Interactions between the helminth and intestinal microbiome in smallholder chicken farming systems

Helminth parasite infections are widespread in smallholder farming systems affecting farmers and livestock animals. There are pathogenic parasites that populate the gut of their host and coexist closely with the gut microbiota. The physical and immunological environment of the gut can be modified by parasites and microbiota creating a wide range of interactions. These interactions modify the development of infection, affects overall host health, and can modify the way a host interacts with its bacterial microbiota. In addition, where there is a high worm burden parasites will affect the health of the host and intestinal tract colonization. This review highlights key studies on the interaction between helminth parasites and the intestinal microbiome to understand the relationship between parasitic worm infections and gut microbiome health in chickens. Finally, the review discusses modulations, molecular changes, and the importance of helminth-microbiome interactions for the host.

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review

Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.

Anticoccidial Vaccination Is Associated with Improved Intestinal Health in Organic Chickens

Simple Summary

In recent years, the number of organic chicken farms has increased. Chickens can be infected by single-cell parasites, coccidia, which cause lesions in the lining of the intestine leading to poor growth and sometimes death (coccidiosis). This infection can also lead to overgrowth in the intestine of a bacterium, Clostridium perfringens, that may cause further damage (necrotic enteritis). Prevention is often achieved by adding substances in the feed that will slow down the development of parasites and bacteria, but this is not allowed in organic farming. The aim of this study was to investigate if vaccination against coccidia can prevent these diseases in organic chickens. Vaccinated chickens developed milder gut lesions, had fewer and less damaging C. perfringens, and had similar or higher body weight compared to unvaccinated chickens six weeks after vaccination. No deaths from coccidiosis or necrotic enteritis occurred among vaccinated chickens while some unvaccinated chickens died from these diseases. We conclude that vaccination against coccidia benefits organic chickens. This study provides knowledge supporting further development of the organic chicken industry. The results are also of relevance to the management of coccidiosis and necrotic enteritis in conventional broilers.

Abstract

Eimeria spp. and Clostridium perfringens (CP) are pathogens associated with coccidiosis and necrotic enteritis (NE) in broiler chickens. In this study we evaluated the effect of anticoccidial vaccination on intestinal health in clinically healthy organic Ross 308 chickens. On each of two farms, one unvaccinated flock (A1 and B1) was compared to one vaccinated flock (A2 and B2) until ten weeks of age (WOA). Faecal oocysts were counted weekly, and species were identified by PCR (ITS-1 gene). Lesion scoring, CP quantification and PCR targeting the CP NetB toxin gene were performed at three, four, and six WOA and chickens were weighed. Necropsies were performed on randomly selected chickens to identify coccidiosis/NE. Oocyst shedding peaked at three WOA in all flocks. Later oocyst shedding (E. tenella/E. maxima) in unvaccinated flocks at 5–7 WOA coincided with coccidiosis/NE. Although results differed somewhat between farms, vaccination was associated with lower intestinal lesion scores, reduced caecal CP counts, lower proportions of netB-positive CP, lower body weight at three–four WOA, and similar or slightly increased body weight at six WOA. In conclusion, the intestinal health of organic broilers can benefit from anticoccidial vaccination when oocyst exposure levels are high.

Prebiotics and alternative poultry production

Alternative poultry production systems continue to expand as markets for organic and naturally produced poultry meat and egg products increase. However, these production systems represent challenges associated with variable environmental conditions and exposure to foodborne pathogens. Consequently, there is a need to introduce feed additives that can support bird health and performance. There are several candidate feed additives with potential applications in alternative poultry production systems. Prebiotic compounds selectively stimulate the growth of beneficial gastrointestinal microorganisms leading to improved health of the host and limiting the establishment of foodborne pathogens. The shift in the gastrointestinal microbiota and modulation of fermentation can inhibit the establishment of foodborne pathogens such as Campylobacter and Salmonella. Both current and potential applications of prebiotics in alternative poultry production systems will be discussed in this review. Different sources and types of prebiotics that could be developed for alternative poultry production will also be explored.

Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains

Recently, there has been a consumer push for natural and organic food products. This has caused alternative poultry production, such as organic, pasture, and free-range systems, to grow in popularity. Due to the stricter rearing practices of alternative poultry production systems, different types of levels of microbiological risks might be present for these systems when compared to conventional production systems. Both conventional and alternative production systems have complex supply chains that present many different opportunities for flocks of birds or poultry meat to be contaminated with foodborne pathogens. As such, it is important to understand the risks involved during each step of production. The purpose of this review is to detail the potential routes of foodborne pathogen transmission throughout the conventional and alternative supply chains, with a special emphasis on the differences in risk between the two management systems, and to identify gaps in knowledge that could assist, if addressed, in poultry risk-based decision making.

An overview of health challenges in alternative poultry production systems

Due to consumer demand and changing welfare standards on health, ecology, equity, and safety concepts, poultry production has changed markedly over the past 20 y. One of the greatest changes to poultry production standards is now offering poultry limited access to the outdoors in alternative and organic poultry production operations. Although operations allowing access to the outdoors are still only a small portion of commercial poultry production, it may impact the gastrointestinal (GIT) health of the bird in different ways than birds raised under conventional management systems. The present review describes current research results in alternative systems by identifying how different poultry production operations (diet, environmental disruptive factors, diseases) impact the ecology and health of the GIT. Various research efforts will be discussed that illustrate the nutritional value of free-range forages and how forages could be beneficial to animal health and production of both meat and eggs. The review also highlights the need for potential interventions to limit diseases without using antibiotics. These alternatives could enhance both economics and sustainability in organic and free-range poultry production.

Gastrointestinal Tract Morphometrics and Content of Commercial and Indigenous Chicken Breeds with Differing Ranging Profiles

Optimal development of the gut is important for nutrient absorption and for poultry to resist diseases. The aim of the study was to compare gastrointestinal tract morphometrics, small intestine microstructure, as well as the amount of pasture matter and feed ingested by the birds with outdoor access presenting either an outdoor-preferring, moderate-outdoor or indoor-preferring ranging profile. Sixty non-beak trimmed birds per strain: broiler hybrid Sasso and Polish indigenous green-legged partridge were housed from week 5 to 10 in groups of 10, under conditions of EU organic meat chicken production. Pens with outdoor ranges were video recorded, to obtain frequencies of the birds' range use. Statistical analysis was conducted applying generalized linear mixed models, applying the ranging profile as a fixed effect and pen as a random factor. The weight of the pasture matter in bird crops was the highest in moderate-outdoor profiled green-legged partridges, as compared to other ranging profiles (p = 0.04). In Sasso, villi in the small intestines were significantly higher in the outdoor-preferring compared to indoor-preferring profiled birds (p = 0.04), while their area was larger in the outdoor-preferring Sasso birds (p = 0.01). The level of development of the gastrointestinal tract and its content may be a potential indicator of the birds' ranging profile and forage consumption.

Standardized ileal digestibility of amino acids and apparent metabolizable energy in corn and soybean meal for organic broiler chicken production in Ontario

Standardized ileal digestibility (SID) of amino acids (AA) and apparent metabolizable energy corrected for nitrogen (AMEn) in samples of organic corn and soybean meal (SBM) were determined. Conventional corn (CC) and SBM (CSBM) samples were tested for comparison. A total of 560, fourteen-day-old male broiler chickens (Cobb 500) were weighed, placed in cages (10 birds per cage), and allocated to seven (n = 8) semi-purified wheat-starch-based diets. Diets were (1) CC, (2) imported organic corn, (3) local organic corn, (4) CSBM, (5) imported organic SBM (OSBMI), (6) local organic SBM (OSBML), and (7) nitrogen-free wheat starch. Only few differences were observed on SID of AA; SID of lysine was lower (P = 0.002) in organic corn samples relative to CC, and SID of methionine was lower (P = 0.002) in OSBML sample relative to CSBM and OSBMI samples. The AMEn of CC was higher (P < 0.01) than that of organic corn samples. The AMEn of OSBML was higher (P < 0.001) than for CSBM and OSBMI; however, the value for OSBMI was higher (P < 0.001) than for CSBM. In conclusion, utilization of AA in conventional and organic feedstuffs was comparable; however, differences in energy utilization warrant considerations in organic broiler feed formulation.

Antimicrobial Susceptibility of Escherichia coli and ESBL-Producing Escherichia coli Diffusion in Conventional, Organic and Antibiotic-Free Meat Chickens at Slaughter

Simple Summary

Following the spread of antibiotic resistance and the high consumption of chicken meat, conventional poultry-producing companies have turned to antibiotic-free and organic lines of products. Our work investigated E. coli susceptibility to different antimicrobials and extended-spectrum β-lactamase (ESBL) E. coli diffusion from samples collected in slaughterhouse from conventional (C), organic (O) and reared without antibiotics (ABF) chickens. Conventional samples showed the highest number of E. coli strains resistant to ampicillin (89.6%), trimethoprim/sulfamethoxazole (62.2%), nalidixic acid (57.8%), ciprofloxacin (44.4%), and cefotaxime (43.7%), with prevalent patterns of multi-resistance to three (35.1%) and to four antimicrobials (31.3%). The highest numbers of ESBL E. coli were observed in conventional and the lowest in organic. Our results are relevant with an influence of farming typology regarding the susceptibility of E. coli and the presence of ESBL E. coli. Conventional farms, in which the use of antibiotics is allowed, showed samples with the highest number of strains resistant to antimicrobials commonly used in poultry as well as the highest amounts of ESBL E. coli. Organic samples exhibited the lowest value for ESBL due to a lack of antimicrobial treatment in chickens and the possibility to have access to the outdoors, limiting contact with litter as a potential source of resistant bacteria.

Abstract

As a result of public health concerns regarding antimicrobial resistance in animal-based food products, conventional poultry companies have turned to ‘raised without antibiotics’ (ABF) and organic farming systems. In this work, we evaluated the influence of rearing systems on antimicrobial susceptibility in E. coli and extended-spectrum β-lactamase (ESLB) E. coli diffusion in conventional (C), organic (O) and antibiotic free (ABF) chicken samples collected from cloacal swabs and skin samples in slaughterhouse. The E. coli isolates from conventional (135), antibiotic-free (131) and organic (140) samples were submitted to the Kirby–Bauer method and ESBL E. coli were analyzed by the microdilution test. Conventional samples showed the highest number of strains resistant to ampicillin (89.6%; p < 0.01), cefotaxime (43.7%; p < 0.01), nalidixic acid (57.8%; p < 0.01), ciprofloxacin (44.4%; p < 0.001), and trimethoprim/sulfamethoxazole (62.2%; p < 0.01), with patterns of multi-resistance to three (35.1%) and to four antimicrobials (31.3%), whereas most of the E. coli isolated from antibiotic-free and organic chicken samples revealed a co-resistance pattern (29.2% and 39%, respectively). The highest number of ESBL E. coli was observed in conventional, in both cloacal and skin samples and the lowest in organic (p < 0.001). Our results are consistent with the effect of conventional farming practices on E. coli antimicrobial resistance and ESBL E. coli number, due to the use of antimicrobials and close contact with litter for most of the production cycle.

Quantifying the effect of inbreeding on average daily gain and Kleiber ratio in Mazandaran native chickens

The aims of this study was to evaluate inbreeding effects for growth rate (average daily gain from hatch to 8 weeks of age (ADG1-8), average daily gain from hatch to 12 weeks of age (ADG1-12), average daily gain from 8 weeks of age to 12 weeks (ADG8-12), average daily gain from hatch to sex maturity (ADG1-SM), average daily gain from 8 weeks of age to sex maturity (ADG8-SM), average daily gain from 12 weeks to sex maturity (ADG12-SM), and Kleiber ratios (KR1-8, KR1-12, KR8-12) in Mazandaran native chickens. The data set of 82,446 pedigreed individuals over 21 generations was analyzed. All individuals were grouped into three classes based on the inbreeding coefficient: First class contained non-inbred birds (F = 0) and second and third classes contained inbred individuals (0 < F ≤ 5% and F > 5%, respectively). The effects of inbreeding coefficient on the studied traits were estimated by the restricted maximum likelihood method (REML) applying the WOMBAT software and fitting individual increase in inbreeding coefficient (ΔFi) of birds as linear covariates under 6 different animal models. ADG8-SM and ADG12-SM increased non-significantly by 0.003 and 0.005 g, respectively, due to 1% increase in ΔFi, while ADG1-8, ADG1-12, ADG8-12, ADG1-SM, KR1-8, and KR1-12 decreased (P < 0.001), respectively, by 0.012 g, 0.011 g, 0.010 g, 0.014 g, 0.003 g, and 0.002 g. Also, KR8-12 non-significantly decreased by 0.001 g. Estimates of direct heritability of traits based on the most appropriate models ranged from 0.05 (KR8-12) to 0.26 (ADG12-SM). Results showed that it is important to regularly analyze inbreeding level in the herd in an attempt to prevent the reduction of performance.

Biorefined grass-clover protein composition and effect on organic broiler performance and meat fatty acid profile

Protein extracted from green biomass can be a sustainable and valuable feed component for organic poultry production. Earlier studies in rats have shown high digestibility of laboratory-scale extracted protein. The aim of this study was to test the effect of upscaling the biorefining process on composition of protein extracted from organic grass-clover and on performance of organic broilers when including grass-clover in the feed. Crude protein content of the extracted grass-clover protein was 36.2% of dry matter (DM) with a higher methionine content, but lower lysine and total sulphur-containing amino acids than that in soybean. Acid-insoluble residue constituted a major fraction of the dietary fibre content, and a large proportion of total CP was bound in this fraction. Alpha-linolenic acid was the dominating fatty acid in the extracted grass-clover protein. One-day-old organic Colour Yield broiler chicks were included in a dose-response trial with grass-clover protein constituting 0%, 8%, 16% or 24% of the feed from day 12 and until slaughter at day 57. Increasing levels of grass-clover protein extract reduced feed intake, growth and slaughter weight; however, at 8% inclusion feed intake and performance were not affected. The fatty acid composition in broiler breast meat reflected the composition of grass-clover protein extract; thus, the increasing dietary addition increased meat alpha-linolenic acid content. A lowered tocopherol content in meat from broilers fed increasing grass-clover protein demonstrated the need for increased amounts of antioxidants due to the high content of unsaturated fat. In conclusion, the study shows that broilers can grow on grass-clover protein from an upscaled biorefining process, but highlights the importance of further optimisation with focus on increased protein content and on avoiding formation of insoluble protein complexes, as these most likely reduce protein digestibility.

Gastrointestinal microbiomes of broilers and layer hens in alternative production systems

Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and maintained in these types of production systems. Exposure to foodborne pathogens and potential for colonization in the gastrointestinal tract has to be considered with these types of production systems. The gastrointestinal tract microbial composition and function of birds grown and maintained in alternative poultry operations may differ depending on diets, breed, and age of bird. Dietary variety and foraging behavior are potential influential factors on bird nutrition. The gastrointestinal tract microbiomes of birds raised under alternative poultry production systems are now being characterized with next-generation sequencing to identify individual microbial members and assess the impact of different factors on the diversity of microbial populations. In this review, the gastrointestinal tract microbiota contributions to free-range or pasture-raised broiler and egg layer production systems, subsequent applications, and potential future directions will be discussed.

Influence of Different Production Systems on the Quality and Shelf Life of Poultry Meat: A Case Study in the German Sector

Production-specific factors, such as breeding, diet, and stress, are known to influence meat quality, but the effect of different husbandry systems on the development of quality parameters and shelf life has hardly been investigated. Thus, the aim of the study was the investigation of an alternative production system based on a slow-growing, corn-fed, and antibiotics-free chicken line compared with conventional poultry production. Additionally, the effect on meat quality, microbiology, and spoilage was analyzed. In total, 221 breast filets from a German poultry meat producer were investigated. Nutritional, biochemical, and cooking loss analyses were conducted on a subset of samples 24 h after storage. The rest of the samples were stored aerobically at 4°C, and the spoilage process was characterized by investigating pH, color, lipid oxidation, microbiology, and sensory attributes subsequently every two days during storage. The alternative production line showed a significantly healthier nutritional profile with a higher protein and lower fat content. Additionally, the amount of L-lactic acid and D-glucose was significantly higher than in the conventional production line. The color values differed between both production lines, with the corn-fed line displaying more yellowish filets. The lipid oxidation and microbial spoilage were not affected by the production line. The shelf life did not differ between the investigation groups and was deemed 7 days in both cases. Despite the highest severity of white striping being observed most in the conventional production line, there was no overall difference in the incidence among groups. The purchase decision was affected by the occurrence of white striping and showed a tendency for a higher acceptance for the alternative production line.

Alterations of Salmonella enterica Serovar Typhimurium Antibiotic Resistance under Environmental Pressure

Microbial horizontal gene transfer is a continuous process that shapes bacterial genomic adaptation to the environment and the composition of concurrent microbial ecology. This includes the potential impact of synthetic antibiotic utilization in farm animal production on overall antibiotic resistance issues; however, the mechanisms behind the evolution of microbial communities are not fully understood. We explored potential mechanisms by experimentally examining the relatedness of phylogenetic inference between multidrug-resistant Salmonella enterica serovar Typhimurium isolates and pathogenic Salmonella Typhimurium strains based on genome-wide single-nucleotide polymorphism (SNP) comparisons. Antibiotic-resistant S Typhimurium isolates in a simulated farm environment barely lost their resistance, whereas sensitive S Typhimurium isolates in soils gradually acquired higher tetracycline resistance under antibiotic pressure and manipulated differential expression of antibiotic-resistant genes. The expeditious development of antibiotic resistance and the ensuing genetic alterations in antimicrobial resistance genes in S Typhimurium warrant effective actions to control the dissemination of Salmonella antibiotic resistance.IMPORTANCE Antibiotic resistance is attributed to the misuse or overuse of antibiotics in agriculture, and antibiotic resistance genes can also be transferred to bacteria under environmental stress. In this study, we report a unidirectional alteration in antibiotic resistance from susceptibility to increased resistance. Highly sensitive Salmonella enterica serovar Typhimurium isolates from organic farm systems quickly acquired tetracycline resistance under antibiotic pressure in simulated farm soil environments within 2 weeks, with expression of antibiotic resistance-related genes that was significantly upregulated. Conversely, originally resistant S Typhimurium isolates from conventional farm systems lost little of their resistance when transferred to environments without antibiotic pressure. Additionally, multidrug-resistant S Typhimurium isolates genetically shared relevancy with pathogenic S Typhimurium isolates, whereas susceptible isolates clustered with nonpathogenic strains. These results provide detailed discussion and explanation about the genetic alterations and simultaneous acquisition of antibiotic resistance in S Typhimurium in agricultural environments.

Comparison of the loads and antibiotic-resistance profiles of Enterococcus species from conventional and organic chicken carcasses in South Korea

Antibiotic-resistant bacteria in poultry meat are a threat to public health. In this study, we compared the Enterococcus spp. loads and antibiotic-resistance profiles between carcasses of conventionally and organically raised chickens. A total of 144 chicken carcasses (72 conventional and 72 organic) was collected from local retail markets in Seoul, South Korea. Overall, 77.7% (112 of 144; 75% conventional and 80% organic) of chicken carcasses were positive for Enterococcus. The mean loads of Enterococcus spp. were greater in conventional chicken carcasses, at 2.9 ± 0.4 log CFU/mL, than those in organic chicken carcasses, at 1.78 ± 0.3 log CFU/mL (p < 0.05). A total of 104 isolates (52 from conventional and 52 from organic chicken carcasses) was randomly selected for further analysis. The predominant species was Enterococcus faecalis in both conventional and organic chicken carcasses (57.7 and 76.9%, respectively; P > 0.05). Rates of resistance to ciprofloxacin and erythromycin, which are used in veterinary medicine in South Korea, were significantly higher in conventional chicken carcasses than in organic chicken carcasses. However, we found no difference between the rates of resistance to antibiotics such as vancomycin and tigecycline, which were not registered for use in veterinary medicine in South Korea, of Enterococcus isolates from conventional and organic chicken carcasses. In addition, although multidrug resistant isolates were obtained from both types of chicken samples, the prevalence of samples positive for Enterococcus was significantly higher in conventional chicken carcasses than in organic chicken carcasses (P < 0.05). The most common multidrug resistance pattern was erythromycin-tetracycline-rifampicin in conventional chicken carcasses and quinupristin-dalfopristin-tetracycline-rifampicin in organic chicken carcasses. A high level of gentamicin resistance was observed in isolates from not only conventional (5.8%) but also organic chicken (1.9%) carcasses, with no significant difference in rates between them (P > 0.05). Despite this, our results suggest that organic food certification is effective in reducing fecal contamination and the burden of antibiotic-resistant Enterococcus spp. in chicken carcasses.

Helminth infections in chickens (Gallus domesticus) raised in different production systems in Brazil

The current study evaluated helminth infections in birds raised in different production systems for different purposes (extensive/dual-purpose, semi-intensive/broiler, semi-intensive/hen, intensive/hen and intensive/broiler) in Brazil. A total of 374 birds was assessed for helminths at necropsy using standard parasitological methods. During the necropsies, organs from the gastrointestinal tract (crop, esophagus, proventriculus, gizzard, small intestine, large intestine and ceca) of each bird were collected and the contents fixed in 70% ethanol. Additionally, the trachea and eyes were assessed for the presence of helminths. The small intestine was examined using a methodology that allowed the recovery of cestode scolices attached to the intestinal mucosa. Stereomicroscopy and optical microscopy were used to detect and identify helminth species based on their morphological characteristics. Fifteen helminth species were found among birds from the different systems. The extensive system presented the highest number of helminth species (six cestodes, seven nematodes and one trematode) and the highest number of parasites (mean helminths/bird), followed by the semi-intensive system (broiler: six cestode and four nematode species; hens: five cestode and three nematode species). Hens from the intensive system were parasitized by five cestode, four nematode and one trematode species. No parasites were detected in broilers raised in the intensive systems. The results obtained in this study highlight the need for special attention and the implementation of biosecurity measures for the prevention of helminth infections in intensive systems (hens) and particularly in extensive and semi-intensive alternative poultry production systems.

Effect of freezing on the quality of meat from broilers raised in different rearing systems

We evaluated the effect of freezing (−18°C) for 12 months on the qualitative characteristics of breast, thigh and drumstick meat. Samples from male Cobb 500 broilers raised in antibiotic-free (n = 125), conventional (n = 125) and organic (n = 125) rearing systems and samples from male Hubbard ISA broilers raised in a free-range (n = 125) rearing system were used. Among the studied systems, up to the ninth month of freezing, the organic chicken breast meat showed lower (P < 0.001) water activity (aw) (0.966, on average). After 12 months of freezing, samples of antibiotic-free and organic poultry showed a pH value similar to that of fresh meat (5.94 and 5.86, respectively). Freezing for 12 months preserved the redness of drumstick meat from conventional broilers (a* = 4.86, on average) and the rearing system did not influence the aw of drumstick meat during the entire experimental period. Freezing preserved the aw of conventional and organic chicken meat samples until the ninth month of evaluation (0.978 and 0.974, respectively). Lipid oxidation in the breast, thigh and drumstick samples from the four rearing systems increased (P < 0.001) from the third month of freezing onwards. There were variations in colour, pH, aw and lipid oxidation of chicken meat among birds raised in different rearing systems. Freezing chicken meat did not prevent colour and pH changes or occurrence of lipid oxidation and did not promote a reduction of aw to levels unfavourable to microbiological development.

Comparisons of management practices and farm design on Australian commercial layer and meat chicken farms: Cage, barn and free range

There are few published studies describing the unique management practices, farm design and housing characteristics of commercial meat chicken and layer farms in Australia. In particular, there has been a large expansion of free range poultry production in Australia in recent years, but limited information about this enterprise exists. This study aimed to describe features of Australian commercial chicken farms, with particular interest in free range farms, by conducting on-farm interviews of 25 free range layer farms, nine cage layer farms, nine barn layer farms, six free range meat chicken farms and 15 barn meat chicken farms in the Sydney basin bioregion and South East Queensland. Comparisons between the different enterprises (cage, barn and free range) were explored, including stocking densities, depopulation procedures, environmental control methods and sources of information for farmers. Additional information collected for free range farms include range size, range characteristics and range access. The median number of chickens per shed was greatest in free range meat chicken farms (31,058), followed by barn meat chicken (20,817), free range layer (10,713), barn layer (9,300) and cage layer farms (9,000). Sheds had cooling pads and tunnel ventilation in just over half of both barn and free range meat chicken farms (53%, n = 8) and was least common in free range layer farms (16%, n = 4). Range access in free range meat chicken farms was from sunrise to dark in the majority (93%, n = 14) of free range meat chicken farms. Over half of free range layer farms (56%, n = 14) granted range access at a set time each morning; most commonly between 9:00 to 10.00am (86%, n = 12), and chickens were placed back inside sheds when it was dusk.

Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform

Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex^® MB40 with 0.2%, and 3) T2: Leiber^® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex^® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

Disease eradication on large industrial farms

Many modern farms exhibit all-in-all-out dynamics in which entire cohorts of livestock are removed from a farm before a new cohort is introduced. This industrialization has enabled diseases to spread rapidly within farms. Here we look at one such example, Marek's disease. Marek's disease is an economically important disease of poultry. The disease is transmitted indirectly, enabling the spread of disease between cohorts of chickens who have never come into physical contact. We develop a model which allows us to track the transmission of disease within a barn and between subsequent cohorts of chickens occupying the barn. It is described by a system of impulsive differential equations. We determine the conditions that lead to disease eradication. For a given level of transmission we find that disease eradication is possible if the cohort length is short enough and/or the cohort size is small enough. Marek's disease can also be eradicated from a farm if the cleaning effort between cohorts is large enough. Importantly complete cleaning is not required for eradication and the threshold cleaning effort needed declines as both cohort duration and size decrease.

Growth performance, carcass traits and physical properties of chicken meat as affected by genotype and production system

Abstract. The results of this study constitute a part of a project aiming at developing a cross-breed suitable for an extensive rearing system, utilising local biodiversity. Hybrids from mating a commercial broiler's male component (C) with Green-legged Partridgenous (GP) or Sussex (Sx) hens were compared with Cobb broilers. The study included 720 chickens of 3 genetic groups. Up to the third week of age, all birds were fed with balanced mixtures recommended for broiler chickens. From the fourth week, the mixture was weekly reduced by 10 % for the birds kept extensively (E). The deducted part was replaced with wheat bran, and from the seventh week with wheat. E groups had access to runs and received green fodder. Birds were slaughtered in 12th week of life. Carcass yield, giblets and proportion of carcass elements were estimated along with meat traits. The body weight at the 6th, 9th, 12th week of rearing and dissection results indicated a good suitability of Cobb chickens for an extensive rearing system. Hybrids were characterised by a considerably smaller proportion of breast muscle and slightly bigger of thighs and drumsticks, compared with Cobb, which could result from their greater motor activity. Results obtained by C × Sx and C × GP chickens, such as final body weight, proportions of abdominal fat and carcass elements, and appropriate value of meat traits, point at the usefulness of these hybrids as a meat-type chicken under extensive housing conditions. Darker colour of chicken meat, derived from C cocks and Sx or GP hens crossbred, can constitute an indicator for their carcasses' identification on the market.

Lower prevalence of antibiotic-resistant Salmonella on large-scale U.S. conventional poultry farms that transitioned to organic practices

As a result of the widespread use of antibiotics in large-scale U.S. poultry production, a significant proportion of Salmonella strains recovered from conventional poultry farms and retail poultry products express antibiotic resistance. We evaluated whether large-scale poultry farms that transitioned from conventional to organic practices and discontinued antibiotic use were characterized by differences in the prevalence of antibiotic-resistant Salmonella compared to farms that maintained conventional practices. We collected poultry litter, water and feed samples from 10 newly organic and 10 conventional poultry houses. Samples were analyzed for Salmonella using standard enrichment methods. Isolates were confirmed using standard biochemical tests and the Vitek®2 Compact System. Antimicrobial susceptibility testing was performed by Sensititre® microbroth dilution. Data were analyzed using Fisher's exact test and generalized linear mixed models. We detected Salmonella in both conventional and newly organic poultry houses. Salmonella Kentucky was the predominant serovar identified, followed by S. Orion, S. Enteritidis, S. Gostrup and S. Infantis. Among S. Kentucky isolates (n=41), percent resistance was statistically significantly lower among isolates recovered from newly organic versus conventional poultry houses for: amoxicillin-clavulanate (p=0.049), ampicillin (p=0.042), cefoxitin (p=0.042), ceftiofur (p=0.043) and ceftriaxone (p=0.042). Percent multidrug resistance (resistance to ≥3 antimicrobial classes) was also statistically significantly lower among S. Kentucky isolates recovered from newly organic poultry houses (6%) compared to those recovered from conventional houses (44%) (p=0.015). To our knowledge, these are the first U.S. data to show immediate, on-farm changes in the prevalence of antibiotic-resistant Salmonella when antibiotics are voluntarily withdrawn from large-scale poultry facilities in the United States.

Prevalence of antibiotic-resistant E. coli in retail chicken: comparing conventional, organic, kosher, and raised without antibiotics

Retail poultry products are known sources of antibiotic-resistant Escherichia coli, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA) - designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant E. coli is unknown. We examined the occurrence of antibiotic-resistant E. coli on raw chicken marketed as conventional, organic, kosher and RWA. From April - June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened E. coli isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant E. coli tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant E. coli, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant E. coli on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant E. coli in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen.

Prevalence of antibiotic-resistant E. coli in retail chicken: comparing conventional, organic, kosher, and raised without antibiotics

Retail poultry products are known sources of antibiotic-resistant Escherichia coli, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA) - designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant E. coli is unknown. We examined the occurrence of antibiotic-resistant E. coli on raw chicken marketed as conventional, organic, kosher and RWA. From April - June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened E. coli isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant E. coli tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant E. coli, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant E. coli on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant E. coli in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen.

Lower prevalence of antibiotic-resistant Enterococci on U.S. conventional poultry farms that transitioned to organic practices

BACKGROUND

In U.S. conventional poultry production, antimicrobials are used for therapeutic, prophylactic, and nontherapeutic purposes. Researchers have shown that this can select for antibiotic-resistant commensal and pathogenic bacteria on poultry farms and in poultry-derived products. However, no U.S. studies have investigated on-farm changes in resistance as conventional poultry farms transition to organic practices and cease using antibiotics.

OBJECTIVE

We investigated the prevalence of antibiotic-resistant Enterococcus on U.S. conventional poultry farms that transitioned to organic practices.

METHODS

Poultry litter, feed, and water samples were collected from 10 conventional and 10 newly organic poultry houses in 2008 and tested for Enterococcus. Enterococcus (n = 259) was identified using the Vitek® 2 Compact System and tested for susceptibility to 17 antimicrobials using the Sensititre™ microbroth dilution system. Data were analyzed using SAS software (version 9.2), and statistical associations were derived based on generalized linear mixed models.

RESULTS

Litter, feed, and water samples were Enterococcus positive. The percentages of resistant Enterococcus faecalis and resistant Enterococcus faecium were significantly lower (p < 0.05) among isolates from newly organic versus conventional poultry houses for two (erythromycin and tylosin) and five (ciprofloxacin, gentamicin, nitrofurantoin, penicillin, and tetracycline) antimicrobials, respectively. Forty-two percent of E. faecalis isolates from conventional poultry houses were multidrug resistant (MDR; resistant to three or more antimicrobial classes), compared with 10% of isolates from newly organic poultry houses (p = 0.02); 84% of E. faecium isolates from conventional poultry houses were MDR, compared with 17% of isolates from newly organic poultry houses (p < 0.001).

CONCLUSIONS

Our findings suggest that the voluntary removal of antibiotics from large-scale U.S. poultry farms that transition to organic practices is associated with a lower prevalence of antibiotic-resistant and MDR Enterococcus.