aeruginosa isolates were collected from three Italian hospitals, located in Rovereto, Trento, and Verona. All strains were typed with the ArrayTube (AT), a DNA-based multimarker microarray. The AT array design and array experiments are available in the ArrayExpress database AZD1390 mouse (http://www.ebi.ac.uk/arrayexpress) under accession numbers E_MTAB_1108 and A-MEXP-2179, respectively. Excluding all isolates with identical AT-profile collected from individual patients, although from different body sites, 124 independent-strains could be selected.
Besides AT-typing, PFGE and MLST were performed on up to 105 strains of our collection, for comparison purposes. The LXH254 in vitro AT-genotypes and virulence markers profiles, PFGE-clone types and MLST genotypes are provided as supplementary material (Additional file 1). Concerning the AT-dataset, the AT-genotype was derived from the 13 SNPs markers plus the fliCa/b multiallelic locus and the exoS/exoU markers, as described by Wielhmann and collaborators [7]. Isolates with identical AT-genotype (i.e. identical
hexadecimal code) and also identical pattern of AT virulence markers were defined as AT-clones, since they are genetically indistinguishable according to the AT approach. Isolates with identical AT-genotype but different pattern of virulence markers were referred to as isolates belonging to the Trichostatin A in vitro same AT-clonal complex. Finally, isolates with different AT-genotypes but related, according to eBURST analysis, were defined as isolates belonging to the same AT-cluster of clones [7]. The AT-genotyping analysis revealed that the 182 collected strains belonged to 41 different AT-genotypes. The relative low genomic variation observed in strain-specific regions within the core genome was concordant Inositol oxygenase with the high genetic conservation previously found by genomic sequencing for P. aeruginosa strains [19]. Each clonal complex, i.e. group of isolates with identical AT-genotype, comprised 3.0 +/− 5.1 isolates. A set of strains of our collection was analyzed also with two genotyping techniques commonly used in microbiology, which are renowned as high resolution reference methods,
i.e. pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) [1]. Comparison with these techniques was performed to gain insights into differences/similarities between approaches and to verify results of previous research groups underlining the feasibility of the AT approach for epidemic strains [18]. The PFGE/SpeI typing was performed on 105 independent strains of our collection, and resolved 77 different fingerprints, defined as different PFGE clones or pulsotypes (Additional file 2), against the 32 AT-genotypes identified by microarray typing within the same set of isolates. Only 24.0% PFGE/SpeI clones appeared to be clonal complexes, according to the phylogenetic analysis, whereas AT-typing identified 15 multi-isolates AT-genotypes out of 32 (42.9%).