Desert locust populations, rainfall and climate change: insights from phenomenological models using gridded monthly data

Using autocorrelation analysis and autoregressive integrated moving average (ARIMA)modelling, we analysed a time series of the monthly number of 1° grid squares infested with desert locust Schistocerca gregaria swarms throughout the geographical range of the species from 1930–1987. Statistically significant first- and higher-order autocorrelations were found in the series. Although endogenous components captured much of the variance, adding rainfall data improved endogenous ARIMA models and resulted in more realistic forecasts. Using a square-root transformation for the locust data improved the fit. The models were only partially successful when accounting for the dramatic changes in abundance which may occur during locust upsurges and declines, in some cases successfully predicting these phenomena but underestimating their severity. Better fitting models were also produced when rainfall data were added to models of an equivalent series for desert locust hoppers (nymphs) that incorporated lagged data for locust swarms as independent variables, representing parent generations. The results are discussed in relation to predicting likely changes in desert locust dynamics with reference to potential effects of climate change

Evidence for a causal relationship between the solar cycle and locust abundance

Time series of abundance indices for Desert Locusts Schistocerca gregaria (Forskål 1775) and Oriental Migratory Locusts Locusta migratoriamanilensis (Meyen 1835) were analysed independently and in relation to measures of solar activity and ocean oscillation systems. Data were compiled on the numbers of territories infested with swarms of the Desert Locust from 1860–2015 and an inferred series that compensated for poor reporting in the 1860 to 1925 period. In addition, data for 1930 to 2014, when reports are considered to have been consistently reliable were converted to numbers of 1° grid squares infested with swarms and separated according to four different geographical regions. Spectral analysis to test the hypothesis that there are cycles in the locust dynamics revealed periodicities of 7.5 and 13.5 years for the inferred series that were significant according to the Ornstein-Uhlenbeck state-space (OUSS) test. Similar periodicities were evident in the 1° grid square data and in each of the regions but even though these were significantly different from white noise, they were not significant according to the OUSS criterion. There were no significant peaks in the Oriental Migratory Locust results with the OUSS test, but the data were significantly different from white noise. To test hypotheses that long term trends in the locust dynamics are driven by solar activity and/or oceanic oscillation systems (the Southern Oscillation Index (SOI), the North Atlantic Oscillation Index (NAO) and the Indian Ocean Dipole (IOD)), the original locust data series and their Kalman-filtered low frequency (LF) components were tested for causality using both spectral coherence tests and convergent cross mapping. Statistically significant evidence was found that solar activity measured by numbers of sunspot groups drive the dynamics, especially the LF components, of both species. In addition, causal links were inferred between both the SOI and NAO data and Desert Locust dynamics. Spectral coherence was also found between sunspot groups and the NAO, the IOD and LF SOI data. The data were also analysed showing that the LF SOI had causal links with the LF inferred Desert Locust series. In addition, the LF NAO was causally linked to the LF 1° grid square data, with the NAO for December-March being most influential. The results suggest that solar activity plays a role in driving locust abundance, but that the mechanisms by which this happens, and whether they are mediated by fluctuations in oceanic systems, is unclear. Furthermore, they offer hope that information on these phenomena might enable a better early warning forecasting of Desert Locust upsurges

The effect of risk-based trading and within-herd measures on Mycobacterium avium subspecies paratuberculosis spread within and between Irish dairy herds

Johne’s disease (bovine paratuberculosis) is an endemic disease caused by Mycobacterium avium subspecies paratuberculosis (Map). Map is transmitted between herds primarily through movement of infected but undetected animals. Within infected herds, possible control strategies include improving herd hygiene by reducing calf exposure to faeces from cows, reducing stress in cows resulting in a longer latently infected period where shedding is minimal, or culling highly test-positive cows soon after detection. Risk-based trading can be a strategy to reduce the risk that Map spreads between herds. Our objective was to assess whether within-herd measures combined with risk-based trading could effectively control Map spread within and between dairy cattle herds in Ireland. We used a stochastic individual-based and between-herd mechanistic epidemiological model to simulate Map transmission. Movement and herd demographic data were available from 1st January 2009–31st December 2018. In total, 13,353 herds, with 4,494,768 dairy female animals, and 72,991 bulls were included in our dataset. The movement dataset consisted of 2,304,149 animal movements. For each herd, a weekly indicator was calculated that reflected the probability that the herd was free from infection. The indicator value increased when a herd tested negative, decreased when animals were introduced into a herd, and became 0 when a herd tested positive. Based on this indicator value, four Johne’s assurance statuses were distinguished: A) ≥ 0.7 – 1.0, B) ≥ 0.3 – 0.0 – < 0.3, and D) 0.0. A is the highest and D the lowest Johne’s assurance status. With risk-based trading some of the observed movements between herds were redirected based on Johne’s assurance status with the aim of reducing the risk that a non-infected herd acquired an infected animal. Risk-based trading effectively reduced the increase in herd prevalence over a 10-year-period in Ireland: from 50% without risk-based trading to 42% with risk-based trading in the metapopulation only, and 26% when external purchases were risk-based as well. However, for risk-based trading to be effective, a high percentage of dairy herds had to participate. The most important within-herd measures were improved herd hygiene and early culling of highly infectious cows. These measures reduced both herd and within-herd prevalence compared to the reference scenario. Combining risk-based trading with within-herd measures reduced within-herd prevalence even more effectively.Department of Agriculture, Food and the Marin

Decision support beyond total savings—Eligibility and potential savings for individual participants from changes in the national surveillance strategy for bovine viral diarrhoea (BVD) in Ireland

Publication history: Accepted - 9 April 2018; Published online - 11 April 2018Surveillance and management of livestock diseases is often evaluated with reference to expected sector-wide costs. In contrast, we calculate losses or savings for individual herd owners of a change in monitoring strategy during a national cattle disease eradication programme: bovine viral diarrhoea (BVD) in Ireland. The alternative strategy differs in how the disease is identified; by its sample- rather than census-based approach; and by its greater cost per test. We examined the costs faced by each breeding herd if testing were conducted using serology on a sample of young stock, in contrast to the current method of tissue-tag testing of all newborn calves. Following best knowledge of the likely costs, the following input values were used: i) €2.50 per test for tissue-tag testing and €7.66 for serology, ii) serology conducted on a sample of 10 young stock per management group from either the 6–12 month or 9–18 month cohorts; iii) 3 scenarios for the number of management groups: one per herd (M∞), one per 100 cows (M100) and one per 50 cows (M50). We found that many herds would often not be able to supply a suitable sample of young stock for serology or would face higher testing costs than when using tissue tag testing. The largest number (25%) of herds would benefit from participating in the change if sampling were done in October. These could annually save between €2.1 million under M∞ and €0.8 million under M50 (€108 - €49 per herd). However, analysing herd-level data we found that 90% of all Irish breeding herds would save less than €1.42 per cow or €99 in total per annum under M∞, and €0.59 per cow or €36 in total under M50. In a sensitivity analysis, we allowed serology costs to vary between €2 and €10 per animal. Herds at the 10 t h percentile of most savings made from switching would save at most €155 (M∞ at €2 per serology test) but would not save anything under M50 at costs ≥ €10. We conclude that, under these assumptions, the expected reduction in testing costs for the majority of beneficiaries would barely outweigh the practical implications of the strategy switch or the risks to the eradication programme associated with sample based surveillance. This study does not assess the cost-effectiveness of alternatives post-eradication.This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors

An observational study of ear-tagged calf mortality (1 to 100 days) on Irish dairy farms and associations between biosecurity practices and calf mortality on farms participating in a Johne's disease control program

Postnatal mortality among replacement stock has a detrimental effect on the social, economic, and environmental sustainability of dairy production. Calf mortality rates vary between countries and show differences in temporal trends; most, however, are characterized by high levels of between-farm variability. Explaining this variation can be difficult because herd-level information on management practices relevant to calf health is often not available. The Irish Johne's Control Programme (IJCP) contains a substantial on-farm monitoring program called the Veterinary Risk Assessment and Management Plan (VRAMP). Although this risk assessment is largely focused on factors relevant to the transmission of paratuberculosis, many of its principles are good practice biocontainment policies that are also advocated for the protection of calf health. The objectives of this study were (1) to quantify mortality in ear-tagged Irish dairy calves between 2016 and 2020 using both survival and risk approaches, (2) to determine risk factors for 100-d cumulative mortality hazard in ear-tagged Irish dairy calves between 2016 and 2020, (3) to determine whether 100-d cumulative mortality hazard was higher in ear-tagged calves within herds registered in the IJCP versus those that were not registered in the IJCP and whether there were differences between these cohorts over time, and (4) within IJCP herds, to determine whether VRAMP score or changes in VRAMP score were associated with 100-d cumulative mortality hazard. Excluding perinatal mortality, the overall 100-d cumulative mortality hazard was 4.1%. Calf mortality was consistently underestimated using risk approaches that did not account for calf censoring. Cox proportional hazards models showed that cumulative mortality hazard was greater in male calves; particularly, calves born to Jersey breed dams and those with a beef breed sire. Mortality hazard increased with increasing herd size, was highest in calves born in herds that contract-reared heifers, and lowest in those born in mixed dairy-beef enterprises. Mortality hazard decreased over time with the mortality hazard in 2020 being 0.83 times that of 2016. Mortality hazard was higher in IJCP-registered herds than nonregistered herds (hazard ratio 1.06, 95% CI 1.01–1.12), likely reflecting differences in herds that enrolled in the national program. However, we detected a significant interaction between IJCP status (enrolled vs. not enrolled) and year (hazard ratio 0.96, 95% CI 0.92–1.00), indicating that the decrease in mortality hazard between 2016 and 2020 was greater in IJCP herds versus non-IJCP herds. Finally, increasing VRAMP scores (indicating higher risk for paratuberculosis transmission) were positively associated with increased calf mortality hazard. Postnatal calf mortality rates in Irish dairy herds declined between 2016 and 2020. Our study suggests that implementation of recommended biocontainment practices to control paratuberculosis in IJCP herds was associated with a reduction in calf mortality hazard.Department of Agriculture, Food and the Marin

Epidemiology of age-dependent prevalence of Bovine Herpes Virus Type 1 (BoHV-1) in dairy herds with and without vaccination

Research Areas: Veterinary SciencesMany studies report age as a risk factor for BoHV-1 infection or seropositivity. However, it is unclear whether this pattern refects true epidemiological causation or is a consequence of study design and other issues. Here, we seek to understand the age-related dynamics of BoHV-1 seroprevalence in seasonal calving Irish dairy herds and provide decision support for the design and implementation of efective BoHV-1 testing strategies. We analysed seroprevalence data from dairy herds taken during two Irish seroprevalence surveys conducted between 2010 and 2017. Age-dependent seroprevalence profles were constructed for herds that were seropositive and unvaccinated. Some of these profles revealed a sudden increase in seroprevalence between adjacent age-cohorts, from absent or low to close to 100% of seropositive animals. By coupling the outcome of our data analysis with simulation output of an individual-based model at the herd scale, we have shown that these sudden increases are related to extensive virus circulation within a herd for a limited time, which may then subsequently remain latent over the following years. BoHV-1 outbreaks in dairy cattle herds afect animals independent of age and lead to almost 100% seroconversion in all age groups, or at least in all animals within a single epidemiological unit. In the absence of circulating infection, there is a year-on-year increase in the age-cohort at which seroprevalence changes from low to high. The fndings of this study inform recommendations regarding testing regimes in the context of contingency planning or an eradication programme in seasonal calving dairy herds.info:eu-repo/semantics/publishedVersio

Seroprevalence of Mycoplasma bovis in bulk milk samples in Irish dairy herds and risk factors associated with herd seropositive status

Mycoplasma bovis is a serious disease of cattle worldwide; mastitis, pneumonia, and arthritis are particularly important clinical presentations in dairy herds. Mycoplasma bovis was first identified in Ireland in 1994, and the reporting of Mycoplasma-associated disease has substantially increased over the last 5 years. Despite the presumed endemic nature of M. bovis in Ireland, there is a paucity of data on the prevalence of infection, and the effect of this disease on the dairy industry. The aim of this observational study was to estimate apparent herd prevalence for M. bovis in Irish dairy herds using routinely collected bulk milk surveillance samples and to assess risk factors for herd seropositivity. In autumn 2018, 1,500 herds out of the 16,858 herds that submitted bulk tank milk (BTM) samples to the Department of Agriculture testing laboratory for routine surveillance were randomly selected for further testing. A final data set of 1,313 sampled herds with a BTM ELISA result were used for the analysis. Testing was conducted using an indirect ELISA kit (ID Screen Mycoplasma bovis). Herd-level risk factors were used as explanatory variables to determine potential risk factors associated with positive herd status (reflecting past or current exposure to M. bovis). A total of 588 of the 1,313 BTM samples were positive to M. bovis, providing an apparent herd prevalence of 0.45 (95% CI: 0.42, 0.47) in Irish dairy herds in autumn 2018. Multivariable analysis was conducted using logistic regression. The final model identified herd size, the number of neighboring farms, in-degree and county as statistically significant risk factors for herd BTM seropositivity to M. bovis. The results suggest a high apparent herd prevalence of seropositivity to M. bovis, and evidence that M. bovis infection is now endemic in the Irish dairy sector. In addition, risk factors identified are closely aligned to what we would expect of an infectious disease. Awareness raising and education about this important disease is warranted given the widespread nature of exposure and likely infection in Irish herds. Further work on the validation of diagnostic tests for herd-level diagnosis should be undertaken as a matter of priority.University College DublinScience Foundation IrelandWellcome Trust -- Submitted for publication after 1 Jan 2021: 0m embargo and CC-BY licenseHealth Research BoardUCD Wellcome Institutional Strategic Support FundSFI-HRB-Wellcome Biomedical Research Partnershi

Regional models of the influence of human disturbance and habitat quality on the distribution of breeding territories of common ringed plover Charadrius hiaticula and Eurasian oystercatcher Haematopus ostralegus

We estimated the influence of human disturbance and environmental factors on territory establishment in common ringed plovers Charadrius hiaticula and Eurasian oystercatchers Haematopus ostralegus, to inform the conservation of these species. We examined a 212 km stretch of coastline in the United Kingdom in 2003, mapping all breeding pairs of both study species, as well as the environmental characteristics of beaches and locations of visitors on the beach, the latter measured by filming from a light aircraft. Of the 1,003 200 m sections of beach surveyed, 183 contained ringed plover territories (267 breeding pairs) and 117 contained oystercatcher territories (226 breeding pairs). 38,634 human visitors to the beach were mapped from three flights. Population densities of both ringed plovers and oystercatchers were lower in locations with high visitor numbers, even when accounting for the influence of the environmental characteristics of the beach. The two bird species showed similar rates of territory establishment at very low visitor rates, but oystercatchers showed a stronger negative response when visitor rates reached higher levels. Binary logistic regression models were used to identify areas where the birds would benefit most from reductions in the number of visitors and we illustrate how this information could be used to inform management around sites otherwise favourable for territory establishment