A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

Abstract

Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.

Harnessing the Diversity of Burkholderia spp. Prophages for Therapeutic Potential

“…Our findings demonstrate that clinically significant Burkholderia isolates host a variety of prophage elements, in agreement with previous studies, showing that lysogeny is relatively common in this genus [ 3 , 49 , 50 ]. While our study was likely underpowered to identify a strong correlation between prophage abundance and phage susceptibility, we found more prophages and greater overall phage resistance in B. multivorans isolates compared to B. cenocepacia isolates.…”

Harnessing the diversity ofBurkholderiaspp. prophages for therapeutic potential

“…Our findings demonstrate that clinically significant Burkholderia isolates are host to a variety of prophage elements, in agreement with previous studies showing that lysogeny is relatively common in this genus (2), ( 47), (16). We found that a higher overall abundance of prophages did not correlate with phage susceptibility in our dataset.…”

“…Small differences in host range within each group of phages could be attributed to differences in titer of the lysate stocks. Notably, with the exception of BCC05 and BCC06, lytic host-range of bacteriophages of prophage origin were comparable to those of environmental origin, both within our study (comparing BCC02-BCC08 with BCh7 and DSMZ107315) and in the literature (16,47).…”

“…There are currently more than 30 known species of Burkholderia, about two thirds of which belong to the Burkholderia cepacia complex (Bcc) (16). The Bcc is made up of 22 phenotypically similar, but genotypically distinct species (Figure 1) (17).…”

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?

“…The B. vietnamiensis G4 capacity to survive harmful compounds in contaminated areas allowed its use in bioremediation experiments, combined with high-performance sequencing techniques and transcription analysis, which enabled the identification of genes differently expressed in its genome [ 23 , 25 – 27 ] and its functions in the biodegradation process [ 28 – 31 ]. The use of new high-performance sequencing tools and transcriptome analysis is important to help us understand microorganism responses under different stress conditions [ 32 ].…”