Comparative genome analysis of a large Dutch Legionella pneumophila strain collection identifies five markers highly correlated with clinical strains.

BMC Genomics
E P F YzermanFrank Schuren

Abstract

Discrimination between clinical and environmental strains within many bacterial species is currently underexplored. Genomic analyses have clearly shown the enormous variability in genome composition between different strains of a bacterial species. In this study we have used Legionella pneumophila, the causative agent of Legionnaire's disease, to search for genomic markers related to pathogenicity. During a large surveillance study in The Netherlands well-characterized patient-derived strains and environmental strains were collected. We have used a mixed-genome microarray to perform comparative-genome analysis of 257 strains from this collection. Microarray analysis indicated that 480 DNA markers (out of in total 3360 markers) showed clear variation in presence between individual strains and these were therefore selected for further analysis. Unsupervised statistical analysis of these markers showed the enormous genomic variation within the species but did not show any correlation with a pathogenic phenotype. We therefore used supervised statistical analysis to identify discriminating markers. Genetic programming was used both to identify predictive markers and to define their interrelationships. A model consisting of five mark...Continue Reading

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Citations

Oct 25, 2012·PloS One·Sjoerd M EuserJeroen W Den Boer
Mar 23, 2011·Plant Science : an International Journal of Experimental Plant Biology·Leighton Pritchard, Paul Birch
Sep 4, 2015·Molecular and Cellular Probes·Seung Min KimMin Ja Kim
Mar 14, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ranadip Pal, Sonal Bhattacharya

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