University of California, San Francisco

Sequencing Infections to Save Lives

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Project Summary

Our failure to rapidly and accurately diagnose infections results in millions of excess patient deaths a year and threatens public health, especially in low-resource developing countries. Clinical tests that can comprehensively diagnose causes of infection in point-of-care settings are lacking. We previously developed and validated the use of metagenomic sequencing technology as a test that can diagnose all infections, whether from viruses, bacteria, fungi, or parasites, from any body fluid, and have proven its clinical utility in saving the lives of patients with mysterious neurological illnesses. Here we will bring this technology to Africa by providing "lab-in-a-suitcase" sequencing kits to diagnose infection and prioritize local clinical and public health needs (e.g. surveillance for viral hemorrhagic fevers such as Ebola). We will leverage existing and sustainable laboratory infrastructure provided by our African partners to train and equip them with the diagnostic tools to guide patient treatments, stop outbreaks, and save lives.

Problem Statement

Infectious diseases are the leading cause of death worldwide and a critical problem of our time. Zika virus was circulating undetected in Brazil for more than a year prior to the appearance of microcephaly-associated birth defects in infants from infected mothers in 2016 [15]. Partly due to the lack of diagnostic testing, the 2013-2016 West African and 2018-2019 ongoing Congo Ebola virus outbreaks spread rapidly and have caused thousands of deaths. Pneumonia and diarrheal disease remain the leading infectious cause of death among children under five worldwide, killing more than 6 million children a year [16]. Even in developed countries, up to 50% of hospitalized patients with acute illnesses remain undiagnosed, resulting in increased morbidity and patient deaths due to delayed or inappropriate therapies.Our collective failure to rapidly and accurately diagnose infections threatens to overwhelm our public health systems. Infectious outbreaks now spread rapidly within hospitals and circulate among a wider population. The problem is especially acute and disproportionate in low-resource countries, which lack the critical tools and infrastructure to diagnosis infections in a timely fashion. Available gold standard microbiological assays to diagnose infection rely on outdated or inefficient approaches (“one bug, one test”) and are thus woefully inadequate to the task. African countries in particular have experienced regular epidemic outbreaks over the past decade. A long-lasting and comprehensive, yet practical, diagnostic solution is needed that will address the continually changing landscape of pathogens, both old and new, that cause life-threatening infections in critically ill patients.

Solution Overview

We conducted the first-ever demonstration of how clinical metagenomic testing improved diagnoses and guided treatment of hospitalized patients with acute infectious diseases [4]. Clinical metagenomic testing saved the life of a patient with a rare brain infection from Nocardia; a separate patient with hepatitis E virus infection was spared from having to undergo a liver transplant. This comprehensive technology has the capacity to diagnose infection from any body fluid – a veritable “portable microbiology lab” that can be brought to any place in the world to diagnose and treat infections in real-time [3].With 100&Change funding, we propose to bring our metagenomic sequencing technology to partner sites in Africa by packaging it as a “lab-in-a-suitcase” kit. The SISL (“Sequencing Infections to Save Lives”) assay will include portable instrumentation, foldable biosafety hoods, a pocket-sized nanopore sequencer, reagents, and a laptop for bioinformatics analysis. We will train local scientists and physicians to process clinical samples and diagnose infections in critically ill patients. SISL kits will be leveraged to address the highest priority clinical and public health unmet needs at each site. We will link to the Health Care/Laboratory Facilities central data management and analysis center through cloud computing interface for real-time metagenomics outcomes data and patient management. A collaborating health economist from UC Berkeley (Dr. Brent Fulton) will assess the overall impact of these efforts on patient outcomes and costs. By leveraging existing laboratory infrastructure at each African site, our efforts to save lives with this technology will be sustainable over time.

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Project Funders

  • NIH/NIAID 2016 - 2021
  • NIH/NIAID 2019 - 2024
  • Wellcome Trust 2016 - 2021

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