Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex

The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases

Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.

The Microbial Community of the Respiratory Tract of Commercial Chickens and Turkeys

Respiratory tract health critically affects the performance of commercial poultry. This report presents data on the microbial community in these organs from a comprehensive study of laying chickens and turkey breeders. The main objective was to characterize and compare the compositions of the respiratory system bacteria isolated from birds of different ages and geographical locations in Poland. Using samples from 28 turkey and 26 chicken flocks, the microbial community was determined by 16S ribosomal RNA sequencing. There was great variability between flocks. The diversity and abundance of upper respiratory tract (URT) bacteria was greater in chickens than in turkeys. At the phyla level, the URT of the chickens was heavily colonized by Proteobacteria, which represented 66.4% of the total microbiota, while in turkeys, this phylum constituted 42.6% of all bacteria. Firmicutes bacteria were more abundant in turkeys (43.2%) than in chickens (24.1%). The comparison of the respiratory tracts at the family and genus levels showed the diversity and abundance of amplicon sequence variants (ASV) differing markedly between the species. Potentially pathogenic bacteria ASV were identified in the respiratory tract, which are not always associated with clinical signs, but may affect bird productivity and performance. The data obtained, including characterization of the bacterial composition found in the respiratory system, may be useful for developing effective interventions strategies to improve production performance and prevent and control disease in commercial laying chickens and turkeys.

Litter Management Strategies and Their Impact on the Environmental and Respiratory Microbiome Might Influence Health in Poultry

Aerial and respiratory tract-associated bacterial diversity has been scarcely studied in broiler production systems. This study examined the relationship between the environmental air and birds’ respiratory microbiome, considering a longitudinal sampling. Total viable bacteria and coliforms in the air were quantified, and the 16S rRNA gene was sequenced from tracheal and air samples obtained through a novelty protocol. Air results showed a decrease in coliforms over time. However, at week 3, we reported an increase in coliforms (from 143 to 474 CFUc/m3) associated with litter management. Additionally, 16S rRNA gene results indicated a distinctive air microbial community, associated primarily with Bacillota phylum particularly of the Bacilli class (>58%), under all conditions. Tracheal results indicated a predominance of Escherichia coli/Shigella at the beginning of the productive cycle, shifting toward the middle and end of the cycle to Gallibacterium. However, at week 3, the dominance of Escherichia coli/Shigella (>99.5%) associated with litter aeration by tumbling stood out. Tracheal and air samples displayed a statistically different community structure, but shared differentially abundant features through time: Enterococcus, Gallibacterium, and Romboutsia ilealis. These results indicate the impact of production management protocols on the birds’ respiratory system that should be considered a breakpoint in poultry farm health.

The first isolation and detection of Ornithobacterium rhinotracheale from swollen head syndrome-infected broiler flocks in Iraq

Background and Aim:

The swollen head syndrome (SHS) makes up complex diseases that infect the upper respiratory tract in poultry and causes several economic losses. Furthermore, this syndrome is considered one of the multifactorial etiological agents. Therefore, this study isolated and molecularly detected Ornithobacterium rhinotracheale (ORT) in poultry.

Materials and Methods:

This study was conducted at 67 broiler farms that had birds observed to be infected with the SHS from September 2018 until August 2019. Subsequently, swabs were collected from their trachea, infraorbital sinuses, and lungs, after which obtained samples were treated through two methods: (a) The direct method, by uploading samples on FTA cards, and the indirect method using a transport media. Afterward, reverse transcription-polymerase chain reaction (RT-PCR) was used to analyze the directly treated samples; howeverAQ1, the culture method, followed by PCR, was used to analyze the indirectly treated samples. Next, a partial 16S RNA gene was isolated using four positive PCR products, after which the effect of 16 antibiotics was studied on the seven local ORT strains isolated.

Results:

The quantity of ORT isolated using the direct method was 28 (41.7%) samples, which were all positive for the strain. Identification was by direct molecular identification (RT-PCR) from samples loaded on FTA cards. Alternatively, 7 (10.4%) ORTs were detected from the indirect method, as obtained using the culture method and biochemical tests. Then, PCR was subsequently used to confirm the results. As observed, 784 bp bands were shown for all seven ORT isolates. Furthermore, results revealed a significant difference in the detection of ORT strains between direct and indirect methods, with p-value (<0.05) and standard deviation of the error±0.038 for the direct, then ±0.061 for the indirect method. For further analysis on the strain types, four 784 bp PCR products were taken, then partial 16S ribosomal sequence typing was conducted. All these four strains were found to be recorded in NCBI for the 1^st time as a local Iraqi strain, with accession numbers (MN931657, MN931656, MN931655, and MN931654). Notably, results also showed that all isolated strains were multidrug-resistant.

Conclusion:

From the results, ORT is proposed to be implicated as one of the etiological factors that cause SHSs in poultry. Phylogenetic analysis of the current ORT bacterial strains also showed that they are closely related to the Egyptian isolates.

Analysis of Microorganism Diversity in Haemaphysalis longicornis From Shaanxi, China, Based on Metagenomic Sequencing

Ticks are dangerous ectoparasites of humans and animals, as they are important disease vectors and serve as hosts for various microorganisms (including a variety of pathogenic microorganisms). Diverse microbial populations coexist within the tick body. Metagenomic next-generation sequencing (mNGS) has been suggested to be useful for rapidly and accurately obtaining microorganism abundance and diversity data. In this study, we performed mNGS to analyze the microbial diversity of Haemaphysalis longicornis from Baoji, Shaanxi, China, with the Illumina HiSeq platform. We identified 189 microbial genera (and 284 species) from ticks in the region; the identified taxa included Anaplasma spp., Rickettsia spp., Ehrlichia spp., and other important tick-borne pathogens at the genus level as well as symbiotic microorganisms such as Wolbachia spp., and Candidatus Entotheonella. The results of this study provide insights into possible tick-borne diseases and reveal new tick-borne pathogens in this region. Additionally, valuable information for the biological control of ticks is provided. In conclusion, this study provides reference data for guiding the development of prevention and control strategies targeting ticks and tick-borne diseases in the region, which can improve the effectiveness of tick and tick-borne disease control.

The Airway Pathobiome in Complex Respiratory Diseases: A Perspective in Domestic Animals

Respiratory infections in domestic animals are a major issue for veterinary and livestock industry. Pathogens in the respiratory tract share their habitat with a myriad of commensal microorganisms. Increasing evidence points towards a respiratory pathobiome concept, integrating the dysbiotic bacterial communities, the host and the environment in a new understanding of respiratory disease etiology. During the infection, the airway microbiota likely regulates and is regulated by pathogens through diverse mechanisms, thereby acting either as a gatekeeper that provides resistance to pathogen colonization or enhancing their prevalence and bacterial co-infectivity, which often results in disease exacerbation. Insight into the complex interplay taking place in the respiratory tract between the pathogens, microbiota, the host and its environment during infection in domestic animals is a research field in its infancy in which most studies are focused on infections from enteric pathogens and gut microbiota. However, its understanding may improve pathogen control and reduce the severity of microbial-related diseases, including those with zoonotic potential.

Ornithobacterium rhinotracheale: An Update Review about An Emerging Poultry Pathogen

Respiratory diseases in birds generate sanitary and economic impacts and may be related to the environment and climate. Mycoplasma gallisepticum, Ornithobacterium rhinotracheale (ORT), Pasteurella multocida, Avibacterium paragallinarum, Escherichia coli, Riemerella anatipestifer, and Bordetella avium are among the most important avian respiratory pathogens. ORT is responsible for causing ornitobacteriosis, a disease characterized by clinical signs ranging from mild to severe respiratory conditions, with high mortality rates, mainly affecting turkeys and chickens. The first report of ornitobacteriosis was in 1981 in Germany. Despite its importance, few studies on ORT have been published. In addition, the presence of this pathogen has been neglected in poultry farms, mainly due to the lack of appropriate diagnostic protocols. The lack of correct isolation and diagnostic protocols along with inappropriate use of antimicrobial agents have been contributing to treatment failure. Due to its economic importance to the poultry industry, ornitobacteriosis should be monitored and included in national programs for the prevention and control of avian respiratory diseases. This review aimed to update and discuss important issues related to ORT since this pathogen has great economic and sanitary implications for the chicken production chain.