Journal Articles
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Item Multidimensional trace metals and nutritional niche differ between sexually immature and mature common dolphins (Delphinus delphis)(Elsevier Ltd., 2023-06-26) Stockin KA; Machovsky-Capuska GE; Palmer EI; Amiot CThere is a need to understand the links between metals and nutrition for apex marine predators, which may be subject to different ecotoxicological effects at different life stages. We combined stomach content analyses (SCA), prey composition analysis (PCA), the Multidimensional Niche Framework (MNNF) with Bayesian multivariate ellipses, trace metal analysis and nicheROVER to investigate nutrition and trace metals across sex, age, and sexual maturity status in common dolphins (Delphinus delphis) from New Zealand. A broader prey composition niche breadth (SEAc) was estimated for immature compared to mature conspecifics, showing a higher degree of prey and nutrient generalism driven by protein (P) intake. Cd and Zn niche similarities suggests these metals were incorporated through similar prey in both immature and mature dolphins, whereas Hg and Se niche divergence indicates uptake occurred via different prey. Our multidisciplinary assessment demonstrated how nutrients and metal interactions differ in common dolphins depending upon sexual maturity. This approach has relevance when considering how marine pollution, environmental fluctuations and climate change may affect nutritional and trace metal interactions during different reproductive stages within marine predators.Item Evaluation of the accuracy of the IDvet serological test for Mycoplasma bovis infection in cattle using latent class analysis of paired serum ELISA and quantitative real-time PCR on tonsillar swabs sampled at slaughter(Public Library of Science (PLoS), 2023-05-11) Marquetoux N; Vignes M; Burroughs A; Sumner E; Sawford K; Jones G; Qi YMycoplasma bovis (Mbovis) was first detected in cattle in New Zealand (NZ) in July 2017. To prevent further spread, NZ launched a world-first National Eradication Programme in May 2018. Existing diagnostic tests for Mbovis have been applied in countries where Mbovis is endemic, for detecting infection following outbreaks of clinical disease. Diagnostic test evaluation (DTE) under NZ conditions was thus required to inform the Programme. We used Bayesian Latent Class Analysis on paired serum ELISA (ID Screen Mycoplasma bovis Indirect from IDvet) and tonsillar swabs (qPCR) for DTE in the absence of a gold standard. Tested samples were collected at slaughter between June 2018 and November 2019, from infected herds depopulated by the Programme. A first set of models evaluated the detection of active infection, i.e. the presence of Mbovis in the host. At a modified serology positivity threshold of SP%> = 90, estimates of animal-level ELISA sensitivity was 72.8% (95% credible interval 68.5%-77.4%), respectively 97.7% (95% credible interval 97.3%-98.1%) for specificity, while the qPCR sensitivity was 45.2% (95% credible interval 41.0%-49.8%), respectively 99.6% (95% credible interval 99.4%-99.8%) for specificity. In a second set of models, prior information about ELISA specificity was obtained from the National Beef Cattle Surveillance Programme, a population theoretically free-or very low prevalence-of Mbovis. These analyses aimed to evaluate the accuracy of the ELISA test targeting prior exposure to Mbovis, rather than active infection. The specificity of the ELISA for detecting exposure to Mbovis was 99.9% (95% credible interval 99.7%-100.0%), hence near perfect at the threshold SP%=90. This specificity estimate, considerably higher than in the first set of models, was equivalent to the manufacturer's estimate. The corresponding ELISA sensitivity estimate was 66.0% (95% credible interval 62.7%-70.7%). These results confirm that the IDvet ELISA test is an appropriate tool for determining exposure and infection status of herds, both to delimit and confirm the absence of Mbovis.Item Prevalence and genetic diversity of Theileria equi from horses in Xinjiang Uygur Autonomous region, China.(Elsevier B.V., 2023-07-01) Zhang Y; Shi Q; Laven R; Li C; He W; Zheng H; Liu S; Lu M; Yang DA; Guo Q; Chahan BTheileria equi is a tick-borne intracellular apicomplexan protozoan parasite that causes equine theileriosis (ET). ET is an economically important disease with a worldwide distribution that significantly impacts international horse movement. Horses are an essential part of the economy in Xinjiang which is home to ∼10% of all the horses in China. However, there is very limited information on the prevalence and genetic complexity of T. equi in this region. Blood samples from 302 horses were collected from May to September 2021 in Ili, Xinjiang, and subjected to PCR examination for the presence of T. equi. In addition, a Bayesian latent class model was employed to estimate the true prevalence of T. equi, and a phylogenetic analysis was carried out based on the 18S rRNA gene of T. equi isolates. Seventy-two horses (23.8%) were PCR positive. After accounting for the imperfect PCR test using a Bayesian latent class model, the estimated true prevalence differed considerably between age groups, being 10.8% (95%CrI: 5.8% - 17.9%) in ≤ 3-year-old horses and 35.7% (95%CrI: 28.1% - 44.5%) in horses that were > 3 year-old. All T. equi isolates had their 18S rRNA gene (430bp) sequenced and analyzed in order to identify whether there were multiple genotypes of T. equi in the Xinjiang horse population. All of the 18S rRNA genes clustered into one phylogenetic group, clade E, which is thus probably the dominant genotype of T. equi in Xinjiang, China. To summarize, we monitored the prevalence of T. equi in horses of Xinjiang, China, with a focus on the association between age and the occurrence of T. equi by Bayesian modelling, accompanied by the genotyping of T. equi isolates. Obtaining the information on genotypes and age structure is significant in monitoring the spread of T. equi and studying the factors responsible for the distribution.Item Source attribution of campylobacteriosis in Australia, 2017-2019.(John Wiley and Sons, Inc., 2023-12-01) McLure A; Smith JJ; Firestone SM; Kirk MD; French N; Fearnley E; Wallace R; Valcanis M; Bulach D; Moffatt CRM; Selvey LA; Jennison A; Cribb DM; Glass KCampylobacter jejuni and Campylobacter coli infections are the leading cause of foodborne gastroenteritis in high-income countries. Campylobacter colonizes a variety of warm-blooded hosts that are reservoirs for human campylobacteriosis. The proportions of Australian cases attributable to different animal reservoirs are unknown but can be estimated by comparing the frequency of different sequence types in cases and reservoirs. Campylobacter isolates were obtained from notified human cases and raw meat and offal from the major livestock in Australia between 2017 and 2019. Isolates were typed using multi-locus sequence genotyping. We used Bayesian source attribution models including the asymmetric island model, the modified Hald model, and their generalizations. Some models included an "unsampled" source to estimate the proportion of cases attributable to wild, feral, or domestic animal reservoirs not sampled in our study. Model fits were compared using the Watanabe-Akaike information criterion. We included 612 food and 710 human case isolates. The best fitting models attributed >80% of Campylobacter cases to chickens, with a greater proportion of C. coli (>84%) than C. jejuni (>77%). The best fitting model that included an unsampled source attributed 14% (95% credible interval [CrI]: 0.3%-32%) to the unsampled source and only 2% to ruminants (95% CrI: 0.3%-12%) and 2% to pigs (95% CrI: 0.2%-11%) The best fitting model that did not include an unsampled source attributed 12% to ruminants (95% CrI: 1.3%-33%) and 6% to pigs (95% CrI: 1.1%-19%). Chickens were the leading source of human Campylobacter infections in Australia in 2017-2019 and should remain the focus of interventions to reduce burden.Item A novel Bayesian Latent Class Model (BLCM) evaluates multiple continuous and binary tests: A case study for Brucella abortus in dairy cattle.(Elsevier B.V., 2024-03-01) Wang Y; Vallée E; Compton C; Heuer C; Guo A; Wang Y; Zhang Z; Vignes MBovine brucellosis, primarily caused by Brucella abortus, severely affects both animal health and human well-being. Accurate diagnosis is crucial for designing informed control and prevention measures. Lacking a gold standard test makes it challenging to determine optimal cut-off values and evaluate the diagnostic performance of tests. In this study, we developed a novel Bayesian Latent Class Model that integrates both binary and continuous testing outcomes, incorporating additional fixed (parity) and random (farm) effects, to calibrate optimal cut-off values by maximizing Youden Index. We tested 651 serum samples collected from six dairy farms in two regions of Henan Province, China with four serological tests: Rose Bengal Test, Serum Agglutination Test, Fluorescence Polarization Assay, and Competitive Enzyme-Linked Immunosorbent Assay. Our analysis revealed that the optimal cut-off values for FPA and C-ELISA were 94.2 mP and 0.403 PI, respectively. Sensitivity estimates for the four tests ranged from 69.7% to 89.9%, while specificity estimates varied between 97.1% and 99.6%. The true prevalences in the two study regions in Henan province were 4.7% and 30.3%. Parity-specific odds ratios for positive serological status ranged from 1.2 to 2.2 for different parity groups compared to primiparous cows. This approach provides a robust framework for validating diagnostic tests for both continuous and discrete tests in the absence of a gold standard test. Our findings can enhance our ability to design targeted disease detection strategies and implement effective control measures for brucellosis in Chinese dairy farms.Item XSim version 2: simulation of modern breeding programs(Oxford University Press on behalf of Genetics Society of America, 2022-04-04) Chen CJ; Garrick D; Fernando R; Karaman E; Stricker C; Keehan M; Cheng H; de Koning D-JSimulation can be an efficient approach to design, evaluate, and optimize breeding programs. In the era of modern agriculture, breeding programs can benefit from a simulator that integrates various sources of big data and accommodates state-of-the-art statistical models. The initial release of XSim, in which stochastic descendants can be efficiently simulated with a drop-down strategy, has mainly been used to validate genomic selection results. In this article, we present XSim Version 2 that is an open-source tool and has been extensively redesigned with additional features to meet the needs in modern breeding programs. It seamlessly incorporates multiple statistical models for genetic evaluations, such as GBLUP, Bayesian alphabets, and neural networks, and it can effortlessly simulate successive generations of descendants based on complex mating schemes by the aid of its modular design. Case studies are presented to demonstrate the flexibility of XSim Version 2 in simulating crossbreeding in animal and plant populations. Modern biotechnology, including double haploids and embryo transfer, can all be simultaneously integrated into the mating plans that drive the simulation. From a computing perspective, XSim Version 2 is implemented in Julia, which is a computer language that retains the readability of scripting languages (e.g. R and Python) without sacrificing much computational speed compared to compiled languages (e.g. C). This makes XSim Version 2 a simulation tool that is relatively easy for both champions and community members to maintain, modify, or extend in order to improve their breeding programs. Functions and operators are overloaded for a better user interface so they may concatenate, subset, summarize, and organize simulated populations at each breeding step. With the strong and foreseeable demands in the community, XSim Version 2 will serve as a modern simulator bridging the gaps between theories and experiments with its flexibility, extensibility, and friendly interface.Item Retention of internal teat sealants over the dry period and their efficacy in reducing clinical and subclinical mastitis at calving(Elsevier Inc and the Federation of Animal Science Societies (Fass) Inc on behalf of the American Dairy Science Association, 2022-06) Bates AJ; King C; Dhar M; Fitzpatrick C; Laven RAInternal teat sealants (ITS) reduce the risk of new intramammary infections over the dry period by forming a physical barrier to pathogen ingress. As the first and last 2 wk of the dry period are high-risk periods for new infections, maintaining an effective barrier in this period is a key requirement. Few studies have systematically examined sealant retention and none have done so under New Zealand pastoral conditions, where cows frequently move to separate grazing for dry periods, typically 80 to 90 d long. This multi-herd study was a split-udder equivalence trial comparing 2 ITS formulations for retention and efficacy in preventing periparturient clinical and subclinical mastitis. Both ITS contained 65% (2.6 g) bismuth salts, which contribute to the barrier within the teat canal, emulsified in ≤1.4 g of mineral oil. However, one ITS additionally contained <10% amorphous silica. At dry-off, treatment was randomly allocated to diagonal teat-pairs within 409 cows on 4 farms. All cows met industry best practice criteria for ITS treatment alone. The study unit was quarter within cow and farm. Outcomes included clinical mastitis (CM) incidence for the last 7 d of the dry period and first 42 d of lactation, subclinical mastitis (SCM) incidence 96 h after calving, and quantity of residual after centrifuging 50 mL of colostrum collected from each quarter within 24 h of calving. Proportional outcomes were analyzed using Bayesian mixed models with a binomial distribution and logit link function, whereas the quantity of residual was analyzed using Bayesian finite mixture models and cluster bootstrapping. We set a region of probable equivalence (ROPE) of ±2.5% between proportions and ±0.2 g for residual weight. Records were available for 1,596 quarters (399 cows). We detected no meaningful difference in incidence of CM or SCM attributable to differences in sealant: the model predicted treatment differences of 0.00 with a 95% highest density interval (HDI) of ±1.00%. Across all cows and farms, the marginal difference in the percentage of quarters with CM was 0.11% (95% HDI: -2.11 to 2.49%), and for SCM 0.00 (95% HDI: -1.98 to 1.94%). Including the quantity of residual recovered at calving did not improve fit or predictive ability of the models predicting CM or SCM, and the coefficient spanned the null value. The distribution of the weight of material recovered at calving was multi-modal; for 25% of quarters, more residual was recovered than inserted. When the residual weight was less than or equal to the median residual weight (2.06 g; range: 0.19-6.03 g), there was a ≥90% probability that any treatment difference in residual was ≤0.2 g. When the residual weight was between the median and 75th percentile (4.40 g; 95% HDI: 4.00 to 4.75 g), there was no clear difference in residual between products. Above the 75th percentile, there was a 90% probability that the residual from quarters differed by product type (difference = 0.36 g, 90% HDI: 0.20 to 0.54 g). In conclusion, both products had equivalent efficacy for SCM and CM. As the quantity of residual increased, the difference in residual weight recovered increased but this may represent increases in debris rather than indicating a more effective barrier.Item The evolution of carotenoid-based plumage colours in passerine birds(John Wiley and Sons Ltd on behalf of British Ecological Society, 2023-01-04) Delhey K; Valcu M; Dale J; Kempenaers B; Willink B1. Many birds use carotenoids to colour their plumage yellow to red. Because birds cannot synthesise carotenoids, they need to obtain these pigments from food, although some species metabolise dietary carotenoids (which are often yellow) into derived carotenoids (often red). 2. Here, we study the occurrence of yellow and red carotenoid-based plumage colours in the passerines, the largest bird radiation and quantify the effects of potential ecological and life-history drivers on their evolution. 3. We scored the presence/absence of yellow and red carotenoid-based plumage in nearly 6,000 species and use Bayesian phylogenetic mixed models to assess the effects of carotenoid-availability in diet, primary productivity, body size, habitat and sexual selection. We also test the widespread assumption that red carotenoid-based colours are more likely to be the result of metabolization. Finally, we analyse the pattern of evolutionary transitions between yellow and red carotenoid-based plumage colours to determine whether, as predicted, the evolution of yellow carotenoid-based colours precedes red. 4. We show that, as expected, both colours are more likely to evolve in smaller species and in species with carotenoid-rich diets. Yellow carotenoid-based plumage colours, but not red, are more prevalent in species that inhabit environments with higher primary productivity and closed vegetation. In general, females were more likely to have yellow and males more likely to have red carotenoid-based plumage colours, closely matching the effects of sexual selection. Our analyses also confirm that red carotenoid-based colours are more likely to be metabolised than yellow carotenoid-based colours. Evolutionary gains and losses of yellow and red carotenoid-based plumage colours indicate that red colours evolved more readily in species that already deposited yellow carotenoids, while the reverse was rarely the case. 5. Our study provides evidence for a general, directional evolutionary trend from yellow to red carotenoid-based colours, which are more likely to be the result of metabolization. This may render them potentially better indicators of quality, and thus favoured by sexual selection.Item Creating symptom-based criteria for diagnostic testing: a case study based on a multivariate analysis of data collected during the first wave of the COVID-19 pandemic in New Zealand(BioMed Central Ltd, 2021-12) French N; Jones G; Heuer C; Hope V; Jefferies S; Muellner P; McNeill A; Haslett S; Priest PBACKGROUND: Diagnostic testing using PCR is a fundamental component of COVID-19 pandemic control. Criteria for determining who should be tested by PCR vary between countries, and ultimately depend on resource constraints and public health objectives. Decisions are often based on sets of symptoms in individuals presenting to health services, as well as demographic variables, such as age, and travel history. The objective of this study was to determine the sensitivity and specificity of sets of symptoms used for triaging individuals for confirmatory testing, with the aim of optimising public health decision making under different scenarios. METHODS: Data from the first wave of COVID-19 in New Zealand were analysed; comprising 1153 PCR-confirmed and 4750 symptomatic PCR negative individuals. Data were analysed using Multiple Correspondence Analysis (MCA), automated search algorithms, Bayesian Latent Class Analysis, Decision Tree Analysis and Random Forest (RF) machine learning. RESULTS: Clinical criteria used to guide who should be tested by PCR were based on a set of mostly respiratory symptoms: a new or worsening cough, sore throat, shortness of breath, coryza, anosmia, with or without fever. This set has relatively high sensitivity (> 90%) but low specificity (< 10%), using PCR as a quasi-gold standard. In contrast, a group of mostly non-respiratory symptoms, including weakness, muscle pain, joint pain, headache, anosmia and ageusia, explained more variance in the MCA and were associated with higher specificity, at the cost of reduced sensitivity. Using RF models, the incorporation of 15 common symptoms, age, sex and prioritised ethnicity provided algorithms that were both sensitive and specific (> 85% for both) for predicting PCR outcomes. CONCLUSIONS: If predominantly respiratory symptoms are used for test-triaging, a large proportion of the individuals being tested may not have COVID-19. This could overwhelm testing capacity and hinder attempts to trace and eliminate infection. Specificity can be increased using alternative rules based on sets of symptoms informed by multivariate analysis and automated search algorithms, albeit at the cost of sensitivity. Both sensitivity and specificity can be improved through machine learning algorithms, incorporating symptom and demographic data, and hence may provide an alternative approach to test-triaging that can be optimised according to prevailing conditions.Item Validation of an Indirect Immunofluorescence Assay and Commercial Q Fever Enzyme-Linked Immunosorbent Assay for Use in Macropods(American Society for Microbiology, 2022-07) Tolpinrud A; Stenos J; Chaber A-L; Devlin JM; Herbert C; Pas A; Dunowska M; Stevenson MA; Firestone SM; Barrs, VRKangaroos are considered to be an important reservoir of Q fever in Australia, although there is limited knowledge on the true prevalence and distribution of coxiellosis in Australian macropod populations. Serological tests serve as useful surveillance tools, but formal test validation is needed to be able to estimate true seroprevalence rates, and few tests have been validated to screen wildlife species for Q fever. In this study, we modified and optimized a phase-specific indirect immunofluorescence assay (IFA) for the detection of IgG antibodies against Coxiella burnetii in macropod sera. The assay was validated against the commercially available ID Screen Q fever indirect multispecies enzyme-linked immunosorbent assay (ELISA) kit (IDVet, Grabels, France) to estimate the diagnostic sensitivity and specificity of each assay, using Bayesian latent class analysis. A direct comparison of the two tests was performed by testing 303 serum samples from 10 macropod populations from the east coast of Australia and New Zealand. The analysis indicated that the IFA had relatively high diagnostic sensitivity (97.6% [95% credible interval [CrI], 88.0 to 99.9]) and diagnostic specificity (98.5% [95% CrI, 94.4 to 99.9]). In comparison, the ELISA had relatively poor diagnostic sensitivity (42.1% [95% CrI, 33.7 to 50.8]) and similar diagnostic specificity (99.2% [95% CrI, 96.4 to 100]) using the cutoff values recommended by the manufacturer. The estimated true seroprevalence of C. burnetii exposure in the macropod populations included in this study ranged from 0% in New Zealand and Victoria, Australia, up to 94.2% in one population from New South Wales, Australia.