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Devine K, Russell CD, Blanco GR, Walker BR, Homer NZM, Denham SG, Simpson JP, Leavy OC, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Greening NJ, Lone NI, Thorpe M, Greenhalf W, Chalmers JD, Ho LP, Horsley A, Marks M, Raman B, Moore SC, Dunning J, Semple MG, Andrew R, Wain LV, Evans RA, Brightling CE, Kenneth Baillie J, Reynolds RM. Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID-19. Clin Endocrinol (Oxf) 2024; 100:317-327. [PMID: 38229583 DOI: 10.1111/cen.15012] [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: 08/23/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024]
Abstract
OBJECTIVE Endocrine systems are disrupted in acute illness, and symptoms reported following coronavirus disease 2019 (COVID-19) are similar to those found with clinical hormone deficiencies. We hypothesised that people with severe acute COVID-19 and with post-COVID symptoms have glucocorticoid and sex hormone deficiencies. DESIGN/PATIENTS Samples were obtained for analysis from two UK multicentre cohorts during hospitalisation with COVID-19 (International Severe Acute Respiratory Infection Consortium/World Health Organisation [WHO] Clinical Characterization Protocol for Severe Emerging Infections in the UK study), and at follow-up 5 months after hospitalisation (Post-hospitalisation COVID-19 study). MEASUREMENTS Plasma steroids were quantified by liquid chromatography-mass spectrometry. Steroid concentrations were compared against disease severity (WHO ordinal scale) and validated symptom scores. Data are presented as geometric mean (SD). RESULTS In the acute cohort (n = 239, 66.5% male), plasma cortisol concentration increased with disease severity (cortisol 753.3 [1.6] vs. 429.2 [1.7] nmol/L in fatal vs. least severe, p < .001). In males, testosterone concentrations decreased with severity (testosterone 1.2 [2.2] vs. 6.9 [1.9] nmol/L in fatal vs. least severe, p < .001). In the follow-up cohort (n = 198, 62.1% male, 68.9% ongoing symptoms, 165 [121-192] days postdischarge), plasma cortisol concentrations (275.6 [1.5] nmol/L) did not differ with in-hospital severity, perception of recovery, or patient-reported symptoms. Male testosterone concentrations (12.6 [1.5] nmol/L) were not related to in-hospital severity, perception of recovery or symptom scores. CONCLUSIONS Circulating glucocorticoids in patients hospitalised with COVID-19 reflect acute illness, with a marked rise in cortisol and fall in male testosterone. These findings are not observed 5 months from discharge. The lack of association between hormone concentrations and common post-COVID symptoms suggests steroid insufficiency does not play a causal role in this condition.
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Affiliation(s)
- Kerri Devine
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK
| | - Giovanny R Blanco
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Brian R Walker
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Natalie Z M Homer
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Scott G Denham
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Joanna P Simpson
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Olivia C Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Omer Elneima
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Hamish J C McAuley
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Aarti Shikotra
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Amisha Singapuri
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Marco Sereno
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ruth M Saunders
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Victoria C Harris
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | | | - Neil J Greening
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nazir I Lone
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Mathew Thorpe
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - James D Chalmers
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | - Alex Horsley
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Michael Marks
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Betty Raman
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jake Dunning
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ruth Andrew
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Rachael A Evans
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | | | - John Kenneth Baillie
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rebecca M Reynolds
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
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Cooper G, Dolby HW, Berry K, Russell CD. Eligibility of patients with Staphylococcus aureus bacteraemia for early oral switch. Lancet Infect Dis 2024; 24:e209-e210. [PMID: 38309279 DOI: 10.1016/s1473-3099(24)00065-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Affiliation(s)
- George Cooper
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Heather W Dolby
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Karla Berry
- Clinical Infection Research Group, Western General Hospital, Edinburgh, UK
| | - Clark D Russell
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK.
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Sidhu JK, Siggins MK, Liew F, Russell CD, Uruchurtu ASS, Davis C, Turtle L, Moore SC, Hardwick HE, Oosthuyzen W, Thomson EC, Semple MG, Baillie JK, Openshaw PJM, Thwaites RS. Delayed mucosal anti-viral responses despite robust peripheral inflammation in fatal COVID-19. J Infect Dis 2023:jiad590. [PMID: 38134401 DOI: 10.1093/infdis/jiad590] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND While inflammatory and immune responses to SARS-CoV-2 infection in peripheral blood are extensively described, responses at the upper respiratory mucosal site of initial infection are relatively poorly defined. We sought to identify mucosal cytokine/chemokine signatures that distinguished COVID-19 severity categories, and relate these to disease progression and peripheral inflammation. METHODS We measured 35 cytokines and chemokines in nasal samples from 274 patients hospitalised with COVID-19. Analysis considered the timing of sampling during disease, as either the early (0-5 days post-symptom onset) or late (6-20 days post-symptom onset). RESULTS Patients that survived severe COVID-19 showed IFN-dominated mucosal immune responses (IFN-γ, CXCL10 and CXCL13) early in infection. These early mucosal responses were absent in patients that would progress to fatal disease despite equivalent SARS-CoV-2 viral load. Mucosal inflammation in later disease was dominated by IL-2, IL-10, IFN-γ, and IL-12p70, which scaled with severity but did not differentiate patients who would survive or succumb to disease. Cytokines and chemokines in the mucosa showed distinctions from responses evident in the peripheral blood, particularly during fatal disease. CONCLUSIONS Defective early mucosal anti-viral responses anticipate fatal COVID-19 but are not associated with viral load. Early mucosal immune responses may define the trajectory of severe COVID-19.
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Affiliation(s)
- Jasmin K Sidhu
- National Heart and Lung Institute, Imperial College London, U.K
| | | | - Felicity Liew
- National Heart and Lung Institute, Imperial College London, U.K
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Edinburgh, U.K
| | | | | | - Lance Turtle
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
- Tropical and Infectious Disease unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), U.K
| | - Shona C Moore
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | - Hayley E Hardwick
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | | | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, U.K
- London School of Hygiene and Tropical Medicine, London, U.K
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, U.K
- Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, U.K
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, U.K
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, U.K
| | | | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, U.K
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4
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Russell CD. Patient Stratification for Oral Transitional Therapy in Bacterial Endocarditis. Clin Infect Dis 2023; 77:494-495. [PMID: 36999920 PMCID: PMC10425185 DOI: 10.1093/cid/ciad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/01/2023] Open
Affiliation(s)
- Clark D Russell
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 619:E61. [PMID: 37433877 PMCID: PMC10371859 DOI: 10.1038/s41586-023-06383-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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Davies PJB, Russell CD, Morgan AR, Taori SK, Lindsay D, Ure R, Brown D, Smith A. Increase of Severe Pulmonary Infections in Adults Caused by M1 UK Streptococcus pyogenes, Central Scotland, UK. Emerg Infect Dis 2023; 29. [PMID: 37343545 PMCID: PMC10370863 DOI: 10.3201/eid2908.230569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
We characterized the epidemiology, host-pathogen characteristics, and outcomes of severe adult pulmonary Streptococcus pyogenes infections that coincided with a high community caseload in central Scotland, UK. The pulmonary infections had high illness and death rates and were associated with socioeconomic deprivation, influenza A co-infection, and the M1UK lineage of S. pyogenes.
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Russell CD, Tsang STJ, Dudareva M, R. W. Simpson AH, Sutherland RK, McNally MA. A Survey of Orthopedic Surgical Management of Pressure Ulcer-Related Pelvic Osteomyelitis. Open Forum Infect Dis 2023; 10:ofad291. [PMID: 37323421 PMCID: PMC10264061 DOI: 10.1093/ofid/ofad291] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
Pressure-ulcer related pelvic osteomyelitis is managed with little high-quality evidence. We undertook an international survey of orthopedic surgical management, covering diagnostic parameters, multidisciplinary input, and surgical approaches (indications, timing, wound closure, and adjunctive therapies). This identified areas of consensus and disagreement, representing a starting point for future discussion and research.
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Affiliation(s)
| | - Shao-Ting Jerry Tsang
- Correspondence: Shao-Ting Jerry Tsang, MBChB, PhD, Department of Orthopaedic Surgery, University of Edinburgh, Chancellor's Bldg, 49 Little France Crescent, Old Dalkeith Rd, Edinburgh EH16 4SB, United Kingdom ()
| | - Maria Dudareva
- The Bone Infection Unit, Nuffield Orthopaedic Centre, Oxford University Hospitals, Oxford, UK
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8
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 617:764-768. [PMID: 37198478 PMCID: PMC10208981 DOI: 10.1038/s41586-023-06034-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).
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Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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Abstract
The influence of comorbidities on COVID-19 outcomes has been recognized since the earliest days of the pandemic. But establishing causality and determining underlying mechanisms and clinical implications has been challenging-owing to the multitude of confounding factors and patient variability. Several distinct pathological mechanisms, not active in every patient, determine health outcomes in the three different phases of COVID-19-from the initial viral replication phase to inflammatory lung injury and post-acute sequelae. Specific comorbidities (and overall multimorbidity) can either exacerbate these pathological mechanisms or reduce the patient's tolerance to organ injury. In this Review, we consider the impact of specific comorbidities, and overall multimorbidity, on the three mechanistically distinct phases of COVID-19, and we discuss the utility of host genetics as a route to causal inference by eliminating many sources of confounding. Continued research into the mechanisms of disease-state interactions will be crucial to inform stratification of therapeutic approaches and improve outcomes for patients.
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Affiliation(s)
- Clark D Russell
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Nazir I Lone
- Usher Institute, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, UK.
| | - J Kenneth Baillie
- Intensive Care Unit, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, UK.
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK.
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10
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Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, de Silva TI, Hardwick HE, Leeming G, Law A, Openshaw PJM, Harrison EM, Baillie JK, Semple MG, Docherty AB. Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study. PLoS Med 2023; 20:e1004086. [PMID: 36719907 PMCID: PMC9928075 DOI: 10.1371/journal.pmed.1004086] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/14/2023] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic. METHODS AND FINDINGS We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent. CONCLUSIONS Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group. TRIAL REGISTRATION ISRCTN 66726260.
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Affiliation(s)
- Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Mathew Thorpe
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas M. Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Maaike Swets
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden University, Leiden, the Netherlands
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, United Kingdom
| | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Clark D. Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Stephen Aston
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel G. Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Alex Richter
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Thushan I. de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, United Kingdom
| | - Hayley E. Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Gary Leeming
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Andy Law
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ewen M. Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - J. Kenneth Baillie
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, United Kingdom
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Annemarie B. Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, United Kingdom
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Jarchow-MacDonald A, Smith M, Seagar AL, Russell CD, Claxton P, Laurenson IF, Moncayo-Nieto OL. Changing Incidence and Characteristics of Nontuberculous Mycobacterial Infections in Scotland and Comparison With Mycobacterium tuberculosis Complex Incidence (2011 to 2019). Open Forum Infect Dis 2022; 10:ofac665. [PMID: 36726549 PMCID: PMC9879710 DOI: 10.1093/ofid/ofac665] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Background An increase in infections with nontuberculous mycobacteria (NTM) has been noted globally, and their incidence has overtaken that of Mycobacterium tuberculosis complex (MTBc) in many countries. Using data from a national reference laboratory, we aimed to determine if this trend could be observed in Scotland. Methods We undertook a retrospective review of all NTM isolates received by the Scottish Mycobacteria Reference Laboratory (SMRL) over 9 years from 2011 to 2019 inclusive. Clinical episodes were defined as per 2017 British Thoracic Society and 2020 American Thoracic Society/European Respiratory Society/European Society of Clinical Microbiology and Infectious Diseases/Infectious Diseases Society of America NTM guidelines. These rates were compared with Scottish tuberculosis rates over the same period. Results Of 8552 NTM isolates from 4586 patients in 2011 to 2019, 7739 (90.5%) were considered clinically relevant. These represented 2409 episodes of NTM infection, with M. avium, M. intracellulare, and M. abscessus complex being most common. A total of 1953 (81.1%) were pulmonary NTM infection episodes from 1470 patients and 456 extrapulmonary episodes from 370 patients. We estimated a rise in incidence from 3.4 to 6.5 per 100 000 person-years (2011-2019 inclusive), with an increase in NTM incidence over MTBc incidence in Scotland by 2017. Conclusions The incidence of NTM infection in Scotland has overtaken MTBc incidence. NTM infection leads to a costly health care burden, possibly as much as UK£1.47 million (US$ and €1.73 million) annually. We recommend standardization of isolate referral with clinical surveillance and implementation of agreed standards of care delivered through multidisciplinary teams. This would improve diagnosis and patient management as well as assessment of diagnostics and novel treatments through clinical trials.
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Affiliation(s)
- Anna Jarchow-MacDonald
- Correspondence: Anna A. Jarchow-MacDonald, MD, MSc, DTMH, Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK (). Dr. Olga-Lucia Moncayo-Nieto, MD, FRCPath, PhD, Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK ()
| | - Michael Smith
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Amie-Louise Seagar
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Clark D Russell
- Queen's Medical Research Institute, University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
| | - Pauline Claxton
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Ian F Laurenson
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
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Dockrell DH, Russell CD, McHugh B, Fraser R. Does autonomous macrophage-driven inflammation promote alveolar damage in COVID-19? Eur Respir J 2022; 60:2201521. [PMID: 36028257 PMCID: PMC9411729 DOI: 10.1183/13993003.01521-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/30/2022] [Accepted: 08/16/2022] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 has caused devastating effects with over 550 million infections by July 2022 and approximately 6.4 million deaths [1]. Societal and economic impacts will reverberate for years, with continuous evolution of SARS-CoV-2 as it persistently spreads through the human population as exemplified by reduced activity of vaccines and monoclonals against Omicron BA.4 or BA.5 subvariants [2]. A greater understanding of pathogenesis and more tailored therapeutic approaches are therefore essential.
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Affiliation(s)
- David H Dockrell
- Centre for Inflammation Research and Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Centre for Inflammation Research and Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Brian McHugh
- Centre for Inflammation Research and Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Rupsha Fraser
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
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13
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Wang B, Law A, Regan T, Parkinson N, Cole J, Russell CD, Dockrell DH, Gutmann MU, Baillie JK. Systematic comparison of ranking aggregation methods for gene lists in experimental results. Bioinformatics 2022; 38:4927-4933. [PMID: 36094347 PMCID: PMC9620830 DOI: 10.1093/bioinformatics/btac621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/18/2022] [Revised: 06/24/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
MOTIVATION A common experimental output in biomedical science is a list of genes implicated in a given biological process or disease. The gene lists resulting from a group of studies answering the same, or similar, questions can be combined by ranking aggregation methods to find a consensus or a more reliable answer. Evaluating a ranking aggregation method on a specific type of data before using it is required to support the reliability since the property of a dataset can influence the performance of an algorithm. Such evaluation on gene lists is usually based on a simulated database because of the lack of a known truth for real data. However, simulated datasets tend to be too small compared to experimental data and neglect key features, including heterogeneity of quality, relevance and the inclusion of unranked lists. RESULTS In this study, a group of existing methods and their variations that are suitable for meta-analysis of gene lists are compared using simulated and real data. Simulated data were used to explore the performance of the aggregation methods as a function of emulating the common scenarios of real genomic data, with various heterogeneity of quality, noise level and a mix of unranked and ranked data using 20 000 possible entities. In addition to the evaluation with simulated data, a comparison using real genomic data on the SARS-CoV-2 virus, cancer (non-small cell lung cancer) and bacteria (macrophage apoptosis) was performed. We summarize the results of our evaluation in a simple flowchart to select a ranking aggregation method, and in an automated implementation using the meta-analysis by information content algorithm to infer heterogeneity of data quality across input datasets. AVAILABILITY AND IMPLEMENTATION The code for simulated data generation and running edited version of algorithms: https://github.com/baillielab/comparison_of_RA_methods. Code to perform an optimal selection of methods based on the results of this review, using the MAIC algorithm to infer the characteristics of an input dataset, can be downloaded here: https://github.com/baillielab/maic. An online service for running MAIC: https://baillielab.net/maic. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tim Regan
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | | - Joby Cole
- University of Sheffield, Sheffield S10 2NT, UK
| | - Clark D Russell
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - David H Dockrell
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Michael U Gutmann
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK
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Sohn SY, Russell CD, Jamjoom AAB, Poon MT, Lawson McLean A, Ahmed AI, Abdulla MAH, Alalade A, Bailey M, Basu S, Baudracco I, Bayston R, Bhattacharya A, Bodkin P, Boissaud-Cooke M, Bojanic S, Brennan PM, Bulters DO, Buxton N, Chari A, Corns R, Coulter C, Coulter I, Critchley G, Dando A, Dardis R, Duddy J, Dyson E, Edwards R, Garnett M, Gatcher S, Georges H, Glancz LJ, Gray WP, Hallet J, Harte J, Haylock-Vize P, Hutchinson PJ, Humphreys H, Jenkinson MD, Joannides AJ, Kandasamy J, Kitchen J, Kolias AG, Loan JJM, Ma R, Madder H, Mallucci CL, Manning A, Mcelligott S, Mukerji N, Narayanamurthy H, O’Brien D, Okasha M, Papadopoulos M, Phan V, Phang I, Poots J, Rajaraman C, Roach J, Ross N, Sharouf F, Shastin D, Simms N, Steele L, Solth A, Tajsic T, Talibi S, Thanabalasundaram G, Vintu M, Wan Y, Wang D, Watkins L, Whitehouse K, Whitfield PC, Williams A, Zaben M. Comparison of suspected and confirmed internal EVD-related infections: a prospective multi-centre U.K. observational study. Open Forum Infect Dis 2022; 9:ofac480. [PMID: 36267249 PMCID: PMC9578167 DOI: 10.1093/ofid/ofac480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/22/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background Diagnosis of internal external ventricular drain (EVD)-related infections (iERI) is an area of diagnostic difficulty. Empiric treatment is often initiated on clinical suspicion. There is limited guidance around antimicrobial management of confirmed versus suspected iERI. Methods Data on patients requiring EVD insertion were collected from 21 neurosurgical units in the United Kingdom from 2014 to 2015. Confirmed iERI was defined as clinical suspicion of infection with positive cerebrospinal fluid (CSF) culture and/or Gram stain. Cerebrospinal fluid, blood, and clinical parameters and antimicrobial management were compared between the 2 groups. Mortality and Modified Rankin Scores were compared at 30 days post-EVD insertion. Results Internal EVD-related infection was suspected after 46 of 495 EVD insertions (9.3%), more common after an emergency insertion. Twenty-six of 46 were confirmed iERIs, mostly due to Staphylococci (16 of 26). When confirmed and suspected infections were compared, there were no differences in CSF white cell counts or glucose concentrations, nor peripheral blood white cell counts or C-reactive protein concentrations. The incidence of fever, meningism, and seizures was also similar, although altered consciousness was more common in people with confirmed iERI. Broad-spectrum antimicrobial usage was prevalent in both groups with no difference in median duration of therapy (10 days [interquartile range {IQR}, 7–24.5] for confirmed cases and 9.5 days [IQR, 5.75–14] for suspected, P = 0.3). Despite comparable baseline characteristics, suspected iERI was associated with lower mortality and better neurological outcomes. Conclusions Suspected iERI could represent sterile inflammation or lower bacterial load leading to false-negative cultures. There is a need for improved microbiology diagnostics and biomarkers of bacterial infection to permit accurate discrimination and improve antimicrobial stewardship.
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Affiliation(s)
- Sei Yon Sohn
- Division of Anaesthesia, University of Cambridge , Cambridge , U.K
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute , Edinburgh , U.K
| | - Aimun AB Jamjoom
- Department of Clinical Neuroscience, Royal Infirmary of Edinburgh , Edinburgh , U.K
| | - Michael T Poon
- Department of Clinical Neuroscience, Royal Infirmary of Edinburgh , Edinburgh , U.K
| | - Aaron Lawson McLean
- Department of Neurosurgery, Jena University Hospital – Friedrich Schiller University Jena , Jena , Germany
| | - Aminul I Ahmed
- Wolfson CARD, King’s College London and Department of Neurosurgery, King’s College Hospital , London , U.K
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Russell CD, Clohisey Hendry S. Defining resistance and tolerance traits in Covid-19: towards a stratified medicine approach. QJM 2022; 115:513-519. [PMID: 35686910 PMCID: PMC9375574 DOI: 10.1093/qjmed/hcac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Successful host defence against infectious disease involves resistance (reduce pathogen load) and tolerance (reduce tissue damage associated with pathogen presence). Integration of clinical, immunologic, genetic and therapeutic discoveries has identified defects in both of these responses in the progression from SARS-CoV-2 infection to life-threatening coronavirus disease 2019 (Covid-19) lung injury. Early after infection with SARS-CoV-2, resistance can be compromised by a failed type 1 interferon (IFN-I) response, due to direct viral antagonism of induction and signalling, deleterious host genetic variants (IFNAR2, IFNA10, TYK2 and PLSCR1), and neutralizing auto-antibodies directed against IFN-I (predominantly IFN-α). Later in the disease, after pathogen sensing has activated a pro-inflammatory response, a failure to appropriately regulate this response compromises tolerance resulting in virus-independent immunopathology involving the lung and reticuloendothelial system. Monocytes are activated in the periphery (involving M-CSF, GM-CSF, IL-6, NLRP1 inflammasomes, TYK2 and afucosylated anti-spike IgG) then recruited to the lung (involving CCR2::MCP-3/MCP-1 and C5a::C5aR1 axes) as pro-inflammatory monocyte-derived macrophages, resulting in inflammatory lung injury. Phenotypic and genotypic heterogeneity is apparent in all these responses, identifying 'treatable traits' (therapeutically relevant components of inter-individual variation) which could be exploited to achieve a stratified medicine approach to Covid-19. Overall, Covid-19 pathogenesis re-affirms the importance of resistance in surviving an infectious disease and highlights that tolerance is also a central pillar of host defence in humans and can be beneficially modified using host-directed therapies.
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Affiliation(s)
- C D Russell
- Address correspondence to C.D Russell, Queen's Medical Research Institute, University of Edinburgh Centre for Inflammation Research, Room C2.16, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
| | - S Clohisey Hendry
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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16
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Garcia-Gallo E, Merson L, Kennon K, Kelly S, Citarella BW, Fryer DV, Shrapnel S, Lee J, Duque S, Fuentes YV, Balan V, Smith S, Wei J, Gonçalves BP, Russell CD, Sigfrid L, Dagens A, Olliaro PL, Baruch J, Kartsonaki C, Dunning J, Rojek A, Rashan A, Beane A, Murthy S, Reyes LF. ISARIC-COVID-19 dataset: A Prospective, Standardized, Global Dataset of Patients Hospitalized with COVID-19. Sci Data 2022; 9:454. [PMID: 35908040 PMCID: PMC9339000 DOI: 10.1038/s41597-022-01534-9] [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: 03/30/2022] [Accepted: 06/29/2022] [Indexed: 12/24/2022] Open
Abstract
The International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) COVID-19 dataset is one of the largest international databases of prospectively collected clinical data on people hospitalized with COVID-19. This dataset was compiled during the COVID-19 pandemic by a network of hospitals that collect data using the ISARIC-World Health Organization Clinical Characterization Protocol and data tools. The database includes data from more than 705,000 patients, collected in more than 60 countries and 1,500 centres worldwide. Patient data are available from acute hospital admissions with COVID-19 and outpatient follow-ups. The data include signs and symptoms, pre-existing comorbidities, vital signs, chronic and acute treatments, complications, dates of hospitalization and discharge, mortality, viral strains, vaccination status, and other data. Here, we present the dataset characteristics, explain its architecture and how to gain access, and provide tools to facilitate its use.
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Affiliation(s)
| | | | - Laura Merson
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom.
- Infectious Diseases Data Observatory (IDDO), University of Oxford, Oxford, United Kingdom.
| | - Kalynn Kennon
- Infectious Diseases Data Observatory (IDDO), University of Oxford, Oxford, United Kingdom
| | - Sadie Kelly
- Infectious Diseases Data Observatory (IDDO), University of Oxford, Oxford, United Kingdom
| | - Barbara Wanjiru Citarella
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | | | - Sally Shrapnel
- The University of Queensland, Brisbane, Australia
- The Australian Research Council Centre of Excellence for Engineered Quantum Systems, St. Lucia, Australia
| | - James Lee
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Sara Duque
- Universidad de La Sabana, Chía, Colombia
| | | | - Valeria Balan
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Sue Smith
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Jia Wei
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Bronner P Gonçalves
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Clark D Russell
- the University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
| | - Louise Sigfrid
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Andrew Dagens
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Piero L Olliaro
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Joaquin Baruch
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Christiana Kartsonaki
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Jake Dunning
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Amanda Rojek
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom
| | - Aasiyah Rashan
- Nat. Intensive Care Surveillance- M.O.R.U, Colombo, Sri Lanka
| | - Abi Beane
- Wellcome-CRIT Care Asia- Africa, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Srinivas Murthy
- Division of Critical Care, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Luis Felipe Reyes
- Universidad de La Sabana, Chía, Colombia.
- International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC), University of Oxford, Oxford, United Kingdom.
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17
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Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [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: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
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Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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18
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Knight SR, Gupta RK, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LCW, Openshaw PJM, Baillie JK, Docherty A, Semple MG, Noursadeghi M, Harrison EM. Prospective validation of the 4C prognostic models for adults hospitalised with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol. Thorax 2022; 77:606-615. [PMID: 34810237 PMCID: PMC8610617 DOI: 10.1136/thoraxjnl-2021-217629] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 05/14/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023]
Abstract
PURPOSE To prospectively validate two risk scores to predict mortality (4C Mortality) and in-hospital deterioration (4C Deterioration) among adults hospitalised with COVID-19. METHODS Prospective observational cohort study of adults (age ≥18 years) with confirmed or highly suspected COVID-19 recruited into the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study in 306 hospitals across England, Scotland and Wales. Patients were recruited between 27 August 2020 and 17 February 2021, with at least 4 weeks follow-up before final data extraction. The main outcome measures were discrimination and calibration of models for in-hospital deterioration (defined as any requirement of ventilatory support or critical care, or death) and mortality, incorporating predefined subgroups. RESULTS 76 588 participants were included, of whom 27 352 (37.4%) deteriorated and 12 581 (17.4%) died. Both the 4C Mortality (0.78 (0.77 to 0.78)) and 4C Deterioration scores (pooled C-statistic 0.76 (95% CI 0.75 to 0.77)) demonstrated consistent discrimination across all nine National Health Service regions, with similar performance metrics to the original validation cohorts. Calibration remained stable (4C Mortality: pooled slope 1.09, pooled calibration-in-the-large 0.12; 4C Deterioration: 1.00, -0.04), with no need for temporal recalibration during the second UK pandemic wave of hospital admissions. CONCLUSION Both 4C risk stratification models demonstrate consistent performance to predict clinical deterioration and mortality in a large prospective second wave validation cohort of UK patients. Despite recent advances in the treatment and management of adults hospitalised with COVID-19, both scores can continue to inform clinical decision making. TRIAL REGISTRATION NUMBER ISRCTN66726260.
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Affiliation(s)
- Stephen R Knight
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Rishi K Gupta
- University College London Institute for Global Health, London, UK
| | - Antonia Ho
- Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Riinu Pius
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Iain Buchan
- Manchester Academic Health Science Centre, Manchester, UK
- Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Gail Carson
- Nuffield Department of Clinical Medicine, ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Thomas M Drake
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jake Dunning
- Public Health England National Infection Service, Salisbury, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carrol Gamble
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Christopher A Green
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Sophie Halpin
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Karl A Holden
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Peter W Horby
- Nuffield Department of Clinical Medicine, ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Clare Jackson
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Kenneth A Mclean
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Laura Merson
- Nuffield Department of Clinical Medicine, ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Lisa Norman
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Piero L Olliaro
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Mark G Pritchard
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Clark D Russell
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Catherine A Shaw
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Aziz Sheikh
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Tom Solomon
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | | | - Olivia V Swann
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Lance C W Turtle
- Clinical Infection, Microbiology and Immunology, University of Liverpool Faculty of Health and Life Sciences, Liverpool, UK
- Liverpool University Hospitals Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Annemarie Docherty
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, University of Liverpool, Liverpool, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
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19
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Dolby HW, Clifford SA, Laurenson IF, Fowler VG, Russell CD. Heterogeneity In Staphylococcus aureus Bacteraemia Clinical Trials Complicates Interpretation Of Findings. J Infect Dis 2022; 226:723-728. [PMID: 35639909 PMCID: PMC9441204 DOI: 10.1093/infdis/jiac219] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
We systematically evaluated randomized-controlled trials (RCTs) for Staphylococcus aureus bacteremia (SAB). There was intertrial heterogeneity in cohort characteristics, including bacteremia source, complicated SAB, and comorbidities. Reporting of cohort characteristics was itself variable, including bacteremia source and illness severity. Selection bias was introduced by exclusion criteria relating to comorbidities, illness severity, infection types, and source control. Mortality was lower in RCT control arms compared with observational cohorts. Differences in outcome definitions impedes meta-analysis. These issues complicate the interpretation and application of SAB RCT results. The value of these trials should be maximized by a standardized approach to recruitment, definitions, and reporting.
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Affiliation(s)
- Heather W Dolby
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, U.K
| | - Sarah A Clifford
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, U.K
| | - Ian F Laurenson
- Clinical Microbiology, Royal Infirmary of Edinburgh, Edinburgh, U.K
| | - Vance G Fowler
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Durham, NC, U.S.A.,Duke Clinical Research Institute, Durham, NC, U.S.A
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, U.K.,Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, U.K.,Clinical Microbiology, Royal Infirmary of Edinburgh, Edinburgh, U.K
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20
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Relph KA, Russell CD, Fairfield CJ, Turtle L, de Silva TI, Siggins MK, Drake TM, Thwaites RS, Abrams S, Moore SC, Hardwick HE, Oosthuyzen W, Harrison EM, Docherty AB, Openshaw PJM, Baillie JK, Semple MG, Ho A. Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission. Open Forum Infect Dis 2022; 9:ofac179. [PMID: 35531376 PMCID: PMC9070482 DOI: 10.1093/ofid/ofac179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Admission procalcitonin measurements and microbiology results were available for 1040 hospitalized adults with coronavirus disease 2019 (from 48 902 included in the International Severe Acute Respiratory and Emerging Infections Consortium World Health Organization Clinical Characterisation Protocol UK study). Although procalcitonin was higher in bacterial coinfection, this was neither clinically significant (median [IQR], 0.33 [0.11-1.70] ng/mL vs 0.24 [0.10-0.90] ng/mL) nor diagnostically useful (area under the receiver operating characteristic curve, 0.56 [95% confidence interval, .51-.60]).
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Affiliation(s)
- Katharine A Relph
- University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
| | - Cameron J Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Lance Turtle
- National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Thushan I de Silva
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals National Health Service Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Matthew K Siggins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Simon Abrams
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Shona C Moore
- National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hayley E Hardwick
- National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Wilna Oosthuyzen
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - J Kenneth Baillie
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm G Semple
- National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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21
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Millar JE, Neyton L, Seth S, Dunning J, Merson L, Murthy S, Russell CD, Keating S, Swets M, Sudre CH, Spector TD, Ourselin S, Steves CJ, Wolf J, Docherty AB, Harrison EM, Openshaw PJM, Semple MG, Baillie JK. Distinct clinical symptom patterns in patients hospitalised with COVID-19 in an analysis of 59,011 patients in the ISARIC-4C study. Sci Rep 2022; 12:6843. [PMID: 35478198 PMCID: PMC9043502 DOI: 10.1038/s41598-022-08032-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/09/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is clinically characterised by fever, cough, and dyspnoea. Symptoms affecting other organ systems have been reported. However, it is the clinical associations of different patterns of symptoms which influence diagnostic and therapeutic decision-making. In this study, we applied clustering techniques to a large prospective cohort of hospitalised patients with COVID-19 to identify clinically meaningful sub-phenotypes. We obtained structured clinical data on 59,011 patients in the UK (the ISARIC Coronavirus Clinical Characterisation Consortium, 4C) and used a principled, unsupervised clustering approach to partition the first 25,477 cases according to symptoms reported at recruitment. We validated our findings in a second group of 33,534 cases recruited to ISARIC-4C, and in 4,445 cases recruited to a separate study of community cases. Unsupervised clustering identified distinct sub-phenotypes. First, a core symptom set of fever, cough, and dyspnoea, which co-occurred with additional symptoms in three further patterns: fatigue and confusion, diarrhoea and vomiting, or productive cough. Presentations with a single reported symptom of dyspnoea or confusion were also identified, alongside a sub-phenotype of patients reporting few or no symptoms. Patients presenting with gastrointestinal symptoms were more commonly female, had a longer duration of symptoms before presentation, and had lower 30-day mortality. Patients presenting with confusion, with or without core symptoms, were older and had a higher unadjusted mortality. Symptom sub-phenotypes were highly consistent in replication analysis within the ISARIC-4C study. Similar patterns were externally verified in patients from a study of self-reported symptoms of mild disease. The large scale of the ISARIC-4C study enabled robust, granular discovery and replication. Clinical interpretation is necessary to determine which of these observations have practical utility. We propose that four sub-phenotypes are usefully distinct from the core symptom group: gastro-intestinal disease, productive cough, confusion, and pauci-symptomatic presentations. Importantly, each is associated with an in-hospital mortality which differs from that of patients with core symptoms.
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Affiliation(s)
- Jonathan E Millar
- Division of Functional Genetics and Development, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Lucile Neyton
- Division of Functional Genetics and Development, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Sohan Seth
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Jake Dunning
- National Infection Service, Public Health England, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Laura Merson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, ISARIC Global Support Centre, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Srinivas Murthy
- BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Clark D Russell
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Maaike Swets
- Division of Functional Genetics and Development, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Carole H Sudre
- School of Biomedical and Imaging Sciences, King's College London, London, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sebastien Ourselin
- School of Biomedical and Imaging Sciences, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.
| | - J Kenneth Baillie
- Division of Functional Genetics and Development, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK.
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22
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Swets MC, Russell CD, Harrison EM, Docherty AB, Lone N, Girvan M, Hardwick HE, Visser LG, Openshaw PJM, Groeneveld GH, Semple MG, Baillie JK. SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses. Lancet 2022; 399:1463-1464. [PMID: 35344735 PMCID: PMC8956294 DOI: 10.1016/s0140-6736(22)00383-x] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Maaike C Swets
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK; Department of Infectious Diseases, Leiden University Medical Centre, Leiden University, Leiden, Netherlands
| | - Clark D Russell
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Nazir Lone
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Leonardus G Visser
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden University, Leiden, Netherlands
| | | | - Geert H Groeneveld
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden University, Leiden, Netherlands
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
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23
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Närhi F, Moonesinghe SR, Shenkin SD, Drake TM, Mulholland RH, Donegan C, Dunning J, Fairfield CJ, Girvan M, Hardwick HE, Ho A, Leeming G, Nguyen-Van-Tam JS, Pius R, Russell CD, Shaw CA, Spencer RG, Turtle L, Openshaw PJM, Baillie JK, Harrison EM, Semple MG, Docherty AB. Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study. Lancet Digit Health 2022; 4:e220-e234. [PMID: 35337642 PMCID: PMC8940185 DOI: 10.1016/s2589-7500(22)00018-8] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/16/2021] [Accepted: 01/13/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care. METHODS We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260. FINDINGS Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70-0·89], p=0·0001, for 70-79 years; 0·52 [0·46-0·58], p<0·0001, for >80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75-80% in January, 2021. INTERPRETATION Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered. FUNDING UK National Institute for Health Research and UK Medical Research Council.
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Affiliation(s)
- Fiina Närhi
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - S Ramani Moonesinghe
- Department for Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK; Health Services Research Centre, National Institute for Academic Anaesthesia, Royal College of Anaesthetists, London, UK
| | | | - Thomas M Drake
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Cara Donegan
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jake Dunning
- Faculty of Medicine, Imperial College London, London, UK
| | | | - Michelle Girvan
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Gary Leeming
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; UK Department of Health and Social Care, Field Epidemiology Service, London, UK
| | - Riinu Pius
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Usher Institute, Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Catherine A Shaw
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | | | - Ewen M Harrison
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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24
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McAllister MJ, Kirkwood K, Chuah SC, Thompson EJ, Cartwright JA, Russell CD, Dorward DA, Lucas CD, Ho GT. Intestinal Protein Characterisation of SARS-CoV-2 Entry Molecules ACE2 and TMPRSS2 in Inflammatory Bowel Disease (IBD) and Fatal COVID-19 Infection. Inflammation 2022; 45:567-572. [PMID: 34697723 PMCID: PMC8545358 DOI: 10.1007/s10753-021-01567-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 05/07/2021] [Revised: 08/21/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023]
Abstract
The coronavirus SARS-CoV-2 contributes to morbidity and mortality mainly as a result of immune-pathology in the lungs. Recent data has shown multi-system involvement with widespread viral tropism. Here we present a detailed intestinal protein characterisation of SARS-Cov-2 entry molecules ACE2 and TMPRSS2 in patients with inflammatory bowel disease ([IBD]; ulcerative colitis [UC] and Crohn's disease [CD]) with age- and sex-matched non-IBD controls, and in those with fatal COVID-19 infection. In our dataset, ACE2 and TMPRSS2 displayed a membrane enterocyte staining in the ileum (due to presence of brush border/microvilli) in contrast to a cytoplasmic pattern in the colon. We also showed a high ACE2/low TMPRSS2 expression pattern in the ileum with a reverse trend in the colon. In UC, colonic ACE2 and TMPRSS2 are cytoplasmic in nature, with significantly higher ACE2 staining intensity compared to non-IBD controls. In inflamed and unaffected IBD mucosa, ileal and colonic enterocyte ACE2 and TMPRSS2 expressions are not modified in the histologic presence of inflammation. We observed immune cells within the lamina propria that expressed ACE2 and TMPRSS2, at higher frequencies in IBD when compared to non-IBD controls. These were identified as plasma cells with multiple myeloma oncogene 1/interferon regulatory factor 4 (MUM1/IRF4) expression. We further analysed the gut histology of six fatal COVID-19 cases, with no difference in colonic and ileal ACE2/TMRPSS2 staining (compared to non-IBD controls) and identified ACE2 + lamina propria plasma cells. Of interest, in this COVID-19 cohort, there was no histologic evidence gut inflammation despite known evidence of viral tropism within the enterocytes. Our data provides evidence for tissue expression of entry molecules ACE2 and TMPRSS2 including a close apposition to plasma cells - both pointing towards a role of the gut in the antecedent immune response to SARS-CoV-2 infection.
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Affiliation(s)
- Milly J McAllister
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Kathryn Kirkwood
- Gastroenterology and Pathology Department, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Shaun C Chuah
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Emily J Thompson
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Jennifer A Cartwright
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Clark D Russell
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
- Regional Infectious Diseases Unit, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - David A Dorward
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
- Department of Pathology, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Christopher D Lucas
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
- Department of Respiratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Gwo-Tzer Ho
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, Scotland, UK.
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25
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Russell CD, Valanciute A, Gachanja NN, Stephen J, Penrice-Randal R, Armstrong SD, Clohisey S, Wang B, Al Qsous W, Wallace WA, Oniscu GC, Stevens J, Harrison DJ, Dhaliwal K, Hiscox JA, Baillie JK, Akram AR, Dorward DA, Lucas CD. Tissue Proteomic Analysis Identifies Mechanisms and Stages of Immunopathology in Fatal COVID-19. Am J Respir Cell Mol Biol 2022; 66:196-205. [PMID: 34710339 PMCID: PMC8845132 DOI: 10.1165/rcmb.2021-0358oc] [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: 08/10/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022] Open
Abstract
Immunopathology occurs in the lung and spleen in fatal coronavirus disease (COVID-19), involving monocytes/macrophages and plasma cells. Antiinflammatory therapy reduces mortality, but additional therapeutic targets are required. We aimed to gain mechanistic insight into COVID-19 immunopathology by targeted proteomic analysis of pulmonary and splenic tissues. Lung parenchymal and splenic tissue was obtained from 13 postmortem examinations of patients with fatal COVID-19. Control tissue was obtained from cancer resection samples (lung) and deceased organ donors (spleen). Protein was extracted from tissue by phenol extraction. Olink multiplex immunoassay panels were used for protein detection and quantification. Proteins with increased abundance in the lung included MCP-3, antiviral TRIM21, and prothrombotic TYMP. OSM and EN-RAGE/S100A12 abundance was correlated and associated with inflammation severity. Unsupervised clustering identified "early viral" and "late inflammatory" clusters with distinct protein abundance profiles, and differences in illness duration before death and presence of viral RNA. In the spleen, lymphocyte chemotactic factors and CD8A were decreased in abundance, and proapoptotic factors were increased. B-cell receptor signaling pathway components and macrophage colony stimulating factor (CSF-1) were also increased. Additional evidence for a subset of host factors (including DDX58, OSM, TYMP, IL-18, MCP-3, and CSF-1) was provided by overlap between 1) differential abundance in spleen and lung tissue; 2) meta-analysis of existing datasets; and 3) plasma proteomic data. This proteomic analysis of lung parenchymal and splenic tissue from fatal COVID-19 provides mechanistic insight into tissue antiviral responses, inflammation and disease stages, macrophage involvement, pulmonary thrombosis, splenic B-cell activation, and lymphocyte depletion.
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Affiliation(s)
- Clark D. Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Asta Valanciute
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Naomi N. Gachanja
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Jillian Stephen
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Stuart D. Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Wael Al Qsous
- Department of Pathology, Western General Hospital, Edinburgh, United Kingdom
| | | | | | - Jo Stevens
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St. Andrews, North Haugh, St. Andrews, United Kingdom
| | - Kevin Dhaliwal
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Respiratory Medicine, and
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; and
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Ahsan R. Akram
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Respiratory Medicine, and
| | - David A. Dorward
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Pathology
| | - Christopher D. Lucas
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
- Department of Respiratory Medicine, and
- Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
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26
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Sullivan MK, Lees JS, Drake TM, Docherty AB, Oates G, Hardwick HE, Russell CD, Merson L, Dunning J, Nguyen-Van-Tam JS, Openshaw P, Harrison EM, Baillie JK, Semple MG, Ho A, Mark PB. Acute kidney injury in patients hospitalized with COVID-19 from the ISARIC WHO CCP-UK Study: a prospective, multicentre cohort study. Nephrol Dial Transplant 2022; 37:271-284. [PMID: 34661677 PMCID: PMC8788218 DOI: 10.1093/ndt/gfab303] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [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: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is common in coronavirus disease 2019 (COVID-19). This study investigated adults hospitalized with COVID-19 and hypothesized that risk factors for AKI would include comorbidities and non-White race. METHODS A prospective multicentre cohort study was performed using patients admitted to 254 UK hospitals with COVID-19 between 17 January 2020 and 5 December 2020. RESULTS Of 85 687 patients, 2198 (2.6%) received acute kidney replacement therapy (KRT). Of 41 294 patients with biochemistry data, 13 000 (31.5%) had biochemical AKI: 8562 stage 1 (65.9%), 2609 stage 2 (20.1%) and 1829 stage 3 (14.1%). The main risk factors for KRT were chronic kidney disease (CKD) [adjusted odds ratio (aOR) 3.41: 95% confidence interval 3.06-3.81], male sex (aOR 2.43: 2.18-2.71) and Black race (aOR 2.17: 1.79-2.63). The main risk factors for biochemical AKI were admission respiratory rate >30 breaths per minute (aOR 1.68: 1.56-1.81), CKD (aOR 1.66: 1.57-1.76) and Black race (aOR 1.44: 1.28-1.61). There was a gradated rise in the risk of 28-day mortality by increasing severity of AKI: stage 1 aOR 1.58 (1.49-1.67), stage 2 aOR 2.41 (2.20-2.64), stage 3 aOR 3.50 (3.14-3.91) and KRT aOR 3.06 (2.75-3.39). AKI rates peaked in April 2020 and the subsequent fall in rates could not be explained by the use of dexamethasone or remdesivir. CONCLUSIONS AKI is common in adults hospitalized with COVID-19 and it is associated with a heightened risk of mortality. Although the rates of AKI have fallen from the early months of the pandemic, high-risk patients should have their kidney function and fluid status monitored closely.
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Affiliation(s)
- Michael K Sullivan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Jennifer S Lees
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Georgia Oates
- Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Hayley E Hardwick
- HPRU in Infection and Emerging Diseases, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Clark D Russell
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Laura Merson
- ISARIC Global Support Centre, University of Oxford, Oxford, UK
| | - Jake Dunning
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Peter Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Malcolm G Semple
- HPRU in Infection and Emerging Diseases, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Patrick B Mark
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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27
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Abbas A, Abdukahil SA, Abdulkadir NN, Abe R, Abel L, Absil L, Acharya S, Acker A, Adachi S, Adam E, Adrião D, Ageel SA, Ahmed S, Ain Q, Ainscough K, Aisa T, Ait Hssain A, Ait Tamlihat Y, Akimoto T, Akmal E, Al Qasim E, Alalqam R, Alam T, Al-dabbous T, Alegesan S, Alegre C, Alessi M, Alex B, Alexandre K, Al-Fares A, Alfoudri H, Ali I, Ali Shah N, Alidjnou KE, Aliudin J, Alkhafajee Q, Allavena C, Allou N, Altaf A, Alves J, Alves JM, Alves R, Amaral M, Amira N, Ammerlaan H, Ampaw P, Andini R, Andrejak C, Angheben A, Angoulvant F, Ansart S, Anthonidass S, Antonelli M, Antunes de Brito CA, Anwar KR, Apriyana A, Arabi Y, Aragao I, Arali R, Arancibia F, Araujo C, Arcadipane A, Archambault P, Arenz L, Arlet JB, Arnold-Day C, Aroca A, Arora L, Arora R, Artaud-Macari E, Aryal D, Asaki M, Asensio A, Ashley E, Ashraf M, Ashraf S, Asim M, Assie JB, Asyraf A, Atique A, Attanyake AMUL, Auchabie J, Aumaitre H, Auvet A, Azemar L, Azoulay C, Bach B, Bachelet D, Badr C, Baig N, Baillie JK, Baird JK, Bak E, Bakakos A, Bakar NA, Bal A, Balakrishnan M, Balan V, Bani-Sadr F, Barbalho R, Barbosa NY, Barclay WS, Barnett SU, Barnikel M, Barrasa H, Barrelet A, Barrigoto C, Bartoli M, Bartone C, Baruch J, Bashir M, Basmaci R, Basri MFH, Bastos D, Battaglini D, Bauer J, Bautista Rincon DF, Bazan Dow D, Bedossa A, Bee KH, Behilill S, Beishuizen A, Beljantsev A, Bellemare D, Beltrame A, Beltrão BA, Beluze M, Benech N, Benjiman LE, Benkerrou D, Bennett S, Bento L, Berdal JE, Bergeaud D, Bergin H, Bernal Sobrino JL, Bertoli G, Bertolino L, Bessis S, Betz A, Bevilcaqua S, Bezulier K, Bhatt A, Bhavsar K, Bianchi I, Bianco C, Bidin FN, Bikram Singh M, Bin Humaid F, Bin Kamarudin MN, Bissuel F, Biston P, Bitker L, Blanco-Schweizer P, Blier C, Bloos F, Blot M, Blumberg L, Boccia F, Bodenes L, Bogaarts A, Bogaert D, Boivin AH, Bolze PA, Bompart F, Bonfasius A, Borges D, Borie R, Bosse HM, Botelho-Nevers E, Bouadma L, Bouchaud O, Bouchez S, Bouhmani D, Bouhour D, Bouiller K, Bouillet L, Bouisse C, Boureau 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D, Treoux T, Trieu HT, Tripathy S, Tromeur C, Trontzas I, Trouillon T, Truong J, Tual C, Tubiana S, Tuite H, Turmel JM, Turtle LC, Tveita A, Twardowski P, Uchiyama M, Udayanga PGI, Udy A, Ullrich R, Umer Z, Uribe A, Usman A, Vajdovics C, Val-Flores L, Valle AL, Valran A, Van de Velde S, van den Berge M, van der Feltz M, van der Valk P, Van Der Vekens N, Van der Voort P, Van Der Werf S, van Dyk M, van Gulik L, Van Hattem J, van Lelyveld S, van Netten C, Van Twillert G, van Veen I, Vanel N, Vanoverschelde H, Varghese P, Varrone M, Vasudayan SR, Vauchy C, Vaughan H, Veeran S, Veislinger A, Vencken S, Ventura S, Verbon A, Vidal JE, Vieira C, Vijayan D, Villanueva JA, Villar J, Villeneuve PM, Villoldo A, Vinh Chau NV, Visseaux B, Visser H, Vitiello C, Vonkeman H, Vuotto F, Wahab NH, Wahab SA, Wahid NA, Wainstein M, Wan Muhd Shukeri WF, Wang CH, Webb SA, Wei J, Weil K, Wen TP, Wesselius S, West TE, Wham M, Whelan B, White N, Wicky PH, Wiedemann A, Wijaya SO, Wille K, Willems S, Williams V, Wils EJ, Wing Yiu N, Wong C, Wong TF, Wong XC, Wong YS, Xian GE, Xian LS, Xuan KP, Xynogalas I, Yacoub S, Yakop SRBM, Yamazaki M, Yazdanpanah Y, Yee Liang Hing N, Yelnik C, Yeoh CH, Yerkovich S, Yokoyama T, Yonis H, Yousif O, Yuliarto S, Zaaqoq A, Zabbe M, Zacharowski K, Zahid M, Zahran M, Zaidan NZB, Zambon M, Zambrano M, Zanella A, Zawadka K, Zaynah N, Zayyad H, Zoufaly A, Zucman D. The value of open-source clinical science in pandemic response: lessons from ISARIC. Lancet Infect Dis 2021; 21:1623-1624. [PMID: 34619109 PMCID: PMC8489876 DOI: 10.1016/s1473-3099(21)00565-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/31/2022]
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McCaughan H, Russell CD, O'Shea DT. Infected deep vein thrombophlebitis in people who inject drugs: missed opportunities and potential for alternative antimicrobial approaches. Infection 2021; 50:507-511. [PMID: 34727367 PMCID: PMC8942891 DOI: 10.1007/s15010-021-01725-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/22/2021] [Indexed: 12/04/2022]
Abstract
Infected deep vein thrombophlebitis (i-DVT) in people who inject drugs (PWID) is a clinically challenging but poorly characterised disease. We undertook a retrospective observational study of 70 PWID presenting acutely with i-DVT to improve the clinical and microbiological characterisation of this disease. i-DVT was frequently associated with bacteraemia (59.1% patients with blood cultures obtained), groin abscesses (in 34.3%; of which 54.2% required surgical drainage), and septic pulmonary emboli (38.6%) requiring anticoagulation. Network analysis identified a cluster of patients presenting with respiratory symptoms but lacking typical DVT symptoms, more likely to have septic pulmonary emboli. A microbiologic diagnosis was frequently achieved (70%). Causative pathogens were predominantly gram-positive (S. aureus and streptococci, especially anginosus group), whereas gram-negative pathogens were identified very infrequently (in 6.1% of microbiological diagnoses). This suggests routine empiric therapy against gram-negative bacteria, though commonly administered, is not required. High rates of clinical cure (88.6%) were observed despite the complex nature of infections and independently of the highly variable intravenous and total antimicrobial durations received. There exists a rationale to devise pragmatic approaches to implement novel individualised treatment plans utilising oral antimicrobial therapy for i-DVT. Despite frequent healthcare interactions, opportunities to address HCV treatment and opioid substitution therapy were frequently missed during these acute admissions.
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Affiliation(s)
- Hugh McCaughan
- Clinical Infection Research Group, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK. .,Centre for Synthetic and Systems Biology, Waddington Building, Kings Buildings, Edinburgh, UK.
| | - Clark D Russell
- Clinical Infection Research Group, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK. .,University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK.
| | - Dáire T O'Shea
- Clinical Infection Research Group, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
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Hurst EA, Mellanby RJ, Handel I, Griffith DM, Rossi AG, Walsh TS, Shankar-Hari M, Dunning J, Homer NZ, Denham SG, Devine K, Holloway PA, Moore SC, Thwaites RS, Samanta RJ, Summers C, Hardwick HE, Oosthuyzen W, Turtle L, Semple MG, Openshaw PJM, Baillie JK, Russell CD. Vitamin D insufficiency in COVID-19 and influenza A, and critical illness survivors: a cross-sectional study. BMJ Open 2021; 11:e055435. [PMID: 34686560 PMCID: PMC8728359 DOI: 10.1136/bmjopen-2021-055435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/30/2021] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES The steroid hormone vitamin D has roles in immunomodulation and bone health. Insufficiency is associated with susceptibility to respiratory infections. We report 25-hydroxy vitamin D (25(OH)D) measurements in hospitalised people with COVID-19 and influenza A and in survivors of critical illness to test the hypotheses that vitamin D insufficiency scales with illness severity and persists in survivors. DESIGN Cross-sectional study. SETTING AND PARTICIPANTS Plasma was obtained from 295 hospitalised people with COVID-19 (International Severe Acute Respiratory and emerging Infections Consortium (ISARIC)/WHO Clinical Characterization Protocol for Severe Emerging Infections UK study), 93 with influenza A (Mechanisms of Severe Acute Influenza Consortium (MOSAIC) study, during the 2009-2010 H1N1 pandemic) and 139 survivors of non-selected critical illness (prior to the COVID-19 pandemic). Total 25(OH)D was measured by liquid chromatography-tandem mass spectrometry. Free 25(OH)D was measured by ELISA in COVID-19 samples. OUTCOME MEASURES Receipt of invasive mechanical ventilation (IMV) and in-hospital mortality. RESULTS Vitamin D insufficiency (total 25(OH)D 25-50 nmol/L) and deficiency (<25 nmol/L) were prevalent in COVID-19 (29.3% and 44.4%, respectively), influenza A (47.3% and 37.6%) and critical illness survivors (30.2% and 56.8%). In COVID-19 and influenza A, total 25(OH)D measured early in illness was lower in patients who received IMV (19.6 vs 31.9 nmol/L (p<0.0001) and 22.9 vs 31.1 nmol/L (p=0.0009), respectively). In COVID-19, biologically active free 25(OH)D correlated with total 25(OH)D and was lower in patients who received IMV, but was not associated with selected circulating inflammatory mediators. CONCLUSIONS Vitamin D deficiency/insufficiency was present in majority of hospitalised patients with COVID-19 or influenza A and correlated with severity and persisted in critical illness survivors at concentrations expected to disrupt bone metabolism. These findings support early supplementation trials to determine if insufficiency is causal in progression to severe disease, and investigation of longer-term bone health outcomes.
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Affiliation(s)
- Emma A Hurst
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Queen's Medical Research Institute, Edinburgh, UK
| | - Richard J Mellanby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ian Handel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David M Griffith
- Molecular, Genetic and Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Adriano G Rossi
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK
| | - Timothy S Walsh
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK
| | - Jake Dunning
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Natalie Z Homer
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Queen's Medical Research Institute, Edinburgh, UK
| | - Scott G Denham
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Queen's Medical Research Institute, Edinburgh, UK
| | - Kerri Devine
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Queen's Medical Research Institute, Edinburgh, UK
| | - Paul A Holloway
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Romit J Samanta
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Hayley E Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Wilna Oosthuyzen
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | | | - J Kenneth Baillie
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
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Russell CD, Fairfield CJ, Drake TM, Turtle L, Seaton RA, Wootton DG, Sigfrid L, Harrison EM, Docherty AB, de Silva TI, Egan C, Pius R, Hardwick HE, Merson L, Girvan M, Dunning J, Nguyen-Van-Tam JS, Openshaw PJM, Baillie JK, Semple MG, Ho A. Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe 2021; 2:e354-e365. [PMID: 34100002 PMCID: PMC8172149 DOI: 10.1016/s2666-5247(21)00090-2] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Microbiological characterisation of co-infections and secondary infections in patients with COVID-19 is lacking, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and secondary infections, and antimicrobial use, in patients admitted to hospital with COVID-19. METHODS The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study is an ongoing, prospective cohort study recruiting inpatients from 260 hospitals in England, Scotland, and Wales, conducted by the ISARIC Coronavirus Clinical Characterisation Consortium. Patients with a confirmed or clinician-defined high likelihood of SARS-CoV-2 infection were eligible for inclusion in the ISARIC WHO CCP-UK study. For this specific study, we excluded patients with a recorded negative SARS-CoV-2 test result and those without a recorded outcome at 28 days after admission. Demographic, clinical, laboratory, therapeutic, and outcome data were collected using a prespecified case report form. Organisms considered clinically insignificant were excluded. FINDINGS We analysed data from 48 902 patients admitted to hospital between Feb 6 and June 8, 2020. The median patient age was 74 years (IQR 59-84) and 20 786 (42·6%) of 48 765 patients were female. Microbiological investigations were recorded for 8649 (17·7%) of 48 902 patients, with clinically significant COVID-19-related respiratory or bloodstream culture results recorded for 1107 patients. 762 (70·6%) of 1080 infections were secondary, occurring more than 2 days after hospital admission. Staphylococcus aureus and Haemophilus influenzae were the most common pathogens causing respiratory co-infections (diagnosed ≤2 days after admission), with Enterobacteriaceae and S aureus most common in secondary respiratory infections. Bloodstream infections were most frequently caused by Escherichia coli and S aureus. Among patients with available data, 13 390 (37·0%) of 36 145 had received antimicrobials in the community for this illness episode before hospital admission and 39 258 (85·2%) of 46 061 patients with inpatient antimicrobial data received one or more antimicrobials at some point during their admission (highest for patients in critical care). We identified frequent use of broad-spectrum agents and use of carbapenems rather than carbapenem-sparing alternatives. INTERPRETATION In patients admitted to hospital with COVID-19, microbiologically confirmed bacterial infections are rare, and more likely to be secondary infections. Gram-negative organisms and S aureus are the predominant pathogens. The frequency and nature of antimicrobial use are concerning, but tractable targets for stewardship interventions exist. FUNDING National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, UK Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, and NIHR HPRU in Respiratory Infections at Imperial College London.
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Affiliation(s)
- Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - R Andrew Seaton
- Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Dan G Wootton
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Louise Sigfrid
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Thushan I de Silva
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, UK
| | - Conor Egan
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Riinu Pius
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Hayley E Hardwick
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Laura Merson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Jake Dunning
- Emerging Infections and Zoonoses Unit, National Infection Service, Public Health England, Colindale, London, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
- UK Department of Health and Social Care, London, UK
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Antonia Ho
- Medical Research Council—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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Drake TM, Riad AM, Fairfield CJ, Egan C, Knight SR, Pius R, Hardwick HE, Norman L, Shaw CA, McLean KA, Thompson AAR, Ho A, Swann OV, Sullivan M, Soares F, Holden KA, Merson L, Plotkin D, Sigfrid L, de Silva TI, Girvan M, Jackson C, Russell CD, Dunning J, Solomon T, Carson G, Olliaro P, Nguyen-Van-Tam JS, Turtle L, Docherty AB, Openshaw PJ, Baillie JK, Harrison EM, Semple MG. Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study. Lancet 2021; 398:223-237. [PMID: 34274064 PMCID: PMC8285118 DOI: 10.1016/s0140-6736(21)00799-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND COVID-19 is a multisystem disease and patients who survive might have in-hospital complications. These complications are likely to have important short-term and long-term consequences for patients, health-care utilisation, health-care system preparedness, and society amidst the ongoing COVID-19 pandemic. Our aim was to characterise the extent and effect of COVID-19 complications, particularly in those who survive, using the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK. METHODS We did a prospective, multicentre cohort study in 302 UK health-care facilities. Adult patients aged 19 years or older, with confirmed or highly suspected SARS-CoV-2 infection leading to COVID-19 were included in the study. The primary outcome of this study was the incidence of in-hospital complications, defined as organ-specific diagnoses occurring alone or in addition to any hallmarks of COVID-19 illness. We used multilevel logistic regression and survival models to explore associations between these outcomes and in-hospital complications, age, and pre-existing comorbidities. FINDINGS Between Jan 17 and Aug 4, 2020, 80 388 patients were included in the study. Of the patients admitted to hospital for management of COVID-19, 49·7% (36 367 of 73 197) had at least one complication. The mean age of our cohort was 71·1 years (SD 18·7), with 56·0% (41 025 of 73 197) being male and 81·0% (59 289 of 73 197) having at least one comorbidity. Males and those aged older than 60 years were most likely to have a complication (aged ≥60 years: 54·5% [16 579 of 30 416] in males and 48·2% [11 707 of 24 288] in females; aged <60 years: 48·8% [5179 of 10 609] in males and 36·6% [2814 of 7689] in females). Renal (24·3%, 17 752 of 73 197), complex respiratory (18·4%, 13 486 of 73 197), and systemic (16·3%, 11 895 of 73 197) complications were the most frequent. Cardiovascular (12·3%, 8973 of 73 197), neurological (4·3%, 3115 of 73 197), and gastrointestinal or liver (0·8%, 7901 of 73 197) complications were also reported. INTERPRETATION Complications and worse functional outcomes in patients admitted to hospital with COVID-19 are high, even in young, previously healthy individuals. Acute complications are associated with reduced ability to self-care at discharge, with neurological complications being associated with the worst functional outcomes. COVID-19 complications are likely to cause a substantial strain on health and social care in the coming years. These data will help in the design and provision of services aimed at the post-hospitalisation care of patients with COVID-19. FUNDING National Institute for Health Research and the UK Medical Research Council.
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Affiliation(s)
- Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Aya M Riad
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Conor Egan
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stephen R Knight
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Riinu Pius
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Hayley E Hardwick
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Lisa Norman
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Catherine A Shaw
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Kenneth A McLean
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - A A Roger Thompson
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Olivia V Swann
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK; Paediatric Infectious Diseases, Royal Hospital for Sick Children, Edinburgh, UK
| | - Michael Sullivan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Felipe Soares
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Karl A Holden
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Laura Merson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Plotkin
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Louise Sigfrid
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Clare Jackson
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jake Dunning
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Emerging Infections and Zoonoses Unit, National Infection Service, Public Health England, London, UK
| | - Tom Solomon
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Clinical Infection Microbiology and Immunology, Institute of Infection, Veterinary, and Zoological Science, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - Gail Carson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piero Olliaro
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Nottingham, UK; United Kingdom Department of Health and Social Care, London, UK
| | - Lance Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Peter Jm Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
| | - J Kenneth Baillie
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Paediatric Infectious Diseases, Royal Hospital for Sick Children, Edinburgh, UK
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Docherty AB, Mulholland RH, Lone NI, Cheyne CP, De Angelis D, Diaz-Ordaz K, Donegan C, Drake TM, Dunning J, Funk S, García-Fiñana M, Girvan M, Hardwick HE, Harrison J, Ho A, Hughes DM, Keogh RH, Kirwan PD, Leeming G, Nguyen Van-Tam JS, Pius R, Russell CD, Spencer RG, Tom BD, Turtle L, Openshaw PJ, Baillie JK, Harrison EM, Semple MG. Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK. Lancet Respir Med 2021; 9:773-785. [PMID: 34000238 PMCID: PMC8121531 DOI: 10.1016/s2213-2600(21)00175-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/14/2021] [Accepted: 03/28/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Mortality rates in hospitalised patients with COVID-19 in the UK appeared to decline during the first wave of the pandemic. We aimed to quantify potential drivers of this change and identify groups of patients who remain at high risk of dying in hospital. METHODS In this multicentre prospective observational cohort study, the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK recruited a prospective cohort of patients with COVID-19 admitted to 247 acute hospitals in England, Scotland, and Wales during the first wave of the pandemic (between March 9 and Aug 2, 2020). We included all patients aged 18 years and older with clinical signs and symptoms of COVID-19 or confirmed COVID-19 (by RT-PCR test) from assumed community-acquired infection. We did a three-way decomposition mediation analysis using natural effects models to explore associations between week of admission and in-hospital mortality, adjusting for confounders (demographics, comorbidities, and severity of illness) and quantifying potential mediators (level of respiratory support and steroid treatment). The primary outcome was weekly in-hospital mortality at 28 days, defined as the proportion of patients who had died within 28 days of admission of all patients admitted in the observed week, and it was assessed in all patients with an outcome. This study is registered with the ISRCTN Registry, ISRCTN66726260. FINDINGS Between March 9, and Aug 2, 2020, we recruited 80 713 patients, of whom 63 972 were eligible and included in the study. Unadjusted weekly in-hospital mortality declined from 32·3% (95% CI 31·8-32·7) in March 9 to April 26, 2020, to 16·4% (15·0-17·8) in June 15 to Aug 2, 2020. Reductions in mortality were observed in all age groups, in all ethnic groups, for both sexes, and in patients with and without comorbidities. After adjustment, there was a 32% reduction in the risk of mortality per 7-week period (odds ratio [OR] 0·68 [95% CI 0·65-0·71]). The higher proportions of patients with severe disease and comorbidities earlier in the first wave (March and April) than in June and July accounted for 10·2% of this reduction. The use of respiratory support changed during the first wave, with gradually increased use of non-invasive ventilation over the first wave. Changes in respiratory support and use of steroids accounted for 22·2%, OR 0·95 (0·94-0·95) of the reduction in in-hospital mortality. INTERPRETATION The reduction in in-hospital mortality in patients with COVID-19 during the first wave in the UK was partly accounted for by changes in the case-mix and illness severity. A significant reduction in in-hospital mortality was associated with differences in respiratory support and critical care use, which could partly reflect accrual of clinical knowledge. The remaining improvement in in-hospital mortality is not explained by these factors, and could be associated with changes in community behaviour, inoculum dose, and hospital capacity strain. FUNDING National Institute for Health Research and the Medical Research Council.
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Affiliation(s)
| | | | - Nazir I Lone
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Christopher P Cheyne
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | | | | | - Cara Donegan
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Thomas M Drake
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | - Jake Dunning
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Sebastian Funk
- London School of Hygiene & Tropical Medicine, London, UK
| | - Marta García-Fiñana
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Janet Harrison
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK
| | - David M Hughes
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Ruth H Keogh
- London School of Hygiene & Tropical Medicine, London, UK
| | - Peter D Kirwan
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Gary Leeming
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Jonathan S Nguyen Van-Tam
- Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Nottingham, UK
| | - Riinu Pius
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- The Usher Institute, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Rebecca G Spencer
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Brian Dm Tom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Lance Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Peter Jm Openshaw
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Ewen M Harrison
- Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
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Russell CD. Exploiting an early immunological window of opportunity in COVID-19. Lancet Respir Med 2021; 9:811-812. [PMID: 34051878 PMCID: PMC8159187 DOI: 10.1016/s2213-2600(21)00225-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Clark D Russell
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK.
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Russell CD, Whittaker E, Dee DP, Farquhar E, Saenz de Villaverde A, Evans MH, Laurenson IF, Mackintosh CL, Cevik M. A Subgroup of Patients With Hospital-acquired Pneumonia Do Not Require Broad-spectrum Gram-negative Antimicrobial Coverage. Clin Infect Dis 2021; 71:e710-e713. [PMID: 32266388 PMCID: PMC7744989 DOI: 10.1093/cid/ciaa391] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/06/2020] [Indexed: 11/26/2022] Open
Abstract
Among 200 patients developing hospital-acquired pneumonia (HAP) outside the intensive care unit, 61% were treated empirically without broad-spectrum Gram-negative coverage, with clinical cure in 69.7%. Lower disease severity markers (systemic inflammatory response syndrome, hypoxia, tachypnoea, neutrophilia) and the absence of diabetes mellitus and prior doxycycline treatment (but not the time to HAP onset) identified patients not requiring broad-spectrum Gram-negative coverage.
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Affiliation(s)
- Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom.,National Health Service Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, United Kingdom.,National Health Service Lothian Infection Service, Clinical Microbiology, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Ed Whittaker
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Dominic P Dee
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Eilidh Farquhar
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Alba Saenz de Villaverde
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Morgan H Evans
- National Health Service Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Ian F Laurenson
- National Health Service Lothian Infection Service, Clinical Microbiology, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Claire L Mackintosh
- National Health Service Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Muge Cevik
- National Health Service Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, United Kingdom.,National Health Service Lothian Infection Service, Clinical Microbiology, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom.,Infection and Global Health Research, School of Medicine, University of St Andrews, Fife, United Kingdom
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35
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Gupta RK, Harrison EM, Ho A, Docherty AB, Knight SR, van Smeden M, Abubakar I, Lipman M, Quartagno M, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Olliaro PL, Pritchard MG, Russell CD, Scott-Brown J, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle L, Openshaw PJM, Baillie JK, Semple MG, Noursadeghi M. Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study. Lancet Respir Med 2021; 9:349-359. [PMID: 33444539 PMCID: PMC7832571 DOI: 10.1016/s2213-2600(20)30559-2] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Prognostic models to predict the risk of clinical deterioration in acute COVID-19 cases are urgently required to inform clinical management decisions. METHODS We developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) among consecutively hospitalised adults with highly suspected or confirmed COVID-19 who were prospectively recruited to the International Severe Acute Respiratory and Emerging Infections Consortium Coronavirus Clinical Characterisation Consortium (ISARIC4C) study across 260 hospitals in England, Scotland, and Wales. Candidate predictors that were specified a priori were considered for inclusion in the model on the basis of previous prognostic scores and emerging literature describing routinely measured biomarkers associated with COVID-19 prognosis. We used internal-external cross-validation to evaluate discrimination, calibration, and clinical utility across eight National Health Service (NHS) regions in the development cohort. We further validated the final model in held-out data from an additional NHS region (London). FINDINGS 74 944 participants (recruited between Feb 6 and Aug 26, 2020) were included, of whom 31 924 (43·2%) of 73 948 with available outcomes met the composite clinical deterioration outcome. In internal-external cross-validation in the development cohort of 66 705 participants, the selected model (comprising 11 predictors routinely measured at the point of hospital admission) showed consistent discrimination, calibration, and clinical utility across all eight NHS regions. In held-out data from London (n=8239), the model showed a similarly consistent performance (C-statistic 0·77 [95% CI 0·76 to 0·78]; calibration-in-the-large 0·00 [-0·05 to 0·05]); calibration slope 0·96 [0·91 to 1·01]), and greater net benefit than any other reproducible prognostic model. INTERPRETATION The 4C Deterioration model has strong potential for clinical utility and generalisability to predict clinical deterioration and inform decision making among adults hospitalised with COVID-19. FUNDING National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, NIHR HPRU in Respiratory Infections at Imperial College London.
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Affiliation(s)
- Rishi K Gupta
- Institute for Global Health, University College London, London, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - Antonia Ho
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Stephen R Knight
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Maarten van Smeden
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | - Marc Lipman
- UCL Respiratory, Division of Medicine, University College London, London, UK; Royal Free Hospitals NHS Trust, London, UK
| | - Matteo Quartagno
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Riinu Pius
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Iain Buchan
- Institute of Population Health Sciences, University of Liverpool, Liverpool, UK
| | - Gail Carson
- ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas M Drake
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Jake Dunning
- National Infection Service, Public Health England, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Carrol Gamble
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Christopher A Green
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Sophie Halpin
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary, and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Karl A Holden
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary, and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Peter W Horby
- ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clare Jackson
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Kenneth A Mclean
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Laura Merson
- ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
| | - Lisa Norman
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Piero L Olliaro
- ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark G Pritchard
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clark D Russell
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Catherine A Shaw
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Aziz Sheikh
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Tom Solomon
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary, and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Walton Centre NHS Foundation Trust, Liverpool, UK
| | | | - Olivia V Swann
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary, and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Royal Liverpool University Hospital, Liverpool, UK
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary, and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK.
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK.
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36
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Sigfrid L, Cevik M, Jesudason E, Lim WS, Rello J, Amuasi J, Bozza F, Palmieri C, Munblit D, Holter JC, Kildal AB, Reyes LF, Russell CD, Ho A, Turtle L, Drake TM, Beltrame A, Hann K, Bangura IR, Fowler R, Lakoh S, Berry C, Lowe DJ, McPeake J, Hashmi M, Dyrhol-Riise AM, Donohue C, Plotkin D, Hardwick H, Elkheir N, Lone NI, Docherty A, Harrison E, Baille JK, Carson G, Semple MG, Scott JT. What is the recovery rate and risk of long-term consequences following a diagnosis of COVID-19? A harmonised, global longitudinal observational study protocol. BMJ Open 2021; 11:e043887. [PMID: 33692181 PMCID: PMC7948153 DOI: 10.1136/bmjopen-2020-043887] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Very little is known about possible clinical sequelae that may persist after resolution of acute COVID-19. A recent longitudinal cohort from Italy including 143 patients followed up after hospitalisation with COVID-19 reported that 87% had at least one ongoing symptom at 60-day follow-up. Early indications suggest that patients with COVID-19 may need even more psychological support than typical intensive care unit patients. The assessment of risk factors for longer term consequences requires a longitudinal study linked to data on pre-existing conditions and care received during the acute phase of illness. The primary aim of this study is to characterise physical and psychosocial sequelae in patients post-COVID-19 hospital discharge. METHODS AND ANALYSIS This is an international open-access prospective, observational multisite study. This protocol is linked with the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) and the WHO's Clinical Characterisation Protocol, which includes patients with suspected or confirmed COVID-19 during hospitalisation. This protocol will follow-up a subset of patients with confirmed COVID-19 using standardised surveys to measure longer term physical and psychosocial sequelae. The data will be linked with the acute phase data. Statistical analyses will be undertaken to characterise groups most likely to be affected by sequelae of COVID-19. The open-access follow-up survey can be used as a data collection tool by other follow-up studies, to facilitate data harmonisation and to identify subsets of patients for further in-depth follow-up. The outcomes of this study will inform strategies to prevent long-term consequences; inform clinical management, interventional studies, rehabilitation and public health management to reduce overall morbidity; and improve long-term outcomes of COVID-19. ETHICS AND DISSEMINATION The protocol and survey are open access to enable low-resourced sites to join the study to facilitate global standardised, longitudinal data collection. Ethical approval has been given by sites in Colombia, Ghana, Italy, Norway, Russia, the UK and South Africa. New sites are welcome to join this collaborative study at any time. Sites interested in adopting the protocol as it is or in an adapted version are responsible for ensuring that local sponsorship and ethical approvals in place as appropriate. The tools are available on the ISARIC website (www.isaric.org). PROTOCOL REGISTRATION NUMBER: osf.io/c5rw3/ PROTOCOL VERSION: 3 August 2020 EUROQOL ID: 37035.
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Affiliation(s)
- Louise Sigfrid
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Heatlh, University of Oxford, Oxford, UK
| | - Muge Cevik
- Infection and Global Health Division, School of Medicine, University of St Andrews, St Andrews, UK
| | - Edwin Jesudason
- Department of Rehabilitation Medicine, NHS Lothian, Edinburgh, UK
| | - Wei Shen Lim
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jordi Rello
- Centro de Investigación Biomédica en Red - Enfermedades Respiratorias (CIBERES), Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Research Department, CHU Nîmes, Université Nîmes-Montpellier, Nîmes, France
| | - John Amuasi
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Livepool, UK
| | - Daniel Munblit
- Department of Paediatrics, I M Sechenov First Moscow State Medical University, Moskva, Russia
- IInflammation, Repair and Development Section, National Heart and Lung Institute, Imperial College London Faculty of Medicine, London, UK
| | - Jan Cato Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anders Benjamin Kildal
- Department of Anesthesiology and Intensive Care, University Hospital of North Norway, Tromso, Norway
| | | | - Clark D Russell
- The University of Edinburgh Centre for Inflammation Research, Edinburgh, UK
| | | | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Thomas M Drake
- Centre for Medical Informatics, The University of Edinburgh, Edinburgh, UK
| | - Anna Beltrame
- Department of Infectious Diseases, Tropical and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Italy
| | - Katrina Hann
- Sustainable Health Systems, Freetown, Sierra Leone
| | | | - Robert Fowler
- Sunnybrook Health Sciences Institute, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | - Colin Berry
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - David J Lowe
- Emergency Department, Queen Elizabeth University Hospital, Glasgow, UK
| | - Joanne McPeake
- NHS Greater Glasgow and Clyde, Glasgow, UK
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Madiha Hashmi
- Department of Critical Care Medicine, Ziauddin University, Karachi, Pakistan
| | | | - Chloe Donohue
- National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Daniel Plotkin
- Nuffield Department of Medicine, ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Hayley Hardwick
- National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | | | - Nazir I Lone
- Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Annemarie Docherty
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Ewen Harrison
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baille
- Division of Genetics and Genomics, The University of Edinburgh The Roslin Institute, Roslin, UK
| | - Gail Carson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Heatlh, University of Oxford, Oxford, UK
| | - Malcolm G Semple
- Health Protection Research Unit In Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- University of Liverpool, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Janet T Scott
- MRC, University of Glasgow Centre for Virus Research, Glasgow, UK
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37
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Thwaites RS, Sanchez Sevilla Uruchurtu A, Siggins MK, Liew F, Russell CD, Moore SC, Fairfield C, Carter E, Abrams S, Short CE, Thaventhiran T, Bergstrom E, Gardener Z, Ascough S, Chiu C, Docherty AB, Hunt D, Crow YJ, Solomon T, Taylor GP, Turtle L, Harrison EM, Dunning J, Semple MG, Baillie JK, Openshaw PJ. Inflammatory profiles across the spectrum of disease reveal a distinct role for GM-CSF in severe COVID-19. Sci Immunol 2021; 6:eabg9873. [PMID: 33692097 PMCID: PMC8128298 DOI: 10.1126/sciimmunol.abg9873] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [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: 02/08/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022]
Abstract
While it is now widely accepted that host inflammatory responses contribute to lung injury, the pathways that drive severity and distinguish coronavirus disease 2019 (COVID-19) from other viral lung diseases remain poorly characterized. We analyzed plasma samples from 471 hospitalized patients recruited through the prospective multicenter ISARIC4C study and 39 outpatients with mild disease, enabling extensive characterization of responses across a full spectrum of COVID-19 severity. Progressive elevation of levels of numerous inflammatory cytokines and chemokines (including IL-6, CXCL10, and GM-CSF) were associated with severity and accompanied by elevated markers of endothelial injury and thrombosis. Principal component and network analyses demonstrated central roles for IL-6 and GM-CSF in COVID-19 pathogenesis. Comparing these profiles to archived samples from patients with fatal influenza, IL-6 was equally elevated in both conditions whereas GM-CSF was prominent only in COVID-19. These findings further identify the key inflammatory, thrombotic, and vascular factors that characterize and distinguish severe and fatal COVID-19.
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Affiliation(s)
- Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, U.K
| | | | | | - Felicity Liew
- National Heart and Lung Institute, Imperial College London, U.K
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Edinburgh, U.K
| | - Shona C Moore
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | - Cameron Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, U.K
| | - Edwin Carter
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, U.K
| | - Simon Abrams
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | - Charlotte-Eve Short
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, U.K
| | | | - Emma Bergstrom
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, U.K
| | - Zoe Gardener
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, U.K
| | - Stephanie Ascough
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, U.K
| | - Christopher Chiu
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, U.K
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, U.K
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, U.K
| | - David Hunt
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, U.K
| | - Yanick J Crow
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, U.K
| | - Tom Solomon
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | - Graham P Taylor
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, U.K
| | - Lance Turtle
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
- Tropical and infectious disease unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), U.K
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, U.K
| | - Jake Dunning
- National Infection Service, Public Health England, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, U.K.
- Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, U.K
| | - J Kenneth Baillie
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, U.K.
- Roslin Institute, University of Edinburgh, Edinburgh, U.K
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38
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Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D, Ling L, McAuley D, Montgomery H, Walsh T, Pereira AC, Renieri A, Shen X, Ponting CP, Fawkes A, Tenesa A, Caulfield M, Scott R, Rowan K, Murphy L, Openshaw PJM, Semple MG, Law A, Vitart V, Wilson JF, Baillie JK. Genetic mechanisms of critical illness in COVID-19. Nature 2021; 591:92-98. [PMID: 33307546 DOI: 10.1038/s41586-020-03065-y] [Citation(s) in RCA: 790] [Impact Index Per Article: 263.3] [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: 09/27/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 × 10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.
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Affiliation(s)
- Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James Furniss
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Elvina Gountouna
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - David Harrison
- Intensive Care National Audit & Research Centre, London, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | | | | | - Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | - Barbara Shih
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Chris Haley
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Paul Klenerman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
- Intensive Care Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | - Hugh Montgomery
- UCL Centre for Human Health and Performance, University College London, London, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Alexandre C Pereira
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Mark Caulfield
- Genomics England, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard Scott
- Genomics England, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust London, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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39
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Dorward DA, Russell CD, Um IH, Elshani M, Armstrong SD, Penrice-Randal R, Millar T, Lerpiniere CEB, Tagliavini G, Hartley CS, Randle NP, Gachanja NN, Potey PMD, Dong X, Anderson AM, Campbell VL, Duguid AJ, Al Qsous W, BouHaidar R, Baillie JK, Dhaliwal K, Wallace WA, Bellamy COC, Prost S, Smith C, Hiscox JA, Harrison DJ, Lucas CD. Tissue-Specific Immunopathology in Fatal COVID-19. Am J Respir Crit Care Med 2021; 203:192-201. [PMID: 33217246 PMCID: PMC7874430 DOI: 10.1164/rccm.202008-3265oc] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [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: 12/15/2022] Open
Abstract
Rationale: In life-threatening coronavirus disease (COVID-19), corticosteroids reduce mortality, suggesting that immune responses have a causal role in death. Whether this deleterious inflammation is primarily a direct reaction to the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or an independent immunopathologic process is unknown. Objectives: To determine SARS-CoV-2 organotropism and organ-specific inflammatory responses and the relationships among viral presence, inflammation, and organ injury. Methods: Tissue was acquired from 11 detailed postmortem examinations. SARS-CoV-2 organotropism was mapped by using multiplex PCR and sequencing, with cellular resolution achieved by in situ viral S (spike) protein detection. Histologic evidence of inflammation was quantified from 37 anatomic sites, and the pulmonary immune response was characterized by using multiplex immunofluorescence. Measurements and Main Results: Multiple aberrant immune responses in fatal COVID-19 were found, principally involving the lung and reticuloendothelial system, and these were not clearly topologically associated with the virus. Inflammation and organ dysfunction did not map to the tissue and cellular distribution of SARS-CoV-2 RNA and protein between or within tissues. An arteritis was identified in the lung, which was further characterized as a monocyte/myeloid-rich vasculitis, and occurred together with an influx of macrophage/monocyte-lineage cells into the pulmonary parenchyma. In addition, stereotyped abnormal reticuloendothelial responses, including excessive reactive plasmacytosis and iron-laden macrophages, were present and dissociated from viral presence in lymphoid tissues. Conclusions: Tissue-specific immunopathology occurs in COVID-19, implicating a significant component of the immune-mediated, virus-independent immunopathologic process as a primary mechanism in severe disease. Our data highlight novel immunopathologic mechanisms and validate ongoing and future efforts to therapeutically target aberrant macrophage and plasma-cell responses as well as promote pathogen tolerance in COVID-19.
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Affiliation(s)
- David A Dorward
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Pathology
| | - Clark D Russell
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Regional Infectious Diseases Unit
| | - In Hwa Um
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Mustafa Elshani
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Stuart D Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tracey Millar
- Centre for Clinical Brain Sciences, Chancellor's Building, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Chris E B Lerpiniere
- Centre for Clinical Brain Sciences, Chancellor's Building, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Giulia Tagliavini
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Catherine S Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nadine P Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Naomi N Gachanja
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Philippe M D Potey
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Wael Al Qsous
- Department of Pathology, Western General Hospital, Edinburgh, United Kingdom
| | | | - J Kenneth Baillie
- Intensive Care Unit, and.,Roslin Institute, Easter Bush Campus, University of Edinburgh, Midlothian, United Kingdom
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Christopher O C Bellamy
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Pathology
| | - Sandrine Prost
- Centre for Inflammation Research, Queen's Medical Research Institute, and
| | - Colin Smith
- Centre for Clinical Brain Sciences, Chancellor's Building, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom.,Department of Pathology
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore; and.,Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, United Kingdom
| | - David J Harrison
- Department of Pathology.,School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Christopher D Lucas
- Centre for Inflammation Research, Queen's Medical Research Institute, and.,Department of Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
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40
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Dolby HW, Potey P, Wilder-Smith AB, Clohisey S, Millar JE, Baillie JK, Dorward DA, Lucas CD, Russell CD. Histological Evidence of Pulmonary Microthrombosis and Vasculitis in Life-Threatening Respiratory Virus Diseases. Open Forum Infect Dis 2021; 8:ofaa640. [PMID: 33553478 PMCID: PMC7798721 DOI: 10.1093/ofid/ofaa640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pulmonary microthrombosis and vasculitis occur in fatal coronavirus disease 2019. To determine whether these processes occur in other life-threatening respiratory virus infections, we identified autopsy studies of fatal influenza (n = 455 patients), severe acute respiratory syndrome ([SARS] n = 37), Middle East respiratory syndrome (n = 2), adenovirus (n = 34), and respiratory syncytial virus (n = 30). Histological evidence of thrombosis was frequently present in adults with fatal influenza and SARS, with vasculitis also reported.
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Affiliation(s)
- Heather W Dolby
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Philippe Potey
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Annika B Wilder-Smith
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Sara Clohisey
- Roslin Institute, Division of Genetics and Genomics, University of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan E Millar
- Roslin Institute, Division of Genetics and Genomics, University of Edinburgh, Edinburgh, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, Division of Genetics and Genomics, University of Edinburgh, Edinburgh, United Kingdom
| | - David A Dorward
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Christopher D Lucas
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
- Roslin Institute, Division of Genetics and Genomics, University of Edinburgh, Edinburgh, United Kingdom
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41
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Parkinson N, Rodgers N, Head Fourman M, Wang B, Zechner M, Swets MC, Millar JE, Law A, Russell CD, Baillie JK, Clohisey S. Dynamic data-driven meta-analysis for prioritisation of host genes implicated in COVID-19. Sci Rep 2020; 10:22303. [PMID: 33339864 PMCID: PMC7749145 DOI: 10.1038/s41598-020-79033-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 09/24/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
The increasing body of literature describing the role of host factors in COVID-19 pathogenesis demonstrates the need to combine diverse, multi-omic data to evaluate and substantiate the most robust evidence and inform development of therapies. Here we present a dynamic ranking of host genes implicated in human betacoronavirus infection (SARS-CoV-2, SARS-CoV, MERS-CoV, seasonal coronaviruses). We conducted an extensive systematic review of experiments identifying potential host factors. Gene lists from diverse sources were integrated using Meta-Analysis by Information Content (MAIC). This previously described algorithm uses data-driven gene list weightings to produce a comprehensive ranked list of implicated host genes. From 32 datasets, the top ranked gene was PPIA, encoding cyclophilin A, a druggable target using cyclosporine. Other highly-ranked genes included proposed prognostic factors (CXCL10, CD4, CD3E) and investigational therapeutic targets (IL1A) for COVID-19. Gene rankings also inform the interpretation of COVID-19 GWAS results, implicating FYCO1 over other nearby genes in a disease-associated locus on chromosome 3. Researchers can search and review the gene rankings and the contribution of different experimental methods to gene rank at https://baillielab.net/maic/covid19 . As new data are published we will regularly update the list of genes as a resource to inform and prioritise future studies.
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Affiliation(s)
- Nicholas Parkinson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Natasha Rodgers
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Max Head Fourman
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Maaike C Swets
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Jonathan E Millar
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Andy Law
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Clark D Russell
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
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42
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Knight SR, Ho A, Pius R, Buchan I, Carson G, Drake TM, Dunning J, Fairfield CJ, Gamble C, Green CA, Gupta R, Halpin S, Hardwick HE, Holden KA, Horby PW, Jackson C, Mclean KA, Merson L, Nguyen-Van-Tam JS, Norman L, Noursadeghi M, Olliaro PL, Pritchard MG, Russell CD, Shaw CA, Sheikh A, Solomon T, Sudlow C, Swann OV, Turtle LC, Openshaw PJ, Baillie JK, Semple MG, Docherty AB, Harrison EM. Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score. BMJ 2020; 370:m3339. [PMID: 32907855 PMCID: PMC7116472 DOI: 10.1136/bmj.m3339] [Citation(s) in RCA: 601] [Impact Index Per Article: 150.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19). DESIGN Prospective observational cohort study. SETTING International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020. PARTICIPANTS: Adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction. MAIN OUTCOME MEASURE In-hospital mortality. RESULTS 35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73). CONCLUSIONS An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations. STUDY REGISTRATION ISRCTN66726260.
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Affiliation(s)
- Stephen R Knight
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Antonia Ho
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
- Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Riinu Pius
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Iain Buchan
- Institute of Population Health Sciences, University of Liverpool, Liverpool, UK
| | - Gail Carson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas M Drake
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Jake Dunning
- National Infection Service, Public Health England, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Carrol Gamble
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Christopher A Green
- Institute of Microbiology & Infection, University of Birmingham, Birmingham, UK
| | - Rishi Gupta
- Institute of Global Health, University College London, London, UK
| | - Sophie Halpin
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Karl A Holden
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Peter W Horby
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clare Jackson
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Kenneth A Mclean
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Laura Merson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
| | - Lisa Norman
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Piero L Olliaro
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark G Pritchard
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clark D Russell
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Catherine A Shaw
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Aziz Sheikh
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Tom Solomon
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Walton Centre NHS Foundation Trust, Liverpool, UK
| | | | - Olivia V Swann
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Lance Cw Turtle
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital, Liverpool, UK
| | - Peter Jm Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
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Bulteel NS, Russell CD, Perry MR, Koch O. Successful reintroduction of tumour necrosis factor-alpha inhibition after treatment of disseminated Lyme borreliosis. J R Coll Physicians Edinb 2020; 49:122-124. [PMID: 31188340 DOI: 10.4997/jrcpe.2019.207] [Citation(s) in RCA: 2] [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: 11/19/2022] Open
Abstract
The importance of tumour necrosis factor-alpha (TNF-α) in the human immune response to Borrelia burgdorferi is uncertain. Murine models suggest a critical role, including spirochaete reactivation following TNF-α inhibition. Our case, combined with a review of the clinical and scientific literature, provides reassurance that TNF-α inhibition can be safely reinstituted after treatment of disseminated borreliosis with standard duration antimicrobial chemotherapy.
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Affiliation(s)
- Naomi S Bulteel
- Regional Infectious Diseases Unit, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK,
| | - Clark D Russell
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, Scotland.,MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, Scotland
| | - Meghan R Perry
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, Scotland.,Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, Scotland
| | - Oliver Koch
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, Scotland
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Watson K, Russell CD, Baillie JK, Dhaliwal K, Fitzgerald JR, Mitchell TJ, Simpson AJ, Renshaw SA, Dockrell DH. Developing Novel Host-Based Therapies Targeting Microbicidal Responses in Macrophages and Neutrophils to Combat Bacterial Antimicrobial Resistance. Front Immunol 2020; 11:786. [PMID: 32582139 PMCID: PMC7289984 DOI: 10.3389/fimmu.2020.00786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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] [Received: 02/14/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial therapy has provided the main component of chemotherapy against bacterial pathogens. The effectiveness of this strategy has, however, been increasingly challenged by the emergence of antimicrobial resistance which now threatens the sustained utility of this approach. Humans and animals are constantly exposed to bacteria and have developed effective strategies to control pathogens involving innate and adaptive immune responses. Impaired pathogen handling by the innate immune system is a key determinant of susceptibility to bacterial infection. However, the essential components of this response, specifically those which are amenable to re-calibration to improve host defense, remain elusive despite extensive research. We provide a mini-review focusing on therapeutic targeting of microbicidal responses in macrophages and neutrophils to de-stress reliance on antimicrobial therapy. We highlight pre-clinical and clinical data pointing toward potential targets and therapies. We suggest that developing focused host-directed therapeutic strategies to enhance "pauci-inflammatory" microbial killing in myeloid phagocytes that maximizes pathogen clearance while minimizing the harmful consequences of the inflammatory response merits particular attention. We also suggest the importance of One Health approaches in developing host-based approaches through model development and comparative medicine in informing our understanding of how to deliver this strategy.
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Affiliation(s)
- Katie Watson
- Department of Infection Medicine, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Clark D Russell
- Department of Infection Medicine, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom.,Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kev Dhaliwal
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - J Ross Fitzgerald
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Timothy J Mitchell
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - A John Simpson
- Institute of Cellular Medicine, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Stephen A Renshaw
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, United Kingdom
| | - David H Dockrell
- Department of Infection Medicine, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
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Docherty AB, Harrison EM, Green CA, Hardwick HE, Pius R, Norman L, Holden KA, Read JM, Dondelinger F, Carson G, Merson L, Lee J, Plotkin D, Sigfrid L, Halpin S, Jackson C, Gamble C, Horby PW, Nguyen-Van-Tam JS, Ho A, Russell CD, Dunning J, Openshaw PJ, Baillie JK, Semple MG. Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study. BMJ 2020; 369:m1985. [PMID: 32444460 PMCID: PMC7243036 DOI: 10.1136/bmj.m1985] [Citation(s) in RCA: 1924] [Impact Index Per Article: 481.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To characterise the clinical features of patients admitted to hospital with coronavirus disease 2019 (covid-19) in the United Kingdom during the growth phase of the first wave of this outbreak who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study, and to explore risk factors associated with mortality in hospital. DESIGN Prospective observational cohort study with rapid data gathering and near real time analysis. SETTING 208 acute care hospitals in England, Wales, and Scotland between 6 February and 19 April 2020. A case report form developed by ISARIC and WHO was used to collect clinical data. A minimal follow-up time of two weeks (to 3 May 2020) allowed most patients to complete their hospital admission. PARTICIPANTS 20 133 hospital inpatients with covid-19. MAIN OUTCOME MEASURES Admission to critical care (high dependency unit or intensive care unit) and mortality in hospital. RESULTS The median age of patients admitted to hospital with covid-19, or with a diagnosis of covid-19 made in hospital, was 73 years (interquartile range 58-82, range 0-104). More men were admitted than women (men 60%, n=12 068; women 40%, n=8065). The median duration of symptoms before admission was 4 days (interquartile range 1-8). The commonest comorbidities were chronic cardiac disease (31%, 5469/17 702), uncomplicated diabetes (21%, 3650/17 599), non-asthmatic chronic pulmonary disease (18%, 3128/17 634), and chronic kidney disease (16%, 2830/17 506); 23% (4161/18 525) had no reported major comorbidity. Overall, 41% (8199/20 133) of patients were discharged alive, 26% (5165/20 133) died, and 34% (6769/20 133) continued to receive care at the reporting date. 17% (3001/18 183) required admission to high dependency or intensive care units; of these, 28% (826/3001) were discharged alive, 32% (958/3001) died, and 41% (1217/3001) continued to receive care at the reporting date. Of those receiving mechanical ventilation, 17% (276/1658) were discharged alive, 37% (618/1658) died, and 46% (764/1658) remained in hospital. Increasing age, male sex, and comorbidities including chronic cardiac disease, non-asthmatic chronic pulmonary disease, chronic kidney disease, liver disease and obesity were associated with higher mortality in hospital. CONCLUSIONS ISARIC WHO CCP-UK is a large prospective cohort study of patients in hospital with covid-19. The study continues to enrol at the time of this report. In study participants, mortality was high, independent risk factors were increasing age, male sex, and chronic comorbidity, including obesity. This study has shown the importance of pandemic preparedness and the need to maintain readiness to launch research studies in response to outbreaks. STUDY REGISTRATION ISRCTN66726260.
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Affiliation(s)
- Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Christopher A Green
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Hayley E Hardwick
- National Institute of Health Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Riinu Pius
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Lisa Norman
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Karl A Holden
- Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jonathan M Read
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Bailrigg, UK
| | - Frank Dondelinger
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Bailrigg, UK
| | - Gail Carson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Merson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - James Lee
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Plotkin
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Louise Sigfrid
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Halpin
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Clare Jackson
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Carrol Gamble
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Peter W Horby
- Centre for Tropical Medicine and International Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
| | - Antonia Ho
- Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Clark D Russell
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jake Dunning
- National Infection Service, Public Health England, London, UK
- Faculty of Medicine, Imperial College London, London, UK
| | - Peter Jm Openshaw
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - J Kenneth Baillie
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
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Russell CD, Tsang STJ, Simpson AHRW, Sutherland RK. Outcomes, Microbiology and Antimicrobial Usage in Pressure Ulcer-Related Pelvic Osteomyelitis: Messages for Clinical Practice. J Bone Jt Infect 2020; 5:67-75. [PMID: 32455097 PMCID: PMC7242403 DOI: 10.7150/jbji.41779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/04/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022] Open
Abstract
Introduction: Pressure ulcer-related pelvic osteomyelitis is a relatively under-studied entity in the field of bone infection. We sought to add to the limited evidence base for managing this challenging syndrome. Methods: Cases were identified retrospectively from a surgical database and hospital discharge codes at a U.K. tertiary centre (2009-2018). Risk factors associated with outcomes were analysed by logistic regression. Results: We identified 35 patients (mean age 57.4 years), 69% managed with a combined medical and surgical approach, with mean follow-up of 3.7 years from index admission. Treatment failure (requiring further surgery or intravenous antimicrobials) occurred in 71% and eventual ulcer healing in 36%. One-year mortality was 23%. Lack of formal care support on discharge, post-traumatic (asensate) neurological deficit and index CRP (>184mg/L) were associated with treatment failure (p=0.001). Age (>59.5 years), lack of attempted soft tissue coverage, haemoglobin (<111g/L) and albumin (<25g/L) were associated with non-healing ulcers (p=0.003). Superficial wound swabs had low sensitivity and specificity compared to deep bone microbiology. Infection (based on deep bone microbiology from 46 infection episodes) was usually polymicrobial (87%), commonly involving S. aureus, Enterococci, GNB and anaerobes. Antimicrobial duration ranged from 0-103 days (mean 54) and was not associated with subsequent treatment failure. Conclusions: Attempted soft tissue coverage after surgical debridement, ensuring appropriate support for personal care after discharge and nutritional optimisation could improve outcomes. Superficial wound swabs are uninformative and deep bone sampling should be pursued. Long antimicrobial courses do not improve outcomes. Clinicians should engage patients in anticipatory care planning.
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Affiliation(s)
- Clark D Russell
- NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, U.K.,University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, U.K
| | - Shao-Ting Jerry Tsang
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, U.K.,Department of Orthopaedic Surgery, University of Edinburgh, Chancellor's Building, Edinburgh, U.K
| | | | - Rebecca K Sutherland
- NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, U.K
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Hill KJ, Russell CD, Clifford S, Templeton K, Mackintosh CL, Koch O, Sutherland RK. The index case of SARS-CoV-2 in Scotland. J Infect 2020; 81:147-178. [PMID: 32205138 PMCID: PMC7118628 DOI: 10.1016/j.jinf.2020.03.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 03/14/2020] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 01/22/2023]
Abstract
Since its identification in December 2019, SARS-CoV-2 has infected 125,048 persons globally with cases identified in 118 countries across all continents. We report on the Scottish index case of SARS-CoV-2 infection, the virus causing COVID-19.
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Affiliation(s)
- Katherine J Hill
- NHS Lothian, Regional Infectious Diseases Unit, Edinburgh, EH4 2XU.
| | - Clark D Russell
- NHS Lothian, Regional Infectious Diseases Unit, Edinburgh, EH4 2XU; University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh EH16 4TJ
| | - Sarah Clifford
- NHS Lothian, Regional Infectious Diseases Unit, Edinburgh, EH4 2XU
| | - Kate Templeton
- NHS Lothian, Diagnostic Virology Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, EH16 4TJ
| | | | - Oliver Koch
- NHS Lothian, Regional Infectious Diseases Unit, Edinburgh, EH4 2XU
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48
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Affiliation(s)
- Clark D Russell
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute Edinburgh, Edinburgh, UK
| | - Jonathan E Millar
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK.
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49
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Cevik M, Russell CD, Ong DSY. Challenges of Interpreting Cytomegalovirus DNAemia and Its Potential Association With Chronic Lung Disease in Children and Adolescents With Perinatally Acquired Human Immunodeficiency Virus Infection. Clin Infect Dis 2020; 70:989-990. [PMID: 31247099 DOI: 10.1093/cid/ciz521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St Andrews.,Regional Infectious Diseases Unit, Western General Hospital, NHS Lothian.,Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Clark D Russell
- Regional Infectious Diseases Unit, Western General Hospital, NHS Lothian.,University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, United Kingdom
| | - David S Y Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam.,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
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50
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Russell CD, Jones ME, O'Shea DT, Simpson KJ, Mitchell A, Laurenson IF. Challenges in the diagnosis of leptospirosis outwith endemic settings: a Scottish single centre experience. J R Coll Physicians Edinb 2019; 48:9-15. [PMID: 29741518 DOI: 10.4997/jrcpe.2018.102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Leptospirosis is a zoonotic infection occurring worldwide but endemic in tropical countries. This study describes diagnostic testing for leptospirosis at our institution in Scotland over a 10-year period. Method We identified patients with blood samples referred to the Public Health England reference laboratory for leptospirosis testing between 2006 and 2016. Results A total of 480 samples were sent for IgM ELISA testing with 26 positive results from 14 patients. Two patients met criteria for 'confirmed' leptospirosis (microscopic agglutination test > 1:320 in one case and a positive PCR in the other) and the remaining 12 were 'probable' on the basis of IgM ELISA positivity, though 9 did not have microscopic agglutination testing performed. Nine infections were imported, mostly from Asia and with a history of fresh water exposure. Three co-infections (respiratory syncytial virus, influenza B and Campylobacter sp.) were identified. Conclusions Practical issues with microscopic agglutination testing (insufficient blood sent to reference laboratory) and PCR (travellers returning > 7 days after illness onset) represent challenges to the laboratory confirmation of a clinical diagnosis of leptospirosis. Co-infection and infectious/auto-immune causes of false positive serology should be evaluated.
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Affiliation(s)
- C D Russell
- CD Russell, Regional Infectious, Diseases Unit, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK,
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