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Biogeochemical catchment models are often developed for a single catchment and, as a result, often generalize poorly beyond this. Evaluating their transferability is an important step in improving their predictive power and application range. We assess the transferability of a recently developed Bayesian Belief Network (BBN) that simulated monthly stream phosphorus (P) concentrations in a poorly-drained grassland catchment through application to three further catchments with different hydrological regimes and agricultural land uses. In all catchments, flow and turbidity were measured sub-hourly from 2009 to 2016 and supplemented with 400-500 soil P test measurements. In addition to a previously parameterized BBN, five further model structures were implemented to incorporate in a stepwise way: in-stream P removal using expert elicitation, additional groundwater P stores and delivery, and the presence or absence of septic tank treatment, and, in one case, Sewage Treatment Works. Model performance was tested through comparison of predicted and observed total reactive P (TRP) concentrations and percentage bias (PBIAS). The original BBN accurately simulated the absolute values of observed flow and TRP concentrations in the poorly and moderately drained catchments (albeit with poor apparent percentage bias scores; 76 % ≤ PBIAS≤94 %) irrespective of the dominant land use, but performed less well in the groundwater-dominated catchments. However, including groundwater total dissolved P (TDP) and Sewage Treatment Works (STWs) inputs, and in-stream P uptake improved model performance (-5 % ≤ PBIAS≤18 %). A sensitivity analysis identified redundant variables further helping to streamline the model applications. An enhanced BBN model capable for wider application and generalisation resulted., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Pastoralism is gaining in recognition for its provision of a broad range of ecosystem services. However, in Western countries, especially in Europe, it has been in decline for decades and its future is uncertain. Professional satisfaction, social appreciation and community integration are key factors for the sustainability of any activity. Using information from 167 traditional Spanish herders, we assessed their perceived degree of satisfaction with their profession and the reasons behind their perceptions. Herders were extremely satisfied with their profession, but they perceived medium and low levels of appreciation by the rural and urban sectors of society, respectively. Herders had negative feelings about the sustainability of their profession, as they felt more appreciated by society in the past than they do today, half of them did not want their offspring to make a living as herders. Improving communication between herders and society could help to enhance herders' appreciation of their profession., (© 2024. The Author(s).)

Background: Louping ill virus (LIV) is a tick-borne flavivirus that can cause fatal meningoencephalomyelitis in dogs. Four dogs with confirmed LIV infection and a case series of dogs with suspected flavivirus infection have been reported in the UK. However, underreporting of LIV infection due to lack of testing is suspected., Methods: Surplus serum/plasma from 220 dogs was used to determine the seroprevalence of LIV by haemagglutination inhibition (HAI) test. Signalment and environmental factors were investigated for potential correlations with a positive titre (serum dilution of 1:20 or more)., Results: Two hundred and two dogs were suitable for inclusion in the study, nine of which (4.5%) were seropositive. Among the dogs investigated for neurological disease (40/202; 19.8%), six (15%) were seropositive. Ectoparasiticide use approached significance (p = 0.055) for being protective against LIV seropositivity., Limitations: The main limitations were the specificity of the HAI test, the relatively small number of samples, the low number of seropositive dogs, the poor geographical distribution of the samples and the inherent limitations of questionnaire-based research., Conclusion: The seroprevalence of LIV in the UK dog population appears to be low. However, LIV should be considered in dogs presenting with unexplained acute or subacute progressive neurological clinical signs, especially because of the recent reports of several dogs with clinical flavivirus infections., (© 2024 British Veterinary Association.)

Chlamydia abortus causes the disease ovine enzootic abortion, which is one of the most infectious causes of foetal death in small ruminants worldwide. While the disease can be controlled using live and inactivated commercial vaccines, there is scope for improvements in safety for both sheep and human handlers of the vaccines. We have previously reported the development of a new prototype vaccine based on a detergent-extracted outer membrane protein preparation of C. abortus that was determined to be more efficacious and safer than the commercial vaccines when administered in two inoculations three weeks apart. In this new study, we have developed this vaccine further by comparing its efficacy when delivered in one or two (1 × 20 µg and 2 × 10 µg) doses, as well as also comparing the effect of reducing the antigen content of the vaccine by 50% (2 × 5 µg and 1 × 10 µg). All vaccine formulations performed well in comparison to the unvaccinated challenge control group, with no significant differences observed between vaccine groups, demonstrating that the vaccine can be administered as a single inoculation and at a lower dose without compromising efficacy. Future studies should focus on further defining the optimal antigen dose to increase the commercial viability of the vaccine.

Winter dormancy is a key process in the phenology of temperate perennials. Climate change is severely impacting its course leading to economic losses in agriculture. A better understanding of the underlying mechanisms, as well as the genetic basis of the different responses, is necessary for the development of climate-resilient cultivars. This study aims to provide an insight into winter dormancy in red raspberry (Rubus idaeus L). We report the transcriptomic profiles during dormancy in two raspberry cultivars with contrasting responses. The cultivar 'Glen Ample' showed a typical perennial phenology, whereas 'Glen Dee' registered consistent dormancy dysregulation, exhibiting active growth and flowering out of season. RNA-seq combined with weighted gene co-expression network analysis identified gene clusters in both genotypes that exhibited time-dependent expression profiles. Functional analysis of 'Glen Ample' gene clusters highlighted the significance of the cell and structural development prior to dormancy entry as well the role of genetic and epigenetic processes such as RNAi and DNA methylation in regulating gene expression. Dormancy release in 'Glen Ample' was associated with up-regulation of transcripts associated with the resumption of metabolism, nucleic acid biogenesis, and processing signal response pathways. Many of the processes occurring in 'Glen Ample' were dysregulated in 'Glen Dee' and 28 transcripts exhibiting time-dependent expression in 'Glen Ample' that also had an Arabidopsis homologue were not found in 'Glen Dee'. These included a gene with homology to Arabidopsis VRN1 (RiVRN1.1) that exhibited a sharp decline in expression following dormancy induction in 'Glen Ample'. Characterization of the gene region in the 'Glen Dee' genome revealed two large insertions upstream of the ATG start codon. We propose that expression below detection level of a specific VRN1 homologue in 'Glen Dee' causes dormancy misregulation as a result of inappropriate expression of a subset of genes that are directly or indirectly regulated by RiVRN1.1., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

The incidence of vector-borne disease is on the rise globally, with burdens increasing in endemic countries and outbreaks occurring in new locations. Effective mitigation and intervention strategies require models that accurately predict both spatial and temporal changes in disease dynamics, but this remains challenging due to the complex and interactive relationships between environmental variation and the vector traits that govern the transmission of vector-borne diseases. Predictions of disease risk in the literature typically assume that vector traits vary instantaneously and independently of population density, and therefore do not capture the delayed response of these same traits to past biotic and abiotic environments. We argue here that to produce accurate predictions of disease risk it is necessary to account for environmentally driven and delayed instances of phenotypic plasticity. To show this, we develop a stage and phenotypically structured model for the invasive mosquito vector, Aedes albopictus, and dengue, the second most prevalent human vector-borne disease worldwide. We find that environmental variation drives a dynamic phenotypic structure in the mosquito population, which accurately predicts global patterns of mosquito trait-abundance dynamics. In turn, this interacts with disease transmission to capture historic dengue outbreaks. By comparing the model to a suite of simpler models, we reveal that it is the delayed phenotypic structure that is critical for accurate prediction. Consequently, the incorporation of vector trait relationships into transmission models is critical to improvement of early warning systems that inform mitigation and control strategies., (© 2024. The Author(s).)

Constructed wetlands (CWs) can play a crucial role in treating wastewater, and in the context of this study, the distillation byproduct of the whisky industry known as 'spent lees'. Here, we assess several different CW substrates (pea gravel, LECA and Alfagrog), with and without the addition of 20% biochar, in mesocosms set up to treat spent lees. Among the substrates tested, LECA + biochar and gravel + biochar showed promising results, with greater dissolved copper (dissCu) reduction, chemical oxygen demand (COD) removal, organic carbon (OC) reduction, and pH modulation. These findings indicate a potentially beneficial role for biochar in enhancing treatment efficacy, particularly in facilitating dissCu remediation and the removal of organic pollutants. In terms of microbial diversity, mesocosms including biochar generally had reduced bacterial alpha diversity, suggesting that 'fresh' (uncolonized) biochar may negatively affect microbial diversity in wetland ecosystems in the short term. After continuously supplying spent lees to mesocosms for 2-months, microbial diversity in each mesocosm dropped substantially, and moderate levels of bacterial community differentiation and high levels of fungal community differentiation were detected among mesocosms. The bacterial and fungal communities were also found to differ between the substrate and outlet water samples. Among the bacterial classes present in the mesocosms that may play a crucial role in water treatment performance, Gammaproteobacteria, Bacteroidia and Alphaproteobacteria should be further investigated. In terms of fungal classes, the role of Sordariomycetes should be explored in greater depth., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the "who-infected-whom" identification problem. We study samples from hosts (130 cattle, 111 badgers) with confirmed infection of M. bovis (causing bovine Tuberculosis), which has an estimated clock rate as slow as ∼0.1-1 variations per year. For each potential pathway between hosts, we calculate the relative likelihood that such a transmission event occurred. This is informed by an epidemiological model of transmission, and host life history data. By including WGS data, we shrink the number of plausible pathways significantly, relative to those deemed likely on the basis of life history data alone. Despite our uncertainty relating to the evolution of M. bovis, the WGS data are therefore a valuable adjunct to epidemiological investigations, especially for wildlife species whose life history data are sparse., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

The parents of broiler (meat) chickens (ie, broiler breeders) are food-restricted until sexual maturity, ensuring good health and reproduction, but resulting in hunger. We investigated whether diets with added insoluble fiber promote satiety and reduce behavioral, motivational, and physiological signs of hunger. Ninety-six broiler breeders were fed 1 of 4 feed treatments (n = 24 per diet) from 6 to 12 wk of age: 1) a commercial diet fed to the recommended ration (R) or 2) ad libitum (AL), the same diet as R but mixed with oat hulls at 3) 20% (OH20%) or 4) 40% (OH40%). The R, OH20% and OH40% diets were approximately iso-energetic and resulted in mean 12 wk of age weights within 2.5% of each other (1.21 kg), while AL birds weighed 221% as much (2.67kg). At 12 wk of age, agouti-related protein (AGRP) expression, was, on average, more than 12 times lower in AL birds (P < 0.001) but did not differ between the fiber diet treatments and R. Pro-opiomelanocortin (POMC) expression, was, on average, over 1.5 times higher in AL birds, but was not statistically significantly affected by feed treatments (P = 0.33). In their home pens, AL birds stood/sat more, foraged less and fed more in total (P < 0.001) and OH40% birds spent longer feeding than R (P = 0.001). Motivation to forage tested by willingness to walk through water to access an area of wood shavings (without food) was not significantly affected by diet (P = 0.33). However, restricted birds were willing to cross in only 7.3% to 12.5% of tests. Mostly birds stayed on the start platform, where AL birds sat more than other treatments and OH40% birds reduced walking relative to R birds (P = 0.016). Across the behavioral and physiological measurements there was a dichotomy of effects in response to approximately iso-energetic diets differing in fiber. There were some potentially beneficial behavioral effects related to reduced foraging and walking. However, there was no evidence that these diets significantly improved physiological measures of satiety of broiler breeders., Competing Interests: DISCLOSURES The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Laura Dixon reports financial support was provided by Biotechnology and Biological Sciences Research Council. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations. We developed an automated, standardized pipeline for the analysis of NGS reads that directly provides users with assemblies and annotations formatted for their submission to NCBI. This pipeline is freely available on GitHub and has been tested through the GARA partners by examining two previously sequenced ASFV genomes; this study also aimed to assess the accuracy and limitations of two strategies present within the pipeline: reference-based (Illumina reads) and de novo assembly (Illumina and Nanopore reads) strategies.

Early nutrition has significant effects on physiological outcomes during adult life. We have analysed the effect of maternal α-casein (CSN1S1) deficiency on the physiological fate of dams and their offspring. α-casein deficiency reduces maternal milk protein concentration by more than 50% and attenuates the growth of pups to 27% (p < 0.001) of controls at the point of weaning. This is associated with a permanent reduction in adult body weight (- 31% at 25 weeks). Offspring nursed by α-casein deficient dams showed a significantly increased lifespan (+ 20%, χ 2 : 10.6; p = 0.001). Liver transcriptome analysis of offspring nursed by α-casein deficient dams at weaning revealed gene expression patterns similar to those found in dwarf mice (reduced expression of somatotropic axis signalling genes, increased expression of xenobiotic metabolism genes). In adult mice, the expression of somatotropic axis genes returned to control levels. This demonstrates that, in contrast to dwarf mice, attenuation of the GH-IGF signalling axis in offspring nursed by α-casein deficient dams is transient, while the changes in body size and lifespan are permanent. Offspring nursed by α-casein deficient dams showed permanent changes in body composition. Absolute and relative adipose tissue weights (p < 0.05), the percentage of body fat (p < 0.001) as well as adipocyte size in epididymal white adipose tissue are all reduced. Serum leptin levels were 25% of those found in control mice (p < 0.001). Liver lipid content and lipid composition were significantly altered in response to postnatal nutrition. This demonstrates the nutrition in early life programmes adult lipid metabolism, body composition and lifespan., (© 2024. The Author(s).)

Behaviour is often the fundamental driver of disease transmission, where behaviours of individuals can be seen to scale up to epidemiological patterns seen at the population level. Here we focus on animal behaviour, and its role in parasite transmission to track its knock-on consequences for parasitism, production and pollution. Livestock face a nutrition versus parasitism trade-off in grazing environments where faeces creates both a nutritional benefit, fertilizing the surrounding sward, but also a parasite risk from infective nematode larvae contaminating the sward. The grazing decisions of ruminants depend on the perceived costs and benefits of the trade-off, which depend on the variations in both environmental (e.g., amounts of faeces) and animal factors (e.g., physiological state). Such grazing decisions determine the intake of both nutrients and parasites, affecting livestock growth rates and production efficiency. This impacts on the greenhouse gas costs of ruminant livestock production via two main mechanisms: (1) slower growth results in longer durations on-farm and (2) parasitised animals produce more methane per unit food intake. However, the sensitivity of behaviour to host parasite state offers opportunities for early detection of parasitism and control. Remote monitoring technology such as accelerometers can detect parasite-induced sickness behaviours soon after exposure, before impacts on growth, and thus may be used for targeting individuals for early treatment. We conclude that livestock host x parasite interactions are at the centre of the global challenges of food security and climate change, and that understanding livestock behaviour can contribute to solving both.

Temperate heathlands and blanket bogs are globally rare and face growing wildfire threats. Ecosystem impacts differ between low and high severity fires, where severity reflects immediate fuel consumption. This study assessed factors influencing fire severity in Scottish heathlands and blanket bogs, including the efficacy of the Canadian Fire Weather Index System (CFWIS). Using remote sensing, we measured the differenced Normalised Burn Ratio at 92 wildfire sites from 2015 to 2021. We used Generalised Additive Mixed Models to investigate the impact of topography, habitat wetness, CFWIS components and 30-day weather on severity. Dry heath exhibited higher severity than wet heath and blanket bog, and slope, elevation and south facing aspect were positively correlated to severity. Weather effects were less clear due to data scale differences, yet still indicated weather's significant role in severity. Rainfall had an increasingly negative effect from approximately 15 days before the fire, whilst temperature had an increasingly positive effect. Vapour Pressure Deficit (VPD) was the weather variable with highest explanatory value, and predicted severity better than any CFWIS component. The best-explained fire severity model (R 2  = 0.25) incorporated topography, habitat wetness wind and VPD on the day of the fire. The Drought Code (DC), predicting organic matter flammability at ≥10 cm soil depth, was the CFWIS component with the highest predictive effect across habitats. Our findings suggest that wildfires in wet heath and blanket bogs are typically characterised by low severity, but that warmer, drier weather may increase the risk of severe, smouldering fires which threaten peatland carbon stores., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Previous vaccination trials have demonstrated that thiol proteins affinity purified from Ostertagia ostertagi excretory-secretory products (O. ostertagi ES-thiol) are protective against homologous challenge. Here we have shown that protection induced by this vaccine was consistent across four independent vaccine-challenge experiments. Protection is associated with reduced cumulative faecal egg counts across the duration of the trials, relative to control animals. To better understand the diversity of antigens in O. ostertagi ES-thiol we used high-resolution shotgun proteomics to identify 490 unique proteins in the vaccine preparation. The most numerous ES-thiol proteins, with 91 proteins identified, belong to the sperm-coating protein/Tpx/antigen 5/pathogenesis-related protein 1 (SCP/TAPS) family. This family includes previously identified O. ostertagi vaccine antigens O. ostertagi ASP-1 and ASP-2. The ES-thiol fraction also has numerous proteinases, representing three distinct classes, including: metallo-; aspartyl- and cysteine proteinases. In terms of number of family members, the M12 astacin-like metalloproteinases, with 33 proteins, are the most abundant proteinase family in O. ostertagi ES-thiol. The O. ostertagi ES-thiol proteome provides a comprehensive database of proteins present in this vaccine preparation and will guide future vaccine antigen discovery projects., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier B.V. All rights reserved.)

Mycotoxins are potent fungal toxins that frequently contaminate agricultural crops and foods. Mycotoxin exposure is frequently reported in humans, and children are known to be particularly at risk of exceeding safe levels of exposure. Urinary biomonitoring is used to assess overall dietary exposure to multiple mycotoxins. This study aims to quantify multi-mycotoxin exposure in UK children and to identify major food groups contributing to exposure. Four repeat urine samples were collected from 29 children (13 boys and 16 girls, aged 2.4-6.8 years), and food diaries were recorded to assess their exposure to eleven mycotoxins. Urine samples ( n = 114) were hydrolysed with β-glucuronidase, enriched through immunoaffinity columns and analysed by LC-MS/MS for deoxynivalenol (DON), nivalenol (NIV), T-2/HT-2 toxins, zearalenone (ZEN), ochratoxin A (OTA) and aflatoxins. Food diaries were analysed using WinDiet software, and the daily intake of high-risk foods for mycotoxin contamination summarised. The most prevalent mycotoxins found in urine samples were DON (95.6% of all samples), OTA (88.6%), HT-2 toxin (53.5%), ZEN (48.2%) and NIV (26.3%). Intake of total cereal-based foods was strongly positively associated with urinary levels of DON and T-2/HT-2 and oat intake with urinary T-2/HT-2. Average daily mycotoxin excretion ranged from 12.10 µg/d (DON) to 0.03 µg/d (OTA), and co-exposure to three or more mycotoxins was found in 66% of samples. Comparing mycotoxin intake estimates to tolerable daily intakes (TDI) demonstrates frequent TDI exceedances (DON 34.2% of all samples, T-2/HT-2 14.9%, NIV 4.4% and ZEN 5.2%). OTA was frequently detected at low levels. When mean daily OTA intake was compared to the reference value for non-neoplastic lesions, the resulting Margin of Exposure (MoE) of 65 was narrow, indicating a health concern. In conclusion, this study demonstrates frequent exposure of UK children to multiple mycotoxins at levels high enough to pose a health concern if exposure is continuous.

Background: Pressure to abolish farrowing crates is increasing, and producers are faced with decisions about which alternative system to adopt. For sow welfare, well designed free farrowing systems without close confinement are considered optimal but producers have concerns about increased piglet mortality, particularly crushing by the sow. Reporting accurate performance figures from commercial farms newly operating such systems could inform the transition process. This study investigated performance on three commercial farms operating four different zero-confinement systems, three of which were newly installed. A total of 3212 litters from 2920 sows were followed from farrowing to weaning over a three-year period with key performance indicators (KPIs) recorded. Mixed Models (LMMs, GLMMs) determined the influence of different factors (e.g. farrowing system, sow parity, management aspects) and litter characteristics on performance, including levels and causes of piglet mortality., Results: Piglet mortality was significantly influenced by farm/system. Live-born mortality ranged from 10.3 to 20.6% with stillbirths ranging from 2.5 to 5.9%. A larger litter size and higher parity resulted in higher levels of mortality regardless of system. In all systems, crushing was the main cause of piglet mortality (59%), but 31% of sows did not crush any piglets, whilst 26% crushed only one piglet and the remaining sows (43%) crushed two or more piglets. System significantly influenced crushing as a percentage of all deaths, with the system with the smallest spatial footprint (m 2 ) compared to the other systems, recording the highest levels of crushing. Time from the start of the study influenced mortality, with significant reductions in crushing mortality (by ~ 4%) over the course of the three-year study. There was a highly significant effect of length of time (days) between moving sows into the farrowing accommodation and sows farrowing on piglet mortality (P < 0.001). The less time between sows moving in and farrowing, the higher the levels of piglet mortality, with ~ 3% increase in total mortality every five days. System effects were highly significant after adjusting for parity, litter size, and days pre-farrowing., Conclusion: These results from commercial farms demonstrate that even sows that have not been specifically selected for free farrowing are able, in many cases, to perform well in these zero-confinement systems, but that a period of adaptation is to be expected for overall farm performance. There are performance differences between the farms/systems which can be attributed to individual farm/system characteristics (e.g. pen design and management, staff expertise, pig genotypes, etc.). Higher parity sows and those producing very large litters provide a greater challenge to piglet mortality in these free farrowing systems (just as they do in crate systems). Management significantly influences performance, and ensuring sows have plenty of time to acclimatise between moving in to farrowing accommodation and giving birth is a critical aspect of improving piglet survival., (© 2024. The Author(s).)

Neosporosis and toxoplasmosis are major causes of abortion in livestock worldwide, leading to substantial economic losses. Detection tools are fundamental to the diagnosis and management of those diseases. Current immunohistochemistry (IHC) tests, using sera raised against whole parasite lysates, have not been able to distinguish between Toxoplasma gondii and Neospora caninum. We used T. gondii and N. caninum recombinant proteins, expressed in Escherichia coli and purified using insoluble conditions, to produce specific polyclonal rabbit antisera. We aimed to develop species-specific sera that could be used in IHC on formalin-fixed, paraffin-embedded (FFPE) tissue sections to improve the diagnosis of ruminant abortions caused by protozoa. Two polyclonal rabbit sera, raised against recombinant proteins, anti- Neospora -rNcSRS2 and anti- Toxoplasma -rTgSRS2, had specificity for the parasite they were raised against. We tested the specificity for each polyclonal serum using FFPE tissue sections known to be infected with T. gondii and N. caninum . The anti- Neospora -rNcSRS2 serum labeled specifically only N. caninum- infected tissue blocks, and the anti- Toxoplasma -rTgSRS2 serum was specific to only T. gondii- infected tissues. Moreover, tissues from 52 cattle and 19 sheep previously diagnosed by lesion profiles were tested using IHC with our polyclonal sera and PCR. The overall agreement between IHC and PCR was 90.1% for both polyclonal anti-rNcSRS2 and anti-rTgSRS2 sera. The polyclonal antisera were specific and allowed visual confirmation of protozoan parasites by IHC, but they were not as sensitive as PCR testing., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla CTX-M-15 serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene Salmonella , identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to repL . Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in S , our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.Salmonella , our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.

Lumpy skin disease virus (LSDV) is a member of the capripoxvirus (CPPV) genus of the Poxviridae family. LSDV is a rapidly emerging, high-consequence pathogen of cattle, recently spreading from Africa and the Middle East into Europe and Asia. We have sequenced the whole genome of historical LSDV isolates from the Pirbright Institute virus archive, and field isolates from recent disease outbreaks in Sri Lanka, Mongolia, Nigeria and Ethiopia. These genome sequences were compared to published genomes and classified into different subgroups. Two subgroups contained vaccine or vaccine-like samples ("Neethling-like" clade 1.1 and "Kenya-like" subgroup, clade 1.2.2). One subgroup was associated with outbreaks of LSD in the Middle East/Europe (clade 1.2.1) and a previously unreported subgroup originated from cases of LSD in west and central Africa (clade 1.2.3). Isolates were also identified that contained a mix of genes from both wildtype and vaccine samples (vaccine-like recombinants, grouped in clade 2). Whole genome sequencing and analysis of LSDV strains isolated from different regions of Africa, Europe and Asia have provided new knowledge of the drivers of LSDV emergence, and will inform future disease control strategies.

Parasites are known for their ability to rapidly adapt to changing conditions. For parasitic helminths, changes in climate, along with farming and management practices associated with the intensification of livestock farming, provide novel challenges which can impact on their epidemiology and control. The sustainability of livestock production partially relies on effective control of helminth infection. Therefore, understanding changes in parasite behaviour, and what drives these, is of great importance. Nematodirus battus is an economically important helminth in the UK and temperate regions. Its infective larvae typically overwinter in eggs on pasture and hatch synchronously in spring, causing acute disease in lambs. Attempts to control disease typically rely on whole-flock benzimidazole (BZ) treatments. In recent years, the emergence of BZ-resistance, alongside the hatching of eggs without the classical over-winter 'chill stimulus', have made N. battus more difficult to control. In three previous studies, after collecting a large number of N. battus populations alongside farm management data from commercial farms, we explored the prevalence of genetic mutations associated with BZ-resistance (n = 253 farms), the ability of eggs to hatch with and without a chill stimulus (n = 90 farms) and how farm management practices varied throughout the UK (n = 187 farms). In the present study, we identify factors which may be acting as drivers, or barriers, to either the development of resistance or the variable hatching behaviour of N. battus eggs. Generalised linear mixed effect models were applied to regress experimental hatching and genotyping data on farm management and additional environmental data. Both variable hatching and resistance development appeared associated with the maintenance of parasite refugia as well as grazing management, particularly reseeding of pasture routinely grazed by young lambs each spring and the practice of set-stocked grazing. Effective quarantine measures were identified as the main protective factor for the development of BZ-resistance whereas set stocked grazing and population bottlenecks, resulting from reseeding heavily contaminated pastures, were risk factors. Spring maximum temperature and other climatic factors were associated with 'typical' hatching of eggs following a chill stimulus whilst several management factors were linked with hatching without prior chilling. For example, practices which reduce parasite numbers on pasture (e.g. re-seeding) or restrict availability of hosts (e.g. resting fields), were found to increase the odds of non-chill hatching. Retention of the timing of lambing and infection level of the host within the fitted model indicated that requirement for a chill stimulus prior to hatching may be plastic, perhaps subject to change throughout the grazing season, in response to immune development or parasite density-dependence within the host. Further investigation of the influence of the factors retained within the fitted models, particularly the theme of parasite refugia which was highlighted in relation to both the presence of BZ-resistance alleles and alternative hatching, is required to establish robust, sustainable parasite control and farm management strategies., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Introduction: In 2020, an estimated 150 million children under the age of 5 years were stunted. Stunting results from early-life adversity and it is associated with significant physical and cognitive deficit, lifelong socioeconomic disadvantage and reduced life expectancy. There is a need to understand the causes of stunting and its effects in order to develop strategies to avoid it and to mitigate the consequences once stunting has occurred. Epigenetics is an important mechanism through which early-life factors are thought to influence biological function, with long-term consequences. We describe a series of epigenetic studies designed to understand how early-life adversity results in stunting and to inform the development of practical tools such as predictive markers and therapeutic targets. This work is part of the UKRI GCRF Action Against Stunting Hub., Methods and Analysis: The project-in India, Indonesia and Senegal-comprises an observational study of mothers, fathers, and offspring (n=500) spanning the first 1000 days of life, and an intervention study in each country. Epigenetic status (DNA methylation) is determined in saliva from babies collected within 1 month of birth and again at 18 months of age, and from mothers and fathers around the time of birth. Epigenome-wide analysis is carried out using the Illumina EPIC array, augmented by high-definition sequencing approaches. Statistical analysis is carried out at the level of candidate genes/regions, higher dimensional epigenetic states and epigenome-wide association. Data analysis focuses on the determinants of stunting, the effectiveness of interventions, population comparisons and the link between epigenetics and other thematic areas, which include anthropometry, microbiome, gut health, parasitology, cognition, nutrition, food hygiene and water sanitation, food systems and the home environment., Ethics and Dissemination: This study has been approved by the relevant Ethics Committees in Indonesia, India and Senegal, and the UK. Research data will be published and posted in public repositories., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.)

Introduction: The use of existing data to provide surveillance intelligence is widely advocated but often presents considerable challenges. Two data sources could be used as proxies for the mortality experienced by the Scottish cattle population: deaths recorded in the mandatory register [Cattle Tracing System (CTS)] and fallen stock collections by the National Fallen Stock Company (NSFCo) with a nationwide voluntary membership., Methods: Data for the period 2011-2016 were described and compared to establish their strengths and limitations. Similarities and differences in their temporal, seasonal and spatial patterns were examined overall, at postcode area level and for different age groups. Temporal aberration detection algorithms (TADA) were fitted., Results: Broadly, similar patterns were observed in the two datasets; however, there were some notable differences. The observed seasonal, annual and spatial patterns match expectations, given knowledge of Scottish cattle production systems. The registry data provide more comprehensive coverage of all areas of Scotland, while collections data provide a more comprehensive measure of the mortality experienced in 0-1-month-old calves., Discussion: Consequently, estimates of early calf mortality and their impact on the livestock sector made using CTS, or successor registers, will be under-estimates. This may apply to other registry-based systems. Fitted TADA detected points of deviations from expected norms some of which coincided in the two datasets; one with a known external event that caused increased mortality. We have demonstrated that both data sources do have the potential to be utilized to provide measures of mortality in the Scottish cattle population that could inform surveillance activities. While neither is perfect, they are complementary. Each has strengths and weaknesses, so ideally, a system where they are analyzed and interpreted in parallel would optimize the information obtained for surveillance purposes for epidemiologists, risk managers, animal health policy-makers and the wider livestock industry sector. This study provides a foundation on which to build an operational system. Further development will require improvements in the timeliness of data availability and further investment of resources., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Eze, Correia-Gomes, Gunn and Tongue.)

The welfare and economic impact of bovine respiratory disease complex (BRDC), and its associated antibiotic usage, are major challenges to cattle rearing and beef cattle finishing industries. Accurate pathogen diagnosis is important to undertake appropriate treatment and long-term management strategies, such as vaccine selection. Conventional diagnostic approaches have several limitations including high costs, long turnaround times and difficulty in test interpretation, which could delay treatment decisions and lead to unnecessary animal losses. We describe the validation of a multiplex-tandem (MT) reverse transcription-polymerase chain reaction (RT-PCR) for the detection of seven common pathogens associated with BRDC. This test has the potential to advance pathogen identification and to overcome many of the limitations of current testing methods. It requires a single sample and results are obtained quickly and not influenced by prior antimicrobial therapy or overgrowth of contaminating organisms. We demonstrated a test specificity of 100% and sensitivity ranging from 93.5% to 100% for these seven common pathogens. This test will be a useful addition to advance BRDC investigation and diagnosis., Competing Interests: Declaration of Competing Interest None of the authors has any financial or personal relationships that could inappropriately influence or bias the content of the paper. Ausdiagnostic played no role in the above study design nor in the collection, analysis and interpretation of data of the field validation, or in the decision to submit the manuscript for publication., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)