The Burkholderia cepacia complex (Bcc) is a collection of genetically distinct but phenotypically similar bacteria that are divided into at least nine species. Bcc bacteria are found throughout the environment, where they can have both beneficial and detrimental effects on plants and some members can also degrade natural and man-made pollutants. Bcc bacteria are now recognized as important opportunistic pathogens that can cause variable lung infections in cystic fibrosis patients, which result in asymptomatic carriage, chronic infection or 'cepacia syndrome', which is characterized by a rapid decline in lung function that can include invasive disease. Here we highlight the unique characteristics of the Bcc, focusing on the factors that determine virulence.

Bacterial pathogens evolve during the infection of their human hosts1-8, but separating adaptive and neutral mutations remains challenging9-11. Here, we identify bacterial genes under adaptive evolution by tracking recurrent patterns of mutations in the same pathogenic strain during the infection of multiple patients. We conducted a retrospective study of a Burkholderia dolosa outbreak among people with cystic fibrosis, sequencing the genomes of 112 isolates collected from 14 individuals over 16 years. We find that 17 bacterial genes acquired non-synonymous mutations in multiple individuals, which indicates parallel adaptive evolution. Mutations in these genes illuminate the genetic basis of important pathogenic phenotypes, including antibiotic resistance and bacterial membrane composition, and implicate oxygen-dependent gene regulation as paramount in lung infections. Several genes have not been previously implicated in pathogenesis, suggesting new therapeutic targets. The identification of parallel molecular evolution suggests key selection forces acting on pathogens within humans and can help predict and prepare for their future evolutionary course.

Infection with

Cystic fibrosis (CF) patients are hypersusceptible to chronic Pseudomonas aeruginosa lung infections. Cultured human airway epithelial cells expressing the ΔF508 allele of the cystic fibrosis transmembrane conductance regulator (CFTR) were defective in uptake of P. aeruginosa compared with cells expressing the wild-type allele. Pseudomonas aeruginosa lipopolysaccharide (LPS)-core oligosaccharide was identified as the bacterial ligand for epithelial cell ingestion; exogenous oligosaccharide inhibited bacterial ingestion in a neonatal mouse model, resulting in increased amounts of bacteria in the lungs. CFTR may contribute to a host-defense mechanism that is important for clearance of P. aeruginosa from the respiratory tract.Among the most serious manifestations of CF are chronic pulmonary infections with the bacterium P. aeruginosa. The basis for hypersusceptibility of CF patients to this bacterium is not well understood, and the role of mutant CFTR, if any, is not clear. Binding and internalization of respiratory pathogens by epithelial cells followed by desquamation could be an important mechanism for clearing bacteria from the lung. This mechanism has been shown to be important in protecting against bladder infections (1).To investigate whether the most common and severe CFTR mutation (ΔF508) affected uptake of P. aeruginosa, we performed bacterial invasion assays (2) with four cell lines: CFT1, an airway epithelial cell line derived from a CF patient homozygous for ΔF508 CFTR and that is transformed with human papilloma virus 18 E6/E7; CFT1-ΔF508, which expresses a third copy of ΔF508 CFTR introduced by a retrovirus; CFT1-LC3, which expresses a control gene (β-galactosidase) introduced by the same retrovirus; and CFT1-LCFSN, which expresses a functional wild-type human CFTR gene (3). We tested a standard laboratory strain of P. aeruginosa, designated PAOI, and two nonmucoid, LPSsmooth clinical isolates from CF patients (4). Compared with CFT1-LCFSN cells, the three lines expressing ΔF508 CFTR internalized significantly fewer bacterial cells (Fig. 1A). The ΔF508 mutation causes inefficient processing of CFTR, a defect that is partially corrected if the cells are grown at 26°C (5). When epithelial cells were cultured for 72 hours at 26°C there were no longer significant differences in uptake of the P. aeruginosa strains by the cells expressing wild-type or mutant CFTR (Fig. 1B). Because the overall uptake of bacteria at 26°C was low, we performed additional experiments with cells grown for 72 hours at 26°C in which the invasion assay was performed at 37°C for 3 hours, conditions under which surface expression of mutant ΔF508 CFTR is maintained (5). No significant difference in bacterial cell uptake was measured (Fig. 1C), and overall amounts of internalization approached those of the CFT1-LCFSN cells at 37°C. Returning cells expressing ΔF508 CFTR to 37°C for 24 hours after growth for 72 hours at 26°C removes CFTR from the cell surface (5); under these conditions internalization of the bacterial strains ...

Mucoid strains of group A Streptococcus have been associated with recent outbreaks ofacute rheumatic fever. The mucoid colony morphology of these strains is a result of abundant production of capsular polysaccharide, which is composed of hyaluronic acid. To study the role of the hyaluronic acid capsule in virulence, we derived an acapsular mutant from a mucoid strain of group A Streptococcus by transposon mutagenesis. M protein expression was not altered in the mutant strain. The mucoid wild-type strain grew in fresh human blood and was resistant to phagocytic killing in vitro. In contrast, the acapsular mutant failed to grow in fresh human blood and was sensitive to phagocytic killing in vitro. Loss of capsule was associated with a 100-fold reduction in virulence of the organisms in mice. We conclude that the hyaluronic acid capsule protects mucoid group A streptococci from phagocytosis and has an important role in virulence.Group A Streptococcus (GAS) continues to be a major cause of morbidity and mortality throughout the world, both from infections and from the postinfectious sequelae of acute rheumatic fever and poststreptococcal glomerulonephritis. Recent reports suggest that after declining in frequency in developed countries for the past half-century, the incidence of life-threatening infections due to GAS and of acute rheumatic fever is increasing (1-5). The reasons for the resurgence of serious human diseases due to GAS are not known; however, it has been suggested that the GAS strains prevalent today may have increased expression of one or more virulence factors (1, 6). One such factor may be the hyaluronic acid capsule. Occasional strains of GAS isolated from clinical sources grow as large, spreading, wet colonies on solid media; this characteristic mucoid colony morphology is due to abundant production by these strains of the GAS capsular polysaccharide, which is composed of hyaluronic acid, a high molecular weight polymer consisting of alternating residues of N-acetylglucosamine and glucuronic acid (7,8). Mucoid strains of GAS have been implicated as causing unusually severe infections and frequently have been associated with individual cases or community outbreaks of rheumatic fever, including clusters of rheumatic fever cases reported recently from several regions of the U.S.A. (3, 5, 9, 10). Kaplan et al. (6) studied 42 GAS strains isolated from sibling contacts or patients with acute rheumatic fever during several outbreaks in the mid-1980s and found 45% to be mucoid.Mucoid isolates are generally rich in M protein and are highly virulent in experimental animals (9, 11). M protein has been considered to be the major surface component responsible for resistance of GAS to phagocytosis (12). The fact that highly virulent, M protein-rich strains usually appear mucoid suggests that the presence of a large hyaluronic acid capsule may also confer special virulence properties on these strains. Hirst (13) attempted to define the role of the hyaluronic acid capsule in virulence by experimentally in...

While complex intra- and interspecies microbial community dynamics are apparent during chronic infections and likely alter patient health outcomes, our understanding of these interactions is currently limited. For example, Pseudomonas aeruginosa and Staphylococcus aureus are often found to coinfect the lungs of patients with cystic fibrosis (CF), yet these organisms compete under laboratory conditions. Recent observations that coinfection correlates with decreased health outcomes necessitate we develop a greater understanding of these interbacterial interactions. In this study, we tested the hypothesis that P. aeruginosa and/or S. aureus adopts phenotypes that allow coexistence during infection. We compared competitive interactions of P. aeruginosa and S. aureus isolates from mono- or coinfected CF patients employing in vitro coculture models. P. aeruginosa isolates from monoinfected patients were more competitive toward S. aureus than P. aeruginosa isolates from coinfected patients. We also observed that the least competitive P. aeruginosa isolates possessed a mucoid phenotype. Mucoidy occurs upon constitutive activation of the sigma factor AlgT/U, which regulates synthesis of the polysaccharide alginate and dozens of other secreted factors, including some previously described to kill S. aureus. Here, we show that production of alginate in mucoid strains is sufficient to inhibit anti-S. aureus activity independent of activation of the AlgT regulon. Alginate reduces production of siderophores, 2-heptyl-4-hydroxyquinolone-N-oxide (HQNO), and rhamnolipids—each required for efficient killing of S. aureus. These studies demonstrate alginate overproduction may be an important factor driving P. aeruginosa coinfection with S. aureus.

Virulence-linked pathways in opportunistic pathogens are putative therapeutic targets that may be associated with less potential for resistance than targets in growth-essential pathways. However, efficacy of virulence-linked targets may be affected by the contribution of virulence-related genes to metabolism. We evaluate the complex interrelationships between growth and virulence-linked pathways using a genome-scale metabolic network reconstruction of Pseudomonas aeruginosa strain PA14 and an updated, expanded reconstruction of P. aeruginosa strain PAO1. The PA14 reconstruction accounts for the activity of 112 virulence-linked genes and virulence factor synthesis pathways that produce 17 unique compounds. We integrate eight published genome-scale mutant screens to validate gene essentiality predictions in rich media, contextualize intra-screen discrepancies and evaluate virulence-linked gene distribution across essentiality datasets. Computational screening further elucidates interconnectivity between inhibition of virulence factor synthesis and growth. Successful validation of selected gene perturbations using PA14 transposon mutants demonstrates the utility of model-driven screening of therapeutic targets.

Quorum sensing (QS) is a bacterial cell-to-cell communication process that relies on the production, release, and response to extracellular signaling molecules called autoinducers. QS controls virulence and biofilm formation in the human pathogen Pseudomonas aeruginosa. P. aeruginosa possesses two canonical LuxI/R-type QS systems, LasI/R and RhlI/R, which produce and detect 3OC12-homoserine lactone and C4-homoserine lactone, respectively. Here, we use biofilm analyses, reporter assays, RNA-seq studies, and animal infection assays to show that RhlR directs both RhlI-dependent and RhlI-independent regulons. In the absence of RhlI, RhlR controls the expression of genes required for biofilm formation as well as genes encoding virulence factors. Consistent with these findings, ΔrhlR and ΔrhlI mutants have radically different biofilm phenotypes and the ΔrhlI mutant displays full virulence in animals whereas the ΔrhlR mutant is attenuated. The ΔrhlI mutant cell-free culture fluids contain an activity that stimulates RhlR-dependent gene expression. We propose a model in which RhlR responds to an alternative ligand, in addition to its canonical C4-homoserine lactone autoinducer. This alternate ligand promotes a RhlR-dependent transcriptional program in the absence of RhlI.