Collaboration gives scientists on-demand access to global superbug data

McMaster University is working with the infectious disease team at the Chan Zuckerberg Initiative (CZI) to improve access to antimicrobial resistance (AMR) data, so scientists across the world can better prevent global health threats.

Leveraging McMaster’s Comprehensive Antibiotic Resistance Database (CARD), the CZI has developed an AMR module for its open-access metagenomics platform, CZ ID. The new module allows for researchers from all over the world to track and investigate drug-resistant bacteria — or superbugs — on demand.

Developed at McMaster by Andrew McArthur and Gerry Wright, professors in the Department of Biochemistry and Biomedical Sciences and members of the Michael G. DeGroote Institute for Infectious Disease Research, CARD is a rigorously curated bioinformatics database that contains the world’s knowledge of antimicrobial resistance genes.

“AMR is a constantly moving target,” McArthur says. “There’s always going to be new antibiotic resistance genes and new mutations. And due to the continued abuse of antibiotics and other factors, this will likely always be the case.

“Tools like CARD and collaborations like this one with the CZI are important if we hope to keep up with resistance.”

The CZI, a philanthropic organization focused on solving a range of important societal challenges, is actively supporting the science and technology that will make it possible to cure, prevent, or manage all diseases. Tools like CZ ID were designed in service of this mission.

“Antimicrobial resistant microorganisms are a major health concern for communities around the world,” says Patricia Brennan, vice president of science technology at the CZI. “CZ ID’s new AMR module helps ensure that researchers have access to the tools and resources that they need to detect, investigate, and track emerging and novel pathogens, including resistant superbugs. We’re grateful for McMaster’s close collaboration on the implementation of reference data from CARD, which is an integral part of this new capability.”

McArthur, whose work is part of McMaster’s Global Nexus School for Pandemic Prevention & Response, says that CARD is unique because it combines computer-assisted technology with human curation to ensure that only the best, most accurate, and most up-to-date data is captured.

“We rely on algorithms to read the scientific literature and to suggest what might be relevant, but the knowledge that appears in CARD is all curated by specialists at McMaster,” he explains. “The core of CARD is a discipline of science called biocuration — it’s hand-driven.”

Today, the database describes over 7,000 resistance genes and mutations leading to treatment failure in people and animals, as well as drug resistance predictions for 377 important pathogens. These data, McArthur says, are used for an array of research activities, ranging from machine-learning and disease surveillance to pharmaceutical R&D.

And now, through this collaboration, these datapoints will allow for CZ ID users to detect and explore AMR genes in a variety of samples via interactive reports. Importantly, CZ ID is already used in 120 different countries, which will help provide the global research community with new levels of access to CARD data.

McArthur says that this new CZ ID module is the latest in a long string of collaborations for CARD, which is now used by public health agencies, industry groups, and academics based all around the world. For him, the growing utility of the tool signals not only the continued importance of solving drug resistance, but also the “critical role” that metagenomics and data science will play in doing so.