Genomics Reveals a Unique Clone of Burkholderia cenocepacia Harboring an Actively Excising Novel Genomic Island

Abstract

Burkholderia cenocepacia is a clinically dominant form among the other virulent species of Burkholderia cepacia complex (Bcc). In the present study, we sequenced and analyzed the genomes of seven nosocomial Bcc isolates, five of which were isolated from the bloodstream infections and two isolates were recovered from the hospital setting during the surveillance. Genome-based species identification of the Bcc isolates using a type strain explicitly identified the species as B. cenocepacia. Moreover, single nucleotide polymorphism analysis revealed that the six isolates were clonal and phylogenetically distinct from the other B. cenocepacia. Comparative genomics distinctly revealed the larger genome size of six clonal isolates as well as the presence of a novel 107 kb genomic island named as BcenGI15, which encodes putative pathogenicity-associated genes. We have shown that the BcenGI15 has an ability to actively excise from the genome and forming an extrachromosomal circular form suggesting its mobile nature. Surprisingly, a homolog of BcenGI15 was also present in the genome of a clinical isolate named Burkholderia pseudomallei strain EY1. This novel genetic element is present only in the variants of B. cenocepacia and B. pseudomallei isolates suggesting its interspecies existence in the main pathogenic species of the genus Burkholderia. In conclusion, the whole genome analysis of the genomically distinct B. cenocepacia clinical isolates has advanced our understanding of the epidemiology and evolution of this important nosocomial pathogen as well as its relatives.

Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches

“…Genome-based taxonomic and phylogenetic analyses that have emerged as present identification standards can provide more accurate genotyping data of clinical isolates and also allow the identification of strains that have rapidly evolved after introduction of novel determinants by horizontal gene transfer ( Juhas et al, 2009 ). For instance, a recent genome-based analysis of Bcc clinical isolates in India identified a previously unknown B. cenocepacia clone characterized by a novel genomic island (i.e., BcenGI15), very similar to that found in Burkholderia pseudomallei strain EY1, and so demonstrated transfer of genomic islands also between different pathogenic species within the Burkholderia genus ( Patil et al, 2017 ).…”

Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria

“…Though, GI type T4SS was not detected, the GIs of S. spongiae KCTC 22492 harbored seven genes encoding for ankyrin-like domains (Figure 3B and Supplementary Table S8). Enrichment of genes coding for ANKs involved in host-parasite interaction has been reported in the GIs of obligate intracellular parasites- Babela massiliensis (lives in Acanthamoeba castellaniiparasitic ) (Pagnier et al, 2015), Orientia tsutsugamushi (lives in trombiculid mites) (Nakayama et al, 2008), and in a bacterium, Burkholderia cenocepacia , for successful pathogenic lifestyle (Patil et al, 2017). The detection of ANks within the GIs of both sponge-associated Shewanella spp.…”

Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster

“…Genomic islands are genomic regions that can serve as a driving force to virulence. They may contain a few or many genes which can be acquired through recombination from other bacteria (Patil et al, 2017). In B. pseudomallei, GIs were a key feature of the genome, accounting for a major source of genomic diversity, as well as being associated with pathogenicity in humans (Sim et al, 2008).…”