Skip to main content

GMCF Activities

Regional Innovative Public Health Laboratory (RIPHL)

The GMCF is the site of the Regional Innovative Public Health Laboratory (RIPHL), a novel public-academic partnership between the Chicago Department of Public Health (CDPH) and RUSH University Medical Center (RUMC). RIPHL was initiated in March 2021 to provide CDPH with flexible molecular laboratory capacity and technical expertise to address emergent public health needs. Its initial focus was on conducting surveillance whole genome sequencing (WGS) for SARS-CoV-2 for the CDPH, and for building a flexible, advanced molecular laboratory capacity for CDPH. RIPHL has since been instrumental in the COVID-19 response in Chicago. Since its inception in March 2021, more than 12,000 samples have been successfully sequenced. Currently, RIPHL is moving into WGS and genetic epidemiological analysis of other pathogens of public health importance, such as Candida auris and mpox. Select publications:

  1. Doyle K, Teran RA, Reefhuis J, Kerins JL, Qiu X, Green SJ, Choi H, Madni SA, Kamal N, Landon E, Albert RC, Pacilli M, Furtado LE, Hayden MK, Kunstman KJ, Bethel C, Megger L, Fricchione MJ, Ghinai I. Multiple Variants of SARS-CoV-2 in a University Outbreak After Spring Break - Chicago, Illinois, March-May 2021. MMWR Morb Mortal Wkly Rep. 2021 Sep 3;70(35):1195-1200. doi: 10.15585/mmwr.mm7035a3. PMID: 34473687; PMCID: PMC8422867.
  2. Ghinai I, Davis ES, Mayer S, Toews KA, Huggett TD, Snow-Hill N, Perez O, Hayden MK, Tehrani S, Landi AJ, Crane S, Bell E, Hermes JM, Desai K, Godbee M, Jhaveri N, Borah B, Cable T, Sami S, Nozicka L, Chang YS, Jagadish A, Chee M, Thigpen B, Llerena C, Tran M, Surabhi DM, Smith ED, Remus RG, Staszcuk R, Figueroa E, Leo P, Detmer WM, Lyon E, Carreon S, Hoferka S, Ritger KA, Jasmin W, Nagireddy P, Seo JY, Fricchione MJ, Kerins JL, Black SR, Butler LM, Howard K, McCauley M, Fraley T, Arwady MA, Gretsch S, Cunningham M, Pacilli M, Ruestow PS, Mosites E, Avery E, Longcoy J, Lynch EB, Layden JE. Risk Factors for Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Homeless Shelters in Chicago, Illinois-March-May, 2020. Open Forum Infect Dis. 2020 Oct 12;7(11):ofaa477. doi: 10.1093/ofid/ofaa477. PMID: 33263069; PMCID: PMC7665740.


RUSH University Medical Center Chicago Department of Public Health
Mary Hayden, Co-PI Alyse Kittner, Director of Lab-based Surveillance 
Stefan Green, Co-PI Massimo Pacilli, Deputy Commissioner 
Kevin Kunstman, Director Dorothy Foulkes, Manager of Quality Assurance 
Hannah Barbian, Genomic Epidemiologist Kayla English, Epidemiologist IV (CDC Foundation)
Félix Araújo-Pérez, Research Bioengineer Diamond Clark-McQueen, PHA II 
Cecelia Chau, Research Scientist  Deniz Yuce, Epidemiologist IV 
Trisha Jeon, Research Associate 3  
Sofiya Bobrovska, MPH, Data Analyst   
Latifah Boyd, MPH, Senior Program Manager  


Microbiome Research in the GMCF

Microbiome research is an area of expertise for the GMCF. Most staff have microbiology backgrounds, and the director of the GMCF, Dr. Stefan Green, is a microbiologist with over 25 years of experience in using molecular tools to interrogate complex microbial communities. Dr. Green has an extensive publication record in microbiome research, and works closely with investigators to design experiments, select appropriate sequencing strategies, analyze data, interpret results, and write manuscripts and proposals. Currently, Dr. Green is a co-I on 8 NIH funded grant proposals, a co-PI on a Chicago Department of Public Health (CDPH) funded program, and co-PI on a Binational Agriculture and Research Development (BARD) program. Dr. Green works on many host-associated microbiome projects in disease and injury states (e.g., Parkinson’s disease, Alzheimer’s disease, Alcohol use disorder, Traumatic brain injury, Bacterial vaginosis, etc) as well as environmental systems (plant rhizosphere, hypersaline microbial mats, contaminated groundwater, landfill, etc). Dr. Green has a particular interest in molecular methodology and in addressing causes of bias during PCR amplification in microbiome analyses. Dr. Green has also been involved in examining the effects of spaceflight on the microbiome of astronauts and mice as part of the NASA Twins study and Rodent Research missions to the International Space Station.

RUSH University Microbiome research highlights include:

  1. Engen, P.A., Green, S.J., Voigt, R.M., Forsyth, C.B. and Keshavarzian, A., 2015. The gastrointestinal microbiome: alcohol effects on the composition of intestinal microbiota. Alcohol research: current reviews, 37(2), p.223.
  2. Garrett-Bakelman, F.E., Darshi, M., Green, S.J., Gur, R.C., Lin, L., Macias, B.R., McKenna, M.J., Meydan, C., Mishra, T., Nasrini, J. and Piening, B.D., 2019. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science, 364(6436), p.eaau8650.
  3. Jochum, S.B., Engen, P.A., Shaikh, M., Naqib, A., Wilber, S., Raeisi, S., Zhang, L., Song, S., Sanzo, G., Chouhan, V. and Ko, F., 2022. Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium–Induced Colitis. Inflammatory Bowel Diseases.
  4. Keshavarzian, A., Green, S.J., Engen, P.A., Voigt, R.M., Naqib, A., Forsyth, C.B., Mutlu, E. and Shannon, K.M., 2015. Colonic bacterial composition in Parkinson's disease. Movement Disorders, 30(10), pp.1351-1360.
  5. Popovich, K.J., Thiede, S.N., Zawitz, C., Payne, D., Aroutcheva, A., Schoeny, M., Green, S.J., Snitkin, E.S. and Weinstein, R.A., 2022, March. Genomic Analysis of Community Transmission Networks for MRSA Among Females Entering a Large Inner-city Jail. In Open forum infectious diseases (Vol. 9, No. 3, p. ofac049). US: Oxford University Press.
  6. Voigt, R.M., Forsyth, C.B., Green, S.J., Mutlu, E., Engen, P., Vitaterna, M.H., Turek, F.W. and Keshavarzian, A., 2014. Circadian disorganization alters intestinal microbiota. PloS one, 9(5), p.e97500.


Center for Emerging Infectious Diseases (CEID)

The Center for Emerging Infectious Diseases (CEID) provides a sustained framework to build on RUSH University's research, training, and community outreach to enhance forward progress and rapid responses to emerging threats. This effort includes the creation of outreach programs designed to produce rapid, community-based response to emerging health threats, especially among underrepresented populations.

CEID has renovated a 500 square foot laboratory with state-of-the-art instruments designed specifically for hands-on training of the latest techniques in genetic and environmental research. This will be used to train Chicagoland high school STEM teachers and students, RUSH University medical students and college students interested in a career in molecular science. CEID also purchased instrumentation to build a lending library of thermocyclers and spectrophotometers for Chicago Public School teachers to deploy in classroom settings.

CEID distributed over $300,000 in pilot awards to infectious disease research programs to further Chicago’s community preparedness for emerging infectious diseases. These research projects included:

  • The RUSH Active Monkeypox Patients (RAMP) Registry (Michael Gottlieb, MD)
  • The Chicago Rat Project: Surveillance and education programs for emerging zoonotic (Supriya Mehta, MHS, PhD)
  • Genomic Sequencing from Non-Culture Based Clinical Neisseria gonorrhoeae Specimens (Kyle Popovich, MD MS)
  • Tracking Antimicrobial Use and Resistance at the RUSH System for Health: A Three-Center Surveillance Study (Carlos Santos, MD, MPHS)
  • Critical Examination of VOC Responses in Respiratory Infections to Support Targeted Antibiotic Therapy (Barbara Swanson, PhD, RN, FAAN)
  • A sequence-based approach to broad infectious disease surveillance in wastewater (Rachel Poretsky, UIC; Ankur Naqib, Rush)
  • Pathogen Surveillance by Ambient Air Monitoring in the Emergency Department (Hannah Barbian, PhD)
  • Experiential Biotechnology for Learners in Chicago Public Schools (Marenda Wilson-Pham, PhD)