Commercial Layer Farms Research Articles

Characterizing the domestic-wild bird interface through camera traps in an area at risk for avian influenza introduction in Northern Italy

Direct or indirect interactions between sympatric wildlife and poultry can lead to interspecies disease transmission. Particularly, avian influenza (AI) is a viral epidemic disease for which the poultry-wild bird interface shapes the risks of new viral introductions into poultry holdings. Given this background, the study hereby presented aimed to identify wild bird species in poultry house surroundings and characterize the spatiotemporal patterns of these visits. Eight camera traps were deployed for a year (January to December 2021) in three commercial chicken layer farms, including free-range and barn-type setups, located in a densely populated poultry area in Northern Italy at high risk for AI introduction via wild birds. Camera traps’ positions were chosen based on wildlife signs identified during preliminary visits to the establishments studied. Various methods, including time series analysis, correspondence analysis, and generalized linear models, were employed to analyze the daily wild bird visits. A total of 1,958 camera trap days yielded 5,978 videos of wild birds from 27 different species and 16 taxonomic families. The animals were predominantly engaged in foraging activities nearby poultry houses. Eurasian magpies (Pica pica), ring-necked pheasants (Phasianus colchicus) and Eurasian collared doves (Streptopelia decaocto) were the most frequent visitors. Mallards (Anas platyrhynchos), an AI reservoir species, were observed only in a farm located next to a fishing sport lake. Time series analysis indicated that wild bird visits increased during spring and winter. Farm and camera trap location also influenced visit frequencies. Overall, the results highlighted specific species that could be prioritized for future AI epidemiological surveys. However, further research is required to assess their susceptibility and infectivity to currently circulating AI viruses, essential for identifying novel bridge hosts.

Seroprevalence and pathology of Mycoplasma gallisepticum infection in layer birds

Avian mycoplasmosis, caused by Mycoplasma gallisepticum (MG), imposes a significant threat to the poultry industry in Bangladesh, leading to considerable economic losses. This study aimed to determine the seroprevalence of MG and characterize the associated pathology in MG-infected layer birds from different geographical areas within the Nilphamari district. Our hypothesis suggested that the seroprevalence of MG infection in layer birds may vary based on geographical location within the Nilphamari district of Bangladesh, with higher prevalence expected in areas with colder temperatures, such as during the winter season, and in densely populated poultry farming regions. For the serum plate agglutination test, 400 random blood samples were collected, while tissue samples from suspected layer birds with respiratory distress were obtained from 40 commercial layer farms for histopathological analysis. The serum plate agglutination test revealed an overall seroprevalence of MG of 64.25%, with the highest prevalence occurring during the winter season (70%), particularly among layer birds aged 20-40 weeks. Moreover, the seroprevalence of MG was significantly higher in Kishoregonj upazila (68%) compared to Nilphamari sadar (62%). Gross examination of MG-infected layer birds unveiled characteristic features such as tracheal hemorrhages and mucous accumulation, pulmonary edema and hemorrhages, and air sac cloudiness. Histopathological observations included tracheal mucosal sloughing and increased goblet cell numbers, as well as lung edema, hemorrhages, and tissue destruction, alongside significant reactive cell infiltration and exudation in the air sacs. By shedding light on the current MG infection status in layer chickens within the Nilphamari district, this study provides valuable insights to aid poultry industry stakeholders in formulating preventive strategies and enhancing the overall health and welfare of poultry flocks. Asian J. Med. Biol. Res. 2024, 10(1), 58-66

Seasonal changes in bird communities on poultry farms and house sparrow-wild bird contacts revealed by camera trapping.

Wild birds are considered reservoirs of poultry pathogens although transmission routes have not been conclusively established. Here we use camera trapping to study wild bird communities on commercial layer and red-legged partridge farms over a one-year timeframe. We also analyze direct and indirect interactions of other bird species with the house sparrow (Passer domesticus), a potential bridge host. We conducted camera trapping events between January 2018 and October 2019, in two caged layer farms, one free-range layer farm, and two red-legged partridge farms in South-Central Spain. We observed wild bird visits on all types of farms, with the significantly highest occurrence on red-legged partridge farms where food and water are more easily accessible, followed by commercial caged layer farms, and free-range chicken farms. The house sparrow (Passer domesticus) followed by spotless starlings (Sturnus unicolor) was the most encountered species on all farms, with the highest frequency in caged layer farms. On partridge farms, the house sparrow accounted for 58% of the wild bird detections, while on the free-range chicken farm, it made up 11% of the detections. Notably, the breeding season, when food and water are scarce in Mediterranean climates, saw the highest number of wild bird visits to the farms. Our findings confirm that the house sparrow, is in direct and indirect contact with layers and red-legged partridges and other wild birds independent of the type of farm. Contacts between house sparrows and other bird species were most frequent during the breeding season followed by the spring migration period. The species most frequently involved in interactions with the house sparrow belonged to the order Passeriformes. The study provides a comparative description of the composition and seasonal variations of bird communities in different types of layer/ poultry farms in Southern Spain i.e. a Mediterranean climate. It confirms the effectiveness of biosecurity measures that restrict access to feed and water. Additionally, it underscores the importance of synanthropic species, particularly the house sparrow, as potential bridge vector of avian pathogens.

Prevalence and characterization of non-typhoidal Salmonella in egg from grading and packing plants in Korea

Egg washing guidelines vary across countries; however, since 2020, Korea has required that all eggs produced from farms with more than 10,000 laying hens must be washed through egg grading and packing (GP) plant. This study investigated the prevalence and characterization of non-typhoidal Salmonella in eggs after washing at GP plants. In total, 16,800 eggs were collected from 60 egg GP plants located inside commercial layer farms, and 840 pooled eggshell and egg contents were tested for Salmonella, respectively. Of the 60 GP plants tested, 11 (18.3%) and 12 (20.0%) plants were positive for Salmonella spp. In the eggshells and egg contents, respectively. In particular, High Salmonella prevalence in the eggshells and egg contents occurred most often in farms with laying hens older than 80 weeks (33.3% and 40.0%, respectively). However, among 840 pooled eggshells and egg content samples, only 19 (2.3%) of each sample type were positive only for non-typhoidal Salmonella spp. The most common Salmonella serovar in both eggshells and egg contents was S. Infantis, which was found in five (8.3%) of 60 GP plants for both samples types. The other Salmonella serovars detected in eggshells were S. Bareilly (5.0%), S. Agona (3.3%), S. Enteritidis (1.7%), and S. Montevideo (1.7%), whereas those detected in egg contents were S. Enteritidis (5.0%), S. Agona (3.3%), S. Newport (3.3%), S. Senftenberg (3.3%), and S. Derby (1.7%). Of the 19 virulence genes tested, 14 genes were detected in all Salmonella. Interestingly, the spvB gene was detected only in S. Enteritidis, and the sefC gene was detected only in S. Enteritidis and S. Senftenberg. Moreover, all S. Infantis isolates showed multidrug resistance (MDR) against five or more classes, and the other serovars only showed MDR against three to four classes or no MDR. These results suggest that comprehensive surveillance and advanced management approaches for egg GP plants are required to minimize egg contamination with non-typhoidal Salmonella.

Association between antimicrobial usage and resistance on commercial broiler and layer farms in Bangladesh.

Antimicrobial resistance has emerged as a significant health problem worldwide, including in Bangladesh, where chickens are an important protein source for human nutrition. One of the factors accelerating the development of antimicrobial resistance is the inappropriate use of antimicrobials on commercial chicken farms. A cross-sectional study was conducted in 2019 on 140 commercial chicken farms in the Chattogram district of Bangladesh to investigate the association between antimicrobial use and resistance in Escherichia coli and Salmonella spp. cultured from cloacal swabs of chickens and from the poultry shed environment. All E. coli and Salmonella spp. isolates were resistant to multiple antimicrobial classes, including those categorized as "Highest Priority Critically Important Antimicrobials" for human medicine. Notably, resistance was observed in E. coli isolates from farms that did not use these antimicrobial classes in the current production cycle. For example, although quinolones were not used on 43.9% of E. coli positive farms, 95.7% of these farms had quinolone-resistant E. coli isolates. The results of the path analysis revealed that there was a "direct effect" of the frequency of antimicrobial usage on "high" resistance, with resistance increasing when antimicrobials were administered more frequently (β = 0.28, p = 0.002). There was a "direct effect" of the purpose of antimicrobial use on "low" resistance, with resistance marginally decreasing when antimicrobials were administered solely for therapeutic use (β = -0.17, p = 0.062), but increasing when they were used prophylactically. Overall, the study results could be used to educate farmers on better practices for antimicrobial administration, and to guide government agencies to update policies on antimicrobial use and resistance surveillance in the poultry sector of Bangladesh.

Diagnosis of Avian Leukosis Virus subgroup J in asymptomatic commercial layers using qPCR

Avian Leukosis Virus (ALV), one of the dangerous retroviruses threatens the poultry industry, is oncogenic and can easily transmit. Over the past three decades, the poultry industry has been significantly affected by subgroup J (ALV-J) in particular, known for its ability to spread both horizontally and vertically. The fact that a commercial vaccine has not yet been developed against ALV increases the risk potential. For these reasons, positive cases should be identified to control ALV infections and minimize infection. A prompt and accurate diagnosis is vital to detecting infected birds. For this purpose, sampling was performed in total 153 blood samples from 14 different asymptomatic commercial layer farm located in Afyonkarahisar, T?rkiye. Herein, the presence, density and prevalence of ALV-J strain and whether it has an oncogenic effect was investigated by qPCR and western blot for the first time in T?rkiye. The average contamination rate of ALV-J was calculated as 70.91% over all samples. However, p27 antigen that is the most abundant polypeptide encoded by the gag gene of ALV could not be detected. High prevalence of ALV-J suggests that ALV strains can be found asymptomatically without showing any symptoms.

Reflections on Drivers for the Emergence and Spread of Antimicrobial Resistant Bacteria Detected from Chickens reared on Commercial Layer Farms in Mukono District, Uganda

Reflections on Drivers for the Emergence and Spread of Antimicrobial Resistant Bacteria Detected from Chickens reared on Commercial Layer Farms in Mukono District, Uganda

Spillover of an endemic avian Influenza H6N2 chicken lineage to ostriches and reassortment with clade 2.3.4.4b H5N1 high pathogenicity viruses in chickens

Prior to 2017, chicken production in South Africa had only ever been affected by an endemic strain of H6N2 low pathogenic avian influenza (LPAI), but since 2017, an outbreak of Goose/Guangdong clade 2.3.4.4b H5N8 high pathogenicity avian influenza (HPAI) introduced by wild birds, followed by clade 2.3.4.4b H5N1 HPAI (2021-present), affected the country. In the present study, the viruses from seven cases of H6N2 LPAI from commercial poultry between October 2019 and August 2020 were genome-sequenced along with an H5N2 HPAI virus, and phylogenetic analysis was performed. The H5N2 HPAI virus caused localized outbreaks in a small-scale chicken farm and a large commercial layer farm in the KwaZulu-Natal province between late October and early December 2022. The phylogenetic results confirmed the first incidence of the chicken-adapted H6N2 lineage in commercial ostriches in the Western Cape province, with a likely epidemiological origin in chickens from the KwaZulu Natal province. The results also showed that the H5N2 HPAI virus was a novel reassortant of PB2, PB1, PA, NP and NA genome segments derived from a parental H6N2 virus that circulated in region, whereas the HA, M and NS genome segments were derived from sub-genotype SA10 H5N1 HPAI parental virus that had circulated in the local wild bird reservoir since July 2021.

Glimpse into the biosecurity, antimicrobial usage, and antimicrobial resistance of fecal <em>Escherichia coli</em> associated with commercial chicken layer farms in a poultry dense area in Sri Lanka

Industrial food animal production plays an essential role in the global food supply chain. In parallel with the growth of the Sri Lankan poultry sector, antimicrobial usage has also been increased with the aim of reducing disease incidents. The development of antimicrobial resistance due to the irrational use of antimicrobials is a global problem. Commensals like Escherichia coli (E. coli) can easily acquire and transfer resistance to pathogenic and zoonotic bacteria which cause treatment failures in both humans and animals. The present study was conducted in 50 poultry layer (commercial chicken layers) farms in Kurunegala district of Sri Lanka during the period from November 2016 to January 2017. A questionnaire-based survey was conducted to collect information mainly on the management, biosecurity, and antimicrobial usage of selected farms. Further, E. coli were isolated from the fecal samples collected from 26 farms among those 50 farms, and their antimicrobial-resistant profiles (AMR) were investigated. Results revealed that 98% of the farms had poor biosecurity management practices while using at least one antimicrobial drug (98%). The most commonly used antimicrobial drug was enrofloxacin (79.6%) followed by amoxicillin (61.2%), both sulfamethoxazole and trimethoprim (49%), tetracycline (26.5%), neomycin (22.4%), and tylosin (4.1%). AMR profile of fecal E. coli revealed that the highest resistance is for tetracycline(81.8%) followed by nalidixic acid (54.5%), trimethoprim-sulfamethoxazole (40.9%), ampicillin (45.5%) and ciprofloxacin (31.8%). Lower levels of resistance, 13.6%, 9.1%, and 4.5% were observed for streptomycin, ceftazidime, and imipenem respectively. All the isolates were susceptible to amikacin and gentamycin; while 68.18% of isolated E. coli were multidrug-resistant (MDR). AMR and MDR findings of this study highlight the need of implementing strategies to regulate the usage of antimicrobial drugs in poultry farms in Sri Lanka, to prevent and control the emergence of antimicrobial-resistant pathogens and diseases from a ‘one health’ perspective.

Flock-level risk factors of litter condition for the occurrence of plumage damage and skin lesions in commercial laying hen farms

Plumage damage (PD) as a result of severe feather pecking (SFP) and skin lesions (SL) due to cannibalism (CA) is serious welfare, performance, and economic problems in commercial layer farms. Genetics, nutrition, and housing conditions are central complexes that contribute to the multifactorial causes of these behavioral disorders. Practical recommendations consider the quality of litter as an important criterion for the prevention of SFP, although systematic longitudinal studies providing evidence-based findings are lacking. Therefore, the aim of this study was to investigate the effects of litter condition on the occurrence of PD and SL in the field using a longitudinal design. Integument scoring (PD and SL; 7 times), litter scoring (structure, cake formation, litter quality, and litter height; 12 times), and laboratory litter analysis (dry matter (DM), nitrogen (N), phosphorus (P) and pH value; 12 times) were performed in 28 laying hen flocks with a median flock size of 12,357 birds, in barn (n=21) or free-range systems (n=7), during the first laying period. Binary logistic regression (BLR) models showed the association of housing type and animal age on PD and SL (P < 0.001), and of the hybrid type on PD (P < 0.001). Furthermore, a significant association with PD and SL was observed for several litter traits. An increase in litter height, DM, and P was associated with lower PD (P ≤ 0.022) and SL (P < 0.001). In contrast, a higher N content of the litter was associated with an increase in SL (P=0.007). Cake formation (P < 0.001) and a low structure (P=0.025) of the litter showed an association with higher PD. In conclusion, this study identified caked litter with less structure, low height, and low contents of DM and P as risk factors for behavioral disorders in commercial laying flocks.

Differences in peripheral and central metabolites and gut microbiome of laying hens with different feather-pecking phenotypes.

Feather pecking (FP) is a maladaptive behavior in laying hens that is associated with numerous physiological traits, including those involving the central neurotransmitter system and the immune system, which have been identified in many species as being regulated by the gut microbiota via the "microbiota-gut-brain" (MGB) axis. Yet, it is unknown whether and how gut microbiota influences FP by regulating multiple central neurotransmission systems and immune system. This study was measured the prevalence of severe FP (SFP) in the commercial layer farm. The chicken flock with the highest frequency of SFP were selected for FP phenotype identification. Nontargeted metabolomics was performed to investigated the differences in the peripheral and central metabolites and 16S rDNA sequencing was performed to investigated the differences in gut microbiome of laying hens with different FP phenotypes. Correlation analysis was performed to determine the potential mechanism by which the disturbed gut microbiota may modulate host physiology and behavior. The results showed that pullets (12 weeks of age) showed significantly higher SFP frequencies than chicks (6 weeks of age) and adults (22 weeks of age; p < 0.05). Compared to neutrals (N), peckers (P) exhibited the stress-induced immunosuppression with the increased plasma levels of corticosterone and norepinephrine, and the decreased plasma levels of IgA, IL-1, IL-6 and tumor necrosis factor α (p < 0.05). In the cecum, the relative abundances of Bacteroides and Gemmiger were higher in the P group, while Roseburia, Ruminococcus2, Anaerostipes, Lachnospiracea_incertae_sedis and Methanobrevibacter were more enriched in the N group. Moreover, increased plasma levels of L-tryptophan, beta-tyrosine and L-histidine were found in the P group (p < 0.05). Notably, in the P group, hippocampal levels of L-tryptophan, xanthurenic acid, L-histidine and histamine were improved and showed a positive association with L-glutamic acid levels. Plasma levels of L-tryptophan, beta-tyrosine and L-histidine were both positively correlated with Bacteroides abundance but negatively correlated with Methanobrevibacter abundance. Overall, these findings suggest that the development of FP may be affected by the gut microbiota, which regulates the central glutamatergic nerve system by altering the metabolism of tryptophan, histidine and tyrosine.

Histopathological changes and sequence analysis of field strains of MDV associated with tumors in commercial layer farms in 2015 to 2019

Histopathological changes and sequence analysis of field strains of MDV associated with tumors in commercial layer farms in 2015 to 2019

Biosecurity practices on commercial layer farms in Abyek county, Qazvin, Iran: A cross-sectional study

Objective: To investigate the biosecurity measures practiced at commercial layer chicken farms in Abyek country, Qazvin, Iran.. Methods: In this cross-sectional study, all licensed and active commercial layer chicken farms in Abyek county, Qazvin province, Iran in 2019 were recruited. We used a risk-based weighted scoring system (Biocheck.UGent) to assess the level of biosecurity according to internal and external classification. Biosecurity was quantified by converting the answers to 169 questions into score from 0 to 100. The minimum score, “0,” represents total absence of any biosecurity measure on the farm, whereas the maximum score, “100,” means full application of all investigated biosecurity measures. Results: The mean score of overall biosecurity in the commercial layer chicken farms in Abyek county, Qazvin province was 72.7. The mean score of internal and external biosecurity measures were 77.1 and 72.2, respectively. The lowest mean score was due to “Disease management” (69.7) among internal biosecurity measures and the lowest mean scores were for "Location of farm” (39.0) and “Removal of manure and dead animals” (42.6) among external biosecurity measures. The highest mean score was for “Transport of the eggs level” (91.0) for external biosecurity measures. Conclusions: This study showed the biosecurity status of commercial layer chicken farms in Abyek county, Qazvin, Iran and revealed some weaknesses in the implementation of these measures at the internal and external levels. It showed the biosecurity measures of these farms, especially at the external levels need to be improved. This information can aid decision-making on efforts used to improve disease control and prevention strategies in poultry farms.

Isolation and antimicrobial resistance of salmonella isolates from commercial layer farms in and around Hyderabad, Telangana

Isolation and antimicrobial resistance of salmonella isolates from commercial layer farms in and around Hyderabad, Telangana

Flock Factors Correlated with Elevated Mortality in Non-Beak Trimmed Aviary-Housed Layers.

The use of non-cage housing systems for layers is increasing in Europe and elsewhere. Knowledge of factors that may affect mortality in these systems is important to be able to improve animal welfare, reduce mortality and enhance sustainability. The aim of this study was to investigate factors that may contribute to increased mortality in non-beak trimmed aviary-housed laying hens in Norway. A total of 39 non-beak trimmed commercial flocks (Lohmann LSL (n = 25) and Dekalb White (n = 14)) were visited between week 70 to 76 of life, and factors related to health, behaviour and management were recorded. Mean mortality in the flocks was 3% (range: 0.5-9%) and increased flock mortality was correlated with total feather loss (p &lt; 0.05); feather loss on the breast (p &lt; 0.02) and feather loss on the head (p &lt; 0.003). There was an association between layer hybrid line and mortality (p = 0.055). Furthermore, a low positive correlation between mortality and dust level inside the barn was found (p &lt; 0.04), showing that mortality was higher when dust level was also high. No correlation between mortality and the provision of environmental enrichment was found. In conclusion, this study found an association between flocks with elevated mortality (&gt;3.0%) and increased feather loss which may indicate feather pecking. The results underline the importance of regularly assessment of plumage condition in commercial layer farms, as a tool to detect early signs of feather pecking in commercial aviary-housed layer flocks. This may help to target feather pecking before cannibalism breaks out.

Farm Environmental Enrichments Improve the Welfare of Layer Chicks and Pullets: A Comprehensive Review.

Simple SummaryLayer industries that are still using cage housing systems should encourage the provision of appropriate farm enrichments, especially at an early stage. Farm environmental enrichments such as litter, sand, alfalfa bales, chick papers, pecking stones, pecking strings, perches, slopes, elevated platforms, aviaries and outdoor access reduce feather and skin damage, as well as abdominal fat content. Additionally, they promote the development of the brain and musculoskeletal systems and improve biological function, productivity and product quality with lifelong benefits for hens by continuously exposing them to free access to forage, dust baths and free locomotion. In this review, we summarize several common and effective methods of farm environmental enrichments, including different manipulable materials, structural equipment, and outdoor access, moreover, the competence of the farm staff is a requirement to achieve useful utilization of these farm environmental enrichments that aim to reduce stress and improve the welfare and productivity of layers. Proper farm environmental enrichments benefit the wellbeing of caged birds.Currently, cage housing is regarded as a global mainstream production system for laying hens. However, limited living space and confinement of birds in cages cause welfare and health problems, such as feather pecking, osteoporosis, obesity, and premature aging. Many studies have been conducted to alleviate layer welfare problems by providing farm environmental enrichments such as litter, sand, alfalfa bales, chick papers, pecking stones, pecking strings, perches, slopes, elevated platforms, aviaries and outdoor access with a trend towards complex enrichments. The provision of appropriate enrichments continuously attracts layers towards pecking, foraging, dust bathing, and locomotion, thereby giving lifelong benefits to laying hens. Hence, raising chicks and pullets under such conditions may reduce feather and skin damage, as well as accumulation of abdominal fat, and improve several biological features such as health, productivity, quality products, and docility of laying hens. Therefore, providing enrichment during the first few days of the layer’s life without any interruption is crucial. In addition, due to different farm conditions, environmental enrichment should be managed by well-trained farm staff. For example, in preventing feather pecking among the birds, litter materials for foraging are superior to dust bath materials or new items. However, a limited supply of litter creates competition and challenges among birds. Therefore, providing farm environmental enrichment for layers requires proper handling, especially in commercial layer farms. Hence, improving the welfare of chicks and pullets through optimizing on-farm environmental enrichments is essential for production systems practicing cage housing.

Phytogen Improves Performance during Spotty Liver Disease by Impeding Bacterial Metabolism and Pathogenicity.

A range of antibiotic alternative products is increasingly studied and manufactured in the current animal agriculture, particularly in the poultry industry. Phytogenic feed additives are known for their remarkable ability to suppress pathogens such as Clostridium spp., Escherichia coli, and Salmonella. Other than enhancing biosecurity, improvements in productivity and performance were also observed. However, clear mechanisms for these improvements were not established. In this study, 20,000 Lohman-Brown layers were provided with phytogenic supplement from 16 to 40 weeks of age, and performance parameters were assessed against the same number of unsupplemented control birds. The performance results showed that the birds with phytogenic supplementation presented consistently reduced mortality, increased rate of lay, and increased average egg weight. Functional analysis through shotgun sequencing of cecal metagenomes confirmed a substantial functional shift in the microbial community, showing that phytogen significantly reduced the range of microbial functions, including the production of essential vitamins, cofactors, energy, and amino acids. Functional data showed that phytogen supplementation induced a phenotypic shift in intestinal bacteria LPS phenotype toward the less pathogenic form. The study corroborates the use of phytogenic products in antibiotic-free poultry production systems. The productivity improvements in the number and weight of eggs produced during Spotty Liver Disease justify further optimizing phytogenic alternatives for use in high-risk open and free-range poultry systems. IMPORTANCE The present study establishes the beneficial effects of the continuous phytogenic supplementation reflected in reduced diarrhea and mortality and higher egg productivity under normal conditions and during a natural outbreak of Spotty Liver Disease. Our data points to the importance of phytogen-driven alteration of microbial pathogenicity and fitness-related functional capabilities revealed on the commercial layer farm. Phytogenic product showed an ability to improve the bird's welfare and sustainability in free-range poultry production systems.

Earlier detection of infectious laryngotracheitis virus by development of Dot-ELISA in commercial layer farms

Earlier detection of infectious laryngotracheitis virus by development of Dot-ELISA in commercial layer farms

Molecular characterisation of hemagglutinin and neuraminidase genes of the first highly pathogenic Avian Influenza H5N1 2.3.2.1c virus isolated from Sabah, Malaysia.

Highly Pathogenic Avian Influenza (HPAI) is a highly contagious disease in poultry. The outbreaks can lead to flock mortality up to 100% in two to three days. In July 2018, high mortality in a commercial layer farm in Kauluan village, Sabah was reported. Samples were sent to Veterinary Research Institute Ipoh for diagnosis. Virus isolation and molecular detection is carried out simultaneously. The causative agent was then identified as AI H5N1 virus by real time reverse transcription-polymerase chain reaction (RT-PCR). The virus was then subjected for further nucleotide sequencing of full length hemagglutinin (HA) and neuraminidase (NA) gene. The PQRERRRKR/GLF motif at the HA cleavage site indicated that the isolate was of HPAI virus. Phylogenetic analysis of the HA gene showed that the isolate was belonged to the clade 2.3.2.1c virus. In the HA gene, besides the S133A substitution, the virus possesses conserved amino acid at most of the avian receptor binding sites including the glutamine (Q) and glycine (G) at position 222 and 224 respectively, indicating that the virus retains the avian-type receptor binding preference. As such, the zoonotic potential of the virus was relatively low. On the other hand, though the N154D and T156A substitution were detected in the same gene, the pandemic potential of this Sabah 2.3.2.1c virus is low in the absence of the Q222L, G224S, H103Y, N220K and T315I. A typical 20 amino acid deletion with loss of four corresponding glycosylation sites in the NA stalk region was visible. Though three NA resistance markers were detected, the virus was predicted to be sensitive to NA inhibitor. This is the first HPAI H5N1 outbreak in Sabah. The introduction of this virus into East Malaysia for the first time raised an alert alarm of the future epidemic potential. Strict farm biosecurity, continuous surveillance programme in poultry, wild birds, migratory birds; molecular epidemiology as well as risk assessment for the virus with pandemic potential are needed in dealing with emergence of new influenza virus in the country.

Relationship between sunlight and range use of commercial free-range hens in Australia

In Australia, summer brings intense, bright sunlight with high ultraviolet (UV) radiation and hot temperatures, which might impact free-range hens’ ranging outside. To determine how range use was correlated with different sunlight variables and weather factors, a study was carried out on three commercial free-range layer farms during the summer/autumn period (December-May) across diverse regions of Australia in Tasmania (TAS), Queensland (QLD), and Western Australia (WA). Hens’ range distribution was determined by counting the number of hens in the direct sunlight (‘sun’) or ‘cloud’ and shaded areas (‘sun-shade’ or ‘cloud-shade’, in sunny or cloudy conditions, respectively) using image snapshots taken at 30 min intervals from video recordings of a portion of one shed comprising 20,000–30,000 hens on each farm during the production phase of the laying cycle. The solar radiation spectrum [UV radiation (UVAB) (288–432 nm), photosynthetically active radiation (PAR; visible light) (400–700 nm), and total solar radiation (TSR) (285 nm-3000 nm)] and weather data (ambient temperature and relative humidity) were recorded through an on-site weather station. Data were analysed separately due to discrepancies between the farms’ layouts. The effects of time of day and months on range use were analysed using General Linear Models in JMP® 16.0 and the relationship of sunlight and weather variables with hens’ distribution in ‘sun’/’sun-shade’ and ‘cloud’/’cloud-shade’ in sunny and cloudy conditions respectively was determined by fitting linear ridge regression models using the ‘lmridge’ package in R. Overall, the time of day and month had significant effects on hens’ distribution on the range (all p < 0.0001). Hens’ range occupancy in the ‘sun’ decreased during the midday period with gradual increases in the late afternoon to evening, and the opposite pattern in the ‘sun-shade’. A linear increase in the number of hens on the range over the months indicated the seasonal effects on hen ranging patterns. Temperature, UVAB and PAR were the most important factors for discouraging hens’ range use in the ‘sun’ suggesting free-range systems in Australia should be designed to account for the extreme sunlight using adequate shade for optimum ranging across summer.