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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 ɸKMV-like phage Ab05.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.
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pone.0130548.g007: Genomic organization of ɸKMV-like phage Ab05.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.

Mentions: Ab05 (43,639bp) showed, on average, 98% sequence similarity with lytic phages LUZ19 from Belgium (43,548bp) [53], and ɸKMV from Russia (42,519bp) [54]. A 431bp DTR was observed, similar to that of LUZ19 (472 bp DTR). Overall the organization of putative genes was that of ɸKMV-like phages [10,55] (Fig 7). Contrarily to the large-genome viruses described above, Ab05 and the other ɸKMV-like genomes were more compact and essentially expressed genes for morphogenesis and replication, in addition to a group of small hypothetical ORFs. An RNA polymerase was found (ORF31), as typically observed in phages of this genus. The first genomic region ending after the gene for RNA polymerase, and encompassing genes for host conversion and DNA replication (early region), was the region showing the most diversity [55]. A lysis cassette formed of a pinholin (ORF49), endolysin (ORF50), and spanins (ORFs 51–52) was similar to the one described in ɸKMV-like phages [56]. Interestingly no putative ORFs were found in the first 1900 nucleotides, a region holding three to five strong promoters in other ɸKMV-like phages. The canonical nucleotide sequence 5’-CGACXXXXXCCTACTCCGG-3’, localized at putative sites for single-strand DNA interruptions [57], was found three times in the Ab05 genome (arrows on Fig 7). Ab05 showed, in addition, the variant sequence 5’-GGGCXXXXXCCTACTCCGG-3’. At these positions an excess of sequencing reads could be observed. Compared to other ɸKMV-like phage genomes, four deletions of putative genes, as well as many regions with low level of similarity at the nucleotide level were observed, reflecting recombination events. The two smaller deletions corresponded in phage LKD6 to a region containing a putative promoter and to an intergenic sequence [55]. Deletion 3 encompassed the short ORF17.1 of phiKF [58]. Deletion 4 encompassed gp20 in LUZ19, a short ORF present in all the sequenced ɸKMV-like phages.


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 ɸKMV-like phage Ab05.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130548.g007: Genomic organization of ɸKMV-like phage Ab05.The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.
Mentions: Ab05 (43,639bp) showed, on average, 98% sequence similarity with lytic phages LUZ19 from Belgium (43,548bp) [53], and ɸKMV from Russia (42,519bp) [54]. A 431bp DTR was observed, similar to that of LUZ19 (472 bp DTR). Overall the organization of putative genes was that of ɸKMV-like phages [10,55] (Fig 7). Contrarily to the large-genome viruses described above, Ab05 and the other ɸKMV-like genomes were more compact and essentially expressed genes for morphogenesis and replication, in addition to a group of small hypothetical ORFs. An RNA polymerase was found (ORF31), as typically observed in phages of this genus. The first genomic region ending after the gene for RNA polymerase, and encompassing genes for host conversion and DNA replication (early region), was the region showing the most diversity [55]. A lysis cassette formed of a pinholin (ORF49), endolysin (ORF50), and spanins (ORFs 51–52) was similar to the one described in ɸKMV-like phages [56]. Interestingly no putative ORFs were found in the first 1900 nucleotides, a region holding three to five strong promoters in other ɸKMV-like phages. The canonical nucleotide sequence 5’-CGACXXXXXCCTACTCCGG-3’, localized at putative sites for single-strand DNA interruptions [57], was found three times in the Ab05 genome (arrows on Fig 7). Ab05 showed, in addition, the variant sequence 5’-GGGCXXXXXCCTACTCCGG-3’. At these positions an excess of sequencing reads could be observed. Compared to other ɸKMV-like phage genomes, four deletions of putative genes, as well as many regions with low level of similarity at the nucleotide level were observed, reflecting recombination events. The two smaller deletions corresponded in phage LKD6 to a region containing a putative promoter and to an intergenic sequence [55]. Deletion 3 encompassed the short ORF17.1 of phiKF [58]. Deletion 4 encompassed gp20 in LUZ19, a short ORF present in all the sequenced ɸKMV-like phages.

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