Abstract
The genus Burkholderia contains large number of diverse species which include many clinically important organisms, phytopathogens, as well as environmental species. However, currently, there is a paucity of biochemical or molecular characteristics which can reliably distinguish different groups of Burkholderia species. We report here the results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus Burkholderia. In phylogenetic trees based upon concatenated sequences for 21 conserved proteins as well as 16S rRNA gene sequence based trees, members of the genus Burkholderia grouped into two major clades. Within these main clades a number of smaller clades including those corresponding to the clinically important Burkholderia cepacia complex (BCC) and the Burkholderia pseudomallei groups were also clearly distinguished. Our comparative analysis of protein sequences from Burkholderia spp. has identified 42 highly specific molecular markers in the form of conserved sequence indels (CSIs) that are uniquely found in a number of well-defined groups of Burkholderia spp. Six of these CSIs are specific for a group of Burkholderia spp. (referred to as Clade I in this work) which contains all clinically relevant members of the genus (viz. the BCC and the B. pseudomallei group) as well as the phytopathogenic Burkholderia spp. The second main clade (Clade II), which is composed of environmental Burkholderia species, is also distinguished by 2 identified CSIs that are specific for this group. Additionally, our work has also identified multiple CSIs that serve to clearly demarcate a number of smaller groups of Burkholderia spp. including 3 CSIs that are specific for the B. cepacia complex, 4 CSIs that are uniquely found in the B. pseudomallei group, 5 CSIs that are specific for the phytopathogenic Burkholderia spp. and 22 other CSI that distinguish two groups within Clade II. The described molecular markers provide highly specific means for the demarcation of different groups of Burkholderia spp. and they also offer novel and useful targets for the development of diagnostic assays for the clinically important members of the BCC or the pseudomallei groups. Based upon the results of phylogenetic analyses, the identified CSIs and the pathogenicity profile of Burkholderia species, we are proposing a division of the genus Burkholderia into two genera. In this new proposal, the emended genus Burkholderia will correspond to the Clade I and it will contain only the clinically relevant and phytopathogenic Burkholderia species. All other Burkholderia spp., which are primarily environmental, will be transferred to a new genus Paraburkholderia gen. nov.
Highlights
The genus Burkholderia is a morphologically, metabolically, and ecologically diverse group of gram-negative bacteria (Yabuuchi et al, 1992; Coenye and Vandamme, 2003; Mahenthiralingam et al, 2005; Palleroni, 2005; Compant et al, 2008)
In this work we have produced a maximum likelihood (ML) phylogenetic tree based on the concatenated amino acid sequences of 21 conserved housekeeping and ribosomal proteins obtained from 45 sequenced Burkholderia species (Figure 1)
The genus contains a variety of bacteria that inhabit a wide range of ecological niches including a number of bacteria that have pathogenic potential (Yabuuchi et al, 1992; Coenye and Vandamme, 2003; Mahenthiralingam et al, 2005; Palleroni, 2005; Compant et al, 2008)
Summary
The genus Burkholderia is a morphologically, metabolically, and ecologically diverse group of gram-negative bacteria (Yabuuchi et al, 1992; Coenye and Vandamme, 2003; Mahenthiralingam et al, 2005; Palleroni, 2005; Compant et al, 2008). Burkholderia species are ubiquitous in the environment (Coenye and Vandamme, 2003). They inhabit a wide range of ecological niches, ranging from soil to the human respiratory tract (Coenye and Vandamme, 2003). A group of 17 closely related Burkholderia species, the Burkholderia cepacia complex (BCC), are responsible for prevalent and potentially lethal pulmonary infections in immunocompromised individuals, such as individuals with cystic www.frontiersin.org. Burkholderia pseudomallei, a Burkholderia species related to the BCC, is the causative agent for the disease melioidosis, a potentially lethal septic infection which accounts for up to 20% of all community-acquired septicemias in some regions (White, 2003; Limmathurotsakul and Peacock, 2011). Other species related to the BCC are the causative agents of major infections in both animals (Burkholderia mallei) and plants (Burkholderia glumae and Burkholderia gladioli) (Whitlock et al, 2007; Nandakumar et al, 2009)
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