Comparison of genomic and MALDI-TOF MS based proteomic clustering in Enterococcus faecalis

The MALDI-TOF MS identification method is based on the comparison of protein profiles of microorganisms with reference profiles. This technique also enables the determination of phylogenetic relationships, such as similarity and divergence, among different species belonging to the same genus. In this study, the concordance between MALDI-TOF MS-based phyloproteomic analysis and ddl gene-based phylogenetic analysis was evaluated in Enterococcus faecalis strains (n = 13). Genomic and proteomic clustering patterns were comparatively assessed. DNA was extracted from E. faecalis strains obtained from the laboratory strain collection, and the ddl gene was amplified by PCR and subsequently sequenced. In addition, phyloproteomic analyses were performed using MATLAB software based on the data obtained from MALDI-TOF MS analyses. A phylogenetic tree was constructed using the UPGMA method based on the Tamura 3-parameter (T92) model. Clustering patterns of the strains were compared using genomic- and proteomic-based dendrograms. Some strains showing genomic similarity were found to be located in different subclusters in proteomic analyses. The findings demonstrated that protein expression profiles play an important role in strain identification; however, they may not directly reflect the genetic similarity relationships among strains. These results suggest that although genomic- and proteomic-based analyses provide compatible results for strain identification, they may reveal different clustering patterns when evaluating relationships among strains. This study contributes to the comparative evaluation of genomic- and proteomic-based analyses and provides insight into the scope and limitations of these methods.