Open Access Research article

Molecular typing and epidemiological investigation of clinical populations of Pseudomonas aeruginosa using an oligonucleotide-microarray

Annalisa Ballarini1*, Giovanna Scalet12*, Malgorzata Kos1, Nina Cramer3, Lutz Wiehlmann3 and Olivier Jousson1

Author Affiliations

1 Centre for Integrative Biology, University of Trento, Trento, Italy

2 Department of Pathology and Diagnostics, University of Verona, Verona, Italy

3 Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany

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BMC Microbiology 2012, 12:152  doi:10.1186/1471-2180-12-152

Published: 27 July 2012

Additional files

Additional file 1:

Database of the 124P. aeruginosaindependent isolates within our collection. The database shows the clinical data of the 124 independent P.aeruginosa isolates and presence/absence of accessory genome genes/islands based on microarray typing. On the right, the corresponding AT- and MLST-genotype are provided, as well as the clone cluster ID, according to each of the three genotyping technique employed. ND = not defined; SC = single clone; SP = single pulsotype.

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Additional file 2:

PFGE dendrogram with assignment of genetically related clones of 162 P. aeruginosaisolates of our strain collection. The UPGMA dendrogram includes a selection of the 124-independent isolates analyzed by microarray typing (in square boxes). The red line represents the 85% similarity value and the square brackets indicate the different clusters identified according to Tenover criteria [32].

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Additional file 3:

Correlation between microarray typing and PFGE typing. Multi-isolates AT-genotypes are listed in the first column. The distribution of the isolates of each multi-isolate AT-genotype among PFGE pulsotypes is shown in each lane. The frequency data and number of isolates refers exclusively to independent isolates.

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Additional file 4:

MLST single allele and allelic profile data for all 80 typed isolates. The database shows for each isolate typed by MLST single allele and allelic profile. Medium-quality allele sequences were not determined (n.d.). Novel allele types and allelic profiles are defined as NEW. The clonal complex corresponding to each ST was added, when available. All data were obtained by comparison to the MLST Public Database (pubmlst.org/paeruginosa).

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Additional file 5:

Distribution of the 41 AT-genotypes identified among hospital locations. Venn’s diagram of the AT-genotype distribution among the three hospital locations: Verona, Rovereto, and Trento. Distributions were calculated from the 124 independent P. aeruginosa isolates of our collection. (PNG 25 kb)

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Additional file 6:

Cluster of AT-clones identified including all available AT-typedP. aeruginosaclinical populations. Cluster of clones were identified by eBurst analysis of our AT-genotypes together with 4 published AT-databases [7,14,15,17]. The colour code indicates the AT-genotypes of our strain collection and for each genotype the% of isolates associated to chronic or acute infections. Novel clones (not described in other studies) are highlighted by a rectangular box. Clones predicted by eBURST as group primary founders are underlined.

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