Emily Lydon, MD
Clinical Fellow
Department of Medicine, Division of Infectious Diseases
University of California San Francisco
About my role
I recently received an ARLG Early Stage Investigator (ESI) Seed Grant to support a research project developing metagenomic sequencing-based diagnostic tests for lower respiratory tract infections in lung transplant recipients.
About my research
Solid organ transplant recipients, particularly those who undergo lung transplantation, are disproportionately susceptible to lower respiratory tract infections (LRTIs) due to the need for lifelong immunosuppression; LRTI is a major contributor to mortality in this population. However, pathogen-based diagnostic tests used during post-transplant bronchoscopy cannot distinguish between true LRTIs and incidental carriage of potential respiratory pathogens, which is much more common, given the non-sterile nature of the respiratory microbiome. This often results in excessive antibiotic administration, which selects for antimicrobial-resistant organisms and causes interactions with immunosuppressants, Clostridioides difficile infection, and quality-of-life-limiting antimicrobial side effects. The research aims to utilize metagenomic sequencing on bronchoscopy samples to develop novel, integrated host-microbial molecular diagnostics to more accurately diagnose LRTIs in this population, specifically distinguishing LRTIs from colonization, while also profiling the impacts of antibiotic exposure on the lung microbiome and resistome.
A key priority of the ARLG scientific agenda is the development of improved diagnostic tests, particularly through the use of host biomarkers and gene expression profiles as alternatives to pathogen-based diagnostics. My project directly addresses this need. I suspect that host gene expression signatures from the lower respiratory tract will more effectively distinguish between true infection from microbial colonization in lung transplant patients compared to standard-of-care pathogen-based diagnostics. If successful and implemented in the clinic, such a test would decrease the number of unnecessary antibiotic prescriptions in this population.
Impact of the ARLG mentoring and funding on my career
In the short term, funding from the ARLG will support sequencing costs for my research project and provide bioinformatics support that will help me grow my bioinformatics and machine learning skill set. I am currently applying for a highly competitive K23 career development award from the NIH. Receiving this funding from the ARLG will hopefully strengthen my application by demonstrating my ability to secure independent research grants and also have access to external mentorship outside of the University of California, San Francisco (UCSF).
I am still early in my involvement as an ARLG mentee, but I have already received valuable guidance from ARLG mentors as I apply for my K23 career development award. I believe receiving this Early Stage Investigator (ESI) Seed Grant will be incredibly helpful in my development as an independent physician-scientist. More importantly, I am excited for this early career connection with such a supportive, well-regarded group of mentors. Before my current work in lung transplant, I contributed to several ARLG-supported projects. Past mentors, including Ephraim Tsalik, MD, MHS, PhD, FIDSA, of Duke, and Sarah Doernberg, MD, MAS, of UCSF had long touted the pivotal role the ARLG played in accelerating their careers, so I am excited to follow in their footsteps.
Receiving an Early Stage Investigator (ESI) Seed Grant is not just about receiving funds to support your research – it also provides access to a wonderful group of potential mentors and opportunities for additional exciting projects that can help launch a career. I am incredibly grateful to have this opportunity so early in my career and am excited to make the most of it.