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

Amplification of avian influenza virus circulation along poultry marketing chains in Bangladesh: A controlled field experiment

The prevalence of avian influenza viruses is commonly found to increase dramatically as birds are transported from farms to live bird markets. Viral transmission dynamics along marketing chains are, however, poorly understood. To address this gap, we implemented a controlled field experiment altering chicken supply to a live bird market in Chattogram, Bangladesh. Broilers and backyard chickens traded along altered (intervention) and conventional (control) marketing chains were tested for avian influenza viruses at different time points. Upon arrival at the live bird market, the odds of detecting avian influenza viruses did not differ between control and intervention groups. However, 12 h later, intervention group odds were lower, particularly for broilers, indicating that viral shedding in live bird markets resulted partly from infections occurring during transport and trade. Curtailing avian influenza virus prevalence in live bird markets requires mitigating risk in marketing chain nodes preceding chickens' delivery at live bird markets.

Farm biosecurity practices affecting avian influenza virus circulation in commercial chicken farms in Bangladesh

Avian influenza virus (AIV) is of major concern to livestock, wildlife, and human health. In many countries in the world, including Bangladesh, AIV is endemic in poultry, requiring improving biosecurity. In Bangladesh, we investigated how variation in biosecurity practices in commercial chicken farms affected their AIV infection status to help guide AIV mitigation strategies. We collected pooled fecal swabs from 225 farms and tested the samples for the AIV matrix gene followed by H5, H7, and H9 subtyping using rRT-PCR. We found that 39.6% of chicken farms were AIV positive, with 13% and 14% being positive for subtypes H5 and H9, respectively. Using a generalized linear mixed effects model, we identified as many as 12 significant AIV risk factors. Two major factors promoting AIV risk that cannot be easily addressed in the short term were farm size and the proximity of the farm to a live bird market. However, the other ten significant determinants of AIV risk can be more readily addressed, of which the most important ones were limiting access by visitors (reducing predicted AIV risk from 42 to 6%), isolation and treatment of sick birds (42 to 7%), prohibiting access of vehicles to poultry sheds (38 to 8%), improving hand hygiene (from 42 to 9%), not sharing farm workers across farms (37 to 8%), and limiting access by wild birds to poultry sheds (37 to 8%). Our findings can be applied to developing practical and cost-effective measures that significantly decrease the prevalence of AIV in chicken farms. Notably, in settings with limited resources, such as Bangladesh, these measures can help governments strengthen biosecurity practices in their poultry industry to limit and possibly prevent the spread of AIV.

Modelling the transmission dynamics of H9N2 avian influenza viruses in a live bird market

H9N2 avian influenza viruses (AIVs) are a major concern for the poultry sector and human health in countries where this subtype is endemic. By fitting a model simulating H9N2 AIV transmission to data from a field experiment, we characterise the epidemiology of the virus in a live bird market in Bangladesh. Many supplied birds arrive already exposed to H9N2 AIVs, resulting in many broiler chickens entering the market as infected, and many indigenous backyard chickens entering with pre-existing immunity. Most susceptible chickens become infected within one day spent at the market, owing to high levels of viral transmission within market and short latent periods, as brief as 5.3 hours. Although H9N2 AIV transmission can be substantially reduced under moderate levels of cleaning and disinfection, effective risk mitigation also requires a range of additional interventions targeting markets and other nodes along the poultry production and distribution network.

EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks

The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.

Fast growing broiler production from genetically different pure lines in Turkey. 2. Broiler traits: growth, feed intake, feed efficiency, livability, body defects and some heterotic effects

The aim of the this study was to reveal the trends in body weight (BW), feed intake (FI), feed conversion ratio (FCR), livability, and body defects (foot pad dermatitis (FPD), hock burn (HB), and breast burn (BB)) in offspring of ANADOLU-T pure lines (PLs), their 12 four-way hybrids and ROSS-308 hybrid, and the observed heterosis values for some performance and body defect traits. A total of 2736 (1368 broilers each) broiler chickens from ANADOLU-T pure lines, their hybrids, and commercial ROSS-308 hybrid were hatched from breeder eggs at 32 and 52 weeks of age and reared for 42 days in 2 experiments. The PL eggs were generally heavier than hybrid eggs (P < 0.001) and day-old BWs (P < 0.001) were also higher in PL chicks (ranging between 44.5 and 45.8 g). The males of ROSS-308 hybrid were heavier than others at 42 d of age (P = 0.035), and the lowest BW values were determined for A1, A2, and A3 line chickens (P < 0.001). ROSS-308 (4453.8 g) showed similar 42-d FI with all of four-way ANADOLU-T hybrids except (B1 × B2) × (A1 × A2) and (B1 × B2) × (A3 × A1). The 42-d FCR was 1.473 for the ROSS-308, while it ranged between 1.654 and 1.715 for the four-way ANADOLU-T hybrids (P < 0.001). The 42-d livability of four-way ANADOLU-T hybrids and ROSS-308 ranged between 92.0 and 100.0%. All ANADOLU-T hybrids, except two, showed higher 42-d livability than ROSS-308. While both genotype and sex were important for HB and BB, only the genotype effect was significant for FPD (P < 0.001). All ANADOLU-T hybrids showed low to moderate and positive heterosis for BW after 28 d. From 14 to 42 d, the magnitudes of heterosis for FCR decreased. Heterosis for livability from 7 to 42 d were not significant between genotypes. Percentages of heterosis for resistance to FPD (- 1.56 to 1.44%), HB (- 37.03 to 18.75%), and BB (- 12.70 to 1.02%) defects were not significant among genotypes. It was concluded that mating of B1 × B2 males with A1 × A2 and A3 × A2 females seems more favorable in terms of higher chick and meat production. However, the fact that the overall performance of ANADOLU-T hybrids is lower than ROSS-308 clearly indicates that genetic selection must be maintained for enhanced body weight and feed efficiency.

Assessment of poultry rearing practices and risk factors of H5N1 and H9N2 virus circulating among backyard chickens and ducks in rural communities

Background

The avian influenza virus (AIV) causes significant economic losses by infecting poultry and occasional spillover to humans. Backyard farms are vulnerable to AIV epidemics due to poor health management and biosecurity practices, threatening rural households’ economic stability and nutrition. We have limited information about the risk factors associated with AIV infection in backyard poultry in Bangladesh. Hence, we conducted a cross-sectional survey comprising epidemiological and anthropological investigations to understand the poultry rearing practices and risk factors of AIV circulation among backyard poultry in selected rural communities.

Methods

We sampled 120 poultry from backyard farms (n = 30) of the three selected communities between February 2017 and January 2018. We tested swab samples for the matrix gene (M gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We applied multivariable logistic regression for risk factor analysis. Furthermore, we conducted an observational study (42 hours) and informal interviews (n = 30) with backyard farmers to record poultry-raising activities in rural communities.

Results

We detected that 25.2% of the backyard poultry tested positive for AIV, whereas 5% tested positive for H5N1 and 10.8% tested positive for H9N2. Results showed that scavenging in both household garden and other crop fields has higher odds of AIV than scavenging in the household garden (AOR: 24.811; 95% CI: 2.11–292.28), and keeping a cage inside the house has higher odds (AOR:14.5; 95% CI: 1.06–198.51) than keeping it in the veranda, cleaning the cage twice a week or weekly has a higher risk than cleaning daily (AOR: 34.45; 95% CI: 1.04–1139.65), dumping litter or droppings (AOR: 82.80; 95% CI: 3.91–1754.59) and dead birds or wastage (AOR: 109.92, 95% CI: 4.34–2785.29) near water bodies and bushes have a higher risk than burring in the ground, slaughtering and consuming sick birds also had a higher odd of AIV (AOR: 73.45, 95% CI: 1.56–3457.73) than treating the birds. The anthropological investigation revealed that household members had direct contact with the poultry in different ways, including touching, feeding, slaughtering, and contacting poultry feces. Poultry is usually kept inside the house, sick poultry are traditionally slaughtered and eaten, and most poultry raisers do not know that diseases can transmit from backyard poultry to humans.

Conclusions

This study showed the circulation of H5N1 and H9N2 virus in backyard poultry in rural communities; associated with species, scavenging area of the poultry, location of the poultry cage, the practice of litter, wastage, droppings, and dead bird disposal, and practice of handling sick poultry. We suggest improving biosecurity practices in backyard poultry and mass awareness campaigns to reduce incidences of AIV in household-level poultry farms in rural communities in Bangladesh.

Village and farm-level risk factors for avian influenza infection on backyard chicken farms in Bangladesh

A cross-sectional study was conducted with 144 small-scale poultry farmers across 42 Bangladeshi villages to explore risk factors associated with avian influenza H5 and H9 seropositivity on backyard chicken farms. Using mixed-effects logistic regression with village as random effect, we identified crow abundance in garbage dumping places and presence of migratory wild birds within villages to be associated with higher odds of H5 and H9 seropositivity. At farm-level, garbage around poultry houses was also associated with higher odds of H5 and H9 seropositivity. In addition, specific trading practices (such as, purchase of chickens from live bird markets (LBM) and neighboring farms to raise them on their own farms, frequency of visits to LBM, purchase of poultry at LBM for consumption) and contact of backyard chickens with other animals (such as, feeding of different poultry species together, using pond water as drinking source for poultry, access of feral and wild animals to poultry houses) were associated with higher odds of H5 or H9 seropositivity. Resource-constrained small-scale poultry farmers should be able to address risk factors identified in this study without requiring large investments into poultry management, thereby reducing the likelihood of avian influenza virus transmission and ultimately occurrence of avian influenza outbreaks.

Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype

Avian influenza viruses of the H9 subtype cause significant losses to poultry production in endemic regions of Asia, Africa and the Middle East and pose a risk to human health. The availability of reliable and updated diagnostic tools for H9 surveillance is thus paramount to ensure the prompt identification of this subtype. The genetic variability of H9 represents a challenge for molecular-based diagnostic methods and was the cause for suboptimal detection and false negatives during routine diagnostic monitoring. Starting from a dataset of sequences related to viruses of different origins and clades (Y439, Y280, G1), a bioinformatics workflow was optimized to extract relevant sequence data preparatory for oligonucleotides design. Analytical and diagnostic performances were assessed according to the OIE standards. To facilitate assay deployment, amplification conditions were optimized with different nucleic extraction systems and amplification kits. Performance of the new real-time RT-PCR was also evaluated in comparison to existing H9-detection methods, highlighting a significant improvement of sensitivity and inclusivity, in particular for G1 viruses. Data obtained suggest that the new assay has the potential to be employed under different settings and geographic areas for a sensitive detection of H9 viruses.

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.

Molecular epidemiology and pathogenicity of H5N1 and H9N2 avian influenza viruses in clinically affected chickens on farms in Bangladesh

Avian influenza virus (AIV) subtypes H5N1 and H9N2 co-circulate in poultry in Bangladesh, causing significant bird morbidity and mortality. Despite their importance to the poultry value chain, the role of farms in spreading and maintaining AIV infections remains poorly understood in most disease-endemic settings. To address this crucial gap in our knowledge, we conducted a cross-sectional study between 2017 and 2019 in the Chattogram Division of Bangladesh in clinically affected and dead chickens in farms with suspected AIV infection. Viral prevalence of each subtype was approximately 10% among farms for which veterinary advice was sought, indicating a high level of virus circulation in chicken farms despite the low number of reported outbreaks. The level of co-circulation of both subtypes on farms was high, with our study suggesting that in the field, the co-circulation of H5N1 and H9N2 can modulate disease severity, which could facilitate an underestimated level of AIV transmission in the poultry value chain. Finally, using newly generated whole-genome sequences, we investigate the evolutionary history of a small subset of H5N1 and H9N2 viruses. Our analyses revealed that for both subtypes, the sampled viruses were genetically most closely related to other viruses isolated in Bangladesh and represented multiple independent incursions. However, due to lack of longitudinal surveillance in this region, it is difficult to ascertain whether these viruses emerged from endemic strains circulating in Bangladesh or from neighbouring countries. We also show that amino acids at putative antigenic residues underwent a distinct replacement during 2012 which coincides with the use of H5N1 vaccines.

Avian influenza transmission risk along live poultry trading networks in Bangladesh

Live animal markets are known hotspots of zoonotic disease emergence. To mitigate those risks, we need to understand how networks shaped by trading practices influence disease spread. Yet, those practices are rarely recorded in high-risk settings. Through a large cross-sectional study, we assessed the potential impact of live poultry trading networks’ structures on avian influenza transmission dynamics in Bangladesh. Networks promoted mixing between chickens sourced from different farming systems and geographical locations, fostering co-circulation of viral strains of diverse origins in markets. Viral transmission models suggested that the observed rise in viral prevalence from farms to markets was unlikely explained by intra-market transmission alone, but substantially influenced by transmission occurring in upstream network nodes. Disease control interventions should therefore alter the entire network structures. However, as networks differed between chicken types and city supplied, standardised interventions are unlikely to be effective, and should be tailored to local structural characteristics.

COVID-19 Impact on Poultry Production and Distribution Networks in Bangladesh

The COVID-19 pandemic has severely affected numerous economic sectors across the world, including livestock production. This study investigates how the pandemic has impacted the poultry production and distribution network (PDN), analyses stakeholders' changing circumstances, and provides recommendations for rapid and long-term resilience. This is based on a literature review, social media monitoring, and key informant interviews (n = 36) from across the poultry sector in Bangladesh. These included key informants from breeder farms and hatcheries, pharmaceutical suppliers, feed companies, dealers, farmers, middlemen, and vendors. We show that the poultry sector was damaged by the COVID-19 pandemic, partly as a result of the lockdown and also by rumors that poultry and their products could transmit the disease. This research shows that hardly any stakeholder escaped hardship. Disrupted production and transportation, declining consumer demand and volatile markets brought huge financial difficulties, even leading to the permanent closure of many farms. We show that the extent of the damage experienced during the first months of COVID-19 was a consequence of how interconnected stakeholders and businesses are across the poultry sector. For example, a shift in consumer demand in live bird markets has ripple effects that impact the price of goods and puts pressure on traders, middlemen, farmers, and input suppliers alike. We show how this interconnectedness across all levels of the poultry industry in Bangladesh makes it fragile and that this fragility is not a consequence of COVID-19 but has been revealed by it. This warrants long-term consideration beyond the immediate concerns surrounding the COVID-19 pandemic.

Risk Areas for Influenza A(H5) Environmental Contamination in Live Bird Markets, Dhaka, Bangladesh

We evaluated the presence of influenza A(H5) virus environmental contamination in live bird markets (LBMs) in Dhaka, Bangladesh. By using Bernoulli generalized linear models and multinomial logistic regression models, we quantified LBM-level factors associated with market work zone–specific influenza A(H5) virus contamination patterns. Results showed higher environmental contamination in LBMs that have wholesale and retail operations compared with retail-only markets (relative risk 0.69, 95% 0.51–0.93; p = 0.012) and in March compared with January (relative risk 2.07, 95% CI 1.44–2.96; p<0.001). Influenza A(H5) environmental contamination remains a public health problem in most LBMs in Dhaka, which underscores the need to implement enhanced biosecurity interventions in LBMs in Bangladesh.

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.