1
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Fennell D, Griffiths D, Eminton Z, Morgan-Fox A, Hill K, Ewings S, Stuart C, Johnson L, Mallard K, Nye M, Darlison L, Dulloo S, Cave J, Luo JL, Taylor P, Spicer J, Poile C, Bzura A, Griffiths G. Evaluating niraparib versus active symptom control in patients with previously treated mesothelioma (NERO): a study protocol for a multicentre, randomised, two-arm, open-label phase II trial in UK secondary care centres. BMJ Open 2023; 13:e073120. [PMID: 37993149 PMCID: PMC10668324 DOI: 10.1136/bmjopen-2023-073120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Malignant mesothelioma is a rapidly lethal cancer that has been increasing at an epidemic rate over the last three decades. Targeted therapies for mesothelioma have been lacking. A previous study called MiST1 (NCT03654833), evaluated the efficacy of Poly (ADP-ribose) polymerase (PARP) inhibition in mesothelioma. This study met its primary endpoint with 15% of patients having durable responses exceeding 1 year. Therefore, there is a need to evaluate PARP inhibitors in relapsed mesothelioma patients, where options are limited. Niraparib is the PARP inhibitor used in NERO. METHODS NERO is a multicentre, two-arm, open-label UK randomised phase II trial designed to evaluate the efficacy of PARP inhibition in relapsed mesothelioma. 84 patients are being recruited. NERO is not restricted by line of therapy; however, eligible participants must have been treated with an approved platinum based systemic therapy. Participants will be randomised 2:1, stratified according to histology and response to prior platinum-based chemotherapy, to receive either active symptom control (ASC) and niraparib or ASC alone, for up to 24 weeks. Participants will be treated until disease progression, withdrawal, death or development of significant treatment limiting toxicity. Participants randomised to niraparib will receive 200 or 300 mg daily in a 3-weekly cycle. The primary endpoint is progression-free survival, where progression is determined by modified Response Evaluation Criteria in Solid Tumors (mRECIST) or RECIST 1.1; investigator reported progression; or death from any cause, whichever comes first. Secondary endpoints include overall survival, best overall response, 12-week and 24 week disease control, duration of response, treatment compliance and safety/tolerability. If NERO shows niraparib to be safe and biologically effective, it may lead to future late phase randomised controlled trials in relapsed mesothelioma. ETHICS AND DISSEMINATION The study received ethical approval from London-Hampstead Research Ethics Committee on 06-May-2022 (22/LO/0281). Data from all centres will be analysed together and published as soon as possible. TRIAL REGISTRATION NUMBER ISCRTN16171129; NCT05455424.
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Affiliation(s)
- Dean Fennell
- Mesothelioma Research Programme, Department of Genetics and Genome Biology, University of Leicester & University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Daniel Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Zina Eminton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Abigail Morgan-Fox
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Kayleigh Hill
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Sean Ewings
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Charlotte Stuart
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Lucy Johnson
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Kim Mallard
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Mavis Nye
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Liz Darlison
- Mesothelioma Research Programme, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Sean Dulloo
- Department of Genetics and Genome Biology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Judith Cave
- Department of Oncology, Wessex NET group ENETS Centre of Excellence, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jin-Li Luo
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Paul Taylor
- Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Jake Spicer
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Charlotte Poile
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Aleksandra Bzura
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
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2
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Khoo SH, Fitzgerald R, Fletcher T, Ewings S, Jaki T, Lyon R, Downs N, Walker L, Tansley-Hancock O, Greenhalf W, Woods C, Reynolds H, Marwood E, Mozgunov P, Adams E, Bullock K, Holman W, Bula MD, Gibney JL, Saunders G, Corkhill A, Hale C, Thorne K, Chiong J, Condie S, Pertinez H, Painter W, Wrixon E, Johnson L, Yeats S, Mallard K, Radford M, Fines K, Shaw V, Owen A, Lalloo DG, Jacobs M, Griffiths G. Optimal dose and safety of molnupiravir in patients with early SARS-CoV-2: a Phase I, open-label, dose-escalating, randomized controlled study. J Antimicrob Chemother 2021; 76:3286-3295. [PMID: 34450619 PMCID: PMC8598307 DOI: 10.1093/jac/dkab318] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES AGILE is a Phase Ib/IIa platform for rapidly evaluating COVID-19 treatments. In this trial (NCT04746183) we evaluated the safety and optimal dose of molnupiravir in participants with early symptomatic infection. METHODS We undertook a dose-escalating, open-label, randomized-controlled (standard-of-care) Bayesian adaptive Phase I trial at the Royal Liverpool and Broadgreen Clinical Research Facility. Participants (adult outpatients with PCR-confirmed SARS-CoV-2 infection within 5 days of symptom onset) were randomized 2:1 in groups of 6 participants to 300, 600 and 800 mg doses of molnupiravir orally, twice daily for 5 days or control. A dose was judged unsafe if the probability of 30% or greater dose-limiting toxicity (the primary outcome) over controls was 25% or greater. Secondary outcomes included safety, clinical progression, pharmacokinetics and virological responses. RESULTS Of 103 participants screened, 18 participants were enrolled between 17 July and 30 October 2020. Molnupiravir was well tolerated at 300, 600 and 800 mg doses with no serious or severe adverse events. Overall, 4 of 4 (100%), 4 of 4 (100%) and 1 of 4 (25%) of the participants receiving 300, 600 and 800 mg molnupiravir, respectively, and 5 of 6 (83%) controls, had at least one adverse event, all of which were mild (≤grade 2). The probability of ≥30% excess toxicity over controls at 800 mg was estimated at 0.9%. CONCLUSIONS Molnupiravir was safe and well tolerated; a dose of 800 mg twice daily for 5 days was recommended for Phase II evaluation.
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Affiliation(s)
- Saye H Khoo
- University of Liverpool, 70 Pembroke Place, Liverpool, UK.,Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Richard Fitzgerald
- Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Thomas Fletcher
- Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Sean Ewings
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Thomas Jaki
- University of Lancaster, Bailrigg, Lancaster, UK.,MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Rebecca Lyon
- Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Nichola Downs
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Lauren Walker
- University of Liverpool, 70 Pembroke Place, Liverpool, UK.,Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Olana Tansley-Hancock
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | | | - Christie Woods
- Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Helen Reynolds
- University of Liverpool, 70 Pembroke Place, Liverpool, UK
| | - Ellice Marwood
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | | | - Emily Adams
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Katie Bullock
- University of Liverpool, 70 Pembroke Place, Liverpool, UK
| | - Wayne Holman
- Ridgeback Biotherapeutics, 3480 Main Highway, Miami, FL, USA
| | - Marcin D Bula
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Jennifer L Gibney
- Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Geoffrey Saunders
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Andrea Corkhill
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Colin Hale
- Liverpool University Hospital NHS Foundation Trust, Prescot Road, Liverpool, UK
| | - Kerensa Thorne
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Justin Chiong
- University of Liverpool, 70 Pembroke Place, Liverpool, UK
| | - Susannah Condie
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Henry Pertinez
- University of Liverpool, 70 Pembroke Place, Liverpool, UK
| | - Wendy Painter
- Ridgeback Biotherapeutics, 3480 Main Highway, Miami, FL, USA
| | - Emma Wrixon
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Lucy Johnson
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Sara Yeats
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Kim Mallard
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Mike Radford
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Keira Fines
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
| | - Victoria Shaw
- University of Liverpool, 70 Pembroke Place, Liverpool, UK
| | - Andrew Owen
- University of Liverpool, 70 Pembroke Place, Liverpool, UK
| | - David G Lalloo
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Michael Jacobs
- Royal Free London NHS Foundation Trust, Pond Street, London, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Tremona Road, Southampton, UK
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3
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Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics 2018; 19:613. [PMID: 30107785 PMCID: PMC6092779 DOI: 10.1186/s12864-018-4988-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and the proportion of heterozygous sites to total SNPs, and (ii) Bayesian model-based clustering of allele frequencies from sequencing reads at heterozygous sites. RESULTS In silico and in vitro artificially mixed and known pure M. tuberculosis samples were analysed to determine the specificity and sensitivity of each method. We found that both approaches were effective in distinguishing between pure strains and mixed infection where there was relatively high (> 10%) proportion of a minor strain in the mixture. A large dataset of clinical isolates (n = 1963) from the Karonga Prevention Study in Northern Malawi was tested to examine correlations with patient characteristics and outcomes with mixed infection. The frequency of mixed infection in the population was found to be around 10%, with an association with year of diagnosis, but no association with age, sex, HIV status or previous tuberculosis. CONCLUSIONS Mixed Mycobacterium tuberculosis infection was identified in silico using whole genome sequence data. The methods presented here can be applied to population-wide analyses of tuberculosis to estimate the frequency of mixed infection, and to identify individual cases of mixed infections. These cases are important when considering the evolution and transmission of the disease, and in patient treatment.
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Affiliation(s)
- Benjamin Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- TB Modelling Group, TB Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Bill Lyons Informatics Centre, University College London, London, UK
| | | | | | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
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4
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Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Ha DM, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Sousa EO, Streicher EM, Van Helden P, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018; 50:764. [PMID: 29674744 DOI: 10.1038/s41588-018-0074-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the URL listed for TubercuList was incorrect. The correct URL is https://mycobrowser.epfl.ch/. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - 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, New South Wales, 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 and Tropical Medicine, London, UK
| | - Shahjahan Ali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah M Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona Alsomali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah O Ahmed
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Stephanie Portelli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yaa Oppong
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, UK.,Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | | | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Keertan Dheda
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicholas Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Louis Grandjean
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dang Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - David J Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nora Mocillo
- Reference Laboratory of Tuberculosis Control, Buenos Aires, Argentina
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Carlos Penha
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Patricia Sheen
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | | | - Frik A Sirgel
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Sola
- Institute for Integrative Cell Biology, CEA, CNRS, Université Paris-Saclay, Orsay, France
| | - Erivelton Oliveira Sousa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Laboratorio Central de Saúde Pública Professor Gonçalo Moniz, Salvador, Brazil
| | - Elizabeth M Streicher
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul Van Helden
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Robert M Warren
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. .,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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5
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Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018; 50:307-316. [PMID: 29358649 DOI: 10.1038/s41588-017-0029-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
Abstract
To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - 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, New South Wales, 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 and Tropical Medicine, London, UK
| | - Shahjahan Ali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah M Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona Alsomali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah O Ahmed
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Stephanie Portelli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yaa Oppong
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, UK
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | | | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Keertan Dheda
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicholas Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Louis Grandjean
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dang Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - David J Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nora Mocillo
- Reference Laboratory of Tuberculosis Control, Buenos Aires, Argentina
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Carlos Penha
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Patricia Sheen
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | | | - Frik A Sirgel
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Sola
- Institute for Integrative Cell Biology, CEA, CNRS, Université Paris-Saclay, Orsay, France
| | - Erivelton Oliveira Sousa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Laboratorio Central de Saúde Pública Professor Gonçalo Moniz, Salvador, Brazil
| | - Elizabeth M Streicher
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul Van Helden
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Robert M Warren
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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Trepanier P, Mallard K, Meunier D, Pike R, Brown D, Ashby JP, Donaldson H, Awad-El-Kariem FM, Balakrishnan I, Cubbon M, Chadwick PR, Doughton M, Doughton R, Hardiman F, Harvey G, Horner C, Lee J, Lewis J, Loughrey A, Manuel R, Parsons H, Perry JD, Vanstone G, White G, Shetty N, Coia J, Wiuff C, Hopkins KL, Woodford N. Carbapenemase-producing Enterobacteriaceae in the UK: a national study (EuSCAPE-UK) on prevalence, incidence, laboratory detection methods and infection control measures. J Antimicrob Chemother 2016; 72:596-603. [DOI: 10.1093/jac/dkw414] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/18/2016] [Accepted: 08/31/2016] [Indexed: 12/25/2022] Open
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Meunier D, Doumith M, Findlay J, Mustafa N, Mallard K, Anson J, Panagea S, Pike R, Wright L, Woodford N, Hopkins KL. Carbapenem resistance mediated by blaOXA-181 in Pseudomonas aeruginosa. J Antimicrob Chemother 2016; 71:2056-7. [PMID: 27009032 DOI: 10.1093/jac/dkw087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Danièle Meunier
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Jacqueline Findlay
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Nazim Mustafa
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Kim Mallard
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - James Anson
- Directorate of Infection and Immunity, Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Prescot St., Liverpool, Merseyside L7 8XP, UK
| | | | - Rachel Pike
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Laura Wright
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, Mallard K, Nair M, Miranda A, Alves A, Perdigão J, Viveiros M, Portugal I, Hasan Z, Hasan R, Glynn JR, Martin N, Pain A, Clark TG. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 2015; 7:51. [PMID: 26019726 PMCID: PMC4446134 DOI: 10.1186/s13073-015-0164-0] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/16/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.
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Affiliation(s)
- 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
| | - Mark D Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Wollaton Road, Nottingham, NG8 1BB UK
| | - Grant Hill-Cawthorne
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia ; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, University of Sydney, Sydney, Australia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mridul Nair
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Anabela Miranda
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - Adriana Alves
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Zahra Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Judith R Glynn
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ; Karonga Prevention Study, Chilumba, Malawi
| | - Nigel Martin
- Department of Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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10
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Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Fine PEM, Parkhill J, Clark TG, Glynn JR. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 2015; 4. [PMID: 25732036 PMCID: PMC4384740 DOI: 10.7554/elife.05166] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/22/2015] [Indexed: 11/13/2022] Open
Abstract
To improve understanding of the factors influencing tuberculosis transmission and the
role of pathogen variation, we sequenced all available specimens from patients
diagnosed over 15 years in a whole district in Malawi. Mycobacterium
tuberculosis lineages were assigned and transmission networks
constructed, allowing ≤10 single nucleotide polymorphisms (SNPs) difference.
We defined disease as due to recent infection if the network-determined source was
within 5 years, and assessed transmissibility from forward transmissions resulting in
disease. High-quality sequences were available for 1687 disease episodes (72% of all
culture-positive episodes): 66% of patients linked to at least one other patient. The
between-patient mutation rate was 0.26 SNPs/year (95% CI 0.21–0.31). We showed
striking differences by lineage in the proportion of disease due to recent
transmission and in transmissibility (highest for lineage-2 and lowest for lineage-1)
that were not confounded by immigration, HIV status or drug resistance. Transmissions
resulting in disease decreased markedly over time. DOI:http://dx.doi.org/10.7554/eLife.05166.001 Tuberculosis is an important public health threat around the globe and is
particularly common in developing countries. It is difficult to control the spread of
the disease because the bacteria that cause it can spread when an infected individual
coughs or sneezes. It may take years for an infected individual to develop symptoms
of tuberculosis so it can be hard to trace the source of an outbreak, and people
infected with HIV are particularly susceptible to the disease. The bacterium that causes the majority of cases of tuberculosis is called
Mycobacterium tuberculosis. There are several different varieties
or ‘lineages’ of M. tuberculosis, and it is thought
that they may vary in their ability to spread and cause disease. However, the results
of previous studies have been inconsistent and there also seems to be a lot of
variation between strains within the same lineage. In this study, Guerra-Assunção et al. used an approach called whole
genome sequencing alongside more traditional methods to study the spread of
tuberculosis in Malawi. They sequenced the genomes of every available sample of
M. tuberculosis collected from patients in the Karonga district
of Malawi over a 15-year period. This produced high-quality DNA sequence data about
the bacteria responsible for almost 1700 cases of disease. Using this massive amount of data, Guerra-Assunção et al. constructed
networks that showed how the bacteria had spread in the community. This revealed that
there were differences between the ability of the various M.
tuberculosis lineages to cause disease and to spread in communities. For
example, lineage 1 was less likely than the other lineages to cause disease soon
after infecting an individual and was less able to spread. The data also show that the proportion of cases of disease due to recent infection
declined substantially during the 15-year period. This indicates that the
tuberculosis and HIV control programmes in the area have been successful. Guerra-Assunção et al.'s findings show that it is possible to
understand how tuberculosis is transmitted on a large scale. The next challenge is to
understand why the lineages differ in their ability to cause disease and spread
between individuals. DOI:http://dx.doi.org/10.7554/eLife.05166.002
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Affiliation(s)
- J A Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - T Mzembe
- Karonga Prevention Study, Malawi, Malawi
| | - K Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - F Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - L Banda
- Karonga Prevention Study, Malawi, Malawi
| | - A Chiwaya
- Karonga Prevention Study, Malawi, Malawi
| | - R P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P E M Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J Parkhill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - T G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Hasan Z, Ali A, McNerney R, Mallard K, Hill-Cawthorne G, Coll F, Nair M, Pain A, Clark TG, Hasan R. Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan. Int J Mycobacteriol 2015. [DOI: 10.1016/j.ijmyco.2014.10.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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12
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Perdigão J, Silva H, Machado D, Macedo R, Maltez F, Silva C, Jordao L, Couto I, Mallard K, Coll F, Hill-Cawthorne GA, McNerney R, Pain A, Clark TG, Viveiros M, Portugal I. Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology. Int J Mycobacteriol 2015. [DOI: 10.1016/j.ijmyco.2015.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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13
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Kanji A, Hasan Z, Ali A, McNerney R, Mallard K, Coll F, Hill-Cawthorne G, Nair M, Clark TG, Zaver A, Jafri S, Hasan R. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. Int J Mycobacteriol 2015; 4:73-9. [PMID: 26655202 DOI: 10.1016/j.ijmyco.2014.11.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/02/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB. MATERIAL AND METHODS Whole genome sequencing analysis was performed on (n=37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n=2); Other lineage 1 (n=3); Lineage 3 (Central Asian, n=24); Other lineage 3 (n=4); Lineage 4 (X3, n=1) and T group (n=3) MTB strains. RESULTS There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in PE_PGRS genes - 6, 9 and 10 - were common in all EAI, CAS, Other lineages (1 and 3), T1 and X3. Deletions (DELs) in PE_PGRS genes - 3 and 19 - were observed in 17 (80.9%) CAS1 and 6 (85.7%) in Other lineages (1 and 3) XDR MTB strains, while DELs in the PE_PGRS49 were observed in all CAS1, CAS, CAS2 and Other lineages (1 and 3) XDR MTB strains. All CAS, EAI and Other lineages (1 and 3) strains showed insertions (INS) in PE_PGRS6 gene, while INS in the PE_PGRS genes 19 and 33 were observed in 20 (95.2%) CAS1, all CAS, CAS2, EAI and Other lineages (1 and 3) XDR MTB strains. CONCLUSION Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.
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Affiliation(s)
| | | | - Asho Ali
- Aga Khan University, Karachi, Pakistan
| | - Ruth McNerney
- London School of Hygiene and Tropical Medicine (LSHTM), United Kingdom
| | - Kim Mallard
- London School of Hygiene and Tropical Medicine (LSHTM), United Kingdom
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine (LSHTM), United Kingdom
| | - Grant Hill-Cawthorne
- Pathogen Genomics Laboratory, 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, NSW 2006, Australia
| | - Mridul Nair
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine (LSHTM), United Kingdom
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14
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Bergval I, Coll F, Schuitema A, de Ronde H, Mallard K, Pain A, McNerney R, Clark TG, Anthony RM. A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture. FEMS Microbiol Lett 2014; 362:1-7. [PMID: 25670707 DOI: 10.1093/femsle/fnu037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We studied genomic variation in a previously selected collection of isogenic Mycobacterium tuberculosis laboratory strains subjected to one or two rounds of antibiotic selection. Whole genome sequencing analysis identified eleven single, unique mutations (four synonymous, six non-synonymous, one intergenic), in addition to drug resistance-conferring mutations, that were fixed in the genomes of six monoresistant strains. Eight loci, present as minority variants (five non-synonymous, three synonymous) in the genome of the susceptible parent strain, became fixed in the genomes of multiple daughter strains. None of these mutations are known to be involved with drug resistance. Our results confirm previously observed genomic stability for M. tuberculosis, although the parent strain had accumulated allelic variants at multiple locations in an antibiotic-free in vitro environment. It is therefore likely to assume that these so-called hitchhiking mutations were co-selected and fixed in multiple daughter strains during antibiotic selection. The presence of multiple allelic variations, accumulated under non-selective conditions, which become fixed during subsequent selective steps, deserves attention. The wider availability of 'deep' sequencing methods could help to detect multiple bacterial (sub)populations within patients with high resolution and would therefore be useful in assisting in the detailed investigation of transmission chains.
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Affiliation(s)
- Indra Bergval
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Anja Schuitema
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands
| | - Hans de Ronde
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands
| | - Kim Mallard
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Arnab Pain
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ruth McNerney
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Richard M Anthony
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, Netherlands
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15
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Perdigão J, Silva H, Machado D, Macedo R, Maltez F, Silva C, Jordao L, Couto I, Mallard K, Coll F, Hill-Cawthorne GA, McNerney R, Pain A, Clark TG, Viveiros M, Portugal I. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC Genomics 2014; 15:991. [PMID: 25407810 PMCID: PMC4289236 DOI: 10.1186/1471-2164-15-991] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/06/2014] [Indexed: 12/04/2022] Open
Abstract
Background Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades. Results In the present study we have genotyped and sequenced the genomes of 56 Mycobacterium tuberculosis isolates recovered mostly from Lisbon. The genotyping data revealed three major clusters associated with MDR-TB, two of which are associated with XDR-TB. Whilst the genomic data contributed to elucidate the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of Mycobacterium tuberculosis clinical isolates, revealed two major clades responsible for M/XDR-TB in the region: Lisboa3 and Q1 (LAM). The data presented by this study yielded insights on microevolution and identification of novel compensatory mutations associated with rifampicin resistance in rpoB and rpoC. The screening for other structural variations revealed putative clade-defining variants. One deletion in PPE41, found among Lisboa3 isolates, is proposed to contribute to immune evasion and as a selective advantage. Insertion sequence (IS) mapping has also demonstrated the role of IS6110 as a major driver in mycobacterial evolution by affecting gene integrity and regulation. Conclusions Globally, this study contributes with novel genome-wide phylogenetic data and has led to the identification of new genomic variants that support the notion of a growing genomic diversity facing both setting and host adaptation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-991) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Isabel Portugal
- Centro de Patogénese Molecular, URIA, Faculdade de Farmácia da Universidade de Lisboa, Av, Prof, Gama Pinto, 1649-003 Lisboa, Portugal.
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16
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Guerra-Assunção JA, Houben RMGJ, Crampin AC, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Harris D, Parkhill J, Clark TG, Glynn JR. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J Infect Dis 2014; 211:1154-63. [PMID: 25336729 PMCID: PMC4354982 DOI: 10.1093/infdis/jiu574] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Recurrent tuberculosis is a major health burden and may be due to relapse with the original strain or reinfection with a new strain. METHODS In a population-based study in northern Malawi, patients with tuberculosis diagnosed from 1996 to 2010 were actively followed after the end of treatment. Whole-genome sequencing with approximately 100-fold coverage was performed on all available cultures. Results of IS6110 restriction fragment-length polymorphism analyses were available for cultures performed up to 2008. RESULTS Based on our data, a difference of ≤10 single-nucleotide polymorphisms (SNPs) was used to define relapse, and a difference of >100 SNPs was used to define reinfection. There was no evidence of mixed infections among those classified as reinfections. Of 1471 patients, 139 had laboratory-confirmed recurrences: 55 had relapse, and 20 had reinfection; for 64 type of recurrence was unclassified. Almost all relapses occurred in the first 2 years. Human immunodeficiency virus infection was associated with reinfection but not relapse. Relapses were associated with isoniazid resistance, treatment before 2007, and lineage-3 strains. We identified several gene variants associated with relapse. Lineage-2 (Beijing) was overrepresented and lineage-1 underrepresented among the reinfecting strains (P = .004). CONCLUSIONS While some of the factors determining recurrence depend on the patient and their treatment, differences in the Mycobacterium tuberculosis genome appear to have a role in both relapse and reinfection.
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Affiliation(s)
| | - Rein M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
| | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine Karonga Prevention Study, Malawi
| | | | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Palwasha Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
| | | | | | - Rui P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Taane G Clark
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
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17
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Clark TG, Mallard K, Coll F, Preston M, Assefa S, Harris D, Ogwang S, Mumbowa F, Kirenga B, O’Sullivan DM, Okwera A, Eisenach KD, Joloba M, Bentley SD, Ellner JJ, Parkhill J, Jones-López EC, McNerney R. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One 2013; 8:e83012. [PMID: 24349420 PMCID: PMC3859632 DOI: 10.1371/journal.pone.0083012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Understanding the emergence and spread of multidrug-resistant tuberculosis (MDR-TB) is crucial for its control. MDR-TB in previously treated patients is generally attributed to the selection of drug resistant mutants during inadequate therapy rather than transmission of a resistant strain. Traditional genotyping methods are not sufficient to distinguish strains in populations with a high burden of tuberculosis and it has previously been difficult to assess the degree of transmission in these settings. We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years. METHODS AND FINDINGS We used high throughput genome sequencing technology to investigate small polymorphisms and large deletions in 51 Mycobacterium tuberculosis samples from 41 treatment-experienced TB patients attending a TB referral and treatment clinic in Kampala. This was a convenience sample representing 69% of MDR-TB cases identified over the four year period. Low polymorphism was observed in longitudinal samples from individual patients (2-15 SNPs). Clusters of samples with less than 50 SNPs variation were examined. Three clusters comprising a total of 8 patients were found with almost identical genetic profiles, including mutations predictive for resistance to rifampicin and isoniazid, suggesting transmission of MDR-TB. Two patients with previous drug susceptible disease were found to have acquired MDR strains, one of which shared its genotype with an isolate from another patient in the cohort. CONCLUSIONS Whole genome sequence analysis identified MDR-TB strains that were shared by more than one patient. The transmission of multidrug-resistant disease in this cohort of retreatment patients emphasises the importance of early detection and need for infection control. Consideration should be given to rapid testing for drug resistance in patients undergoing treatment to monitor the emergence of resistance and permit early intervention to avoid onward transmission.
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Affiliation(s)
- Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Mark Preston
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Samuel Assefa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Sam Ogwang
- Joint Clinical Research Centre, Kampala, Uganda
| | - Francis Mumbowa
- Joint Clinical Research Centre, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bruce Kirenga
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Denise M. O’Sullivan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alphonse Okwera
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Kathleen D. Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Jerrold J. Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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18
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Coll F, Mallard K, Preston MD, Bentley S, Parkhill J, McNerney R, Martin N, Clark TG. SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. ACTA ACUST UNITED AC 2012; 28:2991-3. [PMID: 23014632 PMCID: PMC3496340 DOI: 10.1093/bioinformatics/bts544] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Summary: Spoligotyping is a well-established genotyping technique based on the presence of unique DNA sequences in Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis disease (TB). Although advances in sequencing technologies are leading to whole-genome bacterial characterization, tens of thousands of isolates have been spoligotyped, giving a global view of Mtb strain diversity. To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. Our approach is compared with experimentally and de novo assembly determined strain types in a set of 44 Mtb isolates. In silico and experimental results are identical for almost all isolates (39/44). However, SpolPred detected five experimentally false spoligotypes and was more accurate and faster than the assembling strategy. Application of SpolPred to an additional seven isolates with no laboratory data led to types that clustered with identical experimental types in a phylogenetic analysis using single-nucleotide polymorphisms. Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations. Availability and implementation: SpolPred is written in C and is available from www.pathogenseq.org/spolpred. Contact:francesc.coll@lshtm.ac.uk Supplementary information:Supplementary data are available at Bioinformatics Online.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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19
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McNerney R, Mallard K, Okolo PI, Turner C. Production of volatile organic compounds by mycobacteria. FEMS Microbiol Lett 2012; 328:150-6. [PMID: 22224870 DOI: 10.1111/j.1574-6968.2011.02493.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/03/2011] [Accepted: 12/19/2011] [Indexed: 12/18/2022] Open
Abstract
The need for improved rapid diagnostic tests for tuberculosis disease has prompted interest in the volatile organic compounds (VOCs) emitted by Mycobacterium tuberculosis complex bacteria. We have investigated VOCs emitted by Mycobacterium bovis BCG grown on Lowenstein-Jensen media using selected ion flow tube mass spectrometry and thermal desorption-gas chromatography-mass spectrometry. Compounds observed included dimethyl sulphide, 3-methyl-1-butanol, 2-methyl-1-propanol, butanone, 2-methyl-1-butanol, methyl 2-methylbutanoate, 2-phenylethanol and hydrogen sulphide. Changes in levels of acetaldehyde, methanol and ammonia were also observed. The compounds identified are not unique to M. bovis BCG, and further studies are needed to validate their diagnostic value. Investigations using an ultra-rapid gas chromatograph with a surface acoustic wave sensor (zNose) demonstrated the presence of 2-phenylethanol (PEA) in the headspace of cultures of M. bovis BCG and Mycobacterium smegmatis, when grown on Lowenstein-Jensen supplemented with glycerol. PEA is a reversible inhibitor of DNA synthesis. It is used during selective isolation of gram-positive bacteria and may also be used to inhibit mycobacterial growth. PEA production was observed to be dependent on growth of mycobacteria. Further study is required to elucidate the metabolic pathways involved and assess whether this compound is produced during in vivo growth of mycobacteria.
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Affiliation(s)
- Ruth McNerney
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London, UK.
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20
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Sharaf Eldin GS, Fadl-Elmula I, Ali MS, Ali AB, Salih ALG, Mallard K, Bottomley C, McNerney R. Tuberculosis in Sudan: a study of Mycobacterium tuberculosis strain genotype and susceptibility to anti-tuberculosis drugs. BMC Infect Dis 2011; 11:219. [PMID: 21846389 PMCID: PMC3166935 DOI: 10.1186/1471-2334-11-219] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 08/16/2011] [Indexed: 01/31/2023] Open
Abstract
Background Sudan is a large country with a diverse population and history of civil conflict. Poverty levels are high with a gross national income per capita of less than two thousand dollars. The country has a high burden of tuberculosis (TB) with an estimated 50,000 incident cases during 2009, when the estimated prevalence was 209 cases per 100,000 of the population. Few studies have been undertaken on TB in Sudan and the prevalence of drug resistant disease is not known. Methods In this study Mycobacterium tuberculosis isolates from 235 patients attending three treatment centers in Sudan were screened for susceptibility to isoniazid, rifampicin, ethambutol and streptomycin by the proportion method on Lowenstein Jensen media. 232 isolates were also genotyped by spoligotyping. Demographic details of patients were recorded using a structured questionnaire. Statistical analyses were conducted to examine the associations between drug resistance with risk ratios computed for a set of risk factors (gender, age, case status - new or relapse, geographic origin of the patient, spoligotype, number of people per room, marital status and type of housing). Results Multi drug-resistant tuberculosis (MDR-TB), being resistance to at least rifampicin and isoniazid, was found in 5% (95% CI: 2,8) of new cases and 24% (95% CI: 14,34) of previously treated patients. Drug resistance was associated with previous treatment with risk ratios of 3.51 (95% CI: 2.69-4.60; p < 0.001) for resistance to any drug and 5.23 (95% CI: 2.30-11.90; p < 0.001) for MDR-TB. Resistance was also associated with the geographic region of origin of the patient, being most frequently observed in patients from the Northern region and least in the Eastern region with risk ratios of 7.43 (95%CI:3.42,16.18; p: < 0.001) and 14.09 (95%CI:1.80,110.53; p:0.026) for resistance to any drug and MDR-TB. The major genotype observed was of the Central Asia spoligotype family (CAS1_Delhi), representing 49% of the 232 isolates examined. Conclusions We conclude that emergence of drug resistant tuberculosis has the potential to be a serious public health problem in Sudan and that strengthened tuberculosis control and improved monitoring of therapy is needed. Further surveillance is required to fully ascertain the extent of the problem.
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21
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Glynn JR, Alghamdi S, Mallard K, McNerney R, Ndlovu R, Munthali L, Houben RM, Fine PEM, French N, Crampin AC. Changes in Mycobacterium tuberculosis genotype families over 20 years in a population-based study in Northern Malawi. PLoS One 2010; 5:e12259. [PMID: 20808874 PMCID: PMC2923199 DOI: 10.1371/journal.pone.0012259] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 07/26/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite increasing interest in possible differences in virulence and transmissibility between different genotypes of M. tuberculosis, very little is known about how genotypes within a population change over decades, or about relationships to HIV infection. METHODS AND PRINCIPAL FINDINGS In a population-based study in rural Malawi we have examined smears and cultures from tuberculosis patients over a 20-year period using spoligotyping. Isolates were grouped into spoligotype families and lineages following previously published criteria. Time trends, HIV status, drug resistance and outcome were examined by spoligotype family and lineage. In addition, transmissibility was examined among pairs of cases with known epidemiological contact by assessing the proportion of transmissions confirmed for each lineage, on the basis of IS6110 RFLP similarity of the M tuberculosis strains. 760 spoligotypes were obtained from smears from 518 patients from 1986-2002, and 377 spoligotypes from cultures from 347 patients from 2005-2008. There was good consistency in patients with multiple specimens. Among 781 patients with first episode tuberculosis, the majority (76%) had Lineage 4 ("European/American") strains; 9% had Lineage 3 ("East-African/Indian"); 8% Lineage 1 ("Indo-Oceanic"); and 2% Lineage 2 ("East-Asian"); others unclassifiable. Over time the proportion of Lineage 4 decreased from >90% to 60%, with an increase in the other 3 lineages (p<0.001). Lineage 1 strains were more common in those with HIV infection, even after adjusting for age, sex and year. There were no associations with drug resistance or outcome, and no differences by lineage in the proportion of pairs in which transmission was confirmed. CONCLUSIONS This is the first study to describe long term trends in the four M. tuberculosis lineages in a population. Lineage 4 has probably been longstanding in this population, with relatively recent introductions and spread of Lineages1-3, perhaps influenced by the HIV epidemic.
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Affiliation(s)
- Judith R Glynn
- London School of Hygiene & Tropical Medicine, London, United Kingdom.
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22
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Houben RMGJ, Glynn JR, Mallard K, Sichali L, Malema S, Fine PEM, French N, Crampin AC. Human immunodeficiency virus increases the risk of tuberculosis due to recent re-infection in individuals with latent infection. Int J Tuberc Lung Dis 2010; 14:909-915. [PMID: 20550777 PMCID: PMC3276831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus associated tuberculosis (TB) disease can follow reactivation of latent Mycobacterium tuberculosis infection or recent (re-)infection with M. tuberculosis. If contemporary TB cases share identical M. tuberculosis strains (i.e., are 'clustered'), the episode is likely to have followed recent (re-)infection, irrespective of evidence of previous latent infection. METHODS Individuals experiencing a first TB episode between 1996 and 2008 in Karonga District, Northern Malawi, were included if information on M. tuberculosis infection status (from tuberculin tests) before 1990 and a DNA fingerprint from the TB episode were available. We explored differences in proportion clustered by prior M. tuberculosis infection status and HIV status, adjusting for age, sex, bacille Calmette-Guérin scar status and time since tuberculin testing. RESULTS Of 79 HIV-negative TB cases, those with previous M. tuberculosis infection were much less likely to be clustered than cases without prior infection (29% vs. 77%, adjusted OR = 0.15, 95%CI 0.04-0.59). Among 119 HIV-positive TB cases, clustering was similar in both groups (88% vs. 84%, adjusted OR = 1.85, 95%CI 0.41-8.29). DISCUSSION HIV infection appears to increase the risk of TB following recent re-infection in patients with latent M. tuberculosis infection. Our results add to the mounting evidence that HIV-associated TB mainly follows recent M. tuberculosis infection.
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Affiliation(s)
- R M G J Houben
- Infectious Disease Epidemiology Unit, London School of Hygiene & Tropical Medicine, London, UK.
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23
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Mallard K, Sharaf Eldin GS, McNerney R. ScreenTape as a tool for the rapid differentiation of Mycobacterium tuberculosis isolates. J Med Microbiol 2009; 58:1266-1268. [PMID: 19541780 DOI: 10.1099/jmm.0.008219-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kim Mallard
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Ruth McNerney
- London School of Hygiene and Tropical Medicine, London, UK
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24
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Houben RMGJ, Crampin AC, Mallard K, Mwaungulu JN, Yates MD, Mwaungulu FD, Ngwira BMM, French N, Fine PEM, Glynn JR. HIV and the risk of tuberculosis due to recent transmission over 12 years in Karonga District, Malawi. Trans R Soc Trop Med Hyg 2009; 103:1187-9. [PMID: 19362727 PMCID: PMC2784949 DOI: 10.1016/j.trstmh.2009.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 03/11/2009] [Accepted: 03/12/2009] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) patients with strains common to other recent cases (‘clustering’) suggest recent transmission. HIV status and age may affect proportions clustered. We investigated TB clustering by HIV and age in a population-based study in Malawi. Among 746 patients, HIV infection increased the proportion clustered. Sex-period-adjusted odds ratios for the association of HIV and clustering were 1.26 (95% CI 0.4–4.1) for ages 15–25 years, 1.40 (0.9–2.3) for 25–50 years and 10.44 (2.3–47.9) for >50 years and remained stable over two periods examined. These results suggest that HIV increases the proportion of TB due to recent transmission in the elderly.
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25
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McNerney R, Mallard K, Urassa HMR, Lemma E, Donoghue HD. Colorimetric phage-based assay for detection of rifampin-resistant Mycobacterium tuberculosis. J Clin Microbiol 2007; 45:1330-2. [PMID: 17301279 PMCID: PMC1865820 DOI: 10.1128/jcm.02028-06] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tests based on bacteriophage replication enable rapid screening of Mycobacterium tuberculosis for drug resistance. We describe a novel broth-based colorimetric method for detecting phage replication. When clinical isolates were tested by this novel method, high concordance was observed with both the traditional phage assay and gene mutation analysis for detection of resistance to rifampin.
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Affiliation(s)
- Ruth McNerney
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
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26
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Traore H, Ogwang S, Mallard K, Joloba ML, Mumbowa F, Narayan K, Kayes S, Jones-Lopez EC, Smith PG, Ellner JJ, Mugerwa RD, Eisenach KD, McNerney R. Low-cost rapid detection of rifampicin resistant tuberculosis using bacteriophage in Kampala, Uganda. Ann Clin Microbiol Antimicrob 2007; 6:1. [PMID: 17212825 PMCID: PMC1779803 DOI: 10.1186/1476-0711-6-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2006] [Accepted: 01/09/2007] [Indexed: 11/15/2022] Open
Abstract
Background Resistance to anti-tuberculosis drugs is a serious public health problem. Multi-drug resistant tuberculosis (MDR-TB), defined as resistance to at least rifampicin and isoniazid, has been reported in all regions of the world. Current phenotypic methods of assessing drug susceptibility of M. tuberculosis are slow. Rapid molecular methods to detect resistance to rifampicin have been developed but they are not affordable in some high prevalence countries such as those in sub Saharan Africa. A simple multi-well plate assay using mycobacteriophage D29 has been developed to test M. tuberculosis isolates for resistance to rifampicin. The purpose of this study was to investigate the performance of this technology in Kampala, Uganda. Methods In a blinded study 149 M. tuberculosis isolates were tested for resistance to rifampicin by the phage assay and results compared to those from routine phenotypic testing in BACTEC 460. Three concentrations of drug were used 2, 4 and 10 μg/ml. Isolates found resistant by either assay were subjected to sequence analysis of a 81 bp fragment of the rpoB gene to identify mutations predictive of resistance. Four isolates with discrepant phage and BACTEC results were tested in a second phenotypic assay to determine minimal inhibitory concentrations. Results Initial analysis suggested a sensitivity and specificity of 100% and 96.5% respectively for the phage assay used at 4 and 10 μg/ml when compared to the BACTEC 460. However, further analysis revealed 4 false negative results from the BACTEC 460 and the phage assay proved the more sensitive and specific of the two tests. Of the 39 isolates found resistant by the phage assay 38 (97.4%) were found to have mutations predictive of resistance in the 81 bp region of the rpoB gene. When used at 2 μg/ml false resistant results were observed from the phage assay. The cost of reagents for testing each isolate was estimated to be 1.3US$ when testing a batch of 20 isolates on a single 96 well plate. Results were obtained in 48 hours. Conclusion The phage assay can be used for screening of isolates for resistance to rifampicin, with high sensitivity and specificity in Uganda. The test may be useful in poorly resourced laboratories as a rapid screen to differentiate between rifampicin susceptible and potential MDR-TB cases.
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Affiliation(s)
- Hamidou Traore
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sam Ogwang
- Joint Clinical Research Centre, Plot 893, Ring Road, Butikiro House, Mengo, P.O. Box 10005, Kampala, Uganda
| | - Kim Mallard
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Moses L Joloba
- Makerere University Medical School, Mulago Hospital, Kampala, Uganda
| | - Francis Mumbowa
- Joint Clinical Research Centre, Plot 893, Ring Road, Butikiro House, Mengo, P.O. Box 10005, Kampala, Uganda
| | - Kalpana Narayan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA
| | - Susan Kayes
- Joint Clinical Research Centre, Plot 893, Ring Road, Butikiro House, Mengo, P.O. Box 10005, Kampala, Uganda
| | - Edward C Jones-Lopez
- New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA
| | - Peter G Smith
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jerrold J Ellner
- New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA
| | - Roy D Mugerwa
- Makerere University Medical School, Mulago Hospital, Kampala, Uganda
| | | | - Ruth McNerney
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Mallard K, Schopfer K, Bodmer T. Development of real-time PCR for the differential detection and quantification of Ureaplasma urealyticum and Ureaplasma parvum. J Microbiol Methods 2005; 60:13-9. [PMID: 15567220 DOI: 10.1016/j.mimet.2004.08.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 06/10/2004] [Accepted: 08/23/2004] [Indexed: 11/21/2022]
Abstract
Ureaplasma parvum and Ureaplasma urealyticum are recently recognized species of the genus Ureaplasma. In humans, Ureaplasma spp. can be found on mucosal surfaces, primarily in the respiratory and urogenital tracts. They have been implicated in various human diseases such as nongonococcal urethritis, intrauterine infections in association with adverse pregnancy outcome and fetal morbidity, and pneumonitis in immunocompromised hosts. We have developed two quantitative real-time PCR assays to differentially detect U. parvum and U. urealyticum. Based upon the sequence information of the urease gene (ureB), we designed two TaqMan primer and probe combinations specific for U. parvum and U. urealyticum, respectively. The assays did not react with nucleic acid preparations from 16 bacterial species commonly encountered in relevant clinical specimens, including seven urease-producing species. Each assay had a detection limit of approximately five copies per reaction of the respective gene target. The results suggest that these assays are both sensitive and specific for U. parvum and U. urealyticum. Further investigation of both assays using clinical specimens is appropriate.
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Affiliation(s)
- K Mallard
- Institute for Infectious Diseases, University of Berne, Friedbuehlstrasse 51, CH-3010 Berne, Switzerland
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Mallard K, Jones DB, Richmond J, McGill M, Foulis AK. Expression of the human heat shock protein 60 in thyroid, pancreatic, hepatic and adrenal autoimmunity. J Autoimmun 1996; 9:89-96. [PMID: 8845058 DOI: 10.1006/jaut.1996.0011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Heat shock proteins (hsps) have been proposed to play a role in autoimmune disease. Their highly conserved nature and role as a common antigenic determinant throughout phylogeny has raised the possibility that they may act as cellular targets of an autoimmune response when their expression is altered in stressed tissue cells. Using an antibody to human hsp60 we have demonstrated a wide tissue distribution in normal tissues, including thymus, the degree of staining reflecting the content of mitochondria in the cells, consistent with the known mitochondrial location of this protein. Enhanced staining was also demonstrated in oncocytes (deeply eosinophilic cells which have greatly increased numbers of mitochondria) in both thyroid and adrenal autoimmune disease and also in unrelated conditions where oncocytic change was identified. No enhancement was demonstrated in target cells in organ specific autoimmune diseases where oncocytic change was not seen, for example islet cells in diabetes and bile duct cells in primary biliary cirrhosis. Thus, no alteration of hsp60 expression was demonstrated which was specific to the autoimmune diseases studied.
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Affiliation(s)
- K Mallard
- Department of Pathology, Royal Infirmary, Glasgow, UK
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Desmarchelier PM, Wong FY, Mallard K. An epidemiological study of Vibrio cholerae O1 in the Australian environment based on rRNA gene polymorphisms. Epidemiol Infect 1995; 115:435-46. [PMID: 8557075 PMCID: PMC2271589 DOI: 10.1017/s0950268800058593] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Since 1977, Vibrio cholerae O1 has been isolated from the Australian aquatic environment and periodically cholera cases have occurred following exposure to these environments. To study the relationships between clinical isolates and environmental isolates from rivers and aquatic life, widely distributed throughout the country, a wide range of molecular typing methods were employed. In this paper we report the analysis of the 180 Australian isolates (10 clinical and 170 environmental) using ribotyping. Seven ribotype patterns were observed among the Australian inaba isolates, 2 of which included all clinical inaba isolates and 84% environmental inaba isolates collected from 9 rivers and creeks in eastern Australia during an 8-year period. Isolates from epidemiologically related clinical cases, asymptomatic household contacts and sewage were indistinguishable. The ogawa isolates were more diverse, with 9 ribotypes observed among 24 isolates from 8 rivers during the same period. Ribotype patterns were not shared between the serotypes with the exception of one ogawa isolate which could be distinguished using PFGE. Ribotyping has been useful in confirming an association between epidemiologically related clinical isolates and the aquatic environment and the persistence of several clones of the O1 serovar in the Australian environment during an 8-year period.
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