Table 1.

Summary of major findings obtained in selected genomics and transcriptomics studies related to Burkholderia cepacia complex pathogenesis in the cystic fibrosis (CF) lung.

Experiment	Major Findings	Reference
Genomics
Retrospective study of a B. dolosa outbreak among CF patients by sequencing the genomes of a single colony of 112 isolates collected from 14 individuals over 16 years.	17 bacterial genes acquired non-synonymous mutations in multiple individuals, indicating parallel adaptive evolution. Mutated genes involved in antibiotic resistance, bacterial membrane composition, and oxygen-dependent gene expression regulation.	Lieberman et al., 2011 [13]
Analysis of intraspecies diversity in the sputum of five CF patients infected with B. dolosa.	Several bacterial lineages coexisted within the same patient. Genes subject to strongest selection are involved in outer membrane component synthesis, iron scavenging and antibiotic resistance.	Lieberman et al., 2014 [14]
Genomic and functional evolution analysis of 22 B. multivorans isolates sequentially collected over 20 years.	Population diversified into four primary, coexisting clades, with distinct evolutionary dynamics. Strong selection of genes involved in B. multivorans populations during long-term colonization of CF patient lung targets adherence, metabolism, and cell envelope changes related to adaptation to the biofilm lifestyle.	Silva et al., 2016 [15]
Genome-wide comparative analysis of two B. contaminans isolates, from sputum and from blood culture.	The sputum isolate differs from the bloodstream isolate by over 1400 mutations as a result of a mismatch repair-deficient hypermutable state.	Nunvar et al., 2016 [16]
Transcriptomics
Comparative transcriptomics of two clonal isolates of B. cenocepacia in different stages of chronic infection, recovered from a long-term colonized CF patient deceased with cepacia syndrome.	The later isolate presented upregulated genes involved in translation, iron acquisition, efflux of drugs, and adhesion to respiratory epithelial surface. Alterations related to adaptation to the nutritional environment of the CF lung and to oxygen-limitation.	Mira et al., 2011 [17]
Comparative transcriptomics of two pan-resistant ET12 outbreak isolates recovered two decades after J2315.	The outbreak strains exhibited downregulation of genes involved in flagella production and chemotaxis; upregulation of genes involved in transport and efflux, restriction modification, and transposition.	Sass et al., 2011 [18]
Comparative transcriptomics of B. cenocepacia isolates from the bloodstream of CF patients with cepacia syndrome with isolates recovered from sputum one to two months before the cepacia syndrome.	Blood isolates presented a higher level of expression of virulence genes involved in type III secretion, exopolysaccharide cepacian biosynthesis, and quorum sensing, and reduced expression of flagellar genes.	Kalferstova et al., 2015 [19]
Comparative transcriptomics of two B. contaminans isolates from sputum and blood culture of a CF patient.	Differential expression of quorum sensing-regulated virulence factors, motility, and chemotaxis; the low-oxygen-activated (lxa) locus encoding stress-related proteins; and two clusters responsible for the biosynthesis of the antifungal and hemolytic compounds pyrrolnitrin and occidiofungin.	Nunvar et al., 2016 [16]