Livestock Animals Research Articles

Recent update on enterococcal resistance to the last-resort antimicrobials among livestock animals and retail meats

Recent update on enterococcal resistance to the last-resort antimicrobials among livestock animals and retail meats

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

BackgroundDifferent production systems of livestock animals influence various factors, including the gut microbiota.MethodsWe 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.ResultsOver 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.ConclusionOur 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.

Dairy Farmers’ Perceptions and Adaptation Strategies Towards The Effects of Climate Change in Southern Marmara Region of Turkey

Aims: The study aims to determine dairy farmers' perceptions of climate-related risks, their adaptation strategies and factors affecting their decisions about adaptation strategies in Southern Marmara Region of Turkey. Material and methods: Data was collected from 379 dairy farmers by proportional sampling method. The survey was performed between October and December 2023. Descriptive statistics and probit model were used in the evaluation of the data. Results: Most dairy farmers (70.7%) had a high perception for heavy storms. Changing feed ration seasonally was the most widespread adaptation strategy employed by dairy farmers. It was followed by diversification of animal production activities, livestock insurance and diverseness of feed crops. Among these adaptation strategies, changing feed ration seasonally was the highest choosen adaptation strategy in the study area whereas the diverseness of feed crops was the least choosen adaptation strategy. The probit model results showed that the dairy farmers' age and household size had an adverse the impact on their decisions about all adaptation strategies. Discussion: These results of this study stated that most dairy farmers perceived the rise in temperatures and decline in rainfall as noticeable changes in climate. Few dairy farmers used advanced agricultural applications for dealing with the negative impacts of climatic change, and many dairy farmers continued use to simple adaptation measures. Conclusions:As a result, the present study findings can shed light to policy/decision makers in agricultural research, to practices regarding the climate change impact in dairy farming, and to further studies in the literature.

Seroprevalence and renal carriage of pathogenic Leptospira in livestock in Cotonou, Benin.

Leptospirosis is a zoonotic disease. It is particularly prevalent in tropical countries and has major consequences for human and animal health. In Benin, the disease's epidemiology remains poorly understood, especially in livestock, for which data are lacking. To characterise Leptospira seroprevalence and locally circulating serogroups in livestock from Cotonou and to estimate the prevalence of Leptospira renal carriage in cattle. We conducted a cross-sectional study in February 2020 during which livestock were sampled at an abattoir and in an impoverished city district. We analysed blood samples from 279 livestock animals (i.e. cattle, sheep, goats and pigs) using the microscopic agglutination test. Additionally, samples of renal tissue from 100 cattle underwent 16s rRNA (rrs) real-time PCR analysis. For the 131 cattle, 85 sheep, and 50 goats tested, seroprevalence was 18% (95% confidence interval [CI] [12%, 26%]), 9% (95% CI [4%, 17%] and 2% (95% CI [0%, 9%]), respectively, and most of the seropositive animals were associated with 1:100 titres. All 13 pigs were seronegative. Leptospira DNA was found in the renal tissue of 10% (95% CI [5%, 18%]) of the cattle tested (n=100). Leptospira borgpetersenii was the main species present (n=7), but Leptospira interrogans (n=2) and Leptospira kirschneri (n=1) were also detected. Various serogroups (Canicola, Grippotyphosa, Sejroe, Icterohaemorrhagiae, Pomona, Pyrogenes, Australis and Autumnalis) were detected using microscopic agglutination test without a clear predominance of any of them. These results suggest that abattoir workers and people living in close contact with livestock in poor urban areas are exposed to the risk of Leptospira infection.

Generic methodology to prevent food contamination by soil born legacy POPs in free range livestock

Government monitoring commonly includes regulating POPs in animal feed and products of animal origin, with many countries setting Maximum Residue Levels (MRLs) to ensure safe tolerable concentrations. However, these MRLs do not address the presence of most POP families in soil, where concentrations can be much higher due to the contaminants' strong affinity and persistence in comparison to other environmental matrices. Extensive damage to food and production systems during a pollution incident causing soil contamination by POPs lead to severe economic and social consequences for the affected area. To mitigate these effects, it is crucial to implement necessary measures for consumer protection while also focusing on rehabilitating conditions for food production, tailored to both commercial farms and private holders. In this context, the present work aims to develop and test a methodology for assessing the tolerable concentration of the most cancerogenic legacy POPs in soil for various livestock animals in diverse rearing systems ensuring the safety of food of animal origin. Therefore, we summarize existing knowledge about the risk of POP transfer in different livestock breeding systems via soil exposure, and modeling via a backward calculation from the MRLs the corresponding tolerable quantity of POPs that may be ingested by animals in the considered rearing system. Results of these simulations showed that soil ingestion is a predominant contamination pathway, which is a central factor in the risk assessment of POP exposure on livestock farms, especially in free-range systems. In field conditions of POP exposure, low productive animals may be more susceptible to uptake through soil than high-yielding animals, even if the feed respected MRLs. Results show that PCDD/Fs revealed the lowest security ratio for low productive dairy cows (1.5) compared to high productive ones (52). Laying hens with a productivity of 45% show also as a high sensitivity to POPs exposure via soil ingestion. Indeed, their security ratio for PCDD/Fs, lindane and DDT were 3, 2 and 1, respectively. In perspective, proposed methodology can be adapted for assessing the risk of industrial POPs newly listed in the Stockholm Convention. In practice, it could be useful for food producers to apprehend their own risk of chemical contamination.

Performance evaluation of a prototype for the defense against wolf attacks on livestock animals

This study seeks to evaluate a prototype's effectiveness in safeguarding livestock against wolf attacks. With an increasing imperative to protect livestock from predation, the prototype's performance was systematically examined under diverse conditions. The study primarily aimed at assessing the prototype's ability to detect wolf attacks by analyzing noise variations inherent to predator assaults. Simultaneously, the prototype aimed to mitigate livestock casualties and foster coexistence between wolves and livestock. A series of controlled experiments were meticulously carried out, replicating real-world wolf encounter scenarios. The findings yield valuable insights into the prototype's practical utility and its potential to mitigate conflicts between predator populations and livestock farming. Overall, this research contributes to advancing innovative strategies for sustainable cohabitation between wildlife and agriculture.

Transgenic black soldier flies for production of carotenoids

The black soldier fly (BSF), Hermetia illucens, has gained traction recently as a means to achieve closed-loop production cycles. BSF can subsist off mammalian waste products and their consumption of such waste in turn generates compost that can be used in agricultural operations. Their environmental impact is minimal and BSF larvae are edible, with a nutritional profile high in protein and other essential vitamins. Therefore, it is conceivable to use BSF as a mechanism for both reducing organic waste and maintaining a low-impact food source for animal livestock or humans. The main drawback to BSF as a potential human food source is they are deficient in fat-soluble vitamins such as Vitamins A, D, and E. While loading BSF with essential vitamins may be achieved via diet-based interventions, this undercuts the goal of a closed-loop as specialized diets would require additional supply chains. An alternative is to genetically engineer BSF that can synthesize these essential vitamins. Here we describe a BSF line that has been engineered with the two main carotenoid biosynthetic genes, CarRA and CarB for production of provitamin carotenoids within the Vitamin A family. Our data describe the manipulation of the BSF genome to insert transgenes for expression of functional protein products.

Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host–microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

Knowledge, Attitude, and Prevention Practices towards Common Zoonotic Diseases in and around Bahir Dar City, North Western Ethiopia

The problem of zoonoses diseases is a global public and veterinary health concern. Globally coordinated and well-established research efforts are essential to successfully fighting and reducing the health burden of zoonoses. In our study area, the interplay of intense livestock animals, agricultural activities, and poor health services characterized the high risks of zoonotic diseases. Thus, people suffer from easily preventable diseases with hygiene and good-quality food. The main objectives of this study were to: (i) evaluate the knowledge, attitude, and prevention practices of people handling farm animals and their products toward common zoonotic diseases; and (ii) estimate the associated risk factors influencing their knowledge, attitude, and prevention practices. A questionnaire-based cross-sectional study was conducted from December 2021 to August 2022. A simple random sampling technique was followed to select respondents. Multivariable logistic regression model analysis was conducted using STATA version 14. The overall level of knowledge, attitude, and prevention practice for the major zoonotic disease was 52.5%, 68.6%, and 39.4%, respectively. Rabies, tuberculosis, taeniasis, anthrax, and brucellosis were the major zoonotic diseases selected by respondents in the study areas. The age of respondents, training status, educational status, and farm location were significantly (P <0.05) associated with the level of knowledge and prevention practice against zoonotic diseases. This study revealed that the level of knowledge, attitude, and prevention practices for major zoonotic diseases in Bahir Dar City were relatively poor. Therefore, a concerted effort among various government and nongovernment stakeholders, including veterinarians, public health officials, and environmental experts, is needed to create and raise awareness among livestock producers about the transmission and control methods and the economic and public health importance of zoonotic diseases.

Network visualization of genes involved in skeletal muscle myogenesis in livestock animals

BackgroundMuscle growth post-birth relies on muscle fiber number and size. Myofibre number, metabolic and contractile capacities are established pre-birth during prenatal myogenesis. The aim of this study was to identify genes involved in skeletal muscle development in cattle, sheep, and pigs - livestock.ResultsThe cattle analysis showed significant differences in 5043 genes during the 135–280 dpc period. In sheep, 444 genes differed significantly during the 70–120 dpc period. Pigs had 905 significantly different genes for the 63–91 dpc period.The biological processes and KEGG pathway enrichment results in each species individually indicated that DEGs in cattle were significantly enriched in regulation of cell proliferation, cell division, focal adhesion, ECM-receptor interaction, and signaling pathways (PI3K-Akt, PPAR, MAPK, AMPK, Ras, Rap1); in sheep - positive regulation of fibroblast proliferation, negative regulation of endothelial cell proliferation, focal adhesion, ECM-receptor interaction, insulin resistance, and signaling pathways (PI3K-Akt, HIF-1, prolactin, Rap1, PPAR); in pigs - regulation of striated muscle tissue development, collagen fibril organization, positive regulation of insulin secretion, focal adhesion, ECM-receptor interaction, and signaling pathways (PPAR, FoxO, HIF-1, AMPK). Among the DEGs common for studied animal species, 45 common genes were identified. Based on these, a protein-protein interaction network was created and three significant modules critical for skeletal muscle myogenesis were found, with the most significant module A containing four recognized hub genes - EGFR, VEGFA, CDH1, and CAV1. Using the miRWALK and TF2DNA databases, miRNAs (bta-miR-2374 and bta-miR-744) and transcription factors (CEBPB, KLF15, RELA, ZNF143, ZBTB48, and REST) associated with hub genes were detected. Analysis of GO term and KEGG pathways showed that such processes are related to myogenesis and associated with module A: positive regulation of MAP kinase activity, vascular endothelial growth factor receptor, insulin-like growth factor binding, focal adhesion, and signaling pathways (PI3K-Akt, HIF-1, Rap1, Ras, MAPK).ConclusionsThe identified genes, common to the prenatal developmental period of skeletal muscle in livestock, are critical for later muscle development, including its growth by hypertrophy. They regulate valuable economic characteristics. Enhancing and breeding animals according to the recognized genes seems essential for breeders to achieve superior gains in high-quality muscle mass.

Comparative structure activity and target exploration of 1,2-diphenylethynes in Haemonchus contortus and Caenorhabditis elegans

Infections and diseases caused by parasitic nematodes have a major adverse impact on the health and productivity of animals and humans worldwide. The control of these parasites often relies heavily on the treatment with commercially available chemical compounds (anthelmintics). However, the excessive or uncontrolled use of these compounds in livestock animals has led to major challenges linked to drug resistance in nematodes. Therefore, there is a need to develop new anthelmintics with novel mechanism(s) of action. Recently, we identified a small molecule, designated UMW-9729, with nematocidal activity against the free-living model organism Caenorhabditis elegans. Here, we evaluated UMW-9729's potential as an anthelmintic in a structure-activity relationship (SAR) study in C. elegans and the highly pathogenic, blood-feeding Haemonchus contortus (barber's pole worm), and explored the compound-target relationship using thermal proteome profiling (TPP). First, we synthesised and tested 25 analogues of UMW-9729 for their nematocidal activity in both H. contortus (larvae and adults) and C. elegans (young adults), establishing a preliminary nematocidal pharmacophore for both species. We identified several compounds with marked activity against either H. contortus or C. elegans which had greater efficacy than UMW-9729, and found a significant divergence in compound bioactivity between these two nematode species. We also identified a UMW-9729 analogue, designated 25, that moderately inhibited the motility of adult female H. contortus in vitro. Subsequently, we inferred three H. contortus proteins (HCON_00134350, HCON_00021470 and HCON_00099760) and five C. elegans proteins (F30A10.9, F15B9.8, B0361.6, DNC-4 and UNC-11) that interacted directly with UMW-9729; however, no conserved protein target was shared between the two nematode species. Future work aims to extend the SAR investigation in these and other parasitic nematode species, and validate individual proteins identified here as possible targets of UMW-9729. Overall, the present study evaluates this anthelmintic candidate and highlights some challenges associated with early anthelmintic investigation.

Development strategy of non-GMO organism for increased hemoproteins in Corynebacterium glutamicum: a growth-acceleration-targeted evolution

Heme, found in hemoproteins, is a valuable source of iron, an essential mineral. The need for an alternative hemoprotein source has emerged due to the inherent risks of large-scale livestock farming and animal proteins. Corynebacterium glutamicum, regarded for Qualified Presumption of Safety or Generally Recognized as Safe, can biosynthesize hemoproteins. C. glutamicum single-cell protein (SCP) can be a valuable alternative hemoprotein for supplying heme iron without adversely affecting blood fat levels. We constructed the chemostat culture system to increase hemoprotein content in C. glutamicum SCP. Through adaptive evolution, hemoprotein levels could be naturally increased to address oxidative stress resulting from enhanced growth rate. In addition, we used several specific plasmids containing growth-accelerating genes and the hemA promoter to expedite the evolutionary process. Following chemostat culture for 15 days, the plasmid in selected descendants was cured. The evolved strains showed improved specific growth rates from 0.59 h−1 to 0.62 h−1, 20% enhanced resistance to oxidative stress, and increased heme concentration from 12.95 µg/g-DCW to 14.22–15.24 µg/g-DCW. Notably, the putative peptidyl-tRNA hydrolase-based evolved strain manifested the most significant increase (30%) of hemoproteins. This is the first report presenting the potential of a growth-acceleration-targeted evolution (GATE) strategy for developing non-GMO industrial strains with increased bio-product productivity.

Determinants of animal disease and nontherapeutic antibiotic use on smallholder livestock farms.

Reducing nontherapeutic antibiotic use (ABU) in livestock animals has been identified as an important way of curbing the growth of antimicrobial resistance (AMR). However, nontherapeutic ABU may be important for managing animal disease. In order to reduce nontherapeutic ABU, farmers may need to implement other complementary interventions to safeguard animal health and minimize risk. We should therefore investigate if nontherapeutic ABU is associated with better animal health outcomes before advocating to reduce it. We should also investigate non-antibiotic factors which protect animal health and can make nontherapeutic use less necessary, as well as factors which can encourage farmers to improve their antibiotic stewardship. The study investigated these questions using data from the AMUSE survey, which is designed to evaluate knowledge, attitudes and practices relating to AMR in smallholder livestock farms. The sample included 320 animal herds from 216 smallholder livestock farms in Burkina Faso, with livestock species including poultry, small ruminants, and cattle. The determinants of the occurrence of animal disease and nontherapeutic ABU were investigated using binary logistic regression. Results revealed that nontherapeutic ABU was positively associated with animal disease, although the potential reverse causality of this relationship should be investigated further. Going primarily to a public veterinarian for animal health services, and having a higher level of formal education, were negatively associated with the occurrence of disease. Going primarily to a community animal health worker was positively associated with using antibiotics nontherapeutically, whereas going primarily to a public veterinarian was negatively associated with this outcome. Having an animal health professional (of any kind) provide diagnosis and treatment was positively associated with nontherapeutic antibiotic use for goats and sheep. These findings support the expansion of education access and public veterinary services as a way to encourage better antibiotic stewardship while guarding against any animal health risks associated with doing so. They also highlight that animal health professionals other than public veterinarians may prioritize animal health outcomes over antibiotic stewardship goals.

Towards true prices in food retailing: the value added tax as an instrument transforming agri-food systems

AbstractCurrent crises (i.e., climate crisis, COVID-19 pandemic, Russian invasion of Ukraine, and the resulting energy and food shortages) indicate the need for robust, and sustainable supply chains with regional food production and farmland to secure food supply in the European Union (EU). Recent research shows that organic food is more resilient to supply chain disruptions and price fluctuations. In this context, we examine an approach for the sustainable and resilient transformation of agri-food networks: can an adaptation of value added tax (VAT) levels work as a financial incentive to amplify resilient agricultural practices and sustainable dietary patterns? Within the setting of the amendment of the European framework directive on the use of VAT in 2022, we model the effects of adapting the current German VAT system by (1) reducing VAT on organic vegetarian food to 0% and (2) raising VAT on conventional meat and fish to 19%. Based on historical data on organic sales shares and price elasticities, we project sales shares differentiated by product group for each scenario. Then, we calculate expected tax revenues, changes in consumption patterns, and arising total external climate costs in Germany for both scenarios. Our results show that the overall consumption share of organic food would increase by 21.83% due to the modeled VAT reform compared to the status quo. Despite the VAT reduction to 0% on organic vegetarian products, the measure would yield €2.04 billion in extra tax revenues in Germany per year due to the increased taxation on conventional meat products. We find that annual environmental costs of €5.31 billion can be avoided as a result of lower external climate costs of organic and vegetarian food. Therefore, adjusting VAT rates in the food market can be a political instrument to drive organic food consumption and reduce animal livestock. This supports re-territorialization of agriculture and a more sustainable and resilient European food supply.

Lightweight Small-Tailed Han Sheep Facial Recognition Based on Improved SSD Algorithm

We propose a lightweight detection algorithm based on the Single Shot MultiBox Detector (SSD) algorithm in order to facilitate sheep management and to realize sheep facial identification, and we take the self-constructed dataset as the research object. First, the SSD replaces the VGG16 backbone network with MobileNetv3, a lightweight neural network, to create a hybrid model that is much smaller. Second, the ECA attention mechanism is incorporated into the backend of the 72 × 160 bottleneck layer. Finally, the SmoothL1 loss function is substituted with the BalancedL1 loss function. The optimized model’s size decreases significantly from the original SSD’s 132 MB to just 22.4 MB. It achieves a mean average precision of 83.47% and maintains an average frame rate of 68.53 frames per second. Compared to the basic SSD model, the mean average precision has increased by 3.25 percentage points, the model size has decreased by 109.6 MB, and the detection speed has improved by 9.55 frames per second. In comparative experiments using the same dataset with different object detection models, the proposed model outperforms the SSD, Faster R-CNN, Retinanet, and CenterNet in terms of mean average precision, with improvements of 3.25 percentage points, 4.71 percentage points, 2.38 percentage points, and 8.13 percentage points, respectively. The detection speed has shown significant improvements, increasing by 9.55, 58.55, 53.1, and 12.37 frames per second, respectively. The improved model presented in this paper significantly reduces the model’s size and computational requirements while maintaining an excellent performance. This provides a valuable reference for the digitalization of animal husbandry and livestock farming.

Pigs lacking the SRCR5 domain of CD163 protein demonstrate heritable resistance to the PRRS virus and no changes in animal performance from birth to maturity.

Porcine reproductive and respiratory syndrome (PRRS) is one of the world's most persistent viral pig diseases, with a significant economic impact on the pig industry. PRRS affects pigs of all ages, causing late-term abortions and stillbirths in sows, respiratory disease in piglets, and increased susceptibility to secondary bacterial infection with a high mortality rate. PRRS disease is caused by a positive single-stranded RNA PRRS virus (PRRSV), which has a narrow host-cell tropism limited to monocyte-macrophage lineage cells. Several studies demonstrated that the removal of CD163 protein or, as a minimum, its scavenger receptor cysteine-rich domain 5 (SRCR5) precludes the viral genome release, conferring resistance to PRRSV in live animals. Today, very limited information exists about the impact of such edits on animal performance from birth to maturity in pigs. Using CRISPR-Cas9 with dual-guide RNAs and non-homologous end joining (NHEJ), first-generation (E0) pigs were produced with a deletion of exon 7 in the CD163 gene. The selected pigs were bred to produce the next three generations of pigs to establish multiple lines of pigs homozygous for the edited allele, thereby confirming that the CD163 gene with removed exon 7 was stable during multiple breeding cycles. The pigs were evaluated relative to non-edited pigs from birth to maturity, including any potential changes in meat composition and resistance to PRRSV. This study demonstrates that removing the SRCR5 domain from the CD163 protein confers resistance to PRRSV and, relative to unedited pigs, resulted in no detected differences in meat composition and no changes in the growth rate, health, and ability to farrow. Together, these results support the targeted use of gene editing in livestock animals to address significant diseases without adversely impacting the health and well-being of the animals or the food products derived from them.

Genetic characterization of schistosome species from cattle in Côte d’Ivoire

BackgroundSchistosomiasis is a water-based parasitic disease that affects humans, livestock and wild animals. While considerable resources are dedicated to the surveillance, disease mapping, control and elimination of human schistosomiasis, this is not the case for livestock schistosomiasis. Indeed, there are important data and knowledge gaps concerning the species present, population genetic diversity, infection prevalence, morbidity and economic impact. This study aimed to identify circulating schistosome species in cattle across Côte d’Ivoire and to investigate their population diversity and structuring.MethodsOverall, 400 adult schistosomes were collected from slaughtered cattle at six sites across Côte d’Ivoire. Additionally, 114 miracidia were collected from live cattle at one site: Ferkessédougou, in the northern part of Côte d’Ivoire. DNA from all specimens was extracted and the cox1 and ITS1/2 regions amplified and analysed to confirm species. The genetic diversity and structuring of the schistosome populations were investigated using 12 microsatellite markers.ResultsAll adult schistosomes and miracidia presented Schistosoma bovis mitochondrial cox1 profile. Nuclear ITS1/2 data were obtained from 101 adult schistosomes and four miracidia, all of which presented an S. bovis profile. Genetic diversity indices revealed a deficiency of heterozygotes and signals of inbreeding across all sites, while structure analyses displayed little geographic structuring and differentiation. Cattle in Côte d’Ivoire thus appear to be mono-species infected with S. bovis. Hybrids of Schistosoma haematobium × S. bovis have not been identified in this study. Cattle schistosomes appear to be panmictic across the country.ConclusionsOur results contribute to a deeper understanding of schistosome populations in Ivorian cattle and emphasize a One Health approach of joint human and animal surveillance and prevention and control programmes for schistosomiasis.Graphical

Development and validation of a random forest algorithm for source attribution of animal and human Salmonella Typhimurium and monophasic variants of S. Typhimurium isolates in England and Wales utilising whole genome sequencing data.

Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Salmonella Typhimurium (S. Typhimurium) and monophasic variants (monophasic S. Typhimurium) isolates. To this end, we utilised single nucleotide polymorphism diversity in the core genome MLST alleles obtained from 1,061 laboratory-confirmed human and animal S. Typhimurium and monophasic S. Typhimurium isolates as inputs into a RF model. The algorithm was used for supervised learning to classify 399 animal S. Typhimurium and monophasic S. Typhimurium isolates into one of eight distinct primary source classes comprising common livestock and pet animal species: cattle, pigs, sheep, other mammals (pets: mostly dogs and horses), broilers, layers, turkeys, and game birds (pheasants, quail, and pigeons). When applied to the training set animal isolates, model accuracy was 0.929 and kappa 0.905, whereas for the test set animal isolates, for which the primary source class information was withheld from the model, the accuracy was 0.779 and kappa 0.700. Subsequently, the model was applied to assign 662 human clinical cases to the eight primary source classes. In the dataset, 60/399 (15.0%) of the animal and 141/662 (21.3%) of the human isolates were associated with a known outbreak of S. Typhimurium definitive type (DT) 104. All but two of the 141 DT104 outbreak linked human isolates were correctly attributed by the model to the primary source classes identified as the origin of the DT104 outbreak. A model that was run without the clonal DT104 animal isolates produced largely congruent outputs (training set accuracy 0.989 and kappa 0.985; test set accuracy 0.781 and kappa 0.663). Overall, our results show that RF offers considerable promise as a suitable methodology for epidemiological tracking and source attribution for foodborne pathogens.

Testing of the supramolecular complex of ivermectin Aniverm-2.0% against parasitosis on various types of livestock animals

The purpose of the research is to obtain and test a complex drug Aniverm-2.0% based on the ivermectin substance by free feeding in a mixture with concentrated feed against parasitosis of cattle, sheep, and horses.Materials and methods. Aniverm-2.0% obtained by mechanochemical technology was tested on a farm in the Shatoy Region, the Chechen Republic, on 900 sheep, 180 cattle and 156 horses in March-April 2023. To determine the infection rate, coproovoscopic examinations were conducted on 80 samples from sheep, 20 samples from young cattle and 30 samples from horses using the Fulleborn’s flotation method with a saturated sodium chloride solution. Sheep were dewormed using a group method. The drug was mixed with feed per 0.3 mg/kg for the AS or 60 mg for the drug per animal. The young cattle were kept by tie-up housing and therefore they were given Aniverm-2.0% once at a dose of 0.2 mg/kg for the AS individually in a mixture with feed. The horses were given the drug in a group method at a dose of 0.2 mg/kg for the AS or 1.5 mg/kg for the drug. Fecal samples from all animals were examined before and 2 weeks after the drug.Results and discussion. A 100% rate of infection of the sheep by gastrointestinal nematodes (Strongylata, Nematodirus spp., Trichocephalus spp.) was determined with an average number of eggs 633.3 in 1 g of feces. In 20 fecal samples from the young cattle, 16 were found to have Strongylata eggs (prevalence = 80.0%) with 222.2–280.5 specimens of Strongylata eggs found in 1 g of feces. Strongylata eggs were found in all 30 examined fecal samples from the horses, on average, 253.3 specimens/g of feces (100%). At 2 weeks after treatment, nematode eggs were found in three out of 80 examined fecal samples from the sheep, which can be explained that the sheep did not eat the appropriate dose of the drug. The drug efficacy was determined to be 99.7%. One hundred percent efficacy of the drug was obtained on young cattle and horses.

Prevalence and transmission of extensively drug-resistant Salmonella enterica serovar Kentucky ST198 based on whole-genome sequence in an intensive laying hen farm in Jiangsu, China

Salmonella, which is widely distributed in nature, is an important zoonotic pathogen affecting humans, livestock, and other animals. Salmonella infection not only hinders the development of livestock and poultry-related industries but also poses a great threat to human health. In this study, we collected 1,537 samples including weak chicks, dead embryos, fecal samples and environmental samples from 2020 to 2023 (for a period of 1 to 2 months per year) to keep a long-term monitor the prevalence of Salmonella in an intensive laying hen farm, 105 Salmonella strains were isolated with an isolation rate of 6.83% (105/1,537). It revealed a significant decrease in prevalence rates of Salmonella over time (P < 0.001). Before 2020, the predominant serotype was S. Enteritidis. S. Kentucky was first detected in November 2020 and its proportion was gradually found to exceed that of S. Enteritidis since then. S. Kentucky isolates were distributed in various links of the four regions in the poultry farm. A total of 55 S. Kentucky strains, were assigned to ST198 based on whole genome sequencing. Among them, 54 strains were resistant to 12 to 16 antibiotics, indicating that they were extensively drug-resistant (XDR). Seventeen antimicrobial resistance genes were detected in 55 S. Kentucky isolates. For most of these isolates, antibiotic resistance phenotypes were concordant with their genotypes. All S. Kentucky strains isolated from this farm in 2020 to 2023 showed a high similarity based on their core-genome SNP-based phylogeny. The traceability analysis revealed that S. Kentucky was introduced to the farm through newly purchased flocks. The long-term existence of XDR S. Kentucky ST198 poses a substantial risk because of the multiage management and circulation of workers in this poultry farm. Thus, this study is the first to report extensively drug-resistant S. Kentucky ST198 detected in this intensive poultry farm in China.