Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States

Smith, Emily; Miller, Elizabeth A.; Weber, Bonnie; Aguayo, Jeannette Munoz; Figueroa, Cristian Flores; Huisinga, Jared; Nezworski, Jill; Kromm, Michelle; Wileman, B. W.; Johnson, Timothy J.

doi:10.1128/aem.02874-19

Cited by 6 publications

(7 citation statements)

References 44 publications

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“…Thirty-eight ORT isolates were included in this study (Table 2). These isolates were revived on blood agar (with 5% sheep blood) and incubated for 24-48 h under microaerophilic conditions at 37 °C for 48 h. Characteristic ORT colonies were confirmed by MALDI-TOF [22]. Additionally, nine known ORT-positive clinical samples were obtained from ISU-VDL (Table 3).…”

Section: Ornithobacterium Rhinotracheale Isolates and Clinical Samplesmentioning

confidence: 99%

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

et al. 2022

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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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Section: Ornithobacterium Rhinotracheale Isolates and Clinical Samplesmentioning

confidence: 99%

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

et al. 2022

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“…The mechanism by which VapD confers pathogenicity is not well understood. The expression of the VapD protein is increased during biofilm formation in Xylella fastidiosa [17]. The draft genome MAGN1 was found to contain the ParE toxin-encoding gene, indicating that the toxin ParEI likely targets DNA gyrase and is involved in a RecA-dependent SOS response.…”

Section: Discussionmentioning

confidence: 99%

Draft genome sequence of novel Candidatus Ornithobacterium hominis carrying antimicrobial resistance genes in Egypt

Ahmed,

Azab,

Enany

et al. 2024

BMC Microbiol

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Background Candidatus Ornithobacterium hominis (O. hominis), which was identified in nasopharyngeal swabs from Egypt, has been associated with respiratory disorders in humans. O. hominis, a recently identified member of the Flavobacteriaceae family, belongs to the largest family within the Bacteroidetes phylum. This family includes hundreds of species and 90 genera, including major human pathogens such as Capnocytophaga canimorsus and Elizabethkingia meningoseptica. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The alignment of reads against the O. hominis genome was accomplished using BLASTN, and the reads with significant hits were extracted using Seqtk and assembled using SPAdes. The primary goal of this study was to obtain a more profound understanding of the genomic landscape of O. hominis, with an emphasis on identifying the associated virulence, antimicrobial genes, and distinct defense mechanisms to shed light on the potential role of O. hominis in human respiratory infections. Results The genome size was estimated to be 1.84 Mb, including 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G+C content of 35.62%. Genes encoding gliding motility, antibiotic resistance (20 genes), and the toxA gene were all included in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique genes encoding proteins, such as the ParE1 toxin that defend against the actions of quinolone and other antibiotics. The cobalt-zinc-cadmium resistance gene encoding the protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance genes encoding proteins were identified, such as MexB, MdtK, YheI, and VanC. Conclusion Our study focused on identifying virulence factors, and antimicrobial resistance genes present in the core genome of O. hominis. These findings provide valuable insights into the potential pathogenicity and antibiotic susceptibility of O. hominis.

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“…The mechanism by which VapD confers pathogenicity is not well understood. The expression of the VapD protein is increased during bio lm formation in Xylella fastidiosa (15). The draft genome MAGN1 was found to contain the ParE toxin.…”

Section: Discussionmentioning

confidence: 99%

Draft Genome Sequence of Novel Candidatus Ornithobacterium hominis Carrying Antimicrobial Resistance Genes in Egypt

Ahmed,

Azab,

Enany

et al. 2023

Preprint

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Background Candidatus Ornithobacterium hominis (O. hominis), which was found in Egyptian nasopharyngeal swabs but remains unidentified, has been associated with respiratory disorders in humans. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The primary goal of this study was to present the first O. hominis genome sequence from Egyptian populations. Results The genome size was estimated to be 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G + C content of 35.62%. The toxA gene, 20 antibiotic resistance genes, and gliding motility genes were found in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique proteins, such as the ParE1 toxin, that exhibit a defense mechanism against quinolone and other antibiotic actions. The cobalt-zinc-cadmium resistance protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance proteins were identified, such as MexB, mdtK, yheI, and VanC. Conclusion Numerous virulence factors such as toxA and gliding motility genes, were present in the core O. hominis genome. Additionally, the draft genome contains several antibiotic-resistance genes. These findings may contribute to a better understanding of the genomic landscape of O. hominis and the identification of genes involved in virulence and antibiotic resistance.

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Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States

Cited by 6 publications

References 44 publications

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

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

Draft genome sequence of novel Candidatus Ornithobacterium hominis carrying antimicrobial resistance genes in Egypt

Draft Genome Sequence of Novel Candidatus Ornithobacterium hominis Carrying Antimicrobial Resistance Genes in Egypt

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