Scanning of bacterial genomes to identify essential genes is of biological interest, for understanding the basic functions required for life, and of practical interest, for the identification of novel targets for new antimicrobial therapies. In particular, the lack of efficacious antimicrobial treatments for infections caused by the Burkholderia cepacia complex is causing high morbidity and mortality of cystic fibrosis patients and of patients with nosocomial infections. Here, we present a method based on delivery of the tightly regulated rhamnose-inducible promoter P rhaB for identifying essential genes and operons in Burkholderia cenocepacia. We demonstrate that different levels of gene expression can be achieved by using two vectors that deliver P rhaB at two different distances from the site of insertion. One of these vectors places P rhaB at the site of transposon insertion, while the other incorporates the enhanced green fluorescent protein gene (e-gfp) downstream from P rhaB . This system allows us to identify essential genes and operons in B. cenocepacia and provides a new tool for systematically identifying and functionally characterizing essential genes at the genomic level.As the number of sequenced bacterial genomes rapidly expands, there is increased interest in learning how many and which of the annotated open reading frames (ORFs) fall into the category "essential." Essential genes encode functions that are absolutely required for growth or viability (38). The discovery of novel essential genes not only contributes to the unraveling of previously unrecognized, essential cellular functions but also may help in identifying novel targets for new antibacterial molecules (16,40).Despite vast differences in size and gene repertories among bacterial genomes, a substantial number of essential genes appears to be conserved (24), suggesting that a core set of genes encodes key cellular functions (18). Methods of scanning microbial genomes for essential genes include direct gene disruption strategies such as random transposition (1,17,23,43) and systematic gene-by-gene inactivation (26,29,46). This approach does not consider that many essential genes exist in operons (11,35), and it has the potential to lead to incorrect classifications of nonessential genes as essential due to polar effects in operons containing a mixture of both essential and nonessential genes. This was experimentally assessed by Thanassi et al. (46), who found that 42% of the putative essential genes identified in Streptococcus pneumoniae were misidentified as such due to polar inactivation of true essential genes downstream. Furthermore, recent work has shown not only that essential genes are more likely to exist within operons than are nonessential genes (11, 35) but also that essential genes with related functions have a strong tendency to cluster even when they are not organized in operons (35).Another general strategy for identifying essential genes is functional suppression either by antisense mRNA induction (15,49) or by the trans...