Microbial Genomics and Pathogen Surveillance

The Pathogen Surveillance Program (PSP) brings together a multidisciplinary investigative team to better understand the dissemination and risks posed by viral and bacterial pathogens—most recently exemplified by SARS-CoV-2 and the recent COVID-19 pandemic.

The spread of these viral and bacterial pathogens within communities and health systems poses a significant and potentially fatal threat to individuals and patients. While the COVID-19 pandemic has claimed the lives of millions worldwide, there are countless other pathogens that we need to be aware of, and counteract if necessary.

The PSP brings together scientists from across Mount Sinai with backgrounds in infectious disease, epidemiology, statistical modeling, and the analysis of pathogen genomes and microbiomes. By using the latest whole-genome sequencing technologies the PSP aims to improve our understanding of the molecular basis of evolution and transmission of infectious diseases, host-pathogen interactions, and to identify novel emerging pathogens and their variants. Altogether we anticipate that a better understanding of pathogen genetic diversity will result in improved risk assessments, patient care, and outcomes.

While infectious diseases are caused by specific pathogens, commensal microbes (the microbiome) can also trigger and exacerbate human disease. Using computational and wet lab methods developed by scientists at Mount Sinai, we have identified bacteria associated with inflammatory bowel disease (IBD), allergies, COVID-19, influenza, and cancer—among many other diseases. This has led to innovative approaches to treat these conditions by transplanting microbes from healthy donors to patients, and scientists from our institution currently oversee two clinical trials to treat IBD and food allergies with microbiota transplants. Understanding how commensal microbes interact with the host to educate immune development and to modulate disease risk is an area of active research at Mount Sinai, and developing methods to model such interactions will provide actionable targets to refine microbial therapeutics.

The emergence and invasion of microbial pathogens from microbiomes populating the human organism is an important field of study. In particular, the development of antibiotic resistance and the detrimental effect of opportunistic infections by microbial pathogens is a major concern. Researchers at Mount Sinai have, for example, identified that the host response to influenza infection could indirectly impact antibiotic resistance gene expression in the respiratory tract by affecting the microbiome. Another study revealed that oral commensals are associated with severe COVID-19 disease outcome. New computational and experimental methods have been developed to address the study of lung tissues, which are particularly challenging. A particular focus lies in the typically neglected “co-microbiome” study of bacteria, fungi, and viruses.