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Steglich M, Nübel U. The challenge of detecting indels in bacterial genomes from short-read sequencing data. J Biotechnol 2017; 250:11-15. [PMID: 28267569 DOI: 10.1016/j.jbiotec.2017.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/24/2017] [Accepted: 02/26/2017] [Indexed: 10/20/2022]
Abstract
We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1-2321bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size. All tools tested were able to detect short indels (≤29 basepairs) at sensitivities close to 100%, albeit Pindel reported up to 20% false calls. In contrast, gapped-alignment and split-read tools failed to recover large proportions of long indels (>29bp) even at 120-fold coverage, and again, Pindel produced significant numbers of false-positive calls. Outstandingly, ScanIndel detected and reconstructed 97% of long indels on average (95% confidence intervals, 88%-99%) and, at the same time, produced negligible amounts of false calls. Hence, the combinatorial approach implemented in ScanIndel was able to recover the positions, types and sequences of indels with excellent sensitivity and false-discovery rate, by encompassing the full indel length spectrum present in the datasets.
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Affiliation(s)
| | - Ulrich Nübel
- Leibniz Institute DSMZ, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site, Hannover-Braunschweig, Germany
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202
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Walsh AM, Crispie F, Claesson MJ, Cotter PD. Translating Omics to Food Microbiology. Annu Rev Food Sci Technol 2017; 8:113-134. [DOI: 10.1146/annurev-food-030216-025729] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marcus J. Claesson
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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203
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Crispell J, Zadoks RN, Harris SR, Paterson B, Collins DM, de-Lisle GW, Livingstone P, Neill MA, Biek R, Lycett SJ, Kao RR, Price-Carter M. Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand. BMC Genomics 2017; 18:180. [PMID: 28209138 PMCID: PMC5314462 DOI: 10.1186/s12864-017-3569-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
Background Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being incorporated into routine bTB surveillance. Results A high rate of exchange was evident between the sampled wildlife and cattle populations but directional estimates of inter-species transmission were sensitive to the sampling strategy employed. A relatively high substitution rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing methods, acts to endorse WGS as a typing tool. Conclusions In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with the low prevalence of bTB in New Zealand’s cattle population it is likely that, currently, wildlife populations are acting as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular typing data. The substitution rates estimated here will be an important part of epidemiological investigations using WGS data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3569-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Crispell
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Brent Paterson
- TBfree New Zealand, PO Box 3412, Wellington, 6140, New Zealand
| | | | | | | | - Mark A Neill
- TBfree New Zealand, PO Box 3412, Wellington, 6140, New Zealand
| | - Roman Biek
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Samantha J Lycett
- Infection and Immunity Division, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Rowland R Kao
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK.
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204
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Tuberculosis Outbreak in an Educational Institution in Norway. J Clin Microbiol 2017; 55:1327-1333. [PMID: 28202795 DOI: 10.1128/jcm.01152-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 02/03/2017] [Indexed: 11/20/2022] Open
Abstract
Within 1 week in April 2013, three cases of pulmonary tuberculosis (TB) were reported among students attending training sessions at an educational institution in Oslo, Norway. By the end of October 2013, a total of nine epidemiologically linked cases had been reported. The outbreak encompassed a total of 24 cases from 2009 to 2014, among which all of the 22 Mycobacterium tuberculosis isolates available had identical mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) profiles (MtbC15-9 code 10287-189) belonging to the Beijing lineage. Whole-genome sequencing (WGS) of the M. tuberculosis isolates revealed 20 variable nucleotide positions within the cluster, indicating a clonal outbreak. The most likely index case was identified and diagnosed in Norway in 2009 but was born in Asia. WGS analyses verified that all of the cases were indeed part of a single transmission chain. However, even when combining WGS and intensified contact tracing, we were unable to fully reconstruct the TB transmission events.
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205
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Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, Brand J, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet 2017; 49:395-402. [PMID: 28092681 PMCID: PMC5402762 DOI: 10.1038/ng.3767] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/14/2016] [Indexed: 11/09/2022]
Abstract
Multidrug-resistant tuberculosis (MDR-TB), caused by drug resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. In this study, we examined a dataset of 5,310 M. tuberculosis whole genome sequences from five continents. Despite great diversity with respect to geographic point of isolation, genetic background and drug resistance, patterns of drug resistance emergence were conserved globally. We have identified harbinger mutations that often precede MDR. In particular, the katG S315T mutation, conferring resistance to isoniazid, overwhelmingly arose before rifampicin resistance across all lineages, geographic regions, and time periods. Molecular diagnostics that include markers for rifampicin resistance alone will be insufficient to identify pre-MDR strains. Incorporating knowledge of pre-MDR polymorphisms, particularly katG S315, into molecular diagnostics will enable targeted treatment of patients with pre-MDR-TB to prevent further development of MDR-TB.
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Affiliation(s)
- Abigail L Manson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Keira A Cohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | | | - Derek T Armstrong
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clifton E Barry
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeannette Brand
- Medical Research Council, TB Platform, Pretoria, South Africa
| | | | - Sinéad B Chapman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sang-Nae Cho
- International Tuberculosis Research Center, Changwon and Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institutes of Health, Rockville, Maryland, USA
| | - James Gomez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andreea M Jodals
- Clinical Hospital of Pneumology Leon Daniello, Cluj Napoca, Romania
| | - Moses Joloba
- Department of Medical Microbiology, Mycobacteriology Laboratory, Makerere University, Kampala, Uganda
| | | | - Jong Seok Lee
- International Tuberculosis Research Center, Changwon and Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | | | - Mamoudou Maiga
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Ecaterina Noroc
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | - Elena Romancenco
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Willy Ssengooba
- Department of Medical Microbiology, Mycobacteriology Laboratory, Makerere University, Kampala, Uganda
| | - A A Velayati
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kathryn Winglee
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Aksana Zalutskaya
- Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Laura E Via
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Gail H Cassell
- Department of Global Health and Social Medicine, Harvard Medical School, Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Susan E Dorman
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jerrold Ellner
- Section of Infectious Diseases, Boston Medical Center, Boston, Massachusetts, USA
| | - Parissa Farnia
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - James E Galagan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biomedical Engineering and Microbiology, Boston University, Boston, Massachusetts, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institutes of Health, Rockville, Maryland, USA
| | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Phthisiopneumology Institute, Chisinau, Moldova
| | | | - Po-Ren Hsueh
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | | | - Alexander S Pym
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Alena Skrahina
- Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | | | | | - David Alland
- Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - William R Bishai
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.,Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ted Cohen
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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206
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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207
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Genomic Epidemiology of Tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:79-93. [DOI: 10.1007/978-3-319-64371-7_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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208
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Abstract
As we move into the era of the Sustainable Development Goals (SDGs), the World Health Organization (WHO) has developed the End TB strategy 2016-2035 with a goal to end the global epidemic of tuberculosis (TB) by 2035. Achieving the targets laid out in the Strategy will require strengthening of the whole TB diagnosis and treatment cascade, including improved case detection, the establishment of universal drug susceptibility testing and rapid treatment initiation. An estimated 3.9% of new TB cases and 21% of previously treated cases had rifampicin-resistant (RR) or multidrug-resistant (MDR) TB in 2015. These levels have remained stable over time, although limited data are available from major high burden settings. In addition to the emergence of drug resistance due to inadequate treatment, there is growing evidence that direct transmission is a large contributor to the RR/MDR-TB epidemic. Only 340,000 of the estimated 580,000 incident cases of RR/MDR-TB were notified to WHO in 2015. Among these, only 125,000 were initiated on second-line treatment. RR/MDR-TB epidemics are likely to be driven by direct transmission. The most important risk factor for MDR-TB is a history of previous treatment. Other risk factors vary according to setting but can include hospitalisation, incarceration and HIV infection. Children have the same risk of MDR-TB as adults and represent a diagnostic and treatment challenge. Rapid molecular technologies have revolutionized the diagnosis of drug-resistant TB. Until capacity can be established to test every TB patient for rifampicin resistance, countries should focus on gradually expanding their coverage of testing. DNA sequencing technologies are being increasingly incorporated into patient management and drug resistance surveillance. They offer additional benefits over conventional culture-based phenotypic testing, including a faster turn-around time for results, assessment of resistance patterns to a range of drugs, and investigation of strain clustering and transmission.
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209
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Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2016; 1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
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Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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210
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Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 2016; 23:2-22. [PMID: 27890457 DOI: 10.1016/j.cmi.2016.11.012] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
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Affiliation(s)
- M J Ellington
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - O Ekelund
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - F M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - R Canton
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - M Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - C Giske
- Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - H Grundman
- University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Hasman
- Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark
| | - M T G Holden
- School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK
| | - K L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - J Iredell
- Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia
| | - G Kahlmeter
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - A MacGowan
- Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - D Mevius
- Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - M Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - T Naas
- French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France
| | - T Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - J-M Rolain
- PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Ø Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.
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211
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Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2016; 113:13881-13886. [PMID: 27872285 DOI: 10.1073/pnas.1611283113] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The "Beijing" Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that recent historical events have contributed to the evolution and dispersal of the CAC. Our timing estimates indicate that the clade was likely introduced to Afghanistan during the 1979-1989 Soviet-Afghan war and spread further after population displacement in the wake of the American invasion in 2001. We also find that drug resistance mutations accumulated on a massive scale in Mtb isolates from former Soviet republics after the fall of the Soviet Union, a pattern that was not observed in CAC isolates from Afghanistan. Our results underscore the detrimental effects of political instability and population displacement on tuberculosis control and demonstrate the power of phylodynamic methods in exploring bacterial evolution in space and time.
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212
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Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, Kreiswirth BN, Mathema B. Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009. BMC Genomics 2016; 17:947. [PMID: 27871225 PMCID: PMC5117616 DOI: 10.1186/s12864-016-3298-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
Background Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M. tuberculosis subpopulations, employing both phylogenomic and population genetics methods. Results M. tuberculosis subpopulations in New York City and New Jersey can be distinguished via phylogenomic reconstruction, evidence of demographic expansion and subpopulation-specific signatures of selection, and by determination of subgroup-defining nucleotide substitutions. These methods identified known historical outbreak clusters and previously unidentified subpopulations within relatively monomorphic M. tuberculosis endemic clone groups. Neutrality statistics based on the site frequency spectrum were less useful for identifying M. tuberculosis subpopulations, likely due to the low levels of informative genetic variation in recently diverged isolate groups. In addition, we observed that isolates from New York City endemic clone groups have acquired multiple non-synonymous SNPs in virulence- and growth-associated pathways, and relatively few mutations in drug resistance-associated genes, suggesting that overall pathoadaptive fitness, rather than the acquisition of drug resistance mutations, has played a central role in the evolutionary history and epidemiology of M. tuberculosis subpopulations in New York City. Conclusions Our results demonstrate that some but not all WGS-based methods are useful for detection of emerging M. tuberculosis clone groups, and support the use of phylogenomic reconstruction in routine tuberculosis laboratory surveillance, particularly in areas with relatively less diverse M. tuberculosis populations. Our study also supports the use of wider-reaching phylogenomic and population genomic methods in tuberculosis public health practice, which can support tuberculosis control activities by identifying genetic polymorphisms contributing to epidemiological success in local M. tuberculosis populations and possibly explain why certain isolate groups are apparently more successful in specific host populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3298-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tyler S Brown
- Department of Medicine, Columbia University, New York, NY, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - John R Walker
- The Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Paul J Planet
- Department of Pediatrics, Division of Infectious Diseases, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pablo J Bifani
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | | | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA.
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213
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Aldridge RW, Zenner D, White PJ, Williamson EJ, Muzyamba MC, Dhavan P, Mosca D, Thomas HL, Lalor MK, Abubakar I, Hayward AC. Tuberculosis in migrants moving from high-incidence to low-incidence countries: a population-based cohort study of 519 955 migrants screened before entry to England, Wales, and Northern Ireland. Lancet 2016; 388:2510-2518. [PMID: 27742165 PMCID: PMC5121129 DOI: 10.1016/s0140-6736(16)31008-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Tuberculosis elimination in countries with a low incidence of the disease necessitates multiple interventions, including innovations in migrant screening. We examined a cohort of migrants screened for tuberculosis before entry to England, Wales, and Northern Ireland and tracked the development of disease in this group after arrival. METHODS As part of a pilot pre-entry screening programme for tuberculosis in 15 countries with a high incidence of the disease, the International Organization for Migration screened all applicants for UK visas aged 11 years or older who intended to stay for more than 6 months. Applicants underwent a chest radiograph, and any with results suggestive of tuberculosis underwent sputum testing and culture testing (when available). We tracked the development of tuberculosis in those who tested negative for the disease and subsequently migrated to England, Wales, and Northern Ireland with the Enhanced Tuberculosis Surveillance system. Primary outcomes were cases of all forms of tuberculosis (including clinically diagnosed cases), and bacteriologically confirmed pulmonary tuberculosis. FINDINGS Our study cohort was 519 955 migrants who were screened for tuberculosis before entry to the UK between Jan 1, 2006, and Dec 31, 2012. Cases notified on the Enhanced Tuberculosis Surveillance system between Jan 1, 2006, and Dec 31, 2013, were included. 1873 incident cases of all forms of tuberculosis were identified, and, on the basis of data for England, Wales, and Northern Ireland, the estimated incidence of all forms of tuberculosis in migrants screened before entry was 147 per 100 000 person-years (95% CI 140-154). The estimated incidence of bacteriologically confirmed pulmonary tuberculosis in migrants screened before entry was 49 per 100 000 person-years (95% CI 45-53). Migrants whose chest radiographs were compatible with active tuberculosis but with negative pre-entry microbiological results were at increased risk of tuberculosis compared with those with no radiographic abnormalities (incidence rate ratio 3·2, 95% CI 2·8-3·7; p<0·0001). Incidence of tuberculosis after migration increased significantly with increasing WHO-estimated prevalence of tuberculosis in migrants' countries of origin. 35 of 318 983 pre-entry screened migrants included in a secondary analysis with typing data were assumed index cases. Estimates of the rate of assumed reactivation tuberculosis ranged from 46 (95% CI 42-52) to 91 (82-102) per 100 000 population. INTERPRETATION Migrants from countries with a high incidence of tuberculosis screened before being granted entry to low-incidence countries pose a negligible risk of onward transmission but are at increased risk of tuberculosis, which could potentially be prevented through identification and treatment of latent infection in close collaboration with a pre-entry screening programme. FUNDING Wellcome Trust, UK National Institute for Health Research, UK Medical Research Council, Public Health England, and Department of Health Policy Research Programme.
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Affiliation(s)
- Robert W Aldridge
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK; Farr Institute of Health Informatics Research, University College London, London, UK; Institute for Global Health, University College London, London, UK; Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK.
| | - Dominik Zenner
- Institute for Global Health, University College London, London, UK; Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Peter J White
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK; MRC Centre for Outbreak Analysis and Modelling and NIHR Health Protection Research Unit in Modelling Methodology, Imperial College London, London, UK
| | | | - Morris C Muzyamba
- Institute for Global Health, University College London, London, UK; Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Poonam Dhavan
- Migration Health Division, International Organization for Migration, Geneva, Switzerland
| | - Davide Mosca
- Migration Health Division, International Organization for Migration, Geneva, Switzerland
| | - H Lucy Thomas
- Institute for Global Health, University College London, London, UK; Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Maeve K Lalor
- Institute for Global Health, University College London, London, UK; Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK; Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Andrew C Hayward
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK; Farr Institute of Health Informatics Research, University College London, London, UK
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214
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Ei PW, Aung WW, Lee JS, Choi GE, Chang CL. Molecular Strain Typing of Mycobacterium tuberculosis: a Review of Frequently Used Methods. J Korean Med Sci 2016; 31:1673-1683. [PMID: 27709842 PMCID: PMC5056196 DOI: 10.3346/jkms.2016.31.11.1673] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/06/2016] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units-variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications.
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Affiliation(s)
- Phyu Win Ei
- Advanced Molecular Research Centre, Department of Medical Research, Yangon, Myanmar
| | - Wah Wah Aung
- Advanced Molecular Research Centre, Department of Medical Research, Yangon, Myanmar
| | - Jong Seok Lee
- International Tuberculosis Research Center, Changwon, Korea
| | - Go Eun Choi
- Institute of Convergence Bio-Health, Dong-A University, Busan, Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea.
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215
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Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, Gagneux S. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet 2016; 48:1535-1543. [PMID: 27798628 PMCID: PMC5238942 DOI: 10.1038/ng.3704] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/27/2016] [Indexed: 12/30/2022]
Abstract
Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Leïla Jeljeli
- Forschungszentrum Borstel, Germany.,Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mireia Coscolla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Qingyun Liu
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Lukas Fenner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Liliana Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qian Gao
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | | | - Marie Ballif
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Rita Macedo
- Laboratòrio de Saùde Publica, Lisbon, Portugal
| | - Helmi Mardassi
- Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | | | | | - Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | | | | | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Eddie Wampande
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda.,Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - W Henry Boom
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | - Indira Basu
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - James Bower
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Margarida Saraiva
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | | | | | - Anastasia Koch
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Robert Wilkinson
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa.,Department of Medicine, Imperial College London, UK.,The Francis Crick Institute Mill Hill Laboratory, London, UK
| | - Linda Gail-Bekker
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Bijaya Malla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Serej D Ley
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Papua New Guinea Institute of Medical Research, Goroka, PNG
| | - Hans-Peter Beck
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | | | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | | | - Ana Gil-Brusola
- Department of Microbiology, University Hospital La Fe, Valencia, Spain
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Veronique N Penlap Beng
- Institute Laboratory for Tuberculosis Research (LTR), Biotechnology Center (BTC), University of Yaoundé I, Yaoundé, Cameroon
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Issam Alani
- Department of Medical Laboratory Technology, Faculty of Medical Technology, Baghdad, Iraq
| | - Perpetual Wangui Ndung'u
- Institute of Tropical Medicine and Infectious Diseases (ITROMID), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University Hospital (AKUH), Nairobi, Kenya
| | - Florian Gehre
- Insitute of Tropical Medicine, Antwerp, Belgium.,Medical Research Council, Fajara, the Gambia
| | | | - Francine Ntoumi
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Fondation Congolaise pour la Recherche Médicale, Université Marien Gouabi, Brazzaville, Congo
| | - Lynsey Stewart-Isherwood
- Right to Care and the Clinical HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nyanda E Ntinginya
- National Institute of Medical Research, Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Riga, Latvia
| | - Sven Hoffner
- WHO Supranational TB Reference Laboratory, Department of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
| | - Daiva Bakonyte
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Olga Moldovan
- 'Marius Nasta' Pneumophtisiology Institute, Bucharest, Romania
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Larissa Otero
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - E Jane Carter
- Alpert School of Medicine at Brown University, Providence, Rhode Island, USA.,Moi University School of Medicine, Eldoret, Kenya
| | - Lameck Diero
- Moi University School of Medicine, Eldoret, Kenya
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), 46010, Valencia, Spain.,CIBER Epidemiology and Public Health, Madrid, Spain
| | - Stefan Niemann
- Forschungszentrum Borstel, Germany.,German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
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216
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Walker TM, Merker M, Kohl TA, Crook DW, Niemann S, Peto TEA. Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing. Clin Microbiol Infect 2016; 23:161-166. [PMID: 27789378 DOI: 10.1016/j.cmi.2016.10.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 11/28/2022]
Abstract
Whole genome sequencing (WGS) can help to relate Mycobacterium tuberculosis genomes to one another to assess genetic relatedness and infer the likelihood of transmission between cases. The same sequence data are now increasingly being used to predict drug resistance and susceptibility. Controlling the spread of tuberculosis and providing patients with the correct treatment are central to the World Health Organization's target to 'End TB' by 2035, for which the global prevalence of drug-resistant tuberculosis remains one of the main obstacles to success. So far, WGS has been applied largely to drug-susceptible strains for the purposes of understanding transmission, leaving a number of analytical considerations before transferring what has been learnt from drug-susceptible disease to drug-resistant tuberculosis. We discuss these potential problems here, alongside some of the challenges to characterizing the Mycobacterium tuberculosis 'resistome'-the optimal knowledge-base required for WGS-based assays to successfully direct individualized treatment regimens through the prediction of drug resistance and susceptibility in the future.
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Affiliation(s)
- T M Walker
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - M Merker
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - T A Kohl
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - D W Crook
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute of Health Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - S Niemann
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research, Borstel Site, Borstel, Germany
| | - T E A Peto
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute of Health Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
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217
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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218
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Refrégier G, Abadia E, Matsumoto T, Ano H, Takashima T, Tsuyuguchi I, Aktas E, Cömert F, Gomgnimbou MK, Panaiotov S, Phelan J, Coll F, McNerney R, Pain A, Clark TG, Sola C. Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. INFECTION GENETICS AND EVOLUTION 2016; 45:461-473. [PMID: 27746295 DOI: 10.1016/j.meegid.2016.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/23/2016] [Accepted: 10/12/2016] [Indexed: 12/19/2022]
Abstract
Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term=0.03SNP/genome/year, derived from a tuberculosis ancestor of around 70,000years old; intermediate=0.2SNP/genome/year derived from a Peruvian mummy; short-term=0.5SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as "T3-Osa-Tur") shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800y and 2000years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.
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Affiliation(s)
- Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Edgar Abadia
- Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Tomoshige Matsumoto
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Hiromi Ano
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Tetsuya Takashima
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Izuo Tsuyuguchi
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Elif Aktas
- Şişli Etfal Research and Training Hopital, Istanbul, Turkey
| | - Füsun Cömert
- Faculty of Medicine, Bülent Ecevit University, Zonguldak, Turkey
| | - Michel Kireopori Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Stefan Panaiotov
- National Center of Parasitic and Infectious Diseases, Sofia, Bulgaria
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Cape Town,South Africa
| | - Arnab Pain
- Pathogen Genomics Group, Biological, Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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219
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Casali N, Broda A, Harris SR, Parkhill J, Brown T, Drobniewski F. Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study. PLoS Med 2016; 13:e1002137. [PMID: 27701423 PMCID: PMC5049847 DOI: 10.1371/journal.pmed.1002137] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/23/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A large isoniazid-resistant tuberculosis outbreak centred on London, United Kingdom, has been ongoing since 1995. The aim of this study was to investigate the power and value of whole genome sequencing (WGS) to resolve the transmission network compared to current molecular strain typing approaches, including analysis of intra-host diversity within a specimen, across body sites, and over time, with identification of genetic factors underlying the epidemiological success of this cluster. METHODS AND FINDINGS We sequenced 344 outbreak isolates from individual patients collected over 14 y (2 February 1998-22 June 2012). This demonstrated that 96 (27.9%) were indistinguishable, and only one differed from this major clone by more than five single nucleotide polymorphisms (SNPs). The maximum number of SNPs between any pair of isolates was nine SNPs, and the modal distance between isolates was two SNPs. WGS was able to reveal the direction of transmission of tuberculosis in 16 cases within the outbreak (4.7%), including within a multidrug-resistant cluster that carried a rare rpoB mutation associated with rifampicin resistance. Eleven longitudinal pairs of patient pulmonary isolates collected up to 48 mo apart differed from each other by between zero and four SNPs. Extrapulmonary dissemination resulted in acquisition of a SNP in two of five cases. WGS analysis of 27 individual colonies cultured from a single patient specimen revealed ten loci differed amongst them, with a maximum distance between any pair of six SNPs. A limitation of this study, as in previous studies, is that indels and SNPs in repetitive regions were not assessed due to the difficulty in reliably determining this variation. CONCLUSIONS Our study suggests that (1) certain paradigms need to be revised, such as the 12 SNP distance as the gold standard upper threshold to identify plausible transmissions; (2) WGS technology is helpful to rule out the possibility of direct transmission when isolates are separated by a substantial number of SNPs; (3) the concept of a transmission chain or network may not be useful in institutional or household settings; (4) the practice of isolating single colonies prior to sequencing is likely to lead to an overestimation of the number of SNPs between cases resulting from direct transmission; and (5) despite appreciable genomic diversity within a host, transmission of tuberculosis rarely results in minority variants becoming dominant. Thus, whilst WGS provided some increased resolution over variable number tandem repeat (VNTR)-based clustering, it was insufficient for inferring transmission in the majority of cases.
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Affiliation(s)
- Nicola Casali
- Department of Infectious Diseases and Immunity, Imperial College London, London, United Kingdom
- Centre for Immunology and Infectious Disease, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Agnieszka Broda
- Department of Infectious Diseases and Immunity, Imperial College London, London, United Kingdom
| | - Simon R. Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Timothy Brown
- Public Health England National Mycobacterium Reference Laboratory, London, United Kingdom
| | - Francis Drobniewski
- Department of Infectious Diseases and Immunity, Imperial College London, London, United Kingdom
- Public Health England National Mycobacterium Reference Laboratory, London, United Kingdom
- Departments of Microbiology and Respiratory Medicine, Barts Health NHS Trust, London, United Kingdom
- * E-mail:
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220
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Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2016; 45:359-368. [PMID: 27637931 DOI: 10.1016/j.meegid.2016.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 09/12/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022]
Abstract
Tuberculosis (TB) is an infectious disease of global public health importance caused by Mycobacterium tuberculosis complex (MTC) in which M. tuberculosis (Mtb) is the major causative agent. Recent advancements in genomic technologies such as next generation sequencing have enabled high throughput cost-effective generation of whole genome sequence information from Mtb clinical isolates, providing new insights into the evolution, genomic diversity and transmission of the Mtb bacteria, including molecular mechanisms of antibiotic resistance. The large volume of sequencing data generated however necessitated effective and efficient management, storage, analysis and visualization of the data and results through development of novel and customized bioinformatics software tools and databases. In this review, we aim to provide a comprehensive survey of the current freely available bioinformatics software tools and publicly accessible databases for genomic analysis of Mtb for identifying disease transmission in molecular epidemiology and in rapid determination of the antibiotic profiles of clinical isolates for prompt and optimal patient treatment.
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221
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Bjorn-Mortensen K, Soborg B, Koch A, Ladefoged K, Merker M, Lillebaek T, Andersen AB, Niemann S, Kohl TA. Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland. Sci Rep 2016; 6:33180. [PMID: 27615360 PMCID: PMC5018808 DOI: 10.1038/srep33180] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/19/2016] [Indexed: 12/01/2022] Open
Abstract
In East Greenland, a dramatic increase of tuberculosis (TB) incidence has been observed in recent years. Classical genotyping suggests a genetically similar Mycobacterium tuberculosis (Mtb) strain population as cause, however, precise transmission patterns are unclear. We performed whole genome sequencing (WGS) of Mtb isolates from 98% of culture-positive TB cases through 21 years (n = 182) which revealed four genomic clusters of the Euro-American lineage (mainly sub-lineage 4.8 (n = 134)). The time to the most recent common ancestor of lineage 4.8 strains was found to be 100 years. This sub-lineage further diversified in the 1970s, and massively expanded in the 1990s, a period of lowered TB awareness in Greenland. Despite the low genetic strain diversity, WGS data revealed several recent short-term transmission events in line with the increasing incidence in the region. Thus, the isolated setting and the uniformity of circulating Mtb strains indicated that the majority of East Greenlandic TB cases originated from one or few strains introduced within the last century. Thereby, the study shows the consequences of even short interruptions in TB control efforts in previously TB high incidence areas and demonstrates the potential role of WGS in detecting ongoing micro epidemics, thus guiding public health efforts in the future.
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Affiliation(s)
- K. Bjorn-Mortensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Greenland’s Center of Health Research, Nuuk, Greenland
- Institute of Clinical Medicine, University of Southern Denmark, Odense, Denmark
| | - B. Soborg
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - A. Koch
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - K. Ladefoged
- Department of Internal Medicine, Queen Ingrid’s Hospital, Nuuk, Greenland
| | - M. Merker
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
- German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - T. Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - A. B. Andersen
- Institute of Clinical Medicine, University of Southern Denmark, Odense, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - S. Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
- German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - T. A. Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
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Abstract
The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.
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Arnold A, Witney AA, Vergnano S, Roche A, Cosgrove CA, Houston A, Gould KA, Hinds J, Riley P, Macallan D, Butcher PD, Harrison TS. XDR-TB transmission in London: Case management and contact tracing investigation assisted by early whole genome sequencing. J Infect 2016; 73:210-8. [DOI: 10.1016/j.jinf.2016.04.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/14/2016] [Accepted: 04/20/2016] [Indexed: 11/15/2022]
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Ben-Kahla I, Al-Hajoj S. Drug-resistant tuberculosis viewed from bacterial and host genomes. Int J Antimicrob Agents 2016; 48:353-60. [PMID: 27566907 DOI: 10.1016/j.ijantimicag.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/26/2016] [Accepted: 07/15/2016] [Indexed: 12/14/2022]
Abstract
The outcome of infection with Mycobacterium tuberculosis (MTB) is largely influenced by the host-pathogen interaction in which both the human host and the MTB genetic backgrounds play an important role. Whether this interaction also influences the selection and expansion of drug-resistant MTB strains is the primary focus of this review. We first outline the main and recent findings regarding MTB determinants implicated in the development of drug resistance. Second, we examine data regarding human genetic factors that may play a role in TB drug resistance. We highlight interesting openings for TB research and therapy.
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Affiliation(s)
- Imen Ben-Kahla
- Mycobacteriology Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sahal Al-Hajoj
- Mycobacteriology Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.
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225
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Faksri K, Tan JH, Disratthakit A, Xia E, Prammananan T, Suriyaphol P, Khor CC, Teo YY, Ong RTH, Chaiprasert A. Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients. PLoS One 2016; 11:e0160992. [PMID: 27518818 PMCID: PMC4982626 DOI: 10.1371/journal.pone.0160992] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Multi-drug and extensively drug-resistant tuberculosis (MDR and XDR-TB) are problems that threaten public health worldwide. Only some genetic markers associated with drug-resistant TB are known. Whole-genome sequencing (WGS) is a promising tool for distinguishing between re-infection and persistent infection in isolates taken at different times from a single patient, but has not yet been applied in MDR and XDR-TB. We aim to detect genetic markers associated with drug resistance and distinguish between reinfection and persistent infection from MDR and XDR-TB patients based on WGS analysis. Samples of Mycobacterium tuberculosis (n = 7), serially isolated from 2 MDR cases and 1 XDR-TB case, were retrieved from Siriraj Hospital, Bangkok. The WGS analysis used an Illumina Miseq sequencer. In cases of persistent infection, MDR-TB isolates differed at an average of 2 SNPs across the span of 2–9 months whereas in the case of reinfection, isolates differed at 61 SNPs across 2 years. Known genetic markers associated with resistance were detected from strains susceptible to streptomycin (2/7 isolates), p-aminosalicylic acid (3/7 isolates) and fluoroquinolone drugs. Among fluoroquinolone drugs, ofloxacin had the highest phenotype-genotype concordance (6/7 isolates), whereas gatifloxcain had the lowest (3/7 isolates). A putative candidate SNP in Rv2477c associated with kanamycin and amikacin resistance was suggested for further validation. WGS provided comprehensive results regarding molecular epidemiology, distinguishing between persistent infection and reinfection in M/XDR-TB and potentially can be used for detection of novel mutations associated with drug resistance.
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Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
- * E-mail: (KF); (AC)
| | - Jun Hao Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Areeya Disratthakit
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Eryu Xia
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Therdsak Prammananan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Ministry of Science and Technology, Pathum Thani, Thailand
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Genome Institute of Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Angkana Chaiprasert
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail: (KF); (AC)
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226
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Abstract
ABSTRACT
With the advent of next-generation sequencing technology, the genotyping of clinical
Mycobacterium tuberculosis
strains went through a major breakup that dramatically improved the field of molecular epidemiology but also revolutionized our deep understanding of the
M. tuberculosis
complex evolutionary history. The intricate paths of the pathogen and its human host are reflected by a common geographical origin in Africa and strong biogeographical associations that largely reflect the past migration waves out of Africa. This long coevolutionary history is cardinal for our understanding of the host-pathogen dynamic, including past and ongoing demographic components, strains’ genetic background, as well as the immune system genetic architecture of the host. Coalescent- and Bayesian-based analyses allowed us to reconstruct population size changes of
M. tuberculosis
through time, to date the most recent common ancestor and the several phylogenetic lineages. This information will ultimately help us to understand the spread of the Beijing lineage, the rise of multidrug-resistant sublineages, or the fall of others in the light of socioeconomic events, antibiotic programs, or host population densities. If we leave the present and go through the looking glass, thanks to our ability to handle small degraded molecules combined with targeted capture, paleomicrobiology covering the Pleistocene era will possibly unravel lineage replacements, dig out extinct ones, and eventually ask for major revisions of the current model.
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227
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Lavezzo E, Barzon L, Toppo S, Palù G. Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis. Expert Rev Mol Diagn 2016; 16:1011-23. [PMID: 27453996 DOI: 10.1080/14737159.2016.1217158] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION The diagnosis of infectious diseases is among the most successful areas of application of new generation sequencing technologies. The field has seen the development of numerous experimental and analytical approaches for the detection and the fine description of pathogenic and non-pathogenic microorganisms. AREAS COVERED Without claiming to be exhaustive with respect to all applications and methods developed over the years, this review focuses on the advantages and the issues brought by the new technologies, with an eye in particular to third generation sequencing methods. Both experimental procedures and algorithmic strategies are presented, following the most relevant publications which have led to progress in our ability of detecting infectious agents. Expert commentary: The technical advance brought by third generation sequencing platforms has the potential to significantly expand the range of diagnostic tools that will be available to clinicians. Nonetheless, the implementation of these technologies in clinical practice is still far from being actionable and will temporally follow the path undertaken by second generation methods, which still require the setup of standardized pipelines in both wet and dry laboratory procedures.
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Affiliation(s)
- Enrico Lavezzo
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Luisa Barzon
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Stefano Toppo
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Giorgio Palù
- a Department of Molecular Medicine , University of Padova , Padova , Italy
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228
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Cannas A, Mazzarelli A, Di Caro A, Delogu G, Girardi E. Molecular Typing of Mycobacterium Tuberculosis Strains: A Fundamental Tool for Tuberculosis Control and Elimination. Infect Dis Rep 2016; 8:6567. [PMID: 27403266 PMCID: PMC4927935 DOI: 10.4081/idr.2016.6567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize Mycobacterium tuberculosis isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control.
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Affiliation(s)
- Angela Cannas
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
| | | | - Antonino Di Caro
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
| | - Giovanni Delogu
- National Institute for Infectious Diseases L. Spallanzani, Rome, Italy; Institute of Microbiology, Sacro Cuore Catholic University, Rome, Italy
| | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
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229
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Genomic Diversity of Mycobacterium tuberculosis Complex Strains in Cantabria (Spain), a Moderate TB Incidence Setting. PLoS One 2016; 11:e0157266. [PMID: 27315243 PMCID: PMC4912061 DOI: 10.1371/journal.pone.0157266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 05/26/2016] [Indexed: 12/02/2022] Open
Abstract
Background Tuberculosis (TB) control strategies are focused mainly on prevention, early diagnosis, compliance to treatment and contact tracing. The objectives of this study were to explore the frequency and risk factors of recent transmission of clinical isolates of Mycobacterium tuberculosis complex (MTBC) in Cantabria in Northern Spain from 2012 through 2013 and to analyze their clonal complexity for better understanding of the transmission dynamics in a moderate TB incidence setting. Methods DNA from 85 out of 87 isolates from bacteriologically confirmed cases of MTBC infection were extracted directly from frozen stocks and genotyped using the mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) method. The MIRU-VNTRplus database tool was used to identify clusters and lineages and to build a neighbor joining (NJ) phylogenetic tree. In addition, data were compared to the SITVIT2 database at the Pasteur Institute of Guadeloupe. Results The rate of recent transmission was calculated to 24%. Clustering was associated with being Spanish-born. A high prevalence of isolates of the Euro-American lineage was found. In addition, MIRU-VNTR profiles of the studied isolates corresponded to previously found MIRU-VNTR types in other countries, including Spain, Belgium, Great Britain, USA, Croatia, South Africa and The Netherlands. Six of the strains analyzed represented clonal variants. Conclusion Transmission of MTBC is well controlled in Cantabria. The majority of TB patients were born in Spain. The population structure of MTBC in Cantabria has a low diversity of major clonal lineages with the Euro-American lineage predominating.
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230
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Jia H, Du P, Yang H, Zhang Y, Wang J, Zhang W, Han G, Han N, Yao Z, Wang H, Zhang J, Wang Z, Ding Q, Qiang Y, Barbut F, Gao GF, Cao Y, Cheng Y, Chen C. Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012-2014, traced by whole genome sequencing. BMC Genomics 2016; 17:405. [PMID: 27411304 PMCID: PMC4942892 DOI: 10.1186/s12864-016-2708-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/05/2016] [Indexed: 12/18/2022] Open
Abstract
Background The rapid spread of Clostridium difficile NAP1/BI/027 (C. difficile 027) has become one of the leading threats of healthcare-associated infections worldwide. However, C. difficile 027 infections have been rarely reported in Asia, particularly in China. Results In this study, we identified a rare C. difficile bloodstream infection (BSI) from three isolates of a patient during repeated hospital admission. This finding triggered a retrospective epidemiological study to scan all cases and strains emerged from this ward during the past three years. Using medical personnel interviews, medical record reviews and the genomic epidemiology, two outbreaks in 2012 and 2013–2014 were identified. Through using whole genome sequencing, we succeeded to trace the origin of the BSI strain. Surprisingly, we found the genome sequences were similar to C. difficile 027 strain R20291, indicating the occurrence of a rare C. difficile 027 strain in China. Integrated epidemiological investigation and whole genome sequencing of all strains, we constructed a nosocomial transmission map of these two C. difficile 027 outbreaks and traced the origin of the infection. Conclusions By genome sequencing, spatio-temporal analysis and field epidemiology investigation, we can estimate their complex transform network and reveal the possible modes of transmission in this ward. Based on their genetic diversity, we can assume that the toilets, bathroom, and janitor’s equipment room may be contaminated area, which may be suggested to improve infection control measures in the following health care. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2708-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongbing Jia
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging infectious Diseases, No. 8 Jingshundongjie, Beijing, 100015, China.,State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hui Yang
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Yuanyuan Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging infectious Diseases, No. 8 Jingshundongjie, Beijing, 100015, China.,State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing Wang
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Guiling Han
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Na Han
- State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Zhiyuan Yao
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Haiyin Wang
- State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jing Zhang
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Zhen Wang
- State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Qingming Ding
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China
| | - Yujun Qiang
- State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Frédéric Barbut
- National Reference Laboratory for Clostridium difficile, Faculté de Médecine Pierre et Marie Curie and Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, 75012, France
| | - George F Gao
- The Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongtong Cao
- Department of clinical laboratory, China-Japan Friendship Hospital, No. 2 Yinghua Dongjie, Chaoyang, Beijing, 100029, China.
| | - Ying Cheng
- Key Laboratory of Surveillance and Early-warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing, 102206, China.
| | - Chen Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging infectious Diseases, No. 8 Jingshundongjie, Beijing, 100015, China. .,State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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231
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Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country. J Clin Microbiol 2016; 54:1862-1870. [PMID: 27194683 DOI: 10.1128/jcm.00126-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
Immigrants from regions with a high incidence of tuberculosis (TB) are a risk group for TB in low-incidence countries such as Switzerland. In a previous analysis of a nationwide collection of 520 Mycobacterium tuberculosis isolates from 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, we used whole-genome sequencing (WGS) to revisit these transmission clusters. Genome-based transmission clusters were defined as isolate pairs separated by ≤12 single nucleotide polymorphisms (SNPs). WGS confirmed 17/35 (49%) MIRU-VNTR typing clusters; the other 18 clusters contained pairs separated by >12 SNPs. Most transmission clusters (3/4) of Swiss-born patients were confirmed by WGS, as opposed to 25% (4/16) of the clusters involving only foreign-born patients. The overall clustering proportion was 17% (90 patients; 95% confidence interval [CI], 14 to 21%) by standard genotyping but only 8% (43 patients; 95% CI, 6 to 11%) by WGS. The clustering proportion was 17% (67/401; 95% CI, 13 to 21%) by standard genotyping and 7% (26/401; 95% CI, 4 to 9%) by WGS among foreign-born patients and 19% (23/119; 95% CI, 13 to 28%) and 14% (17/119; 95% CI, 9 to 22%), respectively, among Swiss-born patients. Using weighted logistic regression, we found weak evidence of an association between birth origin and transmission (adjusted odds ratio of 2.2 and 95% CI of 0.9 to 5.5 comparing Swiss-born patients to others). In conclusion, standard genotyping overestimated recent TB transmission in Switzerland compared to WGS, particularly among immigrants from regions with a high TB incidence, where genetically closely related strains often predominate. We recommend the use of WGS to identify transmission clusters in settings with a low incidence of TB.
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232
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Kamath PL, Foster JT, Drees KP, Luikart G, Quance C, Anderson NJ, Clarke PR, Cole EK, Drew ML, Edwards WH, Rhyan JC, Treanor JJ, Wallen RL, White PJ, Robbe-Austerman S, Cross PC. Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock. Nat Commun 2016; 7:11448. [PMID: 27165544 PMCID: PMC4865865 DOI: 10.1038/ncomms11448] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/29/2016] [Indexed: 01/09/2023] Open
Abstract
Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (∼3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.
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Affiliation(s)
- Pauline L Kamath
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana 59715, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Kevin P Drees
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Christine Quance
- USDA-APHIS, National Veterinary Services Laboratories, Ames, Iowa 50010, USA
| | - Neil J Anderson
- Montana Fish Wildlife and Parks, Bozeman, Montana 59718, USA
| | - P Ryan Clarke
- USDA-APHIS, Veterinary Services, Fort Collins, Colorado 80526, USA
| | - Eric K Cole
- USFWS, National Elk Refuge, Jackson, Wyoming 83001, USA
| | - Mark L Drew
- Wildlife Health Laboratory, Idaho Department of Fish and Game, Caldwell, Idaho 83607, USA
| | | | - Jack C Rhyan
- USDA-APHIS, Veterinary Services, Fort Collins, Colorado 80526, USA
| | - John J Treanor
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | - Rick L Wallen
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | - Patrick J White
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | | | - Paul C Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana 59715, USA
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233
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Dowdy DW, Houben R, Cohen T, Pai M, Cobelens F, Vassall A, Menzies NA, Gomez GB, Langley I, Squire SB, White R. Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling. Int J Tuberc Lung Dis 2016; 18:1012-8. [PMID: 25189546 PMCID: PMC4436823 DOI: 10.5588/ijtld.13.0851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The landscape of diagnostic testing for tuberculosis (TB) is changing rapidly, and stakeholders need urgent guidance on how to develop, deploy and optimize TB diagnostics in a way that maximizes impact and makes best use of available resources. When decisions must be made with only incomplete or preliminary data available, modelling is a useful tool for providing such guidance. Following a meeting of modelers and other key stakeholders organized by the TB Modelling and Analysis Consortium, we propose a conceptual framework for positioning models of TB diagnostics. We use that framework to describe modelling priorities in four key areas: Xpert® MTB/RIF scale-up, target product profiles for novel assays, drug susceptibility testing to support new drug regimens, and the improvement of future TB diagnostic models. If we are to maximize the impact and cost-effectiveness of TB diagnostics, these modelling priorities should figure prominently as targets for future research.
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Affiliation(s)
- D W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - R Houben
- Department of Infectious Disease Epidemiology and TB Modelling Group, London School of Hygiene & Tropical Medicine, London, UK
| | - T Cohen
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - M Pai
- Department of Epidemiology and Biostatistics & McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - F Cobelens
- Department of Global Health and Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - A Vassall
- SAME Modelling and Economics, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | - N A Menzies
- Center for Health Decision Science, Harvard School of Public Health, Boston, Massachusetts, USA
| | - G B Gomez
- Department of Global Health and Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - I Langley
- Department of Clinical Sciences and Centre for Applied Health Research & Delivery, Liverpool School of Tropical Medicine, Liverpool, UK
| | - S B Squire
- Department of Clinical Sciences and Centre for Applied Health Research & Delivery, Liverpool School of Tropical Medicine, Liverpool, UK
| | - R White
- Department of Infectious Disease Epidemiology and TB Modelling Group, London School of Hygiene & Tropical Medicine, London, UK
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234
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Brehony C, Hill DM, Lucidarme J, Borrow R, Maiden MC. Meningococcal vaccine antigen diversity in global databases. ACTA ACUST UNITED AC 2016; 20:30084. [PMID: 26676305 DOI: 10.2807/1560-7917.es.2015.20.49.30084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/09/2015] [Indexed: 11/20/2022]
Abstract
The lack of an anti-capsular vaccine against serogroup B meningococcal disease has necessitated the exploration of alternative vaccine candidates, mostly proteins exhibiting varying degrees of antigenic variation. Analysis of variants of antigen-encoding genes is facilitated by publicly accessible online sequence repositories, such as the Neisseria PubMLST database and the associated Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL). We investigated six proposed meningococcal vaccine formulations by deducing the prevalence of their components in the isolates represented in these repositories. Despite high diversity, a limited number of antigenic variants of each of the vaccine antigens were prevalent, with strong associations of particular variant combinations with given serogroups and genotypes. In the MRF-MGL and globally, the highest levels of identical sequences were observed with multicomponent/multivariant vaccines. Our analyses further demonstrated that certain combinations of antigen variants were prevalent over periods of decades in widely differing locations, indicating that vaccine formulations containing a judicious choice of antigen variants have potential for long-term protection across geographic regions. The data further indicated that formulations with multiple variants would be especially relevant at times of low disease incidence, as relative diversity was higher. Continued surveillance is required to monitor the changing prevalence of these vaccine antigens.
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Affiliation(s)
- Carina Brehony
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
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235
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White PJ, Abubakar I. Improving Control of Tuberculosis in Low-Burden Countries: Insights from Mathematical Modeling. Front Microbiol 2016; 7:394. [PMID: 27199896 PMCID: PMC4853635 DOI: 10.3389/fmicb.2016.00394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/14/2016] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis control and elimination remains a challenge for public health even in low-burden countries. New technology and novel approaches to case-finding, diagnosis, and treatment are causes for optimism but they need to be used cost-effectively. This in turn requires improved understanding of the epidemiology of TB and analysis of the effectiveness and cost-effectiveness of different interventions. We describe the contribution that mathematical modeling can make to understanding epidemiology and control of TB in different groups, guiding improved approaches to public health interventions. We emphasize that modeling is not a substitute for collecting data but rather is complementary to empirical research, helping determine what are the key questions to address to maximize the public-health impact of research, helping to plan studies, and making maximal use of available data, particularly from surveillance, and observational studies. We provide examples of how modeling and related empirical research inform policy and discuss how a combination of these approaches can be used to address current questions of key importance, including use of whole-genome sequencing, screening and treatment for latent infection, and combating drug resistance.
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Affiliation(s)
- Peter J White
- MRC Centre for Outbreak Analysis and Modelling and NIHR Health Protection Research Unit in Modelling Methodology, Imperial College London School of Public HealthLondon, UK; Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health EnglandLondon, UK
| | - Ibrahim Abubakar
- TB Section, Respiratory Diseases Department, Centre for Infectious Disease Surveillance and Control, Public Health EnglandLondon, UK; Research Department of Infection and Population Health, University College LondonLondon, UK; MRC Clinical Trials Unit, University College LondonLondon, UK
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236
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Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review. Tuberculosis (Edinb) 2016; 98:77-85. [DOI: 10.1016/j.tube.2016.02.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/22/2016] [Accepted: 02/29/2016] [Indexed: 11/23/2022]
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237
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Pedersen MK, Andersen AB, Andersen PH, Svensson E, Jensen SG, Lillebaek T. Occupational Tuberculosis in Denmark through 21 Years Analysed by Nationwide Genotyping. PLoS One 2016; 11:e0153668. [PMID: 27082745 PMCID: PMC4833408 DOI: 10.1371/journal.pone.0153668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/01/2016] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) is a well-known occupational hazard. Based on more than two decades (1992–2012) of centralized nationwide genotyping of all Mycobacterium tuberculosis culture-positive TB patients in Denmark, we compared M. tuberculosis genotypes from all cases notified as presumed occupational (N = 130) with M. tuberculosis genotypes from all TB cases present in the country (N = 7,127). From 1992 through 2006, the IS6110 Restriction Fragment Length Polymorphism (RFLP) method was used for genotyping, whereas from 2005 to present, the 24-locus-based Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat (MIRU-VNTR) was used. An occupational TB case was classified as clustered if the genotype was 100% identical to at least one other genotype. Subsequently, based on genotype, time period, smear positivity, geography, susceptibility pattern, and any reported epidemiological links between the occupational cases and any potential source cases, the occupational case was categorized as confirmed, likely, possible or unlikely occupationally infected. Among the 130 notified presumed occupational cases, 12 (9.2%) could be classified as confirmed and 46 (35.4%) as unlikely, accounting for nearly half of all cases (44.6%). The remaining 72 cases (55.4%) were categorized as possible. Within this group, 15 cases (11.5%) were assessed to be likely occupational. Our study shows that genotyping can serve as an important tool for disentangle occupational TB in high-income low incidence settings, but still needs to be combined with good epidemiological linkage information.
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Affiliation(s)
- Mathias Klok Pedersen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | | | - Peter Henrik Andersen
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | - Erik Svensson
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
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238
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Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis. J Clin Microbiol 2016; 54:1891-1895. [PMID: 27076659 DOI: 10.1128/jcm.00364-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 11/20/2022] Open
Abstract
When using genome sequencing for molecular epidemiology, short sequence reads are aligned to an arbitrary reference strain to detect single nucleotide polymorphisms. We investigated whether reference genome selection influences epidemiological inferences of Mycobacterium tuberculosis transmission by aligning sequence reads from 162 closely related lineage 4 (Euro-American) isolates to 7 different genomes. Phylogenetic trees were consistent with use of all but the most divergent genomes, suggesting that reference choice can be based on considerations other than M. tuberculosis lineage.
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239
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Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out. Trends Microbiol 2016; 24:637-648. [PMID: 27068531 DOI: 10.1016/j.tim.2016.03.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/13/2016] [Accepted: 03/15/2016] [Indexed: 01/29/2023]
Abstract
Antimicrobial resistance (AMR) threats are typically represented by bacteria capable of extensive horizontal gene transfer (HGT). One clear exception is Mycobacterium tuberculosis (Mtb). It is an obligate human pathogen with limited genetic diversity and a low mutation rate which lacks any evidence for HGT. Such features should, in principle, reduce its ability to rapidly evolve AMR. We identify key features in its biology and epidemiology that allow it to overcome its low adaptive potential. We focus in particular on its innate resistance to drugs, its unusual life cycle, including an often extensive latent phase, and its ability to shelter from exposure to antimicrobial drugs within cavities it induces in the lungs.
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240
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Hoza AS, Mfinanga SG, Moser I, König B. Molecular characterization of Mycobacterium tuberculosis isolates from Tanga, Tanzania: First insight of MIRU-VNTR and microarray-based spoligotyping in a high burden country. Tuberculosis (Edinb) 2016; 98:116-24. [PMID: 27156627 DOI: 10.1016/j.tube.2016.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 11/26/2022]
Abstract
Molecular typing of Mycobacterium tuberculosis(MTB) has greatly enhanced the understanding of the population structure of MTB isolates and epidemiology of tuberculosis (TB). To characterize prevalent genotypes of MTB, microarrays‑based spoligotyping and mycobacterial interspersed repetitive unit‑variable number of tandem repeats (MIRU‑VNTR) were applied on 80 isolates collected from primary health care facilities in Tanga, North‑eastern Tanzania. A total of 18 distinct spoligotypes were identified. The lineages by order of their predominance were EAI and CAS families (26.25%, 21 isolates each), LAM family and T super‑family (10%, 8 isolates each), MANU family (3.75%, 3 isolates), Beijing family (2.5%, 2 isolates) and S family (1.25%, 1 isolate). Overall, sixteen (20%) strains could not be allocated to any lineage according to the SITVIT_WEB database. The allelic diversity (h) for specific MIRU‑VNTR loci showed a considerable variation ranging from 0.826 of VNTR locus 3192 to 0.141 of VNTR locus 2059. The allelic diversity for 11 loci (VNTR 3192, 2996, 2165, 960, 4052, 424, 4156, 2531, 1644, 802 and 3690) exceeded 0.6, indicating highly discriminatory power. Seven loci (VNTR 2163b, 2401, 1955, 577, 4348, 2687 and 580) showed moderate discrimination (0.3 ≤ h ≥ 0.6), and three loci (VNTR3007, 154 and 2059) were less polymorphic. The present study suggests that the TB cases in Tanga might be caused by a diverse array of MTB strain families that may be indicative of a cosmopolitan population with frequent migration and travel. Microarray‑based spoligotyping and MIRU‑VNTR could be reliable tools in detecting different MTB genotypes in high burden settings.
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Affiliation(s)
- Abubakar S Hoza
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Medical Faculty, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany; Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, P.O. Box 3019, Morogoro, Tanzania.
| | - Sayoki G Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P.O. Box 3436 Dar es Salaam, Tanzania
| | - Irmgard Moser
- Friedrich Loeffler Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Brigitte König
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Medical Faculty, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
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241
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den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, Iqbal Z, Kinney A, Limberger R, Musser KA, Shudt M, Strain E, Wiedmann M, Wolfgang WJ. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis. Emerg Infect Dis 2016; 20:1306-14. [PMID: 25062035 PMCID: PMC4111163 DOI: 10.3201/eid2008.131399] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be used in real-time in a public health laboratory is not known. Therefore, we conducted a retrospective and prospective analysis. The retrospective study investigated isolates from 1 confirmed outbreak. Additional cases could be attributed to the outbreak strain on the basis of whole-genome data. The prospective study included 58 isolates obtained in 2012, including isolates from 1 epidemiologically defined outbreak. Whole-genome sequencing identified additional isolates that could be attributed to the outbreak, but which differed from the outbreak-associated PFGE type. Additional putative outbreak clusters were detected in the retrospective and prospective analyses. This study demonstrates the practicality of implementing this approach for outbreak surveillance in a state public health laboratory.
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242
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Hatherell HA, Colijn C, Stagg HR, Jackson C, Winter JR, Abubakar I. Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med 2016; 14:21. [PMID: 27005433 PMCID: PMC4804562 DOI: 10.1186/s12916-016-0566-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/23/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is becoming an important part of epidemiological investigations of infectious diseases due to greater resolution and cost reductions compared to traditional typing approaches. Many public health and clinical teams will increasingly use WGS to investigate clusters of potential pathogen transmission, making it crucial to understand the benefits and assumptions of the analytical methods for investigating the data. We aimed to understand how different approaches affect inferences of transmission dynamics and outline limitations of the methods. METHODS We comprehensively searched electronic databases for studies that presented methods used to interpret WGS data for investigating tuberculosis (TB) transmission. Two authors independently selected studies for inclusion and extracted data. Due to considerable methodological heterogeneity between studies, we present summary data with accompanying narrative synthesis rather than pooled analyses. RESULTS Twenty-five studies met our inclusion criteria. Despite the range of interpretation tools, the usefulness of WGS data in understanding TB transmission often depends on the amount of genetic diversity in the setting. Where diversity is small, distinguishing re-infections from relapses may be impossible; interpretation may be aided by the use of epidemiological data, examining minor variants and deep sequencing. Conversely, when within-host diversity is large, due to genetic hitchhiking or co-infection of two dissimilar strains, it is critical to understand how it arose. Greater understanding of microevolution and mixed infection will enhance interpretation of WGS data. CONCLUSIONS As sequencing studies have sampled more intensely and integrated multiple sources of information, the understanding of TB transmission and diversity has grown, but there is still much to be learnt about the origins of diversity that will affect inferences from these data. Public health teams and researchers should combine epidemiological, clinical and WGS data to strengthen investigations of transmission.
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Affiliation(s)
- Hollie-Ann Hatherell
- CoMPLEX, University College London, London, WC1E 6BT, UK. .,Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK.
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
| | - Helen R Stagg
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK
| | - Charlotte Jackson
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK
| | - Joanne R Winter
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK
| | - Ibrahim Abubakar
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK.,Medical Research Council Clinical Trials Unit, 125 Kingsway, London, WC2B 6NH, UK
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243
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Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE. Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC Genomics 2016; 17:187. [PMID: 26944054 PMCID: PMC4779211 DOI: 10.1186/s12864-016-2531-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND De novo reference assemblies that are affordable, practical to produce, and of sufficient quality for most downstream applications, remain an unattained goal for many taxa. Insects, which may yield too little DNA from individual specimens for long-read sequencing library construction and often have highly heterozygous genomes, can be particularly hard to assemble using inexpensive short-read sequencing data. The large number of insect species with medical or economic importance makes this a critical problem to address. RESULTS Using the assembler DISCOVAR de novo, we assembled the genome of the African malaria mosquito Anopheles arabiensis using 250 bp reads from a single library. The resulting assembly had a contig N50 of 22,433 bp, and recovered the gene set nearly as well as the ALLPATHS-LG AaraD1 An. arabiensis assembly produced with reads from three sequencing libraries and much greater resources. DISCOVAR de novo appeared to perform better than ALLPATHS-LG in regions of low complexity. CONCLUSIONS DISCOVAR de novo performed well assembling the genome of an insect of medical importance, using simpler sequencing input than previous anopheline assemblies. We have shown that this program is a viable tool for cost-effective assembly of a modestly-sized insect genome.
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Affiliation(s)
- R Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, South Bend, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, South Bend, IN, 46556, USA.
| | - Neil I Weisenfeld
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - David B Jaffe
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, South Bend, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, South Bend, IN, 46556, USA.
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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244
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Bates M, Zumla A. The development, evaluation and performance of molecular diagnostics for detection of Mycobacterium tuberculosis. Expert Rev Mol Diagn 2016; 16:307-22. [PMID: 26735769 DOI: 10.1586/14737159.2016.1139457] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The unique pathogenesis of tuberculosis (TB) poses several barriers to the development of accurate diagnostics: a) the establishment of life-long latency by Mycobacterium tuberculosis (M.tb) after primary infection confounds the development of classical antibody or antigen based assays; b) our poor understanding of the molecular pathways that influence progression from latent to active disease; c) the intracellular nature of M.tb infection in tissues means that M.tb and/or its components, are not readily detectable in peripheral specimens; and d) the variable presence of M.tb bacilli in specimens from patients with extrapulmonary TB or children. The literature on the current portfolio of molecular diagnostics tests for TB is reviewed here and the developmental pipeline is summarized. Also reviewed are data from recently published operational research on the GeneXpert MTB/RIF assay and discussed are the lessons that can be taken forward for the design of studies to evaluate the impact of TB diagnostics.
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Affiliation(s)
- Matthew Bates
- a UNZA-UCLMS Research & Training Programme , University Teaching Hospital , Lusaka , Zambia.,b Centre for Clinical Microbiology, Division of Infection and Immunity , University College London , London , UK
| | - Alimuddin Zumla
- a UNZA-UCLMS Research & Training Programme , University Teaching Hospital , Lusaka , Zambia.,b Centre for Clinical Microbiology, Division of Infection and Immunity , University College London , London , UK.,c NIHR Biomedical Research Centre , University College London Hospitals , London , UK
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245
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Trinh QM, Nguyen HL, Nguyen VN, Nguyen TVA, Sintchenko V, Marais BJ. Tuberculosis and HIV co-infection-focus on the Asia-Pacific region. Int J Infect Dis 2016; 32:170-8. [PMID: 25809776 DOI: 10.1016/j.ijid.2014.11.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB) is the leading opportunistic disease and cause of death in patients with HIV infection. In 2013 there were 1.1 million new TB/HIV co-infected cases globally, accounting for 12% of incident TB cases and 360,000 deaths. The Asia-Pacific region, which contributes more than a half of all TB cases worldwide, traditionally reports low TB/HIV co-infection rates. However, routine testing of TB patients for HIV infection is not universally implemented and the estimated prevalence of HIV in new TB cases increased to 6.3% in 2013. Although HIV infection rates have not seen the rapid rise observed in Sub-Saharan Africa, indications are that rates are increasing among specific high-risk groups. This paper reviews the risks of TB exposure and progression to disease, including the risk of TB recurrence, in this vulnerable population. There is urgency to scale up interventions such as intensified TB case-finding, isoniazid preventive therapy, and TB infection control, as well as HIV testing and improved access to antiretroviral treatment. Increased awareness and concerted action is required to reduce TB/HIV co-infection rates in the Asia-Pacific region and to improve the outcomes of people living with HIV.
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Affiliation(s)
- Q M Trinh
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia; Centre for Infectious Disease and Microbiology - Public Health, ICPMR, Westmead Hospital, Sydney, Australia; Tuberculosis Laboratory, Vietnam National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
| | - H L Nguyen
- Vietnam Administration of HIV/AIDS Control, Hanoi, Vietnam
| | - V N Nguyen
- Vietnam National Lung Hospital, Hanoi, Vietnam
| | - T V A Nguyen
- Tuberculosis Laboratory, Vietnam National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - V Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia; Centre for Infectious Disease and Microbiology - Public Health, ICPMR, Westmead Hospital, Sydney, Australia
| | - B J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), The University of Sydney, Sydney, Australia
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246
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Nakauchi A, Wong JH, Mahasirimongkol S, Yanai H, Yuliwulandari R, Mabuchi A, Liu X, Mushiroda T, Wattanapokayakit S, Miyagawa T, Keicho N, Tokunaga K. Identification of ITPA on chromosome 20 as a susceptibility gene for young-onset tuberculosis. Hum Genome Var 2016; 3:15067. [PMID: 27081565 PMCID: PMC4760120 DOI: 10.1038/hgv.2015.67] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a complex disease, and both genetic and environmental factors contribute to disease progression. A previous genome-wide linkage study in Thailand determined that chromosome 20p13-12.3 may contain risk factors for young-onset disease. The present study aimed to identify novel susceptibility genes for young-onset TB within a 1-Mbp target region adjacent to the top-ranking risk marker in Chr.20p13-12.3. We performed next-generation sequencing (NGS) of the region in 13 young patients from multi-case families in Thailand. We then selected the functionally interesting single-nucleotide polymorphisms as candidates for subsequent analyses. The detected candidates rs13830 and rs1127354 in ITPA showed an association with young (<45 years old) TB patients. However, there was no association in old (⩾45 years old) patients. These findings confirm that stratifying patients based on age of TB onset can be important for identifying genetic risk factors for TB susceptibility. In addition, in silico expression quantitative trait loci analyses indicated that ITPA expression was associated with rs13830 genotype. This is the first study to use NGS resequencing to gain insight into host genetic factors associated with TB and to report a significant association for ITPA with host susceptibility in young-onset TB. The study also demonstrated the effectiveness of NGS in identifying susceptibility genes in common diseases.
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Affiliation(s)
- Ayaka Nakauchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Hideki Yanai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | - Rika Yuliwulandari
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Genomic Medicine Research Group, YARSI Research Institute, YARSI University, Jakarta, Indonesia
| | - Akihiko Mabuchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Xiaoxi Liu
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; RIKEN Brain Science Institute, Saitama, Japan
| | - Taisei Mushiroda
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences , Kanagawa, Japan
| | - Sukanya Wattanapokayakit
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Taku Miyagawa
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Naoto Keicho
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA) , Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
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247
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Saini S, Dewan L. Application of discrete wavelet transform for analysis of genomic sequences of Mycobacterium tuberculosis. SPRINGERPLUS 2016; 5:64. [PMID: 26839757 PMCID: PMC4722049 DOI: 10.1186/s40064-016-1668-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/04/2016] [Indexed: 12/04/2022]
Abstract
This paper highlights the potential of discrete wavelet transforms in the analysis and comparison of genomic sequences of Mycobacterium tuberculosis (MTB) with different resistance characteristics. Graphical representations of wavelet coefficients and statistical estimates of their parameters have been used to determine the extent of similarity between different sequences of MTB without the use of conventional methods such as Basic Local Alignment Search Tool. Based on the calculation of the energy of wavelet decomposition coefficients of complete genomic sequences, their broad classification of the type of resistance can be done. All the given genomic sequences can be grouped into two broad categories wherein the drug resistant and drug susceptible sequences form one group while the multidrug resistant and extensive drug resistant sequences form the other group. This method of segregation of the sequences is faster than conventional laboratory methods which require 3–4 weeks of culture of sputum samples. Thus the proposed method can be used as a tool to enhance clinical diagnostic investigations in near real-time.
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Affiliation(s)
- Shiwani Saini
- Department of Electrical Engineering, National Institute of Technology, Kurukshetra, Haryana 136119 India
| | - Lillie Dewan
- Department of Electrical Engineering, National Institute of Technology, Kurukshetra, Haryana 136119 India
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248
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Chindelevitch L, Colijn C, Moodley P, Wilson D, Cohen T. ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. PLoS Comput Biol 2016; 12:e1004475. [PMID: 26829497 PMCID: PMC4734664 DOI: 10.1371/journal.pcbi.1004475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
Genomic tools have revealed genetically diverse pathogens within some hosts. Within-host pathogen diversity, which we refer to as "complex infection", is increasingly recognized as a determinant of treatment outcome for infections like tuberculosis. Complex infection arises through two mechanisms: within-host mutation (which results in clonal heterogeneity) and reinfection (which results in mixed infections). Estimates of the frequency of within-host mutation and reinfection in populations are critical for understanding the natural history of disease. These estimates influence projections of disease trends and effects of interventions. The genotyping technique MLVA (multiple loci variable-number tandem repeats analysis) can identify complex infections, but the current method to distinguish clonal heterogeneity from mixed infections is based on a rather simple rule. Here we describe ClassTR, a method which leverages MLVA information from isolates collected in a population to distinguish mixed infections from clonal heterogeneity. We formulate the resolution of complex infections into their constituent strains as an optimization problem, and show its NP-completeness. We solve it efficiently by using mixed integer linear programming and graph decomposition. Once the complex infections are resolved into their constituent strains, ClassTR probabilistically classifies isolates as clonally heterogeneous or mixed by using a model of tandem repeat evolution. We first compare ClassTR with the standard rule-based classification on 100 simulated datasets. ClassTR outperforms the standard method, improving classification accuracy from 48% to 80%. We then apply ClassTR to a sample of 436 strains collected from tuberculosis patients in a South African community, of which 92 had complex infections. We find that ClassTR assigns an alternate classification to 18 of the 92 complex infections, suggesting important differences in practice. By explicitly modeling tandem repeat evolution, ClassTR helps to improve our understanding of the mechanisms driving within-host diversity of pathogens like Mycobacterium tuberculosis.
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Affiliation(s)
- Leonid Chindelevitch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail:
| | - Caroline Colijn
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Prashini Moodley
- School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Douglas Wilson
- Department of Medicine, Edendale Hospital, Pietermaritzberg, South Africa
- Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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249
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Yates TA, Khan PY, Knight GM, Taylor JG, McHugh TD, Lipman M, White RG, Cohen T, Cobelens FG, Wood R, Moore DAJ, Abubakar I. The transmission of Mycobacterium tuberculosis in high burden settings. THE LANCET. INFECTIOUS DISEASES 2016; 16:227-38. [PMID: 26867464 DOI: 10.1016/s1473-3099(15)00499-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 01/06/2023]
Abstract
Unacceptable levels of Mycobacterium tuberculosis transmission are noted in high burden settings and a renewed focus on reducing person-to-person transmission in these communities is needed. We review recent developments in the understanding of airborne transmission. We outline approaches to measure transmission in populations and trials and describe the Wells-Riley equation, which is used to estimate transmission risk in indoor spaces. Present research priorities include the identification of effective strategies for tuberculosis infection control, improved understanding of where transmission occurs and the transmissibility of drug-resistant strains, and estimates of the effect of HIV and antiretroviral therapy on transmission dynamics. When research is planned and interventions are designed to interrupt transmission, resource constraints that are common in high burden settings-including shortages of health-care workers-must be considered.
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Affiliation(s)
- Tom A Yates
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK; Wellcome Trust Africa Centre for Population Health, Mtubatuba, South Africa, London School of Hygiene & Tropical Medicine, London, UK.
| | - Palwasha Y Khan
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Karonga Prevention Study, Chilumba, Malawi
| | - Gwenan M Knight
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Modelling Group, London School of Hygiene & Tropical Medicine, London, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
| | - Jonathon G Taylor
- UCL Institute for Environmental Design and Engineering, Bartlett School of Environment, Energy and Resources, University College London, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, UK
| | - Marc Lipman
- Division of Medicine, University College London, London, UK
| | - Richard G White
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Modelling Group, London School of Hygiene & Tropical Medicine, London, UK
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Frank G Cobelens
- Department of Global Health, Academic Medical Center, Amsterdam, Netherlands; KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Robin Wood
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; The Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A J Moore
- Tuberculosis Centre, London School of Hygiene & Tropical Medicine, London, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ibrahim Abubakar
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK; MRC Clinical Trials Unit at University College London, University College London, London, UK
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250
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Genomic Analysis of Bacterial Outbreaks. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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