A highly contiguous genome assembly for the California quail (Callipepla californica).

The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.

In vitro susceptibility of Mycoplasma iowae isolates to antimicrobial agents.

ABSTRACTMycoplasma iowae, a potential re-emerging avian pathogen mainly affecting turkeys, has been reported from many parts of the world. Poor hatchability, embryonic death, joint and skeletal abnormalities, poor ossification, runting-stunting, poor feathering and airsacculitis may be observed in infected flocks. The reduction of the severity of clinical signs and short-term control of M. iowae are performed by antibiotic treatment. However, M. iowae develops resistance more rapidly and is considered to be more resistant to antimicrobials than other avian pathogenic mycoplasmas. The aim of the present study was to determine the in vitro susceptibility of 101 M. iowae isolates and strains to ten clinically important antimicrobial agents, and to analyse and compare the susceptibility patterns of isolates of various origins and from a wide time-period. The examined reference strains showed high susceptibility to all antimicrobials except for spectinomycin. Low concentrations of tiamulin, florfenicol and oxytetracycline inhibited the growth of the clinical isolates. Nevertheless, slow tendency of increasing minimum inhibitory concentration (MIC) values was observed over time in the case of the above mentioned agents, while MIC values of enrofloxacin showed relatively rapid changes. Spiramycin, erythromycin, tilmicosin, tylosin, lincomycin and spectinomycin did not inhibit the bacterial growth in most of the cases. Isolates originating from captive game birds showed similar susceptibility profiles to isolates from industrial turkey hosts. The widely detected low susceptibility of M. iowae isolates to macrolides, lincomycin and spectinomycin, and the increase of MIC values of frequently used antimicrobials against this pathogen, emphasize the importance of targeted antibiotic therapy.RESEARCH HIGHLIGHTSAntimicrobial susceptibilities of 101 Mycoplasma iowae isolates were determined.Minimum inhibitory concentrations were determined by broth micro-dilution method.Tiamulin, oxytetracycline and florfenicol showed low MIC values.Isolates rapidly adapted to antimicrobial pressure.

Susceptibility of wild turkeys (Meleagris gallopavo) to experimental West Nile virus infection.

Since the introduction of West Nile virus (WNV) to North America in 1999, WNV is estimated to have contributed to population-level declines in numerous avian species. However, the potential impacts of this virus on many free-ranging upland game bird species, including the wild turkey (Meleagris gallopavo), which is undergoing regional population declines, remain unknown. Herein, two age groups (∼5 to 6 weeks and ∼15 to 16 weeks post-hatch) of juvenile wild turkeys were subcutaneously inoculated with WNV, sampled daily from 1 to 7 days post-inoculation (dpi), and euthanized on 14 dpi. No clinical signs and minimal gross lesions were attributable to WNV infection. Peak viraemia titres were similar between age groups (<101.7 to 104.6 plaque-forming units [PFU]/ml), but the duration of viraemia was longer in the old group (3-4 days) than in the young group (0-3 days). Intermittent oral and/or cloacal viral shedding from 2 to 7 dpi was detected in both age groups. No infectious virus was detected in the heart, brain, kidney, skeletal muscle, spleen, and feathers from WNV-inoculated turkeys euthanized on 14 dpi. All WNV-inoculated birds seroconverted by 14 dpi, as well as two co-housed sham-inoculated birds. The most consistent microscopic lesions among all WNV-inoculated birds were mild lymphoplasmacytic myocarditis and encephalitis. Minimal immunohistochemical labelling was detected in tissues in addition to scant macrophages within the blood, spleen, and bone marrow. These data suggest WNV is unlikely to pose a significant risk to wild turkey populations, although the possibility remains that WNV may indirectly decrease fitness or predispose wild turkeys to other health stressors.RESEARCH HIGHLIGHTS Clinical disease was not observed in wild turkeys experimentally infected with WNV.Pathology attributed to WNV was mild and included brain and heart inflammation.Viraemias suggest WNV-infected wild turkeys do not play a role in WNV transmission.No age-associated differences in WNV clinical disease or pathology were observed.

Excreta quality and digestive function of singly versus couple caged Sardinian partridges (Alectoris barbara barbara Bonnaterre, 1790) as non-invasive indicators of birds' coping ability to forced pairing.

The Sardinian partridge is a monogamous wild bird species of least concern according to IUCN list at present, though formerly accounted among threatened species for decades. The creation of couples is crucial in captivity, because forced pairing in cages can lead to poor welfare of birds, specially of females. This study investigated the impact of single versus couple caging of Sardinian partridges during non-laying period based on the collection and interpretation of indirect and non-invasive parameters (feed intake; space availability; excreta quality; and nutrient utilization). A total of 24 couples of breeding partridges were enrolled for two consequent phases of a same investigation (lasting 15 days each). During phase 1, all couples were fed ad libitum with a pelleted complete diet (DM, 905 g kg-1 of diet; CP, 160 g kg-1 ; and EE, 25 g kg-1 ). In phase 2, each male from 12 out of 24 couples was moved to an identical cage close to that where the female remained alone, to keep visual contact. The rest of couples continued to be kept like in phase 1. During phases 1 and 2, feed intake and excreta outputs were recorded daily. Pooled excreta of the last 3 days from couples and single birds were assessed for pH and DM, CP and ash content. Nutrient digestibility was calculated. No significant differences were noted between single versus couple caging regarding body weight (438 vs. 422 g respectively) or nutrient digestibility. However, singly housed males reduced daily feed intakes and females increased daily feed intake per g-1 BW (0.041 vs. 0.052 g, respectively, p < 0.001). Our results suggest that singly caged partridges from permanent couples can improve the access to feed and reduce competition during the non-mating season.

Hunted game birds - Carriers of foodborne pathogens.

Game birds may carry zoonotic bacteria in their intestines and transmit them to hunters through bird handling or through the handling and consumption of contaminated meat. In this study, the prevalence of foodborne bacteria was screened from game bird faeces and mallard breast meat using PCR. The sampling occurred in southern Finland from August to December during the hunting season. Isolates were characterized by multi-locus sequence typing. Mesophilic aerobic bacteria and Escherichia coli counts were used to assess the microbial contamination of mallard meat. In total, 100 woodpigeon (Columba palumbus), 101 pheasants (Phasianus colchicus), 110 mallards (Anas platyrhynchos), and 30 teals (Anas crecca) were screened during the hunting season. Additionally, 100 mallard breast meat samples were collected. Campylobacter and Listeria were commonly detected in the faeces and Listeria on mallard meat. L. monocytogenes of sequence types associated with human listeriosis were frequently found in game bird faeces and on mallard meat. Good hygiene during game bird handling, storing the game bird meat frozen, and proper heat treatment are important measures to minimize the health risk for hunters and consumers.

Prevalence and genotype diversity of Campylobacter jejuni in hunted reared pheasants (Phasianus colchicus) in Finland.

Campylobacter spp., especially C. jejuni, is the most common zoonotic pathogen in humans worldwide. In Nordic countries, the prevalence of C. jejuni in broilers, which is an important reservoir of human infections, is generally low. Thus, other sources of domestically acquired infections besides chicken meat need to be considered. Game birds are known to carry a variety of zoonotic agents, including Campylobacter. The aim of this study was to investigate Campylobacter spp. carriage in a flock of reared pheasants at hunting in two successive samplings to better understand the dynamics of Campylobacter infections in pheasants. Overall, 72% of the intestinal samples were positive for Campylobacter spp. by direct culture on mCCDA. C. jejuni was the only species identified. The isolates were genotyped using whole genome sequencing (WGS), multilocus sequence typing (MLST), and ad hoc whole genome MLST (wgMLST). Two distinct C. jejuni clones were identified among the 18 isolates studied, representing MLST sequence types (STs) ST-45 and ST-699. The ST-45 isolates were closely related to previous human clinical isolates using core genome MLST (cgMLST). In contrast, the ST-699 isolates forming the dominant clone in the latter sampling were quite distinct from previously described cgMLST profiles from different hosts and sources worldwide. In conclusion, the intestine of reared pheasants is commonly colonized by C. jejuni and may carry genotypes relevant to infections in livestock and humans. Hygienic measures are needed to limit the spread of infection in reared flocks. Especially farmers and hunters having direct contact with pheasant offal need to be aware of the associated zoonosis risk to protect themselves and their working dogs alike. Biosecurity measures to improve the safety and reduce the zoonosis risk associated with pheasant farming should be further investigated.

Pathogenesis and infection dynamics of high pathogenicity avian influenza virus (HPAIV) H5N6 (clade 2.3.4.4b) in pheasants and onward transmission to chickens.

High pathogenicity avian influenza viruses clade 2.3.4.4 H5 have spread among wild birds worldwide during recent years causing annual die-offs among wild birds and outbreaks in poultry in multiple European countries. The outbreaks significantly impact the poultry and game bird sectors. Infected game birds may act as a bridging species potentially enabling spread of virus into commercial and backyard premises. In this study, the pathogenesis and transmission of a HPAIV clade 2.3.4.4b H5N6 virus was investigated in pheasants and chickens. Efficient virus transmission was detected between pheasants over multiple rounds of naïve pheasant introductions and onwards to chickens. Mortality of up to 100% was observed for both infected pheasants and chickens. Intra-species transmission from chicken to chicken was less efficient. The study confirmed that clade 2.3.4.4b H5N6 HPAIV is highly virulent in pheasants and emphasises the role of pheasants as a bridging host for the infection of commercial poultry.

Comparison of Pathology and Immunohistochemistry in Natural and Experimental West Nile Virus Infections in Ruffed Grouse (Bonasa umbellus).

Ruffed Grouse (Bonasa umbellus) populations have declined in much of the eastern US in recent decades. Research suggests that West Nile virus (WNV) contributed to these declines, based on decreasing population indices temporally correlated to WNV introduction into North America, high morbidity and mortality in experimentally infected Ruffed Grouse, and relatively low statewide seroprevalence concurrent with high WNV vector indices. We describe lesions and relevant diagnostic findings in six, free-ranging Ruffed Grouse that directly or indirectly died of natural WNV infection and compare results to experimentally infected Ruffed Grouse. All naturally infected grouse were found moribund or dead from August to December 2015-18 in the northeastern US; 4/6 grouse were subadults. Necropsy, histopathology, immunohistochemistry, and/or ancillary tests contributed to the diagnosis of WNV-associated disease in all cases. The most common lesions in naturally infected grouse were myocardial inflammation, degeneration, and/or necrosis, consistent with lesions in experimentally infected grouse. Evidence of trauma in 6/6 naturally infected grouse suggests the possibility of WNV-associated morbidity as a predisposing factor. Diagnostic findings in 3/6 naturally infected grouse were consistent with experimentally infected grouse with severe disease 7-8 d postinoculation; the remaining naturally infected birds had similar findings to experimentally infected subclinical grouse. Our results further support the notion that WNV contributes to mortality of free-ranging Ruffed Grouse and may be used to improve surveillance strategies and population-level management approaches.

Experimental West Nile Virus Infection in Northern Bobwhite Quail (Colinus virginianus).

West Nile virus (WNV) has been implicated in regional declines of numerous North American bird species, although its potential impact upon many species, including some game birds, remains unknown. Specifically, information about susceptibility to infection and infection outcome are crucial to assessing health risks. Northern bobwhite quail (Colinus virginianus) are a popular and common game bird across much of the United States, as well as in captive breeding programs and as backyard birds. Two age groups of bobwhites were subcutaneously inoculated with WNV and euthanatized on 15 days postinoculation (DPI). Three of 10 inoculated 5-wk-old and 4/10 inoculated 15-wk-old birds developed detectable viremia titers during 1-5 DPI, with low peak titers (101.7-103.0 plaque-forming units [PFU]/ml). Three of 10 inoculated 5-wk-old and 1/10 inoculated 15-wk-old birds shed low viral titers (peak 100.7-101.8 PFU/swab) either orally or cloacally or both for limited periods from 2 to 6 DPI. All inoculated birds (n = 20) remained apparently healthy and seroconverted by 15 DPI. No infectious virus was detected in select tissues: heart, kidney, brain, skeletal muscle, spleen (15-wk-old group only), and feathers from any of the bobwhites. No sham-inoculated, contact control birds (n = 8) became viremic or had virus isolated from tissues or swabs. The most consistent microscopic lesion was minimal to mild, lymphoplasmacytic myocarditis (6/10 in 5-wk-olds; 5/10 in 15-wk-olds). Immunohistochemical labeling was most often in macrophages in spleen and bone marrow, likely reflective of clearance of infection. There were no statistically significant differences in the peak viremia and shedding titers between age groups and no differences in the development of WNV-associated lesions between the two age groups. These results suggest that WNV is unlikely to pose a health risk to bobwhites and that bobwhites likely are an incompetent reservoir host species in WNV transmission.

Infección experimental por el virus del Nilo occidental en codornices de Virginia (Colinus virginianus). El virus del Nilo Occidental (con las siglas en inglés) se ha visto implicado en la disminución regional de numerosas especies de aves en América del Norte, aunque se desconoce su impacto potencial sobre muchas especies, incluidas algunas aves de caza. Específicamente, la información sobre la susceptibilidad a la infección y el resultado de la infección es crucial para evaluar los riesgos para la salud. La codorniz de Virginia (Colinus virginianus) es un ave de caza popular y común en gran parte de los Estados Unidos, así como en programas de cría en cautiverio y como aves de traspatio. Dos grupos de codornices de diferentes edades fueron inoculadas por vía subcutánea con el virus del Nilo Occidental y fueron sacrificadas 15 días después de la inoculación (DPI). Tres de diez aves inoculadas de cinco semanas y cuatro de diez aves inoculadas de 15 semanas desarrollaron títulos de viremia detectables durante uno a cinco días después de la inoculación, con bajos títulos durante la cima de la curva (101.7­103.0 unidades formadoras de placa [PFU]/ml). Tres de diez aves inoculadas de cinco semanas de edad y una de diez aves inoculadas a las 15 semanas de edad mostraron títulos virales bajos (pico 100.7­101.8 PFU/hisopo) ya sea por vía oral, cloacal o ambas durante períodos limitados de dos a seis días después de la inoculación. Todas las aves inoculadas (n = 20) permanecieron aparentemente sanas y mostraron seroconversión a los 15 días después de la inoculación. No se detectó ningún virus infeccioso en tejidos seleccionados: corazón, riñón, cerebro, músculo esquelético, bazo (solo en el grupo de 15 semanas de edad) y plumas de cualquiera de las codornices. Ninguna ave no inoculada o de control por contacto (n = 8) se volvió virémica o mostró aislamiento viral de los tejidos o hisopos. La lesión microscópica más consistente fue miocarditis linfoplasmocítica de mínima a leve (6/10 en aves de cinco semanas; 5/10 en aves de 15 semanas). La tinción inmunohistoquímica se observó con mayor frecuencia en macrófagos del bazo y la médula ósea, lo que probablemente refleja la eliminación de la infección. No hubo diferencias estadísticamente significativas en el pico de viremia y los títulos de eliminación entre los grupos de edad y no hubo diferencias en el desarrollo de lesiones asociadas con el virus del Nilo Occidental entre los dos grupos de edad. Estos resultados sugieren que es poco probable que el virus del Nilo Occidental represente un riesgo para la salud de las codornices de Virginia y que estas aves probablemente sean una especie hospedadora reservorio incompetente en la transmisión del virus del Nilo Occidental.

Surveillance for Heterakis spp. in Game Birds and Cage-Free, Floor-Raised Poultry in Pennsylvania.

Histomoniasis is a significant disease of gallinaceous birds caused by Histomonas meleagridis. Transmission of this parasite is dependent on use of the cecal nematode Heterakis gallinarum. To define the host range of this nematode, cecal contents from 399 game birds and poultry, representing eight species, were examined for Heterakis spp. The majority of these species (five of eight) were infected with Heterakis nematodes. Heterakis gallinarum was detected in free-ranging wild turkeys (Meleagridis gallopovo), captive-raised ring-necked pheasants (Phasianus colchicus), chukars (Alectoris chukar), and domestic chickens (Gallus gallus domesticus), whereas H. isolonche was found in ruffed grouse (Bonasa umbellus). No Heterakis species were identified in the domestic turkey (Meleagridis gallopovo), American woodcock (Scolopax minor), and dabbling duck (Anas spp.) samples. Genetic characterization indicated that nematodes identified as H. gallinarum were present in two distinct clades. One clade of H. gallinarum sequenced from this study grouped with chicken-derived sequences from other countries. The other group of sequences consisted of a sister clade to a group of parasites morphologically identified as H. isolonche. Currently it is unknown if this group represents a genetic variant of H. gallinarum, a variant of H. isolonche, or a novel species. These results indicate Heterakis infection varies among poultry and game bird species but is common among select gallinaceous species in Pennsylvania.

Nota de investigación- Vigilancia de Heterakis spp. en aves de caza y aves comerciales criadas en piso sin jaulas en Pennsylvania. La histomoniasis es una enfermedad importante de las aves gallináceas causada por Histomonas meleagridis. La transmisión de este parásito depende de la interacción con el nematodo cecal Heterakis gallinarum. Para definir el rango de hospedadores de este nematodo, se examinaron los contenidos cecales de 399 aves de caza y aves domésticas, que representaron a ocho especies, para detectar Heterakis spp. La mayoría de estas especies (cinco de ocho) estaban infectadas con nematodos Heterakis. Heterakis gallinarum se detectó en pavos silvestres (Meleagridis gallopavo), faisanes comunes criados en cautiverio (Phasianus colchicus), perdiz chukar (Alectoris chukar) y pollos domésticos (Gallus gallus domesticus), mientras que H. isolonche se encontró en el grévol engolado (Bonasa umbellus). No se identificaron especies de Heterakis en las muestras de pavo doméstico (Meleagridis gallopavo), chocha americana (Scolopax minor) y pato chapuceadores (Anas spp.). La caracterización genética indicó que los nematodos identificados como H. gallinarum estaban presentes en dos clados distintos. Un clado de H. gallinarum secuenciado de este estudio agrupado con secuencias derivadas de pollos de otros países. El otro grupo de secuencias consistió en un clado hermano de un grupo de parásitos identificados morfológicamente como H. isolonche. Actualmente se desconoce si este grupo representa una variante genética de H. gallinarum, una variante de H. isolonche o una especie nueva. Estos resultados indican que la infección por Heterakis varía entre las aves domésticas y las especies de aves de caza, pero es común entre las especies de gallináceas seleccionadas en Pennsylvania.

ECOLOGIC DRIVERS AND POPULATION IMPACTS OF AVIAN TRICHOMONOSIS MORTALITY EVENTS IN BAND-TAILED PIGEONS (PATAGIOENAS FASCIATA) IN CALIFORNIA, USA.

: Avian trichomonosis, a disease typically caused by the protozoan parasite Trichomonas gallinae , is a well recognized cause of death in many avian species. In California, US, trichomonosis has caused periodic epidemics in Pacific Coast Band-tailed Pigeons ( Patagioenas fasciata monilis). We summarize reported mortality events and investigate ecologic drivers and population impacts associated with epidemic mortality due to trichomonosis in Band-tailed Pigeons. Between 1945 and 2014, 59 mortality events involving Band-tailed Pigeons were reported in California with the number of reported events increasing over time. Estimated mortality for these events was variable, ranging between 10 and 10,000 pigeons. Events were most-frequently reported in Monterey (19%; 11/59) and San Luis Obispo (8%; 5/59) counties. Events often started in January (32%; 9/28) and February (50%; 14/28) and lasted 5-68 d. Impacts of mortality events on pigeon populations were indicated by Breeding Bird Survey and Christmas Bird Count abundance indices, which showed a decline in outbreak years compared to nonoutbreak years. Environmental conditions most associated with outbreak years included higher average temperatures between January and March, the period most associated with mortality events, and lower average precipitation in December just prior to mortality events. In Monterey County, events tended to occur in winters following higher acorn production of coast live oaks ( Quercus agrifolia ) in the fall. Weather and food abundance could be related to increased transmission or enhanced viability of Trichomonas spp. Although estimated mortality due to avian trichomonosis was highly variable across years, cumulative losses were substantial and likely to have a negative impact on population size.

Regulatory Considerations for the Approval of Drugs Against Histomoniasis (Blackhead Disease) in Turkeys, Chickens, and Game Birds in the United States.

Histomoniasis, commonly referred to as blackhead disease, is a serious threat to the turkey and game bird industries worldwide, and it is having an increasingly negative impact on the chicken industry as well. The Food and Drug Administration's (FDA) Center for Veterinary Medicine (CVM), charged with the approval and regulation of new animal drugs in the United States, understands the rising need for the availability of therapeutic options against histomoniasis. CVM has actively engaged in discussions with the poultry industry, academic institutions, and animal health companies regarding the current status of histomoniasis in the United States and varied success of past and current management, prophylactic, and therapeutic interventions that have been used against the disease. As effective options against the disease are severely limited, CVM encourages the poultry industry, academic institutions, and animal health companies to work together to research and develop viable management, prophylactic, and therapeutic strategies, such as litter management, deworming programs, vaccines or other biologics, novel technologies, and animal drugs. CVM also recognizes the potential challenges that the poultry industry, academic institutions, and animal health companies may encounter while working towards the approval of safe and effective drug products for the treatment and control of histomoniasis. With that recognition, CVM encourages interested parties to begin discussions with CVM early in order to align research of the drug product against histomoniasis with the drug approval requirements, such that it leads to the approval of a new animal drug in an efficient and expedient manner. This article provides information about the FDA's regulatory process for the approval of new animal drugs in the United States, with especial emphasis on drug products for the treatment and control of histomoniasis in turkeys, chickens, and game birds.