FIG. 1.

Phylogenetic tree from concatenated sequences of MLST loci excepting ddl. The tree shows the relationships between the pneumococcal reference set (indicated by open circles) and nontypeable isolates (closed circles). Nontypeable isolates that had the same ST as members of the reference set are shown in gray. Group 1 contains the reference set of pneumococci and all nontypeable strains clustering with them. Group 1b is defined in the text. Group 2 contains the remaining nontypeable isolates, indicated with the prefix NT in Table 1. Trees were generated using MrBayes as described in Materials and Methods, using all nucleotide sites. The scale bar indicates substitutions per site. The asterisk marks the node that is considered to separate authentic pneumococci from group 2 isolates.