RUSH, Discovery Partners Institute Awarded CDC Contract to Test Wastewater for Antibiotic Resistant Organisms

CHICAGO – RUSH and the Discovery Partners Institute are working together to develop innovative ways to use wastewater to monitor antibiotic resistance in health care facilities.

Under a four-year $2 million contract awarded by the Centers for Disease Control and Prevention, scientists from the two institutions will test methods for sampling wastewater from long-term care facilities to identify antibiotic-resistant organisms. 

“Wastewater produced by healthcare facilities may provide important information about emerging multidrug-resistant organisms of public health importance,” said Michael Lin, MD, MPH, a RUSH University Medical Center infectious diseases specialist and principal investigator for the contract. “We will evaluate cutting edge wastewater sampling and detection methods to monitor antibiotic resistant organism threats.”

The collaboration brings together expertise developed at RUSH, which employs genomic sequencing to analyze COVID-19 test samples for the Chicago Department of Public Health, and DPI, which in partnership with University of Illinois Chicago samples wastewater from dozens of treatment plants and sewers to test for SARS-CoV-2 virus and other pathogens for CDPH and the Illinois Department of Public Health.

“We are using the lessons learned from establishing a SARS-CoV-2-focused wastewater surveillance program to expand to other issues of public health importance,” said Rachel Poretsky, PhD, director of the UIC Microbial Ecology Lab, which will be screening for antibiotic-resistant bacteria in the new effort. “The hope is that, in being one of the first teams to develop a framework for identifying multidrug-resistant genes and organisms in long-term care facilities, we will set the stage for future programs like this nationwide.”

Antibiotic resistance causes more than 35,000 deaths and more than 2.8 million infections a year in the United States, according to the CDC. Certain types of multi-drug resistant infections are especially prevalent in health care settings with chronically ill patients who require longer-term respiratory and medical support. 

The RUSH-DPI project will focus on pathogens designated by CDC as urgent threats, such as carbapenem-resistant bacteria and a multidrug-resistant fungus, Candida auris. The project also is partnering with CDPH.

CDC awarded the four-year contract with the long-term goal of creating a network of facility-level antibiotic resistance testing that will be shared with the National Wastewater Surveillance System, as well as local and regional public health agencies. Wastewater-based epidemiology — the testing of raw sewage for pathogens such as the SARS-CoV-2 virus — provides a potential non-invasive, cost-effective way to measure community health, including in areas where clinical surveillance testing may be underutilized or unavailable.

RUSH and DPI will work together to improve the science of detecting antimicrobial resistant organisms in wastewater, helping to reduce multidrug resistant infections. The team will develop ways to sample and test wastewater that most accurately correlate with the types and levels of antimicrobial resistant organisms among the facility’s patients, Lin said. The work will start at one facility and expand to two more.

RUSH’s infectious disease and microbiome research

RUSH University Medical Center is a select partner with the CDC’s Prevention Epicenters Program, working to implement innovative strategies to improve health care quality and patient safety. In addition to his clinical work, Lin has worked with CDC to enhance the surveillance of health care-acquired infections and prevent the spread of multidrug-resistant organisms. 

RUSH University’s Genomics and Microbiome Core Facility is the site of the Regional Innovative Public Health Laboratory, which provides CDPH with whole genome sequencing for SARS-CoV-2 and other pathogens, as well as large-volume data management and expertise in genomic epidemiology.

DPI and UIC wastewater surveillance

Early in the COVID-19 pandemic, the Discovery Partners Institute, University of Illinois Chicago, Northwestern University and Argonne National Laboratory formed a science team to detect the coronavirus in wastewater, gathering samples from treatment plants as well as directly from sewers in Chicago neighborhoods, O’Hare International Airport and Cook County Jail. The contents are screened for the virus at a high-throughput lab built by UIC; Argonne then sequences the genetic material to provide data on virus variants. Northwestern heads efforts to enhance and customize data analytics for Illinois public health needs while DPI leads program management, including logistics.

Real-time findings are shared with both CDPH and, after DPI built out a much more extensive network of collection points, IDPH to help both agencies track COVID-19’s spread and guide public health policies. Today DPI and its partners collect samples from over 85 locations that cover the output of 9 million Illinoisans. To date, over 6,500 samples have been analyzed and close to 5,000 have been sequenced. Total funding, largely from the city and state public health departments, comes to more than $17 million and extends this surveillance through mid-2023.

About DPI

The Discovery Partners Institute’s ambition is to propel Chicago into a pre-eminent and inclusive tech economy over the next decade. Led by the University of Illinois System in partnership with top research universities, it does three things: tech talent development, applied R&D and business building. DPI prepares diverse students and workers to step into high-demand tech jobs. It also builds research teams and matches them with new funding. With state investment and a new innovation district in development, DPI has the resources to attract, develop and leverage the most ambitious people and companies the region has to offer — and keep them here.

About RUSH

RUSH brings together the brightest minds in medicine, research and academics. Driven by discovery, innovation and a deep responsibility for the health of our communities, Rush University System for Health is a national leader in outstanding patient care, education, research, community partnerships and empowering a new generation of health care providers.

RUSH comprises RUSH University Medical Center, RUSH University, RUSH Copley Medical Center and RUSH Oak Park Hospital, as well as an extensive providers’ network and numerous outpatient care facilities. RUSH Medical College, College of Nursing, College of Health Sciences and Graduate College are educating the next generation of clinicians and health care leaders. RUSH University Medical Center is ranked among the top hospitals in the nation by U.S. News & World Report.