In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, Atopobium vaginae and Lactobacillus spp

Bacterial vaginosis (BV) is a common pathology of women in reproductive age that can lead to serious health complications, and is associated with shifts in the normal microflora from predominance of Lactobacillus spp. to a proliferation of other anaerobes such as G. vaginalis and A vaginae, which ca...

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Bibliographic Details
Published in:BMC research notes 2012-11, Vol.5 (1), p.637-637, Article 637
Main Authors: Henriques, Ana, Cereija, Tatiana, Machado, António, Cerca, Nuno
Format: Article
Language:English
Subjects:
A. vaginae
Actinobacteria - genetics
Adult
Age
Analysis
Atopobium vaginae
Bacteria, Pathogenic
Databases, Nucleic Acid
DNA Primers - genetics
Female
G. vaginalis
Gardnerella vaginalis
Gardnerella vaginalis - genetics
Humans
In silico primer testing
In vitro primer testing
Lactobacillus
Lactobacillus - genetics
Lactobacillus spp
Microbiota (Symbiotic organisms)
Microflora
Microorganisms
Pathogens
Polymerase chain reaction
Polymerase Chain Reaction - methods
Primer sensitivity
Primer specificity
Primers
Sensitivity and Specificity
Short Report
Species Specificity
Vaginosis
Vaginosis, Bacterial - diagnosis
Vaginosis, Bacterial - microbiology
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Summary:Bacterial vaginosis (BV) is a common pathology of women in reproductive age that can lead to serious health complications, and is associated with shifts in the normal microflora from predominance of Lactobacillus spp. to a proliferation of other anaerobes such as G. vaginalis and A vaginae, which can be detected by PCR. The optimal PCR pathogen detection assay relies mainly on the specificity and sensitivity of the primers used. Here we demonstrate that in silico analytical testing of primer specificity is not a synonym to in vitro analytical specificity by testing a range of published and newly designed primers with both techniques for the detection of BV-associated microorganisms. By testing primer in vitro specificity with a sufficient range of bacterial strains, we were able to design primers with higher specificity and sensitivity. Also by comparing the results obtained for the newly designed primers with other previously published primers, we confirmed that in silico analysis is not sufficient to predict in vitro specificity. As such care must be taken when choosing the primers for a detection assay.
ISSN:1756-0500
1756-0500
DOI:10.1186/1756-0500-5-637