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.
Highlights
Burkholderia cepacia complex (Bcc) consists of Gram-negative, oxidase-positive, non-fermenting saprophytic bacilli belonging to the Burkholderiaceae family comprising 20 taxonomically valid species (De Smet et al, 2015; Estrada-de los Santos et al, 2015)
whole genome sequencing (WGS) revealed that all the isolates of Bcc have GC content around 66% and genome size of around 8.6 Mb except one isolate BC-3 having the genome size of 7.8 Mb
General genomic features of nosocomial isolates of Bcc are mentioned in Table 1, and assembly statistics are mentioned in Supplementary Table 2
Summary
Burkholderia cepacia complex (Bcc) consists of Gram-negative, oxidase-positive, non-fermenting saprophytic bacilli belonging to the Burkholderiaceae family comprising 20 taxonomically valid species (De Smet et al, 2015; Estrada-de los Santos et al, 2015). Some GEI encodes their machinery for the excision, conjugative transfer, and the integration This class of GEI is classified as the Integrative and Conjugative Element (ICE) (Wozniak and Waldor, 2010; Johnson and Grossman, 2015; Novick and Ram, 2016). The IMEs are not selfmobilizable but can be mobilized with the help of conjugation machinery of the helper elements such as conjugative plasmids or other ICEs (Guglielmini et al, 2011) These ICEs and IMEs are rapidly growing classes of the mosaic mobile genetic elements (MGE), which are present in both Gram-negative and Grampositive bacteria, and can play important roles in the bacterial genome plasticity or instability (Wozniak and Waldor, 2010; Darmon and Leach, 2014). GEIs play a major role in the adaptive evolution of bacteria by dissemination of antibiotic resistance genes and virulence factors leading to the generation of superbugs as well as the dispersal of catabolic genes in the environmental, symbiotic, and commensal bacteria forming new metabolic pathways (van der Meer and Sentchilo, 2003)
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