Guitor AK, Raphenya AR, Klunk J, Kuch M, Alcock B, Surette MG, McArthur AG, Poinar HN, Wright GD.
Antimicrobial Agents and Chemotherapy 2019 Oct 14. [Epub ahead of print]
The identification and association of the nucleotide sequences encoding antibiotic resistance elements is critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, which are both heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probeset on DNA libraries generated from multi-drug resistant bacteria to selectively capture resistance genes reproducibly produced higher reads on-target at greater length of coverage when compared to shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables sensitive gene detection in diverse environments where antibiotic resistance represents less than 0.1% of the metagenome.
Download the Baits & Protocol at the Comprehensive Antibiotic Resistance Database!
Edalatmand, A. & A.G. McArthur. 2019. Classifying and curating publications on antimicrobial resistance using machine learning. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.
Khan, S., K.K. Tsang, M. Science, D. Kaufman, D. Mertz, J. Pernica, L. Thabane, A.G. McArthur, & M. Loeb. 2019. GloveCare: A pilot study to assess non-sterile glove-based care for the prevention of late onset infection in the NICU. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.
Nasir, J.A., R.A. Kozak, S. Mubareka, H. Poinar, & A.G. McArthur. 2019. Development of virus surveillance tools for clinical diagnostics. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.
Oloni, M., K. Besennov, J. Nash, & A.G. McArthur. 2019. Using the Comprehensive Antimicrobial Resistance Database (CARD) to predict plasmid-borne AMR genes from genome assembly data. Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.
Speicher, D.J., K. Luinstra, J. Maciejewski, K.K. Tsang, S. Patel, V. Allen, A.G. McArthur, & M. Smieja. 2019. Clostridioides difficile strain divergence and prophages in Southern Ontario, Canada (2010-2018). Poster presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.
Tran, H.-K. 2019. In silico prediction of novel type VII polymorphic toxins of the Streptococcus Anginosus Group. Oral presentation at the Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Trainee Day, Hamilton, Ontario, Canada.
The McArthur Lab is very proud to announce Amos Raphenya as 2019 IIDR Michael Kamin Kart Memorial Scholarship Recipient (Staff) and Rachel Tran as 2019 IIDR Michael Kamin Kart Memorial Scholarship Recipient (Undergraduate)! These awards are the highest academic honour for trainees and staff in the Michael G. DeGroote Institute for Infectious Disease Research (IIDR). Awarded during the 2019 IIDR Trainee Day, these awards were accompanied by a talk by Rachel on her summer research: In silico prediction of novel type VII polymorphic toxins in the Streptococcus Anginosus Group.
(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
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.
Waglechner N, McArthur AG, Wright GD.
Nat Microbiol. 2019 Aug 12. [Epub ahead of print]
Glycopeptide antibiotics are produced by Actinobacteria through biosynthetic gene clusters that include genes supporting their regulation, synthesis, export and resistance. The chemical and biosynthetic diversities of glycopeptides are the product of an intricate evolutionary history. Extracting this history from genome sequences is difficult as conservation of the individual components of these gene clusters is variable and each component can have a different trajectory. We show that glycopeptide biosynthesis and resistance in Actinobacteria maps to approximately 150-400 million years ago. Phylogenetic reconciliation reveals that the precursors of glycopeptide biosynthesis are far older than other components, implying that these clusters arose from a pre-existing pool of genes. We find that resistance appeared contemporaneously with biosynthetic genes, raising the possibility that the mechanism of action of glycopeptides was a driver of diversification in these gene clusters. Our results put antibiotic biosynthesis and resistance into an evolutionary context and can guide the future discovery of compounds possessing new mechanisms of action, which are especially needed as the usefulness of the antibiotics available at present is imperilled by human activity.
More details at McMaster’s Brighter World.
PCR detection of mixed and zoonoses Malaria using Plasmodium spp dynein light chain (dlc-tctex) gene
Kariuki MW, Githui E, McArthur AG, Aman RA, Njagi NM, Mwangemi AC, Kamau LW
Annual Research & Review in Biology, 32, 1-12.
Novel gene targets are needed in accurate diagnosis of malaria. Previous studies show that the dynein light chains (dlc) in Plasmodium are uniquely conserved within the species, possibly due to their role as the cargo adptor moiety. This study aimed at the development of PCR assay for the detection of Plasmodium based on the (dlc-Tctex) as a genus and species-specific tool in malaria diagnosis. Multiple primers were designed based on Plasmodium spp dlc(Tctex) genes. The primers were applied on PCR to detect malaria on clinical samples and on laboratory maintained isolates of P. falciparum and P. vivax for human infecting species and P. knowlesi and P. cynomolgi for zoonoses infection involving primates. The amplified PCR fragments were gene cleaned and sequenced. BLASTn e-values output from the raw nucleotide queries supports that the genes are uniquely conserved. Species-specific primers amplified P. falciparum infections with no cross-reactivity to P. vivax, P. knowlesi or P. cynomolgi species. In this assay only 11 out of the 30 microscope positive malaria positive clinical blood samples were positive for PCR detection of P. falciparum infection. Primers designed for Plasmodium genus amplified the target band in all clinical malaria samples but also had another specific band amplification. This preliminary data demonstrate that a species-specific dlc(Tctex) PCR assay can be used for detection of P. falciparum and optimized genus primers can be applied to differentiate mixed malaria infections.
Maguire, F., B. Alcock, A.R. Raphenya, B. Jia. E.J. Griffiths, T.C. Matthews, J. Adam, A. Petkau, G.L. Winsor, IRIDA Consortium, R.G. Beiko, F.S.L. Brinkman, W.W.L. Hsiao. G. Van Domselaar, A.G. McArthur. 2019. Integrated Rapid Infectious Disease Analysis: A comprehensive platform for public health bioinformatics and AMR surveillance using genomic data. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Sherbrooke, Quebec.
Maguire, F., B. Jia, B. Alcock, A.R. Raphenya, F.S.L. Brinkman, A.G. McArthur, & R.G. Beiko. 2019. Precise identification of antimicrobial resistance determinants from metagenomic data. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Sherbrooke, Quebec.
Alcock, B.P., A.R. Raphenya, F. Maguire, F.S. Brinkman, R.G. Beiko, & A.G. McArthur. 2019. Resistome and variant prediction for improved antimicrobial surveillance with the Comprehensive Antibiotic Resistance Database. Poster presentation at the American Society for Microbiology Microbe Meeting, San Francisco, California.
Raphenya, A.R., T.T.Y. Lau, B. Alcock, K.K. Tsang, F. Maguire, F.S. Brinkman, R.G. Beiko, & A.G. McArthur. 2019. Resistance Gene Identifier (RGI) – Prediction of antimicrobial resistance genes and mutations for genomic and metagenomic sequencing data. Oral presentation at the American Society for Microbiology Microbe Meeting, San Francisco, California.
Chen, J. C.-Y., C.G. Clark, A. Bharat, A.G. McArthur, M.R. Graham, G.R. Westmacott, & G. Van Domselaar. 2019. Detection of antimicrobial resistance using proteomics and the Comprehensive Antibiotic Resistance Database: A case study. Presentation at 27th Conference on Intelligent Systems in Molecular Biology & 18th European Conference on Computational Biology, Basel, Switzerland.
Tsang, K.K., F. Maguire, H. Zubyk, S. Chou, G.D. Wright, R.G. Beiko, & A.G. McArthur. 2019. Combining multiple features and algorithms to learn antimicrobial resistance genotype-phenotype relationships. Poster presentation at 27th Conference on Intelligent Systems in Molecular Biology & 18th European Conference on Computational Biology, Basel, Switzerland.
Griffiths, E., D. Dooley, G. Gosal, I. Gill, S. Russell, L. Tindale, V. Pichler, T. Matthews, A. Petkau, J. Adam, D. Fornika, G. Winsor, F. Maguire, B. Alcock, The IRIDA Consortium, A.G. McArthur, R. Beiko, M. Graham, F. Brinkman, G. van Domselaar, & W. Hsiao. 2019. Empowering data sharing for genomics-based public health surveillance using ontologies. Presentation at the 12th International Meeting On Epidemiological Markers (IMMEMXII), Dubrovnik, Croatia.
Matthews, T., F. Bristow, A. Petkau, J. Adam, J. Thiessen, S. Sidhu, P. Kruczkiewicz, D. Dooley, E. Griffiths, D. Fornika, G. Winsor, M. Graham, The IRIDA Consortium, A.G. McArthur, E. Taboada, R. Beiko, F. Brinkman, W. Hsiao, & Gary van Domselaar. 2019. Canada’s Integrated Rapid Infectious Disease Analysis Platform (IRIDA). Presentation at the 12th International Meeting On Epidemiological Markers (IMMEMXII), Dubrovnik, Croatia.
More…
Day, E.A., R.J. Ford, B.K. Smith, P. Mohammadi-Shemirani, M.R. Morrow, R.M. Gutgesel, R. Lu, A.R. Raphenya, A.G. McArthur, N. McInnes, G. Paré, H.C. Gerstein, & G.R. Steinberg. 2019. GDF15 is a metformin stimulated hepatokine that is important for promoting weight loss. Presentation at the Lunenfeld-Tanenbaum International Symposium: Translational Diabetes and Metabolism Research Day, Toronto, Ontario.
Griffiths, E., T. Matthews, A. Petkau, J. Adam, D. Dooley, D. Fornika, G. Winsor, F. Maguire, B. Alcock, The IRIDA Consortium, A.G. McArthur, R. Beiko, M. Graham, F. Brinkman, G. van Domselaar, & W. Hsiao. 2019. Empowering local to global WGS-based surveillance and investigation: The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform. Presentation at the Meeting on Global Microbial Identifier, Singapore.
Matthews, T., J. Adam, A. Petkau, F. Maguire, B. Alcock, A.R. Raphenya, E.J. Griffiths, D. Dooley, B. Jia, G.L. Winsor, The IRIDA Consortium, R.G. Beiko, A.G. McArthur, F.S.L. Brinkman, G.L. Van Domselaar, & W.W.L. Hsiao. 2019. Integrated Rapid Infectious Disease Analysis (IRIDA): a comprehensive and distributed platform for public health genomic epidemiology. Poster presentation at the 2019 Applied Bioinformatics and Public Health Microbiology (ABPHM) Meeting, Cambridge, United Kingdom.
Petkau, A., T. Matthews, F. Bristow, J. Adam, J. Thiessen, S. Sidhu, P. Kruczkiewicz, E. Griffiths, D. Dooley, D. Fornika, G. Winsor, M. Graham, A.R. Raphenya, The IRIDA consortium, E. Taboada, A.G. McArthur, R. Beiko, W. Hsiao, F. Brinkman, G. Van Domselaar. 2019. The IRIDA Platform for Microbial Genomics. Oral presentation at the 2019 Galaxy Community Conference, Freiburg, Germany.
Porter, A.F., A.T. Duggan, J. Klunk, E.C. Holmes, H. Poinar, A.N. Dhody, R. Hicks, G. Smith, M. Humpherys, A. McCollum, W. Davidson, K. Wilkins, Y. Li, A. Burke, H. Polasky, L. Flanders, D. Poinar, A.R. Raphenya, B. Alcock, T.T. Lau, A.G. McArthur, & B. Golding. 2019. Unraveling the evolutionary history of the vaccinia virus, the vaccine for smallpox. Presentation at the Annual Meeting of the Society for Molecular Biology and Evolution, Manchester Central, United Kingdom.
Faltyn, M., B. Alcock, & A.G. McArthur. 2019. Evolution and nomenclature of the trimethoprim resistant dihydrofolate (dfr) reductases. Preprints 2019, 2019050137. [Preprint]
Tsang, K.K., D.J. Speicher, & A.G. McArthur. 2019. Pathogen taxonomy updates at the Comprehensive Antibiotic Resistance Database: Implications for molecular epidemiology. Preprints 2019, 2019070222. [Preprint]
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