Estimation of flock/herd-level true Mycobacterium avium subspecies paratuberculosis prevalence on sheep, beef cattle and deer farms in New Zealand using a novel Bayesian model

Cristobal Verdugo; Geoff Jones; Wes Johnson; Peter Wilson; Lesley Stringer; Cord Heuer

doi:10.1016/j.prevetmed.2014.10.004

Estimation of flock/herd-level true Mycobacterium avium subspecies paratuberculosis prevalence on sheep, beef cattle and deer farms in New Zealand using a novel Bayesian model

Prev Vet Med. 2014 Dec 1;117(3-4):447-55. doi: 10.1016/j.prevetmed.2014.10.004. Epub 2014 Oct 19.

Authors

Cristobal Verdugo¹, Geoff Jones², Wes Johnson³, Peter Wilson⁴, Lesley Stringer⁵, Cord Heuer⁶

Affiliations

¹ Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile; Epicentre, Massey University, Palmerston North, New Zealand. Electronic address: cristobal.verdugo@uach.cl.
² Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
³ Department of Statistics, University of California, Irvine, USA.
⁴ Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
⁵ Epicentre, Massey University, Palmerston North, New Zealand; Veterinary Epidemiology Unit, Department of Agriculture and Rural Development, Belfast, Northern Ireland, United Kingdom.
⁶ Epicentre, Massey University, Palmerston North, New Zealand.

PMID: 25457132
DOI: 10.1016/j.prevetmed.2014.10.004

Abstract

The study aimed to estimate the national- and island-level flock/herd true prevalence (HTP) of Mycobacterium avium subsp. paratuberculosis (MAP) infection in pastoral farmed sheep, beef cattle and deer in New Zealand. A random sample of 238 single- or multi-species farms was selected from a postal surveyed population of 1940 farms. The sample included 162 sheep flocks, 116 beef cattle and 99 deer herds from seven of 16 geographical regions. Twenty animals from each species present on farm were randomly selected for blood and faecal sampling. Pooled faecal culture testing was conducted using a single pool (sheep flocks) or two pools (beef cattle/deer herds) of 20 and 10 samples per pool, respectively. To increase flock/herd-level sensitivity, sera from all 20 animals from culture negative flocks/herds were individually tested by Pourquier(®) ELISA (sheep and cattle) or Paralisa™ (deer). Results were adjusted for sensitivity and specificity of diagnostic tests using a novel Bayesian latent class model. Outcomes were adjusted by their sampling fractions to obtain HTP estimates at national level. For each species, the posterior probability (POPR) of HTP differences between New Zealand North (NI) and South (SI) Islands was obtained. Across all species, 69% of farms had at least one species test positive. Sheep flocks had the highest HTP estimate (76%, posterior probability interval (PPI) 70-81%), followed by deer (46%, PPI 38-55%) and beef herds (42%, PPI 35-50%). Differences were observed between the two main islands of New Zealand, with higher HTP in sheep and beef cattle flocks/herds in the NI. Sheep flock HTP was 80% in the NI compared with 70% (POPR=0.96) in the SI, while the HTP for beef cattle was 44% in the NI and 38% in the SI (POPR=0.80). Conversely, deer HTP was higher in the SI (54%) than the NI (33%, POPR=0.99). Infection with MAP is endemic at high prevalence in sheep, beef cattle and deer flocks/herds across New Zealand.

Keywords: Bayesian analysis; Mycobacterium avium subsp. paratuberculosis; Pastoral systems; Prevalence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bayes Theorem
Cattle
Cattle Diseases / epidemiology*
Cattle Diseases / microbiology
Deer*
Enzyme-Linked Immunosorbent Assay / veterinary
Feces / microbiology
Female
Geography
Male
Mycobacterium avium subsp. paratuberculosis / isolation & purification*
New Zealand / epidemiology
Paratuberculosis / epidemiology*
Paratuberculosis / microbiology
Prevalence
Sheep
Sheep Diseases / epidemiology*
Sheep Diseases / microbiology