Development and Validation of a New TaqMan Real-Time PCR for the Detection of Ornithobacterium rhinotracheale

Development and Validation of PCR Diagnostic Assays for Detection of Avibacterium paragallinarum and Ornithobacterium rhinotracheale

PCR is the most effective method for detecting difficult-to-cultivate pathogens and pathogens that are part of mixed infections in animals, such as Ornithobacterium rhinotracheale, which causes bird ornithobacteriosis, or Avibacterium paragallinarum, which causes infectious coryza. In this work, we developed and validated two efficient and sensitive diagnostic assays for the rapid and accurate detection of A. paragallinarum and O. rhinotracheale DNA in bacterial isolates and clinical samples using real-time PCR with TaqMan-like probes. When designing the PCR assays, we performed in silico analysis, optimized DNA isolation methods and PCR conditions, and assessed the analytical and diagnostic performance of PCR. We designed primers and probes that have no mismatches with published whole-genome sequences of bacteria. The optimization of conditions showed that the PCR assays are sufficiently robust to changes in temperature and oligonucleotide concentration. The validation showed that the developed assays have high analytical and diagnostic sensitivity and specificity. These assays are expected to improve the differential diagnosis of respiratory diseases in chickens and turkeys.

qPCR-Based Monitoring of 2-Methylisoborneol/Geosmin-Producing Cyanobacteria in Drinking Water Reservoirs in South Korea

Cyanobacteria can exist in water resources and produce odorants. 2-Methylisoborneol (2-MIB) and geosmin are the main odorant compounds affecting the drinking water quality in reservoirs. In this study, encoding genes 2-MIB (mic, monoterpene cyclase) and geosmin (geo, putative geosmin synthase) were investigated using newly developed primers for quantitative PCR (qPCR). Gene copy numbers were compared to 2-MIB/geosmin concentrations and cyanobacterial cell abundance. Samples were collected between July and October 2020, from four drinking water sites in South Korea. The results showed similar trends in three parameters, although the changes in the 2-MIB/geosmin concentrations followed the changes in the mic/geo copy numbers more closely than the cyanobacterial cell abundances. The number of odorant gene copies decreased from upstream to downstream. Regression analysis revealed a strong positive linear correlation between gene copy number and odorant concentration for mic (R2 = 0.8478) and geo (R2 = 0.601). In the analysis of several environmental parameters, only water temperature was positively correlated with both mic and geo. Our results demonstrated the feasibility of monitoring 2-MIB/geosmin occurrence using qPCR of their respective synthase genes. Odorant-producing, gene-based qPCR monitoring studies may contribute to improving drinking water quality management.

Space-Time Patterns of Poultry Pathogens in the USA: A Case Study of Ornithobacterium rhinotracheale and Pasteurella multocida in Turkey Populations

Respiratory infections caused by Ornithobacterium rhinotrachealis (ORT) and Pasteurella multocida (PM) bacteria are significant threats to the poultry industry by causing economic losses and welfare issues. Due to characterization difficulties and underutilization of epidemiological tools, description of the spatio-temporal spread of these diseases in the field is limited. The objectives of this retrospective observational cross-sectional study were to (a) investigate the existence of space-time clusters (hotspots); and (b) investigate the association between genetic similarity and spatial proximity for both pathogens using molecular typing and a recently developed Core-Genome Multilocus Sequencing Typing (cgMLST) scheme. ORT (n = 103) and PM (n = 69) isolates from confirmed disease outbreaks from one commercial company between 2013 and 2021 were obtained from a veterinary diagnostic laboratory, characterized using a cgMLST scheme and visualized using a minimum spanning tree. Spatio-temporal cluster analysis using SaTScanTM and a Spearman's rank correlation were performed to investigate clustering and any association between allelic diversity and geospatial distance. The cgMLST sequencing revealed three allelic clusters for ORT and thirteen clusters for PM. The spatio-temporal analysis revealed two significant clusters for PM, one with a 259.3 km cluster containing six cases between May and July 2018 and a 9 km cluster containing five cases between February 2019 and February 2021. No spatio-temporal clusters were found for ORT. A weak negative correlation between allelic diversity and geospatial distance was observed for ORT (r = -0.04, p < 0.01) and a weak positive correlation was observed for PM (r = 0.11, p < 0.01). This study revealed regional spatio-temporal clusters for PM in commercial turkey sites between 2018 and 2021 and provided additional insight into bacterial strain subgroups and the geographical spread of ORT and PM over time.

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.

Complete Genome Sequences of Three Ornithobacterium rhinotracheale Strains from Avian Sources, Using Hybrid Nanopore-Illumina Assembly

Ornithobacterium rhinotracheale has been associated with respiratory disease in poultry, particularly turkeys, leading to significant economic losses. However, O. rhinotracheale is poorly studied, and a very limited number of complete genomes are available. Here, we report the complete genome sequences of three O. rhinotracheale strains, generated using a Nanopore-Illumina hybrid assembly approach.

Common viral and bacterial avian respiratory infections: an updated review

Many pathogens that cause chronic diseases in birds use the respiratory tract as a primary route of infection, and respiratory disorders are the main leading source of financial losses in the poultry business. Respiratory infections are a serious problem facing the poultry sector, causing severe economic losses. Avian influenza virus, Newcastle disease virus, infectious bronchitis virus, and avian pneumovirus are particularly serious viral respiratory pathogens. Mycoplasma gallisepticum, Staphylococcus, Bordetella avium, Pasteurella multocida, Riemerella anatipestifer, Chlamydophila psittaci, and Escherichia coli have been identified as the most serious bacterial respiratory pathogens in poultry. This review gives an updated summary, incorporating the latest data, about the evidence for the circulation of widespread, economically important poultry respiratory pathogens, with special reference to possible methods for the control and prevention of these pathogens.

Correction: Hashish et al. Development and Validation of a New TaqMan Real-Time PCR for the Detection of Ornithobacterium rhinotracheale. Microorganisms 2022, 10, 341

The authors would like to make the following corrections to this paper [...].

Avian Pathogens: Editorial and the Perspectives of Research

In the last ten years, humanity has faced new challenges in the field of human and animal health, including emerging viral infections [...].