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Genome. 2018 May;61(5):359-365. doi: 10.1139/gen-2017-0239. Epub 2018 Mar 16.

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

Author information

1
a Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC, Canada.
2
b Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Quebec City, QC, Canada.
3
c Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC, Canada.
4
d Département de stomatologie, Faculté de médecine dentaire, Université de Montréal, Montreal, QC, Canada.

Abstract

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.

KEYWORDS:

PacBio; Pseudomonas aeruginosa; arrivée d’eau d’un appareil de rinçage dentaire; dental unit waterlines; genomic islands; insertion sequences; introns; mobilome; prophages; séquences d’insertion; îlots génomiques

PMID:
29546998
DOI:
10.1139/gen-2017-0239
[Indexed for MEDLINE]

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