Application of DNA sequence analysis based on five different conserved genes (16S rDNA, rpoB, gdh, est and pgm) for intra-species discrimination of Bacteroides fragilis

In the past few years, many studies revealed a remarkable genetic variability in Bacteroides fragilis species, and the existence of two divisions was proposed according to presence or absence of the cfiA (metallo-β-lactamase/carbapenemase) gene. The aim of this study was to evaluate the use of DNA sequence analysis for glutamate dehydrogenase (gdh), phosphoglucomutase (pgm) and esterase (est) metabolic genes, in comparison to RNA polymerase β subunit (rpoB) and 16S ribosomal RNA (rrs) gene sequencing, to identify the presence of these two groups in seventeen B. fragilis strains. Based on phylogenetic trees, only the est gene sequences generated a classification similar to rrs- and rpoB-genes. On the other hand, the genes pgm and gdh did not allow the discrimination of these divisions. The est gene sequence can be suggested as an additional tool for differentiation of the two groups in B. fragilis, providing highly reproducible and reliable data in B. fragilis taxonomy.

► The genetic diversity concerning resistance genes cfiA e cepA is remarkable.
► DNA sequence analysis was performed on five loci: rrs, rpoB, est, gdh and pgm.
► est gene sequence is an alternative tool for differentiation of the two groups.