e Burkholderia cenocepacia is an emerging opportunistic pathogen causing life-threatening infections in immunocompromised individuals and in patients with cystic fibrosis, which are often difficult, if not impossible, to treat. Understanding the genetic basis of virulence in this emerging pathogen is important for the development of novel treatment regimes. Generation of deletion mutations in genes predicted to encode virulence determinants is fundamental to investigating the mechanisms of pathogenesis. However, there is a lack of appropriate selectable and counterselectable markers for use in B. cenocepacia, making its genetic manipulation problematic. Here we describe a Gateway-compatible allelic exchange system based on the counterselectable pheS gene and the I-SceI homing endonuclease. This system provides efficiency in cloning homology regions of target genes and allows the generation of precise and unmarked gene deletions in B. cenocepacia. As a proof of concept, we demonstrate its utility by deleting the Bcam1349 gene, encoding a cyclic di-GMP (c-di-GMP)-responsive regulator protein important for biofilm formation.
Burkholderia cenocepacia is a member of a group of closely related Gram-negative bacteria referred to as the Burkholderia cepacia complex (Bcc). The Bcc contains at least 18 different species that thrive in diverse ecological niches, including clinical, industrial, and natural environments. These bacteria possess very large genomes separated into multiple replicons and hence are considered one of the most versatile groups of Gram-negative bacteria (1, 2). Some Bcc species have biotechnological potential for use in processes such as the enhancement of plant growth or breakdown of pollutants, while others are opportunistic pathogens causing life-threatening infections in immunocompromised individuals and in patients with cystic fibrosis (CF) (3). Although all members of the Bcc have been isolated from CF patients, B. cenocepacia accounts for the majority of these isolates, comprising the most virulent and transmissible strains associated with a poor clinical course and a high mortality rate (4). Therefore, research on the virulence mechanisms of Bcc bacteria has focused largely on B. cenocepacia.The genomes of several B. cenocepacia strains have recently been sequenced (5-7), enabling bioinformatics-based predictions of virulence determinants in this pathogen. Although a number of genes associated with virulence in B. cenocepacia have been identified (4, 8, 9) and tested in various infection models (10, 11), it seems likely that the list of genes implicated in virulence is far from complete and will expand with genetic tools becoming available to manipulate B. cenocepacia strains. The deletion of genes potentially associated with virulence is a powerful way to investigate their function in bacterial physiology and pathogenesis. Most of the virulence traits of B. cenocepacia, such as antibiotic resistance, motility, biofilm formation, cell invasion, and intracellular survival, are multifactorial, ...