Decoding the Genomes of Microbes to Identify the Kill Switch

Finding novel ways to target parasites and viruses for the control of infections

Dr. Elodie Ghedin wanted to be a scientist from as far back as she could remember. As a young scientist, she traveled to West Africa where she studied the quality of drinking water in the Sahel desert in Senegal. However, she quickly discovered that she was more interested in the parasites infesting the waters than in the levels of contaminants. This triggered her interest in a lifetime of research on neglected tropical diseases and the pathogens underlying their transmission and virulence. Now, at New York University, Dr. Elodie Ghedin uses genomics to look at microbes which spans not only the parasite she was first interested in, but also, worms, viruses, and bacteria.

Dr. Ghedin's study of viral and parasitic pathogens are relevant to infectious diseases that threaten humanity worldwide, especially neglected populations. We have recently seen new human outbreaks of avian influenza virus H7N9 in China, Middle-Eastern respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia, and Ebola virus in West Africa. Analyzing the genomes of these microbes helps scientists understand their evolutionary context and their interactions within their hosts. Armed with this information Dr. Ghedin can aim to find novel ways to push their evolution so they can go from pathogen to commensal, or to identify the kill-switch when necessary. Therefore, Dr. Ghedin's ultimate goal is to identify ways to better target parasites and viruses for the control of infections, through drugs or vaccines. Getting a peek into the blueprint of these organisms also gives her and her team novel insights into complex biological systems.

Current research includes:

  • Decoding the Flu: Using novel methodologies to decode influenza viruses, Dr. Ghedin's lab is determining the extent, structure, and underlying mechanisms of genetic variation in viral populations within infected individuals. This has important consequences for our understanding of the efficacy of vaccines and for the selection of vaccine strains. The goal is to learn what enables a virus to achieve efficient human-to-human transmission during an epidemic and, consequently, inform scientists on how to modify this transmission.

  • Pulmonary Diseases: Dr. Ghedin's work on the influenza virus has branched into a special interest in the microbes both commensal and transient--that can be found in the respiratory tract. In collaboration with a pulmonologist, Dr. Ghedin uses "metagenomic" techniques to characterize the microbial community in the lungs of HIV patients with pulmonary disorders. Their goal is to determine whether there are microbial species that are associated with pulmonary diseases, and could therefore be targeted in treatment regimens. 

  • Predicting Disease Severity: In a systems biology project, Dr. Ghedin and her team are integrating data on virus, bacteria, and host genomics to understand the pathogenesis in influenza infections. The goal is to identify biomarkers that could be used to predict disease severity.

  • Parasitic Worms: Dr. Ghedin studies parasitic worms that cause human diseases. One family of worms (the Filaria) causes elephantiasis and river blindness, and carries bacteria that live in symbiosis with the worm. Dr. Ghedin and her team are studying the molecular interplay between the parasite and the bacteria to identify essential interactions that could be exploited to treat the worm infection.

  • Novel Medicines: A project in need of funding is to characterize the molecules the parasitic worms secrete and identify a few that could be exploited as novel medicines. Parasitic worms are able to "hide" within their infected hosts for years when the host's immune system should have recognized this stranger. This means the worm is spitting out molecules that modulate the immune response. If researchers were able to identify these molecules, they could have an impact on controlling autoimmune diseases, graft rejection, etc. In Dr. Ghedin's lab, they endearingly call this "panning for molecular gold."


After pursuing an undergraduate degree in Biology at McGill University, Dr. Ghedin began a Masters degree in Environmental Sciences where she was originally introduced to the microbes and parasites that continue to captivate her attention. Soon after completing her masters program, she enrolled in doctoral studies at McGill University's Institute of Parasitology where she worked on defining a neglected tropical disease (leishmaniasis) that infects millions of people in more than ninety countries. As a postdoctoral fellow and junior investigator, she pursued work on parasite genomics and was a member of the team that decoded the first parasite genomes. This later led to decoding the genomes of other pathogens, including viruses. As a professor, Dr. Ghedin takes her role as mentor seriously. She is especially drawn towards educating future female scientists. Dr. Ghedin enjoys sharing her own experiences and watching passionate young men and women reach their goals.


In the News

Elodie Ghedin Parasitologist/Virologist

MacArthur Fellows Program


University of Pittsburgh Chancellor's Distinguished Research Award, Junior Scholar, 2010

MacArthur Fellow, 2011

Kavli Frontiers of Science Fellow, 2012