Coccidiosis, caused by Eimeria species parasites, has long been recognised as an economically significant disease of chickens. As the global chicken population continues to grow, and its contribution to food security intensifies, it is increasingly important to assess the impact of diseases that compromise chicken productivity and welfare. In 1999, Williams published one of the most comprehensive estimates for the cost of coccidiosis in chickens, featuring a compartmentalised model for the costs of prophylaxis, treatment and losses, indicating a total cost in excess of £38 million in the United Kingdom (UK) in 1995. In the 25 years since this analysis the global chicken population has doubled and systems of chicken meat and egg production have advanced through improved nutrition, husbandry and selective breeding of chickens, and wider use of anticoccidial vaccines. Using data from industry representatives including veterinarians, farmers, production and health experts, we have updated the Williams model and estimate that coccidiosis in chickens cost the UK £99.2 million in 2016 (range £73.0–£125.5 million). Applying the model to data from Brazil, Egypt, Guatemala, India, New Zealand, Nigeria and the United States resulted in estimates that, when extrapolated by geographical region, indicate a global cost of ~ £10.4 billion at 2016 prices (£7.7–£13.0 billion), equivalent to £0.16/chicken produced. Understanding the economic costs of livestock diseases can be advantageous, providing baselines to evaluate the impact of different husbandry systems and interventions. The updated cost of coccidiosis in chickens will inform debates on the value of chemoprophylaxis and development of novel anticoccidial vaccines.

The phylum Apicomplexa includes serious pathogens of humans and animals. Understanding the distribution and population structure of these protozoan parasites is of fundamental importance to explain disease epidemiology and develop sustainable controls. Predicting the likely efficacy and longevity of subunit vaccines in field populations relies on knowledge of relevant preexisting antigenic diversity, population structure, the likelihood of coinfection by genetically distinct strains, and the efficiency of cross-fertilization. All four of these factors have been investigated for Plasmodium species parasites, revealing both clonal and panmictic population structures with exceptional polymorphism associated with immunoprotective antigens such as apical membrane antigen 1 (AMA1). For the coccidian Toxoplasma gondii only genomic diversity and population structure have been defined in depth so far; for the closely related Eimeria species, all four variables are currently unknown. Using Eimeria tenella, a major cause of the enteric disease coccidiosis, which exerts a profound effect on chicken productivity and welfare, we determined population structure, genotype distribution, and likelihood of crossfertilization during coinfection and also investigated the extent of naturally occurring antigenic diversity for the E. tenella AMA1 homolog. Using genome-wide Sequenom SNP-based haplotyping, targeted sequencing, and single-cell genotyping, we show that in this coccidian the functionality of EtAMA1 appears to outweigh immune evasion. This result is in direct contrast to the situation in Plasmodium and most likely is underpinned by the biology of the direct and acute coccidian life cycle in the definitive host.Eimeria | coccidiosis | population structure | chickens | food security

Graphical abstract

No abstract

SUMMARYFive thousand one hundred and nineteen chicks were obtained from a diallel combination of four breeds of chickens; (Anak Titan (A), Alpha (B), Giriraja (G) and Normal indigenous (N) chickens) in a broiler improvement program. The chicks were reared to 12 weeks in which data on weekly body weight (BW), breast girth (BG) and tibia length (TL) were recorded. Sire and dam genotype significantly (p<0.05) affected all traits. Anak Titan cocks and hens performed best in body weight (BW) with values ranging from 38.45 ± 0.74 g and 40.21 ± 0.66 g at day old to 1135.93 ± 35.67 g and 953.38 ± 35.38 g at week 12 respectively. Normal and Alpha improved indigenous performed better in linear body parameters. Results of diallel analysis to test for general and specific combining abilities of breeds on traits showed that additive genetic effects were important in determining BW and dominance effects were important for BG, while both effects were important in determining TL. This indicates that selection, crossbreeding and combination of both are tools needed to improve BW, BG and TL, respectively. Anak Titan had the best general combining ability (GCA) of 19.49 ± 0.42, 288.54 ± 7.52, 458.78 ± 12.15 and 769.30 ± 4.80 for BW at weeks 1, 4, 8 and 12, respectively and therefore recommended as a good breed for BW in the improvement program. GB crosses had the best SCA for BG and TL of 7. 43 ± 0.11, 8.21 ± 0.16, 11.82 ± 0.22, 5.90 ± 0.29; 8.50 ± 0.10, 9.68 ± 0.10, 7.92 ± 0.34, 0.86 ± 0.30 at weeks 1, 4, 8 and 12 respectively. It is recommended that an improvement process that involves all the breeds should be adapted using reciprocal recurrent selection or modifications of it. RESUMENCinco mil ciento diecinueve pollos fueron obtenidos, en un programa de mejora de pollos de engorde, a partir de una combinación dialélica de cuatro razas: Anak Titan (A), Alpha (B), Giriraja (G) y Normal indígena (N). Los pollos fueron criados a 12 semanas en las que se registraron los datos sobre peso corporal por semana (BW), circunferencia del pecho (BG) y longitud de la tibia (TL). El genotipo de machos y hembras afectó significativamente (p<0,05) a todos los caracteres. Los gallos y las gallinas Anak Titan mostraron el mejor comportamiento en peso corporal (BW) con valores que van desde 38,45 ± 0,74 g a 40,21 ± 0,66 g al día de edad hasta 1135,93 ± 35,67 g y 953,38 ± 35,38 g en la semana 12, respectivamente. Las razas indígenas mejoradas Normal y Alpha obtuvieron mejores resultados en los parámetros lineales del cuerpo. Los resultados del análisis dialélico para probar las capacidad general y específica de combinación de las razas en los caracteres, mostraron que los efectos genéticos aditivos fueron importantes en la determinación BW y los efectos de dominancia fueron importantes para BG, mientras que ambos efectos son importantes en la determinación de TL. Esto indica que la selección, el mestizaje y la combinación de de 19,49 ± 0,42; 7,52 ± 288,54; 458,78 ± 12,15 y 769,30 ± 4,80 para BW en las semanas 1, 4, 8 y 12, respectivamente, por l...