Non-typhoidal Salmonella enterica serovars are enteric pathogens in humans that can be acquired from poultry products. Salmonella colonisation in poultry is an important cause of economic losses. Due to challenges in controlling Salmonella in poultry and the emergence of well-adapted, antibiotic-resistant serovars, there is a need for innovative control strategies, such as vaccines. In this work, plants were used to produce conserved antigenic epitopes of Salmonella FepA, an outer membrane protein involved in iron uptake, genetically fused in tandem to self-assembling lumazine synthase from Brucella spp. (BLS). The recombinant proteins were purified, characterized, and their immunogenicity was assessed in chickens. Results indicated that the recombinant proteins assemble into decameric particles. These proteins elicit antigen-specific antibodies in chickens that bind to the Salmonella’s cell surface. These results demonstrate that the candidate vaccine has the potential to control Salmonella colonization in poultry, helping prevent food chain contamination.

Staphylococcus shinii is a recently proposed staphylococcal species identified in animal-associated microbiomes and fermented foods, with promising probiotic and biotechnological applications. However, its genomic diversity, functional traits and safety profile need to be well established. Here, we report the first recovery and genome sequencing of 41 S. shinii isolates from blueberry fruit washes and surrounding air. Phylogenomic analysis, including reference genomes, revealed at least 15 well-supported intra-species lineages (genomovars) defined by phylogenetic relationship and average nucleotide identity (>99.5% within genomovars; <99.5% between them). Pangenome analysis showed a highly conserved core genome comprising 83.3% of genes, alongside diverse accessory genes across genomovars. Core functions in S. shinii included carbohydrate metabolism, vitamin biosynthesis and short-chain fatty acid production, traits potentially linked to probiotic properties. Biosynthetic gene clusters for bioactive compounds were broadly conserved, although genes encoding ribosomally synthesized and post-translationally modified peptides varied among genomovars. About 10-18 antimicrobial resistance genes (ARGs) were identified per S. shinii genome, several of which were located on the chromosome. Phenotypic testing confirmed susceptibility to ciprofloxacin, gentamicin and ampicillin, while resistance to other antimicrobials varied and was often plasmid-associated. Resistance patterns differed across genomovars, emphasizing the need for intra-species resolution in risk assessment. Although major virulence factors listed in the Virulence Factor Database were absent, putative pathogenicity-related genes were found in the core genome using the Pathogen-Host Interaction Database. Their presence, along with ARGs, underscores the need for caution in clinical contexts. Nonetheless, the absence of major virulence determinants and the presence of beneficial traits in some S. shinii isolates support their potential use in the agri-food system or environmental biotechnology, pending strain-specific safety evaluation.

Salmonella Enteritidis (S. Enteritidis) is a persistent challenge within the poultry industry. The silent colonization allows S. Enteritidis establish themselves in the gut and reproductive tract, leading to persist, spread, and contaminate eggs and meat. This study investigated the anti-virulence potential of a sweet cherry pomace extract (CPE) as a potential natural decontaminant to disrupt S. Enteritidis colonization. The total phenolic content (TPC) and composition of ethanolic extracts from CPE were investigated via HPLC. Antimicrobial activities of CPE were evaluated by minimal inhibitory (MIC) and minimal bactericidal (MBC) concentrations determinations, as well as by growth kinetics and time-kill assays. Anti-virulence at sub-inhibitory concentrations (sub-MICs) was evaluated through swimming/swarming motility, biofilm formation (crystal violet), and auto-aggregation. The efficacy of CPE in reducing S. Enteritidis colonization was validated on chicken skin and visualized through scanning electron microscopy (SEM). The studied CPE was rich in phenolic compounds, predominantly anthocyanins; and exhibited an inhibitory effect against S. Enteritidis at a MIC of 64 mg/mL and MBC of 128 mg/mL. Concentrations ≤8 mg/mL did not significantly affect growth kinetics or viability. Importantly, sub-MIC levels significantly reduced swarming and swimming motility as well as biofilm formation, and auto-aggregation in a dose-dependent manner. SEM topographic analysis confirmed that CPE reduced S. Enteritidis colonization on treated chicken skin. These findings demonstrate that at sub-MICs, CPE functions as a non-bactericidal anti-virulence agent that interferes with S. Enteritidis colonization mechanisms, supporting its potential as a natural decontaminant for poultry processing.

Antimicrobial resistance (AMR) is a significant threat to poultry production and food safety. In laying hens, commensal Escherichia coli can serve as a reservoir of AMR and virulence genes. Although omega-3 fatty acids (N-3 FA), yeast bioactives (YB), and spacing allowance (SA) influence gut health and immunity, their combined effects on AMR profiles of gut bacteria remain unclear. A total of 2,832 chicks were raised in enriched cages under high (HSA, 348 cm2/bird) or low (LSA, 284 cm2/bird) SA and fed a control diet (C), C+3% N-3 FA, or C+0.05% YB. At 4, 16, and 35 weeks of age (woa), cecal contents were cultured on ChromoCult agar to isolate E. coli. Susceptibilities of isolates to 14 antibiotics were determined. Of the 428 isolates, 35.7% were resistant to at least one antimicrobial, and overall AMR prevalence decreased with age (P < 0.05). At each of 4 and 16 woa, N-3 FA-fed birds showed the lowest ampicillin resistance (P < 0.05). Streptomycin resistance was higher in N-3 FA than in YB-fed birds at 16 woa (P = 0.02) but lower than in control-fed birds. Whole-genome sequencing and analysis of 237 selected isolates identified 19 antimicrobial resistance genes (ARGs) and 29 plasmids, with 15 (78.9%) ARGs and 19 (65.5%) plasmid replicons affected by either diet, SA, or age (P < 0.05). Several virulence genes were identified in sequenced E. coli isolates, with those encoding fimbriae, pili, protectin, and toxins being higher in younger pullets (P < 0.05). Overall, isolates from phylogroups A and B1 were predominant; however, at 4 woa, phylogroup D isolates were most prevalent, depending on diet and SA (P < 0.05). Isolates of serotype O23:H16, ST2 were the most prevalent. Of the 237 sequenced isolates, 13 were related to human ExPEC strains. Overall, these findings suggest that N-3 FA YB and SA modulate AMR and virulence genotypes in laying hens, highlighting their potential in mitigating AMR in the poultry production system.

Alternative feed additives are being investigated due to the restriction of antibiotics use to decrease antimicrobial resistance (AMR) in food-producing animals. This study investigated the effects of dietary American cranberry (Vaccinium macrocarpon) and wild blueberry (V. angustifolium) pomaces on the cecal microbiota and resistome profiles as well as the short-chain fatty acid levels. Male broiler chickens Cobb500 were fed a basal diet with either 55 ppm bacitracin methylene disalicylate (BMD); 0.5% (CRP0.5) and 1% (CRP1) cranberry pomace; and 0.5% (LBP0.5) and 1% (LBP1) lowbush blueberry pomace with or without a multienzyme mixture (ENZ). The results showed that at 21 days of age, the total coliform counts decreased in the CRP0.5-fed birds compared to BMD (p < 0.05). The use of pomace significantly increased the abundance of Lactobacillus and Bacteroides regardless of ENZ, while CRP decreased the Proteobacteria phylum abundance. In-feed ENZ tended to increase the relative abundance of genes conferring aminoglycoside resistance. Treatment with CRP0.5 decreased the abundance of cepA genes encoding for macrolide (MACROLIDE) and lincomycin (InuD) resistance while increasing those for tetracycline (tetO and tetX) resistance. These results showed, for the first time, the potential of the studied enzymes in influencing berry pomace’s effects on antimicrobial resistance gene profiles in broilers.

The Canadian Genomics Research and Development Initiative for Antimicrobial Resistance (GRDI-AMR) uses a genomics-based approach to understand how health care, food production and the environment contribute to the development of antimicrobial resistance. Integrating genomics contextual data streams across the One Health continuum is challenging because of the diversity in data scope, content and structure. To better enable data harmonization for analyses, a contextual data standard was developed. However, development of standards does not guarantee their use. Implementation strategies are critical for putting standards into practice. This work focuses on the development of implementation strategies to better operationalize data standards across the Canadian federal genomics ecosystem. Results include improved understanding of complex data models that can create challenges for existing systems. Technical implementation strategies included spreadsheet-based solutions, new exchange formats, and direct standards integration into new databases. Data curation exercises highlighted common data collection and sharing issues, which informed improved practices and evaluation procedures. These new practices are contributing to improved data quality and sharing within the GRDI-AMR consortium as evidenced by publicly available datasets. The implementation strategies and lessons learned described in this work are generalizable for other standards and can be applied more broadly within other initiatives.

Iron is an essential mineral for almost all pathogenic bacteria, including Salmonella enterica serovar Typhimurium and Enteritidis. We have investigated the effect of the deletion of iroN, fepA, and fhu genes on the transcriptomic profiles of S. Typhimurium and S. Enteritidis strains with double (ΔiroNΔfepA) and triple (ΔfhuΔiroNΔfepA) gene deletions and grown under iron-deficient conditions. Significant changes were observed in the expression of genes involved in virulence, stress-response, and energy metabolism in both Salmonella serovars. The pathways most affected were the tricarboxylic acid cycle, electron transport chain, and stress responses all of which were downregulated while cysteine biosynthesis was upregulated. In general, common and/or related genes were affected in the double and triple mutant strains which indicated that the additional deletion of the fhu gene affected a limited number of genes, although S. Typhimurium showed more differences than S. Enteritidis. Nevertheless, the main difference observed between the mutants of the two serovars grown under iron-depleted conditions is the enhanced upregulation of the flagellum genes in S. Enteritidis. This study reveals evidence of novel interactions between metabolic pathways and virulence under iron limitation, providing insights into adaptive strategies that may contribute to the enhanced virulence of these Salmonella serovars.

This study investigated the cecal microbiome of broilers raised under specific antimicrobial feeding programs (AFPs). A total of 2304 day-old Ross-708 male (M, n = 1152) and female (F, n = 1152) chicks were distributed into 48 floor pens which were allocated to one of three AFPs: Conventional, raised without medically important antibiotics (RWMIA), and raised without antibiotics (RWA). At 28 (D28) and 41 (D41) days of age, cecal contents were collected for culture dependent and independent analyses. At both 28 and 41 days, Enterococcus was more abundant in RWA-raised broilers than other groups with the most abundance of this bacterium being found in female birds (P < 0.05). At D41, the most abundant Eimeria tenella counts was observed in RWA-raised broiler ceca (P < 0.05). Sex effects were observed on the abundances of four of the 248 identified antimicrobial resistance genes while abundances of 10 were modulated by AFPs (P < 0.05). Ceca of females birds showed more tssB than males, and ceca of RWMIA-raised birds contained the highest abundance of chuY genes regardless of sex. This study showed that in a specific feeding program, cecal resistome can be affected by chicken's sex contributing to understand the AMR related to the AMU.

In the present study, a Limosilactobacillus reuteri strain isolated from chicken ceca alone or in combination with wild blueberry and American cranberry pomaces were evaluated for their effects on growth performance and body composition in Eimeria-infected broiler. A total of 480 day-old Cobb500 male broilers were placed into 60 cages allocated to 8 treatments: T1: non-infected (NI); T2: Eimeria-infected (EI); T3: EI + anticoccidials (125 mg/kg zoalene for D0-D28, 60 mg/kg salinomycin for D28-D35); T4: EI + 1 % blueberry pomace (BP); T5: EI + 1 % cranberry pomace (CP); T6: EI + 108 CFU Limosilactobacillus reuteri (L. reuteri); T7: EI + 1 % BP + L. reuteri; T8: EI + 1 % CP + L. reuteri. The EI was done by gavaging 2 × 105 oocysts of mixed Eimeria species (E. acervulina, E. maxima and E. tenella). No significant differences were observed between treatments for body weight (BW) and average daily gain, however, berry pomaces reduced average daily feed intake (P < 0.05) and the combination of L. reuteri with berry pomaces reduced feed conversion ratio in broilers when compared to control EI birds (P < 0.05). Eimeria infection reduced both bone mineral content and density as well as fat content at D21 (P < 0.05). At D21, the lowest total fat masses (% of BW) were observed in T4, T5 (pomaces) and T3 (P < 0.05). In conclusion, these findings indicate that berry pomace alone or in combination with the studied L. reuteri isolate may be beneficial for growth performance and body composition in the broiler grower and finisher phases.

One Health genomics initiatives often involve data streams originating from different sources, institutions, sectors, and information management systems. These are often heterogeneous datasets structured in a variety of ways, posing challenges for data harmonization, integration and meaningful interpretation. The Genomics Research and Development Initiative Shared Priority Projects for AMR (GRDI-AMR) uses a genomics-based approach to understand the prevalence and diversity of antimicrobial resistance determinants associated with food production and different environments that can impact human health, as well as how AMR can evolve, spread, and be mitigated. This work is being carried out by six different federal government departments and agencies, academic institutions, as well as agricultural and environmental networks. To facilitate harmonization of data, a modular, interoperable contextual data (metadata) specification was developed, called the GRDI-AMR One Health specification package. The package consists of an ontology-based data standard, built using semantic best practices and existing standards, and is operationalized in a data curation tool called the DataHarmonizer. This tool automates the transformation of contextual data into NCBI’s One Health Enterics BioSample format to support public data sharing. The package also includes different kinds of support materials such as field and term reference guides and a detailed curation protocol highlighting ethical, practical and privacy considerations. Tooling and vocabulary were iteratively improved through multiple rounds of real-world testing. The data standard is continually maintained and version controlled, and has been used to resolve a variety of data harmonization issues experienced throughout numerous collaborative surveillance projects. The standard also encourages the inclusion of prevalence metrics in order to make whole genome sequencing data more useful for risk assessment, and enables communication about data needs between data generators and users. While developed for Canadian surveillance, the GRDI-AMR specification has also been implemented in international harmonization efforts, demonstrating its utility for many types of One Health genomics projects. The specification package is available at (https://github.com/cidgoh/GRDI_AMR_One_Health).

This study evaluated effects of feeding low-bush wild blueberry (LBP) and organic American cranberry (CRP) pomaces without or with multienzyme supplement (ENZ) on growth performance, organ weight and plasma metabolites in broiler chickens. Nonenzyme-fed (no-ENZ: n = 1,575) and enzyme-fed (ENZ: n = 1,575) day-old male Cobb500 broilers were placed in floor pens (45 chicks/pen) and allocated to five corn-soybean meal-based diets: a basal diet supplemented with either bacitracin methylene disalicylate (BMD, 55 mg/kg), 0.5 or 1% of CRP or LBP in a 2 × 5 factorial design for 35-day experiment. Body weight (BW), feed intake (FI) and mortality were recorded whereas BW gain (BWG) and feed conversion ratio (FCR) were calculated. Birds were sampled at days 21 and 35 for organ weights and plasma metabolites. There were no interactions between diet and ENZ on any parameter (P > 0.05) and no effect of ENZ on overall (d 0-35) growth performance and organ weights (P > 0.05). Birds fed BMD were heavier (P < 0.05) at d 35 and had better overall FCR than berry-supplemented birds. Birds fed 1% LBP had poor FCR than birds fed 0.5% CRP. Birds fed LBP exhibited heavier liver (P < 0.05) than birds fed BMD or 1% CRP. The highest plasma concentrations of aspartate transaminase (AST), creatine kinase (CK) at d 28 and gamma-glutamyl transferase (GGT) at d 35 were found in ENZ-fed birds (P < 0.05). At d 28, birds fed 0.5% LBP showed higher plasma AST and CK concentrations (P < 0.05). However, CRP feeding resulted in a lower plasma CK level compared with BMD feeding (P < 0.05). The lowest cholesterol level was detected in 1% CRP-fed birds. In conclusion, this study showed no ENZ effects to potentiate berry pomaces on the overall growth performance of broilers (P < 0.05. However, plasma profiles revealed the potential of ENZ to modulate the metabolism of pomace-fed broilers. LBP increased BW during the starter phase, while CRP increased BW during the grower phase.

Extraintestinal pathogenic Escherichia coli (ExPEC) includes several serotypes that have been associated with colibacillosis in poultry, as well as urinary tract infections and newborn meningitis in humans. This study investigated the antimicrobial activities of ceftriaxone (AXO) and cranberry pomace extracts (CRAN) alone or in combination (CC) against multidrug-resistant (MDR) ExPEC from broiler. The growth-inhibitory activity of CRAN and synergy tests by a checkerboard method were determined in cation-adjusted Mueller–Hinton broth (CAMHB). The transcriptomic profile of the MDR E. coli O7:H18 (ST38) grown in CAMHB supplemented with sub-inhibitory concertation of CRAN and AXO alone or in combination was obtained by RNA-seq. The MIC of CRAN for all isolates was 16 mg/mL. An additive activity was observed between 4 mg/mL of CRAN and 4 μg/mL of AXO. Compared to the control, the transcriptomic analysis revealed that 4 mg/ml of (1/4MIC) CRAN and its combination with 4 μg/mL of (1/8MIC) AXO (CC) exposures resulted in 727 and 712 differentially expressed genes, respectively (false discovery rate < 0.001 and log2-fold change > 2), in the studied E. coli. Major virulence genes including adhesins (fim, flg, csg, and yad), protectins (omp, tra, waa, and hly), secretion systems (hof, pho, and vir), and quorum sensing (lsr), which are energetically expensive for bacteria, were downregulated. Most importantly, 1/4MIC of CRAN or CC downregulated the β-lactamase blaCMY-2 and efflux pump including tolC, mdtEIJ, gadEW, and their regulator gene evgS, while upregulating the cysteine biosynthesis and oxidative stress-related regulatory genes including cys, dmlA, sbp, nrdGHI, soxSR, and rpoH. Downregulation of multiple enzymes involved in TCA cycles and upregulation of Fe–S cluster coordinated by Cys and Isc proteins reflect the regulation of energy metabolism of the studied E. coli upon CRAN or CC exposure. The downregulation of outer membrane protein genes that control permeability barriers, along with different antimicrobial resistance genes, demonstrates that CRAN may have the unique potential to enhance the antimicrobial activities of third-generation cephalosporins such as AXO against MDR E. coli.

American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.

Healthy poultry can be a reservoir for extraintestinal pathogenic Escherichia coli (ExPEC), some of which could be multidrug resistant to antimicrobials. These ExPEC strains could contaminate the environment and/or food chain representing thus, food safety and human health risk. However, few studies have shown the virulence of poultry-source antimicrobial-resistant (AMR) ExPEC in humans. This study characterized AMR ExPEC and investigated the virulence potential of some of their isolates in a Caenorhabditis elegans infection model. A total of 46 E. coli isolates from poultry (chicken, n = 29; turkey, n = 12) retail meats and chicken feces (n = 4), or humans (n = 1) were sequenced and identified as ExPEC. Except eight, all remaining 38 ExPEC isolates were resistant to at least one antibiotic and carried corresponding antimicrobial resistance genes (ARGs). About 27 of the 46 ExPEC isolates were multidrug-resistant (≥3 antibiotic classes). Seven ExPEC isolates from chicken or turkey meats were of serotype O25:H4 and sequence type (ST) 131 which clustered with an isolate from a human urinary tract infection (UTI) case having the same serotype and ST. The C. elegans challenge model using eight of studied ExPEC isolates harboring various ARGs and virulence genes (VGs) showed that regardless of their ARG or VG numbers in tested poultry meat and feces, ExPEC significantly reduced the life span of the nematode (P < 0.05) similarly to a human UTI isolate. This study indicated the pathogenic potential of AMR ExPEC from retail poultry meat or feces, but more studies are warranted to establish their virulence in poultry and human. Furthermore, relationships between specific resistance profiles and/or VGs in these E. coli isolates for their pathogenicity deserve investigations.

With the pressure to reduce antibiotics use in poultry production, cost-effective alternative products need to be developed to enhance the bird's immunity. The present study evaluated the efficacy of cranberry fruit by-products to modulate immunity in broiler chickens. Broiler Cobb 500 chicks were fed a control basal diet, basal diet supplemented with bacitracin (BACI, 55 ppm), cranberry pomace at 1% and 2% (CP2), or cranberry pomace ethanolic extract at 150 and 300 ppm (COH300) for 30 d. Blood sera were analyzed at days 21 and 28 of age for Ig levels by ELISA. The innate and adaptive immune-related gene expression levels in the liver and bursa of Fabricius were investigated at 21 d of age by quantitative polymerase chain reaction arrays. At day 21, the highest IgY level was found in the blood serum of the CP2-fed birds. In the liver, 13 of the 22 differentially expressed genes were downregulated across all treatments compared with the control. Expression of genes belonging to innate immunity such as caspase 1 apoptosis–related cysteine peptidase, chemokine receptor 5, interferon gamma, myeloid differentiation primary response gene 88, and Toll-like receptor 3 were significantly downregulated mainly in BACI- and COH300-fed birds. In the bursa, 5 of 9 genes associated with the innate immunity were differentially expressed. The expression of anti-inflammatory IL-10 gene was upregulated in all treatment groups in bursa compared with the control. The expression of transferrin gene was significantly upregulated in livers of birds fed COH300 and in bursa of birds fed BACI, indicating feeding practices and organ-dependant modulation of this gene in broiler. Overall results of this study showed that cranberry product feed supplementation modulated the innate immune and suppressed proinflammatory cytokines in broilers, providing a platform for future investigations to develop berry products in poultry feeding.

Feeding practices have been found to influence gut microbiota which play a major role in immunity of poultry. In the present study, changes in cecal microbiota and humoral responses resulting in the 55 ppm bacitracin (BACI), 1% each of cranberry (CP1) and wild blueberry (BP1) pomace alone or in combination (CP+BP) feeding in broiler Cobb 500 vaccinated or not against coccidiosis were investigated. In the non-vaccinated group, no significant treatment effects were observed on performance parameters. Vaccination significantly affected bird’s performance parameters particularly during the growing phase from 10 to 20 days of age. In general, the prevalence of coccidiosis and necrotic enteritis (NE) was reduced by vaccination ( P < 0.05). BACI-treated birds showed low intestinal lesion scores, and both CP1 and BP1 feed supplementations reduced Eimeria acervulina and Clostridium perfringens incidences similar to BACI. Vaccination induced change in serum enzymes, minerals, and lipid levels in 21-day old birds while, levels of triglyceride (TRIG) and non-esterified fatty acids (NEFA) were higher ( P < 0.05) in CP1 treated non–vaccinated group than in the control. The levels of NEFA were lower in BACI- and CP1-fed birds than in the control in non-vaccinated day 28 old birds. The highest levels of all estimated three immunoglobulins (IgY, IgM, and IgA) were found in the vaccinated birds. Metagenomics analysis of the cecal bacterial community in 21-day old birds showed the presence of Firmicutes (90%), Proteobacteria (5%), Actinobacteria (2%), and Bacteroidetes (2%). In the vaccinated group, an effect of BACI was noted on Proteobacteria ( P = 0.03). Vaccination and/or dietary treatments influenced the population of Lactobacillaceae , Enterobacteriaceae, Clostridiaceae , and Streptococcaceae which were among the most abundant families. Overall, this study revealed that besides their beneficial effects on performance, alike bacitracin, berry pomaces in poultry feed have profound impacts on the chicken cecal microbiota and blood metabolites that could be influenced by vaccination against coccidiosis.

This study investigated effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN+CIT) on antimicrobial resistance (AMR) phenotypes and genotypes of E. coli isolated from feces of 6-, 16-, 23- and 27-days old broiler chickens. Five dietary treatments included the basal diet (NC), the basal diet supplemented with 55 ppm bacitracin (BAC), 100 ppm encapsulated CIN, CIT, or CIN+CIT. Antimicrobial susceptibility using a Sensititre method of 240 E. coli isolates showed that the most frequent resistances were against b-lactam, aminoglycoside, sulfonamide and tetracycline, however, the prevalence of AMR decreased (P < 0.05) when birds aged. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from CIN or CIN+CIT compared to those from NC or BAC. The whole-genome sequencing analysis of 227 of the 240 isolates detected 26 AMR genes (ARGs) and 19 plasmids but the prevalence of some ARGs and plasmid numbers were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT than NC or BAC. The most prevalent resistance genes included tet(A) (n = 108), aac3_Vla (n = 91), aadA1 (n = 86), blaCMY-2 (n = 78), sul1 (n = 77), aph3_lb (n = 58), aph6_ld (n = 58), and sul2 (n = 24). Interestingly, the number of most virulence genes (VGs) increased (P < 0.05) over time from 6 to 27 days of age. The prevalence of isolates of serotype O21:H16 was lower (P < 0.05) in CIN and CIN+CIT while colibacillosis-associated multi-locus sequence typing (ST117) was the most prevalent in isolates from day 23. A whole genome-based phylogenetic tree revealed a close relationship of 25 of 227 isolates to human or broiler extraintestinal pathogenic E. coli. This study indicates that AMR and virulence genotypes of E. coli could be modulated by encapsulated CIN or CIN+CIT feed supplementations and prompt further investigations on the involved mechanisms.

Antimicrobial resistance is among the most urgent global challenges facing sustainable animal production systems. The use of antibiotics as growth promoters and for infectious disease prevention in intensive animal-farming practices has translated into the selection and spread of antimicrobial resistance genes in an unprecedented fashion. Several multi-resistant bacterial strains have been isolated from food-producing animals, thus constituting an alarming food-safety issue. Many industrial byproducts with potential antimicrobial properties are currently being investigated to identify empirical and affordable solutions/alternatives that can potentially be used in feed for animals. Grape pomace is among such byproducts that gained the attention as a result of its low cost, abundance, and, most importantly, its bioactive and antibacterial properties. This review discusses the recently reported studies with regard to exploring the use of grape pomace (and its extracts) in animal production to control pathogens, along with the promotion of beneficial bacterial species in the gut to ultimately alleviate antibacterial resistance. The review further summarizes realistic expectations connected with grape pomace usage and lists the still-to-be-addressed concerns about its application in animal agriculture.

This study evaluated the performance, gut microbiota, and blood metabolites in broiler chickens fed cranberry and blueberry products for 30 days. A total of 2,800 male day-old broiler Cobb-500 chicks were randomly distributed between 10 diets: control basal diet; basal diet with bacitracin (BACI); four basal diets with 1 and 2% of cranberry (CP1, CP2) and blueberry (BP1, BP2) pomaces; and four basal diets supplemented with ethanolic extracts of cranberry (COH150, COH300) or blueberry (BOH150, BOH300) pomaces. All groups were composed of seven replicates (40 birds per replicate). Cecal and cloacal samples were collected for bacterial counts and 16S rRNA gene sequencing. Blood samples and spleens were analyzed for blood metabolites and gene expressions, respectively. The supplementation of COH300 and BOH300 significantly increased the body weight (BW) during the starting and growing phases, respectively, while COH150 improved (P < 0.05) the overall cumulated feed efficiency (FE) compared to control. The lowest prevalence (P = 0.01) of necrotic enteritis was observed with CP1 and BP1 compared to BACI and control. Cranberry pomace significantly increased the quinic acid level in blood plasma compared to other treatments. At days 21 and 28 of age, the lowest (P < 0.05) levels of triglyceride and alanine aminotransferase were observed in cranberry pomace and blueberry product-fed birds, respectively suggesting that berry feeding influenced the lipid metabolism and serum enzyme levels. The highest relative abundance of Lactobacillaceae was found in ceca of birds fed CP2 (P < 0.05). In the cloaca, BOH300 significantly (P < 0.005) increased the abundances of Acidobacteria and Lactobacillaceae. Actinobacteria showed a significant (P < 0.05) negative correlation with feed intake (FI) and FE in COH300-treated birds, whereas Proteobacteria positively correlated with the BW but negatively correlated with FI and FE, during the growing phase. In the spleen, cranberry products did not induce the release of any pro-inflammatory cytokines but upregulated the expression of several genes (IL4, IL5, CSF2, and HMBS) involved in adaptive immune responses in broilers. This study demonstrated that feed supplementation with berry products could promote the intestinal health by modulating the dynamics of the gut microbiota while influencing the metabolism in broilers.