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

This February 2018 release is our largest to date and includes new data types, a new classification system, an entirely new version of the Resistance Gene Identifier, and website improvements.

CARD Curation: 37 new ADC beta-lactamases, 21 PDC beta-lactamases, new MCR proteins, 23 rRNA mutations, resistant isoleucyl-tRNA synthetases, hundreds of new resistance mutations, and more. While in past releases all curated AMR mutations were those characterized from clinical isolates, CARD now additionally includes mutations discovered via in vitro selection experiments. Ontological improvements have been made to enable an entirely new classification system for CARD data and RGI results: resistance determinants are now systematically categorized by AMR Gene Family, Drug Class, and Resistance Mechanism. The Antibiotic Resistance Ontology is now additionally available via GitHub, https://github.com/arpcard.

Resistance Gene Identifier: Entirely new codebase, compatible with CARD data (card.json) version 2.0.0 and up (download separately). Open Reading Frame (ORF) prediction using Prodigal, homolog detection using BLAST (default) or DIAMOND, and Strict significance based on CARD curated bitscore cut-offs. Addition of rRNA mutation and efflux over-expression models. Hits of 95% identity or better are automatically listed as Strict. All results organized by revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Revised documentation, command line menu, and website graphical interface. The Resistance Gene Identifier is now additionally available via GitHub, https://github.com/arpcard.

Prevalence, Genomes, & Variants: Expansion of our computer-generated data set on the prevalence of AMR genes and variants among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI for clinically important pathogens. CARD Prevalence 2.0.0 is based on sequence data acquired from NCBI on August 28, 2017, analyzed using RGI 4.0.0 (DIAMOND homolog detection) and CARD 2.0.0. Now includes results for protein overexpression models and rRNA mutations. All results organized by the revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Download files now include 35000+ genome annotations and all predicted sequence variants.

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Congratulations to our 3rd year Biochemistry & Biomedical Sciences students upon completion of their research projects! Both will be staying on as summer research students.

 

Tammy Lau – The Importance of Protocol Design for RNA-Seq in the Ongoing Development of a Novel Technology for Tissue Specific Gene Expression Profiling in C. elegans

Arjun Sharma – The Glycopeptide Resistance Predictor

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Congratulations to 4th Year Biomedical Discovery & Commercialization student and McArthur lab member Suman Virdee for her CIHR Undergraduate Summer Studentship Award for her summer project “Development and implementation of computational tools to dissect cancer stem cell circuitry”, a joint project between our laboratory and that of Dr. Kristin Hope!

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genomecanadacolorThe McArthur lab and the Comprehensive Antibiotic Resistance Database are proud to have contributed to the Genome Canada – Canadian Food Inspection Agency Forum on Genomics and Antimicrobial Resistance. The two-day event brought together over sixty leading experts from academic, government, industry and commodities groups to address the challenge of AMR and discuss a path forward. A summary of the Forum and the Workshop Report are now online.

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genome-canada-1A cross-national research consortia co-led by McMaster’s Andrew McArthur is receiving two of 16 federal grants to further develop a big data solution to the growing problem of antimicrobial resistance (AMR). The government’s investment, totaling more than $4M, is the result of Genome Canada’s 2015 Bioinformatics and Computational Biology Competition, a partnership with the Canadian Institutes of Health Research (CIHR). McArthur and his colleagues will receive $500,000 over two years. McArthur will work closely with researchers from the University of British Columbia, Simon Fraser University, Dalhousie University and the Public Health Agency of Canada to design and develop novel software and database systems that will empower public health agencies and the agri-food sector to rapidly respond to threats posed by infectious disease outbreaks and food-borne illnesses.

Full Coverage: Faculty of Health Sciences, Genome Canada, Newswire, Hamilton Spectator

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CIHR (G. Steinberg, McMaster University, Canada) Gene Environment Team on Brown/beige Adipose Tissue (GET_BAT). In this project we will conduct studies in cells, mice and humans to examine how agricultural and food processing practices may regulate brown adipose tissue metabolic activity directly or indirectly by altering the billions of bacteria that reside within our gastrointestinal tract.

NIH/NIEHS (M. Jenny, University of Alabama, USA) The role of MTF-1 as a mediator of ocular toxicity. The major goals of this project are to characterize the role of MTF-1 in regulating genes involved in eye development.

NIH/NIEHS (A. Timme-Laragy, University of Massachusetts Amherst) Activation of Nrf2 during embryonic development: mechanisms and consequences. Examining the possible regulatory role of Nrf2 in early embryonic development, with emphasis upon molecular responses to oxidative stress.

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Fellowship-winners-2016-1Ten undergraduate students from the faculties of Science and Health Sciences have been awarded the prestigious Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Summer Student Fellowship, including our own Briony Lago (third from the right). This highly competitive fellowship, now in its fourth year and worth $1,000, is designed to support students working in the labs of IIDR members during their summer practicum, which runs from May to August. Briony Lago joined the lab as part of her McMaster Chemical Biology Co-Op program, working on our ‘Omic’ Responses & Inactivity in Aging project (a collaboration with colleagues in Kinesiology & Chemistry), our collaboration with Bates College on the role of Nfe2 in oxidative stress response during zebrafish development, and biocuration of our Comprehensive Antibiotic Resistance Database.

See: Q&A with IIDR Summer Fellowship recipient Briony Lago

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