A week of lectures, demos, and training for the Comprehensive Antibiotic Resistance Database

During McMaster Spring Mid-Term Recess (February 18-24), the McArthur lab is pleased to present a series of lectures, demonstrations, and training sessions for the Comprehensive Antibiotic Resistance Database (card.mcmaster.ca) and its associated Resistance Gene Identifier (RGI) software, sponsored by the Michael G. DeGroote Institute for Infectious Disease Research (IIDR).

Questions? Email card@mcmaster.ca

  


Workshop & Lecture material will be available herehttps://github.com/arpcard/state-of-the-card-2019


State of the CARD 2019 Lecture

Tuesday, February 19, 2 – 3 pm MDCL 2232

https://www.eventbrite.ca/e/state-of-the-card-2019-lecture-tickets-55713383229

An introductory lecture on CARD, ARO, and the RGI and their use for data harmonization, AMR surveillance & gene prevalence, genome and metagenome annotation, and their place within the national response to AMR. New efforts on AMR metagenomic analysis, virulence prediction, and identification of mobile elements will be highlighted.

Presenter: Andrew McArthur

Optional Background Reading: Jia et al. 2017. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 45, D566-573.


Web Demo of the CARD, Antibiotic Resistance Ontology (ARO), and Resistance Gene Identifier (RGI)

Tuesday, February 19, 3 – 4 pm MDCL 2232

https://www.eventbrite.ca/e/web-demo-of-the-card-aro-and-rgi-tickets-55713629967

A walkthrough of the CARD website, the Antibiotic Resistance Ontology (ARO), model- and ontological- organization of resistance sequence information, global genome surveillance, and online use of the Resistance Gene Identifier (RGI). Highly recommended if you will be attending one of the subsequent command line training sessions.

Presenter: Andrew McArthur


Hosting your own data on CARD

Wednesday, February 20, 10 – 11 am MDCL 2249

https://www.eventbrite.ca/e/hosting-your-own-data-on-card-tickets-55713736285

Do you have a collection of genome sequences and want them continuously annotated by CARD in a password-secure website? Want your sequencing pipeline to integrate with CARD or use the RGI? Join us for a discussion on how CARD can provide these services.

CARD Members: Andrew McArthur, Brian Alcock


Installing RGI on your Laptop, remote Server, or setting up an RGI server account

Wednesday, February 20, 1 – 3 pm MDCL 2249

https://www.eventbrite.ca/e/installing-rgi-tickets-55713826555

Want to run your own RGI analysis? Need to use options not supported on the CARD website? Want to analyze your metagenomics data? Attend this session to get RGI up and running on your laptop or server or alternatively get registered and started with a RGI server account.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires familiarity with the command line.


Command Line RGI for genomes & genome assemblies: resistome annotation and visualization

Thursday, February 21, 10 am – 12 pm MDCL 2247

https://www.eventbrite.ca/e/command-line-rgi-for-genomes-tickets-55713945912

A training session on how to analyze genomes, genome assemblies, or metagenomic assemblies using RGI at the command line, plus an introduction to publication grade heat map generation.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires RGI installed on your laptop or remote server or a RGI server account. Requires familiarity with the command line.


Command Line RGI for metagenomics & pathogen-of-origin prediction

Thursday, February 21, 2 – 4 pm MDCL 3410

https://www.eventbrite.ca/e/command-line-rgi-for-metagenomics-tickets-55714013113

A training session on CARD’s latest software tools (beta testing) for analysis of metagenomic reads, including an overview of the Burrows Wheeler Transform, the importance of diverse reference sequences, and k-mer algorithms for prediction of pathogen-of-origin of AMR genes.

CARD Members: Amos Raphenya, Brian Alcock, Andrew McArthur

Requires RGI installed on your laptop or remote server or a RGI server account. Requires familiarity with the command line.


Drop-In Session

Visit us in the lab with your questions. No sign up required.

Friday, February 22, 9 am – 4 pm, MDCL 2317

Read more Comments Off on State of the CARD 2019

Antimicrobial Resistance: Emergence, Transmission, and Ecology (ARETE). R. Beiko (PI; Dalhousie University), F. Brinkman (co-PI, Simon Fraser University), A.G. McArthur (co-Applicant) + 4 additional co-Applicants. Genome Canada Bioinformatics and Computational Biology Competition.

 

Bioinformatics Tools to Improve Data Sharing and Re-use in Public Health – applications in antimicrobial resistance profiling and source tracking. W. Hsiao (PI; University of British Columbia), A.G. McArthur (co-Applicant) + 8 additional co-Applicants. CIHR Project Grant.

Read more Comments Off on Some Recent Funding News…

Maguire, F., B. Alcock, F.S. Brinkman, A.G. McArthur, & R.G. Beiko. 2018. AMRtime: Rapid Accurate Identification of Antimicrobial Resistance Determinants from Metagenomic Data. Oral presentation at the Third American Society for Microbiology Meeting on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatics Pipelines, Washington, D.C.

Abstract: Metagenomics, the direct sequencing of the mixture of genomes present in a sample, is an increasingly common workflow within the life sciences. It is frequently used to investigate previously intractable problems such as the functional characterisation of entire microbial environments. One such use-case of global and national public-health importance is analysing the nature and transmission dynamics of antimicrobial resistance (AMR) determinants in human, agri-food and environmental samples. Recently some tools have been developed to profile AMR from metagenomes, however, these are generally limited to profiling at the level of AMR genes clustered by % sequence identity, which may or may not be biologically meaningful. By exploiting the expertly curated ontological structure of the Comprehensive Antibiotic Resistance Database (CARD) and new CARD Prevalence datasets, we have developed an approach using a hierarchical set of machine learning classifiers. This allows us to produce gene-specific AMR profiles to 2386 determinants as well as profiles for higher order, biologically informed, AMR gene family groups. Firstly, DIAMOND based heuristically accelerated homology searches are used to filter out non-AMR related metagenomic reads. This filtering has been optimised to prioritise minimisation of false negatives over minimising false positives. Features generated from these homology searches as well as sequence features are then used to train a random forest classifier to classify filtered reads into one of 227 CARD AMR gene families (e.g. MCR phosphoethanolamine transferase). For each gene family an additional random forest classifier is trained to classify reads into one of the specific AMR determinants belonging to that family (e.g. MCR-1, MCR-2, MCR-3 etc.). This process involves very little computational overhead when classifying beyond the initial homology search. On a fully held out test-set of MiSeq reads simulated from the CARD canonical gene sequences this method resulted in an average precision and recall of 0.993 and 0.987 at the AMR gene family level. Within the 227 AMR families, 70% (158) had an average F1-score greater than 0.99 for classification to specific AMR determinants. A further 10% (24) averaged F1-scores between 0.8 and 0.99. In comparative analyses on the same dataset this outperformed homology searches alone, read mapping and variation graph based methods in terms of average overall accuracy and precision. Further work will aim to improve classification within certain families and expand AMRtime to include variant based AMR models as well as meta-models (e.g. multi-component efflux pump systems).

Read more Comments Off on Third American Society for Microbiology Meeting on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatics Pipelines

Welcome #TeamVirulence, left to right: Rachel Tran (Biochem 3R06), Sally Min (BiomedDC 4A15), Anatoly Miroshnichencko (BiomedDC 4A15), and Rafik El Werfalli (BiomedDC 4A15), who are collectively working on development of CARD:Virulence, a new branch of the Comprehensive Antibiotic Resistance Database dedicated to the molecular surveillance of bacterial virulence factors.

Read more Comments Off on New undergraduate students!

Tsang, K.K., H. Zubyk, S. Chou, G.D. Wright, & A.G. McArthur. Decoding bad bags: Predicting antibiotic resistance phenotypes from genotype. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.

 

Read more Comments Off on Kara Tsang wins Canadian Society of Microbiologists 2018 Top Student Oral Presentation Award!

  • Alcock, B., A.R. Raphenya, A.N. Sharma, K.K. Tsang, T.T.Y. Lau, A. Hernandez-Koutoucheva, & A.G. McArthur. 2018. Data and curation in the Comprehensive Antibiotic Resistance Database. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Lau, T.T.Y., A.R. Raphenya, B. Alcock, & A.G. McArthur. 2018. Optimizing antimicrobial resistance surveillance tools through biological data organization and taxonomic identification of resistance genes. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Maguire, F., A.R. Raphenya, B. Alcock, A.G. McArthur, F.S. Brinkman, & R.G. Beiko. 2018. The cost of speed: evaluating systematic failures in metagenomic AMR profiling. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Raphenya, A.R., B. Alcock, K.K. Tsang, A.N. Sharma, T.T.Y. Lau, A. Hernandez-Koutoucheva, & A.G. McArthur. 2018. The Comprehensive Antibiotic Resistance Database and the Resistance Gene Identifier – Prediction of antimicrobial resistance genes and mutations for genomic and metagenomic sequencing data. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
  • Tsang, K.K., H. Zubyk, S. Chou, G.D. Wright, & A.G. McArthur. Decoding bad bags: Predicting antibiotic resistance phenotypes from genotype. Oral presentation at the Canadian Society of Microbiologists Annual Meeting, Winnipeg, Manitoba.
Read more Comments Off on 68th Annual Canadian Society of Microbiologist Conference in Tweets

Kara Tsang passed her graduate transfer exam today, officially moving from the McMaster Biochemistry & Biomedical Sciences Masters program to the Ph.D. program. Kara’s work focusses on the intersection of biocuration, bioinformatics, machine learning, mutant screening, and phenotypic testing for prediction antimicrobial resistance phenotype from genotype. Well done Kara!

Update: Hot on the heels of becoming a Ph.D. student, Kara has won a 2018/2019 Department of Biochemistry & Biomedical Sciences’s Fred and Helen Knight Enrichment Award!

Read more Comments Off on Kara Tsang, Ph.D. Student

Tammy Lau has been awarded a prestigious Michael G. DeGroote Institute for Infectious Disease Research (IIDR) Summer Student Fellowship for her work on development of k-mer approaches to predicting pathogen-of-origin for metagenomics antimicrobial resistance gene sequences. More details here.

Congratulations Tammy!

Read more Comments Off on Tammy Lau awarded a 2018 IIDR Summer Student Fellowship

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.

Read more Comments Off on Recent Updates to the Comprehensive Antibiotic Resistance Database
The Comprehensive Antibiotic Resistance Database: Expanded tools for molecular surveillance of antimicrobial resistance (AMR) in the environment, agriculture, and clinic. A.G. McArthur (PI), G. Van Domselaar (co-I, Public Health Agency of Canada), R. Beiko (Co-I, Dalhousie University), F. Brinkman (co-I, Simon Frasier University). CIHR Project Grant.

Preventing Clostridium difficile infections by identifying asymptomatic carriers. D. Mertz, M. Loeb, J. Pernica, S. Khan, M. Smieja, A.G. McArthur (Co-Applicants). Hamilton Health Sciences Research Strategic Initiative Program.

Developing a strain-specific test for rapid diagnosis of Clostridium difficile. Y. Li (PI), A.G. McArthur (co-I), C. Lee (co-I). CIHR Antimicrobial Resistance: Point of Care Diagnostics in Human Health.
Read more Comments Off on Some Funding News…