Towards the identification of transmission pathways and early detection of Enterococcus cecorum infection in broiler chickens

Enterococcus cecorum (EC) infection is an emerging endemic disease in UK and global broiler poultry with major economic impact and welfare concerns. There are significant research gaps with regards to EC pathogenesis, source of infection, transmission routes and early detection of disease, which this study aimed to address. In this prospective study, 725 environmental samples were collected from 4 broiler farms (A −D) the day before chick placement (d 1) and through the subsequent crop (d 7, 14, and 21). Cecal swabs were collected from birds that died of natural causes during the study period. A sample of birds that had been found dead or were culled for health reasons, were presented for post-mortem and samples were taken from lesions for EC culture. DNA was extracted from all environmental samples and EC detected using a qPCR and MALDITOF. Two EC isolates from diseased birds were inoculated on concrete slabs and incubated at 23°C and 32°C followed by swabbing of concrete culturing and determination of EC cfu at defined time points. Alongside environmental and bird sampling commercially available, smart camera systems were installed in selected houses on each farm to monitor bird activity and distribution. No EC outbreak occurred during the study, however, it was detected by qPCR in 215/725 (29.7 %) of all samples collected. Also, EC DNA was detected on average in 37% of samples collected on d 1, with approx. 88% of samples from chick paper being positive. Despite this, it was only cultured from 3 ceca samples and joint fluids of two infected birds from farm B on d 14 and 21. The survival experiments using isolates from infected chickens showed EC can survive on concrete for at least 21 d. This study provides invaluable insights into transmission pathways and tenacity of EC. Further studies are needed to determine strain characteristics in relation to their ability to cause disease and to further elucidate the sources of infection on poultry farms

Economics of reducing response time to foreign-animal disease in the United States with point-of-care diagnostic tests

Background As low probability events, United States producers, value chain actors, and veterinary services (VS) have limited experience with identifying foreign animal disease (FAD), which can allow FADs to spread undetected. Point-of-care (POC) diagnostic testing may help reduce the time from detecting an initial suspect case to implementing actionable interventions compared to the current approach of only using laboratory diagnostic testing for disease diagnosis and confirmation. To evaluate the value of the reduced response time, we compare the associated costs between the two diagnostic approaches while accounting for the uncertainty surrounding the size of a FAD event. Methods We apply a state-contingent approach (SCA) to model the uncertainty surrounding a FAD through alternative events, where the event defines the scale of outbreak size and its duration. We apply this approach within a cost-benefit framework (CBA) to determine the economic value from the two testing investment strategies to help explain the policymaker’s response (and costs) to alternative FAD events while also considering the cost impacts on the producers from each event. Results Compared to the current laboratory strategy, a POC strategy that reduces response time by 0.5-days (swine, cattle scenarios) and 1.5-days (poultry scenario) may provide cost-saving to both producers and public response efforts. The benefit-cost analysis further suggests that despite the higher fixed costs to adopt the POC strategy, the swine and cattle sectors may benefit while the benefits may not be as pronounced in the poultry sector. Discussion POC testing that can reduce the time between detection and response during a FAD event may be a sound strategy for public expenditure and provide cost-savings for producers, especially when minimal fixed costs are incurred. However, to fully determine the value of POC testing, the consequences (costs) associated with potential actions if something goes wrong, (e.g. false positive results), should be considered in future studies

Unravelling Enterococcus cecorum infection on UK broiler farms: Correlating clinical signs with genomics, persistence and animal behaviour

Application To combat endemic Enterococcus cecorum disease in UK broilers, it is essential to understand the pathogenesis of the organism and to develop tools for early disease detection and prevention. This will ultimately result in improved animal welfare and reduced economic losses. This pump-priming project provided a scientific basis for future research, by starting to address significant knowledge gaps in E. cecorum epidemiology. Research outputs can be used further to inform farm management practices related to disease management and prevention. This research will also aid the poultry industry with its antibiotics stewardship programme. Introduction E. cecorum infection is an emerging endemic disease in UK and global broiler poultry with significant welfare concerns and results in considerable economic losses to the industry (Wood et al., 2002; De Herdt et al., 2009; Stalker et al., 2010; Dunnam et al., 2023). There are substantial research gaps with regards to E. cecorum pathogenesis, source of infection, transmission routes and strain differences in terms of their ability to cause disease. In addition there is a need to detect E. cecorum infection earlier in the production cycle to aid disease prevention. The aim of this project was to fill knowledge gaps by conducting research into pathogen genomics, transmission and persistence as well as early detection of disease through behavioural monitoring Materials and methods Four commercial UK broiler farms (A-D) with a range of historical performances and history of E. cecorum infections, were chosen for the study. Farms operated an all- in all-out production system with chicks being placed into disinfected sheds at 1 day of age followed by a 37 to 42 day growth cycle. Water and feed intake and environmental parameters were automatically monitored and final performance data was collected. A sample of birds that had been found dead or were culled for any health reasons, were presented for examination by poultry veterinarians. A total of 725 samples were collected on days -1, 7, 14 and 21 (Table 1). DNA was extracted from all samples and E. cecorum was detected using qPCR. Samples were also cultured and E. cecorum was identified using Matrix-assisted laser desorption/ionization (MALDI-TOF). Two E. cecorum strains isolated from joint fluid were tested for tenacity at 23 �C and 32 �C on concrete surfaces in a 21 day long in-vitro experiment. A total of 180 E. cecorum sequences from public repositories (n = 107), APHA archives (n = 74) from 2003 to 2022, and five E. cecorum isolated in this farm study were submitted to whole genome sequencing (WGS) and a maximum likelihood phylogenetic tree constructed. The APHA SeqFinder pipeline was used to detect AMR genes. Finally, commercially available intelligent camera systems were installed on trial farms to record flock activity patterns, cluster movements, distribution and spread. Results No E. cecorum outbreak was observed during the trial period.E. cecorum was detected in 215/725 (29.7%) samples by qPCR (Table 1). It was detected on all farms and in all sample types, including all chick papers suggesting a possible route for entry to farms. qPCR also showed that 99.0% and 88.3% E. cecorum positive samples, respectively, from farms D and C were taken at day -1. E. cecorum was detected throughout the trial on farms A and B. Three E. cecorum were isolated from farm B caecal samples and two from infected birds, which showed sporadic E. cecorum infection; but E. cecorum was not isolated from any environmental source, including from farm B. Survival experiments on concrete showed that both E. cecorum isolates survived longer at 23 �C than at 32 �C. One isolate survived for longer at both temperatures, and was still viable on day 21. Analysis of WGS data indicated several antimicrobial resistance (AMR) genes conferring resistance to aminoglycosides, macrolides and tetracycline were variably present in isolates. Phylogenetic analysis clustered the majority of UK isolates into three groups which are mostly separated from other non-UK isolates collected worldwide. The groups were widely distributed across all the farms included. Data from the cameras indicated that on farms A, C and D bird activity and distribution patterns were consistent with a healthy broiler population. Analysis of data from a house in farm B revealed an unexpected drop in activity and a decrease in distribution after day 15, signalling a potential health concern. This coincided with a noticeable drop in feed consumption from day 12 and diagnosis of dysbacteriosis by the primary veterinarian. Conclusion This study has highlighted a range of possible environmental reservoirs for E. cecorum, by detecting DNA in range of environmental sources. The results indicate that E. cecorum may be present as a harmless commensal at low levels within the farm environment, indicating further work is required to understand conditions that promote changes of this commensal to a pathogen that causes large disease outbreaks on UK farms. Bird activity data from cameras could not be linked to E. cecorum infection, primarily due lack of E. cecorum associated disease on trial farms. Nevertheless the technology shows promises as a reduction in bird activity and change in the distribution was detected on farm B, where gastrointestinal disease was diagnosed. This project has brought together academia, government bodies, veterinarians, poultry farmers and other stakeholders related to the broiler industry. This collaboration has allowed us to harness expertise and knowledge in all areas relevant to the project and to design trials with scientific outputs that can inform farm management practices related to E. cecorum disease prevention and management

Capturing the complexity of veterinarians’ antibiotic prescribing practices in the livestock sector: a meta-ethnography across contexts

Strategies and policies to tackle the global public health threat of antimicrobial resistance are increasingly addressing antimicrobial use prescribing practices in both the human and animal health sectors. Veterinarians’ antibiotic prescribing practices are influenced by different factors and conditioned by the context within which antibiotic prescribing decisions are made, complexifying the implementation of behaviour change interventions. A better understanding of these factors could therefore help in the design and application of such interventions. Meta-ethnography was used to explore the antibiotic prescribing behaviour of veterinarians in different contexts and to construct a new conceptual framework. A search was conducted in PubMed, Web of Science Core Collection and SciELO Citation Index between 2016 and 2024. The final sample consisted of 29 articles, 27 of which were selected from the 561 articles identified in the search and 2 of which were added by the authors. The results were synthesized and presented through four contextual situations influencing antibiotic prescribing by livestock veterinarians: priorities and pressures, uncertain field conditions, systemic challenges and an enabling environment. The results are presented as a conceptual framework that views veterinarians’ antibiotic prescribing behaviour as dynamic, adapting in response to the different contextual situations they encounter. The findings provide an integrated and contextualized understanding of veterinarians’ antibiotic prescribing behaviours, which could be implemented to facilitate the development and application of future antimicrobial stewardship interventions

Comparing Australian public and farmer views on agricultural land use and management practices for sustainability

Using a survey of the public (n = 2032) and broadacre farmers (n = 351) in South Australia and Victoria, Australia, this research compares public and farmers' concerns regarding the acceptability and sustainability of agricultural operations. A principal component analysis was conducted on survey responses to 15 statements capturing environmental, social and governance issues related to agriculture practices and perceptions. This analysis revealed three dimensions: (1) issues related to animal welfare, greenhouse gas emissions and food safety; (2) issues related to farm input use; and (3) the use of socially valuable assets for private profits. Compared to farmers, the public were more concerned about the undersupply of public goods (e.g., farm animal welfare), and issues related to farm input use such as the use of synthetic fertilisers and chemicals. The public and farmers reported a similar level of concern regarding the use of socially valuable assets for private profit (e.g., irrigation water extraction). Regression analyses revealed associations between concerns and socio-demographic characteristics; environmental attitudes; sources of information; and farm characteristics. This study can act as a catalyst for developing practical strategies to analyse and overcome the issues, rather than symptoms, of concern affecting the agricultural industry and its sustainability

Measuring and modelling the impact of outdoor pigs on soil carbon and nutrient dynamics under a changing climate and different management scenarios

A mixed agricultural system that integrates livestock and cropping is essential to organic, agroecological, and regenerative farming. The demand for improved welfare systems has made the practice of outdoor rearing of pigs very popular; it currently makes up 40% of the UK pig industry and has also been integrated into arable rotations. Besides the benefits of outdoor production systems, they also potentially pose environmental risks to farmlands, such as accumulation of nitrogen and phosphorus in the soil, soil erosion and compaction and carbon loss. Despite this, the impact of outdoor pigs and arable crop rotations on soil health has been under-researched relative to other livestock species. This study was conducted at the University of Leeds Research Farm from 2018 to 2020 using a combined experimental and modelling approach to understand the impact of outdoor pigs on soil carbon and nutrient dynamics. The physio-chemical properties of arable soil were measured prior to the introduction of the pigs and after introducing the pigs at the end of first and second years, consecutively. There was assessment of control sites (without pigs, mowing once a year) and pig pens (pigs in a rotation with arable crops). The soil was sampled at two different depths, 0–10 cm and 10–20 cm. It was observed that measured soil organic carbon (SOC) stocks in the soil depths of 0–10 cm and 10–20 cm layer were decreased by 7% and 3%, respectively, in the pig pens from 2019 to 2020, and total available nitrogen and phosphorus were significantly higher in pig pens than the control sites. Hence, at a depth between 0 and 20 cm, the average total available nitrogen was 2.51 and 2.68 mg kg−1 in the control sites and 21.76 and 20.45 mg kg−1 in the pig pens in 2019 and 2020, respectively. The average total available phosphorus at 0–20 cm was 26.54 and 37.02 mg kg−1 in control sites and 48.15 and 63.58 mg kg−1 in pig pens during 2019 and 2020, respectively. A process-based model (DayCent) was used to simulate soil carbon and nitrogen dynamics in the arable rotation with outdoor pigs and showed SOC stock losses of – 0.09 ± 0.23 T C ha−1 year−1 using the future climate CMIP5 RCP 8.5 scenario for 2020 to 2048. To reduce this loss, we modelled the impact of changing the management of the pig rotation and found that the loss of SOC stock could be decreased by shortening the period of pig retention in the field, growing grass in the field, and leguminous crops in the crop rotation

Understanding the roles of economy and society in the relative risks of zoonosis emergence from livestock

The emergence of zoonotic infections that can develop into pathogens of pandemic potential is a major concern for public health. The risks of emergence and transmission relate to multiple factors that range from land use to human–non-human animal contacts. Livestock agriculture plays a potentially significant role in those risks, shaping landscapes and providing hosts that can act as the source or amplifiers of emergent pathogens. The relative risks will be contingent upon the nature of those systems, with comparisons often made between intensive, indoor, biosecure systems and more extensive, outdoor, insecure systems. Microbiological, ecological and veterinary sciences provide useful entry points in specifying and modelling some of the relative risks. Yet, they often do so with little regard for social science inputs and by making assumptions about social and economic conditions. In this article, we respond to recent analyses of relative risks by raising the importance of social and economic drivers of risk. We chart social science insights and research that materially alter the zoonotic risks associated with livestock production. Our purpose is to emphasize the requirement for full appreciation of the social, economic and political components of zoonotic and pandemic risk

UK farmer and grower research priorities

Farmers and growers in the UK are facing rapid changes in policy and trade on top of the emerging pressures relating to climate, nature and public health. There is a need for strategic engagement to ensure that their needs influence UK research and innovation priorities. To address this gap, a group of farming and research organisations have collaborated to understand research and innovation priorities for farmers and growers across the UK. Insights were gathered from 92 farmers and growers, representing all major agricultural sectors across a wide diversity of farming systems, at 12 semi-structured workshops. There are also insights from businesses upstream and downstream of agriculture, as well as from environmental and other organisations that influence the industry’s direction. What we found: • The overarching themes highlighted by farmers and growers in a previous process, in 2013, remain topical today. • The specific priorities within those themes, however, have shifted, particularly with respect to precision agriculture, and training and communications. • The most common priorities were around ‘how’ research and farming is done, rather than ‘what’ it does, with adoption, farmer-led research, and future skills mentioned most often. • The farmers and growers we spoke with are interested in sustainable agriculture, including regenerative farming. In particular, they are interested in understanding socio-economic barriers to sustainable practices and the value of environmentally sustainable farming. • Farmers also raised challenges associated with adapting to new regulations, climate change and public perception. • Agricultural research conducted by universities has limited overlap with the priorities highlighted by farmers and growers. What this means: The differences that this project highlights between the priorities of farmers and growers, and those of researchers and funders, imply there is potential to: • Engage farmers and growers more in innovation that reaches beyond the farm gate, relating to nutrition, waste and circularity, food systems and supply chain development. • Involve farmers and growers more in the development, design and delivery of research, enabling dialogue about priorities in the shorter and longer term, and enhancing the practical relevance of research. • Integrate the social sciences through greater emphasis on interdisciplinary research, given how focused farmers and growers are on questions of adoption, accessibility and impact

Crop species diversity: A key strategy for sustainable food system transformation and climate resilience

The global food system's reliance on a few species threatens food and nutritional security. Species diversification, including indigenous species, is a viable option to address this issue. Diversity enhances food systems' resilience against climatic and economic shocks. It offers resources for improved breeds and allows farmers to mitigate risks. However, successful diversification demands collaboration among farmers, researchers, academics, professionals, retailers, consumers, and policymakers. This review analyzes the role of crop species diversity in food system transformation, focusing on monoculture vulnerabilities, diversification benefits, indigenous species' role in nutrition and food security, and the importance of integrated policies and multi-stakeholder collaborations. We advocate for interdisciplinary research, participatory approaches, and supportive policies to foster diverse, resilient food systems that ensure food security, biodiversity conservation, and enhanced social well-being amidst global challenges. While acknowledging the importance of diversity in animal species for food security, the focus of this review is on crop species diversity and its potential to transform food systems

ZmD11 Gene Regulates Tobacco Plant Floral Development under Drought Stress

Maize is most sensitive to drought stress at the floral stage by reducing tassel and silk quality, and thus improving drought tolerance at this stage may help preserve yield. It has been reported that BRs (brassinosteroids) promote floral development under drought stress. However, the function of the brassinosteroid biosynthesis gene ZmDWARF11 (ZmD11) on floral growth under drought stress has not been elucidated. This study found that under normal growth conditions, the heterologous over-expression of ZmD11 significantly enhanced both the vegetative growth and floral develop-ment of tobacco. Under drought stress, overexpressing ZmD11 reduced stress-induced tobacco flower size reduction, while it did not affect vegetative growth. After drought treatment, the activ-ities of protective enzymes, including CAT (Catalase), SOD (Superoxide Dismutase), and POD (Peroxidase), were higher, while the content of MDA (Malondialdehyde) was lower in ZmD11 over-expression tobacco lines than that in the wild type control. The relative expression of dehy-drin-related genes NtLeat5 and NtERD10 was increased in ZmD11 over-expression tobacco lines compared to that in the control. In summary, we reported that ZmD11 plays a role in tobacco floral development under drought stress. Our data are valuable in understanding the functions of BRs in regulating plant floral development under drought stress