Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms

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 farmsin 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 variablenumber of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefactionanalysis, analysis of molecular variance (AMOVA), Fstpairwise comparisons and propor-tional similarity index (PSI) were used to describe subtype population richness, geneticstructure and potential associations between livestock sectors and New Zealand two mainislands (North and South).The rarefaction analysis suggests a significantly higher subtype richness in dairy cattleherds when compared to the other livestock sectors. AMOVA results indicate that the mainsource of subtype variation is attributable to the livestock sector from which samples weresourced suggesting that subtypes are generally sector-specific. The pairwise Fstresults weresimilar, with low Fstvalues for island differences within a livestock sector when comparedto between sector analyses, representing a low subtype differentiation between islands.However, for a given island, potential associations were seen between dominant subtypesand specific livestock sectors. Three subtypes accounted for 76% of the isolates. The mostcommon of these was isolated from sheep and beef cattle in the North Island, the secondmost frequent subtype was mainly isolated from dairy cattle (either island), while the thirdmost common subtype was associated with deer farmed in the South Island. The PSI analysissuggests similarities in subtypes sourced from sheep and beef cattle. This contrasted withthe isolates sourced from other livestock sectors, which tended to present sector-specificsubtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle