The overall goal of this PhD project was to better understand the general epidemiology
of ovine paratuberculosis (PTb) and the speciﬁc molecular characteristics of the causing
organism Mycobacterium avium subspecies paratuberculosis in New Zealand.
To begin with, current control measures for clinical PTb in New Zealand’s major pastoral
livestock species (dairy cattle, beef cattle, sheep, deer) were reviewed. Infection with Map
is common in all these species and control is voluntary for all livestock industries. Control
measures aim to reduce the incidence rate of clinical PTb rather than to eradicate Map
infection. Dairy and deer industries have developed resources describing best-practice
management options that assist farmers and veterinarians to advise their clients about
speciﬁc control plans. There is no national control programme for sheep and beef cattle.
However, unlike for cattle and deer, the use of a commercial vaccine is licensed for sheep.
Evidence in this thesis suggests that vaccination may be a cost effective option for ﬂocks
that experience a high incidence of clinical disease. For deer, there is a national abattoir
surveillance programme that aims to alert farmers of unusually high rates of PTb-like
lesions in deer at slaughter. Evaluations of the biological and economic effectiveness of
voluntary control still remains to be undertaken for all industries.
Work in this thesis estimated the on-farm economic cost of clinical PTb in sheep (ovine
Johne’s disease, OJD) in New Zealand. It was based on data about the incidence of clinical PTb and overall mortality from 20 OJD-affected farms. The beneﬁt-cost ratio of
vaccination was estimated. Farms were categorized as either ﬁne-wool breed (Merino,
Half-bred, Corriedale) or other breeds and calculations were stratiﬁed for these two farm
categories. The estimated mortality due to OJD was 2.7 times as high in ﬁne-wool as in
other breeds with large variation between farms. A stochastic simulation for a hypothetical ﬂock with 2,000 breeding ewes resulted in an average annual cost of OJD-mortality of
NZ $13,100 in ﬁne-wool and NZ $4,300 in other breeds. Vaccinating replacement lambs against OJD would be cost-effective in most ﬂocks when the pre-vaccination annual OJD
ewe mortality was >1%. Accurate on-farm observation of OJD to establish incidence
would help farmers to make better decisions about vaccination.
Frozen-stored faecal and serum samples of individual sheep with no signs of clinical disease from 45 commercial ﬂocks from a 2013 study that determined pooled faecal culture
(PFC) status were used to determine faecal Map shedding and antibody in serum. A total
of 878 faecal samples were tested with direct faecal real-time quantitative PCR (qPCR) to
determine Map shedding prevalence and abundance in individual animals. In addition, the
qPCR results were compared with Map antibody ELISA results from 837 corresponding
sera to correlate the observed shedding prevalence with sero-prevalence. Overall, 13.1%
of faecal samples and 5.8% of serum samples tested positive. The median intra-ﬂock
prevalence (IFP) of Map shedding in the qPCR positive ﬂocks was 13.5% with a range of
5–95%. The median IFP of Map ELISA antibody positive ﬂocks was 10% with a range
of 5–20%. ELISA results and the DNA concentration in qPCR positive samples were
positively correlated. Nevertheless, ELISA was a poor predictor of individual shedding.
A more robust assessment of the shedding status of ﬂocks can be achieved by using a
combination of qPCR and ELISA of individual animals rather than a single PFC of 20
randomly selected sheep per ﬂock, as was used in the 2013 survey.
Type S1 Map isolates from New Zealand and the Australian Telford strain were char-
acterized based on single nucleotide variant (SNV) analysis of whole genome sequence
data (WGS). A Type S1 genome was completely sequenced and closed for using as a
reference for the SNV analysis. Besides deﬁning the genetic relationship between Map
isolates from New Zealand, Australia and Europe several phenotypic variables used as
surrogates for the severity of PTb in individual hosts were investigated. The New Zealand
and Australian isolates formed a closely related group. They were distinctly different
from the Type S isolates from countries in Europe. Within New Zealand, Map genotypes and region of sheep farm locations were signiﬁcantly associated (p <0.05). There
were no signiﬁcant associations between genotype and surrogates for severity, observed
in the animals which the genotypes were isolated from, such as histopathological scores
of intestinal lesions, host serology or the gross-pathological diagnosis by veterinarians at
necropsy. These results suggested that the phenotypic variation of PTb may depend on
factors other than Map-genotype in Type S strain. Further studies are required to sub-stantiate a hypothesis about varying virulence factors of the Map genome in New Zealand
In summary, PTb control in New Zealand is voluntary in all major ruminant livestock
industries including sheep. In clinically affected commercial sheep farms, estimated mortality due to OJD was 2.7 times as high in ﬁne-wool as in other breeds, but large variations
were observed between farms. PTb vaccination in commercial sheep ﬂocks may be cost
effective if annual incidence of OJD attributable ewe mortality is >1%. In non-clinical
commercial ﬂocks, the median IFP of Map shedding and Map ELISA antibody positive
prevalence was 13.5% and 10% respectively. Approximately 1% ewes in qPCR positive
ﬂocks were supershedders. Based on analysis of WGS data, Type S Map genotypes from
New Zealand sheep were similar across the country and not affected by the type of breed
or disease outcome in hosts.