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Michael G. DeGroote Institute for Infectious Disease Research, McMaster University

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antibiotic resistance COVID19 genomics lab members presentations SARS-CoV-2 software

Canadian Society of Microbiologists 2023

June 28, 2023July 3, 2023 agmcarthur

Baker, S.J.C., J. Maciejewski, M.-T. Usuanlele, J. Gilchrist, D.R. Sharma, D. Bulir, M. Smieja, M. Loeb, M.G. Surette, A.G. McArthur, & D. Mertz. 2023. Investigating

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Happy 10th Anniversary CARD!

June 11, 2023June 12, 2023 agmcarthur

Today the Comprehensive Antibiotic Resistance Database turns 10 years old! While it started a few years before this in the laboratory of Dr. Gerry Wright,

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Chan Zuckerberg ID and the Comprehensive Antibiotic Resistance Database collaborate to add Resistome prediction to the CZ ID platform

May 25, 2023May 25, 2023 agmcarthur

CARD and CZ ID are thrilled to launch a new CZ ID module that allows researchers to detect and analyze antimicrobial resistance (AMR) genes in

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Bonne Chance Arman!

April 30, 2023May 6, 2023 agmcarthur

Volunteer starting in 2019, thesis student, summer student, Masters student (2020-2022), and developer, Arman Edalatmand has been a great lab member for over 4 years,

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Biocuration 2023

April 24, 2023May 6, 2023 agmcarthur

Alcock, B.P., A.R. Raphenya, A. Edalatmand, & A.G. McArthur. 2023. The Comprehensive Antibiotic Resistance Database – curating the global resistome. Oral presentation at the 16th

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CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database

April 21, 2023April 21, 2023 agmcarthur

Arman Edalatmand & Andrew G McArthur. 2023. Database, doi: 10.1093/database/baad023. Scientific literature is published at a rate that makes manual data extraction a highly time-consuming

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CBW & VTEC 2023

April 18, 2023May 6, 2023 agmcarthur

They’re back! Thanks to Karyn Mukiri, Jalees Nasir, and Madeline McCarthy for serving as Teaching Assistants for the re-booted Canadian Bioinformatics Workshop in Infectious Disease

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antibiotic resistance bioinformatics databases genomics lab members

Team Meta-Model Volunteers

January 10, 2023January 10, 2023 agmcarthur

The McArthur Lab welcomes Team Meta-Model, a volunteer curation team led by former BioPharm Co-Op Keaton Smith, working on curating and upgrading the Comprehensive Antibiotic

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IIDR Trainee Day 2022!

November 16, 2022December 9, 2022 agmcarthur

KARYN MUKIRI – Predicting the total resistome KEATON SMITH – Advancements in curation of the Comprehensive Antibiotic Resistance Database JALEES NASIR – Viral fishing expedition:

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antibiotic resistance bioinformatics databases genomics ontologies publications

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

October 20, 2022 agmcarthur

Alcock et al. 2023. Nucleic Acids Res Oct 20, 2022:gkac920. (online ahead of print) The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance

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antibiotic resistance bioinformatics genomics software

Resistome Gene Identifier (RGI) version 6.0.0

September 12, 2022May 25, 2023 agmcarthur

RGI version 6.0.0 – Major release, with parameter and reference data loading changes that may impact scripts. Please see updated README. Added an option (–keep)

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antibiotic resistance bioinformatics genomics lab members

Welcome new M.Sc. student Mateusz Wlodarski!

September 8, 2022October 4, 2022 agmcarthur

The McArthur lab welcomes back past undergraduate student and now newly minted Biochemistry & Biomedical Sciences M.Sc. student Mateusz Wlodarski! Mateusz will be working on

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Congratulations Arman Edalatmand on the completion of your M.Sc.!

September 2, 2022September 8, 2022 agmcarthur
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antibiotic resistance genomics publications

Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation

August 26, 2022September 8, 2022 agmcarthur

Guitor et al. 2022. Microbiome 10(1):136. Background: Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses;

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Summer Conferences 2022

July 2, 2022July 2, 2022 agmcarthur

(presenters in bold; lab members underlined) Baker, S.J.C., S. Yaqoob, M.-T. Usuanlele, J. Gilchrist, M. Smieja, M. Loeb, S. Khan, J. Pernica, M.G. Surette, A.G.

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antibiotic resistance big data bioinformatics genomics publications

Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing

June 15, 2022June 15, 2022 agmcarthur

Raphenya et al. Scientific Data volume 9, Article number: 341 (2022). Whole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria

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antibiotic resistance genomes genomics

MACGENOM Survey Results

June 14, 2022June 14, 2022 Mugdha Dave

The burden of drug-resistant infections continues to threaten our arsenal of antibiotics. Despite the rise in genomic sequencing of clinical isolates, there is a lack

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antibiotic resistance bioinformatics genomics publications

Performance characteristics of next-generation sequencing for the detection of antimicrobial resistance determinants in Escherichia coli genomes and metagenomes

June 1, 2022June 2, 2022 agmcarthur

Rooney et al. 2022 Jun 1;e0002222. Short-read sequencing can provide detection of multiple genomic determinants of antimicrobial resistance from single bacterial genomes and metagenomic samples.

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antibiotic resistance big data genomics publications

Machine learning for antimicrobial resistance prediction: current practice, limitations, and clinical perspective

May 26, 2022May 26, 2022 agmcarthur

Kim et al. Clin Microbiol Rev. 2022 May 25;e0017921. Antimicrobial resistance (AMR) is a global health crisis that poses a great threat to modern medicine.

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antibiotic resistance bioinformatics databases genomics molecular epidemiology publications software

Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks

May 19, 2022 agmcarthur

Bertelli et al. Microb Genom. 2022 May;8(5). doi: 10.1099/mgen.0.000818. Outbreaks of virulent and/or drug-resistant bacteria have a significant impact on human health and major economic

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