Cloud-based platform—IDseq—shows potential to track the causes and spread of infectious diseases worldwide using metagenomic data
Here’s the latest example of how big data and related technologies can give physicians—as well as microbiologists and clinical pathologists—a new tool for understanding infectious disease and tracking outbreaks anywhere in the world. This project is being funded and organized by well-known Silicon Valley entrepreneurs.
The project is known as IDseq. It was announced recently in a press release issued by Chan Zuckerberg Biohub (CZ Biohub), Chan Zuckerberg Initiative (CZI), and the Bill and Melinda Gates Foundation. IDseq is a platform designed to support global disease surveillance and prevention. It will make use of gene sequencing and analysis of metagenomic data. This data will be made accessible to the global medical community.
The system leverages the power of cloud computing to streamline the process of transmitting and analyzing metagenomic data, as well as sharing results with other platform users.
“That will be incredibly valuable. Information sharing is one of the most powerful public-health interventions in an outbreak,” Jennifer Gardy, PhD, an epidemiologist at the University of British Columbia, told The Atlantic.
Designed by Engineers to Be Easily Used by Healthcare Providers and Medical Laboratory Technicians
Coverage in The Atlantic notes that IDseq isn’t the first tool to offer similar features. Joseph DeRisi, PhD, a biochemist at the University of California San Francisco and co-president of CZ Biohub, states, however, that IDseq is one of the first designed by a large team of engineers, security experts, and other tech and medical researchers.
Many tools see their origins in academic research and are less friendly to those without advanced academic expertise. The research team’s goal, according to DeRisi, is for IDseq “To enable people in under-resourced areas to do what we’ve been trying to do in San Francisco.”
Two Trials Show Promise for IDseq Use
While the software is already available for free as a collection of open source tools, the IDseq platform is now in a “soft launch” phase. The Bill and Melinda Gates Foundation is funding training for clinicians at CZ Biohub’s labs in San Francisco through its Grand Challenges Explorations Initiative.
However, the platform has already achieved success in two noted scenarios—one at Dhaka Shishu Hospital in Dhaka, Bangladesh, and another in Tororo District Hospital in Uganda. Both used the system to analyze the samples of children admitted for fevers for which they found no known cause.
In the Dhaka cases, Senjuti Saha, PhD, a microbiologist from Child Health Research Foundation, used the platform to trace unexplained cases of meningitis to an earlier chikungunya virus outbreak. Saha explained to The Atlantic that her colleagues previously thought chikungunya could not cause meningitis. The platform found otherwise, allowing her to analyze a further 478 samples and detect an additional 17 cases of potential chikungunya-related meningitis.
In the Uganda cases, the researchers used metagenomic next-generation sequencing (mNGS) data and the IDseq platform to investigate unknown causes of fever in children.
“As progress is made toward elimination of malaria in sub-Saharan Africa, it will be increasingly important to understand the landscape of pathogens that account for the remaining burden of morbidity and mortality,” researchers state in their study, currently in early access at bioRxiv. “The use of mNGS can contribute importantly to this understanding, offering unbiased identification of infecting pathogens.”
Wide-Spread Use of IDseq Not Without Challenges
While an article in Medium by Charles de Bourcy, PhD, Software Engineer at Chan Zuckerberg Initiative, outlines how the IDseq platform can process up to 480GB in approximately 10 minutes, it doesn’t account for the initial data input, which can be daunting.
For areas with weak infrastructure and/or slow connection speeds, this could add significant delays as medical laboratories and healthcare workers at remote sites attempt to transfer data to the nearest IDseq-enabled location. Saha told The Atlantic, “If the transfer is too slow or the data too large, we just [ship] hard drives.”
Sequencing requirements create additional concerns. Bulky equipment and the skills required to run sequencers could limit the ability to use the IDseq platform to analyze and share results. Clinicians might also face difficulties in sourcing sequencing reagents due to customs and supply chain concerns.
Finally, the platform still requires an expert to interpret findings. “IDseq is an excellent tool, but it needs to be paired with people who have substantive knowledge to guide its use,” Saha told The Atlantic.
Regardless of these issues, Saha believes IDseq can help remote/resource-challenged medical labs chase diseases. “It doesn’t solve all the problems, but it means that groups like ours don’t have to spend time to build up [sequencing] capacity. And anything is better than nothing.”
IDseq might offer an excellent opportunity for microbiology laboratories, clinical laboratories, and medical researchers around the world to share data surrounding outbreaks, track disease on global and community level, and better determine the strains and probable sources of infectious diseases.
“It’s easy for us to sit in our labs dreaming up tools and platforms,” Jennifer Gardy, PhD (above), an epidemiologist at the University of British Columbia, told The Atlantic. “But we need to make sure we’re designing them in a way that makes sense to the doctors, nurses, lab techs, and epidemiologists out there in an outbreak.” (Photo copyright: Michelle Thorpe/University of British Columbia.)
—Jon Stone
Related Information: Chan, Zuckerberg and the Gates Foundation Unveil Open-Source Global Infectious Disease Tracker IDseq: An Open Source Platform for Infectious Disease Detectives Chan Zuckerberg Biohub and Chan Zuckerberg Initiative Announce First-of-Its-Kind “IDseq” Platform and Service to Enable Real-Time Global Disease Surveillance and Prevention A Simpler Way to Get to the Bottom of Mysterious Illnesses in Poor Countries Etiology of Fever in Ugandan Children: Identification of Microbial Pathogens Using Metagenomic Next-Generation Sequencing and IDseq, a Platform for Unbiased Metagenomic Analysis