Epidemiology of Mycobacterium avium subspecies paratuberculosis infection on sheep, beef cattle and deer farms in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
Paratuberculosis (Ptb) is a chronic enteric infection caused by Mycobacterium avium
subspecies paratuberculosis (MAP), affecting wild and domestic ruminants. In domestic
ruminants MAP infection is largely sub-clinical, but can result in chronic diarrhoea
leading to emaciation and death. Clinical disease is commonly observed in adult cattle
and sheep but in deer the disease incidence is higher in young animals (8-12 months). In
the New Zealand pastoral farming system, it is common practice to co-graze Ptb
susceptible livestock species (sheep, cattle, and deer) together, either concurrently or
successively, on the same pasture. Thus several susceptible species have contact at farm
level, being at risk of transmitting MAP between species through contaminated pasture.
Johne’s Disease Research Consortium (JDRC), a partnership between livestock
industries, government and research providers was created to study Ptb in an
overarching approach, involving all susceptible species, aiming to generate scientific
knowledge to support Ptb control policies.
The present research was implemented under the financial support of JDRC, aiming to
generate epidemiological information about Ptb infection and clinical disease on mixedspecies
pastoral farms, grazing sheep, beef cattle, and/or deer. A total of 350 mixedspecies
farms (11,089 animals) were faecal and blood sampled and related
epidemiological information was collected. Data was used to estimate: i) the national
herd level true prevalence (HTP) of MAP infection on sheep, beef cattle and deer, ii) the
risk of MAP infection and clinical disease incidence associated with species co-grazing,iii) the association between infected and affected herds/flocks and production outputs,
and iv) relationships between molecular strain types of MAP isolates and their
distribution across livestock sectors and geographical areas. Finally, data and results
from previous studies allowed v) the development and calibration of a two host-species
(sheep & beef cattle) mathematical model, simulating MAP transmission between
species and the effect of several control measures under mixed species farming.
MAP infection is widely spread in New Zealand. A Bayesian analysis to account for
lack of sensitivity (Se) and specificity (Sp) of testing protocols, indicated that the
highest HTP estimate for sheep flocks (75%, posterior probability interval (PPI) 68-
82%), followed by deer (46%, PPI 39-54%) and beef herds (43%, PPI 359-51%). Sheep
and beef cattle flocks/herds presented a higher prevalence in the North Island (NI),
whereas deer infection was mainly located in the South Island (SI).
Logistic and Poisson regression models using Bayesian inference to adjust for lack of
Se and Sp of diagnostic tests and of farmer’s recall of clinical Ptb indicated that the
shared use of pasture was associated with Ptb prevalence and incidence. When beef
cattle and sheep were co-grazed, the infection risk increased 3-4 times in each species.
Similarly, co-grazing of beef cattle and deer increased 3 times the risk of infection on
deer. Co-grazing beef cattle with sheep, or beef cattle with deer, also was associated
with increased clinical incidence in these species. Conversely, the co-grazing of sheep
and deer was associated with a lower clinical disease incidence in both species.
Classical logistic and Poisson regression models indicated that MAP ‘infection’ status
was significantly (p =0.03) associated with reduced calving rates in beef cattle herds
and lower culling rates in deer herds and sheep flocks. Moreover, in sheep flocks and
deer herds, a significant and a marginally significant (p = 0.05 and 0.09, respectively)Molecular analysis of MAP isolates obtained from sheep, cattle (beef and dairy) and
deer, using a combination of the variable number of tandem repeats (VNTR) method
and the short sequence repeat (SSR) method, rendered 17 MAP subtypes. Analysis
indicated significantly higher subtype richness in dairy cattle and livestock sector as the
main source of subtype variation. Moreover, similar subtypes were sourced from sheep
and beef cattle, which tended to be different to the ones obtained from other livestock
sectors. However, when beef cattle and deer were both present on the same farm, they
harboured similar subtypes. These results provided strong evidence for transmission of
MAP between species through the joint use of pasture.
Simulation results of a mathematical infectious disease model for Ptb indicated that the
length of the co-grazing period was positively associated with the infection prevalence
of sheep and beef cattle. Long pasture spelling periods from 9 to 15 months reduced
MAP contamination up to 99%. However, the infection of naïve animals was still
possible, but the prevalence remained <1% for at least 25 years. The simultaneous
application of control measures on both species was the most efficient approach to
reduce the prevalence and incidence. The separation of co-grazed species in tandem
with an increased farmer surveillance, to reduce the time that clinical animals remained
on the farm, was most effective in sheep, whereas T&C was in beef cattle.
The present research provides evidence that MAP infection is highly endemic in New
Zealand farming livestock, and that the clinical disease incidence is generally low
(<0.5%) in most infected farms. Moreover, inference from molecular pathogen typing
of strategically collected isolates from farms across New Zealand strongly suggested
that MAP is transmitted between species, mainly from sheep to beef cattle and between
beef cattle and deer, all of which are commonly grazed together in the New Zealand
pastoral farming system.