Sampling Frames

Appropriate sampling frames will be identified for each organism. In order to determine transmission characteristics and rates, consecutive samples from potential donors and all identified recipients in an area of transmission will be collected together with appropriate clinical details (potential risk factors for acquisition of pathogen, development of disease and infectiousness), basic demographics and time/space information (including date of hospital admission, date of last hospital admission, dates and times of all ward movements since admission).

Sequencing Platforms

We have access to a range of whole genome sequencing platforms including Illumina Solexa Genome Analyzer II sequencing system and the Roche 454 Genome Sequencer FLX next generation sequencers. All of the pathogens will be sequenced using next generation sequencing.

Further, the translation of sequence-based typing from whole genome sequencing into clinical practice via interrogation of databases by individual practitioners will be a major behaviour change much anticipated by the NHS clinical record system. This will be an opportunity to study and optimise approaches for successful adoption of new technologies.

Bioinformatics and databases

The four exemplar organisms provide a representative range of challenges for the development of a coherent unified informatics platform that could be extended to infectious disease caused by any organism. This will include linked databases for management of large sequence and epidemiological datasets, software tools for general and specific bioinformatic and modelling needs, and a web platform to provide access for clinicians and scientists to upload local data, and view national data and local analyses and predictions. These activities will need considerable development, synergising with ongoing projects at the HPA, and Oxford University (MalariaGEN).

One goal is to develop web-accessible informatics tools which are attractive and easy-to-use, enabling local practitioners to direct their routine infection control practice efficiently; but which are based on a platform that is flexible enough to add further types of data, scaleable for implementation across UK NHS service, and modular, to allow changes that can enable generalisation across the whole range of infection surveillance.

Association studies