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

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.

Fig 1. 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.

Fig 2. Minimum spanning tree representation of PAK_P1-like phages genomes.

The numbers indicated on each branch represent the number of SNPs making this branch. A total of 12125 SNPs were identified and the tree size is 19714 indicating a high level of homoplasia. Homoplasia might result from independent HGT events with unknown phages infecting other Pseudomonas species. Colors indicate the phages country of origin.

Fig 3. 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.

Fig 4. Minimum spanning tree representation of KPP10-like phages genome.

The numbers indicated on each branch are the number of SNPs constituting this branch. A total of 9097 SNPs were identified and the tree size was 12233 indicating a significant level of homoplasia. Colors indicate the phages country of origin.

Fig 5. Genomic organization of PB1-like phage Ab27.

The different ORFs are colored according to their putative function: yellow, unknown; red nucleotide metabolism; orange, terminase; green, morphogenesis; blue, DNA replication; purple, lysis.

Fig 6. Genomic organization of N4-like phage Ab09.

The different ORFs are colored according to their putative function: yellow, unknown; grey, transcription; green, morphogenesis; blue, DNA replication; purple, lysis.

Fig 7. 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.

Fig 8. 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.

Fig 9. 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.

Fig 10. Genomic organization of PA73-like phage Ab26.

The different ORFs are colored according to their putative function: yellow, unknown; orange, terminase; red, biosynthesis; green, morphogenesis; blue, DNA replication; purple, lysis.

Fig 11. Genomic organization of D3112/B3-like phage Ab30.

The different ORFs are colored according to their putative function: yellow, unknown; red, metabolism; green, morphogenesis; pink, transposition.

Fig 12. Electron microscopy examination of nine phages representative of the different genera observed in the present phage collection.

Scale bar represents 100 nm.