Summary: As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases. It contains continually updated, curated and tracked information about Burkholderia cepacia complex genome annotations, plus other Burkholderia species genomes for comparison, providing a high-quality resource for its targeted cystic fibrosis research community.Availability: http://www.burkholderia.com. Source code: GNU GPL.Contact: brinkman@sfu.ca.

Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license.

Pseudomonas aeruginosa strains isolated from patients with persistent lung infections and cystic fibrosis have been found to gradually develop aminoglycoside resistance over time. The aim of this study was to identify potential contributors to low-level aminoglycoside resistance, which may cause such graduated increases in resistance. The Harvard P. aeruginosa PA14 nonredundant library, consisting of approximately 5,800 mutants, was screened for twofold or greater increases in tobramycin resistance. Mutants carrying mutations in a total of 135 unique genes were identified and confirmed to have reduced susceptibility to tobramycin. Many of these genes were involved predominantly in energy metabolism; however, most of these mutants did not exhibit growth defects under the conditions tested, although some exhibited the small-colony phenotype and/or defects in growth under anaerobic conditions. Lipopolysaccharide mutants were also identified, and it was found that tobramycin had a reduced ability to permeabilize the outer membranes of these mutants. The results of this study emphasize the complexity of the interactions that tobramycin may have within the bacterial cell and introduce a large number of novel genes which may play a role in tobramycin resistance.The majority of deaths of cystic fibrosis patients can be attributed to the progressive deterioration of lung function resulting from chronic infection by pathogens such as Pseudomonas aeruginosa (25). Antibiotic treatment of such chronic infections may temporarily suppress symptoms; however, it does not eradicate the pathogen. To overcome the inability of orally and parenterally administered antibiotics to adequately penetrate lung tissue and secretions, the aerosolized aminoglycoside tobramycin was formulated to directly target the site of infection. Clinical trials of aerosolized tobramycin revealed that long-term use of the agent against P. aeruginosa results in small, graduated increases in tobramycin MICs upon repeated isolation of the organism (21, 22), although the mechanisms contributing to this resistance have yet to be described.Tobramycin is a bactericidal agent that targets the 30S ribosome and interferes with protein synthesis. Uptake occurs in three phases: an initial, reversible ionic-binding phase, a phase of slow energized uptake, and finally a phase of very rapid energy-dependent uptake (2, 4, 9). Despite the traditionally held view that antibiotic action can be simplified to interaction with a single target, it is evident that aminoglycosides exert pleiotropic effects on the cell (8, 9), as these effects may be antagonized by a variety of compounds known to affect cellular metabolic processes. Furthermore, the bactericidal nature of aminoglycosides such as tobramycin cannot be accounted for simply by protein synthesis inhibition or misreadings during translation because other protein synthesis inhibitors, such as chloramphenicol, and agents that promote misreading, including modified amino acids, are bacteriostatic. A limited number of cytoch...

Pseudomonas aeruginosa offers substantial therapeutic challenges due to its high intrinsic resistance to many antibiotics and its propensity to develop mutational and/or adaptive resistance. The PA14 comprehensive mutant library was screened for mutants exhibiting either two-to eightfold increased susceptibilities (revealing genes involved in intrinsic resistance) or decreased susceptibilities (mutational resistance) to the fluoroquinolone ciprofloxacin. Thirty-five and 79 mutants with increased and decreased susceptibilities, respectively, were identified, as confirmed by broth dilution.