Prof J Martinez-Urtaza, Prof C Hauton, Dr R Marsh
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
About the Project
Project Rationale:
Vibrio parahaemolyticus (Vp) is a marine bacterium and a natural inhabitant of coastal environments worldwide. Globally, this pathogen is the leading cause of bacterial seafood-borne infections. The geographical distribution of Vp-associated infections has undergone a global expansion over the last 2 decades in phase with climate warming. A key driving factor identified for this process of disease expansion has been the transition from infections caused by locally-restricted strains to the surge and transcontinental expansion of epidemic clonal types. These modern expansions provide an exceptional opportunity to study the evolutionary process of this pathogen first-hand and to understand the mechanisms shaping the epidemic dynamics of diseases associated with these emerging pathogens. This PhD project will determine the factors that drive the emergence, dispersal and successful introduction of these pathogens into new regions, facilitating the global spread of infections. Several fundamental unknowns exist on key features regarding the transmission, dissemination and establishment of these pathogenic environmental bacteria - such as how vibrios emerge in non-endemic areas and how climate change may influence these processes.
The primary objective of this PhD project will be to generate a global map of the geographical distribution of the different genetic variants of Vp and to relate these distributions to the physicochemical marine environments that have driven the evolution and spread of these genetic variants.
Methodology:
Genomes of strains representative of all ranges of environments and geographical regions deposited in public databases along with new genomes belonging to institutional collections of the partners contributing to the project (US FDA, the National Institute of Health in Peru, & Cefas) will be compiled in a central database with the corresponding genomic and associated metadata. Phylogenetic relationships between different Vp populations will be inferred from genomic data and the potential interconnection between populations originating in different geographical areas of the world will be determined.
Thereafter, the student will combine the results of these analyses with environmental and oceanographic data to identify conditions that influence the emergence and distribution of new pathogenic variants. These analyses will elucidate how environmental changes and anthropogenic factors may shape the population structure of these pathogenic organisms.
These findings will further our knowledge of Vp disease dynamics and provide innovative approaches applicable to the other important Vibrio pathogens such as V. cholerae and V. vulnificus as well as emerging strains of Vp that are spreading through the crustacean aquaculture industry, causing diseases such as Acute Hepatopancreatic Necrosis Disease (AHPND).
Training:
The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners.
The student will be registered at the University of Southampton and hosted at Centre for Environment Fisheries and Aquaculture Science, Weymouth Laboratory. Specific training will include: the compilation and phylogenetic analysis of a database of Vp genomic sequences. The database will be used to construct a pangenome analysis using ‘Roary’, an open source tool in Perl, that rapidly builds large-scale pan genomes, identifying core and accessory genes by identifying homologues and orthologous sequences.
Outputs from the pangenome analysis, in the form of Bayesian preidctions of Vp lineage, will be compared to Lagrangian predictions of particle distribution across the world’s oceans and with future climate forecasts of sea surface temperature and salinity profiles in order to predict bi-envelopes for Vp strain emergence and distribution.
Funding Notes
You can apply for fully-funded studentships (stipend and fees) from INSPIRE if you:
Are a UK or EU national.
Have no restrictions on how long you can stay in the UK.
Have been 'ordinarily resident' in the UK for 3 years prior to the start of the project.
Please click http://inspire-dtp.ac.uk/how-apply for more information on eligibilty and how to apply
References
Baker-Austin C. et al 2018 Vibrio spp. infections. Nature Reviews Disease Primers 4: 8: JUL 12 2018
Martinez-Urtaza et al. 2017. Genomic Variation and Evolution of Vibrio parahaemolyticus ST36 over the Course of a Transcontinental Epidemic Expansion. MBIO 8: e01425-17
Baker-Austin, C et al. 2017. Non-Cholera Vibrios: The Microbial Barometer of Climate Change TRENDS IN MICROBIOLOGY 25: 76-84 DOI: 10.1016/j.tim.2016.09.008