Molecular survey and interaction of common respiratory pathogens in chicken flocks (field perspective)

Epidemiological distribution of respiratory viral pathogens in marketable vaccinated broiler chickens in five governorates in the Nile Delta, Egypt, from January 2022 to October 2022

Background and Aim

Respiratory viral infections significantly negatively impact animal welfare and have significant financial implications in the poultry industry. This study aimed to determine the frequency of the most economically relevant respiratory viruses that circulated in Egyptian chicken flocks in 2022.

Materials and Methods

Chickens from 359 broiler flocks in five different Egyptian governorates in the Nile Delta (Beheira, Gharbia, Giza, Monufiya, and Qalyoubia) at marketing time (33-38 days of age) were used in this study. Combined oropharyngeal and cloacal swabs and tissue samples were collected from clinically diseased or freshly dead birds suffering from respiratory disease. Avian influenza (AI)-H5, AI-H9, Newcastle disease (ND), and infectious bronchitis virus (IBV) were analyzed by reverse transcriptase polymerase chain reaction.

Results

Of the 359 flocks examined, 293 tested positive, whereas 66 were completely negative for the four viruses evaluated, with the highest positive results in Beheira. Out of 293 positive flocks, 211 were positive for a single virus, with Beheira having the highest rate, followed by Qalyoubia, Giza, and Monufiya. ND virus (NDV) was found to be the highest across all governorates, followed by IBV, AI-H9, and AI-H5. A double infection was detected in 73 flocks with either H9 or ND, or both H9 and IB could coinfect each other. The most common viral coinfections were H9 + IB, ND + IB, and ND + H9. Giza had the highest prevalence of ND + H9, H9 + IB, and ND + IB coinfection in the governorates, followed by Monufiya and Beheira. Only six out of 359 flocks were tribally infected with ND + H9 + IB in Giza, Monufiya, and Beheira governorates. On the basis of the number of flocks and the month of the year, July had the lowest number of flocks (23), while September and October had the highest number (48 flocks). Positive flock numbers were highest in October and lowest in January.

Conclusion

From January to October 2022, prevalent respiratory viral infections (H5N1, NDV, H9N2, and IBV) were detected in broiler chickens across the Delta area governorate, according to the findings of the present study. In addition, IBV and H9, either alone or in combination, significantly contributed to the respiratory infection observed in broiler chickens. Regardless of the type and origin of the vaccine used, it is not possible to protect broiler chickens from the development of the infection and the subsequent dissemination of the virus into the poultry environment. In the presence of face-infectious field virus mutations, poultry vaccinations must be regularly reviewed and updated, and poultry farms must take further biosecurity measures.

Interactions between the helminth and intestinal microbiome in smallholder chicken farming systems

Helminth parasite infections are widespread in smallholder farming systems affecting farmers and livestock animals. There are pathogenic parasites that populate the gut of their host and coexist closely with the gut microbiota. The physical and immunological environment of the gut can be modified by parasites and microbiota creating a wide range of interactions. These interactions modify the development of infection, affects overall host health, and can modify the way a host interacts with its bacterial microbiota. In addition, where there is a high worm burden parasites will affect the health of the host and intestinal tract colonization. This review highlights key studies on the interaction between helminth parasites and the intestinal microbiome to understand the relationship between parasitic worm infections and gut microbiome health in chickens. Finally, the review discusses modulations, molecular changes, and the importance of helminth-microbiome interactions for the host.

Molecular detection of respiratory avian mycoplasmosis associated bacterial and viral concurrent infections in the poultry flocks

Respiratory tract infections are of serious concern to the poultry industry. The present study was aimed to delineate the extent of respiratory avian mycoplasmosis associated bacterial and viral concurrent infections in the poultry flocks. A total of 146 poultry flocks of Haryana and Rajasthan, India, suspected for chronic respiratory disease (CRD) were screened for avian mycoplasmas, Newcastle disease virus (NDV), infectious bronchitis virus (IBV), and avian pathogenic Escherichia coli (APEC) by conventional polymerase chain reaction (PCR) assays. A total of 49.31% (72/146) flocks were found positive for Mycoplasma infection. Of the Mycoplasma-positive flocks, 80.55% (58/72) represented pathogenic avian mycoplasmas (MG and/or MS), while 19.44% (14/72) flocks were positive for commensal avian mycoplasmas (other than MG and MS). A correlation was deduced between avian mycoplasmosis and bacterial and/or viral co-infections. The results revealed that 17.24% (10/58) flocks had only avian mycoplasmosis infection. However, in the remaining flocks, the avian mycoplasmosis was associated either with APEC infection [17.24% (10/58)], IBV infection [43.10% (25/58)], or both APEC and IBV infections [22.41% (13/58)], respectively. Further epidemiological studies on respiratory avian mycoplasmosis associated concurrent infections with other pathogens are recommended to assess circulating strains, risk factors, and economic losses.

A Multiplex PCR Method for Simultaneous Detection of Infectious Laryngotracheitis Virus and Ornithobacterium rhinotracheale

To date, many fluorescence- and gel-based multiplex polymerase chain reaction (PCR) assays have been developed for the simultaneous detection of multiple infectious agents of respiratory disease in poultry. However, PCR assays are not available for other important emerging respiratory bacteria, such as Ornithobacterium rhinotracheale (ORT). We aimed to fill this gap by establishing a new duplex PCR method for the simultaneous detection of infectious laryngotracheitis virus (ILTV) and ORT. Multiplex primer design software was used to select the compatible multiplex primer pairs. It was determined that an annealing temperature of 65 °C and an initial concentration of 2.5 pmol/µL for each primer set were the most suitable conditions for multiplex PCR. The assay was confirmed to be specific, as it only detected the target pathogens, even in the presence of six non-target agents. The limit of detection was up to 10³ copies/µL of template DNA for both ILTV and ORT. In the screening of 304 field samples, 23, 88, and 44 were positive for both ILTV and ORT, solely for ILTV, and solely ORT, respectively.

Detection of Chicken Respiratory Pathogens in Live Markets of Addis Ababa, Ethiopia, and Epidemiological Implications

A moderate to high seroprevalence of exposure to Newcastle disease (NDV), avian metapneumovirus (aMPV), infectious laryngotracheitis virus (ILTV), infectious bronchitis virus (IBV) and Mycoplasma gallisepticum (MG) has recently been reported in Ethiopia, but it is unclear to what extent these contribute to clinical cases of respiratory disease. This study investigated the presence of these pathogens in chickens exhibiting respiratory disease in two live markets in Addis Ababa. Markets were visited weekly for three months, and 18 chickens displaying respiratory clinical signs were acquired. Swab samples were taken from the choana, trachea, air sac and larynx for bacteriology and PCR tests targeting these five pathogens. PCR-positive samples were sequenced. All 18 chickens were PCR-positive for aMPV, 50% for each of Mg and NDV, 39% for IBV and 11% for ILTV. Infections with >3 pathogens were detected in 17 of 18 chickens. Potentially pathogenic bacteria such as Escherichia coli, Klebsiella spp., Streptococcus spp. and Staphylococcus were found in 16 to 44% of chickens. IBV-positive samples were of the 793B genotype. The results associate the presence of these organisms with clinical respiratory disease and are consistent with recent serological investigations, indicating a high level of exposure to multiple respiratory pathogens.

A study of risk factors associated with Newcastle disease and molecular characterization of genotype XIII Newcastle disease virus in backyard and commercial poultry in Assam, India

The continuous emergence of Newcastle disease virus (NDV) poses a persistent threat to the poultry industry. Recent increasing outbreaks of NDV in the North East region of India have highlighted the need to closely monitor and analyze the potential risk factors for Newcastle disease (ND) outbreaks. In the present study, an attempt was made to genotype the circulating Newcastle disease virus (NDV) in the backyard and commercial poultry flocks in Assam, India. Sera samples from unvaccinated backyard poultry flocks and tissue samples of ND suspected cases were collected and tested for the presence of NDV antibodies using the Haemagglutination inhibition (HI) test. A total of seven NDV isolates were analyzed from different districts of Assam, India, both genotypically and pathotypically. All isolates were characterized as virulent, carrying 112RRKQRF117 amino acid residues at the cleavage site. As determined by phylogenetic analysis, the isolates clustered with members of genotype XIII of class II NDV. Further analysis of risk factors of ND occurrence was conducted through a questionnaire survey. All the results indicated an occurrence of genotype XIII of NDV in the farms with inadequate biosecurity and farming practices.

Concurrent Occurrence of Infectious Bursal Disease and Multicausal Respiratory Infections Caused by Newcastle Disease and Avian Metapneumovirus in Broilers

Control strategy of respiratory complex infections should address precipitating and predisposing causative agents in general and immunosuppressive agents in particular. In both clinical and subclinical forms, infectious bursal disease virus (IBDV) is one of the most immunosuppressive diseases of young chickens. This study aimed to investigate the concurrent occurrence of subclinical infectious bursal disease (IBD) and multicausal respiratory complex infections caused by Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) in broilers. In this study, 800 tissue samples (e.g., trachea, cecal tonsil, bursa of Fabricius, and spleen) and 400 sera samples were collected from broilers with confirmed respiratory signs selected from 20 broiler farms in west Azerbaijan province, Iran, from October 2018 to February 2019. Pathogens in the tissue samples were detected using RT-PCR for the VP2 gene of IBDV, F gen of NDV, and N gene of aMPV. The amplified products were sequenced afterward. At the end of the husbandry period, sera samples were used to detect antibodies against IBDV, aMPV, and NDV using ELISA and HI tests. Molecular results showed that the 45% (9/20), 30% (6/20), and 15% (3/20) of tissue samples were positive for IBDV, NDV, and aMPV, respectively. Regarding co-infection, 5% (1/20) of farm isolates were positive for IBD and ND, while 10% (2/20) of farms isolates were positive for IBD and aMPV. Co-infection of IBD, ND, and aMPV was not detected in farm isolates. Serological results indicated that the IBD co-infected flocks had almost higher (P<0.05) antibody titers against IBD; however, IBDV-NDV co-infected flocks and IBDV-aMPV co-infected flocks had lower antibody titer against NDVand aMPV, respectively. It can be concluded that lower antibody titer against ND and aMPV in IBD-ND and IBD-aMPV co-infections indicated suppressive effects of IBD on these diseases. Therefore, vaccination against IBD even in regions without clinical form of IBD is inevitable for the reduction of immunosuppressive effects of subclinical IBD on immune responses against these diseases.

Rapid and visual detection of Mycoplasma synoviae by recombinase-aided amplification assay combined with a lateral flow dipstick

Mycoplasma synoviae (MS) is an important avian pathogen that has brought substantial economic losses to the global poultry industry. Fast and accurate diagnosis is one of the critical factors for the control of MS infection. This study established a simple, rapid and visual detection method for MS using a recombinase-aided amplification (RAA) combined with a lateral flow dipstick (LFD). The reaction temperature and time of the RAA-LFD assay were optimized after selecting the primers and probe, and the specificity and sensitivity rates were analyzed. The results showed that RAA could amplify the target gene in 20 min at a constant temperature of 38°C, and the amplification products could be visualized by LFD within 5 min. There was no cross-reaction with Mycoplasma gallisepticum (MG), Pasteurella multocida (P. multocida), Escherichia coli (E. coli), Newcastle disease virus (NDV), infectious bursal disease virus (IBDV), infectious bronchitis virus (IBV), and avian reovirus (ARV). Furthermore, the RAA-LFD assay exhibited high sensitivity with a detection limit of 10 copies/μL. A total of 128 clinical samples with suspected infection of MS were tested by RAA-LFD, PCR, and real-time fluorescence quantitative PCR (RFQ-PCR). The coincidence rate of the detection results was 95.3% between RAA-LFD and PCR, and 98.4% between RAA-LFD and RFQ-PCR. These results suggested that the RAA-LFD method established in the present study was easy to use and was associated with strong specificity and high sensitivity. This method was very suitable for the rapid detection of MS in clinical practice.

Concurrent occurrence of infectious bursal disease and respiratory complex caused by infectious bronchitis and avian influenza (H9N2) in broilers

Infectious bursal disease (IBD) virus is considered one of the commonest immunosuppressive diseases in chickens. The aim of this study was to investigate the concurrent occurrence of subclinical IBD in respiratory complex infections caused by avian influenza (AI, H9N2) virus and infectious bronchitis (IB) virus in broilers. During this study, 800 tissue samples of the trachea, caecal tonsil, spleen, and bursa of Fabricius and 400 blood samples were collected from 20 respiratory complex infected flocks. Detection of pathogens in the tissue samples was performed by RT-PCR for amplification of the VP2 gene of IBD, HA region of AI, and S1 gene of IB viruses. The amplified products were subjected to nucleotide sequence analysis. Blood samples were also tested for the detection of antibodies against IBV by using ELISA and against AIV via using the HI test. Molecular results showed that the tissue samples were positive for field isolates of subclinical IBD (45%), IB (45%), and AI-H9N2 (25%). Co-infections of IBD and IB (30%), IBD and AI (20%), and IBD, IB, and AI (5%) were also detected. Serological results indicated that subclinical IBD infected flocks had lower (P<0.05) antibody titres against IB and AI. In conclusion, prior exposure of broilers to IBD virus increased the incidence of respiratory complex caused by IBV and AIV in broilers, and vaccination against IBD is inevitable to reduce subclinical IBD to minimise the incidence/severity of respiratory complex diseases via improving immune responses to commonly used vaccines in broilers.

Molecular epidemiological studies on avian pathogenic Escherichia coli associated with septicemia in chickens in India

Bacterial septicemia causes huge economic losses in the poultry industry and there is no systematic research available in India on the connection of various pathogens associated with septicemia. The present molecular epidemiological study was conducted to investigate the association of different bacterial and immunosuppressive viral pathogens in septicemia suspected chickens. A total of 443 chicken carcasses with septicemic conditions from 71 different flocks were included in this study. Heart blood swabs were subjected to bacterial culture for Salmonella spp., Pasteurella multocida, Escherichia coli, and Gallibacterium anatis. Of these 51 flocks tested for E. coli, 49 (96.1%) flocks were found positive. Among flocks tested for Salmonella spp., 2 flocks were found positive. All tested flocks were found negative for G. anatis and P. multocida as well as air sac swabs tested negative for Mycoplasma spp. Bacterial cultural examination revealed that majority of septicemic chickens were found to be infected with E. coli and these E. coli isolates showed the highest resistance to vancomycin (60%), followed by erythromycin (50%) and cefotaxime (38%) and maximum sensitivity to cefotaxime and clavulanic acid combinations (81.5%), followed by chloramphenicol (69.6%) and ertapenem (67.2%). Among the 5 avian pathogenic E. coli (APEC) virulence genes were detected in 36 flocks and highest frequency of iss (100%), followed by ompT or iutA (97.2%), hly (61.1%) and iroN (47.2%) genes. On polymerase chain reaction (PCR) screening, 10.5, 4.5, 52.2, 19.4, 9.0, 4.5, 20.1 and 19.4% of the flocks were positive for G. anatis, Ornithobacterium rhinotracheale, APEC, Salmonella spp., Mycoplasma gallisepticum, Mycoplasma synoviae, chicken infectious anemia virus and Marek's disease virus, respectively. To our knowledge, the present study is first on the etiology of septicemia in chicken flocks in India. The present study infers that the majority of septicemic deaths in broiler chickens less than 8 weeks have been connected with APEC and majority of E. coli isolates are multidrug resistance, suggesting the need for surveillance and intervention to curb the inadvertent use of antibiotics. Although, incidence of G. anatis association with septicemia was reported, still requires a rigorous epidemiological study to determine the actual prevalence. However, more detailed studies encompassing vast geographical area with large sample size and long duration of the studies are necessary to provide a clear picture of the interaction of different pathogens causing septicemia in chicken.

Low pathogenic avian influenza virus infection retards colon microbiota diversification in two different chicken lines

BACKGROUND

A commensal microbiota regulates and is in turn regulated by viruses during host infection which can influence virus infectivity. In this study, analysis of colon microbiota population changes following a low pathogenicity avian influenza virus (AIV) of the H9N2 subtype infection of two different chicken breeds was conducted.

METHODS

Colon samples were taken from control and infected groups at various timepoints post infection. 16S rRNA sequencing on an Illumina MiSeq platform was performed on the samples and the data mapped to operational taxonomic units of bacterial using a QIIME based pipeline. Microbial community structure was then analysed in each sample by number of observed species and phylogenetic diversity of the population.

RESULTS

We found reduced microbiota alpha diversity in the acute period of AIV infection (day 2-3) in both Rhode Island Red and VALO chicken lines. From day 4 post infection a gradual increase in diversity of the colon microbiota was observed, but the diversity did not reach the same level as in uninfected chickens by day 10 post infection, suggesting that AIV infection retards the natural accumulation of colon microbiota diversity, which may further influence chicken health following recovery from infection. Beta diversity analysis indicated a bacterial species diversity difference between the chicken lines during and following acute influenza infection but at phylum and bacterial order level the colon microbiota dysbiosis was similar in the two different chicken breeds.

CONCLUSION

Our data suggest that H9N2 influenza A virus impacts the chicken colon microbiota in a predictable way that could be targeted via intervention to protect or mitigate disease.