Limits...
Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d'Ivoire.

Essoh C, Latino L, Midoux C, Blouin Y, Loukou G, Nguetta SP, Lathro S, Cablanmian A, Kouassi AK, Vergnaud G, Pourcel C - PLoS ONE (2015)

Bottom Line: The vast majority of the genetic variations among virulent phages from the same genus resulted from seemingly non-random horizontal transfer events, inside a population of P. aeruginosa phages with limited diversity.This is the first study of P. aeruginosa phage diversity in an African city and it shows that a large variety of phage species can be recovered in a limited geographical site at least when different bacterial strains are used.The relative temporal and spatial stability of the Abidjan phage population might reflect equilibrium in the microbial community from which they are released.

View Article: PubMed Central - PubMed

Affiliation: Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France.

ABSTRACT
Twenty two distinct bacteriophages were isolated from sewage water from five locations in the city of Abidjan, Côte d'Ivoire over a two-year period, using a collection of Pseudomonas aeruginosa strains with diverse genotypes. The phages were characterized by their virulence spectrum on a panel of selected P. aeruginosa strains from cystic fibrosis patients and by whole genome sequencing. Twelve virions representing the observed diversity were visualised by electron microscopy. The combined observations showed that 17 phages, distributed into seven genera, were virulent, and that five phages were related to temperate phages belonging to three genera. Some showed similarity with known phages only at the protein level. The vast majority of the genetic variations among virulent phages from the same genus resulted from seemingly non-random horizontal transfer events, inside a population of P. aeruginosa phages with limited diversity. This suggests the existence of a single environmental reservoir or ecotype in which continuous selection is taking place. In contrast, mostly point mutations were observed among phages potentially capable of lysogenisation. This is the first study of P. aeruginosa phage diversity in an African city and it shows that a large variety of phage species can be recovered in a limited geographical site at least when different bacterial strains are used. The relative temporal and spatial stability of the Abidjan phage population might reflect equilibrium in the microbial community from which they are released.

No MeSH data available.


Related in: MedlinePlus

Genomic organization of YuA-like phage Ab18.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; red, DNA repair; green, morphogenesis; blue, DNA replication; purple, lysis, pink, prophage insertion.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4482731&req=5

pone.0130548.g009: Genomic organization of YuA-like phage Ab18.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; red, DNA repair; green, morphogenesis; blue, DNA replication; purple, lysis, pink, prophage insertion.

Mentions: Ab18, Ab19, Ab20 and Ab21, isolated in 2010 and 2011 at two locations and showing related restriction profiles, appeared to be YuA-like phages. Genome sequencing showed that there were in fact only three different phages, Ab19 and Ab21 being identical. The sequencing reads aligned as a circular genome, with no abnormal peaks of reads and consequently the first nucleotide was assigned by comparison with the closest genome, YuA from Russia (58,663 bp) [62]. The genome of the three phages showed at best 70% similarity with that of YuA and MP1412 from South Korea (61,167 bp) [63]. At the protein level, additional similarities could be observed particularly in structural proteins. Moreover, the DNA polymerase (ORF18) and the terminase gene (ORF46) also showed an elevated degree of homology with those of YuA. Fig 9 shows the organisation of the 76 Ab18 ORFs, all oriented in the same direction. Overall the organisation was that of YuA with some remarkable differences, particularly at the level of small ORFs of unknown function. ORF6 and ORF7 of Ab18 and Ab19 encoded the small and large subunits of a ribonuclease reductase of class Ia which corresponded to a single gene in YuA. A putative repressor (ORF21) and an integrase (ORF22) showing 55% identity to that of YuA were present, suggesting that the phage could possibly lysogenize its host. Other parts of the genome had no homology with any phage in the public databases, either at nucleotide or protein level. Ab18, Ab19 and Ab20 genomes showed an average 95% similarity with each other, and displayed several regions of insertion/deletion. The genomes were aligned showing that overall the SNPs were evenly distributed, except for one large region of low percentage of similarity encompassing genes for the tail fiber proteins (S6 Fig). This is in contrast with the high level of divergence observed with the closest phage YuA, and provides a direct estimate of the relative role of mutation by descent versus recombination in this homogenous group of phages. YuA-like phage genomes were reported to be resistant to many restriction enzymes including EcoRI, although EcoRI restriction sites exist in their genome [7,62]. We observed a similar resistance in the four phages from Abidjan suggesting the existence of DNA modifications.


Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d'Ivoire.

Essoh C, Latino L, Midoux C, Blouin Y, Loukou G, Nguetta SP, Lathro S, Cablanmian A, Kouassi AK, Vergnaud G, Pourcel C - PLoS ONE (2015)

Genomic organization of YuA-like phage Ab18.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; red, DNA repair; green, morphogenesis; blue, DNA replication; purple, lysis, pink, prophage insertion.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482731&req=5

pone.0130548.g009: Genomic organization of YuA-like phage Ab18.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; red, DNA repair; green, morphogenesis; blue, DNA replication; purple, lysis, pink, prophage insertion.
Mentions: Ab18, Ab19, Ab20 and Ab21, isolated in 2010 and 2011 at two locations and showing related restriction profiles, appeared to be YuA-like phages. Genome sequencing showed that there were in fact only three different phages, Ab19 and Ab21 being identical. The sequencing reads aligned as a circular genome, with no abnormal peaks of reads and consequently the first nucleotide was assigned by comparison with the closest genome, YuA from Russia (58,663 bp) [62]. The genome of the three phages showed at best 70% similarity with that of YuA and MP1412 from South Korea (61,167 bp) [63]. At the protein level, additional similarities could be observed particularly in structural proteins. Moreover, the DNA polymerase (ORF18) and the terminase gene (ORF46) also showed an elevated degree of homology with those of YuA. Fig 9 shows the organisation of the 76 Ab18 ORFs, all oriented in the same direction. Overall the organisation was that of YuA with some remarkable differences, particularly at the level of small ORFs of unknown function. ORF6 and ORF7 of Ab18 and Ab19 encoded the small and large subunits of a ribonuclease reductase of class Ia which corresponded to a single gene in YuA. A putative repressor (ORF21) and an integrase (ORF22) showing 55% identity to that of YuA were present, suggesting that the phage could possibly lysogenize its host. Other parts of the genome had no homology with any phage in the public databases, either at nucleotide or protein level. Ab18, Ab19 and Ab20 genomes showed an average 95% similarity with each other, and displayed several regions of insertion/deletion. The genomes were aligned showing that overall the SNPs were evenly distributed, except for one large region of low percentage of similarity encompassing genes for the tail fiber proteins (S6 Fig). This is in contrast with the high level of divergence observed with the closest phage YuA, and provides a direct estimate of the relative role of mutation by descent versus recombination in this homogenous group of phages. YuA-like phage genomes were reported to be resistant to many restriction enzymes including EcoRI, although EcoRI restriction sites exist in their genome [7,62]. We observed a similar resistance in the four phages from Abidjan suggesting the existence of DNA modifications.

Bottom Line: The vast majority of the genetic variations among virulent phages from the same genus resulted from seemingly non-random horizontal transfer events, inside a population of P. aeruginosa phages with limited diversity.This is the first study of P. aeruginosa phage diversity in an African city and it shows that a large variety of phage species can be recovered in a limited geographical site at least when different bacterial strains are used.The relative temporal and spatial stability of the Abidjan phage population might reflect equilibrium in the microbial community from which they are released.

View Article: PubMed Central - PubMed

Affiliation: Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France.

ABSTRACT
Twenty two distinct bacteriophages were isolated from sewage water from five locations in the city of Abidjan, Côte d'Ivoire over a two-year period, using a collection of Pseudomonas aeruginosa strains with diverse genotypes. The phages were characterized by their virulence spectrum on a panel of selected P. aeruginosa strains from cystic fibrosis patients and by whole genome sequencing. Twelve virions representing the observed diversity were visualised by electron microscopy. The combined observations showed that 17 phages, distributed into seven genera, were virulent, and that five phages were related to temperate phages belonging to three genera. Some showed similarity with known phages only at the protein level. The vast majority of the genetic variations among virulent phages from the same genus resulted from seemingly non-random horizontal transfer events, inside a population of P. aeruginosa phages with limited diversity. This suggests the existence of a single environmental reservoir or ecotype in which continuous selection is taking place. In contrast, mostly point mutations were observed among phages potentially capable of lysogenisation. This is the first study of P. aeruginosa phage diversity in an African city and it shows that a large variety of phage species can be recovered in a limited geographical site at least when different bacterial strains are used. The relative temporal and spatial stability of the Abidjan phage population might reflect equilibrium in the microbial community from which they are released.

No MeSH data available.


Related in: MedlinePlus