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 Crenigacestat solubility dmso 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 this website 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 selleck compound library 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 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 Quinapyramine 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.