IDSeq is a cloud-based, open-source bioinformatics pipeline for metagenomic sequencing . In non-scientist speak, it’s packages of computer code that comb through all the genetic material extracted from a sample—a tube of human blood, say, or a swab that’s been up someone’s nose. It matches all those mish-mashed bits of DNA and RNA to massive databases of known microbes, telling you which bugs are in the mix. Running IDSeq only requires having a sequencer you know how to use and an internet connection.
IDSeq started out as a research project in the UC San Francisco lab of biochemist Joe DeRisi, where 17 years ago his team built technology that identified the coronavirus that causes SARS. More recently, DeRisi’s lab has been behind a push into clinical metagenomic sequencing , developing tests that have helped solve medical mysteries for patients being treated at nearby hospitals, including the case of a brain-invading tapeworm.In 2016, when pediatrician Priscilla Chan, and her husband, Facebook founder Mark Zuckerberg, pledged $3 billion over 10 years to fight infectious diseases, they chose DeRisi to co-helm their first investment: a new $600 million research center called the Chan Zuckerberg Biohub. Shortly after joining the Biohub, DeRisi brought on a large team of designers and engineers to turn years of cobbled-together code from his lab into an industrial-strength software package. In October, 2018, they soft-launched IDSeq to a small group of test users, with the Facebook fortune footing the bill for all that computational crunching.
To get it into the hands of more scientists, especially in under-resourced places, the Biohub teamed up with the Bill and Melinda Gates Foundation. Grants from the foundation have begun to bring 10 teams of researchers from countries including South Africa, Bangladesh, and Madagascar to the Biohub to learn how to use IDSeq. In addition to training, the grants equip each international team with a small sequencer to bring back to their home labs.Manning received one of those grants to expand her work investigating undiagnosed fevers in Cambodia. At the end of last summer, just as the worst dengue epidemic in Cambodia’s history was peaking, she flew to San Francisco with two technicians from her lab for a week of training at the Biohub. By November, her team had IDSeq up and running, processing blood samples collected from fever patients at field hospitals across Cambodia. In early January, DeRisi brought a Biohub team to visit Manning’s lab and troubleshoot any issues they were having. During the trip, Manning recalls, they discussed news reports of mysterious pneumonia cases coming out of Wuhan, China. At the time, there weren’t wide reports of healthcare workers getting sick, so they expected it to blow over soon. DeRisi’s team flew back to California. “Then everything just hit the roof,” says Manning.
The girl, though, has been receiving a cocktail of three phages from Hatfull’s lab since June—including two that were genetically modified to better attack her bacteria. The Cystic Fibrosis Foundation recently committed $100 million to better detect, prevent, and treat the chronic lung infections that often develop resistance as a result of antibiotic escalation.