Journal Articles
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Item Machine learning for predicting climate change impacts on Pseudopithomyces chartarum spore counts: a risk indicator of facial eczema(Taylor and Francis Group, 2025-11-09) Wada M; Sagarasaeranee O; Cogger N; Marshall J; Cuttance E; Macara G; Sood A; Vallee EAims To determine the importance of 11 climate variables on pasture spore count of Pseudopithomyces chartarum, a risk indicator of facial eczema (FE), and to forecast spore counts in New Zealand until 2100, using longitudinal P. chartarum pasture spore count data. Methods Between 2010 and 2017, spore counts (n = 6,975) were collected from 862 paddocks spread over 102 farms in the North Island of New Zealand. Historical and projected climate data were obtained from the National Institute of Water and Atmospheric Research. The spore count dataset was merged with climate data from corresponding locations, incorporating time lags of 1–53 weeks. Linear regression models were fitted for describing crude associations, while random forest models were fitted for determining variable importance and predicting future spore counts. Results Mixed-effect linear regression models explained up to 11% of the variance of log-transformed spore counts by a single lagged climate covariate. The best-fit random forest model had a testing accuracy of 80% in classifying low or high FE risk (> 20,000 spores) with an R2 value of 43%. The random forest models suggested time-dependent importance of soil temperature at 10 cm depth, solar radiation, potential evapotranspiration, vapour pressure, soil moisture and minimum temperature, while no or weak evidence of variable importance was found for maximum temperature, rainfall, mean sea level atmospheric pressure, relative humidity and wind speed. Over the next 80 years, our model predicted an increase in the seasonal mean spore counts in the study farms by a mean of 17% (min 6, max 30%) under the high-end greenhouse gas emission scenario (representative concentration pathways (RCP) 8.5). Every decade was associated with an increase in the probability of high-risk spore counts (> 20,000) by 14–22% for the moderate to high emission scenarios (RCP 4.5–8.5). The model indicated increased peak spore counts across most regions over the next 80 years. Specifically, the entire North Island and three districts in the South Island were projected to have high mean peak spore counts by 2100. Conclusions and clinical relevance These findings could be used to target high-risk areas to implement mitigation or adaptation measures for FE. In addition, the study highlights the value of ecological data for forecasting environmental disease risks to enhance preparedness for climate change.Item An Investigation of Dairy Cattle Welfare in Commercial Iranian Farms: Results from Management Practices, Resource-Based Measures, and Farm Records(MDPI (Basel, Switzerland), 2025-10-16) Jafari-Gh A; Laven R; Khaloubagheri F; Jafari-Gh S; Mirrahimi MH; Dehghan Banadaky M; Mueller KR; Vallee E; De Rosa GThere is currently no routine systematic assessment of welfare on Iranian dairy farms and no industry-recognised welfare assessment protocols. Therefore, we aimed to design a comprehensive welfare assessment protocol and use it to assess dairy cattle welfare on Iranian dairy farms that could serve as baseline data. Out of the 54 farms on which milking time was measured, 14 had cows spending ≥4 h a day for milking. Additionally, 17/43 farms provided <6 cm of water trough length per cow, and 9/46 farms provided <47 cm of feed trough length per cow, falling short of international guidelines. Hoof trimming was considered a routine procedure with 51/56 farms trimming the hooves ≥2 times a year. The main housing problem in bedded-pack farms was lack of resting areas with 18/29 farms providing less space than the minimum requirement of 5.4 m2/cow, while in free-stall farms bedding depth was the principal housing issue with 16/28 providing ≤10 cm of bedding. Finally, only 31/42 farms that provided farm data kept a record of more than half of the parameters that we asked for. Our findings indicate that a high proportion of farms did not provide sufficient resources or implement management practices necessary to meet welfare requirements of dairy cattle on Iranian farms.Item The association between rainfall and human leptospirosis in Aotearoa New Zealand(Cambridge University Press, 2025-08-26) Tana T; Wada M; Benschop J; Vallee ELeptospirosis remains a significant occupational zoonosis in New Zealand, and emerging serovar shifts warrant a closer examination of climate-related transmission pathways. This study aimed to examine whether total monthly rainfall is associated with reported leptospirosis in humans in New Zealand. Poisson and negative binomial models were developed to examine the relationship between rainfall at 0-, 1-, 2-, and 3-month lags and the incidence of leptospirosis during the month of the report. Total monthly rainfall was positively associated with the occurrence of human leptospirosis in the following month by a factor of 1.017 (95% CI: 1.007–1.026), 1.023 at the 2-month lag (95% CI:1.013–1.032), and 1.018 at the 3-month lag (95% CI: 1.009–1.028) for every additional cm of rainfall. Variation was present in the magnitude of association for each of the individual serovars considered, suggesting different exposure pathways. Assuming that the observed associations are causal, this study supports that additional human cases are likely to occur associated with increased levels of rainfall. This provides the first evidence for including rainfall in a leptospirosis early warning system and to design targeted communication and prevention measures and provide resource allocation, particularly after heavy rainfall in New Zealand.Item The effects of rain and flooding on leptospirosis incidence in sheep and cattle in New Zealand(Taylor and Francis Group on behalf of the New Zealand Veterinary Association, 2025-08-12) Sadler E; Vallee E; Watts J; Wada MAims To describe the spatio-temporal patterns of leptospirosis case counts in sheep and cattle in New Zealand, and to assess their association with climate variables indicative of flooding and surface runoff. As livestock are a major reservoir of Leptospira spp. and an important source of zoonotic transmission, understanding these patterns is critical for informing livestock and public health interventions in the context of climate change. Methods Confirmed cases of bovine and ovine leptospirosis from January 2011 to December 2023 were extracted from the Ministry for Primary Industries’ Animal Health Surveillance programme. Climate data was sourced from the National Institute of Water and Atmospheric Research. Using the χ2 test and Poisson regression models, the association between district-level case counts and four climate indices were examined: seasonal mean rainfall, seasonal frequency of extreme rainfall, seasonal mean soil moisture, and seasonal frequency of estimated surface runoff. Results Findings indicated an average of 13 confirmed cases for sheep annually, with notable surges in 2017 (34 cases) and 2023 (36 cases), aligning with extreme climate events. Poisson regression models for sheep leptospirosis identified significant associations with extreme rainfall (incidence risk ratio (IRR) = 5.03; 95% CI = 1.18–21.45), mean rainfall (IRR = 1.25; 95% CI = 1.15–1.36), surface runoff (IRR = 1.09; 95% CI = 1.04–1.15), and soil moisture (IRR = 1.03; 95% CI = 1.02–1.03). Cattle leptospirosis was positively associated with surface runoff (IRR = 1.06; 95% CI = 1.02–1.10) and soil moisture (IRR = 1.01; 95% CI = 1.00–1.01). Associations with extreme rainfall (IRR = 1.46; 95% CI = 0.49–4.31) and mean rainfall (IRR = 1.07; 95% CI = 1.00–1.14) were not statistically significant. Conclusions The outcomes of this study provide new evidence linking extreme rainfall, surface runoff, and other climate variables with increased leptospirosis case counts in sheep, with less pronounced but notable associations in cattle. These findings highlight the vulnerability of livestock to climate-driven disease pressures and suggest that future extreme weather events may increase the risk of leptospirosis outbreaks. This has important implications for targeted vaccination, surveillance, and public health preparedness in flood-prone rural regions of New Zealand.Item An Investigation of Dairy Cattle Welfare in Commercial Iranian Farms: Results from Animal- and Stockperson-Based Measures.(MDPI (Basel, Switzerland), 2025-01-27) Jafari-Gh A; Laven R; Khaloubagheri F; Mirrahimi MH; Jafari-Gh S; Banadaky MD; Mueller KR; Vallee E; Salari FDairy cow welfare can impact both the economic performance of an individual farm and the public perception of the sector, thus influencing the sustainability of the dairy farming industry. Intensive dairy farming in Iran started in the 1940s, but there is limited data available regarding dairy cattle welfare in the country. Therefore, the aim of this study was to design and use a comprehensive bespoke welfare assessment protocol in intensive Iranian dairy farms to provide baseline data for Iran and other countries with similar farming systems. The protocol consists of animal-based, stockperson-based, and resource-based measures. The first part of the welfare assessment protocol (being presented in this paper) was developed from the existing literature and contained 11 animal-based and 2 stockmanship measures. The protocol was applied in 62 intensive dairy cattle farms in five arid and semi-arid provinces of Iran. Welfare Quality sample size suggestions were used to reach the minimum sample size for all animal-based measures except for the locomotion score, where either the whole milking herd was scored or all cows in the early lactation (<150 days in milk) group. Results show that there was a good focus on nutrition management on the farms. Lameness prevalence and the incidence of hock lesions were too high, although within the range seen in many housed cows outside Iran. In addition, 13.5% of cows had damaged ears. The prevalence of dirty legs was high (≥80% of cows), and the hygiene score was unrelated to the farming system. Finally, the extremely high median prevalence of tail damage (60%) indicates a significant welfare issue that needs to be addressed with urgency.Item Investigating animals and environments in contact with leptospirosis patients in Aotearoa New Zealand reveals complex exposure pathways.(Taylor and Francis Group, 2025-02-12) Benschop J; Collins-Emerson JM; Vallee E; Prinsen G; Yeung P; Wright J; Littlejohn S; Douwes J; Fayaz A; Marshall JC; Baker MG; Quin T; Nisa SCASE HISTORY: Three human leptospirosis cases from a case-control study were recruited for in-contact animal and environment sampling and Leptospira testing between October 2020 and December 2021. These cases were selected because of regular exposure to livestock, pets, and/or wildlife, and sampling was carried out on their farms or lifestyle blocks (sites A-C), with veterinarians overseeing the process for livestock, and cases collecting environmental and wildlife samples. LABORATORY FINDINGS: Across the three sites, a total of 137 cattle, > 40 sheep, 28 possums, six dogs, six rats, three pigs and three rabbits were tested. Herd serology results on Site A, a dairy farm, showed infection with Tarassovi and Pomona; urinary shedding showed Leptospira borgpetersenii str. Pacifica. Animals were vaccinated against Hardjo, Pomona and Copenhageni. The farmer was diagnosed with Ballum. On Site B, a beef and sheep farm, serology showed infection with Pomona; animals were not vaccinated, and the farmer was diagnosed with Hardjo. On Site C, cattle were shedding L. borgpetersenii; animals were not vaccinated, and the case's serovar was indeterminate. Six wild animals associated with Sites A and C and one environmental sample from Site A were positive for pathogenic Leptospira by PCR. CONCLUSION: These findings highlight the complexity of potential exposures and the difficulty in identifying infection sources for human cases. This reinforces the need for multiple preventive measures such as animal vaccination, the use of personal protective equipment, pest control, and general awareness of leptospirosis to reduce infection risk in agricultural settings. CLINICAL RELEVANCE: Farms with unvaccinated livestock had Leptospira infections, highlighting the importance of animal vaccination. Infections amongst stock that were vaccinated emphasise the importance of best practice vaccination recommendations and pest control. Abbreviations: MAT: Microscopic agglutination test; PIC: Person in charge; PPE: Personalprotective equipmentItem The EpiCentre: redefining the future of animal health.(American Veterinary Medical Association, 2024-11-07) Cogger N; Vallee E; Subharat S; Wada M; Sujau M; Han J-H; Isaksen KE; Compton CWRItem Ultrasonographic features of the regressing yolk sac of normal captive Brown kiwi chicks (Apteryx mantelli) vary with age.(John Wiley and Sons, Inc., 2023-09-01) Short E; Owen M; Vallee E; Bolwell C; Morgan KJBrown kiwi (Apteryx mantelli) are a culturally significant ratite species endemic to New Zealand. Chicks can develop diseases of the yolk sac which can be fatal if not promptly recognized and treated. Ultrasound examination of the yolk sac is an important component in the evaluation of chicks with suspected yolk sac disease. However, there are currently no reports of the normal ultrasonographic appearance of the regressing yolk sac in this species. The objective of this prospective reference interval study was to describe the normal ultrasonographic appearance of the yolk sac in brown kiwi chicks. Focused coelomic sonographic examinations were performed on 29 healthy chicks from >1 day of age until the yolk sac was completely absorbed or was <1 mL in volume. 41.6% (57/137) of yolks were round/ovoid in shape and 58.6% (80/137) had lobulated margins with invaginations. All yolks (137/137) were hyperechoic relative to adjacent coelomic structures. The heterogeneity of the echogenicity of the yolk was significantly associated with age (increased heterogeneity in younger birds) and was homogeneous, mildly heterogeneous, and moderately heterogeneous in 33% (46/138), 46% (63/138), and 21% (29/138) of all examinations respectively. Intrasac anechoic pockets were seen in 14% (20/139) of yolk sacs. The rate of yolk sac resorption slowed with age. In all examinations identifying a completely absorbed yolk sac or a yolk sac <1 mL in volume, chicks were less than 21 days old. The results of this study provide a reference of normal for the sonographic appearance of the yolk sac in captive brown kiwi chicks.Item Prevalence and incidence rate of clinical lameness in three New Zealand dairy goat farms(Taylor and Francis Group, 2024-01-01) Jaques N; Turner S-A; Vallee E; Heuer C; Deeming L; Lopez-Villalobos NClinical lameness has an impact on animal welfare and profitability in different livestock industries. The objective of this study was to estimate the prevalence and incidence rate of clinical lameness within New Zealand dairy goat farms. Up to 3246 goats on three dairy goat farms were observed 4–5 times over one year. Data on locomotion scores and animal information were collected between June 2019 and June 2020. A 5-point (0–4) locomotion scoring scale was used, where scores 3 and 4 were classified as clinical lameness. The average herd-level prevalence of clinical lameness for farms A, B, and C were 23, 12, and 10%, respectively. The annual incidence rate of clinical lameness for farms A, B, and C were 104, 56, and 55 cases per 100 goat-years, respectively. Lameness appears to be a significant welfare issue, with incidence varying between farms and between goats. Investigating both farm-level and goat-level factors is required to understand the epidemiology of lameness and design evidence-based control and prevention measures. Further investigation should be undertaken to identify variables affecting the goat's odds of becoming clinically lame. This study sets the foundation for future study of lameness in commercial dairy goat farms nationally and internationally.Item Molecular characterisation and additional morphological descriptions of Eimeria spp. (Apicomplexa: Eimeriidae) from brown kiwi (Apteryx mantelli Bartlett).(Springer Nature, 2023-06-01) Coker SM; McInnes K; Vallee E; Biggs P; Pomroy WE; Howe L; Morgan KJBrown kiwi (Apteryx mantelli Bartlett), a ratite endemic to New Zealand, is currently listed as "Vulnerable" under the IUCN classification system due to predation by introduced mammals. Operation Nest Egg (ONE) raises chicks and juveniles in predator-proof enclosures until they are large enough to defend themselves. These facilities experience an environmental accumulation of coccidial oocysts, which leads to severe morbidity and mortality of these kiwi. Four species of coccidia have been morphologically described from sporulated oocysts with additional opportunistic descriptions of endogenous stages. This research continues the morphological descriptions of these species of Eimeria with an additional novel morphotype also morphologically described. It also provides the first genetic characterisation targeting the mitochondrial cytochrome c oxidase I (COI) gene. Based on these findings, it was determined there are at least five morphotypes of Eimeria that infect brown kiwi and co-infections are common at the ONE facilities surveyed. The COI amplicon targeted for this study was sufficient to provide differentiation from other members of this genus. Sanger sequencing yielded ambiguous bases, indicating the need for more in-depth sequencing.