David Braley Centre for Antibiotic Discovery gives researchers a fighting chance against antimicrobial resistance.
A forward-looking McMaster donor is investing $7 million in a new research centre dedicated specifically to tackling the growing global threat of antimicrobial resistance.
David Braley, whose gifts to the university include a $50-million investment in McMaster teaching, learning and health-care research and delivery, has allocated $7 million from that 2007 gift towards the new David Braley Centre for Antibiotic Discovery.
The centre will operate from the Michael G. DeGroote Institute for Infectious Disease Research, whose labs and offices are located on campus in the Michael G. DeGroote Centre for Learning and Discovery.
Empowering conventional antibiotics with new drug leads targeting the outer-membrane of Gram-negative pathogens. E. Brown (PI), G.D. Wright (co-I), B. Coombes (co-I), A.G. McArthur (co-I), J. Magolan (co-I), C. Whitfield (co-I, Univ. Guelph). Ontario Research Fund – Research Excellence.
Taking control of antibiotic production: establishing and exploiting a systems-level understanding of antibiotic regulation in the actinobacteria. M. Elliot (PI) & A.G. McArthur (co-I). David Braley Center for Antibiotic Discovery (McMaster) Research Grant.
Dr. McArthur and PhD student Kara Tsang taught together at the 2019 MacData Institute Summer School, with Dr. McArthur reviewing biocuration and bioinformatics for genomic surviellence of antimicrobial resistance and Kara following up with a lecture on machine learning techniques to predict clinical antimicrobial resistance from raw genomic sequence.
Also congratulations to Kara for being awarded a 2019 Faculty of Health Sciences Graduate Programs Excellence Award!
Updated August 6, 2019: Congratulations to Kara for also winning an Ontario Graduate Scholarship!
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.
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].
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 firstname.lastname@example.org
Workshop & Lecture material will be available here: https://github.com/arpcard/state-of-the-card-2019