Category Archives: epidemiology

Postdoctoral Position in Bioinformatics – University of Ottawa

The Corradi Lab is currently seeking a postdoctoral fellow in Bioinformatics to work on projects related to Comparative and Population Genomics. The research will be led by Dr. Nicolas Corradi and carried out in a CIFAR (Canadian Institute for Advanced Research) – affiliated laboratory located in the Department of Biology of the University of Ottawa, Canada.


The position is initially funded for one year, with the possibility of renewal for up to three years, depending on performance. The candidate is expected to work on two ongoing lab projects:

  1. Populations genomics of global samples of the bee-pathogen Nosema ceranae

    The recent decline in global populations of honey-bees has been attributed to a many factors, including infections from the microsporidian pathogen Nosema ceranae. Despite the potential threat that this parasite may have on global bee populations, the basic biology of this species is not well understood.
    The present project aims to increase our knowledge of the N. ceranae’s biology by exploring the extent, nature and function of genome diversity that exist both within and between dozens of parasite samples isolated globally (i.e. Spain, France, Turkey, Thailand, USA..etc…).
  2. Population genomics of global isolates of the model plant symbiont, Rhizophagus irregularis

    The Arbuscular Mycorrhizal Fungi (AMF) are ubiquitous plant symbionts that improve the ability of roots to uptake nutrients from soil and provide protection against plant pathogens. These organisms are intriguing as they harbor many nuclei within one cytoplasm throughout their entire life cycle. The genetic organization of these nuclei has been debated for years, but recent genome analyses in our lab are providing essential insights to this debate.

    The proposed projects aims to increase our knowledge of biology and evolution of these curious fungi and critical symbionts by investigating the genome diversity within and across different strains of the model AMF R. irregularis sampled globally.

For specific enquiries please contactDr. Nicolas Corradi (

Applicants are expected to have a strong background in either comparative genomics or populations genomics. Experience in either population genetics, environmental genomics, metagenomics, or ab-initio gene annotation and programming will be seen as an asset for the final selection of the candidate. Some basic training in bioinformatics (Perl, Python, or R) is desired.

A complete application package includes a CV, a one-page description of past research accomplishments and future goals, and the names and e-mail addresses of at least 2 references. The position opens immediately, and evaluation of applications will continue until a suitable candidate is found.

The University of Ottawa is a large, research-intensive university, hosting over 40,000 students and located in the downtown core area of Canada’s capital city. Ottawa is a vibrant, multicultural city with a very high quality of life.

Applications can be sent to Dr. Nicolas Corradi (

Representative publications:

  • Pelin A., Selman M., Laurent Farinelli, Aris-Brosou S. and N. Corradi. 2015. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environmental Microbiology
  • Ropars J. and N. Corradi. 2015. Heterokaryotic vs Homokaryotic Mycelium in the Arbuscular Mycorrhizal Fungi: Different Techniques, Different Results? New Phytologist
  • Corradi, N. 2015. Microsporidians: Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfer. Annual Review of Microbiology
  • Riley R., Charron P., Idnurm A., Farinelli F., Yolande D. , Martin F. and N. Corradi. 2014. Extreme diversification of the mating type–high?mobility group (MATA?HMG) gene family in a plant?associated arbuscular mycorrhizal fungus. New Phytologist
  • Tisserant E., Malbreil M. et al. 2013. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. PNAS

Dynamics of amphibian pathogen infection cycles
Two papers out this week on the population dynamics and epidemiology of the chytrid pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). This is work from the Vredenburg and Briggs labs that includes several decade-long studies of frog declines and the prevalence of Bd.

See Vance in action swabbing a frog

In the Briggs et al paper, they describe a 5-year study on the fungal load in surviving populations of frogs in Sierra Nevada mountain lakes.  They find that adult frogs that have low enough fungal load escape chytridiomycosis and can actually lose and regain infection. They propose that fungal load dynamics are the reason behind differential survival of various populations of mountain frogs. They conclude that:

“Importantly, model results suggest that host persistence versus extinction does not require differences in host susceptibility, pathogen virulence, or environmental conditions, and may be just epidemic and endemic population dynamics of the same host–pathogen system.”

So they propose that differences in the populations that are coming down with the disease is due only to “density-dependent host–pathogen dynamics” not that some populations are resistant. They go on to provide a detailed model of persistence if the host and pathogen, chance of reinfection, and survival of the host which is derived from the long-term study data.  There are many more interesting findings and models proposed in the paper. It also further reinforces (for me) the need to know more about the molecular basis of the host-pathogen interactions and more about how the fungus persists without a host, lifestyle of how it overwinters, and the details of the microbe-host interactions, and the infection dynamic when zoospores disperse from infected frogs.

The Vrendenburg et al paper adresses the dynamics of population decline in the mountain yellow-legged frogs over a periods of 1-5 and 9-13 year study in 3 different study sites at different sampling intervals.  The authors were able to catalog the species decline and conduct skin swabbing to assess Bd prevalence. They found that the fungus spread quickly as it could detected in virtually all the lakes over the course of a year starting with a 2004 survey. The dramatic declines of frog populations in these lakes followed in the years subsequent to the initial detection. This sadly predicts that most if not all of the mountain lakes will go extinct for the frogs as the current tadpoles develop into frogs in the next 3 years and then fall victim to Bd. Based on their sampling work, the authors were also able to correlate what fungal burden predicted a subsequent decline – in populations where more the ~10,000 zoospores were detected in a swab from frog skin, then the frog population was about to experience a sharp decline.  The take-home from this work is that finding ways to keep the intensity of fungal infections down could provide a meaningful intervention that could prolong the viability of the population.

Briggs, C., Knapp, R., & Vredenburg, V. (2010). Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912886107

Vredenburg, V., Knapp, R., Tunstall, T., & Briggs, C. (2010). Dynamics of an emerging disease drive large-scale amphibian population extinctions Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0914111107