Several bacterial species from the Burkholderia cepacia complex (Bcc) are feared opportunistic pathogens that lead to debilitating lung infections with a high risk of developing fatal septicemia in cystic fibrosis (CF) patients. However, the pathogenic potential of other Bcc species is yet unknown. To elucidate clinical relevance of Burkholderia contaminans, a species frequently isolated from CF respiratory samples in Ibero-American countries, we aimed to identify its key virulence factors possibly linked with an unfavorable clinical outcome. We performed a genome-wide comparative analysis of two isolates of B. contaminans ST872 from sputum and blood culture of a female CF patient in Argentina. RNA-seq data showed significant changes in expression for quorum sensing-regulated virulence factors and motility and chemotaxis. Furthermore, we detected expression changes in a recently described low-oxygen-activated (lxa) locus which encodes stress-related proteins, and for two clusters responsible for the biosynthesis of antifungal and hemolytic compounds pyrrolnitrin and occidiofungin. Based on phenotypic assays that confirmed changes in motility and in proteolytic, hemolytic and antifungal activities, we were able to distinguish two phenotypes of B. contaminans that coexisted in the host and entered her bloodstream. Whole genome sequencing revealed that the sputum and bloodstream isolates (each representing a distinct phenotype) differed by over 1,400 mutations as a result of a mismatch repair-deficient hypermutable state of the sputum isolate. The inferred lack of purifying selection against nonsynonymous mutations and the high rate of pseudogenization in the derived isolate indicated limited evolutionary pressure during evolution in the nutrient-rich, stable CF sputum environment. The present study is the first to examine the genomic and transcriptomic differences between longitudinal isolates of B. contaminans. Detected activity of a number of putative virulence factors implies a genuine pathogenic nature of this novel Bcc species.
c Cepacia syndrome (CS) is a fatal septic condition that develops in approximately 20% of cystic fibrosis (CF) patients chronically infected with the Burkholderia cepacia complex (Bcc). The most common causative agent is Burkholderia cenocepacia, a clinically dominant Bcc species that contains the globally distributed epidemic strain sequence type 32 (ST32). Using microarrays, we compared the transcriptomes of ST32 isolates from the bloodstream at the time of CS with their sputum counterparts recovered 1 to 2 months prior to the development of CS. Global gene expression profiles of blood isolates revealed greater activities of the virulence genes involved in the type III secretion system, the bacterial exopolysaccharide cepacian, and quorum sensing, while reduced expression was demonstrated for flagellar genes. Furthermore, a nonmotile phenotype (as evaluated by a swimming motility assay) was identified in blood isolates from 6 out of 8 patients with CS; this phenotype was traceable to 24 months prior to the onset of CS. Loss of motility was not observed in any of the 89 ST32 isolates recovered over the course of chronic infection from 17 patients without CS. In conclusion, the gene expression of Bcc bacteria disseminated during CS has been elucidated for the first time. This study demonstrated marked differences at the transcriptome level between isogenic ST32 isolates that are attributable to the stage and site of infection. The finding of a nonmotile B. cenocepacia isolate may serve as a warning sign for the development of CS in the near future. P atients with cystic fibrosis (CF) spend a lifetime at risk of contracting bacteria from the Burkholderia cepacia complex (Bcc), consisting of a group of 18 genetically closely related bacterial species (1). These microorganisms usually cause chronic respiratory infections in CF patients and result in little chance of treatment success due to their intrinsic resistance to most antimicrobials (2). Moreover, they pose a high risk for the development of a fatal clinical condition termed cepacia syndrome (CS). Because of this unfavorable outcome, Bcc species are considered particularly troublesome CF pathogens associated with not only increased morbidity but also increased mortality (3). Additionally, they spread relatively easily among CF patients and have resulted in several serious Bcc outbreaks in the past. A multicenter outbreak was reported for epidemic lineage ET12 (4), while in a local epidemic identified at the Prague CF Centre in the early 2000s, 30% of the CF population was found to be infected with a single Bcc strain. This strain was designated by multilocus sequence typing (MLST) (5) as sequence type 32 (ST32).Cepacia syndrome (CS) is a worrying terminal phase of Bcc infection characterized by pulmonary exacerbation, high levels of inflammatory markers, new multifocal lung infiltrates visible by chest X-ray, and a positive blood culture for Bcc bacteria. CS is linked mostly to Burkholderia cenocepacia, a species that is clinically dominant among the Bcc mem...
A likely factor contributing to the end of ST32 epidemic was segregation of Bcc infected patients that included also patients with no culture, but PCR positivity. The diagnostic PCR led to timely identification of cases with 'culture-invisible' infection.
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