Antimicrobial resistance (AMR) is a growing global health crisis, making infections harder to treat as
bacteria become resistant to antibiotics. While much research has focused on AMR in harmful bacteria,
less attention has been given to the harmless bacteria in the human gut, which can serve as a hidden
source of resistance genes. These bacteria may transfer antibiotic resistance genes (ARGs) to the
harmful bacteria through a process called horizontal gene transfer (HGT), potentially creating new
drug-resistant infections.

Our study aims to directly track how this transfer happens inside the gut microbiome of critically ill
patients using a new single-cell sequencing technology that can identify the exact bacterial sources of
ARGs. This approach combines expertise from Dr. Lan, a biomedical engineer specializing in new
sequencing technologies, and Dr. Coburn, an infectious disease clinician scientist.

By mapping the HGT of ARGs in hospitalized patients’ gut microbiomes, we aim to provide the first
direct evidence of AMR spread between gut bacteria. These findings could reshape clinical
decision-making, improve antibiotic stewardship policies, and enhance AMR surveillance
strategies to prevent the emergence of new drug-resistant infections.

Each year, hundreds of thousands of children and vulnerable individuals are hospitalized with serious
respiratory infections caused by human parainfluenza viruses (HPIVs). These viruses are among the
most common causes of respiratory illness in young children, yet there are still no approved vaccines or
treatments to prevent them. Our project aims to change that by developing a new vaccine that protects
against multiple types of HPIVs. We are focusing on two key parts of the virus: the fusion protein, which
helps the virus enter human cells, and the matrix protein, which is highly conserved and plays a central
role in virus assembly. By combining both, we aim to trigger a strong and lasting immune response that
includes T-cells—which destroy infected cells—and antibodies—which block the virus from spreading. In
early studies, we found that the matrix protein alone can protect mice from infection. Building on this, we
are now engineering a more powerful version of the vaccine that links the fusion and matrix proteins
together in a single, stable formulation. We will test how well this vaccine protects against different types
of HPIVs and study how it activates the immune system. Because the matrix protein is so similar across
related viruses, this strategy could also help us prepare for future outbreaks caused by other more
pathogenic viruses in the same family, such as Nipah virus, which can spread from animals to humans
and cause severe disease.