Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing.

The Gram-negative bacterium Pseudomonas aeruginosa is found in several habitats, both natural and human-made, and is particularly known for its recurrent presence as a pathogen in the lungs of patients suffering from cystic fibrosis, a genetic disease. Given its clinical importance, several major studies have investigated the genomic adaptation of P. aeruginosa in lungs and its transition as acute infections become chronic. However, our knowledge about the diversity and adaptation of the P. aeruginosa genome to non-clinical environments is still fragmentary, in part due to the lack of accurate reference genomes of strains from the numerous environments colonized by the bacterium. Here, we used PacBio long-read technology to sequence the genome of PPF-1, a strain of P. aeruginosa isolated from a dental unit waterline. Generating this closed genome was an opportunity to investigate genomic features that are difficult to accurately study in a draft genome (contigs state). It was possible to shed light on putative genomic islands, some shared with other reference genomes, new prophages, and the complete content of insertion sequences. In addition, four different group II introns were also found, including two characterized here and not listed in the specialized group II intron database.

Induction, structural characterization, and genome sequence of Lv1, a prophage from a human vaginal Lactobacillus jensenii strain.

The prophage Lv1, harbored by a vaginal Lactobacillus jensenii isolate, was induced by several different anticancer, antimicrobial, and antiseptic agents, suggesting that they contribute to the adverse vaginal effects associated with their therapeutic use. Of special interest with respect to its novelty was the inducing effect of nonoxynol-9, a non-ionic detergent commonly used as a spermicide. The Lv1 genome consists of a 38,934-bp dsDNA molecule with cohesive ends, in which 48 ORFs were recognized, and is organized into functional modules. Lv1 belongs to the family Siphoviridae and, more precisely, to the proposed Sfi21-like genus. The capsid-tail junction of the Lv1 virions is fragile such that most particles become disrupted, suggesting that the virus is defective and thus unable to generate fertile progeny. However, genome analysis did not provide evidence of the defective nature of the prophage, other than the finding that its genome is shorter than those of other, related, phages. Further analysis indicated that prophage Lv1 suffered deletions in its right half to the extent that it no longer fulfill the minimum packaging limits, thereby generating the observed unstable particles.