Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia.

Peter Vandamme,Erin P Price,Charlotte Peeters,Anthony Baker,Derek S Sarovich,Trevor J Hird,Mark Mayo,Aurélien Carlier,Deborah A Henry,Birgit De Smet,Jeffrey Warner,Bart J Currie,James E A Zlosnik

doi:10.3389/fmicb.2017.01679

Abstract

Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154T (=CCUG 65685T). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154T was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway. B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents.

Highlights

A variety of Gram-negative non-fermenting bacteria can colonize the lungs of patients with cystic fibrosis (CF) (Lipuma, 2010; Parkins and Floto, 2015)
The identification of Gram-negative non-fermenting bacteria isolated from respiratory secretions of people with CF may prove challenging, not the least because the CF lung can harbor a range of opportunistic bacteria rarely seen in the general population
The 266152 and type III secretion system based realtime PCR assays (Novak et al, 2006; Price et al, 2012) were negative, which excluded their identification as B. pseudomallei, B. thailandensis, B. humptydooensis or B. oklahomensis

Summary

Introduction

A variety of Gram-negative non-fermenting bacteria can colonize the lungs of patients with cystic fibrosis (CF) (Lipuma, 2010; Parkins and Floto, 2015) The majority of these bacteria are considered opportunists but correct species identification is paramount for the management of infections in these patients. When the genus Burkholderia was created in 1992 it consisted of only seven species which were primarily known as human, animal, and plant pathogens (Yabuuchi et al, 1992). They proved, to be metabolically versatile and biotechnologically appealing, and a large number of novel Burkholderia species were subsequently isolated and formally named. The genus Burkholderia comprises about 100 validly named species and many uncultivated candidate species, which occupy extremely diverse ecological niches (Coenye and Vandamme, 2003; Compant et al, 2008; Suarez-Moreno et al, 2012)

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Results

Conclusion