The remaining 34 isolates were defined as new by the MLST Public Database (pubmlst.org/paeruginosa) (see Additional file 4). However, these 34 new MLST-profiles included 4 profiles deriving from a combination of known alleles not described in the public CP-690550 database, 10 profiles due to the presence of at least one novel allele, and the remaining 20 profiles with medium-quality sequence within one or multiple alleles, for which the allele type could not be univocally determined. Excluding the two isolates with > 2 alleles with medium-quality

sequences, overall 48 MLST STs could be identified among the remaining 78 isolates, the majority of which were single-isolate ST groups (81.3%). The AT-approach identified within the same set TH-302 of isolates a smaller number of AT-genotypes, precisely 24, more than half of which (54.2%) with multiple isolates (see Additional file 1). This data suggested a higher discriminatory power of MLST in comparison to AT-typing, which could be explained by the much higher information content of sequence data on the 7 MLST-marker genes versus presence/absence of polymorphisms in single nucleotides within the 13 ArrayTube SNPs-markers. The Simpson’s index of diversity (DI), calculated on all 78 isolates, was indeed

higher for MSLT than AT microarray typing (DI = 0.966 for MLST (0.946–0.987 95% CI); DI = 0.924 for AT (0.894–0.954 95% CI)), indicating a higher discriminatory ability of MLSTversus AT. However, the difference in discrimination ability was lower than for PFGE versus AT. Also, the global congruence between MLST and AT (adjusted Rand coefficient = 0.559 (95% CI)) was higher than for PFGE versus AT. Focusing on the 3 AT-groups with the most MLST-typed isolates, i.e. F469, 4B9A and EC2A, we observed

that within each of these groups, more than 62% of the isolates (68.8% for the F469 group, 62.5% for 4B9A and 75.0% for EC2A) had an identical MLST-profile, whereas the other isolates differed for 1 to 3 MLST-alleles from the SHP099 nmr dominant clone of the group. By computing the genetic distances between the MLST DNA sequences of the three AT-types, we observed that highest genetic distance was equivalent Metformin to 0.286 (isolate VRPS110) within the F469-group, 0.429 (isolate VRPS97) in the 4B9A-group and 0.143 (isolate FC17) within the EC2A-group (see Figure 1). Figure 1 Genetic distances between MLST DNA sequences within AT-groups. The genetic distance between MLST DNA sequences is shown for AT-groups F469, 4B9A and EC2A. Each graph represents on the horizontal axis the genetic distance to the dominant MLST-ST within the AT-group and, on the vertical axis, the absolute frequency of each ST. Looking at the three larger AT-groups, the exclusion of all isolates with medium-quality allele sequences increased the number of isolates with identical MLST ST within each group. In detail, all 11 isolates from the F469 group had an identical MLST-profile, i.e.