The objective was to study how surveillance for bovine tuberculosis (bTB) could be made more resource-effective in a bTB free country. A stochastic scenario tree model was developed to: (1) evaluate the sensitivity (CSe) of four surveillance system components (SSC) (i.e., meat inspection of slaughtered domestic cattle, farmed deer and pigs, and tuberculin testing of adult export cattle) given that bTB would enter one of these components, (2) estimate the probability of freedom (PFree) from bTB over time, and (3) evaluate how future alternative programmes based on visual meat inspection would affect the confidence in freedom from bTB at the very low animal-level design prevalence 0.0002% and a low probabilities of introduction (1%). All, except the export cattle component reached a PFree above 96% within five years. The PFree was slightly reduced if surveillance was changed to visual inspection, e.g., PFree was reduced from 96.5% to 94.3% in the cattle component, and from 98.5% to 97.7% in the pig component after 24 years. In conclusion, visual meat inspection of pigs and cattle will only reduce the confidence in freedom from bTB slightly. However, with negligible probability of introduction (0.1%) the PFree could be maintained well above 99% in the cattle, pigs and deer components, which highlights the importance of rigid testing and quarantine procedures in trade of livestock. Full article

Current fertiliser recommendations for nitrogen are limited in their accuracy and may be improved by the use of simple on-farm soil rapid tests. This paper investigates the potential for using nitrate (NO₃⁻) ion selective electrodes (ISEs) and dual wavelength UV spectroscopy as part of a rapid soil NO₃⁻ diagnostic test. Three soil types, representing the major soil types for agriculture in the western UK, were tested. For the three soils, the ISE rapid test procedure gave a near 1:1 response (r² = 0.978, 0.968, 0.989) compared to the internationally-approved standard laboratory method. However, the accuracy of the ISE rapid test was reduced at low soil NO₃⁻ concentrations (<10 mg NO₃⁻ L⁻¹). We also show that NO₃⁻ analysis of H₂O soil extracts by dual wavelength UV spectroscopy was also highly correlated (r² = 0.978, 0.983, 0.991) to the standard laboratory method. We conclude that both ISE and dual wavelength UV spectroscopy have clear potential to be used for the rapid on-farm determination of soil NO₃⁻ concentration. Barriers to use of these field-based assessment tools include, farmer perception of cost-benefit, general attitude to new technologies and the ability to generate useful fertiliser use strategies from soil NO₃⁻ measurements. Full article

The objective of the study was to describe the Salmonella prevalence in turkey flocks before and after the implementation of the Salmonella control program in Germany and to identify factors that are potentially associated with the presence of Salmonella in the flocks. To achieve this, all breeding flocks and a representative sample of the fattening flocks were tested for Salmonella. None of the 98 turkey breeding flocks but 31 (10.3%) of 300 turkey fattening flocks were positive for Salmonella spp. in the baseline study during 2006/2007. In 11 (3.7%) fattening flocks S. Enteritidis (1 flock; 0.3%) or S. Typhimurium (8 flocks; 2.7%) or monophasic S. Typhimurium (2 flocks; 0.3%), which are of special public health relevance in Germany, were detected. Logistic regression analysis confirmed that production type and season were significant risk factors for the presence of Salmonella spp. in fattening turkey flocks in Germany. Data from mandatory official testing within the Salmonella control program in 2010 and 2011 revealed that Salmonella prevalence in turkey fattening flocks has decreased significantly to 3.3% and 2.6%. In line with this result, prevalence of S. Enteritidis or S. Typhimurium had decreased to 2.6% and 1.5%. Results indicate that the prevalence of Salmonella in turkey fattening flocks has decreased significantly. Full article

Soil erodibility is among the trickiest erosion factors to estimate. This is especially true for heterogeneous Mediterranean environments, where reliable and dense soil data are rarely available, and interpolation methods give very low accuracies. Towards estimating soil erodibility, research so far has resulted in several alternatives mainly based on empirical formulas, on physics-based equations or on inference with expertise. The aim of this work was to compare erodibility patterns derived by using the empirical United States Department of Agriculture (USDA) formula and by inference from a geological map in a Mediterranean agricultural site. The Kolymvari area, located in the western part of Crete, an area covered by olive groves and citrus orchards, was selected as the study site for this work. Comparison of the spatial patterns of soil erodibility derived from the two alternatives showed significant differences (i.e., a mean normalized difference value of 0.52), while a test of the “inference” alternative indicated very low accuracies (0.1475 RMS error). A comparison, however, of the spatial patterns of erosion values derived from both alternatives indicated that dissimilarities of the two soil erodibility maps faded out. Moreover, the highly risky areas provided by both alternatives were found to be identical for 88% of the whole study site. Full article

Accurate and fast detection of harmful Salmonella is a major concern of food safety. Common Salmonella serotypes responsible for human associated foodborne outbreaks are S. Enteritidis, S. Hadar, S. Heidelberg, and S. Typhimurium are also commonly isolated from poultry. Serology is commonly used to monitor disease in poultry, therefore application of Salmonella serotype-specific test will have added value in Salmonella surveillance or monitoring vaccine efficacy. Recombinant flagellins were purified to be used as antigens in an ELISA. In this study, an ELISA was developed for the serological detection of S. Enteritidis. Once optimized, 500 ng of purified recombinant S. Enteritidis flagellin and a 1:64 dilution were determined to be optimal for testing sera. A negative baseline cutoff was calculated to be an optical density (OD) of 0.35. All sera from birds with history of S. Enteritidis exposure tested positive and all sera from chickens with no exposure tested negative to this Salmonella serotype. Current ELISA for serological detection of Salmonella suffers from cross reactivity inherent in lipopolysaccharide (LPS) or whole cell antigen based serological tests. This new ELISA eliminates common cross reactivity by focusing specifically on the flagellins of the Salmonella serotypes common in poultry and associated with foodborne outbreaks. Full article

Since humans worldwide obtain more than 99.7% of their food (calories) from the land and less than 0.3% from the oceans and aquatic ecosystems, preserving cropland and maintaining soil fertility should be of the highest importance to human welfare. Soil erosion is one of the most serious threats facing world food production. Each year about 10 million ha of cropland are lost due to soil erosion, thus reducing the cropland available for world food production. The loss of cropland is a serious problem because the World Health Organization and the Food and Agricultural Organization report that two-thirds of the world population is malnourished. Overall, soil is being lost from agricultural areas 10 to 40 times faster than the rate of soil formation imperiling humanity’s food security. Full article

This article is one of the first to carry out a non-parametric efficiency analysis of crop production in Uzbekistan. The study applies the bootstrap Data Envelopment Analysis (DEA) to compute bias corrected technical efficiency (TE) scores using a sample of farms located in two regions of Uzbekistan. The study also investigates the determinants of TE in potato and melon production. Results indicate that there is room for efficient use of resources. Farmers are found to be more scale-efficient but not productively efficient. Findings from the second stage DEA model display that soil fertility index, farm size, water availability, crop diversification index, dependency ratio, potential to work in large land area, and longer distance to market contribute positively to production efficiency. Full article

The control of human Campylobacteriosis is a priority in public health agendas all over the world. Poultry is considered a significant risk factor for human infections with Campylobacter and risk assessment models indicate that the successful implementation of Campylobacter control strategies in poultry will translate on a reduction of human Campylobacteriosis cases. Efficient control strategies implemented during primary production will reduce the risk of Campylobacter introduction in chicken houses and/or decrease Campylobacter concentration in infected chickens and their products. Consequently, poultry producers need to make difficult decisions under conditions of uncertainty regarding the implementation of Campylobacter control strategies. This manuscript presents the development of probabilistic graphical models to support decision making in order to control Campylobacter in poultry. The decision support systems are constructed as probabilistic graphical models (PGMs) which integrate knowledge and use Bayesian methods to deal with uncertainty. This paper presents a specific model designed to integrate epidemiological knowledge from the United Kingdom (UK model) in order to assist poultry managers in specific decisions related to vaccination of commercial broilers for the control of Campylobacter. Epidemiological considerations and other crucial aspects including challenges associated with the quantitative part of the models are discussed in this manuscript. The outcome of the PGMs will depend on the qualitative and quantitative data included in the models. Results from the UK model and sensitivity analyses indicated that the financial variables (cost/reward functions) and the effectiveness of the control strategies considered in the UK model were driving the results. In fact, there were no or only small financial gains when using a hypothetical vaccine B (able to decrease Campylobacter numbers from two to six logs in 20% of the chickens with a cost of 0.025 £/chicken) and reward system 1 (based on similar gross profits in relation to Campylobacter levels) under the specific assumptions considered in the UK model. In contrast, significant reductions in expected Campylobacter numbers and substantial associated expected financial gains were obtained from this model when considering the reward system 2 (based on quite different gross profits in relation to Campylobacter levels) and the use of a hypothetical cost-effective vaccine C (able to reduce the level of Campylobacter from two to six logs in 90% of the chickens with a cost of 0.03 £/chicken). The flexibility of probabilistic graphical models allows for the inclusion of more than one Campylobacter vaccination strategy and more than one reward system and consequently, diverse potential solutions for the control of Campylobacter may be considered. Cost-effective Campylobacter control strategies that can significantly reduce the probability of Campylobacter introduction into a flock and/or the numbers of Campylobacter in already infected chickens, and translate to an attractive cost-reward balance will be preferred by poultry producers. Full article

A hilly region in Sri Lanka was considered to be degraded by erosion driven by intensive tobacco production, but what are reliable indicators of erosion? In addition to determining soil chemical and physical traits, maize was cropped with Nitrogen, Phosphorus and Potassium (NPK, PK) recommended mineral fertilization and without fertilizer (ZERO) in two major seasons(October–January in 2007/2008 and 2008/2009—Seasons 1 and 2 respectively) on 92 farms at inclinations ranging from 0% to 65%. In a subset of steep farms (n = 21) an A horizon of 6 cm rather than of 26 cm was strong proof of erosion above 30% inclination. Below the A level, the thickness of the horizon was unaffected by inclination. Soil organic matter contents (SOM) were generally low, more so at higher inclinations, probably due to greater erosion than at lower inclination. Maize yields decreased gradually with increasing inclination; at ZERO, effects of climate and soil moisture on yield were easier determined and were probably due to long-term erosion. However, despite an initial set of 119 farms, an exact metric classification of erosion was impossible. NPK strongly boosted yield. This was a positive sign that the deficits in chemical soil fertility were overriding physical soil weaknesses. The study illustrated that chemical soil fertility in these soils is easily amenable to modifications by mineral and organic manures. Full article

Until recently, the standard method for RNA interference (RNAi)-based reverse genetics in plant parasitic nematodes (PPNs) was based on the use of long double-stranded RNA (dsRNA). This increased the chance of off-target gene silencing through interactions between different short interfering RNAs (siRNAs) and non-cognate mRNA targets. In this work, we applied gene-specific knockdown of Mg-pat-10 and Mg-unc-87 of the root knot nematode Meloidogyne graminicola, using discrete 21 bp siRNAs. The homologue of Mg-pat-10 in C. elegans encodes body wall troponin C, which is essential for muscle contraction, whereas the homologue of Mg-unc-87 encodes two proteins involved in maintenance of the structure of myofilaments in the body wall muscle of C. elegans. The knockdown at the transcript level, as seen by semi-quantitative RT-PCR analysis, indicates that the Mg-pat-10 gene was silenced after soaking the nematodes in a specific siRNA for 48 h. At 72 h post-soaking, the Mg-pat-10 mRNA level was similar to the control, indicating the recovery of expression between 48 h and 72 h post-soaking. For Mg-unc-87 the nematodes started to recover from siRNA silencing 24 h after thorough washing. A migration assay showed that for the nematodes that were soaked in the control (siRNA of β-1,4-endoglucanase), 77% of the nematodes completed migration through the column in a 12 h period. By comparison with the control, nematodes incubated in the siRNA of pat-10 or unc-87 were significantly inhibited in their motility. After 12 h, only 6.3% of the juveniles incubated in the Mg-pat-10 siRNA and 9.3% of those incubated in Mg-unc-87 siRNA had migrated through the column, representing 91.8% and 87.9% inhibition respectively compared to the control. In the present work, we demonstrated that M. graminicola is readily susceptible to siRNAs of two genes involved in nematode motility. This is an important contribution to the progressive use of siRNA for functional analysis. Moreover, the application of RNAi in PPNs opens the way for environmentally friendly control of M. graminicola. Full article

Most source attribution studies for Campylobacter use subtyping data based on single isolates from foods and environmental sources in an attempt to draw epidemiological inferences. It has been suggested that subtyping only one Campylobacter isolate per chicken carcass incurs a risk of failing to recognise the presence of clinically relevant, but numerically infrequent, subtypes. To investigate this, between 21 and 25 Campylobacter jejuni isolates from each of ten retail chicken carcasses were subtyped by pulsed-field gel electrophoresis (PFGE) using the two restriction enzymes SmaI and KpnI. Among the 227 isolates, thirteen subtypes were identified, the most frequently occurring subtype being isolated from three carcasses. Six carcasses carried a single subtype, three carcasses carried two subtypes each and one carcass carried three subtypes. Some subtypes carried by an individual carcass were shown to be potentially clonally related. Comparison of C. jejuni subtypes from chickens with isolate subtypes from human clinical cases (n = 1248) revealed seven of the thirteen chicken subtypes were indistinguishable from human cases. None of the numerically minor chicken subtypes were identified in the human data. Therefore, typing only one Campylobacter isolate from individual chicken carcasses may be adequate to inform Campylobacter source attribution. Full article

According to the IPCC, global temperatures are expected to increase between 1.1 and 6.4 °C during the 21st century and precipitation patterns will be altered. Soils are intricately linked to the atmospheric/climate system through the carbon, nitrogen, and hydrologic cycles. Because of this, altered climate will have an effect on soil processes and properties. Recent studies indicate at least some soils may become net sources of atmospheric C, lowering soil organic matter levels. Soil erosion by wind and water is also likely to increase. However, there are many things we need to know more about. How climate change will affect the N cycle and, in turn, how that will affect C storage in soils is a major research need, as is a better understanding of how erosion processes will be influenced by changes in climate. The response of plants to elevated atmospheric CO₂ given limitations in nutrients like N and P, and how that will influence soil organic matter levels, is another critical research need. How soil organic matter levels react to changes in the C and N cycles will influence the ability of soils to support crop growth, which has significant ramifications for food security. Therefore, further study of soil-climate interactions in a changing world is critical to addressing future food security concerns. Full article

Concern about soil erosion on arable land in Britain dates back at least 40 years. Monitoring schemes and case studies have subsequently identified the areas at risk, the rates and frequencies and the major factors responsible for erosion. Initial concern focused on impacts on the farm and therefore on food production. Latterly the emphasis has shifted to off-farm impacts particularly reservoir sedimentation, muddy flooding of properties and the ecological damage to watercourses due to nutrient enrichment, pesticides and damage to fish spawning grounds from fine-sediment inputs. The shift has therefore been to concerns about a healthy and sustainable environment which includes soils. Government agencies, the water companies and the farming industry have lagged behind scientific studies in recognising and addressing erosion problems. Attempts at mitigation are now largely driven by the need to comply with the EU Water Framework Directive whereby watercourses must reach “good status” by 2015. Future changes in land use and climate will offer further challenges in terms of effective monitoring and compliance. Full article

Soil conservation is threatened by a number of factors, namely the effects of intensive agricultural practices, the increasing pressure for food production linked to the increasing human population, the consumption patterns in developed and emerging economies, and the conversion of agriculture from the production of commodities (which is itself a goal in need of discussion) to the production of biofuels. The extent of human pressure and the effects of conflicting land use systems need to be addressed. Alternative and conservative agricultural practices need to be explored and widely adopted in order to preserve the soil fertility, assessing their pros and cons. In this paper, the main potential alternative practices are reviewed, focusing in particular on organic farming. It is also argued that in order to better plan to preserve soil health a strategy considering the whole food system is required. Full article

Infections with parasitic helminths (nematodes and trematodes) represent a significant economic and welfare burden to the global ruminant livestock industry. The increasing prevalence of anthelmintic resistance means that current control programmes are costly and unsustainable in the long term. Recent changes in the epidemiology, seasonality and geographic distribution of helminth infections have been attributed to climate change. However, other changes in environment (e.g., land use) and in livestock farming, such as intensification and altered management practices, will also have an impact on helminth infections. Sustainable control of helminth infections in a changing world requires detailed knowledge of these interactions. In particular, there is a need to devise new, sustainable strategies for the effective control of ruminant helminthoses in the face of global change. In this paper, we consider the impact of helminth infections in grazing ruminants, taking a European perspective, and identify scientific and applied priorities to mitigate these impacts. These include the development and deployment of efficient, high-throughput diagnostic tests to support targeted intervention, modelling of geographic and seasonal trends in infection, more thorough economic data and analysis of the impact of helminth infections and greater translation and involvement of end-users in devising and disseminating best practices. Complex changes in helminth epidemiology will require innovative solutions. By developing and using new technologies and models, the use of anthelmintics can be optimised to limit the development and spread of drug resistance and to reduce the overall economic impact of helminth infections. This will be essential to the continued productivity and profitability of livestock farming in Europe and its contribution to regional and global food security. Full article

Proliferative enteropathy, commonly known as “ileitis” continues to be a significant production-limiting disease in pig herds throughout the world. The disease can be controlled with a combination of vaccination and antibiotic medication. However, pressure from consumers to reduce antibiotic use in livestock industries highlights the need to better understand the epidemiology of ileitis, the mechanisms of immunity, and to identify management factors that can reduce the load of Lawsonia intracellularis in both pigs and the environment. New diagnostic assays and economic modelling of ileitis will help producers target optimal treatment times and minimize the production losses associated with ileitis. This review aims to outline the current advances in disease diagnosis, epidemiology, control strategies and the economic impact of both clinical and sub-clinical disease. Full article

The authors are sorry to report that some data in the text (Section 2, Section 2.1.1. and Section 2.1.2) and Table 1 were incorrect in reference [1], doi: 10.3390/agriculture2030259, website: https://www.mdpi.com/2077-0472/2/3/259. Our mistake was basically in the calculations of changes observed in the reported values in those references; unfortunately we did not detect the errors at the time of publication. However, since we saw them afterwards, we believed it was pertinent to make the corrections. The authors would, therefore, like to make the following corrections to the paper: [...] Full article