Comparative Genomics of Environmental and Clinical Burkholderia cenocepacia Strains Closely Related to the Highly Transmissible Epidemic ET12 Lineage

Abstract

The Burkholderia cenocepacia epidemic ET12 lineage belongs to the genomovar IIIA including the reference strain J2315, a highly transmissible epidemic B. cenocepacia lineage. Members of this lineage are able to cause lung infections in immunocompromised and cystic fibrosis patients. In this study, we describe the genome of F01, an environmental B. cenocepacia strain isolated from soil in Burkina Faso that is, to our knowledge, the most closely related strain to this epidemic lineage. A comparative genomic analysis was performed on this new isolate, in association with five clinical and one environmental B. cenocepacia strains whose genomes were previously sequenced. Antibiotic resistances, virulence phenotype, and genomic contents were compared and discussed with an emphasis on virulent and antibiotic determinants. Surprisingly, no significant differences in antibiotic resistance and virulence were found between clinical and environmental strains, while the most important genomic differences were related to the number of prophages identified in their genomes. The ET12 lineage strains showed a noticeable greater number of prophages (partial or full-length), especially compared to the phylogenetically related environmental F01 strain (i.e., 5-6 and 3 prophages, respectively). Data obtained suggest possible involvements of prophages in the clinical success of opportunistic pathogens.

Keywords: Burkholderia cenocepacia; Burkina Faso; RND pumps; antibiotic resistance; prophages; virulence factors.

FIGURE 1

Phylogenetic tree from maximum-likelihood analysis of the core-genome alignments of seven Burkholderia cenocepacia strains. In total, 4,555 orthologous proteins were concatenated in an alignment of 1,514,675 amino acids. Bootstraps are indicated in each node. ST, Sequence Type (unique combination of 7 alleles; see Materials and Methods). Two strains belong to the same clonal complex if they share at least four identical alleles.

FIGURE 2

Virulence of B. cenocepacia strains determined using the social amoeba Dictyostelium discoïdeum. Strains of Pseudomonas aeruginosa PT5 and Klebsiella pneumoniae KpGe were used as positive and negative control, respectively. The axenic D. discoïdeum strain AX2 was used for virulence assays. Dilutions of amoebae were spotted on bacterial lawn plates and incubated during 5 days (n = 6).