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Item Case-control study of leptospirosis in Aotearoa New Zealand reveals behavioural, occupational, and environmental risk factors(Cambridge University Press, 2025-06-02) Nisa S; Ortolani E; Vallée E; Marshall J; Collins-Emerson J; Yeung P; Prinsen G; Wright J; Quin T; Fayaz A; Littlejohn S; Baker MG; Douwes J; Benschop J; Hahné SLeptospirosis in NZ has historically been associated with male workers in livestock industries; however, the disease epidemiology is changing. This study identified risk factors amid these shifts. Participants (95 cases:300 controls) were recruited nationwide between 22 July 2019 and 31 January 2022, and controls were frequency-matched by sex (90% male) and rurality (65% rural). Multivariable logistic regression models, adjusted for sex, rurality, age, and season - with one model additionally including occupational sector - identified risk factors including contact with dairy cattle (aOR 2.5; CI: 1.0-6.0), activities with beef cattle (aOR 3.0; 95% CI: 1.1-8.2), cleaning urine/faeces from yard surfaces (aOR 3.9; 95% CI: 1.5-10.3), uncovered cuts/scratches (aOR 4.6; 95% CI: 1.9-11.7), evidence of rodents (aOR 2.2; 95% CI: 1.0-5.0), and work water supply from multiple sources - especially creeks/streams (aOR 7.8; 95% CI: 1.5-45.1) or roof-collected rainwater (aOR 6.6; 95% CI: 1.4-33.7). When adjusted for occupational sector, risk factors remained significant except for contact with dairy cattle, and slaughter without gloves emerged as a risk (aOR 3.3; 95% CI: 0.9-12.9). This study highlights novel behavioural factors, such as uncovered cuts and inconsistent glove use, alongside environmental risks from rodents and natural water sources.Item Loss of production and animal health costs in assessing economic burden of animal disease.(World Organisation for Animal Health, 2024-08) Marsh TL; Pendell D; Schrobback P; Shakil G; Tozer P; Rushton J; Cecchini MThis article focuses on identifying the loss of production and costs (or lack thereof) associated with livestock health as well as animal disease externalities, with the intent to estimate economy-wide burden. It limits its scope to terrestrial livestock and aquaculture, wherein economic burden is predominately determined by market forces. Losses and costs are delineated into both direct losses and costs and indirect losses and costs, as well as ex post costs and ex ante costs. These costs include not only private expenditures but also public expenditures related to the prevention of, treatment of, and response to livestock disease. This distinction is important because a primary role of government is to mitigate externalities. The article then discusses market impacts and investments. Finally, it provides selected examples and illustrative observations and discusses future directions for research and application. Cet article examine les pertes de production et les coûts associés (ou non) à la santé animale ainsi que les externalités liées aux maladies animales, dans le but d’estimer le fardeau pour l’ensemble de l’économie. L’examen se limite à la production d’animaux terrestres et aquatiques, secteurs où le fardeau économique est principalement déterminé par les forces du marché. Les pertes et les coûts sont répartis en pertes et coûts directs et indirects, ainsi qu’en coûts ex post et ex ante. Ces coûts comprennent non seulement les dépenses privées, mais aussi les dépenses publiques liées à la prévention, au traitement et aux réponses aux maladies des animaux d’élevage. Il s’agit d’une distinction importante car l’une des fonctions premières d’un gouvernement est d’atténuer les externalités. Les auteurs examinent ensuite les impacts sur les marchés et les investissements. Pour conclure, à partir d’exemples choisis et d’observations illustrant leur propos, les auteurs proposent des voies d’exploration pour la recherche et ses applications.Item Meta-analysis of New Zealand's nitrous oxide emission factors for ruminant excreta supports disaggregation based on excreta form, livestock type and slope class.(Elsevier B.V., 2020-08-25) van der Weerden TJ; Noble AN; Luo J; de Klein CAM; Saggar S; Giltrap D; Gibbs J; Rys G; Jenerette DGlobally, animal excreta (dung and urine) deposition onto grazed pastures represents more than half of anthropogenic nitrous oxide (N2O) emissions. To account for these emissions, New Zealand currently employs urine and dung emission factor (EF3) values of 1.0% and 0.25%, respectively, for all livestock. These values are primarily based on field studies conducted on fertile, flatland pastures predominantly used for dairy cattle production but do not consider emissions from hill land pastures primarily used for sheep, deer and non-dairy cattle. The objective of this study was to determine the most suitable urine and dung EF3 values for dairy cattle, non-dairy cattle, and sheep grazing pastures on different slopes based on a meta-analysis of New Zealand EF3 studies. As none of the studies included deer excreta, deer EF3 values were estimated from cattle and sheep values. The analysis revealed that a single dung EF3 value should be maintained, although the value should be reduced from 0.25% to 0.12%. Furthermore, urine EF3 should be disaggregated by livestock type (cattle > sheep) and topography (flatland and low sloping hill country > medium and steep sloping hill country), with EF3 values ranging from 0.08% (sheep urine on medium and steep slopes) to 0.98% (dairy cattle on flatland and low slopes). While the mechanism(s) causing differences in urine EF3 values for sheep and cattle are unknown, the 'slope effect' on urine EF3 is partly due to differences in soil chemical and physical characteristics, which influence soil microbial processes on the different slope classes. The revised EF3 values were used in an updated New Zealand inventory approach, resulting in 30% lower national N2O emissions for 2017 compared to using the current EF3 values. We recommend using the revised EF3 values in New Zealand's national greenhouse gas inventory to more accurately capture N2O emissions from livestock grazing.Item Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots.(Springer Nature Limited, 2023-10-27) Muylaert RL; Wilkinson DA; Kingston T; D'Odorico P; Rulli MC; Galli N; John RS; Alviola P; Hayman DTSThe emergence of SARS-like coronaviruses is a multi-stage process from wildlife reservoirs to people. Here we characterize multiple drivers-landscape change, host distribution, and human exposure-associated with the risk of spillover of zoonotic SARS-like coronaviruses to help inform surveillance and mitigation activities. We consider direct and indirect transmission pathways by modeling four scenarios with livestock and mammalian wildlife as potential and known reservoirs before examining how access to healthcare varies within clusters and scenarios. We found 19 clusters with differing risk factor contributions within a single country (N = 9) or transboundary (N = 10). High-risk areas were mainly closer (11-20%) rather than far ( < 1%) from healthcare. Areas far from healthcare reveal healthcare access inequalities, especially Scenario 3, which includes wild mammals and not livestock as secondary hosts. China (N = 2) and Indonesia (N = 1) had clusters with the highest risk. Our findings can help stakeholders in land use planning, integrating healthcare implementation and One Health actions.Item Development of LIME-NZ: a generic tool for prompt estimation of economic impacts of disease for New Zealand livestock.(Taylor and Francis Group, 2024-02-04) Wada M; Compton C; Hickson R; Bingham PAIMS: To develop a simple and robust generic tool to measure the impacts of livestock diseases on New Zealand dairy, beef and sheep farms using enterprise gross margin models. METHODS: The most recent (2018-2020) livestock production benchmarking data was extracted from industry-led economic surveys. Gross margin models were built for each enterprise type, accounting for 11 dairy farm types and 16 farm types for beef and sheep. Disease parameters, including changes in mortality, reproduction performance, milk yield, price of animals and culling rate, as well as additional expenses for veterinary intervention, were applied to the infected compartment of the herd/flock using the assumed annual within-herd disease incidence. Farm-level disease impacts were estimated as the difference in annual profit between the baseline and infected farm. The baseline gross margin models were validated against the industry data. The disease impact models were validated using a recently published study on bovine viral diarrhoea (BVD). The impact assessment tool, LIME-NZ, was developed using the statistical software R and implemented in the web-based R package Shiny. The input parameters can be varied interactively to obtain a range of disease impacts for uncertain disease parameters. RESULTS: The baseline gross margin models demonstrated reasonable accuracy with a mean percentage error of <14% when compared with the industry reports. The estimated annual impacts of BVD were comparable to those reported in the BVD study, NZ$38.5-140.4 thousand and $0.9-32.6 thousand per farm per year for dairy and beef enterprises, respectively. CONCLUSIONS: LIME-NZ can be used to rapidly obtain the likely economic impacts of diseases that are endemic, recently introduced or at increased risk of introduction in the New Zealand context. This will aid communication and decision-making among government agencies and the livestock industry, including veterinarians and livestock producers, about the management of diseases, until refined information becomes available to improve decision-making.Item Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project(American Society for Microbiology, 2023-07-26) Deblais L; Ojeda A; Brhane M; Mummed B; Hassen KA; Ahmedo BU; Weldesenbet YD; Amin JK; Ahmed IA; Usmane IA; Yusuf EA; Seran AJ; Abrahim FI; Game HT; Mummed BA; Usmail MM; Umer KA; Dawid MM; Gebreyes W; French N; Hassen JY; Roba KT; Mohammed A; Yimer G; Saleem C; Chen D; Singh N; Manary MJ; McKune SL; Havelaar AH; Rajashekara G; Elkins CAIn our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r2 = 0.18) and soil collected inside the house (r2 = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r2 < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.Item A cross-sectional investigation of Leptospira at the wildlife-livestock interface in New Zealand(PLOS, 2023-09-06) Moinet M; Oosterhof H; Nisa S; Haack N; Wilkinson DA; Aberdein D; Russell JC; Vallée E; Collins-Emerson J; Heuer C; Benschop J; Stevenson BThere has been a recent upsurge in human cases of leptospirosis in New Zealand, with wildlife a suspected emerging source, but up-to-date knowledge on this topic is lacking. We conducted a cross-sectional study in two farm environments to estimate Leptospira seroprevalence in wildlife and sympatric livestock, PCR/culture prevalence in wildlife, and compare seroprevalence and prevalence between species, sex, and age groups. Traps targeting house mice (Mus musculus), black rats (Rattus rattus), hedgehogs (Erinaceus europaeus) and brushtail possums (Trichosurus vulpecula) were set for 10 trap-nights in March-April 2017 on a dairy (A) and a beef and sheep (B) farm. Trapped wild animals and an age-stratified random sample of domestic animals, namely cattle, sheep and working dogs were blood sampled. Sera were tested by microagglutination test for five serogroups and titres compared using a Proportional Similarity Index (PSI). Wildlife kidneys were sampled for culture and qPCR targeting the lipL32 gene. True prevalence in mice was assessed using occupancy modelling by collating different laboratory results. Infection profiles varied by species, age group and farm. At the MAT cut-point of ≥ 48, up to 78% of wildlife species, and 16-99% of domestic animals were seropositive. Five of nine hedgehogs, 23/105 mice and 1/14 black rats reacted to L. borgpetersenii sv Ballum. The sera of 4/18 possums and 4/9 hedgehogs reacted to L. borgpetersenii sv Hardjobovis whilst 1/18 possums and 1/9 hedgehogs reacted to Tarassovi. In ruminants, seroprevalence for Hardjobovis and Pomona ranged 0-90% and 0-71% depending on the species and age group. Titres against Ballum, Tarassovi and Copenhageni were also observed in 4-20%, 0-25% and 0-21% of domestic species, respectively. The PSI indicated rodents and livestock had the most dissimilar serological responses. Three of nine hedgehogs, 31/105 mice and 2/14 rats were carrying leptospires (PCR and/or culture positive). True prevalence estimated by occupancy modelling in mice was 38% [95% Credible Interval 26, 51%] on Farm A and 22% [11, 40%] on Farm B. In the same environment, exposure to serovars found in wildlife species was commonly detected in livestock. Transmission pathways between and within species should be assessed to help in the development of efficient mitigation strategies against Leptospira.Item Spread of Nontyphoidal Salmonella in the Beef Supply Chain in Northern Tanzania: Sensitivity in a Probabilistic Model Integrating Microbiological Data and Data from Stakeholder Interviews(Wiley Periodicals LLC on behalf of Society for Risk Analysis, 2022-05) Zadoks RN; Barker GC; Benschop J; Allan KJ; Chaters G; Cleaveland S; Crump JA; Davis MA; Mmbaga BT; Prinsen G; Thomas KM; Waldman L; French NPEast Africa is a hotspot for foodborne diseases, including infection by nontyphoidal Salmonella (NTS), a zoonotic pathogen that may originate from livestock. Urbanization and increased demand for animal protein drive intensification of livestock production and food processing, creating risks and opportunities for food safety. We built a probabilistic mathematical model, informed by prior beliefs and dedicated stakeholder interviews and microbiological research, to describe sources and prevalence of NTS along the beef supply chain in Moshi, Tanzania. The supply chain was conceptualized using a bow tie model, with terminal livestock markets as pinch point, and a forked pathway postmarket to compare traditional and emerging supply chains. NTS was detected in 36 (7.7%) of 467 samples throughout the supply chain. After combining prior belief and observational data, marginal estimates of true NTS prevalence were 4% in feces of cattle entering the beef supply and 20% in raw meat at butcheries. Based on our model and sensitivity analyses, true NTS prevalence was not significantly different between supply chains. Environmental contamination, associated with butchers and vendors, was estimated to be the most likely source of NTS in meat for human consumption. The model provides a framework for assessing the origin and propagation of NTS along meat supply chains. It can be used to inform decision making when economic factors cause changes in beef production and consumption, such as where to target interventions to reduce risks to consumers. Through sensitivity and value of information analyses, the model also helps to prioritize investment in additional research.Item Extrapolating incomplete animal population and surveillance data for use in national disease control : examples from Myanmar and New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Epidemiology, School of Veterinary Science at Massey University, Manawatu, New Zealand(Massey University, 2019) van Beest van Andel, MaryNational level databases of animal numbers, locations, and movements provide the essential foundations for disease outbreak investigations, disease control, and disease preparedness activities. These activities are particularly important for managing and mitigating the risks of high impact exotic disease outbreaks like foot-and-mouth disease (FMD) as well as other economically important endemic diseases, which can significantly impact international trade and food security. However, many countries worldwide either lack national animal databases entirely or have multiple, fragmented databases that provide an incomplete picture of animal demographics. Consequently, there has been growing interest in developing novel methods to infer missing information on animal populations from other data sources, to quantify the extent of missing information, and to understand the impacts of missing information on the predictions made from national disease simulation models. This thesis explores these issues in the context of an FMD free country (New Zealand) as well as a country with endemic FMD (Myanmar). In Chapter 3, regression models were used to predict farm-level animal populations in New Zealand based on available data on farm type and location. When the results were compared against a subset of validated animal population data, the predictions at the farm level were found to be inaccurate especially for small-scale farms that keep animals for personal consumption or as a hobby. These properties are of particular interest to animal health authorities as they have been identified as at risk for exotic disease outbreaks. In Chapter 4, the impacts of having inaccurate herd size data on the predictions made by an FMD disease spread simulation model were explored. The results were analysed using cox proportional hazard models and logistic regression models, which showed that simulations run using actual animal population data indicated different optimal control strategies for FMD than models run with imperfect data and these effects differed by the region in New Zealand where the hypothetical disease outbreak was seeded. In Chapter 5, high-resolution local survey data and low-resolution national remote sensor data were used alone and in combination to predict the location of FMD positive villages in Myanmar, which were identified by serological sampling conducted as part of a large OIE funded research project in 2016. The performance of both random forest models and logistic regression models were explored using training and testing data sets. Bovine populations and proximity to cattle markets were found to be significant risk factors for FMD seropositivity and the logistic regression models performed as well as machine learning techniques. Chapter 6 compared verbal reports of FMD outbreaks from village headman and householders against the serological test results from their villages to determine whether using public reports is a viable alternative to conducting resource intensive serological surveys for estimating FMD prevalence in Myanmar. Although village headmen proved to be a better source of FMD reports compared to householders, the verbal reports were still not as accurate as serological tests in an endemic situation where both sensitivity and specificity of observing clinical signs can be complicated by endemic stability and concurrent outbreaks of other diseases. The work in both chapters 5 and 6 was carried out using data from activities of the Livestock Breeding and Veterinary Department and the OIE and as such separate human ethics approval was not required for the surveys described. Chapter 7 addressed the issue of estimating the scale of missing data in a national database by comparing intensively collected interview information with recorded movements at the farm level for farms involved in New Zealand’s Mycoplasma bovis eradication programme. The results showed that dairy farmers often failed to record almost half of high risk movements including leased bulls, calves sent offsite for rearing, and adult cattle sent away for winter grazing. It was also estimated that approximately 60% of animals arriving at abattoirs in New Zealand have multiple movements missing from their life history in the National Animal Identification and Tracing system (NAIT) database. This missing information had a significant impact on the ability of government and industry to effectively respond to the outbreak. However, a positive finding from this study was that the rates of missing data are decreasing over time. Overall, this thesis demonstrated the importance of enhancing efforts to collect accurate and up-to- date national animal population and movement data. For New Zealand, the changes required to improve the national farm animal data landscape include improving compliance with the legislated requirements to record animal movements and modifying the existing databases to record information on the health status of animals against a unique animal identifier. A unique farm identifier is required at the national level and should be agreed upon by industry representatives, government and researchers. The combination of animal health data associated with the unique animal identifier and a single current farm identifier for all farms will result in a robust animal health and biosecurity system.Item Development of a low-cost automated sample presentation and analysis system for counting and classifying nematode eggs : a thesis presented in partial fulfilment of the requirements for the degree of Master of Engineering in Mechatronics at Massey University, Manawatu, New Zealand(Massey University, 2017) Pedersen, BenjaminThis thesis discusses the concept development and design of a low-cost, automated, sample presentation system for faecal egg counting, and classification. The system developed uses microfluidics to present nematode eggs for digital imaging to produce images suitable for image analysis and classification. The system costs are kept low by using simple manufacturing methods and commonly available equipment to produce microfluidic counting chambers, which can be interfaced with conventional microscopes. This thesis includes details of the design and implementation of the software developed to allow capture and processing of images from the presentation system. This thesis also includes details on the measures taken to correct for the optical aberrations introduced by the sample presentation system.