Long-term colonization of the cystic fibrosis lung by Burkholderia cepacia complex bacteria: epidemiology, clonal variation, and genome-wide expression alterations

Abstract

Long-term respiratory infections with Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) patients generally lead to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the "cepacia syndrome." Bcc bacteria are ubiquitous in the environment and are recognized as serious opportunistic pathogens that are virtually impossible to eradicate from the CF lung, posing a serious clinical threat. The epidemiological survey of Bcc bacteria involved in respiratory infections at the major Portuguese CF Treatment Center at Santa Maria Hospital, in Lisbon, has been carried out by our research group for the past 16 years, covering over 500 clinical isolates where B. cepacia and B. cenocepacia are the predominant species, with B. stabilis, B. contaminans, B. dolosa, and B. multivorans also represented. The systematic and longitudinal study of this CF population during such an extended period of time represents a unique case-study, comprehending 41 Bcc-infected patients (29 pediatric and 12 adult) of whom around 70% have been persistently colonized between 7 months and 9 years. During chronic infection, the CF airways represent an evolving ecosystem, with multiple phenotypic variants emerging from the clonal population and becoming established in the patients' airways as the result of genetic adaptation. Understanding the evolutionary mechanisms involved is crucial for an improved therapeutic outcome of chronic infections in CF. This review focuses on our contribution to the understanding of these adaptive mechanisms based on extensive phenotypic, genotypic, and genome-wide expression approaches of selected Bcc clonal variants obtained during long-term colonization of the CF airways.

Keywords: Burkholderia cenocepacia; Burkholderia cepacia complex; chronic respiratory infection; clonal variation; cystic fibrosis; genome-wide expression; long-term colonization.

Figure 1

Characterization of the CF subpopulation that has been monitored at the major Portuguese CF Treatment Center at Santa Maria Hospital, in Lisbon, for the past 16 years. The population was characterized in terms of gender, age, type of colonization, and clinical outcome. Among the deceased patients, at least five had developed the cepacia syndrome at the time of death (each patient marked as *). Based on the information published in Richau et al. (2000), Cunha et al. (2003, 2007), and on other recent unpublished data.

Figure 2

Profiling of the Bcc-infected CF subpopulation. (A) Distribution of the Bcc clinical isolates into the corresponding Bcc species; (B) Chronological distribution of the different Bcc species isolates; (C) Number of patients and date of first Bcc positive isolation (pediatric – white bars and adults – black bars); (D) Number of patients infected with the different species, including co-infection (cen – B. cenocepacia; cep – B. cepacia; stab – B. stabilis; mult – B. multivorans; cont – B. contaminans; dol – B. dolosa); (E) Period of duration of chronic infection and clinical outcome (eradication – white bars, death – black bars, * denotes a confirmed cepacia syndrome). Based on the information published in Richau et al. (2000), Cunha et al. (2003, 2007), and on other recent unpublished data.

Figure 3

Phenotypic characteristics of the B. cenocepacia clonal variants IST439 and IST4113, retrieved from the same CF patient sputum during long-term residence in the lung and whose genomic expression was compared by quantitative proteomic and transcriptomic analyses. (A) Minimum inhibitory concentration (MIC) values; (B) Growth of IST439 and IST4113 under limited or load iron conditions; (C) Fatty acid saturation of the clonal variants obtained during the 41-months of chronic colonization; (D) Colony morphology; (E) Amount of biofilms formed based on crystal violet method; (F) Swarming and swimming motilities; (G) Zeta potential; (H) Cell size; (I) Exopolysaccharide produced; (J) Fraction of cells at the interface of water and n-hexadecane. Based on results from Coutinho et al. (2011) and Madeira et al. (2011).

Figure 4

Proposed mechanistic model of the adaptive responses that might occur during long-term residence of B. cenocepacia in the stressing environment of the CF lung under antimicrobial therapy. The model is based on the results obtained from the comparison of transcriptomic, proteomic, and phenotypic profiling of sequential clinical isolates collected from the same chronically colonized CF patient.