The Lancet: Digital Health (Sep 2023)
Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium
- David Shaw, MBBCh,
- Raquel Abad, PhD,
- Zahin Amin-Chowdhury, MSc,
- Adriana Bautista, MSc,
- Desiree Bennett, PhD,
- Karen Broughton, MSc,
- Bin Cao, ProfMD,
- Carlo Casanova, PhD,
- Eun Hwa Choi, ProfMD,
- Yiu-Wai Chu, PhD,
- Heike Claus, PhD,
- Juliana Coelho, PhD,
- Mary Corcoran, PhD,
- Simon Cottrell, PhD,
- Robert Cunney, MB,
- Lize Cuypers, PhD,
- Tine Dalby, PhD,
- Heather Davies, NZCS,
- Linda de Gouveia, NatDipMedTech,
- Ala-Eddine Deghmane, PhD,
- Walter Demczuk, BSc,
- Stefanie Desmet, PhD,
- Mirian Domenech, PhD,
- Richard Drew, MD,
- Mignon du Plessis, PhD,
- Carolina Duarte, PhD,
- Helga Erlendsdóttir, ProfMSc,
- Norman K Fry, PhD,
- Kurt Fuursted, MD,
- Thomas Hale, ProfPhD,
- Desiree Henares, PhD,
- Birgitta Henriques-Normark, ProfMD,
- Markus Hilty, PhD,
- Steen Hoffmann, MD,
- Hilary Humphreys, ProfMD,
- Margaret Ip, ProfMSc,
- Susanne Jacobsson, PhD,
- Christopher Johnson, PhD,
- Jillian Johnston, MBBS,
- Keith A Jolley, PhD,
- Aníbal Kawabata,
- Jana Kozakova, MD,
- Karl G Kristinsson, ProfMD,
- Pavla Krizova, MD,
- Alicja Kuch, PhD,
- Shamez Ladhani, MD,
- Thiên-Trí Lâm, MD,
- María Eugenia León, MSc,
- Laura Lindholm, MSc,
- David Litt, PhD,
- Martin C J Maiden, ProfPhD,
- Irene Martin, BSc,
- Delphine Martiny, ProfPhD,
- Wesley Mattheus, PhD,
- Noel D McCarthy, ProfDPhil,
- Mary Meehan, PhD,
- Susan Meiring, MBChB,
- Paula Mölling, PhD,
- Eva Morfeldt, PhD,
- Julie Morgan, HND,
- Robert Mulhall, PhD,
- Carmen Muñoz-Almagro, ProfMD,
- David Murdoch, ProfMD,
- Joy Murphy, BA Hons,
- Martin Musilek, PhD,
- Alexandre Mzabi, MD,
- Ludmila Novakova, MSc,
- Shahin Oftadeh, PhD,
- Amaresh Perez-Argüello, MLT,
- Maria Pérez-Vázquez, PhD,
- Monique Perrin, MD,
- Malorie Perry, MSc,
- Benoit Prevost, PhD,
- Maria Roberts, BSc(Hons),
- Assaf Rokney, PhD,
- Merav Ron, PhD,
- Olga Marina Sanabria, MPH,
- Kevin J Scott, PhD,
- Carmen Sheppard, PhD,
- Lotta Siira, PhD,
- Vitali Sintchenko, ProfPhD,
- Anna Skoczyńska, ProfPhD,
- Monica Sloan,
- Hans-Christian Slotved, DMSc,
- Andrew J Smith, ProfFRCPath,
- Anneke Steens, PhD,
- Muhamed-Kheir Taha, ProfMD,
- Maija Toropainen, PhD,
- Georgina Tzanakaki, ProfPhD,
- Anni Vainio, PhD,
- Mark P G van der Linden, PhD,
- Nina M van Sorge, ProfPhD,
- Emmanuelle Varon, MD,
- Sandra Vohrnova, MD,
- Anne von Gottberg, ProfPhD,
- Jose Yuste, PhD,
- Rosemeire Zanella, PhD,
- Fei Zhou, PhD,
- Angela B Brueggemann, ProfDPhil
Affiliations
- David Shaw, MBBCh
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
- Raquel Abad, PhD
- National Reference Laboratory for Meningococci, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Zahin Amin-Chowdhury, MSc
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
- Adriana Bautista, MSc
- Instituto Nacional de Salud, Bogotá, Colombia
- Desiree Bennett, PhD
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
- Karen Broughton, MSc
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
- Bin Cao, ProfMD
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Carlo Casanova, PhD
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Eun Hwa Choi, ProfMD
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
- Yiu-Wai Chu, PhD
- Department of Health, Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Hong Kong Special Administrative Region, China
- Heike Claus, PhD
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
- Juliana Coelho, PhD
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
- Mary Corcoran, PhD
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
- Simon Cottrell, PhD
- Public Health Wales, Cardiff, Wales, UK
- Robert Cunney, MB
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
- Lize Cuypers, PhD
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Tine Dalby, PhD
- Statens Serum Institut, Department of Infectious Disease Epidemiology & Prevention, Copenhagen, Denmark
- Heather Davies, NZCS
- Meningococcal Reference Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
- Linda de Gouveia, NatDipMedTech
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Ala-Eddine Deghmane, PhD
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
- Walter Demczuk, BSc
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Stefanie Desmet, PhD
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Mirian Domenech, PhD
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
- Richard Drew, MD
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Clinical Innovation Unit, Rotunda, Dublin, Ireland
- Mignon du Plessis, PhD
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Carolina Duarte, PhD
- Instituto Nacional de Salud, Bogotá, Colombia
- Helga Erlendsdóttir, ProfMSc
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
- Norman K Fry, PhD
- Immunisation and Vaccine Preventable Diseases Division and Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
- Kurt Fuursted, MD
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
- Thomas Hale, ProfPhD
- Blavatnik School of Government, University of Oxford, Oxford, UK
- Desiree Henares, PhD
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
- Birgitta Henriques-Normark, ProfMD
- Karolinska Institutet, Karolinska University Hospital, Public Health Agency of Sweden, Stockholm, Sweden
- Markus Hilty, PhD
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Steen Hoffmann, MD
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
- Hilary Humphreys, ProfMD
- Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
- Margaret Ip, ProfMSc
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Susanne Jacobsson, PhD
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Christopher Johnson, PhD
- Public Health Wales, Cardiff, Wales, UK
- Jillian Johnston, MBBS
- Public Health Agency, Belfast, UK
- Keith A Jolley, PhD
- Department of Biology, University of Oxford, Oxford, UK
- Aníbal Kawabata
- Laboratorio Central de Salud Pública, Asunción, Paraguay
- Jana Kozakova, MD
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Karl G Kristinsson, ProfMD
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
- Pavla Krizova, MD
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Alicja Kuch, PhD
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
- Shamez Ladhani, MD
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
- Thiên-Trí Lâm, MD
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
- María Eugenia León, MSc
- Laboratorio Central de Salud Pública, Asunción, Paraguay
- Laura Lindholm, MSc
- Finnish Institute for Health and Welfare, Helsinki, Finland
- David Litt, PhD
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
- Martin C J Maiden, ProfPhD
- Department of Biology, University of Oxford, Oxford, UK
- Irene Martin, BSc
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Delphine Martiny, ProfPhD
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium; Faculty of Medicine and Pharmacy, University of Mons, Mons, Belgium
- Wesley Mattheus, PhD
- Meningococcal National Reference Centre, Sciensano, Belgium
- Noel D McCarthy, ProfDPhil
- Population Health Medicine, Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
- Mary Meehan, PhD
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
- Susan Meiring, MBChB
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Paula Mölling, PhD
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Eva Morfeldt, PhD
- Public Health Agency of Sweden, Solna, Sweden
- Julie Morgan, HND
- Streptococcal Reference Laboratory, Institute of Environmental Science and Research Limited, Porirua, New Zealand
- Robert Mulhall, PhD
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
- Carmen Muñoz-Almagro, ProfMD
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain; Medicine Department, Universitat Internacional de Catalunya, Barcelona, Spain
- David Murdoch, ProfMD
- University of Otago, Christchurch, New Zealand
- Joy Murphy, BA Hons
- Public Health Agency, Belfast, UK
- Martin Musilek, PhD
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Alexandre Mzabi, MD
- Ministère de la Santé - Direction de la santé, Luxembourg, Luxembourg
- Ludmila Novakova, MSc
- National Reference Laboratory for Haemophilus Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Shahin Oftadeh, PhD
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia
- Amaresh Perez-Argüello, MLT
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain
- Maria Pérez-Vázquez, PhD
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Monique Perrin, MD
- Laboratoire National de Sante, Dudelange, Luxembourg
- Malorie Perry, MSc
- Public Health Wales, Cardiff, Wales, UK
- Benoit Prevost, PhD
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium
- Maria Roberts, BSc(Hons)
- Public Health Wales, Cardiff, Wales, UK
- Assaf Rokney, PhD
- Public Health Laboratories–Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
- Merav Ron, PhD
- Public Health Laboratories–Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
- Olga Marina Sanabria, MPH
- Instituto Nacional de Salud, Bogotá, Colombia
- Kevin J Scott, PhD
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
- Carmen Sheppard, PhD
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
- Lotta Siira, PhD
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Vitali Sintchenko, ProfPhD
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia; Sydney Institute for Infectious Diseases, University of Sydney, NSW, Australia
- Anna Skoczyńska, ProfPhD
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
- Monica Sloan
- Public Health Agency, Belfast, UK
- Hans-Christian Slotved, DMSc
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
- Andrew J Smith, ProfFRCPath
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK; College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
- Anneke Steens, PhD
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Muhamed-Kheir Taha, ProfMD
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
- Maija Toropainen, PhD
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Georgina Tzanakaki, ProfPhD
- National Meningitis Reference Laboratory, Department of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
- Anni Vainio, PhD
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Mark P G van der Linden, PhD
- Department of Medical Microbiology, German National Reference Centre for Streptococci, University Hospital RWTH Aachen, Aachen, Germany
- Nina M van Sorge, ProfPhD
- Department of Medical Microbiology and Infection Prevention, and Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Emmanuelle Varon, MD
- Laboratory of Medical Biology and National Reference Centre for Pneumococci, Intercommunal Hospital of Créteil, Créteil, France
- Sandra Vohrnova, MD
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Anne von Gottberg, ProfPhD
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Jose Yuste, PhD
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
- Rosemeire Zanella, PhD
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz, São Paulo, Brazil
- Fei Zhou, PhD
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Angela B Brueggemann, ProfDPhil
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK; Correspondence to: Professor Angela Brueggemann, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- Journal volume & issue
-
Vol. 5,
no. 9
pp. e582 – e593
Abstract
Summary: Background: The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. Methods: For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. Findings: Overall, 116 841 cases were analysed: 76 481 in 2018–19, before the pandemic, and 40 360 in 2020–21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40–0·55), H influenzae (0·51; 0·40–0·66) and N meningitidis (0·26; 0·21–0·31), while no significant changes were observed for S agalactiae (1·02; 0·75–1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145–55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. Interpretation: COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. Funding: Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.
