Edalatmand, A. & A.G. McArthur. 2019. Classifying and curating publications on antimicrobial resistance using machine learning. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.

Khan, S., K.K. Tsang, M. Science, D. Kaufman, D. Mertz, J. Pernica, L. Thabane, A.G. McArthur, & M. Loeb. 2019. GloveCare: A pilot study to assess non-sterile glove-based care for the prevention of late onset infection in the NICU. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.

Nasir, J.A., R.A. Kozak, S. Mubareka, H. Poinar, & A.G. McArthur. 2019. Development of virus surveillance tools for clinical diagnostics. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.

Oloni, M., K. Besennov, J. Nash, & A.G. McArthur. 2019. Using the Comprehensive Antimicrobial Resistance Database (CARD) to predict plasmid-borne AMR genes from genome assembly data. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.

Speicher, D.J., K. Luinstra, J. Maciejewski, K.K. Tsang, S. Patel, V. Allen, A.G. McArthur, & M. Smieja. 2019. Clostridioides difficile strain divergence and prophages in Southern Ontario, Canada (2010-2018). Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.

Tran, H.-K. 2019. In silico prediction of novel type VII polymorphic toxins of the Streptococcus Anginosus Group. Oral presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.

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Maguire, F., B. Alcock, A.R. Raphenya, B. Jia. E.J. Griffiths, T.C. Matthews, J. Adam, A. Petkau, G.L. Winsor, IRIDA Consortium, R.G. Beiko, F.S.L. Brinkman, W.W.L. Hsiao. G. Van Domselaar, A.G. McArthur. 2019. Integrated Rapid Infectious Disease Analysis: A comprehensive platform for public health bioinformatics and AMR surveillance using genomic data. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Sherbrooke, Quebec.

Maguire, F., B. Jia, B. Alcock, A.R. Raphenya, F.S.L. Brinkman, A.G. McArthur, & R.G. Beiko. 2019. Precise identification of antimicrobial resistance determinants from metagenomic data. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Sherbrooke, Quebec.

 

Alcock, B.P., A.R. Raphenya, F. Maguire, F.S. Brinkman, R.G. Beiko, & A.G. McArthur. 2019. Resistome and variant prediction for improved antimicrobial surveillance with the Comprehensive Antibiotic Resistance Database. Poster presentation at the American Society for Microbiology Microbe Meeting, San Francisco, California.

Raphenya, A.R., T.T.Y. Lau, B. Alcock, K.K. Tsang, F. Maguire, F.S. Brinkman, R.G. Beiko, & A.G. McArthur. 2019. Resistance Gene Identifier (RGI) – Prediction of antimicrobial resistance genes and mutations for genomic and metagenomic sequencing data. Oral presentation at the American Society for Microbiology Microbe Meeting, San Francisco, California.

Chen, J. C.-Y., C.G. Clark, A. Bharat, A.G. McArthur, M.R. Graham, G.R. Westmacott, & G. Van Domselaar. 2019. Detection of antimicrobial resistance using proteomics and the Comprehensive Antibiotic Resistance Database: A case study. Presentation at 27th Conference on Intelligent Systems in Molecular Biology & 18th European Conference on Computational Biology, Basel, Switzerland.

Tsang, K.K., F. Maguire, H. Zubyk, S. Chou, G.D. Wright, R.G. Beiko, & A.G. McArthur. 2019. Combining multiple features and algorithms to learn antimicrobial resistance genotype-phenotype relationships. Poster presentation at 27th Conference on Intelligent Systems in Molecular Biology & 18th European Conference on Computational Biology, Basel, Switzerland.

Griffiths, E., D. Dooley, G. Gosal, I. Gill, S. Russell, L. Tindale, V. Pichler, T. Matthews, A. Petkau, J. Adam, D. Fornika, G. Winsor, F. Maguire, B. Alcock, The IRIDA Consortium, A.G. McArthur, R. Beiko, M. Graham, F. Brinkman, G. van Domselaar, & W. Hsiao. 2019. Empowering data sharing for genomics-based public health surveillance using ontologies. Presentation at the 12th International Meeting On Epidemiological Markers (IMMEMXII), Dubrovnik, Croatia.

Matthews, T., F. Bristow, A. Petkau, J. Adam, J. Thiessen, S. Sidhu, P. Kruczkiewicz, D. Dooley, E. Griffiths, D. Fornika, G. Winsor, M. Graham, The IRIDA Consortium, A.G. McArthur, E. Taboada, R. Beiko, F. Brinkman, W. Hsiao, & Gary van Domselaar. 2019. Canada’s Integrated Rapid Infectious Disease Analysis Platform (IRIDA). Presentation at the 12th International Meeting On Epidemiological Markers (IMMEMXII), Dubrovnik, Croatia.


More…

Day, E.A., R.J. Ford, B.K. Smith, P. Mohammadi-Shemirani, M.R. Morrow, R.M. Gutgesel, R. Lu, A.R. Raphenya, A.G. McArthur, N. McInnes, G. Paré, H.C. Gerstein, & G.R. Steinberg. 2019. GDF15 is a metformin stimulated hepatokine that is important for promoting weight loss. Presentation at the Lunenfeld-Tanenbaum International Symposium: Translational Diabetes and Metabolism Research Day, Toronto, Ontario.

Griffiths, E., T. Matthews, A. Petkau, J. Adam, D. Dooley, D. Fornika, G. Winsor, F. Maguire, B. Alcock, The IRIDA Consortium, A.G. McArthur, R. Beiko, M. Graham, F. Brinkman, G. van Domselaar, & W. Hsiao. 2019. Empowering local to global WGS-based surveillance and investigation: The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform. Presentation at the Meeting on Global Microbial Identifier, Singapore.

Matthews, T., J. Adam, A. Petkau, F. Maguire, B. Alcock, A.R. Raphenya, E.J. Griffiths, D. Dooley, B. Jia, G.L. Winsor, The IRIDA Consortium, R.G. Beiko, A.G. McArthur, F.S.L. Brinkman, G.L. Van Domselaar, & W.W.L. Hsiao. 2019. Integrated Rapid Infectious Disease Analysis (IRIDA): a comprehensive and distributed platform for public health genomic epidemiology. Poster presentation at the 2019 Applied Bioinformatics and Public Health Microbiology (ABPHM) Meeting, Cambridge, United Kingdom.

Petkau, A., T. Matthews, F. Bristow, J. Adam, J. Thiessen, S. Sidhu, P. Kruczkiewicz, E. Griffiths, D. Dooley, D. Fornika, G. Winsor, M. Graham, A.R. Raphenya, The IRIDA consortium, E. Taboada, A.G. McArthur, R. Beiko, W. Hsiao, F. Brinkman, G. Van Domselaar. 2019. The IRIDA Platform for Microbial Genomics. Oral presentation at the 2019 Galaxy Community Conference, Freiburg, Germany.

Porter, A.F., A.T. Duggan, J. Klunk, E.C. Holmes, H. Poinar, A.N. Dhody, R. Hicks, G. Smith, M. Humpherys, A. McCollum, W. Davidson, K. Wilkins, Y. Li, A. Burke, H. Polasky, L. Flanders, D. Poinar, A.R. Raphenya, B. Alcock, T.T. Lau, A.G. McArthur, & B. Golding. 2019. Unraveling the evolutionary history of the vaccinia virus, the vaccine for smallpox. Presentation at the Annual Meeting of the Society for Molecular Biology and Evolution, Manchester Central, United Kingdom.

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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!

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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.

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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.

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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 herehttps://github.com/arpcard/state-of-the-card-2019


 

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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).
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November 7, 2018; Hamilton, Ontario, Canada; The 9th annual McMaster Innovation Showcase, with focus on biomedical technologies, highlights the role and impact of McMaster research in shaping the future of healthcare. Hosted by the McMaster Industry Liaison Office (MILO) – supporting innovation, commercialization and community engagement. Photo by Ron Scheffler for McMaster University.

Congratulations to #TeamVirulence for winning the 2018 McMaster Innovation Showcase People’s Choice Poster Award for their poster entitled, “Examining the relationship between virulence and antimicrobial resistance via expansion of the Comprehensive Antibiotic Resistance Database (CARD)”! Left to right: Anatoly MiroshnichenkoHiu-Ki Rachel Tran, Sally Yue Min, and Rafik El Werfalli.

#TeamVirulence also presented their work at the 2018 Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day!

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Some invitations are more special than others. Dr. Peixoto da Cruz and I went to graduate school together in British Columbia (a long time ago!) and while we have since lived in different hemispheres, the bond remains strong. It was great to visit PUG Goiás and learn about Peixoto’s impressive training program in genetic screening and counselling, plus talk about our AMR surveillance efforts.

Bioinformatics of antimicrobial resistance in the age of molecular epidemiology. Invited Keynote presentation by A.G. McArthur at Reunião de Citogenética do Brasil Central & XII Workshop de Genética da PUC Goiás, Goiânia, Brazil, October 2018.

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