Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia

Tamieka A Fraser; Mikaela G Bell; Patrick N A Harris; Scott C Bell; Haakon Bergh; Thuy-Khanh Nguyen; Timothy J Kidd; Graeme R Nimmo; Derek S Sarovich; Erin P Price

doi:10.1101/702985

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Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia

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Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia

Tamieka A Fraser, Mikaela G Bell, Patrick N A Harris, Scott C Bell, Haakon Bergh, Thuy-Khanh Nguyen, Timothy J Kidd, Graeme R Nimmo, Derek S Sarovich and Erin P Price

bioRxiv

Cold Spring Harbor Laboratory Press

2019

DOI: https://doi.org/10.1101/702985

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Abstract

Medical Microbiology

Public Health and Health Services

Stenotrophomonas maltophilia is emerging as an important cause of disease in nosocomial and community-acquired settings, including bloodstream, wound and catheter-associated infections. Cystic fibrosis airways also provide optimal growth conditions for various opportunistic pathogens with high antibiotic tolerance, including S. maltophilia. Currently, there is no rapid, cost-effective, and accurate molecular method for detecting this potentially life-threatening pathogen, particularly in polymicrobial specimens, suggesting that its true prevalence may be underestimated. Here, we used large-scale comparative genomics to identify a specific genetic target for S. maltophilia, with subsequent development and validation of a real-time PCR assay for its detection. Analysis of 165 Stenotrophomonas spp. genomes identified a 4kb region specific to S. maltophilia, which was targeted for Black Hole Quencher assay design. Our assay yielded the positive detection of 89 of 89 (100%) clinical S. maltophilia strains, and no amplification of 23 non-S. maltophilia clinical isolates. S. maltophilia was detected in 10/16 CF sputa, demonstrating the utility for direct detection in respiratory specimens. The assay demonstrated good sensitivity, with limits of detection and quantitation on pure culture of ~10 and ~100 genome equivalents, respectively. Our assay provides a highly specific, sensitive, and cost-effective method for the accurate identification of S. maltophilia, and will improve the diagnosis and treatment of this under-recognized pathogen by enabling its accurate and rapid detection from polymicrobial clinical and environmental samples.

Details

Title: Quantitative real-time PCR assay for the rapid identification of the multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia
Authors: Tamieka A Fraser (Author) - University of the Sunshine Coast
Mikaela G Bell (Author) - University of the Sunshine Coast
Patrick N A Harris (Author) - University of Queensland
Scott C Bell (Author) - QIMR Berghofer Medical Research Institute
Haakon Bergh (Author) - Royal Brisbane and Women's Hospital
Thuy-Khanh Nguyen (Author) - QIMR Berghofer Medical Research Institute
Timothy J Kidd (Author) - QIMR Berghofer Medical Research Institute
Graeme R Nimmo (Author) - Royal Brisbane and Women's Hospital
Derek S Sarovich (Author) - University of the Sunshine Coast
Erin P Price (Author) - University of the Sunshine Coast
Publication details: bioRxiv
Publisher: Cold Spring Harbor Laboratory Press
Date published: 2019
DOI: 10.1101/702985
ISSN: 2692-8205
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99451408402621
Output Type: Preprint

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