Typing of Candida glabrata in clinical isolates by comparative sequence analysis of the cytochrome c oxidase subunit 2 gene distinguishes two clusters of strains associated with geographical sequence polymorphisms

We tested whether comparative sequence analysis of the mitochondrion-encode d cytochrome c oxidase subunit 2 gene (COX2) could be used to distinguish i ntraspecific variants of Candida glabrata. Mitochondrial genes are suitable for investigation of close phylogenetic relationships because they evolve much faster than nuclear genes, which in general exhibit very limited intra specific variation. For this survey me used 11 clinical isolates of C. glab rata from three different geographical locations in Brazil, 10 isolates fro m one location in the United States, 1 American Type Culture Collection str ain as an internal control, and the published sequence of strain CBS 138. T he complete coding region of COX2 was amplified from total cellular DNA, an d both strands were sequenced twice for each strain. These sequences were a ligned with published sequences from other fungi, and the numbers of substi tutions and phylogenetic relationships were determined. Typing of these str ains was done by using 17 substitutions, with 8 being nonsynonymous and 9 b eing synonymous. Also, cDNAs made from purified mitochondrial polyadenylate d RNA were sequenced to confirm that our sequences correspond to the expres sed copies and not nuclear pseudogenes and that a frameshift mutation exist s in the 3' end of the coding region (position 673) relative to the Sacchar omyces cerevisiae sequence and the previously published C. glabrata sequenc e. We estimated the average evolutionary rate of COX2 to be 11.4% sequence divergence/10(8) Sears and that phylogenetic relationships of yeasts based on these sequences are consistent with rRNA sequence data. Our analysis of COX2 sequences enables typing of C. glabrata strains based on 13 haplotypes and suggests that positions 51 and 519 indicate a geographical polymorphis m that discriminates strains isolated in the United States and strains isol ated in Brazil. This provides for the first time a means of typing of Candi da strains that cause infections by use of direct sequence comparisons and the associated divergence estimates.