Molecular Characterization of the Recently Emerged Poultry Pathogen Ornithobacterium rhinotracheale by Multilocus Sequence Typing

Thieme, Susann; Mühldorfer, Kristin; Lüschow, Dörte; Hafez, Hafez M.

doi:10.1371/journal.pone.0148158

Cited by 22 publications

(46 citation statements)

References 34 publications

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“…All bacterial hosts of the chromosomal genes in this group, both the representative genes and the members of the families, belonged to the phylum Bacteroidetes. Two of the families in this group consisted of genes located in pathogens, where G29 in family 22 was found on the chromosome of an isolate from the poultry pathogen Ornithobacterium rhinotracheale [37] and G04 in family 4 was present on a plasmid harbored by an isolate of the opportunistic pathogen Myroides odoratimimus [38]. …”

Section: Resultsmentioning

confidence: 99%

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

et al. 2017

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BackgroundMetallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-β-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-β-lactamases of class B1, the most clinically important subclass of these enzymes.ResultsBased on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-β-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-β-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-β-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-β-lactamases. Phylogenetic analysis showed that B1 metallo-β-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 β-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species.ConclusionsThis study more than doubles the number of known B1 metallo-β-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0353-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

et al. 2017

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“…Several studies (Amonsin et al, 1997;Thieme et al, 2016) have proposed that the limited heterogeneity found among isolates can be explained by the fact that the O. rhinotracheale isolates recovered over large geographic areas and long time periods are a small group of closely related clones. Although the number of isolates and the geographic areas from which the isolates were obtained were limited, both the ERIC-PCR and RAPD analyses presented here support this theory.…”

Section: Discussionmentioning

confidence: 99%

“…In conclusion, we were able to discriminate O. rhinotracheale isolates with both ERIC-PCR and RAPD assays using different primers, at least to a certain level. Although a multilocus sequence typing method and database have recently been established (Thieme et al, 2016), repetitive extragenic palindromic PCR and RAPD assays remain relatively cost-efficient, rapid, sensitive, and specific typing methods, and may therefore be useful in epidemiological studies of O. rhinotracheale outbreaks. In this study, ERIC-PCR proved the most useful technique for detecting intraspecies genetic diversity in O. rhinotracheale isolates.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Ornithobacterium rhinotracheale field isolates from Hungary

et al. 2017

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Ornithobacterium rhinotracheale is a widely distributed rod-shaped Gram-negative bacterium that infects several avian species including chickens and turkeys. It is associated with respiratory signs, growth retardation, mortality, and reduced egg production, thus causing severe economic losses to the poultry industries. In this study, 37 field isolates of O. rhinotracheale, collected from various locations in Hungary between 1997 and 2015, were identified and characterized by the analysis of partial 16S rRNA gene sequences, enterobacterial repetitive intergenic consensus (ERIC)-PCR, and random amplified polymorphic DNA (RAPD) PCR assays with the OPG11, OPH19, and M13 primers. Most of the field isolates were serotype A, one was serotype B, and four were serotype D. One isolate could not be typed with antisera against serotypes A-E. In a phylogenetic analysis of the 16S rRNA sequences, the isolates formed two clusters. Thirteen distinct patterns were identified with ERIC-PCR, and the RAPD assay with the M13 primer assigned the isolates to 10 different patterns. The other two RAPD assays were unsuitable for distinguishing and grouping the isolates. Neither ERIC type nor RAPD pattern correlated with the place or year of isolation. However, the strains isolated from chickens were more heterogeneous on ERIC-PCR than the isolates recovered from turkeys. In this study, ERIC-PCR was the most discriminatory method for investigating the genetic diversity of O. rhinotracheale isolates.

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“…The 16S rRNA gene was found to demonstrate identity ranging from 85.1% to 100%. This sequencing protocol can identify and differentiate Ornithobacterium species [72]. Genetic characterization of ORT isolates can also be performed by modified PCR techniques, such as enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), repetitive element palindromic PCR (REP-PCR), random amplified polymorphic DNA-PCR (RAPD-PCR), and MLST [56].…”

Section: Genetic Relatednessmentioning

confidence: 99%

Ornithobacterium rhinotracheale: An Update Review about An Emerging Poultry Pathogen

Barbosa

Cardoso

Silva

et al. 2019

Veterinary Sciences

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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.

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Molecular Characterization of the Recently Emerged Poultry Pathogen Ornithobacterium rhinotracheale by Multilocus Sequence Typing

Cited by 22 publications

References 34 publications

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

Characterization of Ornithobacterium rhinotracheale field isolates from Hungary

Ornithobacterium rhinotracheale: An Update Review about An Emerging Poultry Pathogen

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