Genomic Expression Analysis Reveals Strategies of Burkholderia cenocepacia to Adapt to Cystic Fibrosis Patients' Airways and Antimicrobial Therapy

Abstract

Pulmonary colonization of cystic fibrosis (CF) patients with Burkholderia cenocepacia or other bacteria of the Burkholderia cepacia complex (Bcc) is associated with worse prognosis and increased risk of death. During colonization, the bacteria may evolve under the stressing selection pressures exerted in the CF lung, in particular, those resulting from challenges of the host immune defenses, antimicrobial therapy, nutrient availability and oxygen limitation. Understanding the adaptive mechanisms that promote successful colonization and long-term survival of B. cenocepacia in the CF lung is essential for an improved therapeutic outcome of chronic infections. To get mechanistic insights into these adaptive strategies a transcriptomic analysis, based on DNA microarrays, was explored in this study. The genomic expression levels in two clonal variants isolated during long-term colonization of a CF patient who died from the cepacia syndrome were compared. One of the isolates examined, IST439, is the first B. cenocepacia isolate retrieved from the patient and the other isolate, IST4113, was obtained three years later and is more resistant to different classes of antimicrobials. Approximately 1000 genes were found to be differently expressed in the two clonal variants reflecting a marked reprogramming of genomic expression. The up-regulated genes in IST4113 include those involved in translation, iron uptake (in particular, in ornibactin biosynthesis), efflux of drugs and in adhesion to epithelial lung tissue and to mucin. Alterations related with adaptation to the nutritional environment of the CF lung and to an oxygen-limited environment are also suggested to be a key feature of transcriptional reprogramming occurring during long-term colonization, antibiotic therapy and the progression of the disease.

Variation ofBurkholderia cenocepaciavirulence potential during cystic fibrosis chronic lung infection

“…[1][2][3] During long-term respiratory infections, CF opportunistic pathogens face a highly stressful and fluctuating environment within the patient's airways, in particular due to the host immune system, antimicrobial therapy, reduced availability of oxygen and other nutrients. [4][5][6][7][8] As a consequence, the initial infecting strain undergoes genetic changes resulting in parallel evolution within the lung with diversification of genotypes and phenotypes. 7,[9][10][11][12][13] The understanding of the mechanisms underlying microbial evolution within the CF host and its association with pathogenicity and persistence is crucial to deal with these chronic infections.…”

“…To elucidate these mechanisms, our group has systematically compared the genome-wide expression patterns of 3 of the 11 Burkholderia cenocepacia sequential isolates examined in the present work, which were previously found to exhibit variation in relevant phenotypes in the context of bacterial pathogenesis. [4][5][6]12 These isolates were retrieved from one CF patient (patient J) chronically infected during 3.5 y until death with cepacia syndrome. 12 Late isolates (IST4113 and IST4134) were found to have a higher virulence potential compared to the first isolate (IST439) based on their higher ability to invade epithelial cells and to compromise epithelial monolayer integrity, 5 suggesting an increase of B. cenocepacia virulence throughout the course of long-term lung infection.…”

σ 54 -Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111

“…During CF lung infection, bacteria face an environment with a heterogeneous distribution of oxygen and nutrients, as well as high concentrations of antimicrobials. Several studies have shown that bacteria experience nutrient limitation during chronic lung infection (3)(4)(5)(6). Nitrogen is a major nutrient for cells, and nitrogen metabolism and its regulation have been studied in several bacterial species (7,8).…”

Gene Expression Profiling of Burkholderia cenocepacia at the Time of Cepacia Syndrome: Loss of Motility as a Marker of Poor Prognosis?

“…However, in this study, we aimed to identify key virulence factors; most of these genes are likely common between the genomes of the highly problematic B. cenocepacia clinical strains and, thus, are detectable using this array. Furthermore, analogous data-mining approaches for strains other than J2315 were proven to be valid in several other studies (performed for the H111 [16] and IST439 [17] strains). A total of 36 arrays were performed to capture expression profiles from two sputum and two blood culture isolates that were each incubated in triplicate in (i) sputum, (ii) serum, and (iii) control medium.…”