title: Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms.
abstract: The present study aimed to describe the molecular diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates obtained from sheep, cattle (beef and dairy) and deer farms in New Zealand. A total of 206 independent MAP isolates (15 beef cattle, 89 dairy cattle, 35 deer, 67 sheep) were sourced from 172 species-mobs (15 beef cattle, 66 dairy cattle, 31 deer, 60 sheep). Seventeen subtypes were identified, using a combination of variable number of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefaction analysis, analysis of molecular variance (AMOVA), Fst pairwise comparisons and proportional similarity index (PSI) were used to describe subtype population richness, genetic structure and potential associations between livestock sectors and New Zealand two main islands (North and South). The rarefaction analysis suggests a significantly higher subtype richness in dairy cattle herds when compared to the other livestock sectors. AMOVA results indicate that the main source of subtype variation is attributable to the livestock sector from which samples were sourced suggesting that subtypes are generally sector-specific. The pairwise Fst results were similar, with low Fst values for island differences within a livestock sector when compared to between sector analyses, representing a low subtype differentiation between islands. However, for a given island, potential associations were seen between dominant subtypes and specific livestock sectors. Three subtypes accounted for 76% of the isolates. The most common of these was isolated from sheep and beef cattle in the North Island, the second most frequent subtype was mainly isolated from dairy cattle (either island), while the third most common subtype was associated with deer farmed in the South Island. The PSI analysis suggests similarities in subtypes sourced from sheep and beef cattle. This contrasted with the isolates sourced from other livestock sectors, which tended to present sector-specific subtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle and deer were almost exclusively infected with MAP Type II. However, when beef cattle and deer were both present at farm level, they harboured similar subtypes. This study indicates that cross-species transmission of MAP occurs on New Zealand farms although close contact between species appears to be required, as in the case of sheep and beef cattle which are commonly grazed together in New Zealand.
authors.affiliation: Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile; EpiCentre, Massey University, Private Bag 11-222, Palmerston North, New Zealand. Electronic address: cristobal.verdugo@uach.cl.
authors.forename: Cristobal
authors.initials: C
authors.lastname: Verdugo
authors.affiliation: Infectious Disease Research Centre, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
authors.forename: Eve
authors.initials: E
authors.lastname: Pleydell
authors.affiliation: AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand.
authors.forename: Marian
authors.initials: M
authors.lastname: Price-Carter
authors.affiliation: Infectious Disease Research Centre, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
authors.forename: Deborah
authors.initials: D
authors.lastname: Prattley
authors.affiliation: AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand.
authors.forename: Desmond
authors.initials: D
authors.lastname: Collins
authors.affiliation: AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: de Lisle
authors.affiliation: Livestock Improvement Corporation, Private Bag 3016, Hamilton, New Zealand.
authors.forename: Hinrich
authors.initials: H
authors.lastname: Vogue
authors.affiliation: Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
authors.forename: Peter
authors.initials: P
authors.lastname: Wilson
authors.affiliation: EpiCentre, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
authors.forename: Cord
authors.initials: C
authors.lastname: Heuer
mesh_terms: D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology* / Q000382:microbiology; D003670:Deer; D005243:Feces / Q000382:microbiology; D014644:Genetic Variation; D018598:Minisatellite Repeats; D016927:Mycobacterium avium subsp. paratuberculosis / Q000235:genetics* / Q000302:isolation & purification; D009520:New Zealand / Q000453:epidemiology; D010283:Paratuberculosis / Q000453:epidemiology* / Q000382:microbiology; D016133:Polymerase Chain Reaction / Q000662:veterinary; D012756:Sheep; D012757:Sheep Diseases / Q000453:epidemiology* / Q000382:microbiology
keywords: AMOVA; Mycobacterium avium subsp. paratuberculosis; Pastoral systems; SSR; Subtype diversity; VNTR