Researchers at Sylvester, University of Miami Host Global Metagenomics Conference Spotlighting Biomedical Research Applications of Wastewater Sampling

Members of the Sylvester Comprehensive Cancer Center, part of the University of Miami Miller School of Medicine, together with other investigators at the University of Miami, were organizers of and speakers at the Global Metagenomics Summit that was recently held at the Fontainebleau hotel in Miami Beach.

George Grills giving a presentation.
George Grills, Sylvester’s director of shared resources

Researchers from Sylvester and the University’s College of Engineering hosted satellite events of this conference on the Miller School campus.

The University of Miami is a pioneering institution in using metagenomics analysis of environmental samples like wastewater for pathogen monitoring and human disease prediction. Investigators from the University played a major role at this scientific conference, which included sessions on using metagenomics for pathogen detection, identification, and profiling, and using the results to inform public health decisions.

“I’m so pleased that the University of Miami hosted the global metagenomics conference. This is a significant opportunity to bring scientists from across the world together to share their experiences, and plan for future collaboration,” said Erin Kobetz, Ph.D., M.P.H., vice provost for research and scholarship at Sylvester, who presented “The New View of Public Health.” “Our work in wastewater sampling was a critical part of our institutional COVID mitigation efforts and represents a beautiful example of applied translational science.”

Former FDA Commissioner Scott Gottlieb, M.D., delivered the keynote “Advances in Cell Therapy and Uncontrolled Spread: Why COVID-19 Crushed Us and How We Can Defeat the Next Pandemic.”

Lauren Mak giving a workshop.
Lauren Mak, Weill Cornell Medicine, teaches a bioinformatics analysis workshop during a conference satellite session.

This Global Metagenomics Summit was the seventh annual meeting of the Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) International Consortium.

“MetaSUB is a global community of scientists and clinicians who develop tools for discovering, tracking, and understanding microbes in cities, and then use these tools to map urban biomes and emerging pathogens,” said conference organizer Christopher E. Mason, Ph.D., MetaSUB founder, professor of physiology and biophysics at Weill Cornell Medicine, and director of the WorldQuant Initiative for Quantitative Prediction.

Collaboration Began in 2020

Sylvester’s ties with Dr. Mason and MetaSUB began early in the pandemic. That was when the host organizer of the 2022 Global Metagenomics Summit, George S. Grills, associate director of Shared Resources at Sylvester, joined the cancer center. Grills had previously served as assistant dean for research resources at Weill Cornell. It was in mid-2020, just as the pandemic was getting into full swing.

Grills said it made sense for Sylvester to embark on an environmental surveillance program to do predictive modeling for SARS-CoV-2, the virus that causes COVID-19 disease.

“With the approval and guidance of Dr. Kobetz, I helped bring together faculty from all the campuses at the University of Miami, and as a multidisciplinary team, we started doing environmental monitoring of the virus, which has expanded to include air, surface and wastewater-based surveillance of pathogens.”

Donovan Henry, Ismael Bejerano and Althea Kennedy demostrating wastewater sampling.
Field demonstration of wastewater sampling on the Medical School campus by Donovan Henry, environmental safety officer; Ismael Bejerano, environmental specialist; and Althea Kennedy, director, Environmental Compliance, Sustainability, and Continuity, UHealth Occupational Health, Safety, and Compliance Division.

A diverse group of Sylvester researchers including Grills, who is co-investigator, along with Stephan Schürer, Ph.D., Helena Solo-Gabriele, Ph.D., and Dr. Mason, all principal investigators, are collaborating on the NIH grant for the Rapid Acceleration of Diagnostics – Radical (RADx-rad) program and all played significant roles in the Global Metagenomics Summit.

Dr. Solo-Gabriele, professor of chemical, environmental, and materials engineering at the College of Engineering, had several roles at the meeting, including presenting “Reflections from RADx-rad Wastewater-based Epidemiologic Studies and Potential Future Directions.”

“I talked about how wastewater measurements for the virus that causes COVID-19 can be used to predict illness in the contributing ‘sewershed,’” said Dr. Solo-Gabriele. “Such measurements can be used to predict the proportion of people who are infected, and results can be used to develop mitigation measures to limit disease spread. For example, if the levels of the virus are high in the wastewater, then the corresponding population within the sewershed may be warned of the increased risk for transmission, and they can choose to wear masks, increase hygiene, and/or avoid crowded places.”

Utility of Metadata

Dr. Schürer, associate director of data sciences at Sylvester and professor of molecular and cellular pharmacology at the Miller School, presented “Data Standards and Informatics Infrastructure to Facilitate Effective Surveillance of COVID-19 Outbreaks: Towards a Global Alert and Response Network.” His presentation focused on the informatics infrastructure and required data standards to track samples and data for surveillance and analytics of SARS-CoV2 in wastewater as part of the South Florida RADx research project.

Kausal Trivedi using wastewater field autosampler.
Kausal Trivedi, Teledyne ISCO, illustrates the operation of the company’s new wastewater field autosampler.

“I shared metadata and how metadata enables interoperability of diverse data and thereby facilitate data modeling,” Dr. Schürer said. “I then illustrated the data standards we have developed for the wastewater surveillance projects and the operational informatics that enable data integration and modeling at local, county and state levels.”

The infrastructure, according to Dr. Schürer, also includes a data portal and dashboard to make all data accessible. All data are submitted to NIH and CDC, he said.

“I outlined how a next generation informatics infrastructure could enable a global alert and response network to detect viral threats, natural or man-made, and deploy a response, for example, by integrating variant and mutation detection of viral threats in wastewater with matching that with the most promising available drugs,” Dr. Schürer said.

Lisa Gwynn, D.O., M.B.A., M.S.P.H., FAAP, associate professor of clinical pediatrics and public health sciences; section chief, community pediatrics; and program director of the Pediatric Mobile Clinic and the School Health Initiative at the Miller School, presented “Wastewater Sampling in Schools: New Strategies in Creating a Culture of Safety.”

Dr. Scott Gottlieb presenting.
Scott Gottlieb, M.D., former FDA commissioner

“Our project is an innovative partnership with two RADx projects at the University of Miami, which utilize advanced technologies to isolate COVID-19 in the wastewater of schools and leverages existing relationships in schools through school-based health centers. Our findings about the risk of outbreaks are shared with the school district to inform parents, teachers, and staff and to assist school leaders in implementing mitigation strategies and public health messaging to keep students safe in school,” Dr. Gwynn said.

Presentations from Miller School, College of Engineering

Also presenting were Naresh Kumar, Ph.D., associate professor of environmental health at the Miller School; Kenneth Goodman, Ph.D., FACMI, FACE, director of the Institute for Bioethics and Health Policy and professor of medicine; Mark Sharkey, M.D., assistant professor of medicine, Division of Infectious Diseases; and Pratim Biswas, Ph.D., professor of chemical, environmental and materials engineering and dean of the College of Engineering. A diverse group of students and trainees from the University of Miami gave seven research poster presentations at the meeting.

Grills, who delivered the opening remarks with Dr. Mason and presented “The Role of Shared Resources in Facilitating Human and Environmental Surveillance for SARS-CoV-2,” said the data available from doing wastewater sampling from all three UM campuses, the UHealth Tower hospital, municipal wastewater system in Miami-Dade County, and now nine public schools in Miami-Dade County, has important implications for not only South Florida but both nationally and globally.

“This research has allowed us to build predictive models for the presence of the virus in the environment, to help predict the occurrence of the disease in the human population. We’ve published about a half dozen publications in the past year. Our results indicate that there is good lead time in terms of when you see the virus that causes COVID in the environment and what you can predict that the disease will show up in clinical cases. We are looking to expand this disease predictive modeling to the surveillance of other pathogens in the environment,” Grills said.

Dr. Mason, who presented on “Sewers, Subways, and Space Stations: Genetic Maps of Earth’s Cities and Beyond,” discussed the consortium’s impressive accomplishments.

Sam Comeford describing techniques.
Sam Comeford, research support specialist, University of Miami, describes how to collect wastewater samples.

“We are excited to launch a new data portal for MetaSUB, in partnership with the Rockefeller Foundation and Biotia, as well as the annotation of over 11,000 novel viruses, a full release of new computational tools for metagenomics analytics, and the plan for new global metagenomics studies,” Dr. Mason said.

This year was the first in-person Global Metagenomics Summit since the pandemic began and was among the largest in the seven-year history of the meetings, according to Grills.

“Usually, about 60 people from around the world come to this annual meeting. The meeting this year had 147 attendees, with most attending onsite, from 64 institutions from 13 countries,” Grills said.

Tags: College of Engineering, COVID-19, Dr. Erin Kobetz, Dr. Kenneth Goodman, Dr. Lisa Gwynn, Dr. Mark Sharkey, Dr. Naresh Kumar, Dr. Scott Gottlieb, Global Metagenomics Summit, MetaSUB, Miller School of Medicine, NIH funding, Sylvester Comprehensive Cancer Center