Welcome to our 2019 Summer students Rachel Tran, Megane Bouchard, and Arman Edalatmand, plus curation volunteers Anna-Lisa Nguyen and William Huynh! Rachel is collaborating with the Whitney lab on evolution of bacterial competition, Megane with the Sloboda & Bowdish labs on ageing and maternal health data harmonization, and Arman on new methods for biocuration of quantitative antimicrobial resistance (AMR) data. Anna-Lisa & William will be working on curation of AMR data in the Comprehensive Antibiotic Resistance Database.
Speicher, D.J., K. Luinstra, J. Maciejewski, K.K. Tsang, A.G. McArthur, & M. Smieja. 2019. Clostridioides difficile strain divergence over time. Oral presentation at the Association of Medical Microbiology and Infectious Disease Canada (AMMI Canada) & Canadian Association for Clinical Microbiology and Infectious Diseases (CACMID) Joint Annual Conference, Ottawa, Ontario.
Background: Clostridioides difficileinfection (CDI) is a serious hospital-associated infection with severe outbreaks caused by the hypervirulent NAP1/MLST-1 strain. Whole genome sequencing has shown that most outbreak strains are clonal whereas non-outbreaks display a wide diversity of strains. To examine strain diversity in clinical settings, a subset of C. difficileisolates from symptomatic CDI from an acute care hospital were compared to isolates from C. difficilecolonized (CDC) asymptomatic subjects from the same hospital.
Methods: A subset of PCR-positive stool samples from clinically confirmed CDI isolates from 2016 (13/110), 2017 (8/111), and 2018 (13/65), and CDC from 2017 (17/185) were cultured 3-times consecutively on CHROMagar™ C. difficile, sub-cultured on Columbia colistin-nalidixic acid (CNA) media, had DNA isolated, shotgun sequenced, and genome assembled for both MLST typing and genome-wide SNP phylogenetic analysis.
Results: Based on MLST profiles, the C. difficiletypes detected were diverse. Of the presumed binary toxin positive/NAP1 strains (i.e. PCR tcdA/tcdBpositive) 7/12 (58%) were NAP1/MLST-1 and 3/12 (25%) were NAP7/MLST-11. NAP1/MLST-1 was not detected in any CDC isolate. NAP4/MLST-2,14 were detected in 2016 (n=4), 2017 (n=2), 2018 (n=1), and in CDC isolates (n=3). MLST-42 was dominant in CDC isolates (5/17; 29%) and decreased in prevalence in CDI isolates over time (2016=4; 2017=0; 2018=1).
Conclusion: C. difficilestrains amongst both CDI and CDC individuals are highly divergent. Whilst molecular assays are misclassifying 25% of “NAP1” strains, both NAP1 and NAP7 are hypervirulent. The number of MLST-42 CDC isolates is concerning as it has been reported to be the most common strain causing CDI among U.S. adults. This highlights the need for continued genomic surveillance of both CDI and CDC individuals. Genome-wide SNP phylogenetic analysis is currently being performed.
April 2019 big #card_release #RGI5! Resistance Gene Identifier Version 5: entirely new algorithms for metagenomics data, new options for genomes & assemblies. Extensively updated documentation, http://github.com/arpcard/rgi
Congratulations to Rachel Tran on winning a 2019 DBCAD Summer Fellowship! These competitive awards are designed to support students working in the labs of members from both the David Braley Centre for Antibiotic Discovery and Michael G. DeGroote Institute for Infectious Disease Research during their summer practicum. A full list of awardees can be found here. Learn more about Rachel’s work at Ontario Biology Day 2019:
Tran, H.K.R., S. Ahmad, J.C. Whitney, & A.G. McArthur. 2019. Expanding the Virulence Ontology (VIRO) to determine the evolution of a secretion system effector. Presentation at Ontario Biology Day, London, Ontario, Canada.
The Comprehensive Antibiotic Resistance Database has been updated, http://card.mcmaster.ca
CARD Curation: Expanded MCR, OXA & IMP beta-lactamase, and macrolide phosphotransferase (MPH) sequence curation. Updated nomenclature for MPHs and drug resistant dihydrofolate reductases (dfr). Updated classification of ADC beta-lactamases.
Ontologies: Addition of 518 draft virulence ontology (VIRO) terms.
Prevalence, Resistomes, & Variants: Expansion to 82 pathogens (more Brucella species), 81,000+ resistomes, and 173,000+ AMR allele sequences based on sequence data acquired from NCBI on 28-Feb-2019, analyzed using RGI 4.2.2 (DIAMOND homolog detection) and CARD 3.0.1.
Srinivasan, K.A., S.K. Virdee, & A.G. McArthur. 2019. Strandedness during cDNA synthesis, the stranded parameter in htseq-count, and analysis of RNA-Seq data. Preprints 2019, 2019030124. [Preprint]
Matthews, T., F. Bristow, E. Griffiths, A. Petkau, J. Adam, D. Dooley, P. Kruczkiewicz, J. Curatcha, J. Cabral, D. Fornika, G. Winsor, M. Courtot, C. Bertelli, A. Roudgar, P. Fejaio, P. Mabon, E. Enns, J. Thiessen, A.W.S. Keddy, J. Isaac-Renton, J. Gardy, P. Tang, The IRIDA consortium, J. Carriço, L. Chindelevitch, C. Chauve, M. Graham, A.G. McArthur, E. Taboada, R. Beiko, F.S.L. Brinkman, W.W.L. Hsiao, & G. Van Domselaar. 2018. The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform. BioRxiv 381830 [Preprint].
A week of lectures, demos, and training for the Comprehensive Antibiotic Resistance Database
During McMaster Spring Mid-Term Recess (February 18-24), the McArthur lab is pleased to present a series of lectures, demonstrations, and training sessions for the Comprehensive Antibiotic Resistance Database (card.mcmaster.ca) and its associated Resistance Gene Identifier (RGI) software, sponsored by the Michael G. DeGroote Institute for Infectious Disease Research (IIDR).
Questions? Email card@mcmaster.ca
Workshop & Lecture material will be available here: https://github.com/arpcard/state-of-the-card-2019
We welcome (left to right) Malvika Agarwal, Megane Bouchard, Amro Elrafie, and Hafsa Omer to the lab as data curation volunteers, working collectively to collate important clinical metadata from clinical pathogen sequencing efforts at Hamilton area hospitals and randomized controlled trials in McMaster’s NICU. Malvika and Hafsa are currently in the second year of the Life Sciences program, Megane in the second year of the Bachelor of Health Sciences program, and Amro in second year Biochemistry & Biomedical Sciences program.
A busy year for Dr. McArthur outside of academia…
- Integrated Health Biosystems Chair – Combatting Antimicrobial Resistance in the Age of Molecular Epidemiology. Invited presentation at the Cisco Research Chairs Summit, Toronto.
- The Comprehensive Antibiotic Resistance Database (CARD) and the Resistance Gene Identifier – prediction of antimicrobial resistance genes for genomic and metagenomic sequencing data. Invited presentation at the Integrated Rapid Infectious Disease Analysis (IRIDA) Annual General Meeting, Winnipeg, Manitoba.
- The Comprehensive Antibiotic Resistance Database. Invited presentation at the Agriculture & Agri-Food Canada and Canadian Food Inspection Agency Genomics Research and Development Initiative: GRDI-AMR Annual General Meeting.
- Facilitator & Speaker, Artificial Intelligence: The Art of the Possible, Niagara Health Board of Directors Retreat (Niagara-on-the-Lake, Ontario).
- Represented McMaster University at McMaster – Queen’s Park Government Reception, Gardiner Museum, Toronto.
- Represented McMaster University at Research Canada’s Health Research Caucus – Reshaping Health Research and Innovation: Artificial Intelligence and Machine Learning (Parliament Hill, Ottawa, Ontario).
- Panellist – Artificial Intelligence in Healthcare, Norwegian Health Ministry & Government of Canada Round Table hosted by Hamilton Health Sciences (Hamilton, Ontario).