Australasian Pigeon Circoviruses Demonstrate Natural Spillover Infection.

Pigeon circovirus (PiCV) is considered to be genetically diverse, with a relatively small circular single-stranded DNA genome of 2 kb that encodes for a capsid protein (Cap) and a replication initiator protein (Rep). Australasia is known to be the origin of diverse species of the Order Columbiformes, but limited data on the PiCV genome sequence has hindered phylogeographic studies in this species. To fill this gap, this study was conducted to investigate PiCV in 118 characteristic samples from different birds across Australia using PCR and sequencing. Eighteen partial PiCV Rep sequences and one complete PiCV genome sequence were recovered from reservoir and aberrant hosts. Phylogenetic analyses revealed that PiCV circulating in Australia was scattered across three different subclades. Importantly, one subclade dominated within the PiCV sequenced from Australia and Poland, whereas other PiCV sequenced in this study were more closely related to the PiCV sequenced from China, USA and Japan. In addition, PiCV Rep sequences obtained from clinically affected plumed whistling duck, blue billed duck and Australian magpie demonstrated natural spillover of PiCV unveiled host generalist characteristics of the pigeon circovirus. These findings indicate that PiCV genomes circulating in Australia lack host adapted population structure but demonstrate natural spillover infection.

Bacterial culture and antimicrobial susceptibility results from bovine milk samples submitted to four veterinary diagnostic laboratories in Australia from 2015 to 2019.

A 5-year retrospective study was conducted to describe the mastitis-causing organisms isolated from bovine milk samples submitted to four veterinary diagnostic laboratories in Australia. The aim of this study was to identify temporal, geographical, and seasonal patterns of occurrence for the organisms and report the in vitro susceptibility of the most common mastitis-causing pathogens. In total, 22,102 milk samples were submitted between 2015 and 2019. The results were reported as positive growth for at least one significant organism (n = 11,407; 51.6%), no growth (n = 5,782; 26.2%), and mixed/contaminated growth (n = 4,913; 22.2%). Culture results for no growth, gram-negative bacteria, and eukaryotic organisms were combined for each region, and they were accounted for between 23 and 46% of submissions. These results represent a subset of mastitis cases for which the antibiotic treatment may not be warranted. A total of 11,907 isolates were cultured from 11,407 milk samples. The most common isolated organisms were Streptococcus uberis [41.3%; 95% confidence interval (CI): 40.4-42.1%] and Staphylococcus aureus (23.6%; 95% CI: 22.8-24.3%). For S. uberis and S. aureus, there was an association between a positive culture result and the dairy region. All regions except for the Sub-tropical Dairy region were more likely to culture S. uberis compared to the reference, Dairy NSW (P < 0.001). Similarly, for S. aureus, a positive culture result was more likely in all other dairy regions compared to Dairy NSW (P < 0.001). The LISA cluster analysis identified differences between High-High (hotspot) postcodes for S. aureus and S. uberis throughout all the analyzed dairy regions. These results highlight the need for further investigations into specific risk factors, such as environmental factors and herd-level predictors, which may have influenced the observed regional variations. Common mastitis-causing pathogens showed overall good susceptibility to a range of antimicrobials used in the treatment of mastitis. On-going surveillance of mastitis-causing pathogens and their antimicrobial susceptibilities will facilitate targeted mastitis control and treatment programs.

Social and cognitive factors influencing commercial chicken farmers' antimicrobial usage in Bangladesh.

Adapting the Social Cognitive Theory framework, we conducted a cross-sectional study on 137 commercial chicken farms in Bangladesh to investigate factors influencing the behaviour of farmers towards the application of antimicrobials to their birds. Almost all farmers used antimicrobials to treat poultry diseases, while 38.6% also were using them to promote healthy growth of chickens and 10.2% to increase egg production or improve meat quality. Using Structural Equation Modeling (SEM), we identified that inappropriate usage of antimicrobials (behaviour) was strongly driven by farmers' short-term goals to maintain the health of their chickens in a production cycle (ß = 0.813, p = 0.029), rather than long-term concerns. Farmers' perception about their ability to control antimicrobial administration based on their skills and opportunities (self-efficacy) marginally influenced the short-term goals of antimicrobial usage (ß = 0.301, p = 0.073). The results of this study can be used to develop targeted education programs for farmers, to reduce the application of antimicrobials in their poultry flocks.

Farm-Level Risk Factors Associated With Avian Influenza A (H5) and A (H9) Flock-Level Seroprevalence on Commercial Broiler and Layer Chicken Farms in Bangladesh.

A cross-sectional study was conducted to identify farm-level risk factors associated with avian influenza A H5 and H9 virus exposure on commercial chicken farms in Bangladesh. For broiler farms, both H5 and H9 seropositivity were associated with visits by workers from other commercial chicken farms [odds ratio (OR) for H5 = 15.1, 95% confidence interval (CI): 2.8-80.8; OR for H9 = 50.1, 95% CI: 4.5-552.7], H5 seropositivity was associated with access of backyard ducks (OR = 21.5, 95% CI: 2.3-201.1), and H9 seropositivity with a number of farm employees (OR = 9.4, 95% CI: 1.1-80.6). On layer farms, both H5 and H9 seropositivity were associated with presence of stray dogs (OR for H5 = 3.1, 95% CI: 1.1-9.1; OR for H9 = 4.0, 95% CI: 1.1-15.3), H5 seropositivity with hatcheries supplying chicks (OR = 0.0, 95% CI: 0.0-0.3), vehicles entering farms (OR = 5.8, 95% CI: 1.5-22.4), number of farm employees (OR = 5.8, 95% CI: 1.2-28.2), and burying of dead birds near farms (OR = 4.6, 95% CI: 1.2-17.3); H9 seropositivity with traders supplying feed (OR = 5.9, 95% CI: 1.0-33.9), visits conducted of other commercial poultry farms (OR = 4.7, 95% CI: 1.1-20.6), number of spent layers sold (OR = 24.0, 95% CI: 3.7-155.0), and frequency of replacing chicken droppings (OR = 28.3, 95% CI: 2.8-284.2). Policies addressing these risk factors will increase the effectiveness of prevention and control strategies reducing the risk of avian influenza on commercial chicken farms.

Association between farm biosecurity practices and antimicrobial usage on commercial chicken farms in Chattogram, Bangladesh.

Commercial broiler and layer farming represents an important livestock industry in Bangladesh. Adequate biosecurity practices are considered to be an effective method to prevent infectious disease occurrence on commercial poultry farms, but antimicrobials are also frequently administered to reduce disease risk. We conducted a cross-sectional study on 57 commercial layer and 83 broiler farms in eight subdistricts of the Chattogram district in Bangladesh to investigate the relationship between implemented biosecurity practices and the use of antimicrobials on these farms. We used a causal diagram framework to inform multi-level mixed effects logistic regression models to explore the total and direct effects of biosecurity practices implemented on commercial farms on prophylactic versus therapeutic antimicrobial usage on these farms. Overall, inadequate biosecurity was more common on broiler compared to layer farms and on farms rearing smaller flock sizes. For example, separation of sick from healthy birds was more common on layer farms (85.2 %, 46/54) compared to broiler farms (38.6 %, 32/83) (p = 0.001). Prophylactic administration (compared to therapeutic use) of antimicrobials was less common on farms that were separating sick birds from the healthy birds (total and direct effect OR = 0.1, 95 % CI: 0.1-0.6, p = 0.006) and less common on farms that used a poorer quality source of water for drinking, cooling, cleaning, and washing (total and direct effect OR = 0.3, 95 % CI: 0.1-0.9, p = 0.036). In contrast, farmers that used washing facilities (versus non-usage of washing facilities) were more likely to administer antimicrobials prophylactically (total and direct effect OR = 3.9, 95 % CI: 1.3-11.3, p = 0.012). The null model ICC indicated significant clustering at the subdistrict level (ICC = 0.20, 95 % CI: 0.04-0.60, p = 0.013), but the ICC was reduced after including flock size and farm type, and the biosecurity practices as fixed effects (ICC = 0.14, 95 % CI: 0.02-0.59, p = 0.0661). Overall, our study highlighted that a large proportion of commercial chicken farmers mediated poor biosecurity practices by prophylactic application of antimicrobials. The results of our research can be used to inform awareness programs for commercial poultry farmers emphasizing the importance of improving biosecurity rather than using antimicrobials to reduce the risk of poultry disease occurrence.

Factors influencing chicken farmers' decisions to implement prevention and control measures to reduce avian influenza virus spread under endemic conditions.

The ongoing circulation of Highly Pathogenic Avian Influenza (HPAI) H5N1 poses a threat to both poultry and public health. Adapting the constructs of the Health Belief Model (HBM) framework, we investigated perceptions of backyard, commercial broiler and layer chicken farmers to implement HPAI prevention and control measures in Bangladesh. Two cross-sectional studies were conducted in 2016 and 2017 on 144 backyard, 106 broiler and 113 layer chicken farms. Using Structural Equation Modelling, we modelled the direct and indirect effects on farmers' perceptions on taking HPAI prevention and control actions. Our results indicate that farmers of different chicken production systems have different decision-making processes. While perceived barriers to the implementation of prevention and control measures (e.g. wearing protective equipment when handling chickens) prevented both broiler and backyard farmers to adopt interventions, perceived benefits of measures (e.g. maintaining high biosecurity will reduce the risk of birds becoming sick) strongly influenced commercial farmers' decisions, but not backyard farmers' decisions. Information provided on HPAI through media, meetings or via information campaigns played an important role in farmers' decision-making in all production systems. Outcomes of this research can be used to tailor advice on HPAI control and prevention to different poultry farming groups by accounting for specific factors influencing their decision-making, instead of using one-size-fit-all communication approach.

Patterns of Avian Influenza A (H5) and A (H9) virus infection in backyard, commercial broiler and layer chicken farms in Bangladesh.

In order to control Highly Pathogenic Avian Influenza (HPAI) H5N1 and Low Pathogenic Avian Influenza (LPAI) H9N2 virus spread in endemically infected countries, a detailed understanding of infection patterns is required. We conducted cross-sectional studies in Bangladesh in 2016 and 2017, on 144 backyard, 106 broiler and 113 layer chicken farms. Although all sampled birds were negative for H5 virus by RT-PCR, H5 antibodies were detected in unvaccinated birds on all three farming systems. Higher H5 antibody prevalence was observed in ducks raised on backyard farms, 14.2% (95% CI: 10.0%-19.8%), compared to in-contact backyard chickens, 4.2% (95% CI: 2.8%-6.1%). The H5 antibody prevalence was lower in broiler chickens, 1.5% (95% CI: 0.9%-2.5%), compared to layer chickens, 7.8% (95% CI: 6.1%-9.8%). H9 viruses were detected by RT-PCR in 0.5% (95% CI: 0.2%-1.3%) and 0.6% (95% CI: 0.3%-1.5%) of broilers and layers, respectively, and in 0.2% (95% CI: 0.0%-1.2%) of backyard chickens. Backyard chickens and ducks showed similar H9 antibody prevalence, 16.0% (95% CI: 13.2%-19.2%) and 15.7% (95% CI: 11.3%-21.4%), which was higher compared to layers, 5.8% (95% CI: 4.3%-7.6%), and broilers, 1.5% (95% CI: 0.9%-2.5%). Over the course of a production cycle, H5 and H9 antibody prevalence increased with the age of backyard and layer chickens. Usually, multiple ducks within a flock were H5 antibody positive, in contrast to backyard chickens, broilers and layers where only individual birds within flocks developed H5 antibodies. Our findings highlight low virus circulation in healthy chickens of all production systems in Bangladesh, which is in contrast to high virus circulation reported from live bird markets. Data generated in this project can be used to adopt risk-based surveillance approaches in different chicken production systems in Bangladesh and to inform mathematical models exploring HPAI infection dynamics in poultry from the source of production.

A Cross-Sectional Study of Antimicrobial Usage on Commercial Broiler and Layer Chicken Farms in Bangladesh.

Commercial poultry production is growing rapidly in Bangladesh to address the increasing demand for poultry meat and eggs. Challenges faced by producers include the occurrence of poultry diseases, which are usually treated or controlled by antimicrobials. A cross-sectional study was conducted on 57 commercial layer and 83 broiler farms in eight subdistricts of the Chattogram district, Bangladesh, to assess antimicrobial usage in relation to clinical signs observed in chicken flocks on these farms. Of the 140 commercial chicken farms, 137 (97.9%) used antimicrobials and 24 different antimicrobial agents were administered. On layer farms, the most commonly used antimicrobials were ciprofloxacin (37.0% of farms, 20/54), amoxicillin (33.3%, 18/54), and tiamulin (31.5%, 17/54), while on broiler farms, colistin (56.6%, 47/83), doxycycline (50.6%, 42/83), and neomycin (38.6%, 32/83) were most commonly administered. Only 15.3% (21/137) of farmers used antimicrobials exclusively for therapeutic purposes, while 84.7% (116/137) of farmers used them prophylactically, administering them either for prophylactic purposes only (22.6% of farmers, 31/137) or in combination with therapeutic purposes (62.1% of farmers, 85/137). About 83.3% (45/54) of layer farmers were selling eggs while antimicrobials were being administered compared to 36.1% (30/83) of the broiler farmers selling broiler chickens while administering antimicrobials. Overall, 75.2% (103/137) of farmers reported clinical signs for which they administered antimicrobials, while 24.8% (34/137) of farmers reported no clinical signs but still administered antimicrobials. Respiratory signs (71.8% of farms with clinical signs, 74/103) were most commonly reported, followed by enteric signs (32.0%, 33/103) and increased mortality (16.5%, 17/103). About 37.2% (51/137) of farmers bought antimicrobials exclusively from feed and chick traders, followed by veterinary medical stores (35.0%, 48/137). Purchasing antimicrobials from feed and chick traders was more common among broiler than layer farmers. It is recommended that commercial poultry farmers should keep records of antimicrobials used with dosage and duration of administration along with indication of use. This would allow farmers and veterinarians to review if antimicrobial usage had the desired effects and to evaluate the appropriate use of antimicrobial agents under an antimicrobial stewardship approach.