lineage and Beijing sublineage) acquire drug resistances in vitro more rapidly than M. tuberculosis strains from Lineage 4 (Euro-American lineage) and that this higher rate can be attributed to a higher mutation rate. Moreover, the in vitro mutation rate correlates well with the bacterial mutation rate in humans as determined by whole genome sequencing of clinical isolates. Finally, using a stochastic mathematical model, we demonstrate that the observed differences in mutation rate predict a substantially higher probability that patients infected with a drug susceptible Lineage 2 strain will harbor multidrug resistant bacteria at the time of diagnosis. These data suggest that interventions to prevent the emergence of drug resistant tuberculosis should target bacterial as well as treatment-related risk factors.
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Affiliation(s)
- Christopher B Ford
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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131
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Eliseev PI, Maryandyshev AO, Nikishova EI, Tarasova IV, Gorina GP, Chryssanthou E, Ridell M, Larsson LO. Epidemiological analyses of tuberculosis in Archangelsk, Russia and implementation of a rapid assay for detection of resistance in this high burden setting. Int J Mycobacteriol 2013; 2:103-8. [PMID: 26785897 DOI: 10.1016/j.ijmyco.2013.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/02/2013] [Accepted: 04/02/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major problem in Russia, particularly regarding multidrug-resistant tuberculosis (MDR-TB). Rapid drug susceptibility testing methods are therefore needed. OBJECTIVES To perform epidemiological analyses of TB in the Archangelsk region and to evaluate the molecular method GenoType®MTBDRplus in this type of setting. MATERIALS AND METHODS Clinical and microbiological data of all TB patients in Archangelsk were collected in 2010. Smear-positive sputa were analysed by MTBDRplus and Bactec MGIT 960. RESULTS The number of TB cases was 812 (incidence 65/105) and among these patients, 151 cases were registered in the penitentiary system (incidence 1162/105). Most patients were men, 94% had pulmonary TB and 22% were relapses. Out of all cases, 341 (42%) were smear positive and thus contagious and 176 (22%) had MDR-TB, among which one had extensively drug resistant tuberculosis (XDR-TB). Furthermore, two TB patients had strains being resistant to rifampicin, but susceptible to isoniazid. The number of cases being both contagious and MDR-TB was 128 representing 15.8% of all TB cases (incidence 10.2/105). Among these 128 TB patients 37 were relapses representing 25.7% of all the relapse cases. The results of MTBDRplus and Bactec MGIT analyses corresponded in 98.8%. CONCLUSIONS In Archangelsk many TB patients had contagious MDR-TB thus being hazardous in society and relapsing pulmonary TB was common. The TB situation in the prisons was particularly severe. The analyses showed furthermore that MTBDRplus is of major value in this setting.
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Affiliation(s)
| | | | | | - Irina V Tarasova
- Regional Clinical Antituberculosis Dispensary, Archangelsk, Russia
| | - Galina P Gorina
- Regional Clinical Antituberculosis Dispensary, Archangelsk, Russia
| | - Erja Chryssanthou
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Ridell
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Göteborg, Sweden
| | - Lars-Olof Larsson
- Department of Medicine, Division of Respiratory Medicine, Karolinska University Hospital, Stockholm, Sweden.
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132
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Vesth T, Lagesen K, Acar Ö, Ussery D. CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One 2013; 8:e60120. [PMID: 23577086 PMCID: PMC3618517 DOI: 10.1371/journal.pone.0060120] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 02/24/2013] [Indexed: 01/01/2023] Open
Abstract
Background Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. Results The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. Conclusion This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.
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Affiliation(s)
- Tammi Vesth
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Karin Lagesen
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| | - Öncel Acar
- Department of Electrical Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David Ussery
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
- * E-mail:
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133
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Rifampicin Resistance: Fitness Costs and the Significance of Compensatory Evolution. Antibiotics (Basel) 2013; 2:206-16. [PMID: 27029299 PMCID: PMC4790335 DOI: 10.3390/antibiotics2020206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/28/2013] [Accepted: 03/28/2013] [Indexed: 11/17/2022] Open
Abstract
Seventy years after the introduction of antibiotic chemotherapy to treat tuberculosis, problems caused by drug-resistance in Mycobacterium tuberculosis have become greater than ever. The discovery and development of novel drugs and drug combination therapies will be critical to managing these problematic infections. However, to maintain effective therapy in the long-term and to avoid repeating the mistakes of the past, it is essential that we understand how resistance to antibiotics evolves in M. tuberculosis. Recent studies in genomics and genetics, employing both clinical isolates and model organisms, have revealed that resistance to the frontline anti-tuberculosis drug, rifampicin, is very strongly associated with the selection of fitness compensatory mutations in the different subunits of RNA polymerase. This mode of resistance evolution may also apply to other drugs, and knowledge of the rates and mechanisms could be used to design improved diagnostics and by tracking the evolution of infectious strains, to inform the optimization of therapies.
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134
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Coffee M. Extensively drug-resistant tuberculosis: new strains, new challenges. Microb Drug Resist 2013. [DOI: 10.2217/ebo.12.500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Megan Coffee
- Megan Coffee was born in New York City (NY, USA), and was raised in New Jersey (NJ, USA). She completed her undergraduate degree at Harvard University (MA, USA) with high honors in chemistry. Her PhD from Oxford University (UK) is in mathematical modeling of infectious diseases, focusing on the epidemiology of HIV transmission with migration and other cofactors in South Africa and Zimbabwe. Her MD is from Harvard University, where she studied health sciences and technology, a joint program between
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135
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Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SAFT, Siezen RJ, Borgdorff M, Bentley SD, Parkhill J, van Soolingen D. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis 2013; 13:110. [PMID: 23446317 PMCID: PMC3599118 DOI: 10.1186/1471-2334-13-110] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required. METHODS We attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years. RESULTS Multiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links. CONCLUSIONS This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
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Affiliation(s)
- Josephine M Bryant
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anita C Schürch
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henk van Deutekom
- Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jessica L de Beer
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
| | - Victor de Jager
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
| | - Kristin Kremer
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
| | - Sacha A F T van Hijum
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
- NIZO food research, P.O. Box 206710 BA, Ede, The Netherlands
| | - Roland J Siezen
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
| | - Martien Borgdorff
- Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Dick van Soolingen
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
- Department of Clinical Microbiology and department of Lung Disease, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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136
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Walker TM, Monk P, Smith EG, Peto TEA. Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. Clin Microbiol Infect 2013; 19:796-802. [PMID: 23432709 DOI: 10.1111/1469-0691.12183] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The control of tuberculosis depends on the identification and treatment of infectious patients and their contacts, who are currently identified through a combined approach of genotyping and epidemiological investigation. However, epidemiological data are often challenging to obtain, and genotyping data are difficult to interpret without them. Whole genome sequencing (WGS) technology is increasingly affordable, and offers the prospect of identifying plausible transmission events between patients without prior recourse to epidemiological data. We discuss the current approaches to tuberculosis control, and how WGS might advance public health efforts in the future.
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Affiliation(s)
- T M Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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137
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Ilina EN, Shitikov EA, Ikryannikova LN, Alekseev DG, Kamashev DE, Malakhova MV, Parfenova TV, Afanas’ev MV, Ischenko DS, Bazaleev NA, Smirnova TG, Larionova EE, Chernousova LN, Beletsky AV, Mardanov AV, Ravin NV, Skryabin KG, Govorun VM. Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PLoS One 2013; 8:e56577. [PMID: 23437175 PMCID: PMC3577857 DOI: 10.1371/journal.pone.0056577] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains is a growing problem in many countries. The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. In our work, we sequenced three genomes of Russian MTB strains of different phenotypes--drug susceptible, MDR and XDR. Of them, MDR and XDR strains were collected in Tomsk (Siberia, Russia) during the local TB outbreak in 1998-1999 and belonged to rare KQ and KY families in accordance with IS6110 typing, which are considered endemic for Russia. Based on phylogenetic analysis, our isolates belonged to different genetic families, Beijing, Ural and LAM, which made the direct comparison of their genomes impossible. For this reason we performed their comparison in the broader context of all M. tuberculosis genomes available in GenBank. The list of unique individual non-synonymous SNPs for each sequenced isolate was formed by comparison with all SNPs detected within the same phylogenetic group. For further functional analysis, all proteins with unique SNPs were ascribed to 20 different functional classes based on Clusters of Orthologous Groups (COG). We have confirmed drug resistant status of our isolates that harbored almost all known drug-resistance associated mutations. Unique SNPs of an XDR isolate CTRI-4(XDR), belonging to a Beijing family were compared in more detail with SNPs of additional 14 Russian XDR strains of the same family. Only type specific mutations in genes of repair, replication and recombination system (COG category L) were found common within this group. Probably the other unique SNPs discovered in CTRI-4(XDR) may have an important role in adaptation of this microorganism to its surrounding and in escape from antituberculosis drugs treatment.
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Affiliation(s)
- Elena N. Ilina
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Egor A. Shitikov
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | - Dmitry G. Alekseev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitri E. Kamashev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maja V. Malakhova
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | - Maxim V. Afanas’ev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Nikolai A. Bazaleev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | | | | | | | | | | | | | - Vadim M. Govorun
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
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138
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Champion MD, Gray V, Eberhard C, Kumar S. The evolutionary history of amino acid variations mediating increased resistance of S. aureus identifies reversion mutations in metabolic regulators. PLoS One 2013; 8:e56466. [PMID: 23424663 PMCID: PMC3570469 DOI: 10.1371/journal.pone.0056466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/09/2013] [Indexed: 01/11/2023] Open
Abstract
The evolution of resistance in Staphylococcus aureus occurs rapidly, and in response to all known antimicrobial treatments. Numerous studies of model species describe compensatory roles of mutations in mediating competitive fitness, and there is growing evidence that these mutation types also drive adaptation of S. aureus strains. However, few studies have tracked amino acid changes during the complete evolutionary trajectory of antibiotic adaptation or been able to predict their functional relevance. Here, we have assessed the efficacy of computational methods to predict biological resistance of a collection of clinically known Resistance Associated Mutations (RAMs). We have found that >90% of known RAMs are incorrectly predicted to be functionally neutral by at least one of the prediction methods used. By tracing the evolutionary histories of all of the false negative RAMs, we have discovered that a significant number are reversion mutations to ancestral alleles also carried in the MSSA476 methicillin-sensitive isolate. These genetic reversions are most prevalent in strains following daptomycin treatment and show a tendency to accumulate in biological pathway reactions that are distinct from those accumulating non-reversion mutations. Our studies therefore show that in addition to non-reversion mutations, reversion mutations arise in isolates exposed to new antibiotic treatments. It is possible that acquisition of reversion mutations in the genome may prevent substantial fitness costs during the progression of resistance. Our findings pose an interesting question to be addressed by further clinical studies regarding whether or not these reversion mutations lead to a renewed vulnerability of a vancomycin or daptomycin resistant strain to antibiotics administered at an earlier stage of infection.
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Affiliation(s)
- Mia D Champion
- Center for Evolutionary Medicine & Informatics, Biodesign Institute, Arizona State University, Arizona, United States of America.
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139
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Abstract
Fundamental aspects of the lifestyle of Mycobacterium tuberculosis implicate DNA metabolism in bacillary survival and adaptive evolution. The environments encountered by M. tuberculosis during successive cycles of infection and transmission are genotoxic. Moreover, as an obligate pathogen, M. tuberculosis has the ability to persist for extended periods in a subclinical state, suggesting that active DNA repair is critical to maintain genome integrity and bacterial viability during prolonged infection. In this chapter, we provide an overview of the major DNA metabolic pathways identified in M. tuberculosis, and situate key recent findings within the context of mycobacterial pathogenesis. Unlike many other bacterial pathogens, M. tuberculosis is genetically secluded, and appears to rely solely on chromosomal mutagenesis to drive its microevolution within the human host. In turn, this implies that a balance between high versus relaxed fidelity mechanisms of DNA metabolism ensures the maintenance of genome integrity, while accommodating the evolutionary imperative to adapt to hostile and fluctuating environments. The inferred relationship between mycobacterial DNA repair and genome dynamics is considered in the light of emerging data from whole-genome sequencing studies of clinical M. tuberculosis isolates which have revealed the potential for considerable heterogeneity within and between different bacterial and host populations.
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140
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Abstract
Recent years have witnessed an increased appreciation of the extent and relevance of strain-to-strain variation in Mycobacterium tuberculosis. This paradigm shift can largely be attributed to an improved understanding of the global population structure of this organism, and to the realisation that the various members of the M. tuberculosis complex (MTBC) harbour more genetic diversity than previously realised. Moreover, many studies using experimental models of infection have demonstrated that MTBC diversity translates into significant differences in immunogenecity and virulence . However, linking these experimental phenotypes to relevant clinical phenotypes has been difficult, and to date, largely unsuccessful. Nevertheless, emerging high-throughput technologies, in particular next-generation sequencing , offer new opportunities, and have already lead to important new insights. Given the complexity of the host-pathogen interaction in tuberculosis, systems approaches will be key to define the role of MTBC diversity in the fight against one of humankind's most important pathogens.
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141
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Stucki D, Gagneux S. Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis (Edinb) 2012; 93:30-9. [PMID: 23266261 DOI: 10.1016/j.tube.2012.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/25/2012] [Indexed: 12/12/2022]
Abstract
Recent advances in DNA sequencing have led to the discovery of thousands of single nucleotide polymorphisms (SNPs) in clinical isolates of Mycobacterium tuberculosis complex (MTBC). This genetic variation has changed our understanding of the differences and phylogenetic relationships between strains. Many of these mutations can serve as phylogenetic markers for strain classification, while others cause drug resistance. Moreover, SNPs can affect the bacterial phenotype in various ways, which may have an impact on the outcome of tuberculosis (TB) infection and disease. Despite the importance of SNPs for our understanding of the diversity of MTBC populations, the research community currently lacks a comprehensive, well-curated and user-friendly database dedicated to SNP data. First attempts to catalogue and annotate SNPs in MTBC have been made, but more work is needed. In this review, we discuss the biological and epidemiological relevance of SNPs in MTBC. We then review some of the analytical challenges involved in processing SNP data, and end with a list of features, which should be included in a new SNP database for MTBC.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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142
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Müller B, Borrell S, Rose G, Gagneux S. The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis. Trends Genet 2012; 29:160-9. [PMID: 23245857 DOI: 10.1016/j.tig.2012.11.005] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/18/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
Abstract
Recent surveillance data of multidrug-resistant tuberculosis (MDR-TB) reported the highest rates of resistance ever documented. As further amplification of resistance in MDR strains of Mycobacterium tuberculosis occurs, extensively drug-resistant (XDR) and totally drug-resistant (TDR) TB are beginning to emerge. Although for the most part, the epidemiological factors involved in the spread of MDR-TB are understood, insights into the bacterial drivers of MDR-TB have been gained only recently, largely owing to novel technologies and research in other organisms. Herein, we review recent findings on how bacterial factors, such as persistence, hypermutation, the complex interrelation between drug resistance and fitness, compensatory evolution, and epistasis affect the evolution of multidrug resistance in M. tuberculosis. Improved knowledge of these factors will help better predict the future trajectory of MDR-TB, and contribute to the development of new tools and strategies to combat this growing public health threat.
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Affiliation(s)
- Borna Müller
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
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143
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Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrob Agents Chemother 2012. [PMID: 23208709 DOI: 10.1128/aac.01541-12] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rifampin resistance in clinical isolates of Mycobacterium tuberculosis arises primarily through the selection of bacterial variants harboring mutations in the 81-bp rifampin resistance-determining region of the rpoB gene. While these mutations were shown to infer a fitness cost in the absence of antibiotic pressure, compensatory mutations in rpoA and rpoC were identified which restore the fitness of rifampin-resistant bacteria carrying mutations in rpoB. To investigate the epidemiological relevance of these compensatory mutations, we analyzed 286 drug-resistant and 54 drug-susceptible clinical M. tuberculosis isolates from the Western Cape, South Africa, a high-incidence setting of multidrug-resistant tuberculosis. Sequencing of a portion of the RpoA-RpoC interaction region of the rpoC gene revealed that 23.5% of all rifampin-resistant isolates tested carried a nonsynonymous mutation in this region. These putative compensatory mutations in rpoC were associated with transmission, as 30.8% of all rifampin-resistant isolates with an IS6110 restriction fragment length polymorphism (RFLP) pattern belonging to a recognized RFLP cluster harbored putative rpoC mutations. Such mutations were present in only 9.4% of rifampin-resistant isolates with unique RFLP patterns (P < 0.01). Moreover, these putative compensatory mutations were associated with specific strain genotypes and the rpoB S531L rifampin resistance mutation. Among isolates harboring this rpoB mutation, 44.1% also harbored rpoC mutations, while only 4.1% of the isolates with other rpoB mutations exhibited mutations in rpoC (P < 0.001). Our study supports a role for rpoC mutations in the transmission of multidrug-resistant tuberculosis and illustrates how epistatic interactions between drug resistance-conferring mutations, compensatory mutations, and different strain genetic backgrounds might influence compensatory evolution in drug-resistant M. tuberculosis.
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144
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Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. J Clin Microbiol 2012; 51:611-4. [PMID: 23175259 DOI: 10.1128/jcm.02279-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Two Southeast Asian students attending the same school in the United Kingdom presented with pulmonary tuberculosis. An epidemiological investigation failed to link the two cases, and drug resistance profiles of the Mycobacterium tuberculosis isolates were discrepant. Whole-genome sequencing of the isolates found them to be genetically identical, suggesting a missed transmission event.
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145
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Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TEA. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. THE LANCET. INFECTIOUS DISEASES 2012; 13:137-46. [PMID: 23158499 PMCID: PMC3556524 DOI: 10.1016/s1473-3099(12)70277-3] [Citation(s) in RCA: 661] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background Tuberculosis incidence in the UK has risen in the past decade. Disease control depends on epidemiological data, which can be difficult to obtain. Whole-genome sequencing can detect microevolution within Mycobacterium tuberculosis strains. We aimed to estimate the genetic diversity of related M tuberculosis strains in the UK Midlands and to investigate how this measurement might be used to investigate community outbreaks. Methods In a retrospective observational study, we used Illumina technology to sequence M tuberculosis genomes from an archive of frozen cultures. We characterised isolates into four groups: cross-sectional, longitudinal, household, and community. We measured pairwise nucleotide differences within hosts and between hosts in household outbreaks and estimated the rate of change in DNA sequences. We used the findings to interpret network diagrams constructed from 11 community clusters derived from mycobacterial interspersed repetitive-unit–variable-number tandem-repeat data. Findings We sequenced 390 separate isolates from 254 patients, including representatives from all five major lineages of M tuberculosis. The estimated rate of change in DNA sequences was 0·5 single nucleotide polymorphisms (SNPs) per genome per year (95% CI 0·3–0·7) in longitudinal isolates from 30 individuals and 25 families. Divergence is rarely higher than five SNPs in 3 years. 109 (96%) of 114 paired isolates from individuals and households differed by five or fewer SNPs. More than five SNPs separated isolates from none of 69 epidemiologically linked patients, two (15%) of 13 possibly linked patients, and 13 (17%) of 75 epidemiologically unlinked patients (three-way comparison exact p<0·0001). Genetic trees and clinical and epidemiological data suggest that super-spreaders were present in two community clusters. Interpretation Whole-genome sequencing can delineate outbreaks of tuberculosis and allows inference about direction of transmission between cases. The technique could identify super-spreaders and predict the existence of undiagnosed cases, potentially leading to early treatment of infectious patients and their contacts. Funding Medical Research Council, Wellcome Trust, National Institute for Health Research, and the Health Protection Agency.
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Affiliation(s)
- Timothy M Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
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146
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Diagnostic accuracy of the genotype MTBDRsl assay for rapid diagnosis of extensively drug-resistant tuberculosis in HIV-coinfected patients. J Clin Microbiol 2012; 51:243-8. [PMID: 23152552 DOI: 10.1128/jcm.02513-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Russian Federation is a high-tuberculosis (TB)-burden country with high rates of Mycobacterium tuberculosis multidrug resistance (MDR) and extensive drug resistance (XDR), especially in HIV-coinfected patients. Rapid and reliable diagnosis for detection of resistance to second-line drugs is vital for adequate patient management. We evaluated the performance of the GenoType MTBDRsl (Hain Lifescience GmbH, Nehren, Germany) assay on smear-positive sputum specimens obtained from 90 HIV-infected MDR TB patients from Russia. Test interpretability was over 98%. Specificity was over 86% for all drugs, while sensitivity varied, being the highest (71.4%) for capreomycin and lowest (9.4%) for kanamycin, probably due to the presence of mutations in the eis gene. The sensitivity of detection of XDR TB was 13.6%, increasing to 42.9% if kanamycin (not commonly used in Western Europe) was excluded. The assay is a highly specific screening tool for XDR detection in direct specimens from HIV-coinfected TB patients but cannot be used to rule out XDR TB.
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147
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Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance. Antimicrob Agents Chemother 2012; 56:6080-7. [PMID: 23006760 DOI: 10.1128/aac.01641-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium tuberculosis complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.
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148
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Brandis G, Wrande M, Liljas L, Hughes D. Fitness-compensatory mutations in rifampicin-resistant RNA polymerase. Mol Microbiol 2012; 85:142-51. [PMID: 22646234 DOI: 10.1111/j.1365-2958.2012.08099.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mutations in rpoB (RNA polymerase β-subunit) can cause high-level resistance to rifampicin, an important first-line drug against tuberculosis. Most rifampicin-resistant (Rif(R)) mutants selected in vitro have reduced fitness, and resistant clinical isolates of M. tuberculosis frequently carry multiple mutations in RNA polymerase genes. This supports a role for compensatory evolution in global epidemics of drug-resistant tuberculosis but the significance of secondary mutations outside rpoB has not been demonstrated or quantified. Using Salmonella as a model organism, and a previously characterized Rif(R) mutation (rpoB R529C) as a starting point, independent lineages were evolved with selection for improved growth in the presence and absence of rifampicin. Compensatory mutations were identified in every lineage and were distributed between rpoA, rpoB and rpoC. Resistance was maintained in all strains showing that increased fitness by compensatory mutation was more likely than reversion. Genetic reconstructions demonstrated that the secondary mutations were responsible for increasing growth rate. Many of the compensatory mutations in rpoA and rpoC individually caused small but significant reductions in susceptibility to rifampicin, and some compensatory mutations in rpoB individually caused high-level resistance. These findings show that mutations in different components of RNA polymerase are responsible for fitness compensation of a Rif(R) mutant.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
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