The gyrB gene amplification

was done with the primers described earlier [29]. The 25 μl amplification reactions consisted of 0.25 μM of primers, 0.2 mM dNTP, 2.5 U AmpliTaq Gold (Applied Biosystems, Foster City, USA) and 10 × buffer supplied with the enzyme. The thermal cycle consisted of 10 min denaturation at 94°C, followed by 35 cycles of denaturation for 30 s at 94°C, annealing for 30 s at 51°C, and elongation for 30 s at 72°C and finally for 3 min at 72°C. The PCR fragments were sequenced in both directions with an ABI 3730xl DNA GDC-0449 manufacturer Analyzer (Applied Biosystems). The Diversity indexes for each MLST gene were calculated by eBURST v3 [40, 41]. The MLST sequences of 53 Y. enterocolitica strains obtained in the study were deposited to EMBL/GenBank database under the accession numbers HE803367- HE803737. Analysis of the MLST data Population genetic analyses were performed using BAPS (Bayesian Analysis of Population Structure) software [42–44] with the second-order Markov model

and the standard MLST data input option as in, e.g., [45, 46]. The optimal number of clusters was calculated using 10 runs of the estimation selleckchem algorithm with the prior upper bound of the number of clusters varying in the range (5,15) over the 10 replicates. All estimation runs resulted in an identical partition of the sequence type data with 4 clusters (estimated P = 1.000). Admixture analysis was done using 100 Monte Carlo replicates for allele frequencies and by generating 100 reference genotypes to calculate p-values. For reference selleck chemical cases we used 10 iterations in estimation according to the guidelines of [44, 47]. Mosaicism is defined as sequence types composed of sequence characteristic of more than one BAPS group. Significance of admixture or mosaicism was determined for each sequence type using the threshold p < 0.05. Maximum likelihood tree was constructed by using the concatenated sequences under the general time-reversible model as implemented in the MEGA5 software [48]. 16S RNA gene sequencing and tree

construction 16S rRNA gene sequencing was obtained for 36 Y. enterocolitica BT 1A strains with the primers FD1mod [49], pHr, pDf, and pEr [50] in conditions described earlier [22]. The sequences were used to construct a Neighbour-joining dipyridamole tree using Phylip [51]. The 16S rRNA gene sequences of 28 Y. enterocolitica BT 1A strains obtained during this study were deposited to the EMBL/GenBank database under the accession numbers HE803738 – HE803765. Eight of the BT 1A strains were sequenced during our previous studies and have accession numbers FM958217 – FM958223 and FN812721 [27]. ystA and ystB PCR For the ystA gene specific PCR the forward primer 3-ATC GAC ACC AAT AAC CGC TGAG −5 and reverse primer 3- CCA ATC ACT ACT GAC TTC GGCT −5 were used for 38 Y. enterocolitica BT 1A strains.