2017 - NECC
RACER Pre-proposal Proposal

Name: Ms. Crystal Nicole Ellis
Institution/Firm: University of New Hampshire
Address: 46 College Road
Rudman Hall
Room 201
Durham, NH 03824
Email: crystal_n_ellis@yahoo.com
Telephone: (603) 862-3298
Project Title: Linking genomics to habitat and virulence of V. cholerae and V. parahaemolyticus in the Great Bay Estuary, Durham NH
Abstract: Human pathogens are often acquired from environmental reservoirs, yet the genetic mechanisms that control niche expansion and virulence are poorly characterized, especially in Vibrio species such as V. cholerae and V. parahaemolyticus. These species are ubiquitous and routinely isolated from aquatic habitats with dramatically different environmental characteristics, yet outbreaks are generally localized, caused by strains acquired from warm waters (O'Shea et al., 2004; Joseph et al., 1982). To better understand pathogen emergence in the face of changing environmental conditions, it is essential to understand the interaction between different genotypes of Vibrio species and their habitats. The goal of this project is to determine the pair-wise differences in genome content between Vibrio species isolated from environmental reservoirs to those that were isolated as part of a clinical outbreak in order to link to specialization in a particular environment to genotype. To accomplish this, we will use high throughput Illumina sequencing technology to sequence whole genomes from a collection of environmental V. cholerae and V. parahaemolyticus isolate from the Great Bay Estuary in Durham, NH. Comparing these genomes, which are variable in origin and virulence, to clinical ones previously published online will allow us to identify genetic elements associated with virulence and environmental factors such as temperature and salinity. As it develops, this gene database could be a key resource for investigators studying pathogen emergence in response to global climate change and may also help other investigators identify new virulence mechanisms in other marine pathogens.
Collaborative Project Details: Funding will be used to connect our researchers with those doing similar characterization of environmental Vibrio species in either the Chesapeake Bay area in Delaware or the Gulf of Maine. Potential collaborators include Dr. Vaughn S. Cooper at the University of New Hampshire, NH, Dr. W. Kelley Thomas at the University of New Hampshire, NH and Dr. E. Fidelma Boydof at the University of Delaware, DE.
Project Overview - include goals, general expertise *: Human pathogens adapt rapidly to their newly acquired hosts, even when they are acquired from environmental reservoirs. The genetic mechanisms that underscore the evolution of virulence and niche expansion are poorly understood in many human pathogens, but especially in Vibrio species such as V. cholerae and V. parahaemolyticus. These species are ubiquitous and routinely isolated from aquatic habitats with dramatically different environmental characteristics, yet outbreaks are generally localized, caused by strains acquired from warm waters (O'Shea et al., 2004; Joseph et al., 1982). Vibrio species isolated from cold waters tend to be avirulent, but they still respond to temperature as an environmental cue, becoming more abundant during months when waters are slightly warmer (Jones et al., 2011; Mahoney et al., 2010). Therefore, it is important to understand the interaction between different genotypes of Vibrio species and their habitats in order to predict emergence of pathogenic strains as the result of changing environmental conditions. The goal of this project is to determine the pair-wise differences in genome content between Vibrio species isolated from various environmental reservoirs to those that were isolated as part of a clinical outbreak. We aim to identify genes that are unique to environmental or clinical Vibrio isolates, which could be linked to specialization in a particular environment. To accomplish this, we will use high throughput Illumina sequencing technology to sequence whole genomes from a collection of environmental V. cholerae and V. parahaemolyticus isolate from the Great Bay Estuary in Durham, NH (Schuster et al., submitted, Mahoney et al., 2010). This population is highly diverse with almost no population structure, thus serving as a large pool for genetic variability. Comparing these genomes, which are also variable in origin and virulence, to clinical ones previously sequenced and published online will allow us to identify genetic elements associated with virulence and environmental factors such as temperature and salinity. These genes will also serve as targets for future functional analyses which will allow us to link genotypes to fitness in a particular niche. Additionally, our goals would allow us to discover new genes previously unknown to associate with virulence and may serve to help other investigators identify virulence mechanisms in other pathogens.
The community of Vibrio species we intend to investigate was characterized during a 4-year ongoing study of the population structure and pathogenic potential of Vibrio species in the Great Bay Estuary in Durham, NH. We have maintained a database of >200 isolates characterized as V. cholerae and V. parahaemolyticus by multiplex PCR and MLST analysis (Schuster et al., Jones et al., 2011). We also collected environmental data related to temperature, salinity, and dissolved oxygen (Jones et al., 2011) for each isolate. Additionally, a bioinformatics pipeline was developed at UNH for identifying orthologs, paralogs, and unique genes in large datasets for comparative analyses (V.S. Cooper and P.J. Hatcher, UNH). Use of the NECC data center is integral to this project since Illumina re-sequencing generates large amounts of data that would be difficult to manage without a central database. Furthermore, collaboration with the NECC data center would allow us to maintain our existing collection database and allow other investigators access where they could provide new insight on emergence of pathogens in environmental reservoirs.