Research

Our lab works with experts in genomics, metabolomics and microbiome science to study the intersection between human microbiomes and antimicrobial resistance. We previously studied how commonly prescribed antibiotics affect the healthy gut microbiome and examined associations between the gut microbiome, urinary microbiome and urinary tract infections (UTIs). We are currently using data and specimens from our UTI study to conduct a new study to identify dietary factors associated with antibiotic-resistant UTIs.

Our lab has conducted a series of studies using refined environmental sampling techniques to identify reservoirs of antimicrobial-resistant organisms (AROs), including bacteria and fungi, in the hospital setting. These studies consistently found sink drains to have a high burden of AROs, and one study identified a genetic link between an ARO in hospital sink drains and an ARO implicated in patient infections. This led our team to develop a two-part sink-cleaning intervention protocol, which we have now tested in two different intensive care unit settings.

Building upon the sampling techniques we developed for our human microbiome and healthcare microbiome studies, our lab is working on studies aimed at identifying reservoirs for antimicrobial resistance in community-dwelling adults and the home environment. While much is known about combating antimicrobial-resistant organisms (AROs) in the healthcare environment, these AROs are increasingly introduced from the community. This work, funded by the Centers for Disease Control and Prevention and the Agency for Healthcare Research and Quality, will help identify risk factors for community-associated ARO colonization and infection to inform future interventions.

Working with collaborators at Washington University School of Medicine, the Kwon Lab is leading a project using integrated multi-omics methods to investigate interactions among humans, microbiomes and antibiotic-resistant (AR) Escherichia coli (E. coli), particularly extended-spectrum beta-lactamase-producing E. coli. This work will use existing specimens and data previously collected by our lab for other research projects to advance scientific knowledge to combat antimicrobial resistance by identifying novel biomarkers that can support the development of next-generation diagnostic, preventive and therapeutic interventions. This work is part of the WashU Multi-Omics Unit for Combatting Antibiotic-Resistant Bacteria project, which is an NIH Combatting Antibiotic-Resistant Bacteria Interdisciplinary Research Unit.

Before the lab's transfer to Northwestern University, we served as the lead coordinating center for the CDC-funded Respiratory Virus Transmission Network for Influenza (RVTN-Flu). RVTN-Flu was a multicenter case-ascertained household transmission study designed to study influenza transmission in households and to evaluate the impact of vaccination on infection risk. This study also provided important real-time influenza surveillance data to the CDC. Although study enrollment and data collection ended in 2025, data from this study are being used to investigate several questions related to vaccine effectiveness, the economic impact of influenza, the impact of antivirals on influenza symptoms and related topics.

Using personal protective equipment (PPE), including masks, gowns, gloves, goggles and face shields, can help protect healthcare professionals from infection. Our lab has conducted a series of studies using surrogate markers to track the spread of contamination between PPE, healthcare professionals' hands and clothing, and the healthcare environment. We are currently working on a study using surrogate markers to compare the risk of healthcare professional self-contamination and downstream environmental contamination associated with single-use versus extended-use PPE strategies. The findings of this study will help us to determine whether extended use of PPE is a reasonable strategy, in general and in cases of limited resources.