Journal article
Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp
Microbial Genomics, Vol.6(7), pp.1-10
2020
Abstract
Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans . Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans , with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non- Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
Details
- Title
- Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp
- Authors
- Erin P Price (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - LegacyValentina Soler Arango (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - LegacyTimothy J Kidd (Author) - The University of QueenslandTamieka A Fraser (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - LegacyThuy-Khanh Nguyen (Author) - QIMR Berghofer Medical Research InstituteScott C Bell (Author) - QIMR Berghofer Medical Research InstituteDerek S Sarovich (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
- Publication details
- Microbial Genomics, Vol.6(7), pp.1-10
- Publisher
- Microbiology Society
- Date published
- 2020
- DOI
- 10.1099/mgen.0.000406
- ISSN
- 2057-5858
- Copyright note
- © 2020 The Authors. his is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
- Organisation Unit
- School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99483705402621
- Output Type
- Journal article
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