Characterization of dairy goat production systems in coastal valleys of the Lima region.

Goat farming in Peru is a husbandry activity that, although it is considered secondary in the country, has a great economic and social impact on the rural population, that is why government efforts to develop is so important. The objective of this study was to characterize dairy goat rearing systems in the coastal valleys of the Lima region to identify gaps and opportunities for improvement. This cross-sectional research was conducted in four provinces located in the Lima region, Peru. A total of 62 goat farmers participated in the trial. For data collection, a standard survey was prepared with open and closed questions distributed across two components (socioeconomic and productive). The surveys were processed for qualitative variables using a multiple correspondence analysis (MCA) followed by a hierarchical cluster analysis (HCA) to differentiate the types of farming systems prevalent based on the survey population. The hierarchical cluster analysis resulted in the formation of three separate groups of goat farmers, which can be classified as extensive systems differentiated by management practices and their production and marketing objectives. The test showed a significant difference; therefore, it can be affirmed that they are associated with the groups or clusters formed. These results will allow actors related to goat farming, such as state and regional entities, to focus efforts on addressing specific demands of the different types of goat farmers found in this study.

Association Between Dairy Production System and Milk Functionality Based on Analysis of miRNAs in Exosomes from Milk.

Dairy farming practices significantly affect the nutritional and functional properties of milk. This study compares miRNAs in milk exosomes from extensive and intensive dairy systems and explores their potential implications for human consumers. Extensive systems are believed to produce milk of higher quality with better animal welfare compared to intensive systems. Milk samples from eight extensive and nine intensive dairy farms were analysed. Milk-derived extracellular vesicles were isolated through sequential ultracentrifugation and characterised through Dynamic Light Scattering and Nanosight to determine the size and the concentration of the extracellular vesicles, in addition to immunoblotting to ensure the presence of exosome-specific proteins in their membrane. miRNA levels were quantified using RT-qPCR, and metabolic pathways associated with miRNAs showing significant differences between farm groups were analysed. EVs from extensive farms had higher concentrations. Notably, bta-miR-451 levels were significantly higher in milk from extensive farms (p = 0.021). Like human miRNA hsa-miR-451, it is linked to pathways related to Parkinson's disease and cancer. Our research suggests that milk production in extensive systems not only provides socioeconomic and environmental benefits but may also have positive effects on human health. Further research is warranted to explore the bioactive potential of these miRNAs and their implications for human health.

Exploratory study for implementing a Global Burden of Animal Diseases case study in Senegal. / Etude exploratoire pour la mise en oeuvre d'une étude de cas du programme " Impact mondial des maladies animales " au Sénégal.

Senegal is a West African country with both extensive animal production systems, representative of the environmental, economic and animal health constraints specific to the Sahel region, and thriving commercial poultry and dairy production. An exploratory study was conducted in Senegal between 2021 and 2022 as a prelude to a case study of the Global Burden of Animal Diseases (GBADs) programme. An overview of existing animal production systems as well as the main priorities and issues in animal health on a national level was developed. A national workshop gathering representatives from the livestock production and academic sectors took place in Dakar in June 2022 with the objective of jointly developing a case study. The participants prioritised pastoralist production systems for cattle and agropastoral systems for small ruminants for the application of the GBADs programme. Through a series of activities, the participants highlighted the health, environmental, economic and socio-political challenges surrounding these systems, all of which limit their contribution to the well-being of pastoralist households, consumers and other stakeholders. While Senegal has in the past hosted a large number of research and cooperative projects on these two livestock systems, participants noted difficulties in obtaining, centralising and harmonising the existing data. This exploratory study led to the funding of a focused case study of the agropastoral small-ruminant sector that was carried out in 2023 in partnership with national and international organisations.

Le Sénégal est un pays d'Afrique de l'Ouest comprenant à la fois des systèmes de production animale extensifs représentatifs des contraintes environnementales, économiques et sanitaires propres à la zone sahélienne, et un élevage commercial avicole et laitier en plein essor. Une étude exploratoire en prélude à une étude de cas du programme " Impact mondial des maladies animales " (GBADs) a été menée au Sénégal sur la période 2021-2022. Un état des lieux des systèmes de production animale existants, ainsi que des principales priorités et questions en termes de santé animale au niveau national, a été dressé. Un atelier national rassemblant des représentants de l'administration des productions animales et du secteur académique a eu lieu à Dakar en juin 2022 avec pour objectif de construire l'étude de cas de manière concertée. Les participants ont donné la priorité aux systèmes d'élevage bovins pastoral et petits ruminants agropastoral pour l'application du programme GBADs. Par une série d'activités, les participants ont mis en évidence les enjeux sanitaires, environnementaux, économiques et socio-politiques autour de ces systèmes qui limitent leur contribution au bien-être des ménages d'éleveurs, de consommateurs et autres acteurs de la société. Si le Sénégal a accueilli par le passé un grand nombre de projets de recherche et de coopération portant sur les deux systèmes d'élevage, les participants ont fait remonter les difficultés à obtenir, centraliser et harmoniser les données existantes. Cette étude exploratoire a débouché sur le financement d'une étude de cas focalisée sur le secteur agropastoral des petits ruminants, réalisée en 2023 en partenariat avec des organisations nationales et internationales.

Senegal es un país de África occidental con sistemas de producción animal extensivos, representativos de las limitaciones ambientales, económicas y zoosanitarias propias de la región del Sahel, y una próspera producción comercial avícola y lechera. Entre 2021 y 2022, se llevó a cabo en Senegal un estudio exploratorio como paso previo a la realización de un estudio de caso en el marco del programa sobre el impacto global de las enfermedades animales (GBADs). Se elaboró una reseña de los sistemas de producción animal existentes, así como de las principales prioridades y cuestiones en materia de sanidad animal a escala nacional. En junio de 2022, se celebró en Dakar un taller nacional que reunió a representantes del sector de la producción ganadera y el sector académico con el objetivo de elaborar conjuntamente un estudio de caso. Los participantes priorizaron los sistemas de producción pastoral de ganado vacuno y los sistemas agropastorales de pequeños rumiantes para la aplicación del programa GBADs. A través de una serie de actividades, los participantes pusieron de relieve los retos sanitarios, ambientales, económicos y sociopolíticos en torno a dichos sistemas, que limitan su contribución al bienestar de los hogares pastorales, los consumidores y otras partes interesadas. Aunque Senegal ha acogido en el pasado un gran número de proyectos de investigación y cooperación sobre estos dos sistemas ganaderos, los participantes señalaron las dificultades para obtener, centralizar y armonizar los datos existentes. Este estudio exploratorio condujo a la financiación de un estudio de caso centrado en el sector agropastoril de pequeños rumiantes que se llevó a cabo en 2023 en colaboración con organizaciones nacionales e internacionales.

Constructing Donor-Acceptor Covalent Organic Frameworks for Highly Efficient H2O2 Photosynthesis Coupled with Oxidative Organic Transformations.

The development of photocatalytic systems that enable the simultaneous production of H2O2 and value-added organic chemicals presents a dual advantage: generating valuable products while maximizing the utilization of solar energy. Despite the potential, there are relatively few reports on photocatalysts capable of such dual functions. In this study, we synthesized a series of donor-acceptor covalent organic frameworks (COFs), designated as JUC-675 to JUC-677, to explore their photocatalytic efficiency in the co-production of H2O2 and N-benzylbenzaldimine (BBAD). Among them, JUC-675 exhibited exceptional performance, achieving a H2O2 production rate of 22.8 mmol g-1 h-1 with an apparent quantum yield of 15.7%, and its solar-to-chemical conversion efficiency was calculated to be 1.09%, marking it as the most effective COF-based photocatalyst reported to date. Additionally, JUC-675 demonstrated a high selectivity (99.9%) and yield (96%) for BBAD in the oxidative coupling of benzylamine. The underlying reaction mechanism was thoroughly investigated through validation experiments and density functional theory (DFT) calculations. This work represents a significant advancement in the design of COF-based photocatalysts and the development of efficient dual-function photocatalytic platforms, offering new insights and methodologies for enhanced solar energy utilization and the synthesis of value-added products.

An integral assessment of the impact of diet and manure management on whole-farm greenhouse gas and nitrogen emissions in dairy cattle production systems using process-based models.

Feed management decisions are crucial in mitigating greenhouse gas (GHG) and nitrogen (N) emissions from ruminant farming systems. However, assessing the downstream impact of diet on emissions in dairy production systems is complex, due to the multifunctional relationships between a variety of distinct but interconnected sources such as animals, housing, manure storage, and soil. Therefore, there is a need for an integral assessment of the direct and indirect GHG and N emissions that considers the underlying processes of carbon (C), N and their drivers within the system. Here we show the relevance of using a cascade of process-based (PB) models, such as Dutch Tier 3 and (Manure)-DNDC (Denitrification-Decomposition) models, for capturing the downstream influence of diet on whole-farm emissions in two contrasting case study dairy farms: a confinement system in Germany and a pasture-based system in New Zealand. Considerable variation was found in emissions on a per hectare and per head basis, and across different farm components and categories of animals. Moreover, the confinement system had a farm C emission of 1.01 kg CO2-eq kg-1 fat and protein corrected milk (FPCM), and a farm N emission of 0.0300 kg N kg-1 FPCM. In contrast, the pasture-based system had a lower farm C and N emission averaging 0.82 kg CO2-eq kg-1 FPCM and 0.006 kg N kg-1 FPCM, respectively over the 4-year period. The results demonstrate how inputs and outputs could be made compatible and exchangeable across the PB models for quantifying dietary effects on whole-farm GHG and N emissions.

Partial budget analysis of laying hens' transition from cages to production systems of improved welfare: a case study in Greece.

1. In recent years, public concern regarding animal welfare has increased while, at the same time, cage systems for animal production have been greatly criticised by EU citizens. In addition, large food retailers promote food products that are made with eggs produced in cage-free systems.2. The objective of this study was to evaluate the economic viability of the transition of laying hens' to production systems; from conventional to alternative systems with improved welfare. Three independent scenarios were assumed as follows: transition from enriched colony cages to barn (S1), transition from barn to free-range (S2), and transition from free-range to organic (S3). Economic assessments of each transition was applied to a model farm in Greece with 12 000 hens, through partial budget analysis and net benefits and costs were estimated.3. The results showed a positive economic impact in all transitions to a production system of improved animal welfare (€12,044 in S1, €18,957 in S2 and €7,977 in S3) which indicated that they are economically sustainable. In all scenarios, unit cost increased by 19% in S1, 12% in S2, and 85% in S3.4. In conclusion, transitioning towards improved animal welfare production systems in laying hen farms could be an economically viable option for egg producers in compliance with societal demands and market trends.

A Review on Indigenous Goats of East Africa: A Case for Conservation and Management.

Indigenous goats are important in the livelihoods of rural households in East African countries. This is due to their ability to produce and reproduce in different environments and climatic conditions. Even though these indigenous goats are important, there is little available information on the genetic characterization of these breeds in Africa and at the international level. This paper reviews the status of indigenous goats, highlighting their production systems, phenotypic and genetic characteristics, and genetic diversity, and proposes potential ways for sustainable improvement and conservation in East African countries. Most households use traditional production systems with various uncharacterized goat breeds and ecotypes, which are hence named after the tribe or locality in which they are found. Most of these goats are classified as small East African breeds, with significant variability in morphological features. Some of the challenges to goat production in this region are indiscriminate crossbreeding, lack of pedigree records, parasites and disease incidences, low-quality pastures, and low levels of management. There is a need for a collaborative approach amongst the actors in goat breeding value chains as well as integrating modern genomic tools into breeding programs to enhance selection. This will ensure the resilience and sustainability of these unique indigenous goat populations in East Africa.

The Risk Factors of Dewclaw Dermatitis in Beef Cattle in the Amazon Biome.

Bovine Dewclaw Dermatitis (BDCD) is a hoof disease characterized by inflammation of the second and fifth accessory digits and the skin in this region. This pathology is poorly described in the literature; however, it has recently been observed in beef cattle in the Amazon Biome, Brazil. The objective of this study was to perform a clinical diagnosis and identify the risk factors associated with BDCD onset in cattle in the studied biome. Samples were collected from eight farms with extensive breeding systems located in Xinguara, Rondon do Pará, Curionópolis, and Ipixuna do Pará in the state of Pará, Brazil. A total of 706 Nellore and Nellore crossbred with taurine bovine of both sexes were evaluated, with males aged between 2 and 4 years and a mean weight of 650 kg, and females aged between 2 and 11 years and a mean weight of 400 kg. Distal extremities were inspected during cattle management, and in cases of dewclaw lesions, a specific examination was carried out after proper restraint. Cattle were diagnosed with BDCD on all farms analyzed. Of the 706 cattle inspected, 49 (6.94%) showed BDCD, of which 19 (38.77%) were Nellore and 30 (61.22%) were crossbred. This was the first study to determine BDCD's occurrence in extensive farming systems in the Amazon region, also showing that pastures with large amounts of stumps and stones, the physical structure of pens, and trauma and injury incidence during animal management are the most important predisposing factors for the onset of BDCD.

Addressing the safety of new food sources and production systems.

New food sources and production systems (NFPS) are garnering much attention, driven by international trade, changing consumer preferences, potential sustainability benefits, and innovations in climate-resilient food production systems. However, NFPS can introduce new challenges for food safety agencies and food manufacturers. Most food safety hazards linked to new foods have been identified in traditional foods. However, there can be some food safety challenges that are unique to new foods. New food ingredients, inputs, and processes can introduce unexpected contaminants. To realize the full potential of NFPS, there is a need for stakeholders from governments, the food industry, and the research community to collectively work to address and communicate the safety of NFPS products. This review outlines known food safety hazards associated with select NFPS products on the market, namely, plant-derived proteins, seaweeds, jellyfish, insects, microbial proteins, as well as foods derived from cell-based food production, precision fermentation, vertical farming, and 3D food printing. We identify common elements in emerging NFPS regulatory frameworks in various countries/regions. Furthermore, we highlight current efforts in harmonization of terminologies, use of recent scientific tools to fill in food safety knowledge gaps, and international multi-stakeholder collaborations to tackle safety challenges. Although there cannot be a one-size-fits-all approach when it comes to the regulatory oversight for ensuring the safety of NFPS, there is a need to develop consensus-based structured protocols or workflows among stakeholders to facilitate comprehensive, robust, and internationally harmonized approaches. These efforts increase consumers' confidence in the safety of new foods and contribute toward fair practices in the international trade of such foods.

Effects of season, catching method, and thinning on carcass quality and production parameters in 4 different broiler production systems in the Netherlands.

In the Netherlands, poultry meat production has been evolving in recent years toward broiler production systems with slow-growing broilers. In this study the effects of season, catching method, and thinning on carcass quality and production parameters in four different broiler production systems in the Netherlands was evaluated. The data for this study were collected from slaughterhouse data in 2018, 2019, and 2020 and contained information about four different broiler production systems: conventional (fast growing) broilers (CONV), 2 different indoor slow-growing broilers (SGB1 and SGB2), and Better Life 1 Star (BLS) concept with slow-growing broilers. The data set consisted of 14,976, 1,730, 3,713, and 1,121 records (flocks) for CONV, SGB1, SGB2, and BLS, respectively. All three production systems with slow-growing broilers had a lower slaughter weight, average daily gain (ADG), first-week mortality, and total mortality than CONV (no-thinning). ADG of SGB2 and BLS was lower than that of SGB1. Slaughter weight and ADG were the lowest when day-old chicks were placed in March/April and the highest when they were placed in September/October. All slow-growing broiler production systems had a lower footpad lesion score and a lower incidence of hock burns, leg hematomas, breast hematomas, dead-on-arrival chickens (DOA), and total rejects than CONV. Autumn flocks had more hock burns, a higher footpad lesion score, and more wing hematomas than spring flocks. More scabby hips and fewer total rejects were found during the summer months than during the winter months. Thinning flocks had more scabby hips, ammonia burns, and DOAs and fewer hock burns, footpad lesions, wing hematomas, leg hematomas, breast hematomas, and total rejects than no-thinning flocks. Mechanically caught flocks had more ammonia burns, DOAs, and total rejects than manually caught flocks. In conclusion, this study showed that all three production systems with slow-growing broilers had a lower first-week mortality and total mortality and better scores on most carcass quality parameters and welfare indicators than CONV.

Climate change impacts on temperate fruit and nut production: a systematic review.

Temperate fruit and nut crops require distinctive cold and warm seasons to meet their physiological requirements and progress through their phenological stages. Consequently, they have been traditionally cultivated in warm temperate climate regions characterized by dry-summer and wet-winter seasons. However, fruit and nut production in these areas faces new challenging conditions due to increasingly severe and erratic weather patterns caused by climate change. This review represents an effort towards identifying the current state of knowledge, key challenges, and gaps that emerge from studies of climate change effects on fruit and nut crops produced in warm temperate climates. Following the PRISMA methodology for systematic reviews, we analyzed 403 articles published between 2000 and 2023 that met the defined eligibility criteria. A 44-fold increase in the number of publications during the last two decades reflects a growing interest in research related to both a better understanding of the effects of climate anomalies on temperate fruit and nut production and the need to find strategies that allow this industry to adapt to current and future weather conditions while reducing its environmental impacts. In an extended analysis beyond the scope of the systematic review methodology, we classified the literature into six main areas of research, including responses to environmental conditions, water management, sustainable agriculture, breeding and genetics, prediction models, and production systems. Given the rapid expansion of climate change-related literature, our analysis provides valuable information for researchers, as it can help them identify aspects that are well understood, topics that remain unexplored, and urgent questions that need to be addressed in the future.

Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept.

BACKGROUND: Different production systems of livestock animals influence various factors, including the gut microbiota. METHODS: We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. RESULTS: Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken. CONCLUSION: Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.

Advanced technological adaptations can improve the energy-cum-carbon-efficiency of diverse rice production systems.

Worldwide, there is an urgent need to develop energy-cum-carbon smart and cost-effective rice production systems for farmer's adoption. Data were collected from 280 farmer's fields representing the South Asia rice production system. Out of these 75 fields following transplanted rice (TPR), 55 fields of wet direct seeded rice (WDSR), 60 fields of drill sown direct seeded rice in line (DSR L), 60 fields of traditional direct seeded rice (DSR) and 30 fields of DSR + beushning (DSR + B). Results show that grain and straw yields in the TPR were 6056 and 7752 kg ha-1, respectively; however, they were neither profitable, energy efficient, or eco-friendly. At the same time, the grain and straw yields in DSR L were recorded by 5832 and 7757 kg ha-1, respectively. It was profitable with the highest net returns (1111.5 US$ ha-1), energy use efficiency (12.77), energy productivity (0.41 kg MJ-1), energy profitability (11.77 US$ MJ-1), energy output efficiency (1314.3 MJ day-1) environment friendly in terms of carbon efficiency 7.20, carbon sustainability index (6.20) and had most diminutive carbon footprint (0.14 kg CO2 eq kg-1 grain) with a comparable carbon credit. DSR L is productive, economically viable, energy efficient, and environmentally safer among rice production systems.

Recent Progress in Modular Electrochemical Synthesis of Hydrogen and High-Value-added Chemicals based on Solid Redox Mediator.

Electrochemical synthesis of H2 and high-value-added chemicals is an efficient and cost-effective approach that can be powered using renewable electricity. Compared to a conventional electrochemical production system, the modular electrochemical production system (MEPS) based on a solid redox mediator (SRM) can separate the anodic and cathodic reactions in time and space. The MEPS can avoid the use of membranes and formation of useless products, as well as eliminate the mutual dependence of production rates at anode and cathode. The SRM can temporarily store or release electrons and ions to pair with cathodic and anodic reactions, respectively, in MEPS. Designing of SRMs with large charge capacity and good cyclability is of great significance for constructing a high-performance MEPS. This work summarizes the design principles, recent advances in MEPS based on SRM, and application in redox flow cells. Moreover, structure design strategies as well as in situ characterization techniques and theoretical calculations for SRM is also proposed. It is expected to promote the vigorous development of MEPS based on SRM. Finally, the challenges and perspectives of MEPS based on SRM are discussed.

Analysis of Management Practices and Breeders' Perceptions of Climate Change's Impact to Enhance the Resilience of Sheep Production Systems: A Case Study in the Tunisian Semi-Arid Zone.

Global climate change inflicts unambiguous risks on agricultural systems and food security. Small ruminants are known for their ability to adapt to changing environmental conditions. This paper aims to characterize sheep production systems in a vulnerable agricultural zone and the breeders' perceptions of climate change to apprehend challenges that they are confronting, and formulate resilience actions. The data analysis is based on 94 semi-structured surveys of sheep farmers carried out in the Tunisian semi-arid region. The PCA analysis results revealed three main sheep production systems. The agro-pastoral rain-fed system (AGPRF) is dominant (55%), with large farms and common pastures integrating cereals and fodder. The agro-pastoral irrigated system (AGPI: 20%) is characterized by small-area and forage irrigation (1.8 ha) and a smaller number of ewes but a greater use of animal feed supplementation. The agro-sylvo-pastoral system (AGSP: 25%) is a system where grazing is based on common lands and using tree sub-products, while the agricultural area is exclusively used to cultivate cereal crops. Sheep breeders' climate perceptions are summarized as unpredictable climate events, a decrease in precipitation, and an increase in temperature. Resilience actions principally consist of reducing flocks' numbers, using alternative local feed, fodder, and water resources, and building more shelters and planting more trees in the grazing areas. Nevertheless, cost-effectiveness should be considered in such vulnerable zones to insure the sheep production systems' sustainability.

Production, Composition and Nutritional Properties of Organic Milk: A Critical Review.

Milk is one of the most valuable products in the food industry with most milk production throughout the world being carried out using conventional management, which includes intensive and traditional systems. The intensive use of fertilizers, antibiotics, pesticides and concerns regarding animal health and the environment have given increasing importance to organic dairy and dairy products in the last two decades. This review aims to compare the production, nutritional, and compositional properties of milk produced by conventional and organic dairy management systems. We also shed light on the health benefits of milk and the worldwide scenario of the organic dairy production system. Most reports suggest milk has beneficial health effects with very few, if any, adverse effects reported. Organic milk is reported to confer additional benefits due to its lower omega-6-omega-3 ratio, which is due to the difference in feeding practices, with organic cows predominantly pasture fed. Despite the testified animal, host, and environmental benefits, organic milk production is difficult in several regions due to the cost-intensive process and geographical conditions. Finally, we offer perspectives for a better future and highlight knowledge gaps in the organic dairy management system.

The Bull Breeding Soundness Examination and Its Application in the Production Setting.

breeding soundness for several reasons and at several times during their life span. These include before sale for the reason of affirming their sale ability or before a breeding season to determine their readiness for breeding. Bulls may also be evaluated for diagnostic purposes. The breeding soundness examination (BSE) is universally promoted as an important management tool, but there continues to be a level of inconsistency in its performance. A complete bull BSE consists of a thorough physical examination including internal and external reproductive tract, measurement of the circumference of the scrotum and evaluation of individual sperm motility and morphology.

ICP-OES analysis of total As and Cd in Columbian Oryza sativa L. rice.

Arsenic (As) and cadmium (Cd) are considered toxic elements, even at trace levels. Their accurate quantification in crops can be complex at low levels and due to interference with other elements. The aim of this work was to develop and validate an analytical method for As and Cd quantification in rice stem and grains from the production systems "Irrigated Rice Ecosystems" (IRE) and "Rainfed Rice Ecosystems" (RRE) in Colombia. Mineralisation was carried out by acid digestion using an open system with a heating plate. Metal detection was performed by inductively coupled plasma optical emission spectrometry (ICP-OES). Method adjustment, calibration, and validation were performed in accordance with AOAC standards, considering sensitivity, precision, accuracy, and selectivity parameters. The obtained method was applied to quantify levels in 259 rice stem and 443 grain samples from IRE and RRE.

Prevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark.

The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22). Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply.