AUTHOR=Khrongsee Pacharapong , Irby Iris , Akaphan Pitchaporn , Alami-Rose Mariam A. , Kaewrakmuk Jedsada , Tuanyok Apichai 

TITLE=A comprehensive study of prophage islands in Burkholderia pseudomallei complex

JOURNAL=Frontiers in Bacteriology

VOLUME=3

YEAR=2024

URL=https://www.frontiersin.org/journals/bacteriology/articles/10.3389/fbrio.2024.1339809

DOI=10.3389/fbrio.2024.1339809

ISSN=2813-6144

ABSTRACT=<sec><title>Introduction</title><p>Bacteriophages are known as predators of bacteria and key biological factors influencing genetic recombination through phage transduction in bacteria. Phage transduction is known as one of the most common genetic recombination events found in <italic>Burkholderia pseudomallei</italic>, a diverse bacterial species and the causative agent of a deadly tropical disease melioidosis. The main objective of this study was to catalog prophages or prophage islands that are common in <italic>B. pseudomallei</italic> genomes.</p></sec><sec><title>Methods</title><p>Various bioinformatic tools were used to identify prophages in 106 complete <italic>B. pseudomallei</italic> genomes, and complete and incomplete genomes in other species within the <italic>B. pseudomallei</italic> Complex (BPC). Temperate phages were spontaneously induced from selected <italic>B. pseudomallei</italic> and <italic>B. thailandensis</italic> strains, and further characterized by transmission electron microscopy and whole genome sequencing.</p></sec><sec><title>Results</title><p>Nine phage integration hotspots were identified in <italic>B. pseudomallei</italic> pan-genomes, eight of which were associated with tRNA gene-mediated site-specific recombination (tRNA-SSR) events. These genetic events occurred at various tRNA-genes including tRNA- Phenylalanine (anticodon GAA), - Methionine (CAU), - Proline (UGG), - Arginine (UCU), - Cysteine (GCA), - Arginine (CCG), - Serine (GGA), and – Selenocysteine (UCA) genes. Some of these events were also found in other related species within the <italic>B. pseudomallei</italic> Complex (BPC). We have demonstrated that lysogenic phages from select BPC strains could use <italic>B. pseudomallei</italic> strain Bp82 or 576mn as a host. These phages were classified into one of the two major groups, myoviruses or siphoviruses, based on their morphology and genomic composition.</p></sec><sec><title>Discussion</title><p>We have demonstrated that most <italic>B. pseudomallei</italic> strains are lysogenic, many containing at least one functional prophage in their genomes. Further investigation of the interactions between <italic>B. pseudomallei</italic>, bacteriophages, and other environmental and biological factors would provide a bigger picture of genomic diversity, potentially influence on survival of <italic>B. pseudomallei</italic> in the environment and its pathogenic specialization in hosts.</p></sec>