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

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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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antibiotic resistance epidemiology lab members text mining

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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antibiotic resistance genomics molecular epidemiology presentations SARS-CoV-2 text mining virus epidemiology volunteers

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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