title: Use of a polymerase chain reaction to subtype Mycobacterium avium subspecies paratuberculosis, an increasingly important pathogen from farmed deer in New Zealand.
abstract: OBJECTIVE
  To review the number of microbiologically-confirmed cases of Johne's disease in farmed deer since 2000, and determine the prevalence of the bovine and ovine subtypes of Mycobacterium avium subsp paratuberculosis (M. paratuberculosis), using a highly specific polymerase chain reaction (PCR) test on samples from infected herds.
  
  
  METHODS
  The number of cases of M. paratuberculosis in farmed deer identified by culture or IS900 PCR was documented. A highly specific PCR test was applied to subtype M. paratuberculosis from BACTEC 12B cultures selected on the basis of one culture per deer herd, to give a wide coverage of herds in New Zealand.
  
  
  RESULTS
  From January 2001 to October 2005, M. paratuberculosis was isolated from 1,141 farmed deer, and has now been identified by microbiological testing in over 600 deer herds in New Zealand. The bovine subtype of M. paratuberculosis was shown by a highly specific PCR test to be present in 91/95 herds examined; the ovine subtype was found in the remaining four herds.
  
  
  CONCLUSIONS
  Since 2000, there has been a substantial increase in both the number of microbiologically-confirmed cases of Johne's disease in farmed deer and the number of infected herds. Johne's disease is now widespread and common in deer herds throughout New Zealand. Whilst the bovine subtype of M. paratuberculosis predominates in deer herds in New Zealand in which Johne's disease has been confirmed, the occasional finding of the ovine subtype highlights the need to consider both sheep and cattle as potential sources of infection for farmed deer.
authors.affiliation: AgResearch, Wallaceville Animal Research Centre, PO Box 40-063, Upper Hutt, New Zealand. geoffrey.delisle@agresearch.co.nz
authors.forename: G W
authors.initials: GW
authors.lastname: de Lisle
authors.forename: M C
authors.initials: MC
authors.lastname: Cannon
authors.forename: G F
authors.initials: GF
authors.lastname: Yates
authors.forename: D M
authors.initials: DM
authors.lastname: Collins
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques / Q000662:veterinary; D003670:Deer / Q000382:microbiology*; D004197:Disease Reservoirs / Q000662:veterinary; D016927:Mycobacterium avium subsp. paratuberculosis / Q000145:classification*; D009520:New Zealand / Q000453:epidemiology; D010283:Paratuberculosis / Q000175:diagnosis* / Q000453:epidemiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods / Q000662:veterinary*; D012680:Sensitivity and Specificity