PMC5680771_01
Phylogenetic analysis and population genetic structure of Sequences Type (ST) 1 and related STs. a Maximum-likelihood tree based on the concatenated alignment of the seven housekeeping genes used in the MLST scheme. For phylogenetic reconstructions, sequences of the total STs reported for the clade (associated with hypervirulent strains) and representative STs of the other CD clades (selected under the criteria described in Additional file 1) were used. The red points represent Bootstraps > 80%. The ST-1 (isolates from this study) has been marked with a red asterisk. b Population genetic structure of clonal complex 1, based on the eBURST algorithm. Each box represents the Sequence Type, with the founder STs marked in yellow. A red circle was used to mark the node where the ST-1 is a founder
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Fig1
In the case of C2, it could be identified that 60 STs are grouped in 30 clusters (BT >= 80), and that it is closely related to C1 (Fig. 1a). For this CC1, the predicted founding genotype is ST-3, and in the case of ST-1 it is identified as a founding subgroup for STs: 197, 371, 417 and 418 (Fig. 1b). 
Amplification profiles of the coding regions for the toxins. a Amplification profiles of encoding regions for the major clostridial toxins, located within the PaLoc. b Amplification profiles of coding regions for the binary toxin subunits, located within the CdtLoc. Black rectangles represent a positive result for each test, while white rectangles a negative result
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Fig2
The scheme for describing the toxigenic profile proposed by Griffiths et al. was implemented, which targets the identification of genes encoding the major toxins (tcdA and tcdB), and their negative regulator (tcdC). The results showed that only two of the isolates (Gcol.49 and Gcol.91) were positive for the tcdA and tcdB genes, and the negative tcdC regulator (Fig. 2a). We found that all isolates were positive for the cdtB region, whereas only two (Gcol.51 and Gcol.52) were positive for cdtA (Fig. 2b). 
Evaluation of antibiotic resistance markers a and b Phylogenetic reconstructions inferred by the maximum-likelihood method from alignments of the alleles reported for the gyrA and gyrB genes, respectively, associated with quinolone resistance. c Amplification profiles of loci associated with resistance to erythromycin and clindamycin (ermB) and tetracycline (tet), as well as detection of Tn5397 and Tn916-like elements. In a and b, the red arrows show the allele that carry the isolates for each of the genes. In c, the black rectangles represent a positive result for each test, while white rectangles a negative result
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Fig3
This approach identified 18 clades for gyrA (Fig. 3a), while 16 were identified for gyrB (Fig. 3b). These are described in Fig. 3c.