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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 PAK_P1-like phage Ab02.ORFs are shown as arrows. The different colors correspond to the putative function: yellow, unidentified, red, nucleotide metabolism, orange, terminase, green, morphogenesis and packaging, dark blue, DNA replication, light blue, DTR.
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pone.0130548.g001: Genomic organization of PAK_P1-like phage Ab02.ORFs are shown as arrows. The different colors correspond to the putative function: yellow, unidentified, red, nucleotide metabolism, orange, terminase, green, morphogenesis and packaging, dark blue, DNA replication, light blue, DTR.

Mentions: The twelve phages from this virulent phage genus, including the previously reported phage Ab01 [26], were isolated at four different locations in Abidjan mostly in 2010 but also once in 2011. They were distributed into five different subgroups within which the genome sequences differed at only few nucleotides. They presented more than 90% similarity with the genomes of PAK_P1 from France [45], PAP1 from China [25] and JG004 from Germany [24]. For all twelve phages of this genus, DTRs of 1153 bp (Ab01, Ab07) or 1165bp (Ab02, Ab08, Ab10, Ab13, Ab14, Ab15, Ab16, Ab23, Ab24 and Ab25) were found, similarly to those observed on closely related PAK_P1-like genomes. The DTR size difference was due to insertion/deletions of a few base pairs. All genomes possessed 14 tRNA genes and coded for their own DNA polymerase, and for the control of nucleotide metabolism. Fig 1 shows the organization of ORFs on phage Ab02, and S1 Table lists the ORFs with a putative function. One genome of each subgroup was selected for multiple alignments revealing patches of high heterogeneity, but also several regions (3–9 kb) with only a few single nucleotide polymorphisms (SNPs) (S3 Fig). Patches of sequences showing a high level of divergence and low dN/dS values were observed in the first 17 kb of the genome, reflecting events of horizontal genetic transfer (HGT) [46]. By contrast some regions were devoid of traces of HGT and differed by a few SNPs and high dN/dS values. Presence/absence of sequences was noted. Ab08 possessed a gene encoding a putative endonuclease with an H-N-H motif (Ab08 ORF38, between ORF 39 and ORF40 of Ab02). The gene is absent from the other phages from Abidjan, but present in JG004 (PJG4_036) and PAK_P2 (00161c). In Ab02 a 759bp sequence encoding ORF 104 was inserted into the polymerase gene, separating it into two genes, encoding DNA polymerase part I (ORF103) and part II (ORF105). The insert was related to an intron described in the DNA polymerase gene of LUZ24 (PPLUZ24_gp35), and encoding its own endonuclease. Comparison with other phages of the same genus (JG004, PaP1 and PAK_P1) showed a higher level of diversity as reflected in a minimum spanning tree representation (Fig 2). The very high sequence similarity level in the African phages in regions of the genome not affected by HGT is in favour of a recent diversification from a common founder. A remarkable conservation of protein sequences was observed, such as for the major capsid protein which was identical in all the phages, as previously described [25]. A region of 827bp, present in JG004 only (position 34,438 to 35,264), encompassed the gene for an endonuclease (PJG4_070), inserted between the genes homologous to Ab02 ORF62 and ORF63.


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 PAK_P1-like phage Ab02.ORFs are shown as arrows. The different colors correspond to the putative function: yellow, unidentified, red, nucleotide metabolism, orange, terminase, green, morphogenesis and packaging, dark blue, DNA replication, light blue, DTR.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130548.g001: Genomic organization of PAK_P1-like phage Ab02.ORFs are shown as arrows. The different colors correspond to the putative function: yellow, unidentified, red, nucleotide metabolism, orange, terminase, green, morphogenesis and packaging, dark blue, DNA replication, light blue, DTR.
Mentions: The twelve phages from this virulent phage genus, including the previously reported phage Ab01 [26], were isolated at four different locations in Abidjan mostly in 2010 but also once in 2011. They were distributed into five different subgroups within which the genome sequences differed at only few nucleotides. They presented more than 90% similarity with the genomes of PAK_P1 from France [45], PAP1 from China [25] and JG004 from Germany [24]. For all twelve phages of this genus, DTRs of 1153 bp (Ab01, Ab07) or 1165bp (Ab02, Ab08, Ab10, Ab13, Ab14, Ab15, Ab16, Ab23, Ab24 and Ab25) were found, similarly to those observed on closely related PAK_P1-like genomes. The DTR size difference was due to insertion/deletions of a few base pairs. All genomes possessed 14 tRNA genes and coded for their own DNA polymerase, and for the control of nucleotide metabolism. Fig 1 shows the organization of ORFs on phage Ab02, and S1 Table lists the ORFs with a putative function. One genome of each subgroup was selected for multiple alignments revealing patches of high heterogeneity, but also several regions (3–9 kb) with only a few single nucleotide polymorphisms (SNPs) (S3 Fig). Patches of sequences showing a high level of divergence and low dN/dS values were observed in the first 17 kb of the genome, reflecting events of horizontal genetic transfer (HGT) [46]. By contrast some regions were devoid of traces of HGT and differed by a few SNPs and high dN/dS values. Presence/absence of sequences was noted. Ab08 possessed a gene encoding a putative endonuclease with an H-N-H motif (Ab08 ORF38, between ORF 39 and ORF40 of Ab02). The gene is absent from the other phages from Abidjan, but present in JG004 (PJG4_036) and PAK_P2 (00161c). In Ab02 a 759bp sequence encoding ORF 104 was inserted into the polymerase gene, separating it into two genes, encoding DNA polymerase part I (ORF103) and part II (ORF105). The insert was related to an intron described in the DNA polymerase gene of LUZ24 (PPLUZ24_gp35), and encoding its own endonuclease. Comparison with other phages of the same genus (JG004, PaP1 and PAK_P1) showed a higher level of diversity as reflected in a minimum spanning tree representation (Fig 2). The very high sequence similarity level in the African phages in regions of the genome not affected by HGT is in favour of a recent diversification from a common founder. A remarkable conservation of protein sequences was observed, such as for the major capsid protein which was identical in all the phages, as previously described [25]. A region of 827bp, present in JG004 only (position 34,438 to 35,264), encompassed the gene for an endonuclease (PJG4_070), inserted between the genes homologous to Ab02 ORF62 and ORF63.

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