Analytical verification of a PCR assay for identification of Bordetella avium

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

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.

Bordetella avium-associated endophthalmitis: case report

Background

Bordetella avium, an aerobic bacterium that rarely causes infection in humans, is a species of Bordetella that generally inhabits the respiratory tracts of turkeys and other birds. It causes a highly contagious bordetellosis. Few reports describe B. avium as a causative agent of eye-related infections.

Case presentation

We report a case of acute infectious endophthalmitis associated with infection by B. avium after open trauma. After emergency vitrectomy and subsequent broad-spectrum antibiotic treatment, the infection was controlled successfully, and the patient’s vision improved.

Conclusions

B. avium can cause infection in the human eye, which can manifest as acute purulent endophthalmitis. Nanopore targeted sequencing technology can quickly identify this organism. Emergency vitrectomy combined with lens removal and silicone oil tamponade and the early application of broad-spectrum antibiotics are key for successful treatment.

A Study on Isolation and Molecular Identification of Bordetella avium from Iranian Commercial and Backyard Broiler Turkeys within 2016-2018

Bordetellosis or turkey coryza, caused by Bordetella avium, has been an issue for turkey industry since its first description in 1967 when it was reported for the first time. Bordetella avium causes a highly contagious upper respiratory disease in turkeys. Therefore, this study aimed to isolate and characterize this species from commercial and backyard turkeys in Tehran, Isfahan, and Northern provinces of Iran. For the purpose of the study, 625 tracheal swabs were taken from 425 commercial poults and 200 backyard poults aged 2-6 weeks from September 2016 to September 2018. The swabs were immediately plated on MacConkey and blood agar plates and then pooled (5 swabs/pool) in tubes, containing 2 mL distilled water, to perform direct polymerase chain reaction (PCR) for the identification of B. avium. A total of 17 swab pools were found to be positive for B. avium. A subset of seven positive samples were sequenced for the flanking region of piuA gene. The analysis of the sequences indicated that the sequences were 98%, 96%, and 98% similar to B. avium 197N (AM167904.1), 4142 (AY925058.1), and 4156 (AY925068.1) sequences, respectively. To the best of our knowledge, the current study is the first attempt toward the molecular detection and characterization of B. avium in Iran. It is highly recommended to perform further studies to isolate, characterize, and differentiate the regional isolates in order to help the developing turkey industry of Iran meet the increasing demands for protein in the diet of the citizenry.

In vitro characterization and genetic diversity of Bordetella avium field strains

Bordetella avium (BA) is a respiratory pathogen of particular importance for turkeys. Specific adherence and damage to the respiratory epithelia are crucial steps of the pathogenesis, but knowledge about the mechanisms and the variety of virulence in field strains is limited. We analysed 17 BA field strains regarding their in vitro virulence-associated properties in tracheal organ cultures (TOC) of turkey embryos, and their genetic diversity. The TOC adherence assay indicated that BA field strains differ considerably in their ability to adhere to the tracheal mucosa, while the TOC ciliostasis assay illustrated a high degree of diversity in ciliostatic effects. These two virulence-associated properties were associated with each other in the investigated strains. Three of the investigated strains displayed significantly (P > 0.05) lower in vitro virulence in comparison to other strains. Genetic diversity of BA strains was analysed by core genome multilocus sequence typing (cgMLST). We applied a cgMLST scheme comprising 2667 targets of the reference genome (77.3% of complete genome, BA strain 197N). The results showed a broad genetic diversity in BA field strains but did not demonstrate a correlation between sequence type and virulence-associated properties. The cgMLST analysis revealed that strains with less marked virulence-associated properties had a variety of mutations in the putative filamentous haemagglutinin gene. Likewise, amino acid sequence alignment indicated variations in the protein. The results from our study showed that both adherence and ciliostasis assay can be used for virulence characterization of BA. Variations in the filamentous haemagglutinin protein may be responsible for reduced virulence of BA field strains.

Disclosing respiratory co-infections: a broad-range panel assay for avian respiratory pathogens on a nanofluidic PCR platform

Respiratory syndromes (RS) are among the most significant pathological conditions in edible birds and are caused by complex coactions of pathogens and environmental factors. In poultry, low pathogenic avian influenza A viruses, metapneumoviruses, infectious bronchitis virus, infectious laryngotracheitis virus, Mycoplasma spp. Escherichia coli and/or Ornithobacterium rhinotracheale in turkeys are considered as key co-infectious agents of RS. Aspergillus sp., Pasteurella multocida, Avibacterium paragallinarum or Chlamydia psittaci may also be involved in respiratory outbreaks. An innovative quantitative PCR method, based on a nanofluidic technology, has the ability to screen up to 96 samples with 96 pathogen-specific PCR primers, at the same time, in one run of real-time quantitative PCR. This platform was used for the screening of avian respiratory pathogens: 15 respiratory agents, including viruses, bacteria and fungi potentially associated with respiratory infections of poultry, were targeted. Primers were designed and validated for SYBR green real-time quantitative PCR and subsequently validated on the Biomark high throughput PCR nanofluidic platform (Fluidigm©, San Francisco, CA, USA). As a clinical assessment, tracheal swabs were sampled from turkeys showing RS and submitted to this panel assay. Beside systematic detection of E. coli, avian metapneumovirus, Mycoplasma gallisepticum and Mycoplasma synoviae were frequently detected, with distinctive co-infection patterns between French and Moroccan flocks. This proof-of-concept study illustrates the potential of such panel assays for unveiling respiratory co-infection profiles in poultry.

Detection of Bordetella avium by TaqMan real-time PCR in tracheal swabs from wildlife birds

Bordetella avium, the causing agent of bordetellosis, a highly contagious infection of the respiratory tract in young poultry, causes significant losses in poultry farming throughout the world. Wildlife birds can be a reservoir of various pathogens that infect farm animals. For this reason the studies were conducted to estimate the prevalence of Bordetella avium in wildlife birds in Poland. Tracheal swab samples were collected from 650 birds representing 27 species. The bacterial DNA was isolated directly from the swabs and screened for Bordetella avium by TaqMan real-time PCR. The assay specificity was evaluated by testing DNA isolated from 8 other bacteria that can be present in avian respiratory tract, and there was no amplification from non-Bordetella avium agents. Test sensitivity was determined by preparing standard tenfold serial dilutions of DNA isolated from positive control. The assay revealed to be sensitive, with detection limit of approximately 4.07x10^2 copies of Bordetella avium DNA. The genetic material of Bordetella avium was found in 54.54% of common pheasants, in 9.09% of Eurasian coots, in 3.22% of black-headed gulls and in 2.77% of mallard ducks. The results of this study point to low prevalence of Bordetella avium infections in wildlife birds. The results also show that described molecular assay proved to be suitable for the rapid diagnosis of bordetellosis in the routine diagnostic laboratory.

Development of a PCR for identification of Bordetella hinzii

Bordetella hinzii infects primarily poultry and immunocompromised humans. It is closely related to the etiologic agent of turkey coryza, Bordetella avium. Distinguishing between B. avium and B. hinzii is difficult, and there is no method for identification of B. hinzii suitable for use by diagnostic laboratories. This report details the development of a B. hinzii-specific PCR targeting the ompA gene. Assay sensitivity is 100% based on analysis of 48 B. hinzii isolates from diverse geographic locations representing all known ribotypes. Evaluation of 71 isolates of B. avium and 20 other bacterial isolates from poultry, comprising gram-negative and gram-positive commensals and pathogens of nine genera, demonstrated an assay specificity of 100%. The ompA PCR is a rapid, reliable, and accurate method for identification of B. hinzii and provides a valuable new tool for veterinary diagnostic laboratories investigating poultry respiratory disease outbreaks.

Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus

The pathogenesis of Type 2 highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in 10-week old swine in the United States was investigated. rJXwn06, rescued from an infectious clone of Chinese HP-PRRSV, replicated in swine with at least 100-fold increased kinetics over U.S. strain VR-2332. rJXwn06 caused significant weight loss, exacerbated disease due to bacterial sepsis and more severe histopathological lung lesions in pigs exposed to HP-PRRSV than to those infected with VR-2332. Novel findings include identification of bacterial species present, the degree of thymic atrophy seen, and the inclusion of contact animals that highlighted the ability of HP-PRRSV to rapidly transmit between animals. Furthermore, comprehensive detailed cytokine analysis of serum, bronchoalveolar lavage fluid, and tracheobronchial lymph node tissue homogenate revealed a striking elevation in levels of cytokines associated with both innate and adaptive immunity in HP-PRRSV infected swine, and showed that contact swine differed in the degree of cytokine response.

Genomic sequence and virulence comparison of four Type 2 porcine reproductive and respiratory syndrome virus strains

Porcine reproductive and respiratory syndrome virus (PRRSV) is a ubiquitous and costly virus that exhibits substantial sequence and virulence disparity among diverse isolates. In this study, we compared the whole genomic sequence and virulence of 4 Type 2 PRRSV isolates. Among the 4 isolates, SDSU73, MN184, and NADC30 were all clearly more virulent than NADC31, and among the 3 more virulent isolates, there were subtle differences based on viral replication, lung lesions, lymphadenopathy, febrile response, decreased weight gains, and cytokine responses in the lung. Lesions consistent with bacterial bronchopneumonia were present to varying degrees in pigs infected with PRRSV, and bacteria typically associated with the porcine respiratory disease complex were isolated from the lung of these pigs. Genomic sequence evaluation indicates that SDSU73 is most similar to the nucleotide sequence of JA142, the parental strain of Ingelvac(®) PRRS ATP, while the nucleotide sequences of NADC30 and NADC31 are more similar to strain MN184. Both the NADC30 and NADC31 isolates of PRRSV, isolated in 2008, maintain the nonstructural protein 2 (nsp2) deletion seen in MN184 that was isolated in 2001, but NADC31 has two additional 15 and 36 nucleotide deletions, and these strains are 8-14% different on a nucleotide basis from the MN184 strain. These results indicate that newer U.S. Type 2 strains still exhibit variability in sequence and pathogenicity and although PRRSV strains appear to be reducing the size of the nsp2 over time, this does not necessarily mean that the strain is more virulent.

Bordetella avium antibiotic resistance, novel enrichment culture, and antigenic characterization

Bordetella avium continues to be an economic issue in the turkey industry as the causative agent of bordetellosis, which often leads to serious secondary infections. This study presents a broad characterization of the antibiotic resistance patterns in this diverse collection of B. avium strains collected over the past thirty years. In addition, the plasmid basis for the antibiotic resistance was characterized. The antibiotic resistance pattern allowed the development of a novel enrichment culture method that was subsequently employed to gather new isolates from diseased turkeys and a healthy sawhet owl. While a healthy turkey flock was shown to seroconvert by four weeks-of-age, attempts to culture B. avium from healthy turkey poults were unsuccessful. Western blot of B. avium strains using pooled serum from diseased and healthy commercial turkey flocks revealed both antigenic similarities and differences between strains. In sum, the work documents the continued exposure of commercial turkey flocks to B. avium and the need for development of an effective, inexpensive vaccine to control spread of the disease.

Evaluation of specificity of BP3385 for Bordetella pertussis detection

BP3385 has been proposed as a diagnostic PCR target for discriminating between Bordetella pertussis and other Bordetella species that also infect humans. Our results demonstrate that this gene is also present in some strains of Bordetella hinzii and Bordetella bronchiseptica.

Molecular epidemiology of vancomycin-resistant Enterococcus faecium strains isolated from haematological malignancy patients in a research hospital in Turkey

Infections and outbreaks of vancomycin-resistant enterococci (VRE) still appear to be rare in Turkey. In the present study, VRE strains isolated during an outbreak in a haematology unit of a training and research hospital in Turkey were typed and their antimicrobial-resistance patterns were characterized by molecular methods. Twelve vancomycin-resistant Enterococcus faecium strains isolated from patients with haematological malignancies were investigated by PCR for the presence of genes encoding resistance to vancomycin, tetracycline, chloramphenicol, gentamicin and erythromycin. Their clonal relationship was evaluated by PFGE and multilocus sequence typing. All strains were resistant to vancomycin and erythromycin, and had the vanA and ermB genes, respectively. PFGE was used to determine the presence of two pulsotypes and determine their subtypes. Pulsotype A belonged to sequence type (ST) 17 and pulsotype B belonged to ST 78. All strains with the vanA gene were not the same clone, indicating multiple acquisitions of resistant isolates, even over such a short time period.

Serratia marcescens sepsis outbreak in a neonatal intensive care unit

BACKGROUND

Contaminated parenteral nutrition (PN) is an important source of infection in neonates. Many organisms have been reported to cause contamination resulting in outbreaks in intensive care units. The aim of the present study was to investigate an outbreak caused by Serratia marcescens in a neonatal intensive care unit (NICU).

METHODS

This was a descriptive study of an outbreak of sepsis in an NICU of a university teaching hospital. The outbreak was detected in seven patients from 10 to 12 December 2005 following the administration of PN. Extensive environmental samplings for culture were performed. The clonal relationship among isolates was tested using pulsed-field gel electrophoresis, random amplification of polymorphic DNA-polymerase chain reaction and plasmid DNA typing.

RESULTS

Serratia marcescens was found in blood cultures from infected newborns and from in-use PN solutions. Gestational age of the seven babies ranged from 28 to 34 weeks (median, 32 weeks), birthweight ranged from 1000 g to 2190 g (median, 1469 g), and postnatal age ranged from 8 to 22 days. The mortality rate was 14.3%. All these strains of S. marcescens had the same antibiotic susceptibility pattern and the same genomic DNA profile. Plasmid typing, as well as RAPD-PCR showed that all isolates had the same profile.

CONCLUSION

The source of the nosocomial sepsis in seven neonates was the PN solution. Contamination may occur during storage or repeated handling during PN preparation.

Prevalence and sequence variants of IS481 in Bordetella bronchiseptica: implications for IS481-based detection of Bordetella pertussis

We report the prevalence in Bordetella bronchiseptica of IS481, a frequent target for diagnosis of Bordetella pertussis, as approximately 5%. However, PCR amplicons of the predicted size were detectable in 78% of IS481-negative strains. Our results suggest that PCR targeting IS481 may not be sufficiently specific for reliable identification of B. pertussis.

Analytical verification of a multiplex PCR for identification of Bordetella bronchiseptica and Pasteurella multocida from swine

Bordetella bronchiseptica and Pasteurella multocida are etiologic agents of progressive atrophic rhinitis (PAR) and bronchopneumonia in swine. Only dermonecrotic toxin-producing strains of P. multocida play a role in atrophic rhinitis while both toxigenic and nontoxigenic strains have been associated with pneumonia. Monitoring and investigation of outbreaks involving these bacteria require sensitive and accurate identification and reliable determination of the toxigenic status of P. multocida isolates. In the present study, we report the development, optimization, and performance characteristics of a multiplex PCR assay for simultaneous amplification of up to three different targets, one common to all P. multocida strains, one found only in toxigenic P. multocida strains, and one common to B. bronchiseptica strains. Based on analysis of 94 P. multocida isolates (31 toxigenic) and 126 B. bronchiseptica isolates assay sensitivity is 100% for all amplicons. Evaluation of 22 isolates of other bacterial genera and species commonly found in the swine respiratory tract demonstrated a specificity of 100% for all gene targets. The limit of detection for simultaneous amplification of all targets is 1-10pg of DNA per target, corresponding to a few hundred genomes or less. Amplicon mobility in agarose gels and sequence analysis indicate the amplicons are highly stable. The data presented establish this multiplex PCR as a reliable method for identification of B. bronchiseptica and both toxigenic and nontoxigenic P. multocida that may greatly simplify investigations of swine PAR and bronchopneumonia.