1
|
Timme RE, Woods J, Jones JL, Calci KR, Rodriguez R, Barnes C, Leard E, Craven M, Chen H, Boerner C, Grim C, Windsor AM, Ramachandran P, Muruvanda T, Rand H, Tesfaldet B, Amirzadegan J, Kayikcioglu T, Walsky T, Allard M, Balkey M, Bias CH, Brown E, Judy K, Pfefer T, Tallent SM, Hoffmann M, Pettengill J. SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network. mSystems 2024; 9:e0141523. [PMID: 38819130 DOI: 10.1128/msystems.01415-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA's GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA's laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.
Collapse
Affiliation(s)
- Ruth E Timme
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Jacquelina Woods
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Jessica L Jones
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Kevin R Calci
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Rachel Rodriguez
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Candace Barnes
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Elizabeth Leard
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Mark Craven
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, USA
| | - Haifeng Chen
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, USA
| | - Cameron Boerner
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, USA
| | - Christopher Grim
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Amanda M Windsor
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Padmini Ramachandran
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Tim Muruvanda
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Hugh Rand
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Bereket Tesfaldet
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Jasmine Amirzadegan
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Tunc Kayikcioglu
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
| | - Tamara Walsky
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Marc Allard
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Maria Balkey
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - C Hope Bias
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Eric Brown
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Kathryn Judy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Tina Pfefer
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Sandra M Tallent
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Maria Hoffmann
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - James Pettengill
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| |
Collapse
|
2
|
Griffiths EJ, Mendes I, Maguire F, Guthrie JL, Wee BA, Schmedes S, Holt K, Yadav C, Cameron R, Barclay C, Dooley D, MacCannell D, Chindelevitch L, Karsch-Mizrachi I, Waheed Z, Katz L, Petit Iii R, Dave M, Oluniyi P, Nasar MI, Raphenya A, Hsiao WWL, Timme RE. PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training. Microb Genom 2024; 10. [PMID: 38860884 DOI: 10.1099/mgen.0.001260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments often requires that lower quality datasets be made available for analysis and comparison alongside those of higher quality. This range of data quality in reference sets can complicate the sharing of sub-optimal datasets that are vital for the community and for the reproducibility of assays. Sharing of useful, but sub-optimal datasets requires careful annotation and documentation of known issues to enable appropriate interpretation, avoid being mistaken for better quality information, and for these data (and their derivatives) to be easily identifiable in repositories. Unfortunately, there are currently no standardized attributes or mechanisms for tagging poor-quality datasets, or datasets generated for a specific purpose, to maximize their utility, searchability, accessibility and reuse. The Public Health Alliance for Genomic Epidemiology (PHA4GE) is an international community of scientists from public health, industry and academia focused on improving the reproducibility, interoperability, portability, and openness of public health bioinformatic software, skills, tools and data. To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability. The contextual data tags were developed through consultations with the community including input from the International Nucleotide Sequence Data Collaboration (INSDC), and have been standardized using ontologies - community-based resources for defining the tag properties and the relationships between them. The standardized tags are agnostic to the organism and the sequencing technique used and thus can be applied to data generated from any pathogen using an array of sequencing techniques. The tags can also be applied to synthetic (lab created) data. The list of standardized tags is maintained by PHA4GE and can be found at https://github.com/pha4ge/contextual_data_QC_tags. Definitions, ontology IDs, examples of use, as well as a JSON representation, are provided. The PHA4GE QC tags were tested, and are now implemented, by the FDA's GenomeTrakr laboratory network as part of its routine submission process for SARS-CoV-2 wastewater surveillance. We hope that these simple, standardized tags will help improve communication regarding quality control in public repositories, in addition to making datasets of variable quality more easily identifiable. Suggestions for additional tags can be submitted to PHA4GE via the New Term Request Form in the GitHub repository. By providing a mechanism for feedback and suggestions, we also expect that the tags will evolve with the needs of the community.
Collapse
Affiliation(s)
- Emma J Griffiths
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Inês Mendes
- Theiagen Genomics, LLC, Highlands Ranch, Colorado, USA
| | - Finlay Maguire
- Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada, and Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer L Guthrie
- Department of Microbiology & Immunology, Western University, London, Ontario, Canada
| | - Bryan A Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Sarah Schmedes
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Georgia, USA
| | - Kathryn Holt
- National Microbiology Laboratory, Public health Agency of Canada, Winnipeg, MB, Canada
| | - Chanchal Yadav
- National Microbiology Laboratory, Public health Agency of Canada, Winnipeg, MB, Canada
| | - Rhiannon Cameron
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Charlotte Barclay
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Damion Dooley
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Duncan MacCannell
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Georgia, USA
| | - Leonid Chindelevitch
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zahra Waheed
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Lee Katz
- Center for Food Safety, University of Georgia, Georgia, USA
| | | | - Mugdha Dave
- McMaster University, Hamilton, Ontario, Canada
| | | | - Muhammad Ibtisam Nasar
- Department of Biology, College of Science, United Arab Emirates University- AL Ain, Abu Dhabi, UAE
| | - Amogelang Raphenya
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - William W L Hsiao
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| |
Collapse
|
3
|
Beverley J, Babcock S, Carvalho G, Cowell LG, Duesing S, He Y, Hurley R, Merrell E, Scheuermann RH, Smith B. Coordinating virus research: The Virus Infectious Disease Ontology. PLoS One 2024; 19:e0285093. [PMID: 38236918 PMCID: PMC10796065 DOI: 10.1371/journal.pone.0285093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/12/2023] [Indexed: 01/22/2024] Open
Abstract
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.
Collapse
Affiliation(s)
- John Beverley
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Shane Babcock
- National Center for Ontological Research, Buffalo, NY, United States of America
- Air Force Research Laboratory, Wright Patterson Air Force Base, Riverside, OH, United States of America
| | - Gustavo Carvalho
- Department of Cognitive Science, Northwestern University, Evanston, IL, United States of America
| | - Lindsay G. Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Sebastian Duesing
- Department of Philosophy, Loyola University, Chicago, IL, United States of America
| | - Yongqun He
- Computational Medicine and Bioinformatics, University of Michigan Medical School, He Group, Ann Arbor, MI, United States of America
| | - Regina Hurley
- National Center for Ontological Research, Buffalo, NY, United States of America
- Department of Philosophy, Northwestern University, Evanston, IL, United States of America
| | - Eric Merrell
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Pathology, University of California, San Diego, CA, United States of America
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| |
Collapse
|
4
|
Therrien JD, Thomson M, Sion ES, Lee I, Maere T, Nicolaï N, Manuel DG, Vanrolleghem PA. A comprehensive, open-source data model for wastewater-based epidemiology. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:1-19. [PMID: 38214983 PMCID: wst_2023_409 DOI: 10.2166/wst.2023.409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
The recent SARS-COV-2 pandemic has sparked the adoption of wastewater-based epidemiology (WBE) as a low-cost way to monitor the health of populations. In parallel, the pandemic has encouraged researchers to openly share their data to serve the public better and accelerate science. However, environmental surveillance data are highly dependent on context and are difficult to interpret meaningfully across sites. This paper presents the second iteration of the Public Health Environmental Surveillance Open Data Model (PHES-ODM), an open-source dictionary and set of data tools to enhance the interoperability of environmental surveillance data and enable the storage of contextual (meta)data. The data model describes how to store environmental surveillance program data, metadata about measurements taken on various specimens (water, air, surfaces, sites, populations) and data about measurement protocols. The model provides software tools that support the collection and use of PHES-ODM formatted data, including performing PCR calculations and data validation, recording data into input templates, generating wide tables for analysis, and producing SQL database definitions. Fully open-source and already adopted by institutions in Canada, the European Union, and other countries, the PHES-ODM provides a path forward for creating robust, interoperable, open datasets for environmental public health surveillance for SARS-CoV-2 and beyond.
Collapse
Affiliation(s)
| | - Mathew Thomson
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Eugen-Sorin Sion
- European Commission, European Research Council, Joint Research Centre, Ispra, Italy
| | - Ivan Lee
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Maere
- modelEAU, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Niels Nicolaï
- modelEAU, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Douglas G Manuel
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | | |
Collapse
|
5
|
Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ. Genomics for public health and international surveillance of antimicrobial resistance. THE LANCET. MICROBE 2023; 4:e1047-e1055. [PMID: 37977162 DOI: 10.1016/s2666-5247(23)00283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.
Collapse
Affiliation(s)
- Kate S Baker
- Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Lillian A Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Daniel G Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi
| | | |
Collapse
|
6
|
Timme RE, Karsch-Mizrachi I, Waheed Z, Arita M, MacCannell D, Maguire F, Petit III R, Page AJ, Mendes CI, Nasar MI, Oluniyi P, Tyler AD, Raphenya AR, Guthrie JL, Olawoye I, Rinck G, O’Cathail C, Lees J, Cochrane G, Cummins C, Brister JR, Klimke W, Feldgarden M, Griffiths E. Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications. Microb Genom 2023; 9:001145. [PMID: 38085797 PMCID: PMC10763499 DOI: 10.1099/mgen.0.001145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.
Collapse
Affiliation(s)
- Ruth E. Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Masanori Arita
- DNA Data Bank of Japan, National Institute of Genetics, Mishima, Japan
| | - Duncan MacCannell
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Finlay Maguire
- Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Canada
| | | | - Andrew J. Page
- Quadram Institute Bioscience, Norwich, Norfolk, UK
- Theiagen Genomics LLC, Highlands Ranch, CO, USA
| | | | - Muhammad Ibtisam Nasar
- Department of Biology, College of Science, United Arab Emirates University- Al Ain, Abu Dhabi, UAE
| | - Paul Oluniyi
- Chan Zuckerberg Biohub Network, San Francisco, CA, USA
| | - Andrea D. Tyler
- Science Technology Cores and Services, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Amogelang R. Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer L. Guthrie
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Idowu Olawoye
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Colman O’Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - John Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - J. Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| |
Collapse
|
7
|
Neves A, Cuesta I, Hjerde E, Klemetsen T, Salgado D, van Helden J, Rahman N, Fatima N, Karathanasis N, Zmora P, Åkerström WN, Grellscheid SN, Waheed Z, Blomberg N. FAIR+E pathogen data for surveillance and research: lessons from COVID-19. Front Public Health 2023; 11:1289945. [PMID: 38074768 PMCID: PMC10703184 DOI: 10.3389/fpubh.2023.1289945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy toward addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To address these challenging endeavors, we have started an ELIXIR Focus Group where we invite all interested experts to join in a concerted, expert-driven effort toward sustaining and ensuring high-quality data for global surveillance and research.
Collapse
Affiliation(s)
- Aitana Neves
- SIB Swiss Institute of Bioinformatics, Clinical Bioinformatics, Geneva, Switzerland
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III, Madrid, Spain
| | - Erik Hjerde
- Institute of Chemistry, The Arctic University of Norway, Tromsø, Norway
| | - Terje Klemetsen
- Institute of Chemistry, The Arctic University of Norway, Tromsø, Norway
| | - David Salgado
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Jacques van Helden
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
- Aix-Marseille Univ, INSERM, Lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nazeefa Fatima
- ELIXIR Norway, Centre for Bioinformatics, University of Oslo, Oslo, Norway
| | - Nestoras Karathanasis
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pawel Zmora
- Department of Molecular Virology, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Wolmar Nyberg Åkerström
- NBIS National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Niklas Blomberg
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, United Kingdom
| |
Collapse
|
8
|
Khan W, Kabir F, Kanwar S, Aziz F, Muneer S, Kalam A, Rajab Ali MN, Ansari N, Vanaerschot M, Ahyong V, Fahsbender L, Kalantar K, Black A, Glascock A, Gil J, Ayscue P, Tato C, Jehan F, Nisar I. Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration. BMJ Glob Health 2023; 8:e012589. [PMID: 37984892 PMCID: PMC10660681 DOI: 10.1136/bmjgh-2023-012589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/09/2023] [Indexed: 11/22/2023] Open
Abstract
Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associated with sequencing-equipment and running consumables have created an opportunity for broader adoption. During the COVID-19 pandemic, rapid diagnostics development and DNA sequencing revolutionised the ability to diagnose and sequence SARS-CoV-2 rapidly. Socioeconomic inequalities substantially impact the ability to sequence SARS-CoV-2 strains and undermine a developing country's pandemic preparedness. Low- and middle-income countries face additional challenges in establishing, maintaining and expanding genomic surveillance. We present our experience of establishing a genomic surveillance system at the Aga Khan University, Karachi, Pakistan. Despite being at a leading health sciences research institute in the country, we encountered significant challenges. These were related to collecting standardised contextual data for SARS-CoV-2 samples, procuring sequencing reagents and consumables, and challenges with library preparation, sequencing and submission of high-quality SARS-CoV-2 genomes. Several technical roadblocks ensued during the implementation of the genomic surveillance framework, which were resolved in collaboration with our partners. High-quality genome sequences were then deposited on open-access platforms per the best practices. Subsequently, these efforts culminated in deploying Pakistan's first SARS-CoV-2 phyllo surveillance map as a Nextstrain build. Our experience offers lessons for the successful development of Genomic Surveillance Infrastructure in resource-limited settings struck by a pandemic.
Collapse
Affiliation(s)
- Waqasuddin Khan
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Furqan Kabir
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Samiah Kanwar
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Fatima Aziz
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Sahrish Muneer
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Adil Kalam
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | | | - Nadia Ansari
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Liz Fahsbender
- The Chan Zuckerberg Initiative, Palo Alto, California, USA
| | | | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Juliana Gil
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Cristina Tato
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Fyezah Jehan
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Imran Nisar
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| |
Collapse
|
9
|
Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
Collapse
Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
| |
Collapse
|
10
|
The case for including microbial sequences in the electronic health record. Nat Med 2023; 29:22-25. [PMID: 36646805 DOI: 10.1038/s41591-022-02157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
11
|
Gill IS, Griffiths EJ, Dooley D, Cameron R, Savić Kallesøe S, John NS, Sehar A, Gosal G, Alexander D, Chapel M, Croxen MA, Delisle B, Di Tullio R, Gaston D, Duggan A, Guthrie JL, Horsman M, Joshi E, Kearny L, Knox N, Lau L, LeBlanc JJ, Li V, Lyons P, MacKenzie K, McArthur AG, Panousis EM, Palmer J, Prystajecky N, Smith KN, Tanner J, Townend C, Tyler A, Van Domselaar G, Hsiao WWL. The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information. Microb Genom 2023; 9:mgen000908. [PMID: 36748616 PMCID: PMC9973856 DOI: 10.1099/mgen.0.000908] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.
Collapse
Affiliation(s)
- Ivan S Gill
- University of British Columbia, Vancouver, BC, Canada
| | - Emma J Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Rhiannon Cameron
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Nithu Sara John
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Anoosha Sehar
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Gurinder Gosal
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Madison Chapel
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Matthew A Croxen
- Alberta Precision Labs, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | | | | | - Daniel Gaston
- Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, Canada
| | - Ana Duggan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Mark Horsman
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.,Public Health Ontario Laboratory, Toronto, ON, Canada
| | - Esha Joshi
- Public Health Ontario Laboratory, Toronto, ON, Canada
| | - Levon Kearny
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Natalie Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lynette Lau
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Jason J LeBlanc
- Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, Canada
| | - Vincent Li
- Alberta Precision Labs, Edmonton, AB, Canada
| | - Pierre Lyons
- Public Health Agency of Canada, Moncton, NB, Canada
| | | | - Andrew G McArthur
- Michael G. DeGroote Institute for Infectious Disease Research & Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Emily M Panousis
- Michael G. DeGroote Institute for Infectious Disease Research & Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - John Palmer
- Public Health Ontario Laboratory, Toronto, ON, Canada
| | - Natalie Prystajecky
- University of British Columbia, Vancouver, BC, Canada.,BCCDC Public Health Laboratory, Vancouver, BC, Canada
| | | | - Jennifer Tanner
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Christopher Townend
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Andrea Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - William W L Hsiao
- University of British Columbia, Vancouver, BC, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| |
Collapse
|
12
|
Greenbaum D, Gurwitz D, Joly Y. Editorial: COVID-19 pandemics: Ethical, legal and social issues. Front Genet 2022; 13:1021865. [PMID: 36523760 PMCID: PMC9745311 DOI: 10.3389/fgene.2022.1021865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/18/2022] [Indexed: 08/29/2023] Open
Affiliation(s)
- Dov Greenbaum
- Department of Molecular Biophysics and Biochemistry, New Haven, NY, United States
- Reichman University, Herzliya, Israel
- Zvi Meitar Institute for Legal Implications of Emerging Technologies, Herzliya, Israel
| | - David Gurwitz
- Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, School of Medicine Sackler Faculty of Medicine Tel Aviv University, Tel Aviv, Israel
| | - Yann Joly
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| |
Collapse
|
13
|
Mercer T, Almond N, Crone MA, Chain PSG, Deshpande A, Eveleigh D, Freemont P, Fuchs S, Garlick R, Huggett J, Kammel M, Li PE, Milavec M, Marlowe EM, O'Sullivan DM, Page M, Pestano GA, Suliman S, Simen B, Sninsky JJ, Sopchak L, Tato CM, Vallone PM, Vandesompele J, White TJ, Zeichhardt H, Salit M. The Coronavirus Standards Working Group's roadmap for improved population testing. Nat Biotechnol 2022; 40:1563-1568. [PMID: 36323792 PMCID: PMC9628457 DOI: 10.1038/s41587-022-01538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tim Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, Australia
| | - Neil Almond
- Medicines and Healthcare Products Regulatory Agency, Potters Bar, UK
| | - Michael A Crone
- London Biofoundry, Imperial College Translation and Innovation Hub, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, UK
| | - Patrick S G Chain
- Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Almos, NM, USA
| | - Alina Deshpande
- Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Almos, NM, USA
| | | | - Paul Freemont
- London Biofoundry, Imperial College Translation and Innovation Hub, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, UK
| | - Sebastien Fuchs
- Western University of Health Sciences, College of Osteopathic Medicine of the Pacific, Pomona, CA, USA
| | | | - Jim Huggett
- National Measurement Laboratory, LGC, Teddington, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Martin Kammel
- INSTAND e.V. Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Germany
| | - Po-E Li
- Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Almos, NM, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Denise M O'Sullivan
- National Measurement Laboratory, LGC, Teddington, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Mark Page
- Medicines and Healthcare Products Regulatory Agency, Potters Bar, UK
| | | | - Sara Suliman
- Brigham and Women's Hospital, Division of Rheumatology, Inflammation and Immunity, Harvard Medical School, Boston, MA, USA
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Peter M Vallone
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Thomas J White
- Human Rights Center, School of Law, University of California, Berkeley, CA, USA
| | - Heinz Zeichhardt
- INSTAND e.V. Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Germany
- IQVD GmbH, Institut fuer Qualitaetssicherung in der Virusdiagnostik, Berlin, Germany
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, CA, USA.
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
- MITRE Corporation, McLean, VA, USA.
| |
Collapse
|
14
|
Meumann EM, Krause VL, Baird R, Currie BJ. Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia. Trop Med Infect Dis 2022; 7:tropicalmed7080181. [PMID: 36006273 PMCID: PMC9413455 DOI: 10.3390/tropicalmed7080181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The Northern Territory (NT) is a geographically remote region of northern and central Australia. Approximately a third of the population are First Nations Australians, many of whom live in remote regions. Due to the physical environment and climate, and scale of social inequity, the rates of many infectious diseases are the highest nationally. Molecular typing and genomic sequencing in research and public health have provided considerable new knowledge on the epidemiology of infectious diseases in the NT. We review the applications of genomic sequencing technology for molecular typing, identification of transmission clusters, phylogenomics, antimicrobial resistance prediction, and pathogen detection. We provide examples where these methodologies have been applied to infectious diseases in the NT and discuss the next steps in public health implementation of this technology.
Collapse
Affiliation(s)
- Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
- Correspondence:
| | - Vicki L. Krause
- Northern Territory Centre for Disease Control, Northern Territory Government, Darwin 0810, Australia
| | - Robert Baird
- Territory Pathology, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
| |
Collapse
|
15
|
Schriml LM. A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape. Gigascience 2022; 11:6586815. [PMID: 35579551 PMCID: PMC9112763 DOI: 10.1093/gigascience/giac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/10/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Standardization of omics data drives FAIR data practices through community-built genomic data standards and biomedical ontologies. Use of standards has progressed from a foreign concept to a sought-after solution, moving from efforts to coordinate data within individual research projects to research communities coming together to identify solutions to common challenges. Today we are seeing the benefits of this multidecade groundswell to coordinate, exchange, and reuse data; to compare data across studies; and to integrate data across previously siloed resources.
Collapse
Affiliation(s)
- Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD 21201, USA
| |
Collapse
|