Quick update on the status of the McArthur Lab and the Comprehensive Antibiotic Resistance Database. While our home institution McMaster University is closed to on-site research and undergraduate/graduate teaching, all McArthur Lab members and CARD staff are working from home. However, like many genomics labs in Canada we are directly helping our clinical colleagues in analysis of SARS-CoV-2 sequences, lending processing power, staff time, and expertise. Response time for CARD might be a bit slow as we are stretched a bit thin. But on May 1st, 2020 we will be joined by William Huynh as Junior CARD Curator & Help Desk manager. We are excited to have William join us and expect to come back strong supporting the AMR research community in May.
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.
The McArthur Lab is very proud to announce Amos Raphenya as 2019 IIDR Michael Kamin Kart Memorial Scholarship Recipient (Staff) and Rachel Tran as 2019 IIDR Michael Kamin Kart Memorial Scholarship Recipient (Undergraduate)! These awards are the highest academic honour for trainees and staff in the Michael G. DeGroote Institute for Infectious Disease Research (IIDR). Awarded during the 2019 IIDR Trainee Day, these awards were accompanied by a talk by Rachel on her summer research: In silico prediction of novel type VII polymorphic toxins in the Streptococcus Anginosus Group.
(left to right) Back row: Amos Raphenya, Arman Edalatmand, Brian Alcock, Andrew McArthur, David Speicher, Martins Oloni, Sohaib Syed. Front row: William Huynh, Anna-Lisa Nguyen, Megane Bouchard, Rachel Tran, Hamna Imtiaz, Jalees Nasir, Corie Niu, Hafsa Omer, Kara Tsang. Missing: Marcel Jansen, Sarah Yaqoob. Who’s who?
Welcome 2019-2020 Undergraduates!
Biochem 4T15, BiomedDC 4A15 Thesis – Rachel Tran, Arman Edalatmand, Marcel Jansen, William Huynh, Sohaib Syed
Biochem 3R06, HthSci 3H06 Project – Corie Niu, Hamna Imtiaz, Megane Bouchard
Science 3RP3, LifeSci 3RP3 Inquiry – Hafsa Omer, Sarah Yaqoob
Data Volunteer – Anna-Lisa Nguyen
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.
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.
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, Shigella, Chlamydia trachomatis, and Mycoplasma genitalium. Hear Dr. Speicher talk about his research program on CFMU radio.