Prevalence of Select Intestinal Parasites in Alabama Backyard Poultry Flocks.

Keeping chickens as backyard pets has become increasingly popular in the United States in recent years. However, biosecurity is generally low in backyard flocks. As a consequence, they can serve as reservoirs for various pathogens that pose a risk for commercial poultry or human health. Eighty-four fecal samples, 82 from chickens and two from turkeys, from 64 backyard flocks throughout the state of Alabama were collected in the summers of 2017 and 2018. Coccidia oocysts were seen in 64.1% of flocks with oocyst counts in most samples below 10,000 oocysts per gram. Eggs of Ascaridia spp. or Heterakis gallinarum were observed in 20.3% of the flocks, and eggs of Capillaria spp. in 26.6% of the flocks. Egg counts were low, rarely exceeding 1000 eggs per gram. DNA extracted directly from fecal samples was investigated by PCR for other relevant parasites. The results showed that 4.7% of flocks were positive for Histomonas meleagridis, 18.8% of flocks for Tetratrichomonas gallinarum, 18.8% of flocks for Cryptosporidium spp. and 87.5% of flocks for Blastocystis spp. The results will help to provide information that can be used to design outreach programs to improve health and wellbeing of birds in backyard flocks.

Network meta-analysis comparing the effectiveness of anticoccidial drugs and anticoccidial vaccination in broiler chickens.

With the trend to organic production and concerns about using antibiotic feed additives, the control of infections with Eimeria spp. in broiler flocks has become more difficult. Vaccination against coccidia is an alternative, but there are concerns that the live vaccines used might have negative effects on production parameters and intestinal health. Reports of experiments directly comparing anticoccidial drugs and anticoccidial vaccines are rare. This network meta-analysis (NMA) identified and analyzed 61 articles reporting 63 experiments testing anticoccidial drugs and anticoccidial vaccines under conditions resembling commercial broiler production. The effect sizes were mean differences in body weight/body weight gain (BW/BWG) and feed conversion rate (FCR) between the 175 included groups. The results show that groups vaccinated against coccidia have a similar BW/BWG and FCR at processing age compared to groups given anticoccidial drugs. However, the results tended to be more favorable for anticoccidial drugs than for vaccines. The analysis of eight subsets, containing only groups (1) groups that had not received an AGP in addition to an anticoccidial drug, (2) groups that had not received ionophores, (3) groups that had not received chemicals, (4) groups that had not received an attenuated vaccine, (5) groups that had not received a fully virulent vaccine, (6) groups that were not additionally challenged with bacteria or not challenged, (7) groups that had received a severe challenge as defined by a total infection dose of more than 100,000 oocysts or were not challenged, (8) groups that were challenged on day 15 or earlier or not challenged brought similar results and confirmed the robustness of the NMA. In addition, the analysis exposes unnecessary, as well as inherent, problems with data quality, which every researcher working with coccidia should carefully consider, and identifies under-researched areas that should be addressed in future research.

Influence of Eimeria spp. Infection on Chicken Jejunal Microbiota and the Efficacy of Two Alternative Products Against the Infection.

Eimeria spp. are important intestinal pathogens of chickens (Gallus gallus domesticus). Anticoccidial feed additives, chemicals, and ionophores have traditionally been used to control Eimeria infections in broiler production. Thus, the trend toward antibiotic-free and organic production requires new approaches to coccidiosis prevention. Two not mutually exclusive methods are the use of plant extracts with antiparasitic activity and manipulation of the intestinal microbiota by pre- and probiotics. In the present study, birds were inoculated with a combination of Eimeria acervulina, Eimeria maxima, and Eimeria tenella. We profiled the jejunal microbiome at multiple time points postinfection to investigate the changes in jejunum microbiota and to identify the time point of the maximum difference between infected and noninfected birds. Additionally, we assessed the anticoccidial effects of two anecdotal treatment methods, green tea and apple cider vinegar, as well as amprolium. Green tea and apple cider vinegar had no effect on oocyst shedding, but green tea reduced the mild unspecific lesions in coccidia-infected birds; there was no influence on unspecific lesions in uninfected controls. Jejunal contents were collected on the day of the infection and 1, 2, 4, 6, 10, and 14 days postinfection (dpi) for investigation of the intestinal microbiota by 16S ribosomal (r)RNA gene sequencing. Comparison of the untreated-uninfected and the untreated-infected groups showed a maximum community dissimilarity of 10 dpi. From 4 days after infection, Clostridiales were significantly enriched at the expense of Lactobacillales in infected compared with uninfected birds. Interestingly, treatment with green tea prevented proliferation of Clostridiales induced by the coccidia and increased the relative abundance of Melainabacteria.

Influencia de la infección de Eimeria spp. en el microbiota yeyunal del pollo y en la eficacia de dos productos alternativos contra la infección. Los protozoarios del género Eimeria spp. son importantes patógenos intestinales de los pollos (Gallus gallus domesticus). Los aditivos anticoccidiales en el alimento, los productos químicos y los ionóforos se han utilizado tradicionalmente para controlar las infecciones por Eimeria en la producción de pollos de engorde. Por lo tanto, la tendencia hacia la producción orgánica y libre de antibióticos requiere nuevos enfoques para la prevención de la coccidiosis. Dos métodos no mutuamente excluyentes son el uso de extractos de plantas con actividad antiparasitaria y la manipulación de la microbiota intestinal por prebióticos y probióticos. En el presente estudio, las aves fueron inoculadas con una combinación de Eimeria acervulina, Eimeria maxima y Eimeria tenella. Se determinó el perfil del microbioma yeyunal en múltiples puntos de tiempo después de la infección, para investigar los cambios en la microbiota del yeyuno e identificar el momento donde se observa la diferencia máxima entre las aves infectadas y no infectadas. Además, se evaluaron los efectos anticoccidiales de dos métodos de tratamiento basados por datos anecdóticos, el té verde y el vinagre de sidra de manzana, así como el amprolium. El té verde y el vinagre de sidra de manzana no tuvieron ningún efecto sobre el desprendimiento de oocistos, pero el té verde redujo las lesiones leves inespecíficas en aves infectadas con coccidia; no hubo influencia en lesiones inespecíficas en controles no infectados. Los contenidos yeyunales se recogieron el día de la infección y a los días 1, 2, 4, 6, 10 y 14 después de la infección (dpi) para la investigación de la microbiota intestinal mediante secuenciación del gene del ARN ribosómico 16S. La comparación de los grupos no tratados-no infectados y no tratados-infectados mostró una diferencia máxima en la comunidad a los diez días después de la inoculación. A partir de los cuatro días después de la infección, los agentes Clostridiales se enriquecieron significativamente a expensas de los Lactobacillales en aves infectadas en comparación con las aves no infectadas. Curiosamente, el tratamiento con té verde evitó la proliferación de Clostridiales inducida por los coccidios y aumentó la abundancia relativa de melainabacterias.

Evaluation of Next-Generation Amplicon Sequencing to Identify Eimeria spp. of Chickens.

Identifying Eimeria spp. circulating in a poultry flock assists in designing vaccine preventive programs, as different species do not cross-protect. Because species differ in anticoccidial drug susceptibility, species identification can also be used to optimize anticoccidial medication. In the present study, we designed pan-Eimeria-specific primers for the 18S rDNA and the cytochrome oxidase I (COI) genes, and tested whether next-generation sequencing of their amplicons allowed reliable identification of Eimeria spp. in samples of isolated oocysts. For each gene, two sets of primers to be used in a nested PCR (nPCR) system were designed. In silico evaluation of the primers using published sequences showed that nucleotide sequence identities of the nested amplicons were less than 97% between most species, while only identities of 18S rDNA genes of Eimeria necatrix and Eimeria tenella and between the COI genes of Eimeria mitis and Eimeria mivati were higher than 97%. Three vaccines and five Eimeria samples from chickens in backyard flocks were investigated by nPCRs and by direct PCRs (dPCR) using the nested (inner) primers with genomic DNA as the template. Seventeen further Eimeria samples from chickens in backyard flocks and three Eimeria samples from commercial broiler flocks were investigated only by nPCR. Sequencing nPCR products tended to detect more species than sequencing dPCR products and sequencing 18S rDNA products tended to detect more species than sequencing COI products. Regarding the detected species, there was a clear difference between the commercial broiler flocks and the backyard flocks. Eimeria acervulina, Eimeria maxima, and E. tenella/E. necatrix were the only species detected in broiler flocks, while the population in the backyard flocks was more varied, with Eimeria brunetti and E. mitis/E. mivati and the previously described operational taxonomic unit Y being more prevalent. Several sequences having less than 97% identity with one of the sequences used for clustering were detected in samples from backyard flocks. In conclusion, next-generation amplicon sequencing can be a useful tool to determine which Eimeria spp. are circulating in chicken flocks.

Evaluación de la secuenciación de nueva generación de amplicones para identificar Eimeria spp. de pollos. La identificación de Eimeria spp.que está circulando en una parvada avícola ayuda a diseñar programas preventivos de vacunas, ya que entre las diferentes especies no existe protección cruzada. Debido a que las especies difieren en la susceptibilidad a los medicamentos anticoccidiales, la identificación de especies también se puede utilizar para optimizar la medicación anticoccidial. En el presente estudio, se diseñaron iniciadores específicos genéricos de Eimeria para los genes de ADNr 18S y de citocromo oxidasa I (COI) y se evaluó si la secuenciación de nueva generación de los amplicones permitía la identificación confiable de Eimeria spp. en muestras de ooquistes aislados. Para cada gene, se diseñaron dos conjuntos de iniciadores que se utilizaron en un sistema de PCR anidado (nPCR). La evaluación in silico de los iniciadores usando secuencias publicadas mostró que las identidades de la secuencia de nucleótidos de los amplicones anidados eran inferiores al 97% entre la mayoría de las especies, mientras que solo las identidades de los genes de ADNr 18S de Eimeria necatrix y Eimeria tenella y entre los genes de citocromo oxidasa I de Eimeria mitis y Eimeria mivati fueron superiores al 97%. Se analizaron tres vacunas y cinco muestras de Eimeria de parvadas de pollos de traspatio con el sistema de PCR anidado y con PCR directa (dPCR) utilizando los iniciadores anidados (internos) con ADN genómico como modelo. Diecisiete muestras adicionales de Eimeria de parvadas de pollos de traspatio y tres muestras de Eimeria de parvadas de pollos de engorde comerciales fueron analizadas solo por PCR anidada. La secuenciación de productos PCR anidada tendió a detectar más especies que la secuenciación de productos por el método directo de PCR y la secuenciación de productos de ADNr 18S pareció detectar más especies que la secuenciación de productos de citocromo oxidasa I. Con respecto a las especies detectadas, hubo una clara diferencia entre las parvadas comerciales de engorde y las parvadas de traspatio. Eimeria acervulina, Eimeria maxima y E. tenella/E. Necatrix fueron las únicas especies detectadas en las parvadas de engorde, mientras que la población en las parvadas de traspatio fue más variada, con Eimeria brunetti y E. mitis/E. mivati, también la unidad taxonómica operativa Y descrita anteriormente fue más prevalente. Varias secuencias con menos del 97% de identidad con una de las secuencias utilizadas para la agrupación fueron detectadas en muestras de parvadas de traspatio. En conclusión, la secuenciación de nueva generación de amplicones puede ser una herramienta útil para determinar que especies de Eimeria spp. están circulando en parvadas de pollos.