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


State of the CARD 2019 Lecture

Tuesday, February 19, 2 – 3 pm MDCL 2232

https://www.eventbrite.ca/e/state-of-the-card-2019-lecture-tickets-55713383229

An introductory lecture on CARD, ARO, and the RGI and their use for data harmonization, AMR surveillance & gene prevalence, genome and metagenome annotation, and their place within the national response to AMR. New efforts on AMR metagenomic analysis, virulence prediction, and identification of mobile elements will be highlighted.

Presenter: Andrew McArthur

Optional Background Reading: Jia et al. 2017. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 45, D566-573.


Web Demo of the CARD, Antibiotic Resistance Ontology (ARO), and Resistance Gene Identifier (RGI)

Tuesday, February 19, 3 – 4 pm MDCL 2232

https://www.eventbrite.ca/e/web-demo-of-the-card-aro-and-rgi-tickets-55713629967

A walkthrough of the CARD website, the Antibiotic Resistance Ontology (ARO), model- and ontological- organization of resistance sequence information, global genome surveillance, and online use of the Resistance Gene Identifier (RGI). Highly recommended if you will be attending one of the subsequent command line training sessions.

Presenter: Andrew McArthur


Hosting your own data on CARD

Wednesday, February 20, 10 – 11 am MDCL 2249

https://www.eventbrite.ca/e/hosting-your-own-data-on-card-tickets-55713736285

Do you have a collection of genome sequences and want them continuously annotated by CARD in a password-secure website? Want your sequencing pipeline to integrate with CARD or use the RGI? Join us for a discussion on how CARD can provide these services.

CARD Members: Andrew McArthur, Brian Alcock


Installing RGI on your Laptop, remote Server, or setting up an RGI server account

Wednesday, February 20, 1 – 3 pm MDCL 2249

https://www.eventbrite.ca/e/installing-rgi-tickets-55713826555

Want to run your own RGI analysis? Need to use options not supported on the CARD website? Want to analyze your metagenomics data? Attend this session to get RGI up and running on your laptop or server or alternatively get registered and started with a RGI server account.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires familiarity with the command line.


Command Line RGI for genomes & genome assemblies: resistome annotation and visualization

Thursday, February 21, 10 am – 12 pm MDCL 2247

https://www.eventbrite.ca/e/command-line-rgi-for-genomes-tickets-55713945912

A training session on how to analyze genomes, genome assemblies, or metagenomic assemblies using RGI at the command line, plus an introduction to publication grade heat map generation.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires RGI installed on your laptop or remote server or a RGI server account. Requires familiarity with the command line.


Command Line RGI for metagenomics & pathogen-of-origin prediction

Thursday, February 21, 2 – 4 pm MDCL 3410

https://www.eventbrite.ca/e/command-line-rgi-for-metagenomics-tickets-55714013113

A training session on CARD’s latest software tools (beta testing) for analysis of metagenomic reads, including an overview of the Burrows Wheeler Transform, the importance of diverse reference sequences, and k-mer algorithms for prediction of pathogen-of-origin of AMR genes.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires RGI installed on your laptop or remote server or a RGI server account. Requires familiarity with the command line.


Drop-In Session

Visit us in the lab with your questions. No sign up required.

Friday, February 22, 9 am – 4 pm, MDCL 2317

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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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Dr. David Speicher has joined the McArthur Lab as our new Molecular Epidemiology Postdoctoral Fellow! David joins us via clinical epidemiology research in infectious disease at St. Joseph’s Healthcare Hamilton plus extensive training and experience in Cambodia, India, Sri Lanka, Kenya, and Australia. David has a depth of experience in infectious disease, virology, molecular biology, epidemiology and biostatistics, microbiology, and diagnostic techniques and will be leading infectious disease molecular epidemiology collaborations with McMaster Children’s Hospital, St. Joseph’s Healthcare Hamilton, and Hamilton Health Sciences with an emphasis on antimicrobial resistance, C. difficile, H. pylori, ShigellaChlamydia trachomatis, and Mycoplasma genitalium. Hear Dr. Speicher talk about his research program on CFMU radio.

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Antimicrobial Resistance: Emergence, Transmission, and Ecology (ARETE). R. Beiko (PI; Dalhousie University), F. Brinkman (co-PI, Simon Fraser University), A.G. McArthur (co-Applicant) + 4 additional co-Applicants. Genome Canada Bioinformatics and Computational Biology Competition.

 

Bioinformatics Tools to Improve Data Sharing and Re-use in Public Health – applications in antimicrobial resistance profiling and source tracking. W. Hsiao (PI; University of British Columbia), A.G. McArthur (co-Applicant) + 8 additional co-Applicants. CIHR Project Grant.

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Congratulations to Kara Tsang for winning the 2018 Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Michael Kamin Hart Memorial Scholarship (MSc), the highest academic honour for graduate students in the IIDR. Awarded during the 2018 IIDR Trainee Day, the award was accompanied by a talk by Kara on her Ph.D. research: (Machine) Learning about antibiotic resistance genotype- phenotype relationships”. Well done Kara!

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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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