1 Almost all infectious diseases can be diagnosed with genome testing

Breakthrough in diagnosing rare infectious neurological diseases

Neurological diseases can be very difficult to diagnose, especially when the cause is a rare or previously unknown pathogen. In many cases, if a diagnosis goes undiagnosed, the patient's condition will continue to worsen.

In the early 2010s, Chiu and his UCSF colleagues Joe DeLisiPh.D., and michael wilsonM.D. has developed a new metagenomic sequencing method to test CSF for potential pathogens that cause neurological infections.

The test works by sequencing all the genetic material in the CSF and running a computer analysis pipeline to separate human sequences from sequences derived from bacteria, viruses, fungi, or parasites. Masu.

In 2014, the team used the technology to help doctors in Wisconsin. treat a young boy He was in critical condition in intensive care with an undiagnosed infection.

After a long series of tests that failed to determine what was wrong with the boy, tests at UCSF determined in just 48 hours that the boy had leptospirosis, which is treatable with penicillin. Doctors gave it to him and he made a full recovery.

Our mNGS tests outperform tests for any other category of neurological infections. ”

mNGS testing soon became routine at UCSF, with hospitals and clinics across the country sending samples to be processed at the UCSF Clinical Microbiology Laboratory, which Chiu heads.

From 2016 to 2023, the UCSF team analyzed nearly 5,000 CSF samples with this test, and found that 14.4% of them were infected. In these samples, the test correctly identified the pathogen 86% of the time.

“Our mNGS test outperforms any other category of tests for neurological infections. These results make mNGS testing an important part of the diagnostic arsenal for physicians treating patients with infectious diseases. ”, Chiu said.

To increase access to this technology, Chiu, DeRisi, Wilson and others collaborated to found Delve Bio. Delve Bio is currently the exclusive provider of the mNGS CSF test developed at UCSF.

“These findings support the inclusion of mNGS as a core tool in the clinical workup of CNS infections,” said Steve Miller, MD, chief medical officer at Delve Bio. “mNGS provides the single most unbiased, complete, and definitive tool for pathogen detection. mNGS can rapidly diagnose infections, thereby improving management decisions and treatment of meningitis and encephalitis patients. This can provide guidance and potentially reduce healthcare costs in the future.”

Prepare for the next pandemic

mNGS tests must be fast if they are to serve as an early warning system for a pandemic. Chiu and his colleagues have figured out how to adapt and automate this for processing respiratory fluids.

While a CSF test requires more than 100 separate steps and can take two to seven days to process, a respiratory test requires just 30 minutes of hands-on time before the robots and algorithms take over.

“Our goal was to complete the entire process within 12 to 24 hours, with results available the same or next day,” Chiu says.

In the Nature Communications study, researchers say the test can detect respiratory viruses with pandemic potential, such as SARS-CoV-2, influenza A and B, and RSV, even when only small amounts of the virus are present. It has been demonstrated that it can be detected within one day. With a sample.

They also modeled the technology's ability to detect diverse viruses, or newly evolved strains, and found that it could hypothetically detect all viruses if they emerged in the future.

Both the CSF and respiratory versions of the mNGS test have received breakthrough device designation from the U.S. Food and Drug Administration (FDA).

author: for natural medicine Other UCSF authors of the paper are Patrick Benoit, MD, Noah Brazer, Mikael de Lorenzi-Tognon, MD, PhD, Emily Kelly, MD, MS, Venice Serbellita, MS, Miriam Oseguera, Jenny Nguyen, MD, MA, and Jack Tang. , MHS. , Charles Omura, Jessica Streithorst, PhD, Melissa Hilberg, Daniel Ingebrigsen, MHS, Kelsey Sohn, MHS, Michael R. Wilson, MD. See the paper for all authors.

for nature communications Paper, other UCSF authors include Jessica Kariel Tan, Ph.D., Venice Servelita, M.S., Doug Streich, Emily Kelley, M.D., M.S., Jessica Streithorst, Ph.D., Nanami Sumimoto, Abiodun Foresais, Hee Jae. -Fu, Jenny Nguyen, MD, MS, Miriam Oseguera. , Noah Brazer, Jack Tang, MHS, Danielle Ingebrigtsen, MHS, Becky Fung, Helen Reyes, Melissa Hillberg, Peter M. Mourani, Charles R. Langelier, MD, PhD, Mikael de Lorenzi-Tognon, MD, PhD, and Patrick Benoit , MD. See the paper for all authors.

Funding: of natural medicine This paper was supported in part by BARDA EZ-BAA award 75A50122C00022, US CDC grants 75D30122C15360 and 75D30121C12641, and the Chan Zuckerberg Biohub San Francisco.

of nature communications This paper was supported in part by BARDA EZ-BAA 494 award 75A50122C00022, US CDC grants 75D30122C15360 and 75D30121C12641, Abbott Laboratories, and Chan Zuckerberg Biohub San Francisco.

Disclosure: Chiu is the founder of Delve Bio and serves on the company's scientific advisory board as well as those of Flightpath Biosciences, Biomeme, Mammoth Biosciences, BiomeSense, and Poppy Health. He is also the inventor of US Patent 509 11380421, “Pathogen Detection Using Next Generation Sequencing.” Wilson is a co-founder and serves on Delve Bio's scientific advisory board and board of directors.

Breakthrough in diagnosing rare infectious neurological diseases

Neurological diseases can be very difficult to diagnose, especially when the cause is a rare or previously unknown pathogen. In many cases, if a diagnosis goes undiagnosed, the patient's condition will continue to worsen.

In the early 2010s, Chiu and his UCSF colleagues Joe DeLisiPh.D., and michael wilsonM.D. has developed a new metagenomic sequencing method to test CSF for potential pathogens that cause neurological infections.

The test works by sequencing all the genetic material in the CSF and running a computer analysis pipeline to separate human sequences from sequences derived from bacteria, viruses, fungi, or parasites. Masu.

In 2014, the team used the technology to help doctors in Wisconsin. treat a young boy He was in critical condition in intensive care with an undiagnosed infection.

After a long series of tests that failed to determine what was wrong with the boy, tests at UCSF determined in just 48 hours that the boy had leptospirosis, which is treatable with penicillin. Doctors gave it to him and he made a full recovery.

Our mNGS tests outperform tests for any other category of neurological infections. ”

mNGS testing soon became routine at UCSF, with hospitals and clinics across the country sending samples to be processed at the UCSF Clinical Microbiology Laboratory, which Chiu heads.

From 2016 to 2023, the UCSF team analyzed nearly 5,000 CSF samples with this test, and found that 14.4% of them were infected. In these samples, the test correctly identified the pathogen 86% of the time.

“Our mNGS test outperforms any other category of tests for neurological infections. These results make mNGS testing an important part of the diagnostic arsenal for physicians treating patients with infectious diseases. ”, Chiu said.

To increase access to this technology, Chiu, DeRisi, Wilson and others collaborated to found Delve Bio. Delve Bio is currently the exclusive provider of the mNGS CSF test developed at UCSF.

“These findings support the inclusion of mNGS as a core tool in the clinical workup of CNS infections,” said Steve Miller, MD, chief medical officer at Delve Bio. “mNGS provides the single most unbiased, complete and definitive tool for pathogen detection. Thanks to its ability to quickly diagnose infections, mNGS has become an important tool in the management of meningitis and encephalitis patients. It can help guide decisions and treatments and potentially reduce healthcare costs in the future.”

Prepare for the next pandemic

mNGS tests must be fast if they are to serve as an early warning system for a pandemic. Chiu and his colleagues have figured out how to adapt and automate this for processing respiratory fluids.

While a CSF test requires more than 100 separate steps and can take two to seven days to process, a respiratory test requires just 30 minutes of hands-on time before the robots and algorithms take over.

“Our goal was to complete the entire process within 12 to 24 hours, with results available the same or next day,” Chiu says.

In the Nature Communications study, researchers say the test can detect respiratory viruses with pandemic potential, such as SARS-CoV-2, influenza A and B, and RSV, even when only small amounts of the virus are present. It was demonstrated that it was possible to detect within one day. With a sample.

They also modeled the technology's ability to detect diverse viruses, or newly evolved strains, and found that it could hypothetically detect all viruses if they emerged in the future.

Both the CSF and respiratory versions of the mNGS test have received breakthrough device designation from the U.S. Food and Drug Administration (FDA).

author: for natural medicine Other UCSF authors of the paper are Patrick Benoit, MD, Noah Brazer, Mikael de Lorenzi-Tognon, MD, PhD, Emily Kelly, MD, MS, Venice Serbellita, MS, Miriam Oseguera, Jenny Nguyen, MD, MA, and Jack Tang. , MHS. , Charles Omura, Jessica Streithorst, PhD, Melissa Hilberg, Daniel Ingebrigsen, MHS, Kelsey Sohn, MHS, Michael R. Wilson, MD. See the paper for all authors.

for nature communications Paper, other UCSF authors include Jessica Kariel Tan, Ph.D., Venice Servelita, M.S., Doug Streich, Emily Kelley, M.D., M.S., Jessica Streithorst, Ph.D., Nanami Sumimoto, Abiodun Foresais, Hee Jae. -Fu, Jenny Nguyen, MD, MS, Miriam Oseguera. , Noah Brazer, Jack Tang, MHS, Danielle Ingebrigtsen, MHS, Becky Fung, Helen Reyes, Melissa Hillberg, Peter M. Mourani, Charles R. Langelier, MD, PhD, Mikael de Lorenzi-Tognon, MD, PhD, and Patrick Benoit , MD. See the paper for all authors.

Funding: of natural medicine This paper was supported in part by BARDA EZ-BAA award 75A50122C00022, US CDC grants 75D30122C15360 and 75D30121C12641, and the Chan Zuckerberg Biohub San Francisco.

of nature communications This paper was supported in part by BARDA EZ-BAA 494 award 75A50122C00022, US CDC grants 75D30122C15360 and 75D30121C12641, Abbott Laboratories, and Chan Zuckerberg Biohub San Francisco.

Disclosure: Chiu is the founder of Delve Bio and serves on the company's scientific advisory board as well as those of Flightpath Biosciences, Biomeme, Mammoth Biosciences, BiomeSense, and Poppy Health. He is also the inventor of US Patent 509 11380421, “Pathogen Detection Using Next Generation Sequencing.” Wilson is a co-founder and serves on Delve Bio's scientific advisory board and board of directors.

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