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

Abstract

BackgroundDiscrimination 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.ResultsMicroarray 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 markers was developed that together correctly predicted 100% of the clinical strains and 69% of the environmental strains.ConclusionsA novel approach for identifying predictive markers enabling discrimination between clinical and environmental isolates of L. pneumophila is presented. Out of over 3000 possible markers, five were selected that together enabled correct prediction of all the clinical strains included in this study. This novel approach for identifying predictive markers can be applied to all bacterial species, allowing for better discrimination between strains well equipped to cause human disease and relatively harmless strains.

Genome Analysis of Legionella pneumophila Strains Using a Mixed-Genome Microarray

“…A supervised statistical analysis using Genetic Programming was used to identity DNA markers that could discriminate between clinical and environmental Legionella strains, and a model consisting of five markers was developed to predict the origin of a strain: clinical or environmental. The final model correctly predicted 100% of the clinical strains and 69% of the environmental strains [12]. Despite these promising results, there might be other methodological approaches that could lead to (at least) comparable predictive performances.…”

“…Together with the implementation of new governmental laws and guidelines to prevent growth of Legionella bacteria in potential sources, it was attempted to diminish the overall impact of Legionnaires’ disease in the Netherlands. Nevertheless, despite these excessive efforts the incidence of Legionnaires’ disease has only increased since 1999 [11] .This unexpected trend might partly be due to the unfocussed broad scope of preventive measures that do not take virulence factors into account [12] – [14] . Previous studies have shown that the majority (>90%) of Legionnaires’ disease cases are caused by the species Legionella pneumophila , and about 80% more specifically by L. pneumophila serogroup 1 [15] , [16] .…”

Prediction of the origin of French Legionella pneumophila strains using a mixed-genome microarray

“…The mixed-genome microarray used in this study has been described elsewhere, and was developed using a systematic collection of Dutch Legionella strains [19]. In short, four clinical Legionella isolates and four environmental L .…”

Microbial Growth in Drinking-Water Supplies: Problems, Causes, Control and Research Needs

“…Despite the positive PCR results, L. pneumophila could not be cultivated from the same water sample on a selective agar medium (buffered charcoal yeast extract agar) for Legionella. The discrepancy between the qPCR and cultivation results can be caused by several factors: (i) the observed mip gene of L. pneumophila came from dead L. pneumophila cells, (ii) not all L. pneumophila strains in drinking water can be cultivated on the selective agar medium or (iii) the agar plates were overgrown with other Legionella species, preventing the detection of L. pneumophila. The consequence of these findings for public health remains uncertain, also because not all L. pneumophila strains are pathogenic (Yzerman et al 2010).…”