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

Yuan Jin,Jing Zhou,Na Kong,Junjie Yue,Hongguang Ren,Qi Zhang,Long Liang,Jianglin Zhou,Mingda Hu

doi:10.1186/s13062-020-0258-5

Abstract

BackgroundAccurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed.MethodsWe compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering.ResultsWe showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species.ConclusionsThis is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species.ReviewerThis article was reviewed by Dr. Xianwen Ren.

Highlights

Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research
Burkholderia cepacia complex (BCC) is a group of gram-negative bacteria comprising more than 20 valid species names, including B. cepacia, B. multivorans, B. cenocepacia, B. vietnamiensis, B. stabilis, B. ambifaria, B. dolosa, B. anthina, B. pyrrocinia and B. ubonensis, etc. [1,2,3]
Four BCC genomes with a Contig-level assembly were included in our data set because they were assembled from type material and their species did not have a better genomes from the type strain

Summary

Introduction

Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. Burkholderia cepacia complex (BCC) is a group of gram-negative bacteria comprising more than 20 valid species names, including B. cepacia, B. multivorans, B. cenocepacia, B. vietnamiensis, B. stabilis, B. ambifaria, B. dolosa, B. anthina, B. pyrrocinia and B. ubonensis, etc. The B. cepacia complex bacteria have been reported as opportunistic (2020) 15:6 pathogens that caused pneumonia in people with cystic fibrosis (CF) or chronic granulomatous disease [8]. These organisms are associated with accelerated decline in pulmonary functions, increasing morbidity and mortality and reducing survival following lung transplantation [9]. Outbreaks of different BCC species are often reported, and there is a large body of evidence showing that BCC bacteria are capable of patient-to-patient spread [11]

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