Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia
Open Access
- 23 June 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Microbiology
- Vol. 20 (1), 1-13
- https://doi.org/10.1186/s12866-020-01842-3
Abstract
The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray. The DNA microarray detection limit was 103 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay. We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.Keywords
Other Versions
This publication has 38 references indexed in Scilit:
- Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300BMC Genomics, 2012
- British Thoracic Society guidelines for the management of community acquired pneumonia in children: update 2011Thorax, 2011
- Development and Evaluation of Oligonucleotide Chip Based on the 16S-23S rRNA Gene Spacer Region for Detection of Pathogenic Microorganisms Associated with SepsisJournal of Clinical Microbiology, 2010
- Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD)Journal of Microbiological Methods, 2010
- Evaluation of different nucleic acid amplification techniques for the detection of M. pneumoniae, C. pneumoniae and Legionella spp. in respiratory specimens from patients with community-acquired pneumoniaJournal of Microbiological Methods, 2008
- A nanoplex PCR assay for the rapid detection of vancomycin and bifunctional aminoglycoside resistance genes in Enterococcus speciesBMC Microbiology, 2007
- Design and validation of a low density array (Nosochip) for the detection and identification of the main pathogenic bacteria and fungi responsible for nosocomial pneumoniaEuropean Journal of Clinical Microbiology & Infectious Diseases, 2007
- 16S rRNA sequencing in routine bacterial identification: A 30-month experimentJournal of Microbiological Methods, 2006
- Development and Evaluation of Chlamylege, a New Commercial Test Allowing Simultaneous Detection and Identification of Legionella , Chlamydophila pneumoniae , and Mycoplasma pneumoniae in Clinical Respiratory Specimens by Multiplex PCRJournal of Clinical Microbiology, 2005
- Efficacy of species-specificrecAPCR tests in the identification ofBurkholderia cepaciacomplex environmental isolatesFEMS Microbiology Letters, 2005