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Viruses 2018, 10(6), 297; https://doi.org/10.3390/v10060297

Burkholderia cenocepacia Prophages—Prevalence, Chromosome Location and Major Genes Involved

1
Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland
2
School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
*
Author to whom correspondence should be addressed.
Received: 12 April 2018 / Revised: 28 May 2018 / Accepted: 29 May 2018 / Published: 31 May 2018
(This article belongs to the Special Issue Phage-Host Interactions)
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Abstract

Burkholderia cenocepacia, is a Gram-negative opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC) group. BCC representatives carry various pathogenicity factors and can infect humans and plants. Phages as bacterial viruses play a significant role in biodiversity and ecological balance in the environment. Specifically, horizontal gene transfer (HGT) and lysogenic conversion (temperate phages) influence microbial diversification and fitness. In this study, we describe the prevalence and gene content of prophages in 16 fully sequenced B. cenocepacia genomes stored in NCBI database. The analysis was conducted in silico by manual and automatic approaches. Sixty-three potential prophage regions were found and classified as intact, incomplete, questionable, and artifacts. The regions were investigated for the presence of known virulence factors, resulting in the location of sixteen potential pathogenicity mechanisms, including toxin–antitoxin systems (TA), Major Facilitator Superfamily (MFS) transporters and responsible for drug resistance. Investigation of the region’s closest neighborhood highlighted three groups of genes with the highest occurrence—tRNA-Arg, dehydrogenase family proteins, and ABC transporter substrate-binding proteins. Searches for antiphage systems such as BacteRiophage EXclusion (BREX) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in the analyzed strains suggested 10 sequence sets of CRISPR elements. Our results suggest that intact B. cenocepacia prophages may provide an evolutionary advantage to the bacterium, while domesticated prophages may help to maintain important genes. View Full-Text
Keywords: Burkholderia cenocepacia; prophages; prevalence; in silico analyses Burkholderia cenocepacia; prophages; prevalence; in silico analyses
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Roszniowski, B.; McClean, S.; Drulis-Kawa, Z. Burkholderia cenocepacia Prophages—Prevalence, Chromosome Location and Major Genes Involved. Viruses 2018, 10, 297.

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