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1. An early warning system for emerging SARS-CoV-2 variants

Author

Lorenzo Subissi, Anne von Gottberg, Lipi Thukral, Nathalie Worp, Bas B. Oude Munnink, Surabhi Rathore, Laith J. Abu-Raddad, Ximena Aguilera, Erik Alm, Brett N. Archer, Homa Attar Cohen, Amal Barakat, Wendy S. Barclay, Jinal N. Bhiman, Leon Caly, Meera Chand, Mark Chen, Ann Cullinane, Tulio de Oliveira, Christian Drosten, Julian Druce, Paul Effler, Ihab El Masry, Adama Faye, Simani Gaseitsiwe, Elodie Ghedin, Rebecca Grant, Bart L. Haagmans, Belinda L. Herring, Shilpa S. Iyer, Zyleen Kassamali, Manish Kakkar, Rebecca J. Kondor, Juliana A. Leite, Yee-Sin Leo, Gabriel M. Leung, Marco Marklewitz, Sikhulile Moyo, Jairo Mendez-Rico, Nada M. Melhem, Vincent Munster, Karen Nahapetyan, Djin-Ye Oh, Boris I. Pavlin, Thomas P. Peacock, Malik Peiris, Zhibin Peng, Leo L. M. Poon, Andrew Rambaut, Jilian Sacks, Yinzhong Shen, Marilda M. Siqueira, Sofonias K. Tessema, Erik M. Volz, Volker Thiel, Sylvie van der Werf, Sylvie Briand, Mark D. Perkins, Maria D. Van Kerkhove, Marion P. G. Koopmans, Anurag Agrawal, World Health Organisation (WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), National Institute for Communicable Diseases [Johannesburg] (NICD), University of the Witwatersrand [Johannesburg] (WITS), Central Scientific Instruments Organisation (CSIR), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Weill Cornell Medicine [Qatar], Universidad del Desarollo [Santiago, Chile] (UDD), European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), Imperial College London, Victorian Infectious Diseases Reference Laboratory [Melbourne, Australia] (VIDRL), UK Health Security Agency [London] (UKHSA), World Organisation for Animal Health (WOAH), Stellenbosch University, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], German Center for Infection Research, Partnersite Munich (DZIF), The University of Western Australia (UWA), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Botswana Harvard AIDS Institute Partnership, Harvard T.H. Chan School of Public Health, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), World Health Organization [Kinshasa, Democratic Republic of Congo] (WHO-DRC), United States Centers for Disease Control and Prevention, The University of Hong Kong (HKU), American University of Beirut [Beyrouth] (AUB), Robert Koch Institute [Berlin] (RKI), Chinese Center for Disease Control and Prevention, University of Edinburgh, Fudan University [Shanghai], Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centers for Disease Control and Prevention [Pretoria, South Africa] (CDC-South Africa), Centers for Disease Control and Prevention (CDC), University of Bern, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Ashoka University, We acknowledge scientists, public health professionals and Ministries of Health across the world for early generation and sharing of data on SARS-CoV-2 variants., and Virology

Subjects
630 Agriculture, SARS-CoV-2, [SDV]Life Sciences [q-bio], COVID-19, Humans, General Medicine, General Biochemistry, Genetics and Molecular Biology
Abstract

International audience

Published
2022
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2. Rapidly adapting primary care sentinel surveillance across seven countries in Europe for COVID-19 in the first half of 2020: strengths, challenges, and lessons learned

Author

Bagaria, Jayshree, Jansen, Tessa, Marques, Diogo Fp, Hooiveld, Mariette, McMenamin, Jim, de Lusignan, Simon, Vilcu, Ana-Maria, Meijer, Adam, Rodrigues, Ana-Paula, Brytting, Mia, Mazagatos, Clara, Cogdale, Jade, van der Werf, Sylvie, Dijkstra, Frederika, Guiomar, Raquel, Enkirch, Theresa, Valenciano, Marta, I-MOVE-COVID-19 study team, Larrauri, Amparo, Pozo Sanchez, Francisco, Casas Flecha, Inmaculada, Unión Europea. Comisión Europea. H2020, Public Health Scotland [Glasgow], Netherlands Institute for Health Services Research [Utrecht] (NIVEL), EpiConcept [Paris], University of Oxford, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] (INSA), Public Health Agency of Sweden, Institute of Health Carlos III, UK Health Security Agency (UKHSA), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101003673., MOVE-COVID-19 study team: Esther Kissling, Lisa Domegan, Joan O'Donnell, Josephine Murray, Virginia Sandonis Martín, Iván Martínez-Baz, Ausenda Machado, Itziar Casado, Sylvie Behillil, Amparo Larrauri, Ruby Tsang, Marit de Lange, Maximilian Riess, Jesús Castilla, Mark Hamilton, Alessandra Falchi, Francisco Pozo, Linda Dunford, Cristina Burgui, Debbie Sigerson, Thierry Blanchon, Eva María Martínez Ochoa, Jeff Connell, Joanna Ellis, Rianne van Gageldonk-Lafeber, Irina Kislaya, Angela Mc Rose, Jamie Lopez Bernal, Nick Andrews, Inmaculada Casas Flecha, Janine Thoulass, Baltazar Nunes, Verónica Gomez, Rita Sa Machado, Vincent Enouf, Pedro Licinio Pinto Leite, Anna Molesworth, Adele McKenna, Janine Thoulass, European Project: 101003673,H2020-SC1-PHE-CORONAVIRUS-2020,I-MOVE-COVID-19(2020), HAL-SU, Gestionnaire, Multidisciplinary European network for research, prevention and control of the COVID-19 Pandemic - I-MOVE-COVID-19 - - H2020-SC1-PHE-CORONAVIRUS-20202020-03-16 - 2022-06-15 - 101003673 - VALID, UK Health Security Agency [London] (UKHSA), and Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur)

Subjects
Epidemiology, Sentinel surveillance, primary care, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Influenza, Human, Humans, Influenza-Like Illness, Pandemics, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Primary Health Care, SARS-CoV-2, Cuidados de Saúde, Public Health, Environmental and Occupational Health, Influenza-Like Illness (ILI), COVID-19, Estados de Saúde e de Doença, Primary care, Europe, Vigilância Epidemiológica, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Influenza Vaccines, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Sentinel Surveillance
Abstract

I-MOVE-COVID-19 study team: Esther Kissling, Lisa Domegan, Joan O’Donnell, Josephine Murray, Virginia Sandonis Martín, Iván Martínez-Baz, Ausenda Machado, Itziar Casado, Sylvie Behillil, Amparo Larrauri, Ruby Tsang, Marit de Lange, Maximilian Riess, Jesús Castilla, Mark Hamilton, Alessandra Falchi, Francisco Pozo, Linda Dunford, Cristina Burgui, Debbie Sigerson, Thierry Blanchon, Eva María Martínez Ochoa, Jeff Connell, Joanna Ellis, Rianne van Gageldonk-Lafeber, Irina Kislaya, Angela MC Rose, Jamie Lopez Bernal, Nick Andrews, Inmaculada Casas Flecha, Janine Thoulass, Baltazar Nunes, Verónica Gomez, Rita Sa Machado, Vincent Enouf, Pedro Licinio Pinto Leite, Anna Molesworth, Adele McKenna, Janine Thoulass As the COVID-19 pandemic began in early 2020, primary care influenza sentinel surveillance networks within the Influenza - Monitoring Vaccine Effectiveness in Europe (I-MOVE) consortium rapidly adapted to COVID-19 surveillance. This study maps system adaptations and lessons learned about aligning influenza and COVID-19 surveillance following ECDC / WHO/Europe recommendations and preparing for other diseases possibly emerging in the future. Using a qualitative approach, we describe the adaptations of seven sentinel sites in five European Union countries and the United Kingdom during the first pandemic phase (March–September 2020). Adaptations to sentinel systems were substantial (2/7 sites), moderate (2/7) or minor (3/7 sites). Most adaptations encompassed patient referral and sample collection pathways, laboratory testing and data collection. Strengths included established networks of primary care providers, highly qualified testing laboratories and stakeholder commitments. One challenge was the decreasing number of samples due to altered patient pathways. Lessons learned included flexibility establishing new routines and new laboratory testing. To enable simultaneous sentinel surveillance of influenza and COVID-19, experiences of the sentinel sites and testing infrastructure should be considered. The contradicting aims of rapid case finding and contact tracing, which are needed for control during a pandemic and regular surveillance, should be carefully balanced. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101003673. info:eu-repo/semantics/publishedVersion

Published
2022
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3. Effectiveness of complete primary vaccination against COVID-19 at primary care and community level during predominant Delta circulation in Europe: multicentre analysis, I-MOVE-COVID-19 and ECDC networks, July to August 2021

Author

Kissling, Esther, Hooiveld, Mariëtte, Martínez-Baz, Iván, Mazagatos, Clara, William, Naoma, Vilcu, Ana-Maria, Kooijman, Marjolein N, Ilić, Maja, Domegan, Lisa, Machado, Ausenda, de Lusignan, Simon, Lazar, Mihaela, Meijer, Adam, Brytting, Mia, Casado, Itziar, Larrauri, Amparo, Murray, Josephine-L K, Behillil, Sylvie, de Gier, Brechje, Mlinarić, Ivan, O'Donnell, Joan, Rodrigues, Ana Paula, Tsang, Ruby, Timnea, Olivia, de Lange, Marit, Riess, Maximilian, Castilla, Jesús, Pozo Sanchez, Francisco, Hamilton, Mark, Falchi, Alessandra, Knol, Mirjam J, Kurečić Filipović, Sanja, Dunford, Linda, Guiomar, Raquel, Cogdale, Jade, Cherciu, Carmen, Jansen, Tessa, Enkirch, Theresa, Basile, Luca, Connell, Jeff, Gomez, Verónica, Sandonis-Martin, Virginia, Bacci, Sabrina, Rose, Angela Mc, Pastore Celentano, Lucia, Valenciano, Marta, I-MOVE-COVID-19, ECDC primary care study teams, Conde-San Román, Patricia, Casas Flecha, Inmaculada, Oliva Dominguez, Jesus Angel, Delgado-Sanz, Concepcion, EpiConcept [Paris], Netherlands Institute for Health Services Research [Utrecht] (NIVEL), Navarra Institute for Health Research / Instituto de Investigación Sanitaria de Navarra (IdiSNA), Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA)-Universidad de Navarra [Pamplona] (UNAV)-Clínica Universidad de Navarra [Pamplona], CIBER de Epidemiología y Salud Pública (CIBERESP), Institute of Health Carlos III, Public Health Scotland [Glasgow], Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Croatian Institute of Public Health [Zagreb] (CIPH), Health Service Executive [Dublin] (HSE), Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] (INSA), University of Oxford, Cantacuzino Institute [Romania], Réseau International des Instituts Pasteur (RIIP), Public Health Agency of Sweden, Instituto de Salud Carlos III [Madrid] (ISC), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Biologie des ARN et virus influenza - RNA Biology of Influenza Virus (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University College Dublin [Dublin] (UCD), UK Health Security Agency [London] (UKHSA), European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), I-MOVE-COVID-19 and ECDC primary care study team Katica Čusek Adamić, Ivana Ferenčak, Bernard Kaić, Mirjana Lana Kosanović Ličina, Danijela Lakošeljac, Ivana Mihin Huskić, Diana Nonković, Nick Andrews, Jamie Lopez Bernal, Joanna Ellis, Heather Whitaker, Thierry Blanchon, Caroline Guerrisi, Titouan Launay, Shirley Masse, Sylvie van der Werf, Vincent Enouf, John Cuddihy, Lois O'Connor, Adele McKenna, Michael Joyce, Cillian de Gascun, Joanne Moran, Rianne van Gageldonk-Lafeber, Susan J Hahné, Hester E de Melker, Ewout B Fanoy, Stijn Raven, Marit Middeldorp, Irina Kislaya, Baltazar Nunes, Rita Roquete, Adriana Silva, Aryse Melo, Inês Costa, Nuno Verdasca, Patrícia Conde, Amélia Soeiro, Maria Elena Mihai, Iulia Bistriceanu, Alina Ivanciuc, Diana Dintoi, Catalina Pascu, Adrian Jidovu, Debbie Sigerson, Diogo Fp Marques, Anna Molesworth, Leanne Quinn, Miranda Leyton, Selin Campbell, Janine Thoulass, Jim McMenamin, Inmaculada Casas Flecha, Ana Martínez Mateo, Daniel Castrillejo, Eva María Martínez Ochoa, Carmen Quiñones Rubio, Concepción Delgado-Sanz, Jesús Oliva, Ana Miqueleiz, Ana Navascués, Camino Trobajo-Sanmartín, Carmen Ezpeleta, Paula López Moreno, Javier Gorricho, Eva Ardanaz, Fernando Baigorria, Aurelio Barricarte, Cristina Burgui, Enrique de la Cruz, Nerea Egüés, Manuel García Cenoz, Marcela Guevara, Conchi Moreno-Iribas, Carmen Sayón, Pasi Penttinen, Christiana Carstairs, University of St Andrews. School of Medicine, Unión Europea. Comisión Europea. H2020, and European Centre for Disease Prevention and Control

Subjects
Test-negative design, RM, Delta variant, COVID-19 Vaccines, Epidemiology, [SDV]Life Sciences [q-bio], Multicentre study, Influenza, Human/prevention & control, MESH: Primary Health Care, Europe/epidemiology, MESH: Influenza Vaccines, SDG 3 - Good Health and Well-being, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Virology, Influenza, Human, Humans, MESH: COVID-19, MESH: SARS-CoV-2, COVID-19/epidemiology, Vaccine effectiveness, QR355, MESH: Humans, Primary Health Care, vaccine effectiveness, SARS-CoV-2, MESH: Influenza, Human, Vaccination, test-negative design, Public Health, Environmental and Occupational Health, COVID-19, 3rd-DAS, MESH: Vaccination, NIS, multicentre study, RM Therapeutics. Pharmacology, Europe, Influenza Vaccines, MESH: COVID-19 Vaccines, SARS-COV-2, vaccine efffectiveness, MESH: Europe, QR355 Virology
Abstract

Introduction In July and August 2021, the SARS-CoV-2 Delta variant dominated in Europe. Aim Using a multicentre test-negative study, we measured COVID-19 vaccine effectiveness (VE) against symptomatic infection. Methods Individuals with COVID-19 or acute respiratory symptoms at primary care/community level in 10 European countries were tested for SARS-CoV-2. We measured complete primary course overall VE by vaccine brand and by time since vaccination. Results Overall VE was 74% (95% CI: 69–79), 76% (95% CI: 71–80), 63% (95% CI: 48–75) and 63% (95% CI: 16–83) among those aged 30–44, 45–59, 60–74 and ≥ 75 years, respectively. VE among those aged 30–59 years was 78% (95% CI: 75–81), 66% (95% CI: 58–73), 91% (95% CI: 87–94) and 52% (95% CI: 40–61), for Comirnaty, Vaxzevria, Spikevax and COVID-19 Vaccine Janssen, respectively. VE among people 60 years and older was 67% (95% CI: 52–77), 65% (95% CI: 48–76) and 83% (95% CI: 64–92) for Comirnaty, Vaxzevria and Spikevax, respectively. Comirnaty VE among those aged 30–59 years was 87% (95% CI: 83–89) at 14–29 days and 65% (95% CI: 56–71%) at ≥ 90 days between vaccination and onset of symptoms. Conclusions VE against symptomatic infection with the SARS-CoV-2 Delta variant varied among brands, ranging from 52% to 91%. While some waning of the vaccine effect may be present (sample size limited this analysis to only Comirnaty), protection was 65% at 90 days or more between vaccination and onset.

Published
2022
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4. A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Author

Brankin, Alice, Malone, Kerri, Barilar, Ivan, Battaglia, Simone, Borroni, Emanuele, Pires Brandao, Angela, Cabibbe, Andrea Maurizio, Carter, Joshua, Chetty, Darren, Cirillo, Daniela María, Claxton, Pauline, Clifton, David, Cohen, Ted, Coronel, Jorge, Crook, Derrick, Dreyer, Viola, Earle, Sarah, Escuyer, Vincent, Ferrazoli, Lucilaine, Gāo, George Fú, Gardy, Jennifer, Gharbia, Saheer, Teixeira Ghisi, Kelen, Ghodousi, Arash, Gibertoni Cruz, Ana Lúıza, Grandjean, Louis, Grazian, Clara, Groenheit, Ramona, Guthrie, Jennifer, He, Wencong, Hoffmann, Harald, J., Sarah, Hunt, Martin, Ismail, Nazir Ahmed, Jarrett, Lisa, Joseph, Lavania, Jou, Ruwen, Kambli, Priti, Khot, Rukhsar, Knaggs, Jeff, Koch, Anastasia, Kohlerschmidt, Donna, Kouchaki, Samaneh, Lachapelle, Alexander, Lalvani, Ajit, Grandjean Lapierre, Simon, Laurenson, Ian, Letcher, Brice, Lin, Wan-Hsuan, Liu, Chunfa, Liu, Dongxin, Mandal, Ayan, Mansjö, Mikael, Matias, Daniela, Meintjes, Graeme, de Freitas Mendes, Flávia, Merker, Matthias, Mihalic, Marina, Millard, James, Miotto, Paolo, Mistry, Nerges, Moore, David, Musser, Kimberlee A., Ngcamu, Dumisani, Ngoc Nhung, Hoang, Niemann, Stefan, Soli Nilgiriwala, Kayzad, Nimmo, Camus, O'Donnell, Max, Okozi, Nana, Siqueira Oliveira, Rosangela, Omar, Shaheed Vally, Paton, Nicholas, Peto, Timothy Ea, Watanabe Pinhata, Juliana Maira, Plesnik, Sara, Puyen, Zully, Rabodoarivelo, Marie, Rakotosamimanana, Niaina, Rancoita, Paola, Rathod, Priti, Robinson, Esther, Rodger, Gillian, Rodrigues, Camilla, Rodwell, Timothy, Roohi, Aysha, Santos-Lazaro, David, Shah, Sanchi, Kohl, Thomas Andreas, Smith, Grace, Solano, Walter, Spitaleri, Andrea, Supply, Philip, Steyn, Adrie, Surve, Utkarsha, Tahseen, Sabira, Thuong, Nguyen, Thwaites, Guy, Todt, Katharina, Trovato, Alberto, Utpatel, Christian, van Rie, Annelies, Vijay, Srinivasan, Walker, Timothy, Walker, A. Sarah, Warren, Robin M., Werngren, Jim, Wijkander, Maria, Wilkinson, Robert, Wilson, Daniel, Wintringer, Penelope, Xiao, Yu-Xin, Yang, Yang, Zhao, Yanlin, Yao, Shen-Yuan, Zhu, Baoli, Fowler, Philip, Iqbal, Zamin, Consortium, The CRyPTIC, University of Oxford, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Forschungszentrum Borstel - Research Center Borstel, IRCCS San Raffaele Scientific Institute [Milan, Italie], Casa de Oswaldo Cruz [Rio de Janeiro] (COC), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Instituto Adolfo Lutz [São Paulo, Brazil], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Africa Health Research Institute [Durban/Mtubatuba] (AHRI), University of Edinburgh, Yale School of Public Health (YSPH), Universidad Peruana de Ciencias Aplicadas (Lima) (UPC), Wadsworth Center, New York State Department of Health [Albany], Chinese Center for Disease Control and Prevention, Bill & Melinda Gates Foundation [Seattle], UK Health Security Agency [London] (UKHSA), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), University College of London [London] (UCL), University of New South Wales [Sydney] (UNSW), Public Health Agency of Sweden, University of British Columbia [Vancouver], Public Health Ontario - Santé publique Ontario, Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, National Institute for Communicable Diseases [Johannesburg] (NICD), Taipei Medical University, PD Hinduja Hospital & Research Institute, Mumbai, University of Cape Town, University of Surrey (UNIS), Imperial College London, Université de Montréal (UdeM), PRA Health sciences [Mumbai], London School of Hygiene and Tropical Medicine (LSHTM), Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), Columbia University Irving Medical Center (CUIMC), National University of Singapore (NUS), Socios En Salud [Lima, Peru], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Foundation for Innovative New Diagnostics (FIND), University of California [San Diego] (UC San Diego), University of California (UC), Universidad Peruana Cayetano Heredia (UPCH), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), National TB control Program [Islamabad, Pakistan], University of Antwerp (UA), Stellenbosch University, Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, Department of Medicine, University of Cape Town, The Francis Crick Institute [London], Shanghai Jiao Tong University School of Medicine, Chinese Academy of Sciences [Beijing] (CAS), and Wellcome Trust (200205/Z/15/Z)Bill and Melinda Gates Foundation (OPP1133541)National Institute for Health Research Oxford Biomedical Research CentreNational Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial ResistanceWellcome Trust (203919/Z/16/Z)National Mega Project on Major Infectious Disease Prevention (2018ZX10103001)H2020 Marie Skłodowska-Curie Actions (EIPOD3)Unitaid (2019-32-FIND MDR)FAPESP (17/16082-7)FAPESP (2012/51756-5)National Natural Science Foundation of China (81991534)Beijing Municipal Science and Technology Commission (Z201100005520041)Wellcome Trust International Intermediate Fellowship (206724/Z/17/Z)Wellcome TrustSouth African Medical Research Councilthe Rhodes Trust and Stanford Medical Scientist Training Program (T32 GM007365)National Institute for Health Research (NIHR) Health Protection Research Unit in Respiratory Infections at Imperial College LondonFonds de Recherche en Santé du QuébecWellcome Trust (203583/Z/16/Z)Research Foundation Flanders (G0F8316N)Wellcome Trust (98316)Wellcome Trust (214321/Z/18/Z)Wellcome Trust (203135/Z/16/Z)National Research Foundation South Africa (64787)Wellcome Trust (201470/Z/16/Z)National Institute of Allergy and Infectious Diseases (1R01AI146338)GOSH (1R01AI146338)GOSH/ICH Biomedical Research CentreOxford Medical Research Council Doctoral Training Partnership (NDM Prize Studentship)Nuffield Department of Clinical MedicineSir Henry Dale Fellowship (101237/Z/13/B)The Robertson FoundationNIHRWellcome Trust (214560/Z/18/Z)Rhodes TrustWellcome Trust (FC0010218)UK Research and Innovation (FC0010218)Cancer Research UK (FC0010218)National Institutes of HealthCenters for Disease Control and PreventionUSAIDBill and Melinda Gates FoundationWellcome Trust (203141/Z/16/Z)NIHR Oxford Biomedical Research Centre (BRC BRC-1215-20008)Deutsches Zentrum für InfektionsforschungPublic Health ScotlandCenters for Disease Control and Prevention (U60OE000103)Division of Intramural Research, National Institute of Allergy and Infectious Diseases (AI-117312)

Subjects
General Immunology and Microbiology, General Neuroscience, Extensively Drug-Resistant Tuberculosis, Antitubercular Agents, Microbial Sensitivity Tests, Mycobacterium tuberculosis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, General Biochemistry, Genetics and Molecular Biology, Phenotype, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Resistance, Multiple, Bacterial, Mutation, Tuberculosis, Multidrug-Resistant, Humans, Rifampin, General Agricultural and Biological Sciences
Abstract

The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured in a single assay. It is the largest matched phenotypic and genotypic dataset for M. tuberculosis to date. Here, we provide a summary detailing the breadth of data collected, along with a description of how the isolates were selected, collected, and uniformly processed in CRyPTIC partner laboratories across 23 countries. The compendium contains 6,814 isolates resistant to at least 1 drug, including 2,129 samples that fully satisfy the clinical definitions of rifampicin resistant (RR), multidrug resistant (MDR), pre-extensively drug resistant (pre-XDR), or extensively drug resistant (XDR). The data are enriched for rare resistance-associated variants, and the current limits of genotypic prediction of resistance status (sensitive/resistant) are presented by using a genetic mutation catalogue, along with the presence of suspected resistance-conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid, and linezolid. Finally, a case study of rifampicin monoresistance demonstrates how this compendium could be used to advance our genetic understanding of rare resistance phenotypes. The data compendium is fully open source and it is hoped that it will facilitate and inspire future research for years to come.

Published
2022
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5. Investigation of an international outbreak of multidrug-resistant monophasic Salmonella Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022

Author

Lesley Larkin, Maria Pardos de la Gandara, Ann Hoban, Caisey Pulford, Nathalie Jourdan-Da Silva, Henriette de Valk, Lynda Browning, Gerhard Falkenhorst, Sandra Simon, Raskit Lachmann, Rikard Dryselius, Nadja Karamehmedovic, Stefan Börjesson, Dieter van Cauteren, Valeska Laisnez, Wesley Mattheus, Roan Pijnacker, Maaike van den Beld, Joël Mossong, Catherine Ragimbeau, Anne Vergison, Lin Thorstensen Brandal, Heidi Lange, Patricia Garvey, Charlotte Salgaard Nielsen, Silvia Herrera León, Carmen Varela, Marie Chattaway, François-Xavier Weill, Derek Brown, Paul McKeown, UK Health Security Agency [London] (UKHSA), Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR - laboratoire coordonnateur), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Public Health Scotland [Glasgow], Robert Koch Institute [Berlin] (RKI), Robert Koch Institute [Wernigerode], Public Health Agency of Sweden, Sciensano [Bruxelles], Réseau International des Instituts Pasteur (RIIP), European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Laboratoire National de Santé [Luxembourg] (LNS), Norwegian Institute of Public Health [Oslo] (NIPH), Health Protection Surveillance Centre (HPSC), Instituto de Salud Carlos III [Madrid] (ISC), Scottish Microbiology Reference Laboratories, UK Health Security Agency (UKHSA), Institut Pasteur [Paris]-Université Paris Cité (UPC), Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), and European Centre for Disease Prevention and Control (ECDC)

Subjects
Monophasic Salmonella Typhimurium, Salmonella typhimurium, Epidemiology, Public Health, Environmental and Occupational Health, Chocolate products, Outbreak, Multi-country collaboration, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, United Kingdom, Disease Outbreaks, Core-genome multi locus sequence typing, Descriptive epidemiological evidence, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Whole genome sequencing, Child, Preschool, Humans, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Antimicrobial resistance profile, Chocolate, Child, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

An extensive multi-country outbreak of multidrug-resistant monophasic Salmonella Typhimurium infection in 10 countries with 150 reported cases, predominantly affecting young children, has been linked to chocolate products produced by a large multinational company. Extensive withdrawals and recalls of multiple product lines have been undertaken. With Easter approaching, widespread product distribution and the vulnerability of the affected population, early and effective real-time sharing of microbiological and epidemiological information has been of critical importance in effectively managing this serious food-borne incident.

Published
2022
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