Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.

Abstract

The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database.

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

“…3 and 5), indicating that they were previously misidentified and BCC26 should represent a putative novel species. Cluster BCC29 was represented by B. pyrrocinia DSM 10685 T and contained another strain (LA20W) that was previously misidentified as B. stabillis, which is also supported by another study [1]. Core genome phylogeny and dDDH/ANI similarity suggests that strain previously named as B. stabillis FERMP-21014 in BCC29 also should be reclassified as B. pyrrocinia, because it shared a middle dDDH value of 49.4% and ANI value of 93.3% with B. stabillis ATCC BAA-67 T that both lower than species delineation threshold.…”

“…Two isolates previously identified as B. cenocepacia, DDS 22E-1 and DWS 37E-2, are more likely to be B. pseudomultivorans and B. latens, respectively. B. stabilis LA20W seems to be more similar to the type strain B. pyrrocinia than B. stabilis, which was also confirmed by another study [1]. Two additional strains, LO6 and DDS 7H-2, were previously identified as B. cepacia and probably belong to B. dolosa and B. cenocepacia, respectively.…”

“…Examples are shown by B. contaminans, B. lata (former taxon K), B. stagnalis, B. territorii (former group B and L), and the recently described B. catarinensis (formerly Burkholderia sp. 89) [1,19,20]. Hence, these clusters or putative novel species, at least somewhat, might be formally described and validly named in the near future.…”

“…Our inferred species tree of BCC reconstructed by these markers provided us with an accurate phylogenetic relationship. Together with dDDH and ANI, two methods that are useful for species demarcation and are powerful in BCC species differentiation [1,64,65], we delineated BCC species as 36 clusters. The results showed that the 22 currently known species correspond to 22 of these clusters (Fig.…”

Burkholderia multivorans septicemia in a pediatric liver transplant patient

“…The Burkholderia cepacia complex (Bcc), consisting of 22 species, is a group of aerobic, gram‐negative, non–spore‐forming bacilli that are phenotypically similar but genotypically distinct . Bcc are well recognized opportunistic pathogens associated with high morbidity and mortality in persons with cystic fibrosis (CF) .…”