Bovine tuberculosis (bTB) is a serious disease that threatens the health of livestock, wildlife, and the agricultural economy, particularly in the United Kingdom. Although every cow in the UK is subjected to a yearly bTB test, with those testing positive being slaughtered, efficient disease containment and control has not yet been achieved. This suggests that there is a source of the bacterial pathogen, Mycobacterium bovis (M. bovis), which causes bTb, that is being maintained somewhere outside of the cattle population, allowing the bTB epidemic to be sustained. M. bovis is related to Mycobacterium tuberculosis, which causes human tuberculosis, and can be transmitted between cows and humans, often through drinking unpasteurised milk. Controlling and eradicating bTB is therefore an important public health and economic issue.
Historically, the badger (Meles meles) has been implicated as a wild reservoir for M. bovis. This has mostly been based on circumstantial evidence: for example, large badger populations have been noted in areas where bovine tuberculosis outbreaks frequently occur. Ultimately, the role of badgers in transmitting bTB has not been well defined and remains tremendously controversial. Badger infection control strategies have nevertheless been implemented, ranging from vaccination to licensed culls.
Now, recently published research shows very clearly that exactly the same strains of M. bovis bacteria can be found in infected badgers and infected cattle living in the same place at the same time. This was based on a forensic genetic analysis, known as whole genome sequencing, carried out on the DNA of M. bovis bacteria isolated over a period of 10 years from both badgers and cows living in a test area of neighbouring farms in Northern Ireland where outbreaks of bTB were common. This means one of two things: either the bacterium had been directly transmitted between badgers and cows, or both animals had stumbled upon and been exposed to the same infectious source somewhere in their habitat (M. bovis can survive for months in the soil).
By modelling the transmission of the 31 identified strains of M. bovis, it was apparent that different patterns of bacterial circulation could drive bTB outbreaks: transmission in some herds was sustained through cow-to-cow infections, while in other herds, transmission was heavily influenced by new interactions with a local reservoir of unknown origin. Thus, local rather than distant interactions were the principal drivers of M. bovis infection outbreaks, with very little transmission being attributed to the movement of livestock between farms or hidden low levels of infection being missed by the annual bTB test.
This is the first direct evidence that badgers infected with M. bovis show a genetic interaction with persistently infected herds of cows, suggesting the potential for direct transmission of bTB between these two species.
Biek R, O'Hare A, Wright D, Mallon T, McCormick C, Orton RJ, McDowell S, Trewby H, Skuce RA, & Kao RR (2012). Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations. PLoS pathogens, 8 (11) PMID: 23209404
mmmbitesizescience 
Are you sure that M.bovis can survive in soil for months? My understanding is that it degrades rapidly under the affects of ultraviolet light.
This is taken from the entry for Wednesday March 27th 2013 at http://bovinetb.blogspot.co.uk/ regarding Owen Paterson’s Parliamentary question asked on 6 Jan 2004:
“Mr. Paterson: To ask the Secretary of State for Environment, Food and Rural Affairs what assessment has been made of whether badgers infected by TB may excrete urine from which viable M. bovis bacilli may be isolated; what the typical quantities per millilitre are; and whether such levels are capable of causing infection in cattle through (a) contamination of feed and (b) other mechanisms. [144445]
Mr. Bradshaw: Some badgers develop TB infection in the kidneys 37 per cent. of infected badgers sampled post mortem between 1971 and 1978 m. bovis was isolated from the kidneys and may excrete M. bovis bacilli in urine. Urine is typically left in trails up to a metre or more in length and may be focused at a latrine or distributed more randomly as the badger forages. Concentrations of up to 300,000 bacilli per ml of badger urine have been reported and experimental nasal inoculation of cattle suggests that, at this concentration of viable microbes, less than 0.03 ml would need to be inhaled by cattle in order to promote slow infection.
Investigations into infection of cattle from feed and other sources contaminated with infected badger urine are lacking. However, risk of infection to cattle by infected badger urine on cattle feed would be a function of the survival of the microbe in the feed (which is dependent on, for example, duration since excretion, moisture content of the environment, exposure to UV rays) the number of microbes consumed by the cattle and the method of consumption (i.e. ingestion or inhalation). I am unaware of measurements of M. bovis survival in cattle feed but the environment inside farm buildings is generally considered to be conducive to longer periods of survival than at pasture, where M. bovis in badger urine has survived for three days in summer and 28 days in winter.”
My understanding is that the bacillus survives longer in the absence of natural light but , as the evidence above suggests, this is not the case in the open fields where soil tends to be. Some clarification to your claim ‘(M. bovis can survive for months in the soil)’ would be appreciated.
Hi Dave! Thanks for your comment. You are absolutely right – the survival of M. tb is dependent upon environmental conditions, especially UV levels. So in Winter and Autumn, the bacteria can survive in the soil for 4-5 months, but in Summer, they stick around for less than 2 months (see http://goo.gl/63Ab5; section II). Optimal environmental conditions for survival are a nice moist 37dC, −20 kPa; 30% [vol/wt] (see http://goo.gl/DHhGF). This is a really good 2006 article that addresses the issue of environmental persistence: http://goo.gl/Z6gRx