25 U GoTaq Polymerase (Invitrogen, Carlsbad, California). The same PCR program was used consisting of 30 cycles of denaturation at 95°C for 1 min, annealing at 55°C for 30 sec, and primer extension at 72°C for 1 min. Followed by 10 min incubation at 72°C to complete extension. Data analysis Statistical association between serotypes, PFGE clusters, antimicrobial Combretastatin A4 resistance or endonuclease restriction phenotype and pherotype where

characterized by odds ratios (OR) with 95% confidence intervals (CI) computed through the Fisher method implemented in the epitools package for the R language. OR significance was evaluated with the Fisher exact test. The resulting p-values were corrected for multiple testing by controlling the False Discovery Rate (FDR) under or equal to 0.05 through the linear procedure of Benjamini and Hochberg [55]. Wallace coefficients (W) and respective 95% confidence intervals were computed as previously described [26, 27]. The relationship between cross-pherotype pair frequency and the number of divergent alleles between STs was validated for statistical significance by permutation tests. The https://www.selleckchem.com/products/arn-509.html latter consisted in repeating the computation of frequencies of cross-pherotype strain pairs for 1,000 times, randomly

shuffling the pherotype assignment of the strains before each repetition. The p-values were obtained from the fraction of the 1,000 random runs where the cross-pherotype pair frequency was lower than the respective values with the correct pherotype assignment. A permutation Foretinib test was Amobarbital also performed to evaluate the significance of the probability that a divergent allele in an SLV pair was donated from a strain with a different pherotype. In this case, in each of the 1,000 runs, the divergent allele was randomly sampled from the corresponding locus in the collection of STs. The determination of π, FST, K*ST and Snn for the analysis of sequence data was done using the DNASP v4.50.3 program. The values of K*ST and Snn were used to assess population differentiation in combination with permutation tests (1,000 permutations). Neutral Multilocus Infinite Allele Model The model

presented by Fraser et al. [36] was expanded to include an additional CSP locus and a new IPR parameter. The CSP locus has only two possible alleles, CSP-1 and CSP-2 that can interchange by recombination but are not affected by mutations. The parameter IPR defines the inter-pherotype recombination probability. The model was simulated with the parameter values determined in [36] for the pneumococcal population. Namely, the population size was 1,000, the population mutation and recombination rates were 5.3 and 17.3, respectively. All the analyses were repeated with a population recombination rate reduced in 50% and the results were qualitatively similar. All simulations were run for 1,000 generations, after which the sequence type diversity was stable, as measured by the Simpson’s index of diversity [56].