Poultry Science

The respiratory microbiome plays important roles in poultry health, immune regulation, and pathogen resistance, yet its development throughout the broiler production cycle remains poorly understood. This study investigated temporal changes in the tracheal microbiome of broiler chickens across production phases. Tracheal samples were collected during the starter (day 12), grower (day 21), early finisher (day 26), and late finisher (day 35) phases and analyzed using 16S ribosomal RNA gene sequencing. Tracheal microbial richness, diversity, community structure, and taxonomic composition changed significantly across broiler production stages, including starter, grower, early finisher, and late finisher feeding phases. Alpha diversity increased progressively throughout production, with significant increases in richness, diversity, and phylogenetic diversity during later stages. Beta diversity analysis revealed distinct microbial communities associated with each production phase, with starter-phase samples clearly separated from later phases. Taxonomic profiling showed dominance of Proteobacteria during the starter and grower phases, with enrichment of Methylobacterium-Methylorubrum and Pseudomonas during the starter phase and of Escherichia-Shigella during the grower phase. In contrast, the finisher phases exhibited reduced Proteobacteria abundance and increased Firmicutes and Actinobacteriota, including Lactobacillus, Ligilactobacillus, Faecalibacterium, Streptococcus, Staphylococcus, Romboutsia, and Corynebacterium. Overall, the tracheal microbiome underwent progressive maturation, shifting from a Proteobacteria-dominated community to a more diverse, complex, Firmicutes-rich ecosystem. These findings provide new insights into the development of the respiratory microbiome in broiler chickens and may support strategies to improve poultry respiratory health. Because dietary transitions occurred concurrently with age progression, the observed microbiome shifts should be interpreted as production-stage-associated changes rather than diet-specific effects.

The relationship between Campylobacter levels in broiler caeca and on carcass skin is central to quantitative microbial risk assessment along the poultry production chain, underpinning modelling of intervention impacts, including EFSA assessments of the public health impact of control measures. However, this relationship is typically inferred from monitoring data generated under sampling designs that do not preserve pairing between specimens and may involve pooling. In this study, we used a simulation framework to evaluate whether commonly used sampling strategies allow reliable recovery of the caecal-skin relationship. A simulated broiler population was generated, assigning caecal and skin loads to individual birds based on a specified linear relationship. Sampling was conducted under paired and unpaired designs, with and without pooling, reflecting approaches used in surveillance programmes and in policy-oriented models. Regression models were fitted to sampled data across 1,000 simulations for a range of assumed slopes. Under paired sampling, estimated slopes closely matched the true relationship across most scenarios. In contrast, unpaired sampling consistently failed to recover the association, with estimated slopes centred around zero regardless of the true slope. These findings were robust to variation in within-flock prevalence, residual error, and intercept. The results show that sampling design fundamentally affects identifiability of relationships between stages of the production chain. This has implications for interpretation of parameters derived from monitoring data and used in quantitative Campylobacter risk assessments informing policy. Parameters derived from unpaired and pooled monitoring data should therefore be interpreted with caution when used to support risk assessment and decision-making. Campylobacter; broiler chickens; sampling strategy; unpaired sampling; carcass contamination; quantitative microbial risk assessment; simulation.

Salmonellosis continues to be one of the most important causes of food-borne illness in the U.S. An additional concern with this bacterial pathogen is that infections with multiple-antibiotic-resistant Salmonella strains are becoming untreatable infectious diseases. Poultry meat and eggs are major sources of Salmonella food-borne illness, due to carriage of these bacterial pathogens in the intestinal microbiome of chickens. A food safety priority, as stated by the USDA, is a significant reduction in carriage of pathogenic Salmonella species in poultry which would significantly improve food safety and reduce cases of human salmonellosis contracted from consumption of contaminated poultry. While this goal has been a priority for many years, basic research and animal management efforts have not achieved significant control of Salmonella carriage. This study represents an alternative approach to reduce or eliminate carriage of Salmonella in poultry flocks. We characterized a type 1 fimbrial allele of Salmonella that confers high levels of adherence to various host cells. We then engineered an E. coli Nissle 1917 probiotic strain that expresses this Salmonella adherence factor at high levels. The E. coli Nissle 1917 is used as the scaffold strain for this work since this E. coli strain has received the FDA designation of Generally Regarded As Safe (GRAS) and has been used for many years as a probiotic to treat human intestinal disorders. Our E. coli Nissle strain was engineered to use an in vivo selection system for a plasmid carrying the cloned Salmonella type 1 fimbrial genes, so that the strain can be used as a probiotic without any antibiotic resistance-encoding genes requiring antibiotic selection for maintenance of the desired phenotype. Our probiotic strain displays high levels of adherence to host cells, in fact higher levels of adherence than a Salmonella strain carrying the same type 1 fimbrial genes. We demonstrate that the probiotic strain significantly outcompetes pathogenic Salmonella strains for adherence to tissue culture cells and in vivo experimental challenges revealed that the probiotic strain mediates a significant exclusion of Salmonella from the intestines of broilers, layers, and turkeys.

BackgroundRaw broiler meat products are highly perishable, and microbial activity is the main factor limiting their shelf lives. The spoilage microbiomes of broiler meat products have been studied mainly using traditional culturing methods and 16S rRNA gene amplicon sequencing, neither of which can show the activity of whole microbiome. Previous metatranscriptomic research of broiler spoilage has also remained limited to specific spoilage organisms rather than entire microbiomes. ResultsOur longitudinal study of broiler meat spoilage discovered the successions of active bacterial microbiomes and metabolic pathway activities of spoilers at 4{degrees}C and 6{degrees}C. Samples taken daily were subjected to metatranscriptomic analyses in combination with non-targeted metabolomic, traditional microbiology, and sensory analyses until advanced spoilage took place. Carnobacterium divergens, Carnobacterium maltaromaticum and Vagococcus proximus were the most active species at both temperatures. Carnobacteria are known poultry spoilers whereas Vagococcus proximus, a species recently described, played an unexpected active role in the microbiome. It became dominant in samples stored at 6{degrees}C and its activity increased also at 4{degrees}C after the use-by date. Central carbohydrate metabolism was the most common KEGG orthology pathway module of the microbiome at both temperatures. C. divergens and C. maltaromaticum showed stable metabolic profiles during the spoilage process, whereas V. proximus displayed a shift from high ATP synthesis activity to increased fatty acid and carbohydrate metabolism when spoilage advanced in samples stored at 4{degrees}C. Non-targeted metabolomics showed similar metabolomic trends across both temperatures. At 6{degrees}C, time-dependent changes were generally more pronounced, and the spoilage markers tyramine and spermidine showed greater accumulation. ConclusionsAs expected, the rate of spoilage is higher at 6 than 4{degrees}C, however we did not anticipate a similar overall trajectory of the spoilage processes. Our results link V. proximus as a key active spoiler in broiler meat and demonstrate the efficacy of using RNA-seq together with metabolomics to decode the function of a meat spoilage microbiome. This demonstrates that spoilage microbiomes consist of active species we have been neglecting due to the technological limitations of the standard methods. Future studies targeting to the metabolism and detecting of Vagococcus are warranted.

Across the United States, backyard poultry (BYP) are becoming increasingly popular as a food source as well as pets. Unfortunately, they have also been a source of annual human salmonellosis outbreaks for over a decade. Previous CDC analyses suggest baby poultry are the main source of live poultry-associated outbreaks as opposed to adult birds. However, there are few data on the frequency of pathogens, such as Salmonella enterica, in baby poultry sold to the BYP market. Further, there is a lack of data on the serovars and antimicrobial resistance (AMR) rates in these baby poultry. We collected 643 soiled bedding and shipping box samples from agricultural supply stores primarily located in Vermont. S. enterica was detected in 23.5% (151/643) of samples, with the highest rates of detection in 2021-2022. Rates of S. enterica varied by species. Turkey poult bedding samples had the highest rates of S. enterica (44.4%; 8/18), while laying chick bedding samples had the lowest (19.4%; 68/350). Meat chick bedding samples had an intermediate rate, at 36% (32/89). The most common serovar detected was Salmonella Enteritidis, which represented 51.2% (64/125) of sequenced isolates. AMR genes or AMR-associated point mutations were detected in 21.6% (27/125) of samples, but only in non-Enteritidis serovars. These data indicate that baby poultry intended for the BYP market pose a substantial risk of salmonellosis to consumers.

Dietary protein restriction challenges the allocation of amino acids to growth and other physiological functions and therefore requires coordinated metabolic adaptation. Domestic pigs provide an informative system in which to study such responses, because nitrogen retention directly affects lean growth and can be quantified accurately under controlled feeding and housing conditions. Under reduced-protein diets, pigs differ in how effectively they retain nitrogen, and this variation has a genetic basis, making them well suited to investigate the molecular regulation of nitrogen use efficiency (NUE). Here, we characterise differential gene expression and enriched pathways in liver and skeletal muscle of more than 80 pigs with two divergent NUE phenotypes (high and low) maintained under the same protein-reduced, ad libitum dietary conditions. The two NUE phenotypes were clearly distinct at the transcriptomic level, with 177 differentially expressed genes in the liver and 133 in the muscle. In the liver, differential expression and enrichment analyses indicate reduced amino acid catabolism, lower inflammatory and detoxification activity, and a metabolic state that favours lipid processing and insulin-related regulation over the use of amino acids as energy sources. In skeletal muscle, they point to reduced lipid uptake, lower reliance on amino acid oxidation, and a greater emphasis on protein synthesis, translational regulation, mitochondrial energy metabolism, and growth-related processes. These gene-level patterns were supported and extended by pathway and gene-set enrichment analyses. Together, the results suggest that high and low-NUE pigs differ through coordinated, tissue-specific molecular adaptations. Overall, variation in NUE appears to reflect coordinated, tissue-specific differences in how nutrients are allocated between energy use, storage, and lean tissue growth.

The gut microbiota is crucial for immune development and overall health in chickens. In commercial production, birds routinely receive multiple vaccines during early life. While individual vaccines are known to affect microbial composition, the impact of complex, multi-vaccine programs, as used in the poultry industry, is not well understood. This longitudinal study examined the impact of multiple live and inactivated vaccines, given at commercially relevant times from an early age, on gut microbial diversity and composition in layer chickens. We characterised microbiota profiles using 16S rRNA gene sequencing at pre- and post-vaccination timepoints across different vaccine groups. Overall, microbial diversity remained stable across most vaccines, indicating strong resilience of the gut microbiota to repeated immunological interventions. Differential abundance analyses identified changes in selected bacterial taxa following vaccination, with responses varying among vaccine groups. Notably, these changes were not sustained, as the gut microbial community returned to a stable state after the vaccination schedule. These findings underscore the robustness of the chicken gut ecosystem and lay a foundation for future research into microbiome-vaccine interactions and their implications for poultry health, immunity, and production efficiency.

Colibacillosis, caused by Avian Pathogenic Escherichia coli (APEC), result in substantial economic losses in global poultry production. The emergence of multidrug-resistant (MDR) APEC poses zoonotic risks through horizontal transfer of antimicrobial resistance (AMR) genes. Bacteriophage therapy emerges as a safe alternative to antibiotherapy; however, comprehensive characterization of phages targeting MDR-APEC from diverse geographical regions remains limited. We isolated five lytic bacteriophages from poultry fecal samples collected from five Indian states and characterized them through morphological analysis, physiological stability testing, whole-genome sequencing, and in vivo efficacy assessment. Host range was determined against APEC isolates, and therapeutic potential was validated in Galleria mellonella infection model. All five phages showed Myovirus-like morphology and stability across physiologically relevant temperatures (up to 55-70{degrees}C) and pH conditions (3-11). Their genome size ranges from 170 to 356 kb, belonging to three distinct genera; Dhakavirus, Gaprivervirus, and Asteriusvirus. Genomic analysis confirmed absence of antimicrobial resistance, virulence, toxin, or lysogeny genes. 51 APEC strains were isolated, of which 23 (45.1%) were MDR. Individual phages lysed 37-51% of tested APEC and 17-39% of MDR strains. Three Escherichia phages (fBSZT1, fUAMT1, fPKPT2) significantly improved larval survival to 60-80% at MOI 10 in G. mellonella infection models compared to untreated controls. This study establishes a well-characterized phage bank targeting MDR-APEC strains, providing foundation for developing phage-based interventions to reduce antibiotic dependency and mitigate AMR transmission risks under One Health framework.

Gastropods are a highly diverse and often overlooked taxonomic group of significant ecological and economic importance. Some terrestrial gastropods are critical pests of commercial agriculture and home gardens worldwide. Malacopathogenic nematodes offer an effective biological control method of managing pest slugs and snails as a natural enemy. Pellioditis (syn. Phasmarhabditis) hermaphrodita and Pellioditis (syn. Phasmarhabditis) californica are two species of biocontrol nematodes that have been commercialized, sold as Nemaslug(R) and Nemaslug(R) 2.0 respectively on three continents. Although there is interest in bringing Nemaslug(R) products to the US, they are currently not permitted due to limited knowledge on their North American distribution and effects on non-target and native species. In this study, we investigated the impact of P. hermaphrodita and P. californica on Ariolimax columbianus across two slug-host life stages, in laboratory infectivity assays. The objectives were to 1. determine whether P. hermaphrodita and P. californica nematodes impact survival of A. columbianus, and 2. evaluate whether there are differential effects on survival in juvenile and adult life stages of A. columbianus, in laboratory infectivity trials. We found that P. hermaphrodita caused significant mortality in A. columbianus with 100% mortality observed in both juvenile and adult slug hosts. The P. californica treatment had significant effects on the juvenile A. columbianus group only, with 80% mortality. By contrast, only 16% of unexposed control juveniles and 4% of control adult slugs died during the experiment. These results indicate that P. hermaphrodita and P. californica are lethal to the native, non-target Pacific banana slug (A. columbianus) under laboratory conditions, with mortality differing between juvenile and adult host life stages. Given the ecological importance of A. columbianus, these findings raise concerns for potential non-target effects of P. californica and P. hermaphrodita on terrestrial gastropod communities and emphasize the need for testing biocontrol agents against multiple life stages.

The recent shift in Bangladesh from tradition backyard rearing system to modern commercial layer farming has made the birds immune to infectious diseases. Pediculosis, however, continues to pose a challenge in modern production system due to its invasive nature, often going unnoticed and neglected as it is typically non-lethal, yet capable of causing significant production losses. Lice infestation is a persistent threat in poultry production; however, its implications in battery-caged commercial layer hens in Bangladesh remain insufficiently characterized. The study aimed to identify the causative louse species and evaluate its associations with clinical pathology, hematological alteration and productive performance in 30 white-feathered (15 infested + 15 non-infested) and 30 brown-feathered (15 infested + 15 non-infested) laying birds from two commercial farms in Tangail. Morphological characterization confirmed the parasite as Menacanthus stamineus, distinguished by a dorsoventrally flattened body, parabolicallly rounded head wider than long, concealed club-shaped antennae, an oblong-oval abdomen with fine setae and three pairs of short legs each bearing paired claws. Infested birds exhibited consistent clinical pathology, including pale combs, petechial hemorrhages around the vent, severe feather damage with alopecic and exudative areas and incidence of irregular and broken-shelled eggs. Production performance analysis revealed significant reduction in hen-day egg production, egg weight, and feed intake, accompanied by significantly increased feed conversion ratios. Hematological evaluation demonstrated significantly reduced hemoglobin concentration, hematocrit and erythrocyte counts in infested hens, indicating mild anemia and compromised oxygen-carrying capacity. Collectively, pediculosis was strongly associated with lice-induced self-inflicted injury and cannibalism, systemic physiological stress, impaired erythropoiesis, reduced production efficiency and compromised welfare in caged laying hens. To best of our knowledge, it was the first integrative reports from Bangladesh documenting M. stramineus infestation in battery-caged commercial layer system with concurrent evidence of hematological disruption and measurable productivity losses, underscoring its epidemiological and economic significance and urgent need for targeted, evidence-based ectoparasite control strategies.

Many pathogens, both those with human spillover potential as well as avian-specific viruses, are maintained in wild bird populations. While routine surveillance for influenza A viruses (IAVs) is performed annually, surveillance for other pathogens is limited. Sampling of wild birds is time-consuming, labour-intensive, often limited in sample size, and involves handling of wild and potentially infected birds, posing an increased risk of direct exposure for personnel. Additional methods for surveillance are needed given these significant challenges. Longitudinal fecal and sediment sampling was performed at various sites in southern Manitoba, Canada, particularly focused in Winnipeg from May to October 2025. Sites were chosen based on the suitability of the area for waterfowl habitat, the presence of waterfowl in the area, as well as proximity to reported outbreaks of H5N1 influenza virus. Fecal and sediment samples were collected and screened for the presence of influenza A virus (IAV), Newcastle disease virus (NDV), avian reovirus (ARV), and avian poxvirus (APXV). In total, 782 combined fecal and sediment samples were collected. Of the 714 fecal samples, 34 tested positive for IAV RNA (4.8% prevalence). None of the IAV-positive fecal samples tested positive for H5 RNA. Of the 68 sediments, 15 were positive for IAV RNA (22.1% prevalence), four of which were positive for H5 RNA. NDV RNA positivity was low, with only four positive fecal samples (0.6% prevalence) that were all collected on the same day. ARV RNA positivity was also low, with five positive sediment samples (7.4% prevalence in sediment samples). None of the samples tested positive for APXV DNA. This study builds on previous work showing the utility of environmental sampling for a variety of avian and zoonotic pathogens using a One Health approach that is low-risk, efficient, and high-throughput.

ObjectiveStall housing of pregnant sows raises welfare concerns, whereas conventional group housing systems often reduce space efficiency. This study evaluated the effects of periodic group housing (PG) on reproductive performance and welfare compared with continuous stall housing (CS). MethodsSows in the CS group (n = 15) were continuously housed in stalls. In the PG group (n = 15), sows were housed in groups of three and allocated 1 day of group housing and 6 days of stall housing per week over 10 weeks. During group housing sessions, the sows had access to a group housing area containing sawdust. Behavioral observations and salivary cortisol measurements were conducted on the first day of the stall housing session in weeks 1, 6, and 10. Behavioral indices were expressed as proportions based on 90 sampling points recorded at 1-min intervals. ResultsThe number of stillbirths was significantly lower in the PG group than in the CS group (0.63 vs. 1.49 piglets per litter). whereas other reproductive outcomes, including total litter size and average birth weight, did not differ. In older parity sows, the PG treatment markedly increased the proportion of time spent lying, suggesting reduced discomfort associated with restricted movement. Furthermore, the proportion of exploratory behavior decreased markedly, and drinking behavior showed a decreasing trend across parity levels in the PG group, suggesting partial satisfaction of motivations for environmental exploration and oral manipulation. The proportion of oral abnormal behavior showed a pronounced interaction between housing treatment and experimental week, increasing from week 1 to week 6 in the PG group. Salivary cortisol concentrations did not differ between the groups. ConclusionPG may improve reproductive performance and partially satisfy the behavioral motivations restricted under continuous stall housing. This system may represent a practical alternative for improving animal welfare while minimizing economic losses.

The corticotropin-releasing factor (CRF) system bidirectionally interacts with cytokines and other immune-related components in mammals. However, the nature of these interactions remains poorly characterized in other vertebrates, including teleost fishes. To gain insight into the relationship between immune responses and the CRF system in teleosts, we explored how CRF system components were transcriptionally regulated in immune organs of rainbow trout (Oncorhynchus mykiss). We first characterized the CRF system in the spleen and head kidney--two primary immune organs in teleosts--and found that many CRF system components were present in both tissues, but splenic expression was consistently greater. Changes in the abundance of splenic CRF system components following vaccination (which transiently stimulated inflammatory responses and cytokine production) indicated contrasting and time-dependent regulation of CRF receptor 1 (CRFR1; suppression) and CRFR2 (stimulation) activities in response to an inflammatory challenge. Using spleen explant cultures, we then evaluated whether these effects were mediated by either of nuclear factor kappa B (NF-{kappa}B; a pro-inflammatory transcription factor) or cortisol (an anti-inflammatory hormone). At baseline, cultured spleens increased cytokine production and exhibited transcriptional changes in CRF system components comparable to those observed following vaccination. Cortisol treatment and NF-{kappa}B inhibition both attenuated the rise in cytokine transcription; however, cortisol treatment generally affected transcripts influencing CRFR1 activity, while NF-{kappa}B inhibition reduced CRFR2 activity. Overall, our data provide novel insight into CRF system regulation in the spleen and suggest that cortisol and inflammatory cytokines differentially regulate CRFR1 and CRFR2 activity within this organ.

BackgroundSalmonella enterica is a major cause of foodborne and invasive infections worldwide. Increasing antimicrobial resistance and adaptation to diverse ecological niches require an improved understanding of the genetic and epigenetic diversity of circulating strains. This study investigated the genomic and epigenetic diversity of S. enterica isolates collected in Kazakhstan from clinical, animal, and environmental sources. MethodsWhole-genome sequencing was performed using the Illumina sequencing platform. Several selected strains were additionally sequenced using PacBio SMRT technology for DNA methylation profiling. Genome assembly, plasmid reconstruction, MLST genotyping, and analyses of virulence genes, antimicrobial resistance determinants, and genome methylation associated with restriction-modification (RM) systems and orphan methyltransferases were performed using established bioinformatics tools. ResultsThe ST11 genotype predominated among clinical isolates, but these strains formed distinct clusters differing in plasmid composition, virulence-associated genes, and resistance determinants. Most strains carried two large plasmids associated with environmental persistence and virulence, whereas the recent hospital isolate 19S, belonging to the ST11 group, carried two alternative plasmids enriched in virulence and antibiotic resistance genes. All genomes demonstrated conserved DAM-associated adenine methylation at GATC motifs, partial DCM-mediated cytosine methylation at CCWGG motifs, and widespread adenine methylation at CAGAG motifs linked to type III RM system. In contrast, the type I RM system present in the majority of sequenced strains was suppressed under laboratory growth conditions and remained active only in strain 19S, possibly due to mutations identified in the hsdM gene that may have released this methyltransferase from suppression. Novel epigenetic modification signals involving cytosine and guanine in replichore-biased tandem repeats were also identified. ConclusionsS. enterica strains circulating in Kazakhstan exhibit substantial genomic and epigenetic diversity associated with different survival and transmission strategies. DNA methylation profiling provided additional insights beyond conventional MLST genotyping and identified strain 19S as a promising model for future studies of epigenetic regulation in bacterial virulence and adaptation mediated through genomic DNA methylation.

BackgroundBeef feedlots are increasing concerns that antibiotic use in beef cattle selects for antibiotic resistance, but limitations of primary studies and previous syntheses make it difficult to confirm a consistent effect. We conducted a rigorous systematic review and meta-analysis to summarise: 1) the effect during and after antibiotic administration; 2) its moderation by time since administration started/ended. MethodsEligible studies longitudinally compared beef cattle administered antibiotics to those that were not, measuring resistance determinants in faeces and/or environments. Information sources included Web of Science, CAB Abstracts, and Medline (last searches: 05/03/25). Risk of bias was assessed using RoB 2 and ROBINS-I. Meta-analysis was conducted where feasible, using individual participant data where necessary. ResultsThe 33 included studies were mostly small trials of North American feedlot cattle, all with high risks of bias. Meta-analysis of 11 studies of tylosin, ceftiofur, and chlortetracycline indicated positive effects on absolute abundance of resistance both during (SMDH = 0.4; 95% CI = 0.11 to 0.69, p = <0.01) and after (SMDH = 0.52; 95% CI = 0.33 to 0.71, p = <0.01) antibiotic administration. Log-transformed time was positively associated with effect size during (Slope = 0.63; 95% CI = 0.1 to 1.16, p = 0.02), and negatively associated after (Slope = -0.65; 95% CI = -1.24 to -0.06, p = 0.03) DiscussionAvailable evidence indicates time-dependent selection for antibiotic resistance in beef cattle, warranting further regulation to limit human health risks. Simultaneously, uncertainty about precise effect sizes warrants further research. FundingBBSRC Registrationhttps://doi.org/10.17605/OSF.IO/RXQHT

Mycoplasma bovis is a minimal bacterium infecting cattle, which causes a wide variety of symptoms and is impacting dairy and beef producers worldwide. Part of the difficulty in research surrounding M. bovis, and other mycoplasmas, is the lack of efficient genome editing tools. As a proof of concept, we previously presented a transposon-based CRISPR-Base Editor system to introduce targeted mutations in M. bovis. In this work, the existing tool has been greatly improved: multi-loci targeting through addition of a second guide RNA; increased number of targetable loci by using an engineered Cas9 with AT-rich PAM specificity, and elimination of the CRISPR-Base Editor from the generated mutants through either transposon excision or use of a curable plasmid. We also propose a dedicated bioinformatic tool to identify target sequences in genes of a given genome. This software was applied to demonstrate the potential of our improved tools in M. bovis and other mycoplasmas of veterinary and human interest that currently lack genome editing methods.

Soil-transmitted helminth (STH) infections are a major public health burden, and there are programmes of mass drug administration that attempt to ameliorate the harm that they cause. There has been increasing use of genomics to study STH infections and other parasitic nematodes, with particular interest in whole genome sequencing (WGS). For such studies, samples are commonly stored frozen, but in settings where these infections are endemic this can be difficult, and so there would be advantages to having ambient temperature storage methods. We investigated two ambient temperature storage methods - FTA cards and DESS buffer - for infective larvae of the rat parasites Nippostrongylus brasiliensis and Strongyloides ratti, prior to DNA extraction and then WGS. Our results showed that for individual larvae stored on FTA cards or in DESS buffer, this resulted in a lower proportion of sequence reads that mapped to the reference genomes, compared to the frozen control samples. Generally, for individual larvae, DESS-storage resulted in better sequencing results than FTA-storage. However, for pools of 10 or 50 larvae, then these ambient temperature storage methods generally resulted in comparable sequence read mapping to the frozen control samples.

Staphylococcus aureus and Streptococcus pyogenes are major causative bacteria responsible for skin and soft-tissue infections (SSTIs) such as impetigo. Increasing resistance to commonly used topical antibiotics necessitates evaluation of newer agents for the treatment of skin infections. Ozenoxacin, a novel non-fluorinated topical quinolone, has shown promise, exhibiting potent activity against a wide range of pathogens, including methicillin-resistant Staphylococcus (MRSA) and Streptococcus pyogenes. The present study compared the in vitro activity of ozenoxacin and comparator agents against clinical isolates of Staphylococcus aureus and Streptococcus pyogenes from multiple sources including skin and soft-tissue, wound, abscess, and blood. Ozenoxacin was assessed for in vitro antimicrobial activity against 109 methicillin-susceptible (MSSA), methicillin-resistant S. aureus (MRSA), and 24 Streptococcus pyogenes isolates by broth microdilution method recommended by the Clinical and Laboratory Standards Institute (CLSI). Ozenoxacin demonstrated potent in-vitro activity against all 109 S. aureus (MIC50/90= 0.125/0.5 {micro}g/ml) and 24 S. pyogenes (MIC50/90= 0.015/0.03 {micro}g/ml) strains. In contrast, higher MICs were observed for fusidic acid and mupirocin among a subset of S. aureus isolates. A comparison of MIC90values demonstrated that ozenoxacin (0.5 {micro}g/ml) was more active against S. aureus isolates than 8 of the 9 comparator agents tested including vancomycin and linezolid (MIC90= 2 & 4 {micro}g/ml) respectively. In vitro studies of ozenoxacin showed potency against staphylococci and streptococci including resistant S. aureus strains. These findings support its role as an effective first-in-class quinolone topical therapeutic option in the management of various SSTIs.

Charrs (Salvelinus spp.) are strong candidates for cyclical feed-restriction strategies due to their documented exceptional ability to withstand and recover from feed resources scarcity during winter (Drouin-Johnson et al. 2026; Le Francois et al. 2023; Savoie et al. 2017). Dietary nucleotides (NT) are supplements used to improve growth and health in fish, yet their integration into feed-restriction programs to enhance growth recovery remains largely unexplored. The one-carbon (1C) metabolism offers a mechanistic framework to investigate these effects, as it relies on vitamin B status and supports methylation reactions central to biosynthesis and growth. A large-scale trial involving S. alpinus x S. fontinalis was conducted, comprising a 90-day fasting period followed by refeeding on a commercial feed with or without NT. Growth and feeding metrics were evaluated alongside key metabolites of 1C metabolism to assess adaptations to fasting-induced vitamin B deficiency and the role of NT in recovery. Starved fish lost 5.2 % of body mass (p < 0.05) but displayed accelerated growth upon refeeding, further enhanced by NT supplementation by 27.8 % (p < 0.05), forecasting full compensation after 125 days. Starvation increased homocysteine and decreased methionine concentrations (p < 0.05), while S-adenosylmethionine, S-adenosylhomocysteine, and formate showed only minor fluctuations. These patterns indicate moderate but reversible fluctuations of 1C metabolism. NT supplementation may exert a methyl-unit sparing effect during refeeding, potentially supporting anabolic recovery. This study uniquely combines commercial-scale growth trials and molecular analyses, providing new insights into a species-adapted feeding strategy that enhances growth recovery performances and metabolic resilience.

In 2020, highly pathogenic avian influenza (HPAI) isolates from clade 2.3.4.4b emerged in Europe and spread globally, including in bovine hosts in the USA. Viruses from this clade cause minimal disease in dairy cattle, characterized by decreased milk production but low mortality rates. Infections have also occurred in feline hosts. In contrast to cows, infection of cats (and closely related species, including skunks and foxes) can result in severe neurological signs and mortality. Documented feline H5N1 infections from clade 2.3.4.4.b have a mortality rate of approximately 80% following rapid onset of clinical signs. No antiviral compounds have been tested in an experimental feline model; however, anecdotal clinical evidence suggests early treatment with oseltamivir may improve outcomes in felines with HPAI. Here, we show the in vitro efficacy of several influenza inhibitors in feline glial astrocyte (PG-4) and kidney (CRFK) cell culture models using the clade 2.3.4.4.b virus Tx2/24 (H5N1). The neuraminidase inhibitor oseltamivir carboxylate did not effectively inhibit viral replication in either cell line. The cap-dependent endonuclease inhibitor baloxavir exhibited the strongest inhibition of this virus, with EC50 values of 30 nM in PG-4 and 1 M in CRFK cells. Amantadine and rimantadine, M2 ion channel inhibitors, were unable to completely inhibit viral replication in either cell line at any concentration utilized. The broad-spectrum nucleoside analog GS-441524 demonstrated little to no inhibition of viral replication in either cell line. Additionally, the mutagenic NHC analogs EIDD-1931 and EIDD-2801 successfully inhibited viral replication at the maximum tested concentration of 100 M but exhibited significant cytotoxicity. Our findings suggest that baloxavir should be considered by veterinary clinicians as the first-line drug of choice when presented with felines or other species infected with HPAI.