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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 LUZ24-like phage Ab22.The different ORFs are colored according to their putative function: yellow, unknown; red, biosynthesis; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.
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pone.0130548.g008: Genomic organization of LUZ24-like phage Ab22.The different ORFs are colored according to their putative function: yellow, unknown; red, biosynthesis; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.

Mentions: The Ab22 genome was 45,808 bp long and showed 86–96% similarity with lytic phage LUZ24 from Belgium (45,625 bp; AM910650 [59]) and lysogenic phage PaP3 from China (45,503bp NC_004466 [60]). The genome was also close to that of phage 1-14Or01 that we previously isolated in France [26]. Ab22 possessed a 184 bp DTR as observed for 1-14Or01 (182bp) [26]. Annotation predicted the existence of 71 putative ORFs and three tRNAs (tRNAPro, tRNATyr and tRNAAsn) (Fig 8). By comparison, LUZ24 showed 74 ORFs and two tRNAs, and PaP3 71 ORFs and 4 tRNAs. Several regions of insertion or deletion with respect to LUZ24 were observed. The longest (1206 bp) was present in Ab22 (ORF17) and absent in LUZ24, and all other closely related P. aeruginosa phages. It showed 100% identity with the transposase fusion protein of phage TL from Russia (YP_009007804), suggesting that this gene possibly contributes to the insertion of the phage genome in the bacterial DNA. The second largest region of difference was a 665 bp fragment, absent in Ab22, encoding the gp35 endonuclease (self-splicing intron) in LUZ24, separating the polymerase part II and III (ORF34 and ORF36). These two genes were fused into a single ORF in Ab22 (ORF38). The first 1000 nucleotides did not encode any putative protein and probably contained promoters, although the consensus sequence described by Ceyssens et al. [59] could not be found at this position. At six positions (arrows on Fig 8), an excess number of reads corresponded to the sequence 5’-GTACTATGAC-3’, or to the variant 5’-GTACTGTGAC-3’ marking the single-strand DNA interruptions observed on the viral genome. We and others previously reported the existence of such sites with phages of LUZ24-family [26,61].


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 LUZ24-like phage Ab22.The different ORFs are colored according to their putative function: yellow, unknown; red, biosynthesis; 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.g008: Genomic organization of LUZ24-like phage Ab22.The different ORFs are colored according to their putative function: yellow, unknown; red, biosynthesis; green, morphogenesis; blue, DNA replication; purple, lysis. Vertical arrows indicate the position of single-strand DNA interruptions.
Mentions: The Ab22 genome was 45,808 bp long and showed 86–96% similarity with lytic phage LUZ24 from Belgium (45,625 bp; AM910650 [59]) and lysogenic phage PaP3 from China (45,503bp NC_004466 [60]). The genome was also close to that of phage 1-14Or01 that we previously isolated in France [26]. Ab22 possessed a 184 bp DTR as observed for 1-14Or01 (182bp) [26]. Annotation predicted the existence of 71 putative ORFs and three tRNAs (tRNAPro, tRNATyr and tRNAAsn) (Fig 8). By comparison, LUZ24 showed 74 ORFs and two tRNAs, and PaP3 71 ORFs and 4 tRNAs. Several regions of insertion or deletion with respect to LUZ24 were observed. The longest (1206 bp) was present in Ab22 (ORF17) and absent in LUZ24, and all other closely related P. aeruginosa phages. It showed 100% identity with the transposase fusion protein of phage TL from Russia (YP_009007804), suggesting that this gene possibly contributes to the insertion of the phage genome in the bacterial DNA. The second largest region of difference was a 665 bp fragment, absent in Ab22, encoding the gp35 endonuclease (self-splicing intron) in LUZ24, separating the polymerase part II and III (ORF34 and ORF36). These two genes were fused into a single ORF in Ab22 (ORF38). The first 1000 nucleotides did not encode any putative protein and probably contained promoters, although the consensus sequence described by Ceyssens et al. [59] could not be found at this position. At six positions (arrows on Fig 8), an excess number of reads corresponded to the sequence 5’-GTACTATGAC-3’, or to the variant 5’-GTACTGTGAC-3’ marking the single-strand DNA interruptions observed on the viral genome. We and others previously reported the existence of such sites with phages of LUZ24-family [26,61].

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