3
|
Tsang KK, Ahmad S, Aljarbou A, Al Salem M, Baker SJC, Panousis EM, Derakhshani H, Rossi L, Nasir JA, Bulir DC, Surette MG, Lee RS, Smaill F, Mertz D, McArthur AG, Khan S. SARS-CoV-2 Outbreak Investigation Using Contact Tracing and Whole-Genome Sequencing in an Ontario Tertiary Care Hospital. Microbiol Spectr 2023; 11:e0190022. [PMID: 37093060 PMCID: PMC10269621 DOI: 10.1128/spectrum.01900-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
Genomic epidemiology can facilitate an understanding of evolutionary history and transmission dynamics of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak. We used next-generation sequencing techniques to study SARS-CoV-2 genomes isolated from patients and health care workers (HCWs) across five wards of a Canadian hospital with an ongoing SARS-CoV-2 outbreak. Using traditional contact tracing methods, we show transmission events between patients and HCWs, which were also supported by the SARS-CoV-2 lineage assignments. The outbreak predominantly involved SARS-CoV-2 B.1.564.1 across all five wards, but we also show evidence of community introductions of lineages B.1, B.1.1.32, and B.1.231, falsely assumed to be outbreak related. Altogether, our study exemplifies the value of using contact tracing in combination with genomic epidemiology to understand the transmission dynamics and genetic underpinnings of a SARS-CoV-2 outbreak. IMPORTANCE Our manuscript describes a SARS-CoV-2 outbreak investigation in an Ontario tertiary care hospital. We use traditional contract tracing paired with whole-genome sequencing to facilitate an understanding of the evolutionary history and transmission dynamics of this SARS-CoV-2 outbreak in a clinical setting. These advancements have enabled the incorporation of phylogenetics and genomic epidemiology into the understanding of clinical outbreaks. We show that genomic epidemiology can help to explore the genetic evolution of a pathogen in real time, enabling the identification of the index case and helping understand its transmission dynamics to develop better strategies to prevent future spread of SARS-CoV-2 in congregate, clinical settings such as hospitals.
Collapse
Affiliation(s)
- Kara K. Tsang
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Shehryar Ahmad
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alanoud Aljarbou
- Department of Pediatrics, College of Medicine, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohammed Al Salem
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Sheridan J. C. Baker
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Emily M. Panousis
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hooman Derakhshani
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Laura Rossi
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jalees A. Nasir
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - David C. Bulir
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael G. Surette
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Robyn S. Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Fiona Smaill
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Dominik Mertz
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G. McArthur
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sarah Khan
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
4
|
Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya A, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy M, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray K, Hoad GR, Jia B, Bhando T, Carfrae L, Farha M, French S, Gordzevich R, Rachwalski K, Tu M, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko R, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2022; 51:D690-D699. [PMID: 36263822 PMCID: PMC9825576 DOI: 10.1093/nar/gkac920] [Citation(s) in RCA: 187] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.
Collapse
Affiliation(s)
- Brian P Alcock
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - William Huynh
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Romeo Chalil
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keaton W Smith
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mateusz A Wlodarski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Aaron Petkau
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sohaib A Syed
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kara K Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mugdha Dave
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Madeline C McCarthy
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Karyn M Mukiri
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jalees A Nasir
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bahar Golbon
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hamna Imtiaz
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Xingjian Jiang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Komal Kaur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan Kwong
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Zi Cheng Liang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keyu C Niu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Prabakar Shan
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jasmine Y J Yang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gemma R Hoad
- Research Computing Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Timsy Bhando
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lindsey A Carfrae
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Maya A Farha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rodion Gordzevich
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan M Tu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Emily Bordeleau
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Haley L Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada,Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William W L Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew G McArthur
- To whom correspondence should be addressed. Tel: +1 905 525 9140 (Ext 21663);
| |
Collapse
|