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Concept: Poultry farming

169

Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including , and . After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as , , , and multiple sequence types. Retail products were dominated by , but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of . These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.

Concepts: Food, Foodborne illness, Sequence, Poultry farming, Poultry, Pathogen, Bacteria, Microbiology

109

Two broiler trials were designed to investigate the relationship between the concentration of non-starch polysaccharides (NSP) in wheat and 1) its nutritional value for broilers and 2) the efficacy of exogenous enzymes. In a balance trial, diets were formulated with 3 wheat cultivars (Rustic and Viscount-medium NSP, Centenaire-high NSP) and were tested with or without the addition of an exogenous enzyme mixture. The diets were fed to 144 male Ross 308 broiler chickens housed in digestibility cages. Total tract nutrient digestibilities and AMEn were measured from 18 to 22 d of age. In a performance trial, diets were formulated with wheat (medium NSP diet) or with wheat mixed with rye and barley (high NSP diet) and were tested with or without the addition of an exogenous enzyme mixture. The diets were fed to 960 male Ross 308 broilers housed in pens and broiler performance during starter, grower and finisher periods was measured.In the balance trial, wheat cultivar did not affect nutrient digestibility or AMEn. Enzyme addition caused a significant increase in nutrient digestibilities and AMEn for the diet formulated with the high NSP wheat Centenaire only. In the performance trial, feeding the high NSP diet resulted in a higher feed conversion ratio and lower final body weight compared to the medium NSP diet. The largest improvements by enzyme addition were observed in the high NSP diet.In conclusion, the study was not able to show a consistent relationship between the NSP concentration of wheat and its nutritional value, but did demonstrate that the effect of an enzyme mixture on nutrient digestibility or broiler performance depends upon the NSP concentration in the diet.

Concepts: Starch, Metabolism, Poultry farming, Chicken, Feed conversion ratio, Broiler, Protein, Nutrition

24

The present study represents the first description of ionophore resistance in recovered from commercial Algerian (Jijel-Algeria) broiler farms. Microscopy and intervening transcribed sequence 1 PCR (ITS1 PCR) revealed only 2 Eimeria species present in litter from these farms- namely Eimeria acervulina and Eimeria maxima. A pool of these isolates were evaluated in broiler chickens (Cobb 500) for sensitivity to 5 anticoccidial compounds-diclazuril (1ppm), lasalocid (125ppm), monensin (125ppm), narasin (70ppm) and salinomycin (60ppm). As indicated by anticoccidial sensitivity profiles based on lesion scores and anticoccidial index (ACI), complete resistance to monensin and narasin, partial resistance to salinomycin and lasalocid, and complete sensitivity to diclazuril was observed. While lack of sensitivity to monensin is not surprising given its use for years as the sole anticoccidial compound, the resistance to monoether (narasin) and polyether (lasalocid) ionophores suggests that cross-resistance has developed in a segment of the Eimeria population. The fairly uniform Eimeria species composition among all poultry farms suggests that E. acervulina and E. maxima more rapidly develop resistance to ionophore drugs.

Concepts: Apicomplexa, Ionophores, Poultry farming, Monensin, Coccidiostat, Salinomycin, Ionophore, Eimeria

23

With the increasing production of ethanol for biofuels, a by-product of corn-based ethanol fermentation, dried distillers grains with solubles (DDGS) is finding its way into the feed of agricultural animals including cattle, pigs, poultry, sheep, goats, aquaculture species and horses. Corn DDGS contains very high levels of non-starch polysaccharides and could be considered a good source of fibre. Despite knowledge of the role of the fibre in modulating intestinal microbiota and consequently influencing health, there is currently little information on the interactions between DDGS and intestinal microbiota. We assessed the changes in the cecal microbiota of broilers feed rations supplemented with DDGS (five concentrations: 0, 6, 12, 18 and 24% w/w) with and without presence of digestive enzymes. DDGS concentration was strongly positively correlated (P = 3.7e(-17), r = 0.74) with feed conversion efficiency (FCR), diminishing broiler performance with higher concentrations. Additionally, DDGS concentrations positively correlated with Richness index (P = 1.5e(-3), r = 0.5), increasing the number of detectable species in the cecum. Among the most affected genera, Faecalibacterium (P = 0.032, r = -0.34) and Streptococcus (P = 7.9e(-3), r = -0.39) were negatively correlated with DDGS, while Turicibacter (P = 2.8e(-4), r = 0.52) was positively correlated with the DDGS concentration. Enzymes showed minimal effect on cecal microbiota.

Concepts: Poultry farming, Biofuel, Distillers grains, Fodder, Starch, Yeast, Bacteria, Ethanol fuel

21

The effect of commercial selection on the growth, efficiency, and yield of broilers was studied using 2 University of Alberta Meat Control strains unselected since 1957 and 1978, and a commercial Ross 308 strain (2005). Mixed-sex chicks (n = 180 per strain) were placed into 4 replicate pens per strain, and grown on a current nutritional program to 56 d of age. Weekly front and side profile photographs of 8 birds per strain were collected. Growth rate, feed intake, and measures of feed efficiency including feed conversion ratio, residual feed intake, and residual maintenance energy requirements were characterized. A nonlinear mixed Gompertz growth model was used to predict BW and BW variation, useful for subsequent stochastic growth simulation. Dissections were conducted on 8 birds per strain semiweekly from 21 to 56 d of age to characterize allometric growth of pectoralis muscles, leg meat, abdominal fat pad, liver, gut, and heart. A novel nonlinear analysis of covariance was used to test the hypothesis that allometric growth patterns have changed as a result of commercial selection pressure. From 1957 to 2005, broiler growth increased by over 400%, with a concurrent 50% reduction in feed conversion ratio, corresponding to a compound annual rate of increase in 42 d live BW of 3.30%. Forty-two-day FCR decreased by 2.55% each year over the same 48-yr period. Pectoralis major growth potential increased, whereas abdominal fat decreased due to genetic selection pressure over the same time period. From 1957 to 2005, pectoralis minor yield at 42 d of age was 30% higher in males and 37% higher in females; pectoralis major yield increased by 79% in males and 85% in females. Over almost 50 yr of commercial quantitative genetic selection pressure, intended beneficial changes have been achieved. Unintended changes such as enhanced sexual dimorphism are likely inconsequential, though musculoskeletal, immune function, and parent stock management challenges may require additional attention in future selection programs.

Concepts: Sexual dimorphism, Gender, Immune system, Natural selection, Sex, Poultry farming, Feed conversion ratio, Pectoralis major muscle

7

By 2030, the global population will be 8.5 billion, placing pressure on international poultry production, of which China is a key producer(1). From April 2017, China will implement the withdrawal of colistin as a growth promoter, removing over 8,000 tonnes per year from the Chinese farming sector(2). To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using blaNDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies. Here, we show that mcr-1, but not blaNDM, is prevalent in hatcheries, but blaNDM quickly contaminates flocks through dogs, flies and wild birds. We also screened samples directly for resistance genes to understand the true breadth and depth of the environmental and animal resistome. Direct sample testing for blaNDM and mcr-1 in hatcheries, commercial farms, a slaughterhouse and supermarkets revealed considerably higher levels of positive samples than the blaNDM- and mcr-1-positive E. coli, indicating a substantial segment of unseen resistome-a phenomenon we have termed the ‘phantom resistome’. Whole-genome sequencing identified common blaNDM-positive E. coli shared among farms, flies, dogs and farmers, providing direct evidence of carbapenem-resistant E. coli transmission and environmental contamination.

Concepts: Escherichia, Poultry farming, Enterobacteriaceae, Sample, People's Republic of China, Farm, China, Escherichia coli

7

Arsenicals (roxarsone and nitarsone) used in poultry production likely increase inorganic arsenic (iAs), monomethylarsonic acid (MMA), dimethylarsinic acid (DMA), and roxarsone or nitarsone concentrations in poultry meat. The association between poultry intake and exposure to these arsenic species, as reflected in elevated urinary arsenic concentrations, however, is unknown.

Concepts: Game, White meat, Arsine, Poultry farming, Livestock, Meat, Arsenic, Poultry

4

Antimicrobial use for growth promotion in food animal production is now widespread. A major concern is the rise of antimicrobial resistance and the subsequent impact on human health. The antimicrobials of concern are used in concentrated animal feeding operations (CAFOs) which are responsible for almost all meat production including swine and poultry in the US. With global meat consumption rising, the CAFO model has been adopted elsewhere to meet this demand. One such country where this has occurred is China, and evidence suggests 70% of poultry production now occurs outside of traditional small farms. Moreover, China is now the largest aggregate consumer of meat products in the world. With this rapid rise in consumption, the Chinese production model has changed along with the use of antimicrobials in feeds. However, the specific antibiotic use in the Chinese food animal production sector is unclear. Additionally, we are aware of high quantities of antimicrobial use because of reports of high concentrations of antimicrobials in animal waste and surface waters surrounding animal feeding operations.

Concepts: Egg, China, Concentrated Animal Feeding Operation, Antibiotic resistance, Nutrition, Livestock, Factory farming, Poultry farming

3

The incidence of human infections caused by Campylobacter jejuni and C. coli, the main bacterial agents of gastrointestinal disease, has been increasing worldwide. Here, we review the role of poultry as a source and reservoir for Campylobacter. Contamination and subsequent colonization of broiler flocks at the farm level often lead to transmission of Campylobacter along the poultry production chain and contamination of poultry meat at retail. Yet, Campylobacter prevalence in poultry as well as the contamination level of poultry products vary greatly between different countries and thus, urge differences in the intervention strategies that need to be applied. In addition, temporal patterns in poultry do not always coincide with those found in human infections. Moreover, studies in rural and urban areas have revealed differences in Campylobacter infections attributed to poultry, as poultry seems to be the predominant reservoir in urban, but not necessarily in rural settings. Furthermore, foreign travel is considered a major risk factor in acquiring the disease, especially for individuals living in the northern European countries. Intervention strategies aimed at reducing Campylobacter colonization in poultry and focused on the farm level have been successful in reducing the number of Campylobacter cases in several countries. Increasing farm biosecurity and education of consumers are likely to limit the risk of infection. Overall, poultry is an important reservoir and source of human campylobacteriosis, although the contribution of other sources, reservoirs and transmission warrants more research.

Concepts: Meat, Campylobacteriosis, Epidemiology, Poultry, Poultry farming, Disease, Campylobacter, Campylobacter jejuni

2

In poultry production intestinal health and function is paramount to achieving efficient feed utilisation and growth. Uncovering the localised molecular mechanisms that occur during the early and important periods of growth that allow birds to grow optimally is important for this species. The exposure of young chicks to used litter from older flocks, containing mixed microbial populations, is a widely utilised model in poultry research. It rarely causes mortality but effects an immunogenic stimulation sufficient enough to cause reduced and uneven growth that is reflective of a challenging growing environment.

Concepts: Effects unit, Challenge, Causality, Effect, Biology, Chicken, Poultry farming, Broiler