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DNA extraction from archived TB cultures from badgers: a resource to study fine-scale transmission dynamics using next-generation sequencing - SD0502

Description
We propose performing DNA extraction on archived Mycobacterium bovis culture isolates from badgers at Woodchester Park from 2000-present. This material constitutes a valuable resource for studying fine-scale TB transmission dynamics using next-generation whole genome sequencing. The project will seek to maximise the value of archived samples from this unique long-term study of a wildlife population. Current methods for investigating variation in M.bovis isolates from the study population are crude (spoligotyping, VNTR) by comparison with the high degree of resolution available by genome sequencing. Whole genome sequencing offers great promise as an epidemiological tool, as it has already been used to identify fine scale spatial and temporal patterns in M. bovis dynamics amongst cattle and a very small sample of badgers1 .

This approach has yet to be used to investigate dynamics of TB in the wildlife host population. If we are able to demonstrate the successful isolation of DNA from these archived samples, and to identify sufficient genetic variation then this opens the door to routine use of this technique as an epidemiological tool in our on-going Defra-funded work on TB in badgers.
Initially, we propose to sequence approximately 30 isolates from a cohort of resident and immigrant badgers in order to compare sequence diversity. Targeting our efforts at these samples should maximise our chances of success as the immigration of infected hosts is a potential source of genetic variation in M. bovis isolates2. This strategy will also allow us to investigate disease dynamics related to movement of individuals and provide a potentially compelling demonstration of the applied value of the approach.
Objective
We propose performing DNA extraction on archived Mycobacterium bovis culture isolates from badgers at Woodchester Park from 2000-present. This material constitutes a valuable resource for studying fine-scale TB transmission dynamics using next-generation whole genome sequencing. The project will seek to maximise the value of archived samples from this unique long-term study of a wildlife population. This will be the first attempt to collate whole genome sequence data from M. bovis isolates from UK badgers and represents an initial exploration of the use of such information in unravelling epidemiological patterns in TB infection in badgers and cattle in this study area. The project benefits from material already collected and archived from the long-term Woodchester Park badger study and from the availability of corresponding ecological and epidemiological data.
Time-Scale and Cost
From: 2013

To: 2013

Cost: £23,000
Contractor / Funded Organisations
F E R A (FERA)
Keywords
Analytical Chemistry