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Background: A new reassortant influenza A (H7N9) virus emerged early 2013 in eastern China. Exposure to H7N9 infected poultry at live bird markets (LBM) was implicated as the main risk factor for human infection. We aimed to identify the role of LBM biosecurity indicators and poultry movement in the affected areas.Methods: A cross-sectional survey was carried out in 24 LBMs at the beginning of H7N9 outbreak in all affected provinces. We used univariable analysis to identify the biosecurity factors associated with the H7N9 presence in LBMs and social network and spatial analysis to quantify the connectivity and geographic variation in the connectivity of poultry movements.Results: Chickens were the predominant poultry species traded by affected LBMs. The presence of H7N9 in LBMs was significantly associated with the type of LBM and with LBMs that sold chicken to other markets. The chicken movements were significantly spatially clustered and was highest in counties from Jiangsu and Anhui provinces.Conclusion: LBM biosecurity and chicken movement played an important role in the emergence of H7N9. This study identified highly connected areas in eastern China which continue to report human infections highlighting candidate areas for more detailed epidemiological investigations. [ABSTRACT FROM AUTHOR]

Live bird markets (LBMs) are essential for marketing poultry, but have been linked to many outbreaks of avian influenza (AI) and its spread. In Uganda, it has been observed that demographic characteristics of poultry traders/handlers influence activities and decision-making in LBMs. The study investigated the influence of socio-demographic characteristics of poultry handlers: age, sex, religion, educational background, level of income, location of residence and region of operation on 20 potential risk factors for introduction and spread of AI in LBMs. Study sites included 39 LBMs in the four regions of Uganda. Data was collected using a semi-structured questionnaire administered to 424 poultry handlers. We observed that background of education was a predictor for slaughter and processing of poultry in open sites. Location of residence was associated with slaughter of poultry from open sites and selling of other livestock species. Region influenced stacking of cages, inadequate cleaning of cages, feeders and drinkers, and provision of dirty feed and water. Specifically, bird handlers with secondary level of education (OR = 12.9, 95% CI: 2.88-57.4, P < 0.01) were more likely to be involved in open site slaughter of poultry than their counterparts without formal education. Comparatively, urbanite bird handlers were less likely to share poultry equipment (OR = 0.4, 95% CI: 0.22-0.63, P < 0.01) than rural resident handlers. Poultry handlers in Northern were 3.5 times more likely to practise insufficient cleaning of cages (OR = 3.5, 95% CI: 1.52-8.09) compared to those in Central region. We demonstrated that some socio-demographic characteristics of poultry handlers were predictors to risky practices for introduction and spread of AI viruses in LBMs in Uganda. [ABSTRACT FROM AUTHOR]

The article discusses surveillance conducted at the Live Bird Markets (LBMs) at Vietnam for avian influenza (AI) viruses in poultry. Topics discussed include virus of highly pathogenic avian influenza (HPAI) A (H5N1), virus isolation, and appearance of Clade viruses in poultry. Also discussed are genetic variants of the viruses and poultry vaccines used in Vietnam.

Clade 2.3.4.4 H5Nx influenza viruses have further diversified into several subclades. Sub-clade 2.3.4.4b H5N1 viruses have been widely circulating in wild birds and detected in Europe, Africa, Asia, and North America since October 2020. In this study, we report the first detection of highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses in wild birds and domestic ducks from live bird markets in Egypt. Phylogenetic analysis revealed that the Egyptian H5N1 virus retained the genomic composition of Eurasian strains. Mutations in the viral proteins associated with zoonotic potential and pathogenicity were detected in Egyptian isolates. Egypt is considered a hot spot for the evolution of the influenza virus, so active surveillance of avian influenza viruses in Egypt is warranted.

Background: Newcastle disease is still a serious disease of poultry especially in backyard free-range production systems despite the availability of cross protective vaccines. Healthy-looking poultry from live bird markets have been suspected as a major source of disease spread although limited studies have been conducted to ascertain the presence of the virulent strains in the markets and to understand how they are related to outbreak strains. Methods: This study evaluated the occurrence of Newcastle disease virus in samples collected from poultry in live bird markets across Uganda. The isolates were pathoyped using standard methods (mean death time (MDT), intracelebral pathogenicity index (ICPI), and sequencing of the fusion protein cleavage site motif) and also phylogenetically analysed after sequencing of the full fusion and hemagglutin-neuraminidase genes. The isolates were classified into genotypes and subgenotypes based on the full fusion protein gene classification system and compared with other strains in the region and world-wide. Results: Virulent avian paramyxovirus type I (APMV-1) (Newcastle disease virus) was isolated in healthy-looking poultry in live bird markets. The viruses belonged to a new subgenotype, Vd, in genotype V, and clustered together with Tanzania and Kenya strains. They harbored low genetic diversity. Conclusion: The occurrence of virulent AMPV-1 strains in live bird markets may serve as sources of Newcastle disease outbreaks in non-commercial farms. [ABSTRACT FROM AUTHOR]

Abstract: Indonesia continues to report the highest number of human and poultry cases of highly pathogenic avian influenza H5N1. The disease is considered to be endemic on the island of Bali. Live bird markets are integral in the poultry supply chain on Bali and are important, nutritionally and culturally, for the rural and urban human populations. Due to the lack of biosecurity practiced along the supply chain from producer to live bird markets, there is a need to understand the risks associated with the spread of H5N1 through live bird movements for effective control. Resources to control H5N1 in Indonesia are very limited and cost effective strategies are needed. We assessed the probability a live bird market is infected through live poultry movements and assessed the effects of implementing two simple and low cost control measures on this risk. Results suggest there is a high risk a live bird market is infected (0.78), and risk mitigation strategies such as detecting and removing infected poultry from markets reduce this risk somewhat (range 0.67–0.76). The study demonstrates the key role live poultry movements play in transmitting H5N1 and the need to implement a variety of control measures to reduce disease spread. [Copyright &y& Elsevier]

Background: The endemic H5N1 high pathogenicity avian influenza virus (A/H5N1) in poultry in Egypt continues to cause heavy losses in poultry and poses a significant threat to human health. Methods: Here we describe results of A/H5N1 surveillance in domestic poultry in 2009 and wild birds in 2009-2010. Tracheal and cloacal swabs were collected from domestic poultry from 22024 commercial farms, 1435 backyards and 944 live bird markets (LBMs) as well as from 1297 wild birds representing 28 different types of migratory birds. Viral RNA was extracted from a mix of tracheal and cloacal swabs media. Matrix gene of avian influenza type A virus was detected using specific real-time reverse-transcription polymerase chain reaction (RT-qPCR) and positive samples were tested by RT-qPCR for simultaneous detection of the H5 and N1 genes. Results: In this surveillance, A/H5N1 was detected from 0.1% (n = 23/) of examined commercial poultry farms, 10.5% (n = 151) of backyard birds and 11.4% (n = 108) of LBMs but no wild bird tested positive for A/H5N1. The virus was detected from domestic poultry year-round with higher incidence in the warmer months of summer and spring particularly in backyard birds. Outbreaks were recorded mostly in Lower Egypt where 95.7% (n = 22), 68.9% (n = 104) and 52.8% (n = 57) of positive commercial farms, backyards and LBMs were detected, respectively. Higher prevalence (56%, n = 85) was reported in backyards that had mixed chickens and waterfowl together in the same vicinity and LBMs that had waterfowl (76%, n = 82). Conclusion: Our findings indicated broad circulation of the endemic A/H5N1 among poultry in 2009 in Egypt. In addition, the epidemiology of A/H5N1 has changed over time with outbreaks occurring in the warmer months of the year. Backyard waterfowl may play a role as a reservoir and/or source of A/H5N1 particularly in LBMs. The virus has been established in poultry in the Nile Delta where major metropolitan areas, dense human population and poultry stocks are concentrated. Continuous surveillance, tracing the source of live birds in the markets and integration of multifaceted strategies and global collaboration are needed to control the spread of the virus in Egypt. [ABSTRACT FROM AUTHOR]

Please cite this paper as: Chander et al. (2012) Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. Influenza and Other Respiratory Viruses 7(4), 513-520. Background Wild birds are the natural hosts for influenza A viruses (IAVs) and provide a niche for the maintenance of this virus. Objectives This study was undertaken to analyze nucleotide sequences of the matrix (M) gene of AIVs isolated from wild birds and live bird markets (LBMs) to index the changes occurring in this gene. Methods M-gene of 229 avian influenza virus (AIV) isolates obtained from wild birds and LBMs was amplified and sequenced. Full-length sequences (∼900 nt.) thus obtained were analyzed to identify changes that may be associated with resistance to adamantanes. Phylogenetic analysis of all sequences was performed using clustalw, and evolutionary distances were calculated by maximum composite likelihood method using mega ( ver. 5.0) software. Results Twenty-seven different viral subtypes were represented with H3N8 being the most dominant subtype in wild birds and H7N2 being the predominant subtype among isolates from LBMs. Phylogenetic analysis of the M-gene showed a high degree of nucleotide sequence identity with US isolates of AIVs but not with those of Asian or European lineages. While none of the isolates from wild birds had any antiviral resistance-associated mutations, 17 LBM isolates carried polymorphisms known to cause reduced susceptibility to antiviral drugs (adamantanes). Of these 17 isolates, 16 had S31N change and one isolate had V27A mutation. Conclusions These results indicate independent evolution of M-gene in the absence of any antiviral drugs leading to mutations causing resistance indicating the need for continued active surveillance of AIVs. [ABSTRACT FROM AUTHOR]

Please cite this paper as: Munyua et al. (2013) Detection of influenza A virus in live bird markets in Kenya, 2009-2011. Influenza and Other Respiratory Viruses 7(2), 113-119. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub-Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. Objectives This surveillance project aimed to detect influenza A virus in poultry traded in five LBMs in Kenya. Methods We visited each market monthly and collected oropharyngeal and cloacal specimens from poultry and environmental specimens for virological testing for influenza A by real time RT-PCR. On each visit, we collected information on the number and types of birds in each market, health status of the birds, and market practices. Results During March 24, 2009-February 28, 2011, we collected 5221 cloacal and oropharyngeal swabs. Of the 5199 (99·6%) specimens tested, influenza A virus was detected in 42 (0·8%), including 35/4166 (0·8%) specimens from chickens, 3/381 (0·8%) from turkeys, and 4/335 (1·2%) from geese. None of the 317 duck specimens were positive. Influenza was more commonly detected in oropharyngeal [33 (1·3%)] than in cloacal [9 (0·4%)] specimens. None of the 485 environmental specimens were positive. Virus was detected in all five markets during most (14/22) of the months. Ducks and geese were kept longer at the market (median 30 days) than chickens (median 2 days). Conclusions Influenza A was detected in a small percentage of poultry traded in LBMs in Kenya. Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs. [ABSTRACT FROM AUTHOR]

The article focuses on a study related to the impact of live bird markets (LBMs) in the development of avian influenza virus (AIV). It informs that scientists used primary virus isolation methods and subtype-specific reverse-transcription-polymerase chain reaction (PCR). It states that the isolation rates if AIV are higher in winter and spring season as compared to summer and autumn season in China. It also mentions that geese and swans harbor low pathogenic avian influenza (LPAI) during grazing in the field so poultry farms need to look into the grazing system of poultry animals.

Live bird markets and contacts between them through poultry traders are known risk factors in the spread of diseases such as Newcastle disease. A traders' questionnaire survey was used to build networks of chicken movements among 29 shared markets during and outside festive seasons in the Oromia region of Ethiopia. A comparison was made between typologies built using centrality indexes (in-degree, out-degree, in-closeness, out-closeness and random-walk betweenness) and descriptive characteristics of the markets (number of chickens, number and type of sellers and the frequency with which they use different markets). The festive seasons did not appear to have an impact on the network structure, implying that it was not necessary to make structural changes to surveillance targets during these periods. Based on centrality indices, three markets (Meki, Debre Zeit and Adulala) emerged from the typology as being central to the network, which would not have been deduced from their descriptive characteristics alone. These three poultry markets ideally would be chosen in a risk-based type of surveillance system and in targeted control policies. [ABSTRACT FROM AUTHOR]

Abstract: Live bird markets (LBMs) are at risk of contamination with the avian influenza H5N1 virus. There are a number of methods for prioritizing LBMs for intervention to curb the risk of contamination. Selecting a method depends on diagnostic objective and disease prevalence. In a low resource setting, options for prioritization are constricted by the cost of and resources available for tool development and administration, as well as the resources available for intervention. In this setting, tools can be developed using previously collected data on risk factors for contamination, and translated into prediction equations, including decision trees (DTs). DTs are a graphical type of classifier that combine simple questions about the data in an intuitive way. DTs can be used to develop tools tailored to different diagnostic objectives. To demonstrate the utility of this method, risk factor data arising from a previous cross-sectional study in 83 LBMs in Indonesia were used to construct DTs. A DT with high specificity was selected for the initial stage of an LBM intervention campaign in which authorities aim to focus intervention resources on a small set of LBMs that are at near-certain risk of contamination. Another DT with high sensitivity was selected for later stages in an intervention campaign in which authorities aim to detect and prioritize all LBMs with the risk factors for virus contamination. The best specific DT achieved specificity of 77% and the best sensitive DT achieved sensitivity of 90%. The specific DT had two variables: the size of the duck population in the LBM and the human population density in the LBM''s district. The sensitive DT had three variables: LBM location, whether solid waste was removed from the LBM daily and whether the LBM was zoned to separate the bird holding, slaughtering and sale areas. High specificity or sensitivity will be preferred by authorities depending on the stage of the intervention campaign. The study demonstrates that simple tools utilizing DTs can be developed to prioritize LBMs for intervention to control H5N1-virus. DT tools are simple to apply, suitable for low-resource settings and can be tailored to the particular needs and stage of the disease control program. [Copyright &y& Elsevier]

Background: Uninterrupted transmission of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.2.1 in Egypt since 2006 resulted in establishment of two main genetic clusters. The 2.2.1/C group where all recent human and majority of backyard origin viruses clustered together, meanwhile the majority of viruses derived from vaccinated poultry in commercial farms grouped in 2.2.1.1 clade. Findings: In the present investigation, an HPAIV H5N1 was isolated from twenty weeks old layers chickens that were vaccinated with a homologous H5N1 vaccine at 1, 7 and 16 weeks old. At twenty weeks of age, birds showed cyanosis of comb and wattle, decrease in egg production and up to 27% mortality. Examined serum samples showed low antibody titer in HI test (Log2 3.2± 4.2). The hemagglutinin (HA) and neuraminidase (NA) genes of the isolated virus were closely related to viruses in 2.2.1/C group isolated from poultry in live bird market (LBM) and backyards or from infected people. Conspicuous mutations in the HA and NA genes including a deletion within the receptor binding domain in the HA globular head region were observed. Conclusions: Despite repeated vaccination of layer chickens using a homologous H5N1 vaccine, infection with HPAIV H5N1 resulted in significant morbidity and mortality. In endemic countries like Egypt, rigorous control measures including enforcement of biosecurity, culling of infected birds and constant update of vaccine virus strains are highly required to prevent circulation of HPAIV H5N1 between backyard birds, commercial poultry, LBM and humans. [ABSTRACT FROM AUTHOR]

Neuraminidase (NA) gene of avian influenza viruses isolated from Live Bird Markets (LBMs) on the east coast of the United States was sequenced and analyzed for mutations associated with antiviral resistance. In total, 189 isolates collected from 1994 to 2005 were used in this study. Full length sequences of the NA gene were obtained from 183 of the 189 isolates. Four different lengths of NA gene were observed; 40 isolates had full length (about 1400 nt), 132 isolates had a deletion of 48 nt, 10 isolates had a deletion of 66 nt, and one isolate had a deletion of 72 nt. Amino acid analysis of the sequence data showed point mutations distributed throughout the gene length. None of these deletions was in the catalytic region and most of the mutations were observed in the flanking regions. None of the isolates had mutations which are known to confer antiviral resistance. These results indicate that though NA gene is prone to mutational changes, much of those changes occur outside the catalytic domain. [ABSTRACT FROM AUTHOR]

Abstract: Live bird markets can become contaminated with and become a source of transmission for avian influenza viruses including the highly pathogenic H5N1 strain. Many countries affected by the H5N1-virus have limited resources for programs in environmental health, sanitation and disease control in live bird markets. This study proposes five critical control points (CCPs) to reduce the risk of H5N1-virus contamination in markets in low resource settings. The CCPs were developed based on three surveys conducted in Indonesia: a cross-sectional survey in 119 markets, a knowledge, attitudes and practice survey in 3 markets and a microbiological survey in 83 markets. These surveys assessed poultry workflow, market infrastructure, hygiene and regulatory practices and microbiological contamination with the H5N1-virus. The five CCPs identified were (1) reducing risk of receiving infected birds into the market, (2) reducing the risk of virus spread between different bird flocks in holding cages, (3) reducing surface contamination by isolating slaughter processes from other poultry-related processes, (4) minimizing the potential for contamination during evisceration of carcasses and (5) reducing the risk of surface contamination in the sale zone of the market. To be relevant for low resource settings, the CCPs do not necessitate large infrastructure changes. The CCPs are suited for markets that slaughter poultry and have capacity for daily disposal and removal of solid waste from the market. However, it is envisaged that the CCPs can be adapted for the development of risk-based programs in various settings. [Copyright &y& Elsevier]

The article offers information on a study which analyzed avian influenza virus (AIV) present in live bird markets (LBM) in Korea during the winter seasons of 2006 to 2008. A brief review of the related literature is presented. Materials and methods used included sampling for virus isolation, virus isolation and subtyping and phylogenetic and molecular analysis. It discusses the findings of the study such as the replication of influenza virus isolates in experimental animals. It concludes that viral gene transfer exists among different animal species in LBM.

The article focuses on a comprehensive avian influenza control program created for the live bird market (LBM) system in New York City. The program was designed to eradicate avian influenza virus (AIV) from the LBM system. Sanitation and a break in continuous-flow operations for thorough cleaning and disinfection have been used to control agricultural disease in the LBM. According to the authors, the implementation of the program, along with voluntary cooperation from LBM owners and poultry dealers and haulers, resulted to the isolation of H7 low pathogenic avian influenza virus (LPAIV) from the New York LBM.

The article focuses on a study which characterized Clade 7 high pathogenicity avian influenza H5N1 viruses in chickens in Vietnam. The study identified nucleotide and amino acid divergence across the hemagglutinin (HA) protein gene. Study authors conducted an antigenic analysis of the isolates from the live bird markets and found cross-reactivity between clade 7 viruses that belong to the same subgroups. A reassortant virus from A/chicken/Vietnam/NCVD-016/2008 was developed by the authors as a prepandemic vaccine candidate for veterinary or human vaccination.

Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand the ecology and epidemiology of AI in Nigeria, we performed whole-genome sequencing of nineteen H9N2 viruses recovered, from apparently healthy poultry species, during active surveillance conducted in nine LBMs across Nigeria in 2019. Analyses of the HA gene segment of these viruses showed that the H9N2 strains belong to the G1 lineage, which has zoonotic potential, and are clustered with contemporary H9N2 identified in Africa between 2016 and 2020. We observed two distinct clusters of H9N2 viruses in Nigeria, suggesting different introductions into the country. In view of the zoonotic potential of H9N2 and the co-circulation of multiple subtypes of AI virus in Nigeria, continuous monitoring of the LBMs across the country and molecular characterization of AIVs identified is advocated to mitigate economic losses and public health threats. [ABSTRACT FROM AUTHOR]

Live bird markets are considered high-risk environments facilitating viral transfer and replication of influenza A H5N1. In Indonesia, these markets have been the source for multiple human infections of H5N1 resulting in death, and thus have been the focus of government-led interventions. This paper examines the aftermath of an intervention in one market in Bali, Indonesia. It highlights the social and economic factors influencing the adoption of risk prevention behaviour and concludes by arguing for further qualitative research to understand why at-risk individuals fail to adopt biosecurity measures, even after recently experiencing an outbreak of avian influenza. [ABSTRACT FROM AUTHOR]

Yellow broilers are the primary source of poultry consumption in China and the predominant trade of live poultry. However, knowledge of the value chain is limited, which is vital evidence for the effective control of H7N9 and other zoonotic avian influenzas. The aim of the study was to map the yellow broiler value chain in Guangxi Zhuang Autonomous Region, China and investigate its governance structure and practices relevant to the risk of H7N9 transmission. A value chain analysis was conducted in five areas of Guangxi from May to August 2018. To map the value chain, three focus group discussions (FGDs) were conducted and stakeholders, products and premises involved and their interactions were identified. Then, 55 key informant interviews (KIIs) collected qualitative data on stakeholders' profile, practices and interactions with other stakeholders and rules/norms that exist along the value chain. On-site observations were also carried out at different types of premises along the value chain to complement and validate findings of KIIs and FGDs. Participants were also asked to provide proportional estimates of each component in the value chain where possible. The qualitative data from FGDs, KIIs and on-site observations were analysed to create stakeholder profiles and a diagram of product flows and stakeholders' interactions. Thematic analysis was used to identify the governance structure of the value chains and practices relevant to the risk of H7N9 transmission. The stakeholders and premises involved in Guangxi yellow broiler production, wholesale and retail were described, as well as their interactions. Contract farming is extensively adopted in Guangxi; consequently yellow broiler grower companies are the dominant stakeholders. The trading platform was identified as a key premise linking farms and live bird markets. The thematic analysis highlighted poor biosecurity practices in different premises along the value chain, which was supported by on-site observations. The operation of trading platforms reported in this study presents a disease risk but is not considered in the current H7N9 control programs. The study suggested that biosecurity management gaps need to be addressed through government-industry partnerships that require engagement with private stakeholders in the planning and implementation of H7N9 control strategies incentivising participation of grower companies, wholesalers and retailers. [ABSTRACT FROM AUTHOR]

Wild migratory birds are often implicated in the introduction, maintenance, and global dissemination of different pathogens, such as influenza A viruses (IAV) and antimicrobial-resistant (AMR) bacteria. Trapping of migratory birds during their resting periods at the northern coast of Egypt is a common and ancient practice performed mainly for selling in live bird markets (LBM). In the present study, samples were collected from 148 wild birds, representing 14 species, which were being offered for sale in LBM. All birds were tested for the presence of AIV and enterobacteriaceae . Ten samples collected from Northern Shoveler birds ( Spatula clypeata ) were positive for IAV and PCR sub-typing and pan HA/NA sequencing assays detected H5N8, H9N2, and H6N2 viruses in four, four, and one birds, respectively. Sequencing of the full haemagglutinin (HA) gene revealed a high similarity with currently circulating IAV in Egypt. From all the birds, E.coli was recovered from 37.2% and Salmonella from 20.2%, with 66%-96% and 23%-43% isolates being resistant to at least one of seven selected critically important antimicrobials (CIA), respectively. The presence of enzootic IAV and the wide prevalence of AMR enterobacteriaceae in wild birds highlight the potential role of LBM in the spread of different pathogens from and to wild birds. Continued surveillance of both AIV and antimicrobial-resistant enterobacteriaceae in wild birds' habitats is urgently needed.

Cryptosporidium is an opportunistic parasite that has been reported in >30 avian hosts worldwide, however, there is no information regarding Cryptosporidium spp. in poultry in Bangladesh. Accordingly, we investigated the prevalence of Cryptosporidium spp. in poultry at open live bird markets in Bangladesh. A total of 197 samples were randomly collected from poultry at open live bird markets in Bangladesh and screened for the detection of Cryptosporidium. Initial microscopic examination revealed Cryptosporidium spp. was observed in 19.8% (39/197) of the poultry specimens. Subsequent nested PCR targeting the 18S rRNA gene revealed that 15.7% (31/197) of the samples were Cryptosporidium positive. Of these 31 samples, 17 were Cryptosporidium baileyi (8.7%), 12 were Cryptosporidium meleagridis (6.0%), and 2 were Cryptosporidium parvum (1.0%). Nucleotide sequence analysis of the GP60 gene of the C. meleagridis revealed that two subtypes (IIIbA21G1R1 and IIIbA23G1R1), which were found in broiler, native and sonali chickens and a pigeon, matched those previously reported in humans and poultry. We identified two novel subtypes (IIIbA21G2R1 and IIIbA20G2R1) in sonali chickens, a broiler chicken and a layer chicken. We also amplified the GP60 gene of C. parvum and found two subtypes (IIaA11G2R1 and IIaA13G2R1) in a sonali and a broiler chicken that were previously reported in calf. These findings suggest that poultry can be a source of cryptosporidial infections for humans and animals in Bangladesh. This is the first molecular investigation of Cryptosporidium genotypes and subtypes in poultry at open live bird markets in Bangladesh., Competing Interests: The authors have no conflicts of interest to declare., (© 2020 The Authors.)

We conducted a cross-sectional study in live bird markets (LBMs) in Dhaka and Chittagong, Bangladesh, to estimate the prevalence of avian influenza A(H5) and A(H9) viruses in different types of poultry and environmental areas by using Bayesian hierarchical logistic regression models. We detected these viruses in nearly all LBMs. Prevalence of A(H5) virus was higher in waterfowl than in chickens, whereas prevalence of A(H9) virus was higher in chickens than in waterfowl and, among chicken types, in industrial broilers than in cross-breeds and indigenous breeds. LBMs with >1 wholesaler were more frequently contaminated by A(H5) virus than retail-only LBMs. Prevalence of A(H9) virus in poultry and level of environmental contamination were also higher in LBMs with >1 wholesaler. We found a high level of circulation of both avian influenza viruses in surveyed LBMs. Prevalence was influenced by type of poultry, environmental site, and trading.

Highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Vietnam since 2003, whilst outbreaks of HPAI H5N6 virus are more recent, having only been reported since 2014. Although the spatial distribution of H5N1 outbreaks and risk factors for virus occurrence has been extensively studied, there have been no comparative studies for H5N6. Data collected through active surveillance of Vietnamese live bird markets (LBMs) between 2011 and 2015 were used to explore and compare the spatiotemporal distributions of H5N1- and H5N6-positive LBMs. Conditional autoregressive models were developed to quantify spatiotemporal associations between agroecological factors and the two HPAI strains using the same set of predictor variables. Unlike H5N1, which exhibited a strong north-south divide, with repeated occurrence in the extreme south of a cluster of high-risk provinces, H5N6 was homogeneously distributed throughout Vietnam. Similarly, different agroecological factors were associated with each strain. Sample collection in the months of January and February and higher average maximum temperature were associated with higher likelihood of H5N1-positive market-day status. The likelihood of market days being positive for H5N6 increased with decreased river density, and with successive Rounds of data collection. This study highlights marked differences in spatial patterns and risk factors for H5N1 and H5N6 in Vietnam, suggesting the need for tailored surveillance and control approaches.

Longitudinal surveillance of 2 live bird markets in Cambodia revealed year-round, high co-circulation of H5, H7, and H9 influenza viruses. We detected influenza A viruses in 51.3% of ducks and 39.6% of chickens, and co-infections, mainly by H5 and H9 viruses, in 0.8% of ducks and 4.5% of chickens.

This study was conducted to determine the prevalence of antimicrobial resistance in Campylobacter spp. isolates from broilers in live bird markets (LBMs). A total of 209 Campylobacter spp. isolates (84 Campylobacter jejuni; 125 Campylobacter coli) were recovered from 364 broiler cecum samples collected from five LBMs in Shanghai, China. Minimum inhibitory concentrations of 13 antimicrobials were determined using agar dilution method. More than 96% of the Campylobacter spp. isolates were resistant to quinolones and tetracyclines. A high prevalence of macrolide resistance (erythromycin, 84.0%; azithromycin, 80.8%) was observed in C. coli, but not in C. jejuni (erythromycin, 6.0%; azithromycin, 2.4%). C. coli also showed significantly higher resistance than C. jejuni to clindamycin, gentamicin, and kanamycin. In contrast, C. coli isolates had lower resistance to florfenicol than the C. jejuni isolates. The majority of the C. jejuni (88.1%) and C. coli (97.6%) isolates exhibited multidrug resistance (MDR) to three or more classes of antimicrobials. All of the 208 ciprofloxacin-resistant Campylobacter spp. isolates were positive for the C257T mutation of the gyrA gene. In addition, the tet(O) gene was identified in all of the 202 doxycycline-resistant Campylobacter spp. isolates. Furthermore, 75.7% and 20.4% of the 103 azithromycin-resistant Campylobacter spp. isolates were positive for the A2075G mutation of the 23S rRNA gene and the presence of the erm(B) gene, respectively. Moreover, the cat gene was found in 14.3% (8/56) and 76.8% (73/95) of the chloramphenicol-resistant C. jejuni and C. coli isolates, respectively. To the best of our knowledge, this is the first report of the prevalence of antimicrobial resistance among Campylobacter spp. isolates originating from LBMs. The high prevalence of MDR Campylobacter spp. isolates in LBMs highlights the need to implement efficient intervention measures to control not only Campylobacter contamination in LBMs but also dissemination of antimicrobial resistance among Campylobacter spp. in poultry production.

Highly pathogenic H5N1 and low pathogenic H9N2 influenza viruses are endemic to poultry markets in Bangladesh and have cocirculated since 2008. H9N2 influenza viruses circulated constantly in the poultry markets, whereas highly pathogenic H5N1 viruses occurred sporadically, with peaks of activity in cooler months. Thirty highly pathogenic H5N1 influenza viruses isolated from poultry were characterized by antigenic, molecular, and phylogenetic analyses. Highly pathogenic H5N1 influenza viruses from clades 2.2.2 and 2.3.2.1 were isolated from live bird markets only. Phylogenetic analysis of the 30 H5N1 isolates revealed multiple introductions of H5N1 influenza viruses in Bangladesh. There was no reassortment between the local H9N2 influenza viruses and H5N1 genotype, despite their prolonged cocirculation. However, we detected two reassortant H5N1 viruses, carrying the M gene from the Chinese H9N2 lineage, which briefly circulated in the Bangladesh poultry markets and then disappeared. On the other hand, interclade reassortment occurred within H5N1 lineages and played a role in the genesis of the currently dominant H5N1 viruses in Bangladesh. Few 'human-like' mutations in H5N1 may account for the limited number of human cases. Antigenically, clade 2.3.2.1 H5N1 viruses in Bangladesh have evolved since their introduction and are currently mainly homogenous, and show evidence of recent antigenic drift. Although reassortants containing H9N2 genes were detected in live poultry markets in Bangladesh, these reassortants failed to supplant the dominant H5N1 lineage.