Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers

The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex...

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Bibliographic Details
Published in:Journal of microbiological methods 2015-10, Vol.117, p.108-112
Main Authors: Perrin, Elena, Fondi, Marco, Maida, Isabel, Mengoni, Alessio, Chiellini, Carolina, Mocali, Stefano, Cocchi, Priscilla, Campana, Silvia, Taccetti, Giovanni, Vaneechoutte, Mario, Fani, Renato
Format: Article
Language:English
Subjects:
Bacteria
Burkholderia cepacia
Burkholderia cepacia complex
Burkholderia cepacia complex - genetics
Burkholderia cepacia complex - isolation & purification
Burkholderia Infections - diagnosis
Burkholderia Infections - microbiology
Cystic Fibrosis - microbiology
DNA, Bacterial - genetics
Genes, Overlapping - genetics
Genetic Markers - genetics
Genome, Bacterial - genetics
Genomes
Humans
Identification
marC–hisH
Molecular Typing - methods
Overlapping genes
Polymerase Chain Reaction
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Summary:The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera. •Comparative microbial genomes analysis could be used in the field of microbial identification.•The use of overlapping genes for this purpose was evaluated.•The phylogenetic distribution of an overlap between marC and hisH genes was analyzed.•A PCR on this overlap, specific for Burkholderia, was designed, set up and tested.
ISSN:0167-7012
1872-8359
DOI:10.1016/j.mimet.2015.07.025