Association of biosecurity and hygiene practices with avian influenza A/H5 and A/H9 virus infections in turkey farms.

High pathogenicity avian influenza (HPAI) H5N1 outbreaks pose a significant threat to the health of livestock, wildlife, and humans. Avian influenza viruses (AIVs) are enzootic in poultry in many countries, including Bangladesh, necessitating improved farm biosecurity measures. However, the comprehension of biosecurity and hygiene practices, as well as the infection of AIV in turkey farms, are poorly understood in Bangladesh. Therefore, we conducted this study to determine the prevalence of AIV subtypes and their association with biosecurity and hygiene practices in turkey farms. We collected oropharyngeal and cloacal swabs from individual turkeys from 197 farms across 9 districts in Bangladesh from March to August 2019. We tested the swab samples for the AIV matrix gene (M gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We found 24.68% (95% CI:21.54-28.04) of turkey samples were AIV positive, followed by 5.95% (95% CI: 4.33-7.97) for H5, 6.81% (95% CI: 5.06-8.93) for H9 subtype and no A/H7 was found. Using a generalized linear mixed model, we determined 10 significant risk factors associated with AIV circulation in turkey farms. We found that the absence of sick turkeys, the presence of footbaths, the absence of nearby poultry farms, concrete flooring, and the avoidance of mixing newly purchased turkeys with existing stock can substantially reduce the risk of AIV circulation in turkey farms (odds ratio ranging from 0.02 to 0.08). Furthermore, the absence of nearby live bird markets, limiting wild bird access, no visitor access, improved floor cleaning frequency, and equipment disinfection practices also had a substantial impact on lowering the AIV risk in the farms (odds ratio ranging from 0.10 to 0.13). The results of our study underscore the importance of implementing feasible and cost-effective biosecurity measures aimed at reducing AIV transmission in turkey farms. Particularly in resource-constrained environments such as Bangladesh, such findings might assist governmental entities in enhancing biosecurity protocols within their poultry sector, hence mitigating and potentially averting the transmission of AIV and spillover to humans.

Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh.

Waterfowl are considered to be natural reservoirs of the avian influenza virus (AIV). However, the dynamics of transmission and evolutionary patterns of AIV and its subtypes within duck farms in Bangladesh remain poorly documented. Hence, a cross-sectional study was conducted in nine districts of Bangladesh between 2019 and 2021, to determine the prevalence of AIV and its subtypes H5 and H9, as well as to identify risk factors and the phylodynamics of H5N1 clades circulating in domestic duck farms. The oropharyngeal and cloacal swab samples were tested for the AIV Matrix gene (M-gene) followed by H5, H7, and H9 subtypes using rRT-PCR. The exploratory analysis was performed to estimate AIV and its subtype prevalence in different production systems, and multivariable logistic regression model was used to identify the risk factors that influence AIV infection in ducks. Bayesian phylogenetic analysis was conducted to generate a maximum clade credibility (MCC) tree and the maximum likelihood method to determine the phylogenetic relationships of the H5N1 viruses isolated from ducks. AIV was detected in 40% (95% CI: 33.0-48.1) of the duck farms. The prevalence of AIV was highest in nomadic ducks (39.8%; 95% CI: 32.9-47.1), followed by commercial ducks (24.6%; 95% CI: 14.5-37.3) and backyard ducks (14.4%; 95% CI: 10.5-19.2). The H5 prevalence was also highest in nomadic ducks (19.4%; 95% CI: 14.0-25.7). The multivariable logistic regression model revealed that ducks from nomadic farms (AOR: 2.4; 95% CI: 1.45-3.93), juvenile (AOR: 2.2; 95% CI: 1.37-3.61), and sick ducks (AOR: 11.59; 95% CI: 4.82-32.44) had a higher risk of AIV. Similarly, the likelihood of H5 detection was higher in sick ducks (AOR: 40.8; 95% CI: 16.3-115.3). Bayesian phylogenetic analysis revealed that H5N1 viruses in ducks belong to two distinct clades, 2.3.2.1a, and 2.3.4.4b. The clade 2.3.2.1a (reassorted) has been evolving silently since 2015 and forming at least nine subgroups based on >90% posterior probability. Notably, clade 2.3.4.4b was introduced in ducks in Bangladesh by the end of the year 2020, which was genetically similar to viruses detected in wild birds in Japan, China, and Africa, indicating migration-associated transmission of an emerging panzootic clade. We recommend continuing AIV surveillance in the duck production system and preventing the intermingling of domestic ducks with migratory waterfowl in wetlands.

Prevalence and risk factors for avian influenza virus (H5 and H9) contamination in peri-urban and rural live bird markets in Bangladesh.

Avian influenza viruses (AIV) have been frequently detected in live bird markets (LBMs) around the world, primarily in urban areas, and have the ability to spillover to other species, including humans. Despite frequent detection of AIV in urban LBMs, the contamination of AIV on environmental surfaces in rural and peri-urban LBMs in Bangladesh is poorly documented. Therefore, we conducted this study to determine the prevalence of AIV subtypes within a subset of peri-urban and rural LBMs in Bangladesh and to further identify associated risk factors. Between 2017 and 2018, we collected faecal and offal samples from 200 stalls in 63 LBMs across four sub-districts. We tested the samples for the AIV matrix gene (M-gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We performed a descriptive analysis of market cleanliness and sanitation practices in order to further elucidate the relationship between LBM biosecurity and AIV subtypes by species, sample types, and landscape. Subsequently, we conducted a univariate analysis and a generalized linear mixed model (GLMM) to determine the risk factors associated with AIV contamination at individual stalls within LBMs. Our findings indicate that practices related to hygiene and the circulation of AIV significantly differed between rural and peri-urban live bird markets. 42.5% (95% CI: 35.56-49.67) of stalls were positive for AIV. A/H5, A/H9, and A HA/Untyped were detected in 10.5% (95% CI: 6.62-15.60), 9% (95% CI: 5.42-13.85), and 24.0% (95% CI: 18.26-30.53) of stalls respectively, with no detection of A/H7. Significantly higher levels of AIV were found in the Sonali chicken strain compared to the exotic broiler, and in offal samples compared to fecal samples. In the GLMM analysis, we identified several significant risk factors associated with AIV contamination in LBMs at the stall level. These include: landscape (AOR: 3.02; 95% CI: 1.18-7.72), the number of chicken breeds present (AOR: 2.4; 95% CI: 1.01-5.67), source of birds (AOR: 2.35; 95% CI: 1.0-5.53), separation of sick birds (AOR: 3.04; 95% CI: 1.34-6.92), disposal of waste/dead birds (AOR: 3.16; 95% CI: 1.41-7.05), cleaning agent (AOR: 5.99; 95% CI: 2.26-15.82), access of dogs (AOR: 2.52; 95% CI: 1.12-5.7), wild birds observed on site (AOR: 2.31; 95% CI: 1.01-5.3). The study further revealed a substantial prevalence of AIV with H5 and H9 subtypes in peri-urban and rural LBMs. The inadequate biosecurity measures at poultry stalls in Bangladesh increase the risk of AIV transmission from poultry to humans. To prevent the spread of AIV to humans and wild birds, we suggest implementing regular surveillance at live bird markets and enhancing biosecurity practices in peri-urban and rural areas in Bangladesh.