(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

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Jalees Nasir transferred from the McMaster Biochemistry & Biomedical Sciences Masters program to the Ph.D. program today! Jalees’s work focusses on the developing new genomic tools for clinical surveillance of viral infections.

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David Braley Centre for Antibiotic Discovery gives researchers a fighting chance against antimicrobial resistance.

A forward-looking McMaster donor is investing $7 million in a new research centre dedicated specifically to tackling the growing global threat of antimicrobial resistance.

David Braley, whose gifts to the university include a $50-million investment in McMaster teaching, learning and health-care research and delivery, has allocated $7 million from that 2007 gift towards the new David Braley Centre for Antibiotic Discovery.

The centre will operate from the Michael G. DeGroote Institute for Infectious Disease Research, whose labs and offices are located on campus in the Michael G. DeGroote Centre for Learning and Discovery.

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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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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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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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