This study focuses on virus isolation of avian reoviruses from a tenosynovitis outbreak between September 2015 and June 2018, the molecular characterization of selected isolates based on partial S1 gene sequences, and the full genome characterization of seven isolates. A total of 265 reoviruses were detected and isolated, 83.3% from tendons and joints, 12.3% from the heart and 3.7% from intestines. Eighty five out of the 150 (56.6%) selected viruses for sequencing and characterization were successfully detected, amplified and sequenced. The characterized reoviruses grouped in six distinct genotypic clusters (GC1 to GC6). The most represented clusters were GC1 (51.8%) and GC6 (24.7%), followed by GC2 (12.9%) and GC4 (7.2%), and less frequent GC5 (2.4%) and GC3 (1.2%). A shift on cluster representation throughout time occurred. A reduction of GC1 and an increase of GC6 classified strains was noticed. The highest homologies to S1133 reovirus strain were detected in GC1 (~77%) while GC2 to GC6 homologies ranged between 58.5 and 54.1%. Over time these homologies have been maintained. Seven selected isolates were full genome sequenced. Results indicated that the L3, S1 and M2 genes, coding for proteins located in the virus capsid accounted for most of the variability of these viruses. The information generated in the present study helps the understanding of the epidemiology of reoviruses in California. In addition, provides insights on how other genes that are not commonly studied add variability to the reovirus genome.

SUMMARY Except for the important role coccidia have as predisposing factors of necrotic enteritis, the role parasites play in the dynamics of a healthy microbiota of chickens is not well explored. This review describes the interactions of relevant intestinal parasites of chickens with bacteria. Infection with Eimeria spp. favor the growth of Clostridium perfringens and suppress the growth of many other bacteria by increasing viscosity and passage time of the ingesta, and by causing lesions to the intestinal mucosa that improve the availability of nutrients for C. perfringens. Conversely, there are indications that bacteria influence the course of disease after infections with Eimeria spp. Not much is known about intestinal cryptosporidiosis in chickens, but results in mice show that the intestinal microbiota induces some resistance against infection with Cryptosporidium parvum and that the innate immune response triggered by infections with cryptosporidia might have an effect on other intestinal microbes.... RESUMEN Estudio Recapitulativo- Interacciones entre parásitos y la microbiota bacteriana en los pollos. Excepto por el papel importante que tienen las coccidias como factores predisponentes de la enteritis necrótica, el papel que juegan los parásitos en la dinámica de una microbiota sana de pollos no ha sido bien explorado. En esta revisión describen las interacciones de parásitos intestinales relevantes de pollos con bacterias. La infección con Eimeria spp. favorece el crecimiento de Clostridium perfringens y disminuye el crecimiento de muchas otras bacterias aumentando la viscosidad y el tiempo de paso de la ingesta y causando lesiones a la mucosa intestinal que mejoran la disponibilidad de nutrientes para C. perfringens. Por otro lado, hay indicios de que las bacterias influyen en el curso de la enfermedad posterior a las infecciones con Eimeria spp. No se sabe mucho sobre la criptosporidiosis intestinal en pollos, pero los resultados en ratones muestran que la microbiota intestinal induce cierta resis...

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.

Increased consumer concern for animal welfare has led some poultry producers to alter their stunning methods from electrical to controlled atmosphere stunning. The potential for different impacts on meat quality between commercially applied controlled atmosphere stunning (CAS) and electrical stunning (ES) using current US parameters needs further evaluation. Three trials were conducted in a commercial broiler processing facility that uses separate processing lines for ES and CAS. Blood glucose concentrations were measured from broilers stunned by either CAS or ES at: 1) lairage, 2) pre-stunning, and 3) post-stunning, using a glucose monitor. Occurrence of visible wing damage was evaluated post-defeathering and breast fillet meat quality was evaluated through measurement of pH, color, and drip loss at deboning and after 24 h. Data were analyzed using GLM or chi-square with a significance at P ≤ 0.05 and means were separated by Tukey's HSD. Blood glucose concentrations (mg/dL) from CAS and ES birds were not different at lairage (284, 272, P = 0.2646) or immediately prior to stunning (274, 283, P = 0.6425). Following stunning and neck cut, circulating blood glucose from birds stunned by CAS was higher than ES (418, 259, P < 0.0001). CAS carcasses had more visible wing damage than ES carcasses (3.6%, 2.2%, P < 0.0001). Breast fillet pH was lower, L* was higher, and a* was lower at debone for CAS fillets (5.81, 54.65, 1.96) compared to ES fillets (5.92, 53.15, 2.31, P < 0.0001, P = 0.0005, P = 0.0303). Drip loss did not differ between breast fillets from CAS or ES broilers (4.83, 4.84; P = 0.0859). The implications of increased blood glucose concentration post-CAS are unknown and require further evaluation. However, the increase in visible wing damage observed post-defeathering from CAS carcasses indicated a need for equipment parameter adjustments during the process from stunning through defeathering when using CAS for broiler stunning. Although differences were observed in breast fillet attributes at deboning, these differences would have minimal practical application and were no longer present at 24 h. Overall, use of CAS in a commercial facility resulted in differences in subsequent product quality when compared to ES.

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.

The aim of this study was to evaluate and quantify the parasitological challenge in pastured poultry production in the state of Georgia. Over the course of 1 yr, fecal samples from six turkey flocks, 10 broiler flocks, and 13 layer flocks were collected on a pastured farm in 2-wk intervals to determine counts of Eimeria oocysts and nematode eggs. Average coccidia counts were 10,198 oocysts per gram of feces (OPG) in broiler flocks, 1470 OPG in layer flocks, and 695 OPG in turkey flocks. The means in broiler and turkey flocks were higher at their first week on pasture. Counts in broilers and layers were significantly higher in spring than in winter and summer. Coccidia counts in broilers were lower than published numbers in conventionally reared poultry, indicating the rotation system of the pastures might effectively reduce the infection pressure. Next-generation sequencing of PCR products showed the presence of most described Eimeria spp. in broilers, layers, and turkeys. In addition, operational taxonomic units (OTUs) x, y, and z were found. The frequency of species was similar for broilers and layers, with the exception that Eimeria praecox and OTU z were more common in layers. In layer flocks, the average count of roundworm eggs per gram of feces (EPG) was 509 EPG with 80% of the samples being positive. The mean counts had no clear pattern related to age. There was an increase of EPG with the increase of temperatures during spring and summer with the peak at midfall. Worm eggs from laying hens were identified as Ascaridia galli. The seasonal differences suggest that higher temperatures might result in an increase of egg survival and sporulation in the environment.