WP2-T4 Production of a database and data collection

Participants :

  • 5 - IRTA
  • 9 - CEFAS

The production of a database related to site and pathogen characterization will be used for evaluating epidemiological criteria affecting disease manifestation (pathogen presence and mortality). From a disease and epidemiological point of view, ‘pattern and frequency’ can be interpreted through the level of mortalities. In addition, the mortalities may be seasonal and could only occur, for instance, in the spring, although this may vary
with the pathogen and the water temperature or salinity.

The database design will provide a platform for handling information related to rearing and environmental parameters and pathogen detection for selected pathogens. Data will be collected at different levels, e.g. batch, farm, bay, etc…..

Consequently, the design will be closely related to the experimental design of WP2 and WP3 to enable the most adequate data to be collected for subsequent data analysis, although the following database fields will be initially carefully considered for their relevance:

i) Agent
Infectivity, pathogenicity, virulence, genotype, available sequences;

ii) Host
Survival, species, phenotype, age, sex, nutritional status, physiological status, pathological status, origin of stock, time since movement, population density, prevalence rates, estimated mortality

iii) Environment (site)
Climate/weather, rainfall events, prevailing wind, water system, water quality, temperature, salinity, turbidity, oxygen, food availability, geology/sea bed type, tidal currents (direction and speed), presence of blooms, characterization or presence of plankton/copepod species, lat/long/GPS identifier, local run off (channels, outfalls, sluices), type of production system.

It is envisaged that approximately 15 factors would be needed to create the database fields, and the relevant factors from the above list will be decided on by all the partners at the first project meeting. The basic input data will be derived from the characterization of bivalve mollusc sites in five European countries (France, Ireland, Italy, Netherlands and Spain) with the recorded presence of five specific pathogens (OsHV-1, 2 Vibrio spp., Nocardia crassostreae and Marteilia refringens).

The database will be designed in MS Access for the duration of the project and the data will be exported to MS
Excel for analysis using standard software packages (see WP3, Task 5).