Longitudinal monitoring for respiratory pathogens in broiler chickens reveals co-infection of Chlamydia psittaci and Ornithobacterium rhinotracheale

Case Report: Pneumonia Caused by Chlamydia Psittaci and Cryptococcus Co-Infection

This study presents a rare case of pneumonia caused by a co-infection of Chlamydia psittaci and Cryptococcus, confirmed by metagenomic next-generation sequencing (mNGS). The patient, who had underlying chronic hepatitis B, had adopted a stray pigeon before the onset of the disease. The primary symptoms were fever, and a productive cough. The patient recovered following treatment with moxifloxacin and itraconazole. C. psittaci and Cryptococcus infections may both have been transmitted from the stray pigeon. This report highlights the potential for infections caused by multiple zoonotic pathogens and the value of mNGS for making the diagnosis of these infections.

Uncovering the core principles of the gut-lung axis to enhance innate immunity in the chicken

Research in mammals has evidenced that proper colonization of the gut by a complex commensal microbial community, the gut microbiota (GM), is critical for animal health and wellbeing. It greatly contributes to the control of infectious processes through competition in the microbial environment while supporting proper immune system development and modulating defence mechanisms at distant organ sites such as the lung: a concept named ‘gut-lung axis’. While recent studies point to a role of the GM in boosting immunity and pathogen resilience also in poultry, the mechanisms underlying this role are largely unknown. In spite of this knowledge gap, GM modulation approaches are today considered as one of the most promising strategies to improve animal health and welfare in commercial poultry production, while coping with the societal demand for responsible, sustainable and profitable farming systems. The majority of pathogens causing economically important infectious diseases in poultry are targeting the respiratory and/or gastrointestinal tract. Therefore, a better understanding of the role of the GM in the development and function of the mucosal immune system is crucial for implementing measures to promote animal robustness in commercial poultry production. The importance of early gut colonization in the chicken has been overlooked or neglected in industrial poultry production systems, where chicks are hampered from acquiring a complex GM from the hen. Here we discuss the concept of strengthening mucosal immunity in the chicken through GM modulation approaches favouring immune system development and functioning along the gut-lung axis, which could be put into practice through improved farming systems, early-life GM transfer, feeding strategies and pre-/probiotics. We also provide original data from experiments with germ-free and conventional chickens demonstrating that the gut-lung axis appears to be functional in chickens. These key principles of mucosal immunity are likely to be relevant for a variety of avian diseases and are thus of far-reaching importance for the poultry sector worldwide.

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.

Novel and Alternative Therapeutic Strategies for Controlling Avian Viral Infectious Diseases: Focus on Infectious Bronchitis and Avian Influenza

The growth of poultry farming has enabled higher spread of infectious diseases and their pathogens among different kinds of birds, such as avian infectious bronchitis virus (IBV) and avian influenza virus (AIV). IBV and AIV are a potential source of poultry mortality and economic losses. Furthermore, some pathogens have the ability to cause zoonotic diseases and impart human health problems. Antiviral treatments that are used often lead to virus resistance along with the problems of side effects, recurrence, and latency of viruses. Though target hosts are being vaccinated, the constant emergence and re-emergence of strains of these viruses cause disease outbreaks. The pharmaceutical industry is gradually focusing on plant extracts to develop novel herbal drugs to have proper antiviral capabilities. Natural therapeutic agents developed from herbs, essential oils (EO), and distillation processes deliver a rich source of amalgams to discover and produce new antiviral drugs. The mechanisms involved have elaborated how these natural therapeutics agents play a major role during virus entry and replication in the host and cause inhibition of viral pathogenesis. Nanotechnology is one of the advanced techniques that can be very useful in diagnosing and controlling infectious diseases in poultry. In general, this review covers the issue of the poultry industry situation, current infectious diseases, mainly IB and AI control measures and, in addition, the setup of novel therapeutics using plant extracts and the use of nanotechnology information that may help to control these diseases.

Molecular characterization of Chlamydia species in commercial and backyard poultry farms in Costa Rica

Outbreaks caused by Chlamydia psittaci and other chlamydial species have recently been reported in poultry farms worldwide, causing considerable economic losses. The objective of this study was to determine the presence of chlamydial species in these birds in Costa Rica. One hundred and fifty pools of lung tissue samples from industrial poultry with respiratory problems and 112 pools of tracheal swabs from asymptomatic backyard poultry were analysed by real-time quantitative polymerase chain reaction (qPCR), end-point PCR and sequencing. A total of 16.8% (44/262) samples were positive for Chlamydia spp., most of them detected in asymptomatic backyard poultry (28.6%, 32/112) and fewer in industrial poultry (8%, 12/150). Of these positive samples, 45.5% (20/44) were determined to be C. psittaci . For the first time C. psittaci genotype A is reported in poultry in Latin America. In addition, the presence of Chlamydia gallinacea in backyard poultry and of Chlamydia muridarum in industrial and backyard poultry is reported for the first time in Central America. In 40.9% (18/44) of the positive samples, it was not possible to identify the infecting chlamydial species. These findings reveal a zoonotic risk, particularly for poultry farm and slaughterhouse workers having direct contact with these birds.

Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing

Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases.

Feed-borne Bacillus cereus exacerbates respiratory distress in chickens infected with Chlamydia psittaci by inducing haemorrhagic pneumonia

Chlamydia psittaci is an important zoonotic pathogen and its oral route of infection plays an important role in the transmission and persistence. Bacillus cereus (B. cereus) strain, a common contaminant of animal feed and feedstuffs, can cause severe diarrhoea and malnutrition in poultry. In our previous study, a B. cereus strain (Dawu C), isolated from the haemorrhagic lungs of infected chickens, was shown to harbour two virulence genes (hblC and cytk) and was able to induce haemorrhagic lesions in the lungs, as well as gizzard erosion and ulceration (GEU) syndrome in broilers. In the present study, we tested the hypothesis that B. cereus-induced GEU would aggravate C. psittaci infection. Our results showed that SPF chickens exposed to B. cereus developed a severe GEU syndrome. More interestingly, prior infection with B. cereus facilitated C. psittaci infection, and aggravated GEU and respiratory distress, which were accompanied by high chlamydial loads in the lungs and severe lesions in respiratory organs. Moreover, levels of local inflammatory cytokines were elevated and T cell responses were impaired in the infected birds. In conclusion, GEU caused by B. cereus may facilitate chlamydial transmission from the ventriculus to the lungs.RESEARCH HIGHLIGHTS Bacillus cereus contributes to the gizzard erosion and ulceration syndrome in chickens.Exposure to Bacillus cereus exacerbates pneumonia in birds following chlamydial infection.Bacillus cereus facilitates persistent chlamydial infection and exacerbates immune responses.

Human psittacosis: a review with emphasis on surveillance in Belgium

Chlamydia psittaci causes psittacosis in humans, mainly in persons in contact with birds in either the setting of occupational or companion bird exposure. Infection is associated with a range of clinical manifestations from asymptomatic infection to severe atypical pneumonia and systemic disease. This paper reviews new knowledge on psittacosis, its legal and regulatory aspects and presents epidemiological data on psittacosis in Belgium. In Belgium, the number of reported positive laboratory results increased slowly since 2010, and in 2017, the number almost doubled compared to the two previous years. The number of psittacosis cases in Belgium, as in other countries, is probably highly underestimated, because of underdiagnoses and underreporting. Over the 3-year period, the mandatory notification system registered 24% only of all reported positive laboratory result. Therefore, increased awareness among general and occupational physicians, clinicians and the public is needed. Policies aimed at reducing psittacosis disease burden are justified, nevertheless national health authorities should provide more legal and financial support to implement more adequate C. psittaci diagnostic tools.

Genetic analysis on body weight at different ages in broiler chicken raised in commercial environment

A multivariate model was developed and used to estimate genetic parameters of body weight (BW) at 1-6 weeks of age of broilers raised in a commercial environment. The development of model was based on the predictive ability of breeding values evaluated from a cross-validation procedure that relied on half-sib correlation. The multivariate model accounted for heterogeneous variances between sexes through standardization applied to male and female BWs differently. It was found that the direct additive genetic, permanent environmental maternal and residual variances for BW increased drastically as broilers aged. The drastic increase in variances over weeks of age was mainly due to scaling effects. The ratio of the permanent environmental maternal variance to phenotypic variance decreased gradually with increasing age. Heritability of BW traits ranged from 0.28 to 0.33 at different weeks of age. The direct genetic effects on consecutive weekly BWs had high genetic correlations (0.85-0.99), but the genetic correlations between early and late BWs were low (0.32-0.57). The difference in variance components between sexes increased with increasing age. In conclusion, the permanent environmental maternal effect on broiler chicken BW decreased with increasing age from weeks 1 to 6. Potential bias of the model that considered identical variances for sexes could be reduced when heterogeneous variances between sexes are accounted for in the model.

Use of genomic information to exploit genotype-by-environment interactions for body weight of broiler chicken in bio-secure and production environments

BACKGROUND

The increase in accuracy of prediction by using genomic information has been well-documented. However, benefits of the use of genomic information and methodology for genetic evaluations are missing when genotype-by-environment interactions (G × E) exist between bio-secure breeding (B) environments and commercial production (C) environments. In this study, we explored (1) G × E interactions for broiler body weight (BW) at weeks 5 and 6, and (2) the benefits of using genomic information for prediction of BW traits when selection candidates were raised and tested in a B environment and close relatives were tested in a C environment.

METHODS

A pedigree-based best linear unbiased prediction (BLUP) multivariate model was used to estimate variance components and predict breeding values (EBV) of BW traits at weeks 5 and 6 measured in B and C environments. A single-step genomic BLUP (ssGBLUP) model that combined pedigree and genomic information was used to predict EBV. Cross-validations were based on correlation, mean difference and regression slope statistics for EBV that were estimated from full and reduced datasets. These statistics are indicators of population accuracy, bias and dispersion of prediction for EBV of traits measured in B and C environments. Validation animals were genotyped and non-genotyped birds in the B environment only.

RESULTS

Several indications of G × E interactions due to environmental differences were found for BW traits including significant re-ranking, heterogeneous variances and different heritabilities for BW measured in environments B and C. The genetic correlations between BW traits measured in environments B and C ranged from 0.48 to 0.54. The use of combined pedigree and genomic information increased population accuracy of EBV, and reduced bias of EBV prediction for genotyped birds compared to the use of pedigree information only. A slight increase in accuracy of EBV was also observed for non-genotyped birds, but the bias of EBV prediction increased for non-genotyped birds.

CONCLUSIONS

The G × E interaction was strong for BW traits of broilers measured in environments B and C. The use of combined pedigree and genomic information increased population accuracy of EBV substantially for genotyped birds in the B environment compared to the use of pedigree information only.

A Bird's-Eye View of Chronic Unilateral Conjunctivitis: Remember about Chlamydia psittaci

Chlamydia psittaci causes psittacosis in humans, mainly in people in contact with birds in either the setting of occupational or companion bird exposure. Infection is associated with a range of clinical manifestations from asymptomatic infection to severe atypical pneumonia and systemic disease. C. psittaci has also been associated with ocular adnexal lymphoma in human patients. The current paper describes successful doxycycline treatment of a male patient suffering from C. psittaci chronic unilateral conjunctivitis, most probably linked to the visit of a South African wildlife reserve. Increased awareness among general and occupational physicians, ophthalmologists, clinicians, and the public on the potential of C. psittaci to cause ocular infection is needed.

Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens

The digestive and respiratory tracts of chickens are colonized by bacteria that are believed to play important roles in the overall health and performance of the birds. Most of the current research on the commensal bacteria (microbiota) of chickens has focused on broilers and gut microbiota, and less attention has been given to layers and respiratory microbiota. This research bias has left significant gaps in our knowledge of the layer microbiome. This study was conducted to define the core microbiota colonizing the upper respiratory tract (URT) and lower intestinal tract (LIT) in commercial layers under field conditions. One hundred eighty-one chickens were sampled from a flock of >80,000 birds at nine times to collect samples for 16S rRNA gene-based bacterial metabarcoding. Generally, the body site and age/farm stage had very dominant effects on the quantity, taxonomic composition, and dynamics of core bacteria. Remarkably, ileal and URT microbiota were compositionally more related to each other than to that from the cecum. Unique taxa dominated in each body site yet some taxa overlapped between URT and LIT sites, demonstrating a common core. The overlapping bacteria also contained various levels of several genera with well-recognized avian pathogens. Our findings suggest that significant interaction exists between gut and respiratory microbiota, including potential pathogens, in all stages of the farm sequence. The baseline data generated in this study can be useful for the development of effective microbiome-based interventions to enhance production performance and to prevent and control disease in commercial chicken layers.IMPORTANCE The poultry industry is faced with numerous challenges associated with infectious diseases and suboptimal performance of flocks. As microbiome research continues to grow, it is becoming clear that poultry health and production performance are partly influenced by nonpathogenic symbionts that occupy different habitats within the bird. This study has defined the baseline composition and overlaps between respiratory and gut bacteria in healthy, optimally performing chicken layers across all stages of the commercial farm sequence. Consequently, the study has set the groundwork for the development of interventions that seek to enhance production performance and to prevent and control infectious diseases through the modulation of gut and respiratory bacteria.

Co-infection of Chlamydia psittaci with H9N2, ORT and Aspergillus fumigatus contributes to severe pneumonia and high mortality in SPF chickens

Since 2007, most areas of China have seen outbreaks of poultry airsacculitis, which causes hugely economic losses to the poultry industry. However, there are no effective measures to combat the problem. In this study, 105 rations were collected to isolate Aspergillus spp. from the diseased farms. In subsequent experiments, SPF chickens were inoculated with Ornithobacterium rhinotracheale (ORT), Chlamydia psittaci (C. psittaci) and Aspergillus fumigatus (A. fumigatus), and mortality rate, body weight gain and lesion score were evaluated. Of these ration samples, 63 (60.0%) were A. fumigates, 21 (20.0%) were Aspergillus niger (A. niger) and 11 (10.5%) were Aspergillus candidus (A. candidus). Furthermore, SPF birds infected with C. psittaci, ORT, H9N2 virus and A. fumigatus conidia exhibited a mortality rate of 40%, while simultaneous co-infection with C. psittaci, ORT and A. fumigatus resulted in a mortality rate of 20%. The avian airsacculitis was manifested in the C. psittaci + ORT/A. fumigatus, C. psittaci + H9N2 + ORT/A. fumigatus and C. psittaci + H9N2/A. fumigatus groups while others had transient respiratory diseases without mortality. Our survey indicates that feed-borne A. fumigatus is prevalent in poultry rations. The combination of C. psittaci, ORT, H9N2 and A. fumigatus conidia contributes to the replication of avian airsacculitis by aggravating the severe damage to the air sacs and lungs of chickens.

Chlamydia psittaci infection increases mortality of avian influenza virus H9N2 by suppressing host immune response

Avian influenza virus subtype H9N2 (H9N2) and Chlamydia psittaci (C. psittaci) are frequently isolated in chickens with respiratory disease. However, their roles in co-infection remain unclear. We tested the hypothesis that C. psittaci enhances H9N2 infection through suppression of host immunity. Thus, 10-day-old SPF chickens were inoculated intra-tracheally with a high or low virulence C. psittaci strain, and were simultaneously vaccinated against Newcastle disease virus (NDV). Significant decreases in body weight, NDV antibodies and immune organ indices occurred in birds with the virulent C. psittaci infection, while the ratio of CD4+/CD8+ T cells increased significantly compared to that of the lower virulence strain. A second group of birds were inoculated with C. psittaci and H9N2 simultaneously (C. psittaci+H9N2), C. psittaci 3 days prior to H9N2 (C. psittaci/H9N2), or 3 days after H9N2 (H9N2/C. psittaci), C. psittaci or H9N2 alone. Survival rates were 65%, 80% and 90% in the C. psittaci/H9N2, C. psittaci+H9N2 and H9N2/C. psittaci groups, respectively and respiratory clinical signs, lower expression of pro-inflammatory cytokines and higher pathogen loads were found in both C. psittaci/H9N2 and C. psittaci+H9N2 groups. Hence, virulent C. psittaci infection suppresses immune response by inhibiting humoral responses and altering Th1/Th2 balance, increasing mortality in H9N2 infected birds.

Oral Uptake of Chlamydia psittaci by Ducklings Results in Systemic Dissemination

Enteric infections caused by Chlamydia (C.) psittaci are frequent in ducks, but mostly remain subclinical under field conditions. To emulate natural infection, we investigated the pathogenic potential of a C. psittaci field strain in orally inoculated 4-day-old ducklings. Three different challenge doses were tested and seven contact animals were also mock-inoculated with buffer in each group. Over the course of ten days, the birds were monitored for clinical symptoms and chlamydial dissemination before final examination of tissues using histopathology and immunohistochemistry. While the challenge strain disseminated systemically to all internal organs, mild signs of diarrhea were confined to ducklings inoculated with the highest dose (4.3 x 10⁸ IFU/mL, Group 1). No other clinical symptoms or histopathological lesions were seen. The chlamydial load in internal organs as measured by PCR depended on the challenge dose and was unevenly distributed, i.e. high loads in spleen, liver, and distal small and large intestinal tract (ileum, cecum and rectum) vs. ten times lower values in lungs and proximal small intestinal tract (duodenum and jejunum). Notably, the C. psittaci infection of contact birds became evident on day 10 post-infection, with bacterial loads comparable to those of experimentally-infected animals, thus suggesting rapid bird-to-bird transmission of the challenge strain.