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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 KPP10-like phage Ab06.The different ORFs are colored according to their putative function: yellow, unknown; red, nucleotide metabolism; orange, terminase; green, morphogenesis; blue, DNA replication.
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pone.0130548.g003: Genomic organization of KPP10-like phage Ab06.The different ORFs are colored according to their putative function: yellow, unknown; red, nucleotide metabolism; orange, terminase; green, morphogenesis; blue, DNA replication.

Mentions: Five phages (Ab03, Ab04, Ab06, Ab11, Ab17) isolated in 2010 and 2011 at four different locations in Abidjan, belonged to the KPP10-like virulent phage genus. They were all different, and shared 88–96% sequence identity with the genomes of KPP10 from Japan [27], and PAK_P3 from France [23,45]. At position 23,000, a region with very low read coverage was observed in all phages except Ab17 and corresponded to an AT-rich region. A putative DTR of 771bp (Ab03, Ab04, Ab11, Ab17) showing an internal 15 bp deletion in Ab06, was found, defining the genome ends. The inferred nucleotide one position was different from the reported first nucleotide of phage KPP10. The genomes of the five phages were annotated (Ab06 is shown on Fig 3) showing that, overall, the ORF organization was very similar to that of the related phages, with a few differences for some very short hypothetical proteins. In keeping with KPP10, these phages had three tRNA genes (tRNAAsn, tRNATyr and tRNAGln). Upon alignment of the five genomes using Geneious, several regions of variability were observed within otherwise largely similar sequences (S4 Fig). In regions most probably encountering frequent HGTs, the percentage of SNPs was 20% as compared to 0.1% on average in the rest of the genome, and dN/dS ratios were low. Similarly to PAK_P1 phages, the first 22 kb, and the last 8kb showed the largest traces of HGT. It is interesting to note that some recombination sites appeared to be inside coding regions leading to the production of putative proteins with high levels of heterogeneity. This was the case for example for ORF14, encoding an hypothetical protein corresponding to ORF120 in KPP10, which was very different in the five phages, and appeared to be a patchwork of short regions from different origins. Similarly to PAK_P1-like phages, the five KPP10-like phages from Abidjan clustered at a large genetic distance to phages isolated in other countries (Fig 4). Several regions of short insertion/deletions were observed between the different phages, sometimes resulting in the fusion of two putative ORFs. Ab17 lacked a 3271 bp region encompassing seven hypothetical ORFs (ORF89 to ORF96 in Ab06), perfectly conserved in the other phages. As a result, a putative RNA ligase (ORF91 in Ab17) was formed by the fusion of the beginning of ORF89 and ORF97 (also a putative RNA ligase in the other phages) in Ab06. This region corresponded to nucleotides 22,874 to 26,077 in KPP10, and also encompassed seven putative genes of unknown function (ORF34 to ORF40). Another region of 528 bp was absent in Ab03 and Ab06, and corresponded to DNA with no homology in Genbank/EMBL at the nucleotide level.


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 KPP10-like phage Ab06.The different ORFs are colored according to their putative function: yellow, unknown; red, nucleotide metabolism; orange, terminase; green, morphogenesis; blue, DNA replication.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130548.g003: Genomic organization of KPP10-like phage Ab06.The different ORFs are colored according to their putative function: yellow, unknown; red, nucleotide metabolism; orange, terminase; green, morphogenesis; blue, DNA replication.
Mentions: Five phages (Ab03, Ab04, Ab06, Ab11, Ab17) isolated in 2010 and 2011 at four different locations in Abidjan, belonged to the KPP10-like virulent phage genus. They were all different, and shared 88–96% sequence identity with the genomes of KPP10 from Japan [27], and PAK_P3 from France [23,45]. At position 23,000, a region with very low read coverage was observed in all phages except Ab17 and corresponded to an AT-rich region. A putative DTR of 771bp (Ab03, Ab04, Ab11, Ab17) showing an internal 15 bp deletion in Ab06, was found, defining the genome ends. The inferred nucleotide one position was different from the reported first nucleotide of phage KPP10. The genomes of the five phages were annotated (Ab06 is shown on Fig 3) showing that, overall, the ORF organization was very similar to that of the related phages, with a few differences for some very short hypothetical proteins. In keeping with KPP10, these phages had three tRNA genes (tRNAAsn, tRNATyr and tRNAGln). Upon alignment of the five genomes using Geneious, several regions of variability were observed within otherwise largely similar sequences (S4 Fig). In regions most probably encountering frequent HGTs, the percentage of SNPs was 20% as compared to 0.1% on average in the rest of the genome, and dN/dS ratios were low. Similarly to PAK_P1 phages, the first 22 kb, and the last 8kb showed the largest traces of HGT. It is interesting to note that some recombination sites appeared to be inside coding regions leading to the production of putative proteins with high levels of heterogeneity. This was the case for example for ORF14, encoding an hypothetical protein corresponding to ORF120 in KPP10, which was very different in the five phages, and appeared to be a patchwork of short regions from different origins. Similarly to PAK_P1-like phages, the five KPP10-like phages from Abidjan clustered at a large genetic distance to phages isolated in other countries (Fig 4). Several regions of short insertion/deletions were observed between the different phages, sometimes resulting in the fusion of two putative ORFs. Ab17 lacked a 3271 bp region encompassing seven hypothetical ORFs (ORF89 to ORF96 in Ab06), perfectly conserved in the other phages. As a result, a putative RNA ligase (ORF91 in Ab17) was formed by the fusion of the beginning of ORF89 and ORF97 (also a putative RNA ligase in the other phages) in Ab06. This region corresponded to nucleotides 22,874 to 26,077 in KPP10, and also encompassed seven putative genes of unknown function (ORF34 to ORF40). Another region of 528 bp was absent in Ab03 and Ab06, and corresponded to DNA with no homology in Genbank/EMBL at the nucleotide level.

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