Phylogenetic analysis of Calymmatobacterium granulomatis based on 16S rRNA gene sequences

Abstract

Calymmatobacterium granulomatis is the aetiological agent of granuloma inguinale -a chronic granulomatous genital infection -and is morphologically similar to members of the genus Klebsiella. This study determined the 16s rRNA gene sequence of C. granulomatis and the taxonomic position of the organism in relation to the genus Klebsiella. Genomic DNA was extracted from C. granulomatis-infected monocytes and from frozen and formalin-fixed paraffin wax-embedded tissue biopsy specimens from patients with histologically proven granuloma inguinale. The 16s rDNA was amplified by PCR with broad range oligonucleotide primers. The amplified DNA fragments were cloned into PMOS vector, digested with Bum HI and Pstl restriction endonucleases, hybridised with a gram-negative bacterial probe (DL04), sequenced in both directions by the automated ALFTM DNA sequencer, verified on an ABI Prism 377 automated sequencer and analysed with DNASIS and MEGA software packages. Sequence analysis revealed DNA homology of 99% in C. granulomatis from the different sources, supporting the belief that the bacteria in the culture and the biopsy specimens belonged to the same species, although there was some diversity within the species. Phylogenetically, the strains were closely related to the genera Klebsiella and Enterobacter with similarities of 95% and 94% respectively. C. granulomatis is a unique species, distinct from other related organisms belonging to the y subclass of Proteobacteria.

Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping.

“…Altogether, at least seven distinct sequence clusters can be distinguished in Klebsiella. Whether the newly described Klebsiella granulomatis species (Carter et al, 1999 ;Kharsany et al, 1999) belongs to one of the K. pneumoniae groups identified herein, or to a new cluster, remains to be determined. Moreover, additional sampling within K. pneumoniae and K. oxytoca, for example with isolates from outside Europe and from other ecological environments, may well lead to the identification of additional clusters.…”

Phylogenetic Relationships of Bacteria with Special Reference to Endosymbionts and Enteric Species

“…And for those enteric genera containing but a single species [e.g., Calymmatobacterium (Kharsany et al 1999), Candidatus (Zreik et al 1998) and Hafnia (Hauben et al 1998, Sproer et al 1999, their relationships to other members of the Enterobacteriaceae (as well as their identification as unique genera) has typically been established by the analysis of SSU rRNA sequences.…”

Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov.

“…The last two of these species were subsequently combined as K. planticola on the basis of their extensive DNA-DNA homology (Gavini et al, 1986). Finally, Calymmatobacterium granulomatis, the presumed causative agent of donovanosis, was recently reclassified as Klebsiella granulomatis on the basis of phylogenetic data (Kharsany et al, 1999 ;Carter et al, 1999). The latest edition of (Ørskov, 1984) classified the genus Klebsiella into five species, namely K. pneumoniae, Klebsiella oxytoca, K. terrigena, K. ornithinolytica and K. planticola.…”