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Krylova E, Bogomazova A, Kirsanova N, Putintseva A, Gorbacheva N, Prasolova O, Soltynskaya I, Ivanova O. Development and Validation of PCR Diagnostic Assays for Detection of Avibacterium paragallinarum and Ornithobacterium rhinotracheale. Vet Sci 2023; 11:7. [PMID: 38250913 PMCID: PMC10819020 DOI: 10.3390/vetsci11010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
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.
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Affiliation(s)
- Ekaterina Krylova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
| | - Alexandra Bogomazova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
- Laboratory of Cell Biology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia (Lopukhin FRCC PCM), 119435 Moscow, Russia
| | - Nataliya Kirsanova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
| | - Anastasiya Putintseva
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
| | - Natalia Gorbacheva
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
| | - Olga Prasolova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
| | - Irina Soltynskaya
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
| | - Olga Ivanova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), 123022 Moscow, Russia; (A.B.); (A.P.); (O.P.)
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Nguyen VG, Cao TBP, Le VT, Truong HT, Chu TTH, Dang HA, Nguyen TH, Le TL, Huynh TML. A Multiplex PCR Method for Simultaneous Detection of Infectious Laryngotracheitis Virus and Ornithobacterium rhinotracheale. Vet Sci 2023; 10:vetsci10040272. [PMID: 37104427 PMCID: PMC10144794 DOI: 10.3390/vetsci10040272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 04/28/2023] Open
Abstract
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.
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Affiliation(s)
- Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Thi-Bich-Phuong Cao
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Van-Truong Le
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Ha-Thai Truong
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Thi-Thanh-Huong Chu
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Huu-Anh Dang
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Thi-Hoa Nguyen
- Key Laboratory for Veterinary Biotechnology, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Thi-Luyen Le
- Key Laboratory for Veterinary Biotechnology, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Thi-My-Le Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
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Welchman D, Tasker J, Poulos C, Ellis C, Bradbury JM. Survey of respiratory disease associated with Mycoplasma gallisepticum in British gamebirds (2016-2019): In vitro antibiotic sensitivity, pathology and detection of other pathogens. Vet Rec 2022; 191:e1972. [PMID: 36008358 DOI: 10.1002/vetr.1972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/21/2022] [Accepted: 05/11/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The causes of respiratory disease in British gamebirds were investigated during 2016-2019 following concerns about poorer responses to antibiotic treatment. Emphasis was placed on Mycoplasma gallisepticum, but other possible bacterial and viral causes were included, along with gross and histopathological examination. METHODS Clinical respiratory disease outbreaks were investigated. RESULTS Mycoplasma gallisepticum was detected by PCR in 65 of 69 outbreaks in pheasants and partridges and isolated from 56 of these. Partial mgc2 gene sequences from 28 M. gallisepticum isolates were compared, and 26 proved identical, suggesting the prevalence of a dominant sequence type. Minimum inhibitory concentration values for tiamulin, tylosin, tylvalosin, doxycycline and tetracycline were significantly higher than the reference strain but could not be correlated with treatment failures. Other bacterial species were isolated from sinuses but were not consistently correlated with disease. RT-PCRs detected coronaviruses in 18% of 49 outbreaks and avian metapneumovirus in 8%. Histopathological lesions were typical of M. gallisepticum sinusitis and significantly associated with M. gallisepticum PCR outbreak positivity. CONCLUSION Mycoplasma gallisepticum remains an important cause of respiratory disease in gamebirds. Synergism with other pathogens may have played a role in some outbreaks. Specific reasons for variable responses to antibacterial treatment were not identified.
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Affiliation(s)
| | - John Tasker
- Veterinary Pharmaceutical Consultancy, Colchester, UK
| | | | - Christine Ellis
- Veterinary Microbiology Diagnostics Laboratory, Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - Janet M Bradbury
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
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Occurrence of Ornithobacterium rhinotracheale in Polish turkey flocks. J Vet Res 2022; 66:77-84. [PMID: 35582491 PMCID: PMC8959689 DOI: 10.2478/jvetres-2022-0014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/03/2022] [Indexed: 11/20/2022] Open
Abstract
Abstract
Introduction
Ornithobacterium rhinotracheale (ORT) causes significant economic losses to the poultry industry around the world. The bacterium often affects poultry as part of multiple infections causing very serious clinical signs that are usually not limited only to the respiratory system. This study’s main objective was the retrospective detection and identification of ORT in turkey flocks.
Material and Methods
ORT identification was performed in 6,225 samples taken from 133 different flocks between 2015 and 2020. Molecular methods were used, specifically real-time PCR and traditional PCR. We focused on partial 16S rRNA gene sequences of isolates, which were compared with sequences obtained from GenBank. The reaction products were analysed phylogenetically. Molecular methods indicating secondary infections was carried out, and the bacterial composition of the upper respiratory tract was 16S metasequenced for selected flocks to identify any other pathogens.
Results
The presence of ORT was detected in 30.83% of samples by real-time PCR and 28.57% by PCR. Phylogenetic analysis of the PCR products from the turkeys samples showed that their sequences resolved into two main genetic groups. Tests for the occurrence of secondary infections showed the presence of Mycoplasma gallisepticum and M. synoviae in some samples but the total absence of Bordetella avium. The upper respiratory tract in turkeys was dominated by two major phyla Firmicutes and Proteobacteria. At the genus level, the genera Ornithobacterium, Mycoplasma, Gallibacterium, Avibacterium, and Escherichia-Shigella were found which may include pathogenic bacteria that can cause clinical symptoms.
Conclusion
The results of the analysis of multiple infection carried out in flocks with respiratory signs are probably associated with outbreaks of ornithobacteriosis in turkey flocks in Poland.
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Development and Validation of a New TaqMan Real-Time PCR for the Detection of Ornithobacterium rhinotracheale. Microorganisms 2022; 10:microorganisms10020341. [PMID: 35208796 PMCID: PMC8875355 DOI: 10.3390/microorganisms10020341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/17/2022] [Accepted: 01/29/2022] [Indexed: 02/01/2023] Open
Abstract
Ornithobacterium rhinotracheale (ORT) has been associated with poultry respiratory disease worldwide. The organism is fastidious and isolation is challenging. One TaqMan real-time PCR (qPCR) assay has been developed for the detection of ORT. However, during validating the ORT qPCR, the assay performance was suboptimal. During the in silico evaluation, deviations from the basic parameters for primers and probes designs (e.g., presence of stable undesirable primer-dimers) were observed. The suboptimal design led to low efficiency and low sensitivity of the assay. Initially, modification on the probe was carried out to improve the performance of the assay. However, the assay’s performance (efficiency and sensitivity) was still suboptimal. In this manuscript, we describe the development of a new qPCR assay and the comparison of its performance with the currently available assay. A highly efficient, sensitive, and specific qPCR assay was developed with approximately 1000-folds reduction in the limit of detection (from 3 × 106 plasmid DNA copies/mL to 1 × 103 plasmid DNA copies/mL). Additionally, the efficiency of the new assay (E = 98.70%) was significantly better than the current assay (E = 73.18%). The newly developed assay is an improved diagnostic tool for the sensitive and efficient diagnosis of ORT from clinical samples.
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Hashish A, Sinha A, Mekky A, Sato Y, Macedo NR, El-Gazzar M. Development and Validation of Two Diagnostic Real-Time PCR (TaqMan) Assays for the Detection of Bordetella avium from Clinical Samples and Comparison to the Currently Available Real-Time TaqMan PCR Assay. Microorganisms 2021; 9:microorganisms9112232. [PMID: 34835358 PMCID: PMC8619015 DOI: 10.3390/microorganisms9112232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
Bordetella avium (BA) is one of many pathogens that cause respiratory diseases in turkeys. However, other bacterial species can easily overgrow it during isolation attempts. This makes confirming the diagnosis of BA as the causative agent of turkey coryza more difficult. Currently, there are two PCR assays for the molecular detection of BA. One is conventional gel-based PCR and the other is TaqMan real-time PCR (qPCR) assay. However, multiple pitfalls were detected in both assays regarding their specificity, sensitivity, and efficiency, which limits their utility as diagnostic tools. In this study, we developed and validated two TaqMan qPCR assays and compared their performance to the currently available TaqMan qPCR. The two assays were able to correctly identify all BA isolates and showed negative results against a wide range of different microorganisms. The two assays were found to have high efficiency with a detection limit of approximately 1 × 103 plasmid DNA Copies/mL with high repeatability and reproducibility. In comparison to the currently available TaqMan qPCR assay, the newly developed assays showed significantly higher PCR efficiencies due to superior primers and probes design. The new assays can serve as a reliable tool for the sensitive, specific, and efficient diagnosis of BA.
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Affiliation(s)
- Amro Hashish
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (A.H.); (A.S.); (Y.S.); (N.R.M.)
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt;
| | - Avanti Sinha
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (A.H.); (A.S.); (Y.S.); (N.R.M.)
| | - Amr Mekky
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt;
| | - Yuko Sato
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (A.H.); (A.S.); (Y.S.); (N.R.M.)
| | - Nubia R. Macedo
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (A.H.); (A.S.); (Y.S.); (N.R.M.)
| | - Mohamed El-Gazzar
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (A.H.); (A.S.); (Y.S.); (N.R.M.)
- Correspondence: ; Tel.: +1-706-540-3037
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Veiga IB, Mühldorfer K, Hafez HM, Lüschow D. Whatman® FTA® Cards Performance for Ornithobacterium rhinotracheale DNA Amplification. Avian Dis 2021; 64:496-498. [PMID: 33570099 DOI: 10.1637/aviandiseases-d20-00030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/25/2020] [Indexed: 11/05/2022]
Abstract
The avian pathogen Ornithobacterium rhinotracheale (ORT) has been implied in the etiology of poultry respiratory disease in recent years. To evaluate whether Whatman® Flinders Technology Associates (FTA®) cards can be used for hazard-free transport and storage of ORT samples for posterior DNA amplification, a controlled assay was performed. Three 10-fold dilutions of an ORT culture suspension were spotted on FTA cards and stored at room temperature (RT) for 6 mo. Sterile swabs were immersed in the same three 10-fold culture dilutions and stored at RT and 4 and -20 C without storage medium for the same time. DNA was extracted from both the FTA cards and swabs 1 day, 1 and 6 wk, and 6 mo following sample preparation and stored at -20 C. At the end of the experiment, real-time PCR amplification of the 16S ribosomal RNA gene was performed from DNA extracted throughout a 6-mo period from all ORT samples stored on both FTA cards and swabs. The obtained threshold cycle values for each ORT DNA extraction date were within the same range for all samples in a dilution-dependent fashion, regardless of storage temperature or used material. Pure ORT colonies could be reisolated 1 day after sample preparation from the swab dilutions stored at all temperatures but not from the FTA cards. We conclude that the efficiency of ORT DNA amplification from samples stored on FTA cards or in swabs is similar. However, FTA cards have the advantage of preventing microorganism growth, thus allowing safe transport and storage, for at least 6 mo, for bacterial dilutions down to at least 104-105 colony-forming units/ml.
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Affiliation(s)
- Inês Berenguer Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Kristin Mühldorfer
- Leibniz Institute for Zoo and Wildlife Research, Department of Wildlife Diseases, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Hafez Mohamed Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Freie Universität Berlin, Königsweg 63, 14163 Berlin, Germany
| | - Dörte Lüschow
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Freie Universität Berlin, Königsweg 63, 14163 Berlin, Germany
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Xue J, Lv C, He P, Xu M, Zhang G. Research Note: Serological investigation of Ornithobacterium rhinotracheale infection in China. Poult Sci 2020; 99:4814-4817. [PMID: 32988517 PMCID: PMC7598332 DOI: 10.1016/j.psj.2020.06.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/18/2020] [Accepted: 06/07/2020] [Indexed: 11/27/2022] Open
Abstract
Ornithobacterium rhinotracheale (ORT) has been associated with avian respiratory disease. On coinfection with other pathogens, ORT can cause serious health problems in avian species, leading to financial losses. To monitor the serologic prevalence of ORT in chicken flocks in China, 1,280 sera were collected to determine ORT antibodies among 64 flocks from 15 provinces of China using a commercial ELISA kit. The overall seroprevalence of ORT among the birds tested was 44.06%. In younger chickens, the serum positive rate was lower than that in older chickens, and with increased age, the serum positive rates increased. Older chickens had not only higher positive rates but also higher antibody levels. These data indicated that ORT infections were common in China. Because an ORT vaccine is currently not available, good disease management and biosecurity measures are required for effective disease control.
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Affiliation(s)
- Jia Xue
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Chunmei Lv
- Diagnostic & Research Center of Livestock and Poultry Epidemic Diseases, China Agricultural University, Beijing 100193, China
| | - Pei He
- Diagnostic & Research Center of Livestock and Poultry Epidemic Diseases, China Agricultural University, Beijing 100193, China
| | - Meiyu Xu
- Diagnostic & Research Center of Livestock and Poultry Epidemic Diseases, China Agricultural University, Beijing 100193, China
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Smith EA, Miller EA, Weber BP, Munoz Aguayo J, Flores Figueroa C, Huisinga J, Nezworski J, Kromm M, Wileman B, Johnson TJ. Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States. Appl Environ Microbiol 2020; 86:e02874-19. [PMID: 32245763 PMCID: PMC7237767 DOI: 10.1128/aem.02874-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/25/2020] [Indexed: 01/02/2023] Open
Abstract
Ornithobacterium rhinotracheale is a causative agent of respiratory tract infections in avian hosts worldwide but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of O. rhinotracheale, which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between O. rhinotracheale populations through comparative genomics of clinical isolates from different U.S. turkey producers. O. rhinotracheale clinical isolates were collected from four major U.S. turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucleotide polymorphism (SNP)-based analysis, and then assembly and annotations were performed to identify genes encoding putative virulence factors and antimicrobial resistance determinants. A pangenome approach was also used to establish a core set of genes consistently present in O. rhinotracheale and to highlight differences in gene content between phylogenetic clades. A total of 1,457 nonrecombinant SNPs were identified from 157 O. rhinotracheale genomes, and four distinct phylogenetic clades were identified. Isolates clustered by company on the phylogenetic tree, however, and each company had isolates in multiple clades with similar collection dates, indicating that there are multiple O. rhinotracheale strains circulating within each of the companies examined. Additionally, several antimicrobial resistance proteins, putative virulence factors, and the pOR1 plasmid were associated with particular clades and multilocus sequence types, which may explain why the same strains seem to have persisted in the same turkey operations for decades.IMPORTANCE The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods. Additionally, differentiating O. rhinotracheale isolates at the whole-genome level may provide insight into selection of the most appropriate autogenous vaccine strain, or groups of strains, for a given population of clinical isolates.
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Affiliation(s)
- Emily A Smith
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Bonnie P Weber
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jeannette Munoz Aguayo
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
| | | | | | | | | | | | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
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Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens. Appl Environ Microbiol 2019; 85:AEM.03137-18. [PMID: 30824436 DOI: 10.1128/aem.03137-18] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023] Open
Abstract
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.
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Ha HJ, Christensen N, Humphrey S, Haydon T, Bernardi G, Rawdon T. The First Detection of Ornithobacterium rhinotracheale in New Zealand. Avian Dis 2016; 60:856-859. [PMID: 27902894 DOI: 10.1637/11457-062116-case] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ornithobacterium rhinotracheale (ORT) has been considered exotic to New Zealand and thus, any samples from poultry suspected of ORT infection are submitted as part of an exotic disease investigation managed by Ministry for Primary Industries (MPI) and subjected to standardized test protocols carried out in the physical containment level 3+ laboratory at MPI's Animal Health Laboratory (AHL). All previous exotic disease investigations concerning ORT produced negative results by bacterial culture and conventional PCR. Following the recent introduction of a real-time PCR for ORT at the AHL, several tracheal wash fluids from backyard chickens ( Gallus gallus domesticus ) were tested positive. This identification constituted the first detection of ORT in New Zealand poultry. As a result, a second premise was investigated with further samples testing positive for ORT by molecular assays. This paper describes the two exotic disease investigations associated with the first detection of ORT in New Zealand poultry and its implications.
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Affiliation(s)
- H J Ha
- A Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Wallaceville, Upper Hutt 5018, New Zealand
| | - N Christensen
- B Avivet Ltd., 257 Patumahoe Road, Pukekohe 2678, New Zealand
| | - S Humphrey
- A Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Wallaceville, Upper Hutt 5018, New Zealand
| | - T Haydon
- A Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Wallaceville, Upper Hutt 5018, New Zealand
| | - G Bernardi
- C Pacificvet Limited, 3 Hickory Place, Christchurch 8042, New Zealand
| | - T Rawdon
- D Investigation and Diagnostics Centres and Response, Ministry for Primary Industries, 66 Ward Street, Wallaceville, Upper Hutt 5018, New Zealand
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