Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail
ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that can cause sinus infections and pneumonia in cystic fibrosis (CF) patients. Bacteriophage therapy is being investigated as a treatment for antibiotic-resistant P. aeruginosa infections. Although virulent bacteriophages have shown promi...
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American Society for Microbiology
2025-05-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.02149-24 |
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| author | Stephanie A. Fong George Bouras Ghais Houtak Roshan Nepal Sholeh Feizi Sandra Morales Alkis J. Psaltis Peter-John Wormald Sarah Vreugde |
| author_facet | Stephanie A. Fong George Bouras Ghais Houtak Roshan Nepal Sholeh Feizi Sandra Morales Alkis J. Psaltis Peter-John Wormald Sarah Vreugde |
| author_sort | Stephanie A. Fong |
| collection | DOAJ |
| description | ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that can cause sinus infections and pneumonia in cystic fibrosis (CF) patients. Bacteriophage therapy is being investigated as a treatment for antibiotic-resistant P. aeruginosa infections. Although virulent bacteriophages have shown promise in treating P. aeruginosa infections, the development of bacteriophage-insensitive mutants (BIMs) in the presence of bacteriophages has been described. The aim of this study was to examine the genetic changes associated with the BIM phenotype. Biofilms of three genetically distinct P. aeruginosa strains, including PAO1 (ATCC 15692), and two clinical respiratory isolates (one CF and one non-CF) were grown for 7 days and treated with either a cocktail of four bacteriophages or a vehicle control for 7 consecutive days. BIMs isolated from the biofilms were detected by streak assays, and resistance to the phage cocktail was confirmed using spot test assays. Comparison of whole genome sequencing between the recovered BIMs and their respective vehicle control-treated phage-sensitive isolates revealed structural variants in two strains, and several small variants in all three strains. These variations involved a TonB-dependent outer membrane receptor in one strain, and mutations in lipopolysaccharide synthesis genes in two strains. Prophage deletion and induction were also noted in two strains, as well as mutations in several genes associated with virulence factors. Mutations in genes involved in susceptibility to conventional antibiotics were also identified in BIMs, with both decreased and increased antibiotic sensitivity to various antibiotics being observed. These findings may have implications for future applications of lytic phage therapy.IMPORTANCELytic bacteriophages are viruses that infect and kill bacteria and can be used to treat difficult-to-treat bacterial infections, including biofilm-associated infections and multidrug-resistant bacteria. Pseudomonas aeruginosa is a bacterium that can cause life-threatening infections. Lytic bacteriophage therapy has been trialed in the treatment of P. aeruginosa infections; however, sometimes bacteria develop resistance to the bacteriophages. This study sheds light on the genetic mechanisms of such resistance, and how this might be harnessed to restore the sensitivity of multidrug-resistant P. aeruginosa to conventional antibiotics. |
| format | Article |
| id | doaj-art-a8ee51be9426405fb5447b92ea54fe65 |
| institution | OA Journals |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
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| series | Microbiology Spectrum |
| spelling | doaj-art-a8ee51be9426405fb5447b92ea54fe652025-08-20T02:11:31ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-05-0113510.1128/spectrum.02149-24Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktailStephanie A. Fong0George Bouras1Ghais Houtak2Roshan Nepal3Sholeh Feizi4Sandra Morales5Alkis J. Psaltis6Peter-John Wormald7Sarah Vreugde8Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaAmpliPhi Australia, Brookvale, New South Wales, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaDepartment of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide, Adelaide, AustraliaABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that can cause sinus infections and pneumonia in cystic fibrosis (CF) patients. Bacteriophage therapy is being investigated as a treatment for antibiotic-resistant P. aeruginosa infections. Although virulent bacteriophages have shown promise in treating P. aeruginosa infections, the development of bacteriophage-insensitive mutants (BIMs) in the presence of bacteriophages has been described. The aim of this study was to examine the genetic changes associated with the BIM phenotype. Biofilms of three genetically distinct P. aeruginosa strains, including PAO1 (ATCC 15692), and two clinical respiratory isolates (one CF and one non-CF) were grown for 7 days and treated with either a cocktail of four bacteriophages or a vehicle control for 7 consecutive days. BIMs isolated from the biofilms were detected by streak assays, and resistance to the phage cocktail was confirmed using spot test assays. Comparison of whole genome sequencing between the recovered BIMs and their respective vehicle control-treated phage-sensitive isolates revealed structural variants in two strains, and several small variants in all three strains. These variations involved a TonB-dependent outer membrane receptor in one strain, and mutations in lipopolysaccharide synthesis genes in two strains. Prophage deletion and induction were also noted in two strains, as well as mutations in several genes associated with virulence factors. Mutations in genes involved in susceptibility to conventional antibiotics were also identified in BIMs, with both decreased and increased antibiotic sensitivity to various antibiotics being observed. These findings may have implications for future applications of lytic phage therapy.IMPORTANCELytic bacteriophages are viruses that infect and kill bacteria and can be used to treat difficult-to-treat bacterial infections, including biofilm-associated infections and multidrug-resistant bacteria. Pseudomonas aeruginosa is a bacterium that can cause life-threatening infections. Lytic bacteriophage therapy has been trialed in the treatment of P. aeruginosa infections; however, sometimes bacteria develop resistance to the bacteriophages. This study sheds light on the genetic mechanisms of such resistance, and how this might be harnessed to restore the sensitivity of multidrug-resistant P. aeruginosa to conventional antibiotics.https://journals.asm.org/doi/10.1128/spectrum.02149-24bacteriophagePseudomonas aeruginosacystic fibrosismultidrug resistance |
| spellingShingle | Stephanie A. Fong George Bouras Ghais Houtak Roshan Nepal Sholeh Feizi Sandra Morales Alkis J. Psaltis Peter-John Wormald Sarah Vreugde Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail Microbiology Spectrum bacteriophage Pseudomonas aeruginosa cystic fibrosis multidrug resistance |
| title | Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail |
| title_full | Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail |
| title_fullStr | Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail |
| title_full_unstemmed | Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail |
| title_short | Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail |
| title_sort | genomic variation in pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail |
| topic | bacteriophage Pseudomonas aeruginosa cystic fibrosis multidrug resistance |
| url | https://journals.asm.org/doi/10.1128/spectrum.02149-24 |
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