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Coats T, Conroy S, de Groot B, Heeren P, Lim S, Lucke J, Mooijaart S, Nickel CH, Penfold R, Singler K, van Oppen JD, Polyzogopoulou E, Kruis A, McNamara R, de Groot B, Castejon-Hernandez S, Miro O, Karamercan MA, Dündar ZD, van Oppen JD, Pavletić M, Libicherová P, Balen F, Benhamed A, Dubucs X, Hernu R, Laribi S, Singler K, Fraidakis O, Fyntanidou VP, Polyzogopoulou E, Gaal S, Jónsdóttir AB, Kelly-Friel ME, McAteer CA, Sibthorpe LD, Synnott A, Zazzara MB, Coffeng SM, de Groot B, Lucke JA, Smits RAL, Castejon-Hernandez S, Llauger L, Mir SA, Ortiz MS, Padilla EE, Rodeles SC, Rojewski-Rojas W, Fadini D, Jegerlehner NS, Nickel CH, Rezzonico S, Zucconi EC, Cakmak S, Demir HA, Dündar ZD, Güven R, Karamercan MA, Sogut O, Tayfur I, Adams JA, Bernardo J, Brown L, Burton J, Butler MJ, Claassen RI, Compton F, Cooper JG, Heyes R, Ko S, Lightbody CJ, Masoli JAH, McKenzie STG, Mawhinney D, Moultrie NJ, Price A, Raman R, Rothwell LH, Shashikala RP, Smith EJ, Sorice V, van Oppen JD, Wallace JM, Young T, Benvin A, Breški E, Ćefo A, Dumić D, Ferenac R, Jurica I, Otočan M, Zinaić PŠ, Clement B, Jacquin L, Royer B, Apfelbacher SI, Bezati S, Gkarmiri S, Kaltsidou CV, Klonos G, Korka Z, Koufogianni A, Mavros V, Nano A, Ntousopoulos A, Papadopoulos N, Sason R, Zagalioti SC, Hjaltadottir I, Sigurþórsdóttir I, Skuladottir SS, Thorsteinsdottir T, Breslin D, Byrne CP, Dolan A, Harte O, Kazi D, McCarthy A, McMillan SS, Moiloa DN, O’Shaughnessy ÍL, Ramiah V, Williams S, Giani T, Levati E, Montenero R, Russo A, Salini S, van den Berg B, Booijen AM, Sir O, Vermeulen AE, ter Voert MA, Alvarez-Galarraga AC, Azeli Y, Gómez RGG, González González R, Lizardo D, Pérez ML, Madan CN, Medina JÁ, Moreno JS, Patiño EVB, Posada DMC, Rodrigo IC, Vitucci CF, Ballinari M, Dreher T, Gianinazzi L, Espejo T, Hautz WE, Rezzonico S, Bayramoğlu B, Cakmak S, Comruk B, Dogan T, Köse F, Allen TP, Ardley R, Beith CM, Boath KA, Britton HL, Campbell MMF, Capel J, Catney C, Clements S, Collins BP, Compton F, Cook A, Cosgriff EJ, Coventry T, Doyle N, Evans Z, Fasina TA, Ferrick JF, Fleming GM, Gallagher C, Golden M, Gorania D, Glass L, Greenlees H, Haddock ZP, Harris R, Hollas C, Hunter A, Ingham C, Ip SSY, James JA, Kenenden C, Jenkinson GE, Lee E, Lovick SA, McFadden M, McGovern R, Medhora J, Merchant F, Mishra S, Moreland GB, Narayanasamy S, Neal AR, Nicholls EL, Omar MT, Osborne N, Oteme FO, Pearson J, Price R, Sajan M, Sandhu LK, Scott-Murfitt H, Sealey B, Sharp EP, Spowage-Delaney BAC, Stephen F, Stevenson L, Tyrrell I, Ukoh CK, Walsh R, Watson AM, Whiteford JEC, Allston-Reeve C, Barson TJ, Giorgi MG, Godhania YL, Inchley V, Mirkes E, Rahman S. Prevalence of Frailty in European Emergency Departments (FEED): an international flash mob study. Eur Geriatr Med 2024; 15:463-470. [PMID: 38340282 PMCID: PMC10997678 DOI: 10.1007/s41999-023-00926-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/19/2023] [Indexed: 02/12/2024]
Abstract
INTRODUCTION Current emergency care systems are not optimized to respond to multiple and complex problems associated with frailty. Services may require reconfiguration to effectively deliver comprehensive frailty care, yet its prevalence and variation are poorly understood. This study primarily determined the prevalence of frailty among older people attending emergency care. METHODS This cross-sectional study used a flash mob approach to collect observational European emergency care data over a 24-h period (04 July 2023). Sites were identified through the European Task Force for Geriatric Emergency Medicine collaboration and social media. Data were collected for all individuals aged 65 + who attended emergency care, and for all adults aged 18 + at a subset of sites. Variables included demographics, Clinical Frailty Scale (CFS), vital signs, and disposition. European and national frailty prevalence was determined with proportions with each CFS level and with dichotomized CFS 5 + (mild or more severe frailty). RESULTS Sixty-two sites in fourteen European countries recruited five thousand seven hundred eighty-five individuals. 40% of 3479 older people had at least mild frailty, with countries ranging from 26 to 51%. They had median age 77 (IQR, 13) years and 53% were female. Across 22 sites observing all adult attenders, older people living with frailty comprised 14%. CONCLUSION 40% of older people using European emergency care had CFS 5 + . Frailty prevalence varied widely among European care systems. These differences likely reflected entrance selection and provide windows of opportunity for system configuration and workforce planning.
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Coats T, Bouamra O, Edwards A, Lecky F, Mirkes E, Sergeant J, Ivan T. 1750 Prediction of 6 month Trauma PROMS using in-hospital data. J Accid Emerg Med 2022. [DOI: 10.1136/emermed-2022-rcem2.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aims, Objectives and BackgroundTrauma audit has used lived/died as an outcome for 30 years, but Patient Reported Outcome Measures (PROMS) have also been collected by the Trauma Audit and Research Network (TARN) for the past 5 years across major trauma centres. These are measured at 6 months after injury and include two measures of health-related quality of life, EQ5D-5 and GOSE, employment status and three patient experience questions. It is not known if 6-month PROMS can be predicted after major trauma.Method and DesignThe TARN PROMS data was extracted and randomly divided into a model development (training) and a model testing (test) dataset. There is no standard way of using this type of complex data, so three different modelling approaches were used: (1) conventional logistic regression, (2) artificial intelligence (AI) selection of ‘nearest neighbours’, and (3) AI decision trees. The performance of each model was evaluated using the test dataset.Results and ConclusionThere were 5791 patients in the training set and 1447 patients in the test set. All three of the methods achieved an ROC AUC between 0.69 and 0.77 – implying that this might be the limit of prediction based on this type of data. When tested against the binary Glasgow Outcome Score the results are shown in the table 1. The AI method of ‘k Nearest Neighbours’ achieved a balance between sensitivity (72%) and specificity (71%).Abstract 1750 Table 1GOSE Groupk Nearest NeighboursLogistic RegressionDecision treesSensitivity72%91%79%Specificity71%26%65%PPV90%82%39%NPV42%45%91%ROC0.7640.6850.77ROC 95% CI0.733 – 0.7950.648 – 0.723Conclusionpatient reported outcomes at 6 months after injury can be predicted from in-hospital data. This potentially gives a new method for clinical audit and comparison of trauma outcomes using a measure that is more relevant to survivors of major trauma than the current ‘lived/died’.
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Yates T, Summerfield A, Razieh C, Banerjee A, Chudasama Y, Davies MJ, Gillies C, Islam N, Lawson C, Mirkes E, Zaccardi F, Khunti K, Nafilyan V. A population-based cohort study of obesity, ethnicity and COVID-19 mortality in 12.6 million adults in England. Nat Commun 2022; 13:624. [PMID: 35110546 PMCID: PMC8810846 DOI: 10.1038/s41467-022-28248-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 07/02/2021] [Accepted: 01/05/2022] [Indexed: 12/19/2022] Open
Abstract
Obesity and ethnicity are known risk factors for COVID-19 outcomes, but their combination has not been extensively examined. We investigate the association between body mass index (BMI) and COVID-19 mortality across different ethnic groups using linked national Census, electronic health records and mortality data for adults in England from the start of pandemic (January 2020) to December 2020. There were 30,067 (0.27%), 1,208 (0.29%), 1,831 (0.29%), 845 (0.18%) COVID-19 deaths in white, Black, South Asian and other ethnic minority groups, respectively. Here we show that BMI was more strongly associated with COVID-19 mortality in ethnic minority groups, resulting in an ethnic risk of COVID-19 mortality that was dependant on BMI. The estimated risk of COVID-19 mortality at a BMI of 40 kg/m2 in white ethnicities was equivalent to the risk observed at a BMI of 30.1 kg/m2, 27.0 kg/m2, and 32.2 kg/m2 in Black, South Asian and other ethnic minority groups, respectively.
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Affiliation(s)
- Thomas Yates
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK.
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre (BRC), Leicester General Hospital, Leicester, LE5 4PW, UK.
| | | | - Cameron Razieh
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre (BRC), Leicester General Hospital, Leicester, LE5 4PW, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Amitava Banerjee
- Institute of Health Informatics, University College London, London, UK
- Department of Cardiology, Barts Health NHS Trust, London, UK
| | - Yogini Chudasama
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Melanie J Davies
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre (BRC), Leicester General Hospital, Leicester, LE5 4PW, UK
- Leicester Diabetes Centre, University Hospitals of Leicester NHS Trust, Leicester General Hospital, Leicester, UK
| | - Clare Gillies
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
- NIHR Applied Research Collaboration - East Midlands (ARC-EM), Leicester General Hospital, Leicester, UK
| | - Nazrul Islam
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Claire Lawson
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Evgeny Mirkes
- Department of Mathematics, University of Leicester, Leicester, UK
| | - Francesco Zaccardi
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Kamlesh Khunti
- Diabetes Research Centre, University of Leicester, Leicester General Hospital, Leicester, LE5 4PW, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
- Leicester Diabetes Centre, University Hospitals of Leicester NHS Trust, Leicester General Hospital, Leicester, UK
- NIHR Applied Research Collaboration - East Midlands (ARC-EM), Leicester General Hospital, Leicester, UK
| | - Vahé Nafilyan
- Office for National Statistics, Newport, UK
- Faculty of Public Health, Environment and Society, London School of Hygiene and Tropical Medicine, London, UK
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Albergante L, Mirkes E, Bac J, Chen H, Martin A, Faure L, Barillot E, Pinello L, Gorban A, Zinovyev A. Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. Entropy (Basel) 2020; 22:E296. [PMID: 33286070 PMCID: PMC7516753 DOI: 10.3390/e22030296] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/19/2022]
Abstract
Multidimensional datapoint clouds representing large datasets are frequently characterized by non-trivial low-dimensional geometry and topology which can be recovered by unsupervised machine learning approaches, in particular, by principal graphs. Principal graphs approximate the multivariate data by a graph injected into the data space with some constraints imposed on the node mapping. Here we present ElPiGraph, a scalable and robust method for constructing principal graphs. ElPiGraph exploits and further develops the concept of elastic energy, the topological graph grammar approach, and a gradient descent-like optimization of the graph topology. The method is able to withstand high levels of noise and is capable of approximating data point clouds via principal graph ensembles. This strategy can be used to estimate the statistical significance of complex data features and to summarize them into a single consensus principal graph. ElPiGraph deals efficiently with large datasets in various fields such as biology, where it can be used for example with single-cell transcriptomic or epigenomic datasets to infer gene expression dynamics and recover differentiation landscapes.
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Affiliation(s)
- Luca Albergante
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- Sensyne Health, Oxford OX4 4GE, UK
| | - Evgeny Mirkes
- Center for Mathematical Modeling, University of Leicester, Leicester LE1 7RH, UK; (E.M.); (A.G.)
- Lobachevsky University, 603000 Nizhny Novgorod, Russia
| | - Jonathan Bac
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- Centre de Recherches Interdisciplinaires, Université de Paris, F-75000 Paris, France
| | - Huidong Chen
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA; (H.C.); (L.P.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexis Martin
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- ECE Paris, F-75015 Paris, France
| | - Louis Faure
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- Center for Brain Research, Medical University of Vienna, 22180 Vienna, Austria
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
| | - Luca Pinello
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA; (H.C.); (L.P.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Gorban
- Center for Mathematical Modeling, University of Leicester, Leicester LE1 7RH, UK; (E.M.); (A.G.)
- Lobachevsky University, 603000 Nizhny Novgorod, Russia
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
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Bell AJ, Foy BH, Richardson M, Singapuri A, Mirkes E, van den Berge M, Kay D, Brightling C, Gorban AN, Galbán CJ, Siddiqui S. Functional CT imaging for identification of the spatial determinants of small-airways disease in adults with asthma. J Allergy Clin Immunol 2019; 144:83-93. [PMID: 30682455 DOI: 10.1016/j.jaci.2019.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Asthma is a disease characterized by ventilation heterogeneity (VH). A number of studies have demonstrated that VH markers derived by using impulse oscillometry (IOS) or multiple-breath washout (MBW) are associated with key asthmatic patient-related outcome measures and airways hyperresponsiveness. However, the topographical mechanisms of VH in the lung remain poorly understood. OBJECTIVES We hypothesized that specific regionalization of topographical small-airway disease would best account for IOS- and MBW-measured indices in patients. METHODS We evaluated the results of paired expiratory/inspiratory computed tomography in a cohort of asthmatic (n = 41) and healthy (n = 11) volunteers to understand the determinants of clinical VH indices commonly reported by using IOS and MBW. Parametric response mapping (PRM) was used to calculate the functional small-airways disease marker PRMfSAD and Hounsfield unit (HU)-based density changes from total lung capacity to functional residual capacity (ΔHU); gradients of ΔHU in gravitationally perpendicular (parallel) inferior-superior (anterior-posterior) axes were quantified. RESULTS The ΔHU gradient in the inferior-superior axis provided the highest level of discrimination of both acinar VH (measured by using phase 3 slope analysis of multiple-breath washout data) and resistance at 5 Hz minus resistance at 20 Hz measured by using impulse oscillometry (R5-R20) values. Patients with a high inferior-superior ΔHU gradient demonstrated evidence of reduced specific ventilation in the lower lobes of the lungs and high levels of PRMfSAD. A computational small-airway tree model confirmed that constriction of gravitationally dependent, lower-zone, small-airway branches would promote the largest increases in R5-R20 values. Ventilation gradients correlated with asthma control and quality of life but not with exacerbation frequency. CONCLUSIONS Lower lobe-predominant small-airways disease is a major driver of clinically measured VH in adults with asthma.
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Affiliation(s)
- Alex J Bell
- NIHR Respiratory Biomedical Research Centre (BRC), Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Brody H Foy
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Matthew Richardson
- NIHR Respiratory Biomedical Research Centre (BRC), Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Amisha Singapuri
- NIHR Respiratory Biomedical Research Centre (BRC), Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Evgeny Mirkes
- Department of Mathematics, University of Leicester, Leicester, United Kingdom
| | - Maarten van den Berge
- Department of Pulmonology, University Medical Centre Groningen, Groningen, the Netherlands
| | - David Kay
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Chris Brightling
- NIHR Respiratory Biomedical Research Centre (BRC), Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Alexander N Gorban
- Department of Mathematics, University of Leicester, Leicester, United Kingdom
| | - Craig J Galbán
- Department of Radiology, University of Michigan, Ann Arbor, Mich
| | - Salman Siddiqui
- NIHR Respiratory Biomedical Research Centre (BRC), Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.
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Settipani J, Karim K, Chauvin A, Ibnou-Ali SM, Paille-Barrere F, Mirkes E, Gorban A, Larcombe L, Whitcombe MJ, Cowen T, Piletsky SA. Theoretical aspects of peptide imprinting: screening of MIP (virtual) binding sites for their interactions with amino acids, di- and tripeptides. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/22243682.2018.1467279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Julie Settipani
- Leicester Biotechnology Group, University of Leicester, Leicester, UK
| | - Kal Karim
- Leicester Biotechnology Group, University of Leicester, Leicester, UK
| | - Alienor Chauvin
- Leicester Biotechnology Group, University of Leicester, Leicester, UK
| | | | | | - Evgeny Mirkes
- Department of Mathematics, University of Leicester, Leicester, UK
| | - Alexander Gorban
- Department of Mathematics, University of Leicester, Leicester, UK
| | - Lee Larcombe
- Applied Exomics, Stevenage Bioscience Catalyst, Stevenage, UK
| | | | - Todd Cowen
- Leicester Biotechnology Group, University of Leicester, Leicester, UK
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Bell A, Richardson M, Singapuri A, Mirkes E, Gorban A, Galban C, van den Berge M, Brightling C, Siddiqui S. Parametric response map registered CT feature and small airway physiology analysis in asthma. IMAGING 2017. [DOI: 10.1183/1393003.congress-2017.oa4647] [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: 11/05/2022] Open
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Manso AS, Chai MH, Atack JM, Furi L, De Ste Croix M, Haigh R, Trappetti C, Ogunniyi AD, Shewell LK, Boitano M, Clark TA, Korlach J, Blades M, Mirkes E, Gorban AN, Paton JC, Jennings MP, Oggioni MR. A random six-phase switch regulates pneumococcal virulence via global epigenetic changes. Nat Commun 2014; 5:5055. [PMID: 25268848 PMCID: PMC4190663 DOI: 10.1038/ncomms6055] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [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: 03/19/2014] [Accepted: 08/21/2014] [Indexed: 01/27/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is the world’s foremost bacterial pathogen in both morbidity and mortality. Switching between phenotypic forms (or ‘phases’) that favour asymptomatic carriage or invasive disease was first reported in 1933. Here, we show that the underlying mechanism for such phase variation consists of genetic rearrangements in a Type I restriction-modification system (SpnD39III). The rearrangements generate six alternative specificities with distinct methylation patterns, as defined by single-molecule, real-time (SMRT) methylomics. The SpnD39III variants have distinct gene expression profiles. We demonstrate distinct virulence in experimental infection and in vivo selection for switching between SpnD39III variants. SpnD39III is ubiquitous in pneumococci, indicating an essential role in its biology. Future studies must recognize the potential for switching between these heretofore undetectable, differentiated pneumococcal subpopulations in vitro and in vivo. Similar systems exist in other bacterial genera, indicating the potential for broad exploitation of epigenetic gene regulation. Pneumococci can alternate between harmless and highly virulent forms. Here the authors show that such variation may be due to random rearrangements in a genetic locus encoding a restriction-modification system, resulting in epigenetic changes that affect expression of many genes.
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Affiliation(s)
- Ana Sousa Manso
- 1] Department of Genetics, University of Leicester, Leicester LE1 7RH, UK [2] Dipartimento di Biotechnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Melissa H Chai
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia
| | - Leonardo Furi
- 1] Department of Genetics, University of Leicester, Leicester LE1 7RH, UK [2] Dipartimento di Biotechnologie Mediche, Università di Siena, 53100 Siena, Italy
| | | | - Richard Haigh
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Claudia Trappetti
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Abiodun D Ogunniyi
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lucy K Shewell
- Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia
| | | | - Tyson A Clark
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Matthew Blades
- Bioinformatics and Biostatistics Analysis Support Hub, University of Leicester, Leicester LE1 7RH, UK
| | - Evgeny Mirkes
- Department of Mathematics, University of Leicester, Leicester LE1 7RH, UK
| | - Alexander N Gorban
- Department of Mathematics, University of Leicester, Leicester LE1 7RH, UK
| | - James C Paton
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Michael P Jennings
- 1] Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia [2]
| | - Marco R Oggioni
- 1] Department of Genetics, University of Leicester, Leicester LE1 7RH, UK [2] Dipartimento di Biotechnologie Mediche, Università di Siena, 53100 Siena, Italy [3]
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Mirkes E, Ohnemus J. Angular distributions of Drell-Yan lepton pairs at the Fermilab Tevatron: Order alpha s2 corrections and Monte Carlo studies. Phys Rev D Part Fields 1995; 51:4891-4904. [PMID: 10018965 DOI: 10.1103/physrevd.51.4891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Decker R, Finkemeier M, Mirkes E. Pseudoscalar mass effects in the decays of tau with three pseudoscalar mesons. Phys Rev D Part Fields 1994; 50:6863-6871. [PMID: 10017664 DOI: 10.1103/physrevd.50.6863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Driesen VM, Kühn JH, Mirkes E. Testing J/ psi production and decay properties in e+e- annihilation. Phys Rev D Part Fields 1994; 49:3197-3208. [PMID: 10017316 DOI: 10.1103/physrevd.49.3197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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