• Alcock, B., A.R. Raphenya, A.N. Sharma, K.K. Tsang, T.T.Y. Lau, A. Hernandez-Koutoucheva, & A.G. McArthur. 2018. Data and curation in the Comprehensive Antibiotic Resistance Database. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Lau, T.T.Y., A.R. Raphenya, B. Alcock, & A.G. McArthur. 2018. Optimizing antimicrobial resistance surveillance tools through biological data organization and taxonomic identification of resistance genes. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Maguire, F., A.R. Raphenya, B. Alcock, A.G. McArthur, F.S. Brinkman, & R.G. Beiko. 2018. The cost of speed: evaluating systematic failures in metagenomic AMR profiling. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Raphenya, A.R., B. Alcock, K.K. Tsang, A.N. Sharma, T.T.Y. Lau, A. Hernandez-Koutoucheva, & A.G. McArthur. 2018. The Comprehensive Antibiotic Resistance Database and the Resistance Gene Identifier – Prediction of antimicrobial resistance genes and mutations for genomic and metagenomic sequencing data. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Tsang, K.K., H. Zubyk, S. Chou, G.D. Wright, & A.G. McArthur. Decoding bad bags: Predicting antibiotic resistance phenotypes from genotype. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
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Kara Tsang passed her graduate transfer exam today, officially moving from the McMaster Biochemistry & Biomedical Sciences Masters program to the Ph.D. program. Kara’s work focusses on the intersection of biocuration, bioinformatics, machine learning, mutant screening, and phenotypic testing for prediction antimicrobial resistance phenotype from genotype. Well done Kara!

Update: Hot on the heels of becoming a Ph.D. student, Kara has won a 2018/2019 Department of Biochemistry & Biomedical Sciences’s Fred and Helen Knight Enrichment Award!

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Kara Tsang wins the McMaster Faculty of Health Sciences Graduate Programs Outstanding Achievement & Excellence in Oral Presentation Awards! Her happy supervisor is honoured to win the Graduate Student Federation Excellence in Graduate Supervision Award!

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Morgan TD, Graham CF, McArthur AG, Raphenya AR, Boreham DR, Manzon RG, Wilson JY, Lance SL, Howland KL, Patrick PH, Somers CM

Canadian Journal of Fisheries and Aquatic Sciences 2018 75(6):836-849.

Round whitefish (Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning.

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Tammy Lau has been awarded a prestigious Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Summer Student Fellowship for her work on development of k-mer approaches to predicting pathogen-of-origin for metagenomics antimicrobial resistance gene sequences. More details here.

Congratulations Tammy!

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The McArthur lab welcomes Pardeep Gill, who will be performing a Biochem 3R06 project on the phylogenetic origins of AraC and NeuB proteins in collaboration with the Knodler lab at Washington State University and the Berti lab of McMaster’s Chemistry & Chemical Biology department, respectively.

Tammy Lau is continuing her k-mer algorithm development for AMR gene pathogen-of-origin prediction thesis work as a summer student (as part of the IRIDA consortium) and Bhavya Singh and Alexandra Florescu will be volunteering part-time on ontology development (as part of the GenEpiO consortium).

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Dr. McArthur has been busy doing some Government outreach. In early 2018 he was a Panellist on Artificial Intelligence in Healthcare at Norwegian Health Ministry & Government of Canada Round Table hosted by Hamilton Health Sciences and then in May 2018 represented McMaster University at Research Canada’s Health Research Caucus – Reshaping Health Research and Innovation: Artificial Intelligence and Machine Learning at Parliament Hill, Ottawa.

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The Comprehensive Antibiotic Resistance Database has been updated, http://card.mcmaster.ca

CARD Curation: Addition of HERA, TRU, & ACI beta-lactamases, sul4, and new quinolone efflux pumps.

Antibiotic Resistance Ontology: Expanded to include an entirely new branch describing AMR phenotypic testing methods. ARO additionally now officially available at the OBO Foundry, allowing formal integration with other ontological resources, most notably the Genomic Epidemiology Application Ontology (GenEpiO), https://github.com/genepio/genepio.

Resistance Gene Identifier: Resistome prediction for low quality or low coverage assemblies, merged metagenomics reads, and small plasmids or assembly contigs. Includes prediction of partial AMR genes. Support added for Docker operating-system-level virtualization (i.e. containerization).

Prevalence, Resistomes, & Variants: Expanded to 67 important pathogens, with a focus on ESKAPEs, WHO Priority Pathogens, and agents of sepsis.

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Congratulations to Jonsson Lui & Kirill Pankov, both alumni of the McArthur, for being awarded Biogen Scholarships as part of their Masters in Biomedical Discovery & Commercialization. Well done! (Jonsson Liu shown)

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Florescu, A., B. Alcock, A. Raphenya, & A.G. McArthur. 2018. Incorporating phenotypic testing into ontological data sharing paradigms. Presentation at Ontario Biology Day, Waterloo, Ontario, Canada.

Lau, T. & A.G. McArthur. 2018. The optimization of antimicrobial resistance surveillance tools. Poster presentation at Ontario Biology Day, Waterloo, Ontario, Canada.

Singh, B., A.G. McArthur, & J. Stone. 2018. Ontological classification of resistance gene annotations for antimicrobial surveillance. Presentation at Ontario Biology Day, Waterloo, Ontario, Canada.

Jenny, M.J., K. Srinivasan, B. O’Shields, & A.G. McArthur. 2018. Sex and age-related differences in cadmium-induced global transcriptomic profiles in adult zebrafish eye tissues. Presentation at the Society of Toxicology 57th Annual Meeting, San Antonio, Texas.

Srinivasan, K., M.J. Jenny, & A.G. McArthur. 2018. Global changes in gene expression in human lens epithelial cells in response to cadmium exposure. Poster presentation at the Society of Toxicology 57th Annual Meeting, San Antonio, Texas

Lau, T. & A.G. McArthur. 2018. The optimization of antimicrobial resistance surveillance tools. Presentation at McMaster Women in Science and Engineering (WISE) Current Research in Engineering, Science & Technology (CREST) Meeting, Hamilton, Ontario, Canada.

Singh, B., A.G. McArthur, & J. Stone. 2018. Ontological classification of resistance gene annotations for antimicrobial surveillance. Presentation at McMaster Women in Science and Engineering (WISE) Current Research in Engineering, Science & Technology (CREST) Meeting, Hamilton, Ontario, Canada.

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