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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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252
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McArthur AG, Tsang KK. Antimicrobial resistance surveillance in the genomic age. Ann N Y Acad Sci 2016; 1388:78-91. [PMID: 27875856 DOI: 10.1111/nyas.13289] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 12/31/2022]
Abstract
The loss of effective antimicrobials is reducing our ability to protect the global population from infectious disease. However, the field of antibiotic drug discovery and the public health monitoring of antimicrobial resistance (AMR) is beginning to exploit the power of genome and metagenome sequencing. The creation of novel AMR bioinformatics tools and databases and their continued development will advance our understanding of the molecular mechanisms and threat severity of antibiotic resistance, while simultaneously improving our ability to accurately predict and screen for antibiotic resistance genes within environmental, agricultural, and clinical settings. To do so, efforts must be focused toward exploiting the advancements of genome sequencing and information technology. Currently, AMR bioinformatics software and databases reflect different scopes and functions, each with its own strengths and weaknesses. A review of the available tools reveals common approaches and reference data but also reveals gaps in our curated data, models, algorithms, and data-sharing tools that must be addressed to conquer the limitations and areas of unmet need within the AMR research field before DNA sequencing can be fully exploited for AMR surveillance and improved clinical outcomes.
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Affiliation(s)
- Andrew G McArthur
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Kara K Tsang
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada
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253
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Faksri K, Xia E, Tan JH, Teo YY, Ong RTH. In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer. BMC Genomics 2016; 17:847. [PMID: 27806686 PMCID: PMC5093977 DOI: 10.1186/s12864-016-3213-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole-genome sequencing is increasingly used in clinical diagnosis of tuberculosis and study of Mycobacterium tuberculosis complex (MTC). MTC consists of several genetically homogenous mycobacteria species which can cause tuberculosis in humans and animals. Regions of difference (RDs) are commonly regarded as gold standard genetic markers for MTC classification. RESULTS We develop RD-Analyzer, a tool that can accurately infer the species and lineage of MTC isolates from sequence reads based on the presence and absence of a set of 31 RDs. Applied on a publicly available diverse set of 377 sequenced MTC isolates from known major species and lineages, RD-Analyzer achieved an accuracy of 98.14 % (370/377) in species prediction and a concordance of 98.47 % (257/261) in Mycobacterium tuberculosis lineage prediction compared to predictions based on single nucleotide polymorphism markers. By comparing respective sequencing read depths on each genomic position between isolates of different sublineages, we were able to identify the known RD markers in different sublineages of Lineage 4 and provide support for six potential delineating markers having high sensitivities and specificities for sublineage prediction. An extended version of RD-Analyzer was thus developed to allow user-defined RDs for lineage prediction. CONCLUSIONS RD-Analyzer is a useful and accurate tool for species, lineage and sublineage prediction using known RDs of MTC from sequence reads and is extendable to accepting user-defined RDs for analysis. RD-Analyzer is written in Python and is freely available at https://github.com/xiaeryu/RD-Analyzer .
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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
| | - Eryu Xia
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Jun Hao Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Tahir Foundation Building, 12 Science Drive 2, #10-01, Singapore, 117549, Singapore
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Tahir Foundation Building, 12 Science Drive 2, #10-01, Singapore, 117549, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Tahir Foundation Building, 12 Science Drive 2, #10-01, Singapore, 117549, Singapore.
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254
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Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nat Med 2016; 22:1470-1474. [PMID: 27798613 DOI: 10.1038/nm.4205] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/14/2016] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
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255
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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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256
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Papaventsis D, Casali N, Kontsevaya I, Drobniewski F, Cirillo DM, Nikolayevskyy V. Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review. Clin Microbiol Infect 2016; 23:61-68. [PMID: 27665704 DOI: 10.1016/j.cmi.2016.09.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/10/2016] [Accepted: 09/15/2016] [Indexed: 01/02/2023]
Abstract
OBJECTIVES We conducted a systematic review to determine the diagnostic accuracy of whole genome sequencing (WGS) of Mycobacterium tuberculosis for the detection of resistance to first- and second-line anti-tuberculosis (TB) drugs. METHODS The study was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews group. A total of 20 publications were included. The sensitivity, specificity, positive-predictive value and negative-predictive value of WGS using phenotypic drug susceptibility testing methods as a reference standard were determined. RESULTS Anti-TB agents tested included all first-line drugs, a variety of reserve drugs, as well as new drugs. Polymorphisms in a total of 53 genes were tested for associations with drug resistance. Pooled sensitivity and specificity values for detection of resistance to selected first-line drugs were 0.98 (95% CI 0.93-0.98) and 0.98 (95% CI 0.98-1.00) for rifampicin and 0.97 (95% CI 0.94-0.99) and 0.93 (95% CI 0.91-0.96) for isoniazid, respectively. Due to high heterogeneity in study designs, lack of data, knowledge of resistance mechanisms and clarity on exclusion of phylogenetic markers, there was a significant variation in analytical performance of WGS for the remaining first-line, reserved drugs and new drugs. CONCLUSIONS Whole genome sequencing could be considered a promising alternative to existing phenotypic and molecular drug susceptibility testing methods for rifampicin and isoniazid pending standardization of analytical pipelines. To ensure clinical relevance of WGS for detection of M. tuberculosis complex drug resistance, future studies should include information on clinical outcomes.
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Affiliation(s)
- D Papaventsis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - N Casali
- Department of Medicine, Imperial College London, London, UK
| | - I Kontsevaya
- Department of Medicine, Imperial College London, London, UK
| | - F Drobniewski
- Department of Medicine, Imperial College London, London, UK
| | - D M Cirillo
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - V Nikolayevskyy
- Department of Medicine, Imperial College London, London, UK; PHE National Mycobacterium Reference Laboratory, London, UK.
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257
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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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258
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Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med 2016; 194:621-30. [PMID: 26910495 PMCID: PMC5027209 DOI: 10.1164/rccm.201510-2091oc] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/22/2016] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The development of molecular diagnostics that detect both the presence of Mycobacterium tuberculosis in clinical samples and drug resistance-conferring mutations promises to revolutionize patient care and interrupt transmission by ensuring early diagnosis. However, these tools require the identification of genetic determinants of resistance to the full range of antituberculosis drugs. OBJECTIVES To determine the optimal molecular approach needed, we sought to create a comprehensive catalog of resistance mutations and assess their sensitivity and specificity in diagnosing drug resistance. METHODS We developed and validated molecular inversion probes for DNA capture and deep sequencing of 28 drug-resistance loci in M. tuberculosis. We used the probes for targeted sequencing of a geographically diverse set of 1,397 clinical M. tuberculosis isolates with known drug resistance phenotypes. We identified a minimal set of mutations to predict resistance to first- and second-line antituberculosis drugs and validated our predictions in an independent dataset. We constructed and piloted a web-based database that provides public access to the sequence data and prediction tool. MEASUREMENTS AND MAIN RESULTS The predicted resistance to rifampicin and isoniazid exceeded 90% sensitivity and specificity but was lower for other drugs. The number of mutations needed to diagnose resistance is large, and for the 13 drugs studied it was 238 across 18 genetic loci. CONCLUSIONS These data suggest that a comprehensive M. tuberculosis drug resistance diagnostic will need to allow for a high dimension of mutation detection. They also support the hypothesis that currently unknown genetic determinants, potentially discoverable by whole-genome sequencing, encode resistance to second-line tuberculosis drugs.
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MESH Headings
- Antitubercular Agents/pharmacology
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genes, Bacterial/drug effects
- Genes, Bacterial/genetics
- Humans
- Molecular Diagnostic Techniques
- Mutation/drug effects
- Mutation/genetics
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Multidrug-Resistant/microbiology
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Affiliation(s)
- Maha R. Farhat
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | - Razvan Sultana
- Genomics England, Queen Mary University, London, United Kingdom
| | - Oleg Iartchouk
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - James Galagan
- Department of Biomedical Engineering
- Department of Microbiology, and
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | | | | | - Hanna Nebenzahl-Guimaraes
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3Bs, PT Government Associate Laboratory, Braga/Guimaraes, Portugal
| | - Karen Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Alexander Sloutsky
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Devinder Kaur
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barry N. Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Natalia Kurepina
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Leen Rigouts
- Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Biomedical Sciences, Antwerp University, Antwerp, Belgium; and
| | - Elizabeth M. Streicher
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tommie C. Victor
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M. Warren
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Dick van Soolingen
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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Swaminathan S, Sundaramurthi JC, Palaniappan AN, Narayanan S. Recent developments in genomics, bioinformatics and drug discovery to combat emerging drug-resistant tuberculosis. Tuberculosis (Edinb) 2016; 101:31-40. [PMID: 27865394 DOI: 10.1016/j.tube.2016.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/21/2016] [Accepted: 08/08/2016] [Indexed: 11/16/2022]
Abstract
Emergence of drug-resistant tuberculosis (DR-TB) is a big challenge in TB control. The delay in diagnosis of DR-TB leads to its increased transmission, and therefore prevalence. Recent developments in genomics have enabled whole genome sequencing (WGS) of Mycobacterium tuberculosis (M. tuberculosis) from 3-day-old liquid culture and directly from uncultured sputa, while new bioinformatics tools facilitate to determine DR mutations rapidly from the resulting sequences. The present drug discovery and development pipeline is filled with candidate drugs which have shown efficacy against DR-TB. Furthermore, some of the FDA-approved drugs are being evaluated for repurposing, and this approach appears promising as several drugs are reported to enhance efficacy of the standard TB drugs, reduce drug tolerance, or modulate the host immune response to control the growth of intracellular M. tuberculosis. Recent developments in genomics and bioinformatics along with new drug discovery collectively have the potential to result in synergistic impact leading to the development of a rapid protocol to determine the drug resistance profile of the infecting strain so as to provide personalized medicine. Hence, in this review, we discuss recent developments in WGS, bioinformatics and drug discovery to perceive how they would transform the management of tuberculosis in a timely manner.
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Affiliation(s)
- Soumya Swaminathan
- National Institute for Research in Tuberculosis (ICMR), Chetpet, Chennai, 600031, India.
| | - Jagadish Chandrabose Sundaramurthi
- Division of Biomedical Informatics, Department of Clinical Research, National Institute for Research in Tuberculosis (ICMR), Chetpet, Chennai, 600031, India
| | - Alangudi Natarajan Palaniappan
- Department of Clinical Research, National Institute for Research in Tuberculosis (ICMR), Chetpet, Chennai, 600031, India
| | - Sujatha Narayanan
- Department of Immunology, National Institute for Research in Tuberculosis (ICMR), Chetpet, Chennai, 600031, India
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260
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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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261
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Multidrug-Resistant Tuberculosis in Children: Recent Developments in Diagnosis, Treatment and Prevention. CURRENT PEDIATRICS REPORTS 2016. [DOI: 10.1007/s40124-016-0100-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Ninan MM, Gowri M, Christopher DJ, Rupali P, Michael JS. The diagnostic utility of line probe assays for multidrug-resistant tuberculosis. Pathog Glob Health 2016; 110:194-9. [PMID: 27499239 PMCID: PMC5072114 DOI: 10.1080/20477724.2016.1214350] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Owing to the burden of multidrug-resistant tuberculosis, molecular techniques have been approved by the WHO for the rapid diagnosis of the same. The objectives of this prospective, diagnostic study, conducted at Christian Medical College, a tertiary care center in South India, were to compare the performance of line probe assay (GenoTypeMTBDRplus) with culture, as well as the Xpert MTB/Rif assay on sputum samples. Ninety-one consecutive suspects of multidrug-resistant pulmonary tuberculosis patients from January 2013 to June 2013 were enrolled in this study and the results of line probe assay compared to culture and Xpert MTB/Rif. Compared to culture, the assay demonstrated a sensitivity and specificity of 81.5% (95%CI 67.4-91.1%) and 87.5% (95%CI 71-96.5%) for the detection of tuberculosis, with sensitivity and specificity of 100% (95%CI 85.2-100%) and 93.8% (95%CI 69.8-99.8%), respectively, for rifampicin resistance. For isoniazid resistance, sensitivity and specificity were 89.3% (95%CI 71.8-97.7%) and 100% (95%CI 71.5-100%), respectively. Compared to Xpert MTB/Rif assay, the assay showed a sensitivity of 80% (95%CI 68.2-88.9%) and specificity of 100% (95%CI 85.8-100%) for the detection of tuberculosis a sensitivity of 94.3% (95%CI 80.8-99.3%) and specificity of 94.1% (95%CI 71.3-99.9%) for rifampicin resistance was attained. This assay performed well on smear positive samples, but poorly on smear negative and scanty samples, and can serve as a rapid diagnostic tool, particularly in isoniazid monoresistant cases of tuberculosis, which are not diagnosed by Xpert MTB/Rif.
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Affiliation(s)
- Marilyn M Ninan
- Department of Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Mahasampath Gowri
- Department of Biostatistics, Christian Medical College and Hospital, Vellore, India
| | - D. J. Christopher
- Department of Pulmonary Medicine, Christian Medical College and Hospital, Vellore, India
| | - Priscilla Rupali
- Department of Infectious Diseases, Christian Medical College and Hospital, Vellore, India
| | - Joy S. Michael
- Department of Microbiology, Christian Medical College and Hospital, Vellore, India
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263
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Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol 2016; 54:2058-67. [PMID: 27225403 PMCID: PMC4963505 DOI: 10.1128/jcm.00535-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022] Open
Abstract
Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.
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264
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Silva Feliciano C, Rodrigues Plaça J, Peronni K, Araújo Silva W, Roberto Bollela V. Evaluation of resistance acquisition during tuberculosis treatment using whole genome sequencing. Braz J Infect Dis 2016; 20:290-3. [PMID: 27004922 PMCID: PMC9425402 DOI: 10.1016/j.bjid.2016.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB) is still considered a major global public health problem in the world and there is a concern about the worldwide increase of drug-resistance (DR). This paper describes the analysis of three Mycobacterium tuberculosis isolates from a single patient collected over a long treatment period of time. DR was initially investigated through phenotypic testing, followed by line probe assays (LPAs) and whole genome sequencing (WGS). It presents an intriguing situation where a multidrug-resistant (MDR-) TB case was diagnosed and treated based only on late phenotypic drug susceptibility testing of isolate 1. During the treatment, another two isolates were cultivated: isolate 2, nine months after starting MDR-TB treatment; and isolate 3, cultivated five months later, during regular use of anti-TB drugs. These two isolates were evaluated using molecular LPA and WGS, retrospectively. All mutations detected by LPA were also detected in the WGS, including conversion from fluoroquinolones susceptibility to resistance from isolate 2 to isolate 3. WGS showed additional mutations, including some which may confer resistance to other drugs not tested (terizidone/cycloserine) and mutations with no correspondent resistance in drug susceptibility testing (streptomycin and second-line injectable drugs).
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265
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Coker OO, Chaiprasert A, Ngamphiw C, Tongsima S, Regmi SM, Clark TG, Ong RTH, Teo YY, Prammananan T, Palittapongarnpim P. Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand. PeerJ 2016; 4:e1905. [PMID: 27114869 PMCID: PMC4841212 DOI: 10.7717/peerj.1905] [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: 11/30/2015] [Accepted: 03/16/2016] [Indexed: 01/27/2023] Open
Abstract
Genome sequencing plays a key role in understanding the genetic diversity of Mycobacterium tuberculosis (M.tb). The genotype-specific character of M. tb contributes to tuberculosis severity and emergence of drug resistance. Strains of M. tb complex can be classified into seven lineages. The Nonthaburi (NB) genotype, belonging to the Indo-Oceanic lineage (lineage 1), has a unique spoligotype and IS6110-RFLP pattern but has not previously undergone a detailed whole genome analysis. In addition, there is not much information available on the whole genome analysis of M. tb isolates from tuberculous meningitis (TBM) patients in public databases. Isolates CSF3053, 46-5069 and 43-13838 of NB genotype were obtained from the cerebrospinal fluids of TBM Thai patients in Siriraj Hospital, Bangkok. The whole genomes were subjected to high throughput sequencing. The sequence data of each isolate were assembled into draft genome. The sequences were also aligned to reference genome, to determine genomic variations. Single nucleotide polymorphisms (SNPs) were obtained and grouped according to the functions of the genes containing them. They were compared with SNPs from 1,601 genomes, representing the seven lineages of M. tb complex, to determine the uniqueness of NB genotype. Susceptibility to first-line, second-line and other antituberculosis drugs were determined and related to the SNPs previously reported in drug-resistant related genes. The assembled genomes have an average size of 4,364,461 bp, 4,154 genes, 48 RNAs and 64 pseudogenes. A 500 base pairs deletion, which includes ppe50, was found in all isolates. RD239, specific for members of Indo Oceanic lineage, and RD147c were identified. A total of 2,202 SNPs were common to the isolates and used to classify the NB strains as members of sublineage 1.2.1. Compared with 1,601 genomes from the seven lineages of M. tb complex, mutation G2342203C was found novel to the isolates in this study. Three mutations (T28910C, C1180580T and C152178T) were found only in Thai NB isolates, including isolates from previous study. Although drug susceptibility tests indicated pan-susceptibility, non-synonymous SNPs previously reported to be associated with resistance to anti-tuberculous drugs; isoniazid, ethambutol, and ethionamide were identified in all the isolates. Non-synonymous SNPs were found in virulence genes such as the genes playing roles in apoptosis inhibition and phagosome arrest. We also report polymorphisms in essential genes, efflux pumps associated genes and genes with known epitopes. The analysis of the TBM isolates and the availability of the variations obtained will provide additional resources for global comparison of isolates from pulmonary tuberculosis and TBM. It will also contribute to the richness of genomic databases towards the prediction of antibiotic resistance, level of virulence and of origin of infection.
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Affiliation(s)
- Olabisi Oluwabukola Coker
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Angkana Chaiprasert
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency , Pathum Thani , Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency , Pathum Thani , Thailand
| | - Sanjib Mani Regmi
- Department of Microbiology, Gandaki Medical College , Pokhara Kaski , Nepal
| | - Taane G Clark
- Faculty of Epidemiology and Population Health, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, University of London , London , United Kingdom
| | - Rick Twee Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore , Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore , Singapore
| | - Therdsak Prammananan
- Tuberculosis Research Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency , Pathum Thani , Thailand
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266
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Phelan J, Coll F, McNerney R, Ascher DB, Pires DEV, Furnham N, Coeck N, Hill-Cawthorne GA, Nair MB, Mallard K, Ramsay A, Campino S, Hibberd ML, Pain A, Rigouts L, Clark TG. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Med 2016; 14:31. [PMID: 27005572 PMCID: PMC4804620 DOI: 10.1186/s12916-016-0575-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/02/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. METHODS To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. RESULTS The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. CONCLUSIONS Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistance mutations to improve the design of tuberculosis control measures, such as diagnostics, and inform patient management.
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Affiliation(s)
- Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,University of Cape Town Lung Institute, Lung Infection & Immunity Unit, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Douglas E V Pires
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima 1715, Belo Horizonte, 30190-002, Brazil
| | - Nick Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Nele Coeck
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Grant A Hill-Cawthorne
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mridul B Nair
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Andrew Ramsay
- Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organisation, Geneva, Switzerland
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. .,Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK.
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267
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Haas CT, Roe JK, Pollara G, Mehta M, Noursadeghi M. Diagnostic 'omics' for active tuberculosis. BMC Med 2016; 14:37. [PMID: 27005907 PMCID: PMC4804573 DOI: 10.1186/s12916-016-0583-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/08/2016] [Indexed: 12/12/2022] Open
Abstract
The decision to treat active tuberculosis (TB) is dependent on microbiological tests for the organism or evidence of disease compatible with TB in people with a high demographic risk of exposure. The tuberculin skin test and peripheral blood interferon-γ release assays do not distinguish active TB from a cleared or latent infection. Microbiological culture of mycobacteria is slow. Moreover, the sensitivities of culture and microscopy for acid-fast bacilli and nucleic acid detection by PCR are often compromised by difficulty in obtaining samples from the site of disease. Consequently, we need sensitive and rapid tests for easily obtained clinical samples, which can be deployed to assess patients exposed to TB, discriminate TB from other infectious, inflammatory or autoimmune diseases, and to identify subclinical TB in HIV-1 infected patients prior to commencing antiretroviral therapy. We discuss the evaluation of peripheral blood transcriptomics, proteomics and metabolomics to develop the next generation of rapid diagnostics for active TB. We catalogue the studies published to date seeking to discriminate active TB from healthy volunteers, patients with latent infection and those with other diseases. We identify the limitations of these studies and the barriers to their adoption in clinical practice. In so doing, we aim to develop a framework to guide our approach to discovery and development of diagnostic biomarkers for active TB.
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Affiliation(s)
- Carolin T Haas
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Jennifer K Roe
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Meera Mehta
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK.
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268
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Witney AA, Cosgrove CA, Arnold A, Hinds J, Stoker NG, Butcher PD. Clinical use of whole genome sequencing for Mycobacterium tuberculosis. BMC Med 2016; 14:46. [PMID: 27004841 PMCID: PMC4804576 DOI: 10.1186/s12916-016-0598-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/11/2016] [Indexed: 02/07/2023] Open
Abstract
Drug-resistant tuberculosis (TB) remains a major challenge to global health and to healthcare in the UK. In 2014, a total of 6,520 cases of TB were recorded in England, of which 1.4 % were multidrug-resistant TB (MDR-TB). Extensively drug-resistant TB (XDR-TB) occurs at a much lower rate, but the impact on the patient and hospital is severe. Current diagnostic methods such as drug susceptibility testing and targeted molecular tests are slow to return or examine only a limited number of target regions, respectively. Faster, more comprehensive diagnostics will enable earlier use of the most appropriate drug regimen, thus improving patient outcomes and reducing overall healthcare costs. Whole genome sequencing (WGS) has been shown to provide a rapid and comprehensive view of the genotype of the organism, and thus enable reliable prediction of the drug susceptibility phenotype within a clinically relevant timeframe. In addition, it provides the highest resolution when investigating transmission events in possible outbreak scenarios. However, robust software and database tools need to be developed for the full potential to be realized in this specialized area of medicine.
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Affiliation(s)
- Adam A Witney
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - Catherine A Cosgrove
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK.,Clinical Infection Unit, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London, SW17 0QT, UK
| | - Amber Arnold
- Clinical Infection Unit, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London, SW17 0QT, UK
| | - Jason Hinds
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Neil G Stoker
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Philip D Butcher
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
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269
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Phelan JE, Coll F, Bergval I, Anthony RM, Warren R, Sampson SL, Gey van Pittius NC, Glynn JR, Crampin AC, Alves A, Bessa TB, Campino S, Dheda K, Grandjean L, Hasan R, Hasan Z, Miranda A, Moore D, Panaiotov S, Perdigao J, Portugal I, Sheen P, de Oliveira Sousa E, Streicher EM, van Helden PD, Viveiros M, Hibberd ML, Pain A, McNerney R, Clark TG. Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics 2016; 17:151. [PMID: 26923687 PMCID: PMC4770551 DOI: 10.1186/s12864-016-2467-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/12/2016] [Indexed: 11/23/2022] Open
Abstract
Background Approximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised to be important virulence factors involved with host-pathogen interactions, but their high genetic variability and complexity of analysis means they are typically disregarded in genome studies. Results To elucidate the structure of these genes, 518 genomes from a diverse international collection of clinical isolates were de novo assembled. A further 21 reference M. tuberculosis complex genomes and long read sequence data were used to validate the approach. SNP analysis revealed that variation in the majority of the 168 pe/ppe genes studied was consistent with lineage. Several recombination hotspots were identified, notably pe_pgrs3 and pe_pgrs17. Evidence of positive selection was revealed in 65 pe/ppe genes, including epitopes potentially binding to major histocompatibility complex molecules. Conclusions This, the first comprehensive study of the pe and ppe genes, provides important insight into M. tuberculosis diversity and has significant implications for vaccine development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2467-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jody E Phelan
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - Francesc Coll
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - Indra Bergval
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, Netherlands.
| | - Richard M Anthony
- KIT Biomedical Research, Royal Tropical Institute, Amsterdam, Netherlands.
| | - Rob Warren
- Department of Science and Technology and National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, and Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Samantha L Sampson
- Department of Science and Technology and National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, and Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Nicolaas C Gey van Pittius
- Department of Science and Technology and National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, and Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK.
| | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK. .,Karonga Prevention Study, Lilongwe, Malawi.
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal.
| | - Theolis Barbosa Bessa
- Centro de Pesquisas Goncalo Moniz, Fundacao Oswaldo Cruz Bahia R, Salvador, Bahia, Brazil.
| | - Susana Campino
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - Keertan Dheda
- Department of Medicine, Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, University of Cape Town, Cape Town, Western Cape, South Africa. .,Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.
| | - Louis Grandjean
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK. .,Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi, Pakistan.
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi, Pakistan.
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal.
| | - David Moore
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, 1504, Sofia, Bulgaria.
| | | | | | - Patricia Sheen
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | | | - Elizabeth M Streicher
- Department of Science and Technology and National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, and Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Paul D van Helden
- Department of Science and Technology and National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, and Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa (IHMT/UNL), Lisbon, Portugal.
| | - Martin L Hibberd
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
| | - Ruth McNerney
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - Taane G Clark
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK.
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270
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Colijn C, Cohen T. Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond. THE LANCET RESPIRATORY MEDICINE 2016; 4:6-8. [DOI: 10.1016/s2213-2600(15)00510-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 11/27/2015] [Indexed: 11/26/2022]
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271
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Lee RS, Behr MA. The implications of whole-genome sequencing in the control of tuberculosis. Ther Adv Infect Dis 2015; 3:47-62. [PMID: 27034776 DOI: 10.1177/2049936115624630] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The availability of whole-genome sequencing (WGS) as a tool for the diagnosis and clinical management of tuberculosis (TB) offers considerable promise in the fight against this stubborn epidemic. However, like other new technologies, the best application of WGS remains to be determined, for both conceptual and technical reasons. In this review, we consider the potential value of WGS in the clinical laboratory for the detection of Mycobacterium tuberculosis and the prediction of antibiotic resistance. We also discuss issues pertaining to data generation, interpretation and dissemination, given that WGS has to date been generally performed in research labs where results are not necessarily packaged in a clinician-friendly format. Although WGS is far more accessible now than it was in the past, the transition from a research tool to study TB into a clinical test to manage this disease may require further fine-tuning. Improvements will likely come through iterative efforts that involve both the laboratories ready to move TB into the genomic era and the front-line clinical/public health staff who will be interpreting the results to inform management decisions.
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Affiliation(s)
- Robyn S Lee
- McGill University, Department of Epidemiology, Biostatistics and Occupational Health, The Research Institute of the McGill University Health Centre and McGill International TB Centre, Montreal, QC, Canada
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272
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Theron G, Jenkins HE, Cobelens F, Abubakar I, Khan AJ, Cohen T, Dowdy DW. Data for action: collection and use of local data to end tuberculosis. Lancet 2015; 386:2324-33. [PMID: 26515676 PMCID: PMC4708262 DOI: 10.1016/s0140-6736(15)00321-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Accelerating progress in the fight against tuberculosis will require a drastic shift from a strategy focused on control to one focused on elimination. Successful disease elimination campaigns are characterised by locally tailored responses that are informed by appropriate data. To develop such a response to tuberculosis, we suggest a three-step process that includes improved collection and use of existing programmatic data, collection of additional data (eg, geographic information, drug resistance, and risk factors) to inform tailored responses, and targeted collection of novel data (eg, sequencing data, targeted surveys, and contact investigations) to improve understanding of tuberculosis transmission dynamics. Development of a locally targeted response for tuberculosis will require substantial investment to reconfigure existing systems, coupled with additional empirical data to evaluate the effectiveness of specific approaches. Without adoption of an elimination strategy that uses local data to target hotspots of transmission, ambitious targets to end tuberculosis will almost certainly remain unmet.
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Affiliation(s)
- Grant Theron
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and South African Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Lung Infection and Immunity Unit, Department of Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Helen E Jenkins
- Department of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Cobelens
- KNCV Tuberculosis Foundation, The Hague, Netherlands; Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, Netherlands
| | | | - Aamir J Khan
- Interactive Research & Development, Karachi, Pakistan
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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273
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Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. THE LANCET RESPIRATORY MEDICINE 2015; 4:49-58. [PMID: 26669893 PMCID: PMC4698465 DOI: 10.1016/s2213-2600(15)00466-x] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/17/2015] [Accepted: 10/28/2015] [Indexed: 12/01/2022]
Abstract
Background Slow and cumbersome laboratory diagnostics for Mycobacterium tuberculosis complex (MTBC) risk delayed treatment and poor patient outcomes. Whole-genome sequencing (WGS) could potentially provide a rapid and comprehensive diagnostic solution. In this prospective study, we compare real-time WGS with routine MTBC diagnostic workflows. Methods We compared sequencing mycobacteria from all newly positive liquid cultures with routine laboratory diagnostic workflows across eight laboratories in Europe and North America for diagnostic accuracy, processing times, and cost between Sept 6, 2013, and April 14, 2014. We sequenced specimens once using local Illumina MiSeq platforms and processed data centrally using a semi-automated bioinformatics pipeline. We identified species or complex using gene presence or absence, predicted drug susceptibilities from resistance-conferring mutations identified from reference-mapped MTBC genomes, and calculated genetic distance to previously sequenced UK MTBC isolates to detect outbreaks. WGS data processing and analysis was done by staff masked to routine reference laboratory and clinical results. We also did a microcosting analysis to assess the financial viability of WGS-based diagnostics. Findings Compared with routine results, WGS predicted species with 93% (95% CI 90–96; 322 of 345 specimens; 356 mycobacteria specimens submitted) accuracy and drug susceptibility also with 93% (91–95; 628 of 672 specimens; 168 MTBC specimens identified) accuracy, with one sequencing attempt. WGS linked 15 (16% [95% CI 10–26]) of 91 UK patients to an outbreak. WGS diagnosed a case of multidrug-resistant tuberculosis before routine diagnosis was completed and discovered a new multidrug-resistant tuberculosis cluster. Full WGS diagnostics could be generated in a median of 9 days (IQR 6–10), a median of 21 days (IQR 14–32) faster than final reference laboratory reports were produced (median of 31 days [IQR 21–44]), at a cost of £481 per culture-positive specimen, whereas routine diagnosis costs £518, equating to a WGS-based diagnosis cost that is 7% cheaper annually than are present diagnostic workflows. Interpretation We have shown that WGS has a scalable, rapid turnaround, and is a financially feasible method for full MTBC diagnostics. Continued improvements to mycobacterial processing, bioinformatics, and analysis will improve the accuracy, speed, and scope of WGS-based diagnosis. Funding National Institute for Health Research, Department of Health, Wellcome Trust, British Colombia Centre for Disease Control Foundation for Population and Public Health, Department of Clinical Microbiology, Trinity College Dublin.
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274
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Bryant JM, Lipman M, Breuer J. Personalizing therapy for multidrug resistant TB: the potential of Rapid Whole Genome Sequencing. Expert Rev Anti Infect Ther 2015; 14:1-3. [PMID: 26559223 DOI: 10.1586/14787210.2016.1116385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Multidrug resistant tuberculosis is an increasing problem globally. The current gold standard in drug sensitivity testing is slow and cumbersome. To tackle drug resistance effectively, a more rapid method of testing is required. Current molecular tests are fast, but only offer information on a limited number of genetic loci. Whole genome sequencing presents an attractive alternative that can provide comprehensive, clinically relevant information on all described loci. Although the standard approach to whole genome sequencing of Mycobacterium tuberculosis is slow due to the requirement of culture, this article will describe recent advances that mean it has the potential to provide results within days.
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Affiliation(s)
| | - Marc Lipman
- b Centre for Respiratory Medicine, Royal Free London NHS Foundation Trust , University College London , London , UK
| | - Judith Breuer
- a Division of Infection and Immunity , UCL , London , UK
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275
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Takiff HE, Feo O. Clinical value of whole-genome sequencing of Mycobacterium tuberculosis. THE LANCET. INFECTIOUS DISEASES 2015; 15:1077-1090. [PMID: 26277037 DOI: 10.1016/s1473-3099(15)00071-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/27/2015] [Accepted: 05/20/2015] [Indexed: 01/25/2023]
Abstract
Whole-genome sequencing (WGS) is now common as a result of new technologies that can rapidly sequence a complete bacterial genome for US$500 or less. Many studies have addressed questions about tuberculosis with WGS, and knowing the sequence of the entire genome, rather than only a few fragments, has greatly increased the precision of molecular epidemiology and contact tracing. Additionally, topics such as the mutation rate, drug resistance, the target of new drugs, and the phylogeny and evolution of the Mycobacterium tuberculosis complex bacteria have been elucidated by WGS. Nonetheless, WGS has not explained differences in transmissibility between strains, or why some strains are more virulent than others or more prone to development of multidrug resistance. With advances in technology, WGS of clinical specimens could become routine in high-income countries; however, its relevance will probably depend on easy to use software to efficiently process the sequences produced and accessible genomic databases that can be mined in future studies.
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Affiliation(s)
- Howard E Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela; Unité de Génétique Mycobactérienne, Insitut Pasteur, Paris, France.
| | - Oscar Feo
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela
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276
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Glynn JR, Guerra-Assunção JA, Houben RMGJ, Sichali L, Mzembe T, Mwaungulu LK, Mwaungulu JN, McNerney R, Khan P, Parkhill J, Crampin AC, Clark TG. Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. PLoS One 2015; 10:e0132840. [PMID: 26181760 PMCID: PMC4504505 DOI: 10.1371/journal.pone.0132840] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/18/2015] [Indexed: 12/12/2022] Open
Abstract
Background The proportion of tuberculosis attributable to transmission from close contacts is not well known. Comparison of the genome of strains from index patients and prior contacts allows transmission to be confirmed or excluded. Methods In Karonga District, Malawi, all tuberculosis patients are asked about prior contact with others with tuberculosis. All available strains from culture-positive patients were sequenced. Up to 10 single nucleotide polymorphisms between index patients and their prior contacts were allowed for confirmation, and ≥ 100 for exclusion. The population attributable fraction was estimated from the proportion of confirmed transmissions and the proportion of patients with contacts. Results From 1997–2010 there were 1907 new culture-confirmed tuberculosis patients, of whom 32% reported at least one family contact and an additional 11% had at least one other contact; 60% of contacts had smear-positive disease. Among case-contact pairs with sequences available, transmission was confirmed from 38% (62/163) smear-positive prior contacts and 0/17 smear-negative prior contacts. Confirmed transmission was more common in those related to the prior contact (42.4%, 56/132) than in non-relatives (19.4%, 6/31, p = 0.02), and in those with more intense contact, to younger index cases, and in more recent years. The proportion of tuberculosis attributable to known contacts was estimated to be 9.4% overall. Conclusions In this population known contacts only explained a small proportion of tuberculosis cases. Even those with a prior family contact with smear positive tuberculosis were more likely to have acquired their infection elsewhere.
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Affiliation(s)
- Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - José Afonso Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | | | | | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Palwasha Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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277
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Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG. PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics 2015; 16:155. [PMID: 25968323 PMCID: PMC4429496 DOI: 10.1186/s12859-015-0603-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/29/2015] [Indexed: 12/04/2022] Open
Abstract
Background Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting. Results We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates. Conclusion PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms (http://sourceforge.net/projects/phylotrack).
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Affiliation(s)
- Ernest D Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. .,Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK.
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.
| | - Nick Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.
| | - Susana Campino
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
| | - Fady R Mohareb
- Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.
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