Isolation, genomic and comparative proteomic characterization of three lytic Pseudomonas aeruginosa bacteriophages from wastewater in Bobo-Dioulasso, Burkina Faso

Abstract Background. Pseudomonas aeruginosa is a leading cause of opportunistic and healthcare-associated infections and is listed by the World Health Organization among the pathogens for which new therapeutic options are most urgently needed. Lytic bacteriophages are one of the few alternatives that can be deployed rapidly and at low cost, but phage collections and phage genome sequences remain very unevenly distributed geographically, and West Africa is particularly under-represented. Wastewater, which combines high bacterial densities with continuous inputs of faecal, hospital and industrial effluent, is the most productive environment for recovering phages that are locally adapted to circulating clinical strains. We therefore set out to isolate lytic phages active against clinical P. aeruginosa isolates from wastewater in Bobo-Dioulasso, Burkina Faso, and to characterize their genomes. Results. Twenty-eight lytic phages were isolated from five wastewater sites using six P. aeruginosa host strains, and screened against a panel of eleven clinical and reference strains. Host ranges were broad: eleven isolates lysed at least ten of the eleven strains and three lysed all eleven, while only two isolates were restricted to four strains. Five phages were selected for whole-genome sequencing and three yielded complete, high-quality assemblies. All three belong to the class Caudoviricetes . vB_PaeM_CM0001 (57,614 bp; 63.5% GC; 88 CDSs) is a member of the family Mesyanzhinovviridae , subfamily Bradleyvirinae , genus Abidjanvirus . vB_PaeP_CM0002 (43,491 bp) and vB_PaeP_CM0003 (43,177 bp), each encoding 65 CDSs with 62.3–62.6% GC, belong to the family Autographiviridae , subfamily Krylovirinae , genus Phikmvvirus . Intergenomic similarities indicate that vB_PaeM_CM0001 is a new isolate of an existing Abidjanvirus species, whereas vB_PaeP_CM0002 and vB_PaeP_CM0003 represent two new Phikmvvirus species. The two Phikmvvirus genomes share 91.9% nucleotide identity and 62 orthogroups and are fully collinear with each other and with their closest relatives; their divergence is confined to nucleotide substitution and to a single 2.0 kb region spanning the tail fibre locus. vB_PaeM_CM0001 shares no detectable orthogroups with them. Conclusions. These three genomes are the first P. aeruginosa phage genomes reported from Burkina Faso. Two of them represent new species. Their broad host ranges, strictly lytic gene repertoires and absence of resistance determinants make them credible starting points for a national phage bank and for future therapeutic evaluation.