1
|
Ning Y, Teng T, Wu X, Wang M, Jiao X, Qiao J. Development of an enzyme-linked phage receptor-binding protein assay (ELPRA) based on a novel biorecognition molecule- receptor-binding protein Gp130 of Pseudomonas aeruginosa bacteriophage Henu5. Enzyme Microb Technol 2024; 177:110442. [PMID: 38593554 DOI: 10.1016/j.enzmictec.2024.110442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium associated with life-threatening healthcare-associated infections (HAIs), including burn wound infections, pneumonia and sepsis. Moreover, P. aeruginosa has been considered a pathogen of global concern due to its rising antibiotic resistance. Efficient identification of P. aeruginosa would significantly benefit the containment of bacterial infections, prevent pathogen transmission, and provide orientated treatment options. The accuracy and specificity of bacterial detection are primarily dictated by the biorecognition molecules employed. Lytic bacteriophages (or phages) could specifically attach to and lyse host bacterial cells. Phages' host specificity is typically determined by their receptor-binding proteins (RBPs), which recognize and adsorb phages to particular bacterial host receptors. This makes RBPs promising biorecognition molecules in bacterial detection. This study identified a novel RBP (Gp130) from the P. aeruginosa phage Henu5. A modified enzyme-linked phage receptor-binding protein assay (ELPRA) was developed for P. aeruginosa detection employing Gp130 as biorecognition molecules. Optimized conditions provided a calibration curve for P. aeruginosa with a range from 1.0 × 103 to 1.0 × 107 CFU/mL, with a limit of detection as low as 10 CFU/mL in phosphate-buffered saline (PBS). With VITEKⓇ 2 Compact system identification (40 positives and 21 negatives) as the gold standard, the sensitivity of ELPRA was 0.950 (0.818-0.991), and the specificity was 0.905 (0.682-0.983) within a 95 %confidence interval. Moreover, the recovery test in spiked mouse serum showed recovery rates ranging from 82.79 %to 98.17%, demonstrating the prospect of the proposed ELPRA for detecting P. aeruginosa in biological samples.
Collapse
Affiliation(s)
- Yu Ning
- Department of Medical Laboratory, Shandong Second Medical University, Weifang, Shandong 261053, PR China
| | - Tieshan Teng
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, PR China
| | - Xuehan Wu
- Department of Medical Laboratory, Shandong Second Medical University, Weifang, Shandong 261053, PR China
| | - Menglu Wang
- Department of Medical Laboratory, Shandong Second Medical University, Weifang, Shandong 261053, PR China
| | - Xin Jiao
- Department of Medical Laboratory, Shandong Second Medical University, Weifang, Shandong 261053, PR China
| | - Jinjuan Qiao
- Department of Medical Laboratory, Shandong Second Medical University, Weifang, Shandong 261053, PR China; Institutional Key Laboratory of Clinical Laboratory Diagnostics, 12th 5-Year Project of Shandong Province, Shandong Second Medical University, Weifang, Shandong 261053, PR China.
| |
Collapse
|
2
|
Schmidt AK, Schwartzkopf CM, Pourtois JD, Burgener EB, Faith DR, Joyce A, Lamma T, Kumar G, Bollyky PL, Secor PR. Targeted deletion of Pf prophages from diverse Pseudomonas aeruginosa isolates has differential impacts on quorum sensing and virulence traits. J Bacteriol 2024; 206:e0040223. [PMID: 38687034 PMCID: PMC11112994 DOI: 10.1128/jb.00402-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that commonly causes medical hardware, wound, and respiratory infections. Temperate filamentous Pf phages that infect P. aeruginosa impact numerous virulence phenotypes. Most work on Pf phages has focused on Pf4 and its host P. aeruginosa PAO1. Expanding from Pf4 and PAO1, this study explores diverse Pf phages infecting P. aeruginosa clinical isolates. We describe a simple technique targeting the Pf lysogeny maintenance gene, pflM (PA0718), that enables the effective elimination of Pf prophages from diverse P. aeruginosa hosts. The pflM gene shows diversity among different Pf phage isolates; however, all examined pflM alleles encode the DUF5447 domain. We demonstrate that pflM deletion results in prophage excision but not replication, leading to total prophage loss, indicating a role for lysis/lysogeny decisions for the DUF5447 domain. This study also assesses the effects different Pf phages have on host quorum sensing, biofilm formation, pigment production, and virulence against the bacterivorous nematode Caenorhabditis elegans. We find that Pf phages have strain-specific impacts on quorum sensing and biofilm formation, but nearly all suppress pigment production and increase C. elegans avoidance behavior. Collectively, this research not only introduces a valuable tool for Pf prophage elimination from diverse P. aeruginosa isolates but also advances our understanding of the complex relationship between P. aeruginosa and filamentous Pf phages.IMPORTANCEPseudomonas aeruginosa is an opportunistic bacterial pathogen that is frequently infected by filamentous Pf phages (viruses) that integrate into its chromosome, affecting behavior. Although prior work has focused on Pf4 and PAO1, this study investigates diverse Pf in clinical isolates. A simple method targeting the deletion of the Pf lysogeny maintenance gene pflM (PA0718) effectively eliminates Pf prophages from clinical isolates. The research evaluates the impact Pf prophages have on bacterial quorum sensing, biofilm formation, and virulence phenotypes. This work introduces a valuable tool to eliminate Pf prophages from clinical isolates and advances our understanding of P. aeruginosa and filamentous Pf phage interactions.
Collapse
Affiliation(s)
- Amelia K. Schmidt
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Julie D. Pourtois
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Elizabeth B. Burgener
- Division of Pediatric Pulmonology and Sleep Medicine, Children’s Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Alex Joyce
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Tyrza Lamma
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Geetha Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Paul L. Bollyky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| |
Collapse
|
3
|
Hernandez CA, Delesalle VA, Krukonis GP, DeCurzio JM, Koskella B. Genomic and phenotypic signatures of bacteriophage coevolution with the phytopathogen Pseudomonas syringae. Mol Ecol 2024; 33:e16850. [PMID: 36651263 DOI: 10.1111/mec.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 01/19/2023]
Abstract
The rate and trajectory of evolution in an obligate parasite is critically dependent on those of its host(s). Adaptation to a genetically homogeneous host population should theoretically result in specialization, while adaptation to an evolving host population (i.e., coevolution) can result in various outcomes including diversification, range expansion, and/or local adaptation. For viruses of bacteria (bacteriophages, or phages), our understanding of how evolutionary history of the bacterial host(s) impacts viral genotypic and phenotypic evolution is currently limited. In this study, we used whole genome sequencing and two different metrics of phage impacts to compare the genotypes and phenotypes of lytic phages that had either coevolved with or were repeatedly passaged on an unchanging (ancestral) strain of the phytopathogen Pseudomonas syringae. Genomes of coevolved phages had more mutations than those of phages passaged on a constant host, and most mutations were in genes encoding phage tail-associated proteins. Phages from both passaging treatments shared some phenotypic outcomes, including range expansion and divergence across replicate populations, but coevolved phages were more efficient at reducing population growth (particularly of sympatric coevolved hosts). Genotypic similarity correlated with infectivity profile similarity in coevolved phages, but not in phages passaged on the ancestral host. Overall, while adaptation to either host type (coevolving or ancestral) led to divergence in phage tail proteins and infectivity patterns, coevolution led to more rapid molecular changes that increased bacterial killing efficiency and had more predictable effects on infectivity range. Together, these results underscore the important role of hosts in driving viral evolution and in shaping the genotype-phenotype relationship.
Collapse
Affiliation(s)
- Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, California, Berkeley, USA
| | | | - Greg P Krukonis
- Department of Biology, Angelo State University, San Angelo, Texas, USA
| | - Jenna M DeCurzio
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, Berkeley, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
4
|
Daugelavičius R, Daujotaitė G, Bamford DH. Lysis Physiology of Pseudomonas aeruginosa Infected with ssRNA Phage PRR1. Viruses 2024; 16:645. [PMID: 38675985 PMCID: PMC11054506 DOI: 10.3390/v16040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The phage PRR1 belongs to the Leviviridae family, a group of ssRNA bacteriophages that infect Gram-negative bacteria. The variety of host cells is determined by the specificity of PRR1 to a pilus encoded by a broad host range of IncP-type plasmids that confer multiple types of antibiotic resistance to the host. Using P. aeruginosa strain PAO1 as a host, we analyzed the PRR1 infection cycle, focusing on cell lysis. PRR1 infection renders P. aeruginosa cells sensitive to lysozyme approximately 20 min before the start of a drop in suspension turbidity. At the same time, infected cells start to accumulate lipophilic anions. The on-line monitoring of the entire infection cycle showed that single-gene-mediated lysis strongly depends on the host cells' physiological state. The blockage of respiration or a reduction in the intracellular ATP concentration during the infection resulted in the inhibition of lysis. The same effect was observed when the synthesis of PRR1 lysis protein was induced in an E. coli expression system. In addition, lysis was strongly dependent on the level of aeration. Dissolved oxygen concentrations sufficient to support cell growth did not ensure efficient lysis, and a coupling between cell lysis initiation and aeration level was observed. However, the duration of the drop in suspension turbidity did not depend on the level of aeration.
Collapse
Affiliation(s)
| | - Greta Daujotaitė
- Department of Biochemistry, Vytautas Magnus University, LT-44248 Kaunas, Lithuania;
- Molecular and Integrative Biosciences Research Programme, Department of Biological and Environmental Sciences and Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Dennis H. Bamford
- Molecular and Integrative Biosciences Research Programme, Department of Biological and Environmental Sciences and Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| |
Collapse
|
5
|
Whiteley LE, Whiteley M. Characterization of a new Pseudomonas aeruginosa Queuovirinae bacteriophage. Microbiol Spectr 2024; 12:e0371923. [PMID: 38345389 PMCID: PMC10913419 DOI: 10.1128/spectrum.03719-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/17/2024] [Indexed: 03/06/2024] Open
Abstract
The ESKAPEE pathogen Pseudomonas aeruginosa is a common cause of chronic wound and cystic fibrosis lung infections, as well as acute burn and nosocomial infections. Many of these infections are recalcitrant to conventional antibiotic therapies due to both traditional antibiotic resistance mechanisms and antimicrobial tolerance. Recent successes with bacteriophage (phage) therapy to treat chronic human P. aeruginosa infections have led to a renewed interest in isolating and characterizing new P. aeruginosa phages. Here, we isolated and characterized a new lytic phage (termed PIP, pili-infecting phage) capable of infecting P. aeruginosa PA14. PIP is a tailed phage with an icosahedral head and flexible tail containing a genome that is 57,462 bp in length. Phylogenetic analysis reveals that PIP belongs to the subfamily Queuovirinae and genus Nipunavirus but is highly divergent in gene content from known Nipunaviruses. By isolating and characterizing a P. aeruginosa strain that spontaneously evolved resistance to PIP, we show that the receptor for PIP is Type IV pili. In summary, we isolated a new P. aeruginosa phage species with a unique genome, thus increasing the diversity of phages known to infect this important human pathogen.IMPORTANCEThe opportunistic pathogen Pseudomonas aeruginosa causes both acute and chronic human infections. These infections are notoriously difficult to treat due to both antibiotic resistance and antibiotic tolerance. The increasing frequency of antibiotic failure in P. aeruginosa infections has led scientists to explore other treatment options, including bacteriophage (phage) therapy. To this end, there has been a significant effort to identify new Pseudomonas phages. Here, we isolated and characterized a bacteriophage (termed PIP, pili-infecting phage) that infects P. aeruginosa PA14. Examination of the PIP genome revealed that this phage represents a new species in the subclass Queuovirinae. The isolation and characterization of spontaneous PA14 mutants that are resistant to PIP infection revealed Type IV pili as the PIP receptor. Ultimately, this study characterizes a new species of Pseudomonas phage, thus enhancing the known diversity of phages that infect this important pathogen.
Collapse
Affiliation(s)
- Lauren E. Whiteley
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Marvin Whiteley
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| |
Collapse
|
6
|
Ipoutcha T, Racharaks R, Huttelmaier S, Wilson CJ, Ozer EA, Hartmann EM. A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages. Microbiol Spectr 2024; 12:e0289723. [PMID: 38294230 PMCID: PMC10913387 DOI: 10.1128/spectrum.02897-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024] Open
Abstract
The rise in the frequency of antibiotic resistance has made bacterial infections, specifically Pseudomonas aeruginosa, a cause for greater concern. Phage therapy is a promising solution that uses naturally isolated phages to treat bacterial infections. Ecological limitations, which stipulate a discrete host range and the inevitable evolution of resistance, may be overcome through a better understanding of phage biology and the utilization of engineered phages. In this study, we developed a synthetic biology approach to construct tailed phages that naturally target clinically relevant strains of Pseudomonas aeruginosa. As proof of concept, we successfully cloned and assembled the JG024 and DMS3 phage genomes in yeast using transformation-associated recombination cloning and rebooted these two phage genomes in two different strains of P. aeruginosa. We identified factors that affected phage reboot efficiency like the phage species or the presence of antiviral defense systems in the bacterial strain. We have successfully extended this method to two other phage species and observed that the method enables the reboot of phages that are naturally unable to infect the strain used for reboot. This research represents a critical step toward the construction of clinically relevant, engineered P. aeruginosa phages.IMPORTANCEPseudomonas aeruginosa is a bacterium responsible for severe infections and a common major complication in cystic fibrosis. The use of antibiotics to treat bacterial infections has become increasingly difficult as antibiotic resistance has become more prevalent. Phage therapy is an alternative solution that is already being used in some European countries, but its use is limited by the narrow host range due to the phage receptor specificity, the presence of antiviral defense systems in the bacterial strain, and the possible emergence of phage resistance. In this study, we demonstrate the use of a synthetic biology approach to construct and reboot clinically relevant P. aeruginosa tailed phages. This method enables a significant expansion of possibilities through the construction of engineered phages for therapy applications.
Collapse
Affiliation(s)
- Thomas Ipoutcha
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Ratanachat Racharaks
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Cole J. Wilson
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| |
Collapse
|
7
|
Su Q, Lu D, Kong J, Lin H, Xuan G, Wang J. PqsA mutation-mediated enhancement of phage-mediated combat against Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 14:1296777. [PMID: 38469347 PMCID: PMC10925624 DOI: 10.3389/fcimb.2024.1296777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/17/2024] [Indexed: 03/13/2024] Open
Abstract
Phage therapy is a potential approach in the biocontrol of foodborne pathogens. However, the emergence of phage resistance and the narrow host range of most phage isolates continue to limit the antimicrobial efficacy of phages. Here, we investigated the potential of the pqsA gene, encoding the anthranilate-CoA ligase enzyme, as an adjuvant for phage therapy. The knockout of the pqsA gene significantly enhanced the bactericidal effect of phages vB_Pae_QDWS and vB_Pae_S1 against Pseudomonas aeruginosa. Under phage infection pressure, the growth of the PaΔpqsA was significantly inhibited within 8 h compared to the wild-type PAO1. Furthermore, we found that altering phage adsorption is not how PaΔpqsA responds to phage infection. Although pqsA represents a promising target for enhancing phage killing, it may not be applicable to all phages, such as types vB_Pae_W3 and vB_Pae_TR. Our findings provide new material reserves for the future design of novel phage-based therapeutic strategies.
Collapse
Affiliation(s)
| | | | | | | | - Guanhua Xuan
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jingxue Wang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| |
Collapse
|
8
|
Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. Sci Adv 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
Collapse
Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| |
Collapse
|
9
|
Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
Collapse
Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
| |
Collapse
|
10
|
García-Cruz JC, Rebollar-Juarez X, Limones-Martinez A, Santos-Lopez CS, Toya S, Maeda T, Ceapă CD, Blasco L, Tomás M, Díaz-Velásquez CE, Vaca-Paniagua F, Díaz-Guerrero M, Cazares D, Cazares A, Hernández-Durán M, López-Jácome LE, Franco-Cendejas R, Husain FM, Khan A, Arshad M, Morales-Espinosa R, Fernández-Presas AM, Cadet F, Wood TK, García-Contreras R. Resistance against two lytic phage variants attenuates virulence and antibiotic resistance in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 13:1280265. [PMID: 38298921 PMCID: PMC10828002 DOI: 10.3389/fcimb.2023.1280265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024] Open
Abstract
Background Bacteriophage therapy is becoming part of mainstream Western medicine since antibiotics of clinical use tend to fail. It involves applying lytic bacteriophages that self-replicate and induce cell lysis, thus killing their hosts. Nevertheless, bacterial killing promotes the selection of resistant clones which sometimes may exhibit a decrease in bacterial virulence or antibiotic resistance. Methods In this work, we studied the Pseudomonas aeruginosa lytic phage φDCL-PA6 and its variant φDCL-PA6α. Additionally, we characterized and evaluated the production of virulence factors and the virulence in a Galleria mellonella model of resistant mutants against each phage for PA14 and two clinical strains. Results Phage φDCL-PA6α differs from the original by only two amino acids: one in the baseplate wedge subunit and another in the tail fiber protein. According to genomic data and cross-resistance experiments, these changes may promote the change of the phage receptor from the O-antigen to the core lipopolysaccharide. Interestingly, the host range of the two phages differs as determined against the Pseudomonas aeruginosa reference strains PA14 and PAO1 and against nine multidrug-resistant isolates from ventilator associated pneumonia. Conclusions We show as well that phage resistance impacts virulence factor production. Specifically, phage resistance led to decreased biofilm formation, swarming, and type III secretion; therefore, the virulence towards Galleria mellonella was dramatically attenuated. Furthermore, antibiotic resistance decreased for one clinical strain. Our study highlights important potential advantages of phage therapy's evolutionary impact that may be exploited to generate robust therapy schemes.
Collapse
Affiliation(s)
- Juan Carlos García-Cruz
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Xareni Rebollar-Juarez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Aldo Limones-Martinez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Cristian Sadalis Santos-Lopez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Universidad Univer Milenium, Toluca de Lerdo, Mexico
| | - Shotaro Toya
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Corina Diana Ceapă
- Microbiology Laboratory, Chemistry Institute, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Lucia Blasco
- Microbiología Traslacional y Multidisciplinar (MicroTM), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
- Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - María Tomás
- Microbiología Traslacional y Multidisciplinar (MicroTM), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
- Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores (FES) Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores (FES) Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Miguel Díaz-Guerrero
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Daniel Cazares
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Adrián Cazares
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Melisa Hernández-Durán
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación, Luis Guillermo Ibarra Ibarra, Mexico, Mexico
| | - Luis Esaú López-Jácome
- Laboratorio de Microbiología Clínica, División de Infectología, Instituto Nacional de Rehabilitación, Luis Guillermo Ibarra Ibarra, Mexico, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rafael Franco-Cendejas
- Subdirección de Investigación Biomédica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico, Mexico
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Altaf Khan
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Arshad
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ana María Fernández-Presas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Frederic Cadet
- PEACCEL, Artificial Intelligence Department, AI for Biologics, Paris, France
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| |
Collapse
|
11
|
Wang SY, Tan X, Liu ZQ, Ma H, Liu TB, Yang YQ, Ying Y, Gao RY, Zhang DZ, Ma YF, Chen K, Lin L, Jiang ZH, Yu JL. Pharmacokinetics and safety evaluation of intravenously administered Pseudomonas phage PA_LZ7 in a mouse model. Microbiol Spectr 2024; 12:e0188223. [PMID: 38014983 PMCID: PMC10783130 DOI: 10.1128/spectrum.01882-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Phage therapy is gaining traction as an alternative to antibiotics due to the rise of multi-drug-resistant (MDR) bacteria. This study assessed the pharmacokinetics and safety of PA_LZ7, a phage targeting MDR Pseudomonas aeruginosa, in mice. After intravenous administration, the phage showed an exponential decay in plasma and its concentration dropped significantly within 24 h for all dosage groups. Although there was a temporary increase in certain plasma cytokines and spleen weight at higher dosages, no significant toxicity was observed. Therefore, PA_LZ7 shows potential as an effective and safe candidate for future phage therapy against MDR P. aeruginosa infections.
Collapse
Affiliation(s)
- Si-yun Wang
- Department of Neonatology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Xin Tan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zi-qiang Liu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Ma
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Tian-bin Liu
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Yong-qing Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yong Ying
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Ru-yue Gao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Dai-zhou Zhang
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Ying-fei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kai Chen
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Lin Lin
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Zhi-huan Jiang
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, Ji'nan, China
- Shandong Innovation Center of Engineered Bacteriophage Therapeutics, Ji'nan, China
| | - Jia-lin Yu
- Department of Neonatology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Chongqing, China
- Department of Neonatology, Southern University of Science and Technology Hospital, Shenzhen, China
| |
Collapse
|
12
|
Schroven K, Voet M, Lavigne R, Hendrix H. Targeted Genome Editing of Virulent Pseudomonas Phages Using CRISPR-Cas3. Methods Mol Biol 2024; 2793:113-128. [PMID: 38526727 DOI: 10.1007/978-1-0716-3798-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The vast number of unknown phage-encoded ORFan genes and limited insights into the genome organization of phages illustrate the need for efficient genome engineering tools to study bacteriophage genes in their natural context. In addition, there is an application-driven desire to alter phage properties, which is hampered by time constraints for phage genome engineering in the bacterial host. We here describe an optimized CRISPR-Cas3 system in Pseudomonas for straightforward editing of the genome of virulent bacteriophages. The two-vector system combines a broad host range CRISPR-Cas3 targeting plasmid with a SEVA plasmid for homologous directed repair, which enables the creation of clean deletions, insertions, or substitutions in the phage genome within a week. After creating the two plasmids separately, a co-transformation to P. aeruginosa cells is performed. A subsequent infection with the targeted phage allows the CRISPR-Cas3 system to cut the DNA specifically and facilitate or select for homologous recombination. This system has also been successfully applied for P. aeruginosa and Pseudomonas putida genome engineering. The method is straightforward, efficient, and universal, enabling to extrapolate the system to other phage-host pairs.
Collapse
Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| |
Collapse
|
13
|
Böhning J, Graham M, Letham SC, Davis LK, Schulze U, Stansfeld PJ, Corey RA, Pearce P, Tarafder AK, Bharat TAM. Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa. Nat Commun 2023; 14:8429. [PMID: 38114502 PMCID: PMC10730611 DOI: 10.1038/s41467-023-44160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Inoviruses are filamentous phages infecting numerous prokaryotic phyla. Inoviruses can self-assemble into mesoscale structures with liquid-crystalline order, termed tactoids, which protect bacterial cells in Pseudomonas aeruginosa biofilms from antibiotics. Here, we investigate the structural, biophysical, and protective properties of tactoids formed by the P. aeruginosa phage Pf4 and Escherichia coli phage fd. A cryo-EM structure of the capsid from fd revealed distinct biochemical properties compared to Pf4. Fd and Pf4 formed tactoids with different morphologies that arise from differing phage geometries and packing densities, which in turn gave rise to different tactoid emergent properties. Finally, we showed that tactoids formed by either phage protect rod-shaped bacteria from antibiotic treatment, and that direct association with a tactoid is required for protection, demonstrating the formation of a diffusion barrier by the tactoid. This study provides insights into how filamentous molecules protect bacteria from extraneous substances in biofilms and in host-associated infections.
Collapse
Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Miles Graham
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Suzanne C Letham
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Luke K Davis
- Department of Mathematics, University College London, London, WC1H 0AY, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Philip Pearce
- Department of Mathematics, University College London, London, WC1H 0AY, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Abul K Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| |
Collapse
|
14
|
Cobián Güemes AG, Ghatbale P, Blanc AN, Morgan CJ, Garcia A, Leonard J, Huang L, Kovalick G, Proost M, Chiu M, Kuo P, Oh J, Karthikeyan S, Knight R, Pogliano J, Schooley RT, Pride DT. Jumbo phages are active against extensively drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. Antimicrob Agents Chemother 2023; 67:e0065423. [PMID: 37931230 PMCID: PMC10720484 DOI: 10.1128/aac.00654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/08/2023] [Indexed: 11/08/2023] Open
Abstract
Antibiotic-resistant bacteria present an emerging challenge to human health. Their prevalence has been increasing across the globe due in part to the liberal use of antibiotics that has pressured them to develop resistance. Those bacteria that acquire mobile genetic elements are especially concerning because those plasmids may be shared readily with other microbes that can then also become antibiotic resistant. Serious infections have recently been related to the contamination of preservative-free eyedrops with extensively drug-resistant (XDR) isolates of Pseudomonas aeruginosa, already resulting in three deaths. These drug-resistant isolates cannot be managed with most conventional antibiotics. We sought to identify alternatives to conventional antibiotics for the lysis of these XDR isolates and identified multiple bacteriophages (viruses that attack bacteria) that killed them efficiently. We found both jumbo phages (>200 kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the three separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.
Collapse
Affiliation(s)
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Alisha N. Blanc
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Chase J. Morgan
- Department of Biology, University of California San Diego, La Jolla, California, USA
| | - Andrew Garcia
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Jesse Leonard
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Lina Huang
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Marissa Proost
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Megan Chiu
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Joseph Oh
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Smruthi Karthikeyan
- Department of Environmental Science and Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Sciences & Engineering, University of California San Diego, La Jolla, California, USA
| | - Joe Pogliano
- Department of Biology, University of California San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
| | - Robert T. Schooley
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
15
|
Evseev P, Bocharova J, Shagin D, Chebotar I. Analysis of Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis Revealed Novel Groups of Filamentous Bacteriophages. Viruses 2023; 15:2215. [PMID: 38005892 PMCID: PMC10675462 DOI: 10.3390/v15112215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause infections in humans, especially in hospital patients with compromised host defence mechanisms, including patients with cystic fibrosis. Filamentous bacteriophages represent a group of single-stranded DNA viruses infecting different bacteria, including P. aeruginosa and other human and animal pathogens; many of them can replicate when integrated into the bacterial chromosome. Filamentous bacteriophages can contribute to the virulence of P. aeruginosa and influence the course of the disease. There are just a few isolated and officially classified filamentous bacteriophages infecting P. aeruginosa, but genomic studies indicated the frequent occurrence of integrated prophages in many P. aeruginosa genomes. An analysis of sequenced genomes of P. aeruginosa isolated from upper respiratory tract (throat and nasal swabs) and sputum specimens collected from Russian patients with cystic fibrosis indicated a higher diversity of filamentous bacteriophages than first thought. A detailed analysis of predicted bacterial proteins revealed prophage regions representing the filamentous phages known to be quite distantly related to known phages. Genomic comparisons and phylogenetic studies enabled the proposal of several new taxonomic groups of filamentous bacteriophages.
Collapse
Affiliation(s)
- Peter Evseev
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Julia Bocharova
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Dmitriy Shagin
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Igor Chebotar
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| |
Collapse
|
16
|
Mäntynen S, Salomaa MM, Poranen MM. Diversity and Current Classification of dsRNA Bacteriophages. Viruses 2023; 15:2154. [PMID: 38005832 PMCID: PMC10674327 DOI: 10.3390/v15112154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Half a century has passed since the discovery of Pseudomonas phage phi6, the first enveloped dsRNA bacteriophage to be isolated. It remained the sole known dsRNA phage for a quarter of a century and the only recognised member of the Cystoviridae family until the year 2018. After the initial discovery of phi6, additional dsRNA phages have been isolated from globally distant locations and identified in metatranscriptomic datasets, suggesting that this virus type is more ubiquitous in nature than previously acknowledged. Most identified dsRNA phages infect Pseudomonas strains and utilise either pilus or lipopolysaccharide components of the host as the primary receptor. In addition to the receptor-mediated strictly lytic lifestyle, an alternative persistent infection strategy has been described for some dsRNA phages. To date, complete genome sequences of fourteen dsRNA phage isolates are available. Despite the high sequence diversity, similar sets of genes can typically be found in the genomes of dsRNA phages, suggesting shared evolutionary trajectories. This review provides a brief overview of the recognised members of the Cystoviridae virus family and related dsRNA phage isolates, outlines the current classification of dsRNA phages, and discusses their relationships with eukaryotic RNA viruses.
Collapse
Affiliation(s)
- Sari Mäntynen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; (M.M.S.); (M.M.P.)
| | | | | |
Collapse
|
17
|
Tsai YC, Lee YP, Lin NT, Yang HH, Teh SH, Lin LC. Therapeutic effect and anti-biofilm ability assessment of a novel phage, phiPA1-3, against carbapenem-resistant Pseudomonas aeruginosa. Virus Res 2023; 335:199178. [PMID: 37490958 PMCID: PMC10430585 DOI: 10.1016/j.virusres.2023.199178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
Multiple drug-resistant (MDR) Pseudomonas aeruginosa commonly causes severe hospital-acquired infections. The gradual emergence of carbapenem-resistant P. aeruginosa has recently gained attention. A wide array of P. aeruginosa-mediated pathogenic mechanisms, including its biofilm-forming ability, limits the use of effective antimicrobial treatments against it. In the present study, we isolated and characterized the phenotypic, biological, and genomic characteristics of a bacteriophage, vB_PaP_phiPA1-3 (phiPA1-3). Biofilm eradication and phage rescue from bacterial infections were assessed to demonstrate the efficacy of the application potential. Host range spectrum analysis revealed that phiPA1-3 is a moderate host range phage that infects 20% of the clinically isolated strains of P. aeruginosa tested, including carbapenem-resistant P. aeruginosa (CRPA). The phage exhibited stability at pH 7.0 and 9.0, with significantly reduced viability below pH 5.0 and beyond pH 9.0. phiPA1-3 is a lytic phage with a burst size of 619 plaque-forming units/infected cell at 37 °C and can effectively lyse bacteria in a multiplicity of infection-dependent manner. The genome size of phiPA1-3 was found to be 73,402 bp, with a G+C content of 54.7%, containing 93 open reading frames, of which 62 were annotated as hypothetical proteins and the remaining 31 had known functions. The phage possesses several proteins similar to those found in N4-like phages, including three types of RNA polymerases. This study concluded that phiPA1-3 belongs to the N4-like Schitoviridae family, can potentially eradicate P. aeruginosa biofilms, and thus, serve as a valuable tool for controlling CRPA infections.
Collapse
Affiliation(s)
- Yu-Chuan Tsai
- Institute of Medical Sciences, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Yi-Pang Lee
- Department of Dentistry, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Nien-Tsung Lin
- Master Program in Biomedical Science, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Hsueh-Hui Yang
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Soon-Hian Teh
- Division of Infectious Diseases, Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC.
| | - Ling-Chun Lin
- Institute of Medical Sciences, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC; Master Program in Biomedical Science, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC.
| |
Collapse
|
18
|
Fei B, Li D, Liu X, You X, Guo M, Ren Y, Liu Y, Wang C, Zhu R, Li Y. Characterization and genomic analysis of a broad-spectrum lytic phage HZ2201 and its antibiofilm efficacy against Pseudomonas aeruginosa. Virus Res 2023; 335:199184. [PMID: 37532140 PMCID: PMC10407953 DOI: 10.1016/j.virusres.2023.199184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
Pseudomonas aeruginosa is a clinically common conditionally pathogenic bacterium, and the abuse of antibiotics has exacerbated its drug resistance in recent years. This has resulted in extensive reports about the usage of Pseudomonas aeruginosa phage as a novel antibacterial drug. In this study, we isolated a novel phage HZ2201 with a broad lytic spectrum. The lytic rate of this phage against Pseudomonas aeruginosa reached 78.38% (29/37), including 25 multi-drug- and carbapenem-resistant Pseudomonas aeruginosa strains. Transmission electron microscopy revealed that phage HZ2201 belongs to the class Caudoviricetes. Biological characterization showed that phage HZ2201 had an latent period of 40 min, a lytic period of 20 min, and a burst size of 440 PFU/cell, with improved tolerance to temperature and pH. Considering genomic analysis, the HZ2201 genome was a circular double-stranded DNA with a size of 45,431 bp and a guanine-cytosine (G + C) content of 52.16%, and contained 3 tRNAs. 27 of the 74 open reading frames (ORFs) annotated by the Rapid Annotation using Subsystem Technology (RAST) tool could be matched to the genomes of known functions, and no genes related to virulence and antibiotic resistance were found. The phylogenetic tree suggests that phage HZ2201 is highly related to the phage ZCPS1 and PaP3, and ORF57 and ORF17 are predicted to encode a holin and an endolysin, respectively. Cell lysis by HZ2201 proceeds through the holin-endolysin system, suggesting that it is a novel phage. Additionally, we demonstrated that phage HZ2201 has a high inhibitory capacity against Pseudomonas aeruginosa biofilms. The results of our study suggest that phage HZ2201 is a novel potential antimicrobial agent for treating drug-resistant Pseudomonas aeruginosa infection.
Collapse
Affiliation(s)
- Bing Fei
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Dengzhou Li
- Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450002, China; The Key Laboratory of Pathogenic Microbes &Antimicrobial Resistance Surveillance of Zhengzhou, Zhengzhou, 450002, China; Henan Engineering Research Center for Identification of Pathogenic Microbes, Zhengzhou, 450002, China; Henan Provincial Key Laboratory of Antibiotics-Resistant Bacterial Infection Prevention & Therapy with Traditional Chinese Medicine, Zhengzhou, 450002, China
| | - Xinwei Liu
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China; Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Xiaojuan You
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China; Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Mengyu Guo
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Yanying Ren
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Ying Liu
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Chunxia Wang
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China; Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Rui Zhu
- Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450002, China; The Key Laboratory of Pathogenic Microbes &Antimicrobial Resistance Surveillance of Zhengzhou, Zhengzhou, 450002, China; Henan Engineering Research Center for Identification of Pathogenic Microbes, Zhengzhou, 450002, China; Henan Provincial Key Laboratory of Antibiotics-Resistant Bacterial Infection Prevention & Therapy with Traditional Chinese Medicine, Zhengzhou, 450002, China.
| | - Yongwei Li
- The Second Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, 450002, China.
| |
Collapse
|
19
|
Olsen NS, Nielsen TK, Cui L, Dedon P, Neve H, Hansen L, Kot W. A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 protection in vitro. Nucleic Acids Res 2023; 51:8663-8676. [PMID: 37503841 PMCID: PMC10484667 DOI: 10.1093/nar/gkad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Deazaguanine DNA modifications are widespread in phages, particularly in those with pathogenic hosts. Pseudomonas phage iggy substitutes ∼16.5% of its genomic 2'-deoxyguanosine (G) with dPreQ0, and the iggy deazaguanine transglycosylase (DpdA) is unique in having a strict GA target motif, not observed previously. The iggy PreQ0 modification is shown to provide protection against both restriction endonucleases and Cas9 (when present in PAM), thus expanding our understanding of the deazaguanine modification system, its potential, and diversity. Phage iggy represents a new genus of Pseudomonas phages within the Queuovirinae subfamily; which have very little in common with other published phage genomes in terms of nucleotide similarity (<10%) and common proteins (<2%). Interestingly, shared similarity is concentrated in dpdA and preQ0 biosynthesis genes. TEM imaging confirmed a siphovirus morphology with a prolate icosahedral head and a non-contractile flexible tail with one long central tail spike. The observed protective effect of the deazaguanine modification on the iggy DNA may contribute to its broad within-species host range. Phage iggy was isolated on Pseudomonas aeruginosa PAO1, but also infects PDO300, PAK, PA14, as well as 10 of 27 tested environmental isolates and 13 of 20 tested clinical isolates of P. aeruginosa from patients with cystic fibrosis.
Collapse
Affiliation(s)
- Nikoline S Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Peter Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, US
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| |
Collapse
|
20
|
Stante M, Weiland-Bräuer N, Repnik U, Werner A, Bramkamp M, Chibani CM, Schmitz RA. Four Novel Caudoviricetes Bacteriophages Isolated from Baltic Sea Water Infect Colonizers of Aurelia aurita. Viruses 2023; 15:1525. [PMID: 37515211 PMCID: PMC10383413 DOI: 10.3390/v15071525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The moon jellyfish Aurelia aurita is associated with a highly diverse microbiota changing with provenance, tissue, and life stage. While the crucial relevance of bacteria to host fitness is well known, bacteriophages have often been neglected. Here, we aimed to isolate virulent phages targeting bacteria that are part of the A. aurita-associated microbiota. Four phages (Pseudomonas phage BSwM KMM1, Citrobacter phages BSwM KMM2-BSwM KMM4) were isolated from the Baltic Sea water column and characterized. Phages KMM2/3/4 infected representatives of Citrobacter, Shigella, and Escherichia (Enterobacteriaceae), whereas KMM1 showed a remarkably broad host range, infecting Gram-negative Pseudomonas as well as Gram-positive Staphylococcus. All phages showed an up to 99% adsorption to host cells within 5 min, short latent periods (around 30 min), large burst sizes (mean of 128 pfu/cell), and high efficiency of plating (EOP > 0.5), demonstrating decent virulence, efficiency, and infectivity. Transmission electron microscopy and viral genome analysis revealed that all phages are novel species and belong to the class of Caudoviricetes harboring a tail and linear double-stranded DNA (formerly known as Siphovirus-like (KMM3) and Myovirus-like (KMM1/2/4) bacteriophages) with genome sizes between 50 and 138 kbp. In the future, these isolates will allow manipulation of the A. aurita-associated microbiota and provide new insights into phage impact on the multicellular host.
Collapse
Affiliation(s)
- Melissa Stante
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Urska Repnik
- Central Microscopy Facility, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany;
| | - Almut Werner
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
- Central Microscopy Facility, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany;
| | - Cynthia M. Chibani
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| |
Collapse
|
21
|
Li F, Hou CFD, Lokareddy RK, Yang R, Forti F, Briani F, Cingolani G. High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217. Nat Commun 2023; 14:4052. [PMID: 37422479 PMCID: PMC10329688 DOI: 10.1038/s41467-023-39756-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023] Open
Abstract
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4.
Collapse
Affiliation(s)
- Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
| |
Collapse
|
22
|
Prokopczuk FI, Im H, Campos-Gomez J, Orihuela CJ, Martínez E. Engineered Superinfective Pf Phage Prevents Dissemination of Pseudomonas aeruginosa in a Mouse Burn Model. mBio 2023; 14:e0047223. [PMID: 37039641 PMCID: PMC10294672 DOI: 10.1128/mbio.00472-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023] Open
Abstract
Pf is a filamentous bacteriophage integrated in the chromosome of most clinical isolates of Pseudomonas aeruginosa. Under stress conditions, mutations occurring in the Pf genome result in the emergence of superinfective variants of Pf (SI-Pf) that are capable of circumventing phage immunity; therefore, SI-Pf can even infect Pf-lysogenized P. aeruginosa. Here, we identified specific mutations located between the repressor and the excisionase genes of Pf4 phage in the P. aeruginosa PAO1 strain that resulted in the emergence of SI-Pf. Based on these findings, we genetically engineered an SI-Pf (eSI-Pf) and tested it as a phage therapy tool for the treatment of life-threatening burn wound infections caused by PAO1. In validation experiments, eSI-Pf was able to infect PAO1 grown in a lawn as well as biofilms formed in vitro on polystyrene. eSI-Pf also infected PAO1 present in burned skin wounds on mice but was not capable of maintaining a sustained reduction in bacterial burden beyond 24 h. Despite not lowering bacterial burden in burned skin tissue, eSI-Pf treatment completely abolished the capability of P. aeruginosa to disseminate from the burn site to internal organs. Over the course of 10 days, this resulted in bacterial clearance and survival of all treated mice. We subsequently determined that eSI-Pf induced a small-colony variant of P. aeruginosa that was unable to disseminate systemically. This attenuated phenotype was due to profound changes in virulence determinant production and altered physiology. Our results suggest that eSI-Pf has potential as a phage therapy against highly recalcitrant antimicrobial-resistant P. aeruginosa infections of burn wounds. IMPORTANCE Pseudomonas aeruginosa is a major cause of burn-related infections. It is also the most likely bacterial infection to advance to sepsis and result in burn-linked death. Frequently, P. aeruginosa strains isolated from burn patients display a multidrug-resistant phenotype necessitating the development of new therapeutic strategies and prophylactic treatments. In this context, phage therapy using lytic phages has demonstrated exciting potential in the control P. aeruginosa infection. However, lytic phages can present a set of drawbacks during phage therapy, including the induction of bacterial resistance and limited bacteria-phage interactions in vivo. Here, we propose an alternative approach to interfere with P. aeruginosa pathogenesis in a burn infection model, i.e., by using an engineered superinfective filamentous phage. Our study demonstrates that treatment with the engineered Pf phage can prevent sepsis and death in a burn mouse model.
Collapse
Affiliation(s)
- Federico I. Prokopczuk
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hansol Im
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Javier Campos-Gomez
- Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Carlos J. Orihuela
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eriel Martínez
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|
23
|
Dai F, Yang G, Lou J, Zhao X, Chen M, Sun G, Yu Y. Isolation and Characterization of Pseudomonas aeruginosa Phages with a Broad Host Spectrum from Hospital Sewage Systems and Their Therapeutic Effect in a Mouse Model. Am J Trop Med Hyg 2023; 108:1220-1226. [PMID: 37094788 PMCID: PMC10540096 DOI: 10.4269/ajtmh.22-0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 02/01/2023] [Indexed: 04/26/2023] Open
Abstract
This study aimed to isolate and characterize phages as an alternative treatment of multidrug- or pan-drug-resistant Pseudomonas aeruginosa. Phage titers and bacterial densities correlated, with the phages disappearing after bacteria were eliminated. We isolated phages in filtered sewage water by a double-layered agar spot test. Fifty-eight P. aeruginosa strains were used to screen the host spectrum of the 14 phages isolated. Random amplification of polymorphic DNA-typing polymerase chain reaction was used to analyze the genomic homologies of the 58 host bacteria strains and four phages with a broad host spectrum. Transmission electron microscopy was used to observe the morphology of the four phages with a broad host spectrum. Mice with intraabdominal P. aeruginosa infection were used as an in vivo animal model to investigate the therapeutic effect of the selected phage. Four virulent phages with a broad host spectrum specific to P. aeruginosa strains were isolated. They were all double-stranded DNA viruses and belonged to four different genotypes. The test curve showed that phage I had the highest adsorption rate, the shortest latent period, and the largest burst size. The infected mouse model indicated that small doses of phage I could prevent the death of infected mice. Phage titers and bacterial densities correlated, with phages disappearing after bacteria were eliminated. Phage I was the most effective and promising treatment of drug-resistant P. aeruginosa.
Collapse
Affiliation(s)
- Fangfang Dai
- Department of Clinical Laboratory, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Gengxia Yang
- General Surgical Center, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Jinli Lou
- Department of Clinical Laboratory, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Xiuying Zhao
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Ming Chen
- Department of Clinical Laboratory, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Guizhen Sun
- Department of Clinical Laboratory, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yanhua Yu
- Department of Clinical Laboratory, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| |
Collapse
|
24
|
Sun L, You J, Li D, Zhang Z, Qin X, Pang W, Li P, Han Q, Li Y, Huang Z, Zhang X, Gong M, Yang H. Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8. Microbiome 2023; 11:18. [PMID: 36721246 PMCID: PMC9887876 DOI: 10.1186/s40168-022-01459-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/31/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Narrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins. RESULTS Here, we report that Pseudomonas phage K8 can evolve broader host range and higher killing efficiency at the cost of virion stability. Phage K8 host range mutant K8-T239A carries a mutant version of the putative baseplate wedge protein GP075, termed GP075m. While phage K8 adsorbs to hosts via the O-specific antigen of bacterial LPS, phage K8-T239A uses GP075m to also bind the bacterial core oligosaccharide, enabling infection of bacterial strains resistant to K8 infection due to modified O-specific antigens. This mutation in GP075 also alters inter-protein interactions among phage proteins, and reduces the stability of phage particles to environmental stressors like heat, acidity, and alkalinity. We find that a variety of mutations in gp075 are widespread in K8 populations, and that the gp075-like genes are widely distributed among the domains of life. CONCLUSION Our data show that a typical life history tradeoff occurs between the stability and the host range in the evolution of phage K8. Reservoirs of viral gene variants may be widely present in phage communities, allowing phages to rapidly adapt to any emerging environmental stressors. Video Abstract.
Collapse
Affiliation(s)
- Li Sun
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jiajia You
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xuying Qin
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenjing Pang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Peize Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qingzhu Han
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yueying Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiwei Huang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xixi Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | | | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| |
Collapse
|
25
|
Mabrouk SS, Abdellatif GR, Abu Zaid AS, Aziz RK, Aboshanab KM. In Vitro and Pre-Clinical Evaluation of Locally Isolated Phages, vB_Pae_SMP1 and vB_Pae_SMP5, Formulated as Hydrogels against Carbapenem-Resistant Pseudomonas aeruginosa. Viruses 2022; 14:v14122760. [PMID: 36560763 PMCID: PMC9780878 DOI: 10.3390/v14122760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The inadequate therapeutic opportunities associated with carbapenem-resistant Pseudomonas aeruginosa (CRPA) clinical isolates impose a search for innovative strategies. Therefore, our study aimed to characterize and evaluate two locally isolated phages formulated in a hydrogel, both in vitro and in vivo, against CRPA clinical isolates. The two phages were characterized by genomic, microscopic, phenotypic characterization, genomic analysis, in vitro and in vivo analysis in a Pseudomonas aeruginosa-infected skin thermal injury rat model. The two siphoviruses belong to class Caudovirectes and were named vB_Pae_SMP1 and vB_Pae_SMP5. Each phage had an icosahedral head of 60 ± 5 nm and a flexible, non-contractile tail of 170 ± 5 nm long, while vB_Pae_SMP5 had an additional base plate containing a 35 nm fiber observed at the end of the tail. The hydrogel was prepared by mixing 5% w/v carboxymethylcellulose (CMC) into the CRPA propagated phage lysate containing phage titer 108 PFU/mL, pH of 7.7, and a spreadability coefficient of 25. The groups were treated with either Phage vB_Pae_SMP1, vB_Pae_SMP5, or a two-phage cocktail hydrogel cellular subepidermal granulation tissues with abundant records of fibroblastic activity and mixed inflammatory cell infiltrates and showed 17.2%, 25.8%, and 22.2% records of dermal mature collagen fibers, respectively. In conclusion, phage vB_Pae_SMP1 or vB_Pae_SMP5, or the two-phage cocktails formulated as hydrogels, were able to manage the infection of CRPA in burn wounds, and promoted healing at the injury site, as evidenced by the histopathological examination, as well as a decrease in animal mortality rate. Therefore, these phage formulae can be considered promising for clinical investigation in humans for the management of CRPA-associated skin infections.
Collapse
Affiliation(s)
- Samar S. Mabrouk
- Department of Microbiology, Faculty of Pharmacy, Ahram Canadian University (ACU), 6th October City, Giza 12566, Egypt
| | - Ghada R. Abdellatif
- Department of Microbiology, Faculty of Pharmacy, Ahram Canadian University (ACU), 6th October City, Giza 12566, Egypt
| | - Ahmed S. Abu Zaid
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Ramy K. Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Department of Microbiology and Immunology, Children’s Cancer Hospital Egypt 57357, Cairo 11617, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Correspondence:
| |
Collapse
|
26
|
Górniak M, Zalewska A, Jurczak-Kurek A. Recombination Events in Putative Tail Fibre Gene in Litunavirus Phages Infecting Pseudomonas aeruginosa and Their Phylogenetic Consequences. Viruses 2022; 14:v14122669. [PMID: 36560673 PMCID: PMC9786124 DOI: 10.3390/v14122669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Recombination is the main driver of bacteriophage evolution. It may serve as a tool for extending the phage host spectrum, which is significant not only for phages' ecology but also for their utilisation as therapeutic agents of bacterial infections. The aim of this study was to detect the recombination events in the genomes of Litunavirus phages infecting Pseudomonas aeruginosa, and present their impact on phylogenetic relations within this phage group. The phylogenetic analyses involved: the whole-genome, core-genome (Schitoviridae conserved genes), variable genome region, and the whole-genome minus variable region. Interestingly, the recombination events taking place in the putative host recognition region (tail fibre protein gene and the adjacent downstream gene) significantly influenced tree topology, suggesting a strong phylogenetic signal. Our results indicate the recombination between phages from two genera Litunavirus and Luzeptimavirus and demonstrate its influence on phage phylogeny.
Collapse
|
27
|
Hungaro HM, Vidigal PMP, do Nascimento EC, Gomes da Costa Oliveira F, Gontijo MTP, Lopez MES. Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry. Viruses 2022; 14:v14030629. [PMID: 35337036 PMCID: PMC8951688 DOI: 10.3390/v14030629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and more than 50% of the genes encoding proteins with unknown functions. Nevertheless, UFJF_PfDIW6’s genome was organised into five functional modules: DNA packaging, structural proteins, DNA metabolism, lysogenic, and host lysis. Comparative genome analysis revealed that the UFJF_PfDIW6’s genome is distinct from other viral genomes available at NCBI databases, displaying maximum coverages of 5% among all alignments. Curiously, this phage showed higher sequence coverages (38–49%) when aligned with uncharacterised prophages integrated into Pseudomonas genomes. Phages compared in this study share conserved locally collinear blocks comprising genes of the modules’ DNA packing and structural proteins but were primarily differentiated by the composition of the DNA metabolism and lysogeny modules. Strategies for taxonomy assignment showed that UFJF_PfDIW6 was clustered into an unclassified genus in the Podoviridae clade. Therefore, our findings indicate that this phage could represent a novel genus belonging to the Podoviridae family.
Collapse
Affiliation(s)
- Humberto Moreira Hungaro
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Campus da UFV, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil;
| | - Edilane Cristina do Nascimento
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Felipe Gomes da Costa Oliveira
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Marco Túlio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-872, SP, Brazil;
| | - Maryoris Elisa Soto Lopez
- Departamento de Engenharia de Alimentos, Universidade de Córdoba (UNICORDOBA), Córdoba 230002, Colombia
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
| |
Collapse
|
28
|
Castledine M, Sierocinski P, Inglis M, Kay S, Hayward A, Buckling A, Padfield D. Greater Phage Genotypic Diversity Constrains Arms-Race Coevolution. Front Cell Infect Microbiol 2022; 12:834406. [PMID: 35310856 PMCID: PMC8931298 DOI: 10.3389/fcimb.2022.834406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Antagonistic coevolution between hosts and parasites, the reciprocal evolution of host resistance and parasite infectivity, has important implications in ecology and evolution. The dynamics of coevolution—notably whether host or parasite has an evolutionary advantage—is greatly affected by the relative amount of genetic variation in host resistance and parasite infectivity traits. While studies have manipulated genetic diversity during coevolution, such as by increasing mutation rates, it is unclear how starting genetic diversity affects host–parasite coevolution. Here, we (co)evolved the bacterium Pseudomonas fluorescens SBW25 and two bacteriophage genotypes of its lytic phage SBW25ɸ2 in isolation (one phage genotype) and together (two phage genotypes). Bacterial populations rapidly evolved phage resistance, and phage reciprocally increased their infectivity in response. When phage populations were evolved with bacteria in isolation, bacterial resistance and phage infectivity increased through time, indicative of arms-race coevolution. In contrast, when both phage genotypes were together, bacteria did not increase their resistance in response to increasing phage infectivity. This was likely due to bacteria being unable to evolve resistance to both phage via the same mutations. These results suggest that increasing initial parasite genotypic diversity can give parasites an evolutionary advantage that arrests long-term coevolution. This study has important implications for the applied use of phage in phage therapy and in understanding host–parasite dynamics in broader ecological and evolutionary theory.
Collapse
|
29
|
Kazantseva OA, Buzikov RM, Pilipchuk TA, Valentovich LN, Kazantsev AN, Kalamiyets EI, Shadrin AM. The Bacteriophage Pf-10-A Component of the Biopesticide "Multiphage" Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae. Viruses 2021; 14:42. [PMID: 35062246 PMCID: PMC8779105 DOI: 10.3390/v14010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Phytopathogenic pseudomonads are widespread in the world and cause a wide range of plant diseases. In this work, we describe the Pseudomonas phage Pf-10, which is a part of the biopesticide "Multiphage" used for bacterial diseases of agricultural crops caused by Pseudomonas syringae. The Pf-10 chromosome is a dsDNA molecule with two direct terminal repeats (DTRs). The phage genomic DNA is 39,424 bp long with a GC-content of 56.5%. The Pf-10 phage uses a packaging mechanism based on T7-like short DTRs, and the length of each terminal repeat is 257 bp. Electron microscopic analysis has shown that phage Pf-10 has the podovirus morphotype. Phage Pf-10 is highly stable at pH values from 5 to 10 and temperatures from 4 to 60 °C and has a lytic activity against Pseudomonas strains. Phage Pf-10 is characterized by fast adsorption rate (80% of virions attach to the host cells in 10 min), but has a relatively small number of progeny (37 ± 8.5 phage particles per infected cell). According to the phylogenetic analysis, phage Pf-10 can be classified as a new phage species belonging to the genus Pifdecavirus, subfamily Studiervirinae, family Autographiviridae, order Caudovirales.
Collapse
Affiliation(s)
- Olesya A. Kazantseva
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Rustam M. Buzikov
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Tatsiana A. Pilipchuk
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Leonid N. Valentovich
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Andrey N. Kazantsev
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Pushchino Radio Astronomy Observatory, 142290 Pushchino, Russia;
| | - Emilia I. Kalamiyets
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Andrey M. Shadrin
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| |
Collapse
|
30
|
Liu Y, Zhang L, Guo M, Chen L, Wu B, Huang H. Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2. J Biol Chem 2021; 297:101357. [PMID: 34756887 PMCID: PMC8633003 DOI: 10.1016/j.jbc.2021.101357] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/26/2022] Open
Abstract
It has been shown that phages have evolved anti-CRISPR (Acr) proteins to inhibit host CRISPR-Cas systems. Most acr genes are located upstream of anti-CRISPR-associated (aca) genes, which is instrumental for identifying these acr genes. Thus far, eight Aca families (Aca1-Aca8) have been identified, all proteins of which share low sequence homology and bind to different target DNA sequences. Recently, Aca1 and Aca2 proteins were discovered to function as repressors by binding to acr-aca promoters, thus implying a potential anti-anti-CRISPR mechanism. However, the structural basis for the repression roles of Aca proteins is still unknown. Here, we elucidated apo-structures of Aca1 and Aca2 proteins and their complex structures with their cognate operator DNA in two model systems, the Pseudomonas phage JBD30 and the Pectobacterium carotovorum template phage ZF40. In combination with biochemical and cellular assays, our study unveils dimerization and DNA-recognition mechanisms of Aca1 and Aca2 family proteins, thus revealing the molecular basis for Aca1-and Aca2-mediated anti-CRISPR repression. Our results also shed light on understanding the repression roles of other Aca family proteins and autoregulation roles of acr-aca operons.
Collapse
Affiliation(s)
- Yanhong Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China; Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Linsheng Zhang
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Maochao Guo
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Liu Chen
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Hongda Huang
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China.
| |
Collapse
|
31
|
Liu Y, Liu M, Hu R, Bai J, He X, Jin Y. Isolation of the Novel Phage PHB09 and Its Potential Use against the Plant Pathogen Pseudomonas syringae pv. actinidiae. Viruses 2021; 13:v13112275. [PMID: 34835081 PMCID: PMC8622976 DOI: 10.3390/v13112275] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are viruses that specifically infect target bacteria. Recently, bacteriophages have been considered potential biological control agents for bacterial pathogens due to their host specificity. Pseudomonas syringae pv. actinidiae (Psa) is a reemerging pathogen that causes bacterial canker of kiwifruit (Actinidia sp.). The economic impact of this pest and the development of resistance to antibiotics and copper sprays in Psa and other pathovars have led to investigation of alternative management strategies. Phage therapy may be a useful alternative to conventional treatments for controlling Psa infections. Although the efficacy of bacteriophage φ6 was evaluated for the control of Psa, the characteristics of other DNA bacteriophages infecting Psa remain unclear. In this study, the PHB09 lytic bacteriophage specific to Psa was isolated from kiwifruit orchard soil. Extensive host range testing using Psa isolated from kiwifruit orchards and other Pseudomonas strains showed PHB09 has a narrow host range. It remained stable over a wide range of temperatures (4-50 °C) and pH values (pH 3-11) and maintained stability for 50 min under ultraviolet irradiation. Complete genome sequence analysis indicated PHB09 might belong to a new myovirus genus in Caudoviricetes. Its genome contains a total of 94,844 bp and 186 predicted genes associated with phage structure, packaging, host lysis, DNA manipulation, transcription, and additional functions. The isolation and identification of PHB09 enrich the research on Pseudomonas phages and provide a promising biocontrol agent against kiwifruit bacterial canker.
Collapse
|
32
|
Knezevic P, Petrovic Fabijan A, Gavric D, Pejic J, Doffkay Z, Rakhely G. Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case. Viruses 2021; 13:1965. [PMID: 34696396 PMCID: PMC8540360 DOI: 10.3390/v13101965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10-4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.
Collapse
Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Aleksandra Petrovic Fabijan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Jovana Pejic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Zsolt Doffkay
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| |
Collapse
|
33
|
Ismail MH, Michie KA, Goh YF, Noorian P, Kjelleberg S, Duggin IG, McDougald D, Rice SA. The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression. Viruses 2021; 13:1614. [PMID: 34452479 PMCID: PMC8402870 DOI: 10.3390/v13081614] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homologue of the P2 phage repressor C and was recently named Pf4r. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show a critical site in repressor C (Pf4r) where a mutation in the site, 788799A>G (Ser4Pro), causes Pf4r to lose its function as the immunity factor against reinfection by Pf4. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation, Pf4r*, associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by multi-angle light scattering (MALS) analysis, where the Pf4r* protein only forms monomers. The loss of dimerisation also explains the loss of Pf4r's immunity function. Phenotypic assays showed that Pf4r increased LasB activity and was also associated with a slight increase in the percentage of morphotypic variants. ChIPseq and transcriptomic analyses suggest that Pf4r also likely functions as a transcriptional regulator for other host genes. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.
Collapse
Affiliation(s)
- Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Katharine A. Michie
- Structural Biology Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia;
| | - Yu Fen Goh
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
| | - Parisa Noorian
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Iain G. Duggin
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore; (M.H.I.); (Y.F.G.); (S.K.); (D.M.)
- The School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- The iThree Institute, The University of Technology Sydney, Sydney, NSW 2007, Australia; (P.N.); (I.G.D.)
| |
Collapse
|
34
|
Markwitz P, Olszak T, Gula G, Kowalska M, Arabski M, Drulis-Kawa Z. Emerging Phage Resistance in Pseudomonas aeruginosa PAO1 Is Accompanied by an Enhanced Heterogeneity and Reduced Virulence. Viruses 2021; 13:1332. [PMID: 34372538 PMCID: PMC8310095 DOI: 10.3390/v13071332] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Bacterial surface structures of a proteinic nature and glycoconjugates contribute to biofilm formation and provide shields to host defense mechanisms (e.g., the complement system and phagocytosis). A loss or alteration of these molecules, leading to phage resistance, could result in fewer virulent bacteria. In this study, we evaluate the biology and phenotype changes in Pseudomonas aeruginosa PAO1 phage-resistant clones, which emerge in phage-treated biofilms. We characterize these clones for phage-typing patterns, antibiotic resistance, biofilm formation, pathogenicity, and interactions with the innate immune system. Another important question that we address is whether phage-resistant mutants are also generated incidentally, despite the phage treatment-selective pressure, as the natural adaptation of the living biofilm population. It is found that the application of different phages targeting a particular receptor selects similar phage resistance patterns. Nevertheless, this results in a dramatic increase in the population heterogeneity, giving over a dozen phage-typing patterns, compared to one of the untreated PAO1 sessile forms. We also confirm the hypothesis that "phage-resistant bacteria are more susceptible to antibiotics and host-clearance mechanisms by the immune system". These findings support phage application in therapy, although the overall statement that phage treatment selects the less virulent bacterial population should be further verified using a bigger collection of clinical strains.
Collapse
Affiliation(s)
- Pawel Markwitz
- Department of Pathogen Biology and Immunology, University of Wroclaw, 51-148 Wroclaw, Poland; (P.M.); (T.O.); (G.G.)
| | - Tomasz Olszak
- Department of Pathogen Biology and Immunology, University of Wroclaw, 51-148 Wroclaw, Poland; (P.M.); (T.O.); (G.G.)
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, University of Wroclaw, 51-148 Wroclaw, Poland; (P.M.); (T.O.); (G.G.)
| | - Magdalena Kowalska
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland; (M.K.); (M.A.)
| | - Michal Arabski
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland; (M.K.); (M.A.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, 51-148 Wroclaw, Poland; (P.M.); (T.O.); (G.G.)
| |
Collapse
|
35
|
Shmidov E, Zander I, Lebenthal-Loinger I, Karako-Lampert S, Shoshani S, Banin E. An Efficient, Counter-Selection-Based Method for Prophage Curing in Pseudomonas aeruginosa Strains. Viruses 2021; 13:v13020336. [PMID: 33670076 PMCID: PMC7926659 DOI: 10.3390/v13020336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 01/28/2023] Open
Abstract
Prophages are bacteriophages in the lysogenic state, where the viral genome is inserted within the bacterial chromosome. They contribute to strain genetic variability and can influence bacterial phenotypes. Prophages are highly abundant among the strains of the opportunistic pathogen Pseudomonas aeruginosa and were shown to confer specific traits that can promote strain pathogenicity. The main difficulty of studying those regions is the lack of a simple prophage-curing method for P. aeruginosa strains. In this study, we developed a novel, targeted-curing approach for prophages in P. aeruginosa. In the first step, we tagged the prophage for curing with an ampicillin resistance cassette (ampR) and further used this strain for the sacB counter-selection marker’s temporal insertion into the prophage region. The sucrose counter-selection resulted in different variants when the prophage-cured mutant is the sole variant that lost the ampR cassette. Next, we validated the targeted-curing with local PCR amplification and Whole Genome Sequencing. The application of the strategy resulted in high efficiency both for curing the Pf4 prophage of the laboratory wild-type (WT) strain PAO1 and for PR2 prophage from the clinical, hard to genetically manipulate, 39016 strain. We believe this method can support the research and growing interest in prophage biology in P. aeruginosa as well as additional Gram-negative bacteria.
Collapse
Affiliation(s)
- Esther Shmidov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Itzhak Zander
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ilana Lebenthal-Loinger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
| | - Sarit Karako-Lampert
- Scientific Equipment Center, The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University, Ramat Gan 5290002, Israel;
| | - Sivan Shoshani
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- Correspondence:
| |
Collapse
|
36
|
Aghaee BL, Khan Mirzaei M, Alikhani MY, Mojtahedi A, Maurice CF. Improving the Inhibitory Effect of Phages against Pseudomonas aeruginosa Isolated from a Burn Patient Using a Combination of Phages and Antibiotics. Viruses 2021; 13:334. [PMID: 33670028 PMCID: PMC7926668 DOI: 10.3390/v13020334] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance causes around 700,000 deaths a year worldwide. Without immediate action, we are fast approaching a post-antibiotic era in which common infections can result in death. Pseudomonas aeruginosa is the leading cause of nosocomial infection and is also one of the three bacterial pathogens in the WHO list of priority bacteria for developing new antibiotics against. A viable alternative to antibiotics is to use phages, which are bacterial viruses. Yet, the isolation of phages that efficiently kill their target bacteria has proven difficult. Using a combination of phages and antibiotics might increase treatment efficacy and prevent the development of resistance against phages and/or antibiotics, as evidenced by previous studies. Here, in vitro populations of a Pseudomonas aeruginosa strain isolated from a burn patient were treated with a single phage, a mixture of two phages (used simultaneously and sequentially), and the combination of phages and antibiotics (at sub-minimum inhibitory concentration (MIC) and MIC levels). In addition, we tested the stability of these phages at different temperatures, pH values, and in two burn ointments. Our results show that the two-phages-one-antibiotic combination had the highest killing efficiency against the P. aeruginosa strain. The phages tested showed low stability at high temperatures, acidic pH values, and in the two ointments. This work provides additional support for the potential of using combinations of phage-antibiotic cocktails at sub-MIC levels for the treatment of multidrug-resistant P. aeruginosa infections.
Collapse
Affiliation(s)
- Bahareh Lashtoo Aghaee
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 65178-38678, Iran;
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764 Neuherberg, Germany;
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 0B1, Canada
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 65178-38678, Iran;
| | - Ali Mojtahedi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht 41938-33697, Iran
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 0B1, Canada
| |
Collapse
|
37
|
Abstract
In the era where antibiotic resistance is considered one of the major worldwide concerns, bacteriophages have emerged as a promising therapeutic approach to deal with this problem. Genetically engineered bacteriophages can enable enhanced anti-bacterial functionalities, but require cloning additional genes into the phage genomes, which might be challenging due to the DNA encapsulation capacity of a phage. To tackle this issue, we designed and assembled for the first time synthetic phages with smaller genomes by knocking out up to 48% of the genes encoding hypothetical proteins from the genome of the newly isolated Pseudomonas aeruginosa phage vB_PaeP_PE3. The antibacterial efficacy of the wild-type and the synthetic phages was assessed in vitro as well as in vivo using a Galleria mellonella infection model. Overall, both in vitro and in vivo studies revealed that the knock-outs made in phage genome do not impair the antibacterial properties of the synthetic phages, indicating that this could be a good strategy to clear space from phage genomes in order to enable the introduction of other genes of interest that can potentiate the future treatment of P. aeruginosa infections.
Collapse
Affiliation(s)
- Diana P Pires
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal.
| | - Rodrigo Monteiro
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal
| | - Dalila Mil-Homens
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Lisboa, Portugal
| | - Arsénio Fialho
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal.
| |
Collapse
|
38
|
Krylov V, Bourkaltseva M, Pleteneva E, Shaburova O, Krylov S, Karaulov A, Zhavoronok S, Svitich O, Zverev V. Phage phiKZ-The First of Giants. Viruses 2021; 13:149. [PMID: 33498475 PMCID: PMC7909554 DOI: 10.3390/v13020149] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
The paper covers the history of the discovery and description of phiKZ, the first known giant bacteriophage active on Pseudomonas aeruginosa. It also describes its unique features, especially the characteristic manner of DNA packing in the head around a cylinder-shaped structure ("inner body"), which probably governs an ordered and tight packaging of the phage genome. Important properties of phiKZ-like phages include a wide range of lytic activity and the blue opalescence of their negative colonies, and provide a background for the search and discovery of new P. aeruginosa giant phages. The importance of the phiKZ species and of other giant phage species in practical phage therapy is noted given their broad use in commercial phage preparations.
Collapse
Affiliation(s)
- Victor Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Maria Bourkaltseva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Elena Pleteneva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Olga Shaburova
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Sergey Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia;
| | - Sergey Zhavoronok
- Department of Infectious Diseases, Belarusian State Medical University, 220116 Minsk, Belarus;
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| |
Collapse
|
39
|
Storey N, Rabiey M, Neuman BW, Jackson RW, Mulley G. Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. Viruses 2020; 12:E1286. [PMID: 33182769 PMCID: PMC7696170 DOI: 10.3390/v12111286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 01/16/2023] Open
Abstract
Bacterial diseases of the edible white button mushroom Agaricus bisporus caused by Pseudomonas species cause a reduction in crop yield, resulting in considerable economic loss. We examined bacterial pathogens of mushrooms and bacteriophages that target them to understand the disease and opportunities for control. The Pseudomonastolaasii genome encoded a single type III protein secretion system (T3SS), but contained the largest number of non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes that can play a role in pathogenicity, including a putative tolaasin-producing gene cluster, a toxin causing blotch disease symptom. However, Pseudomonasagarici encoded the lowest number of NRPS and three putative T3SS while non-pathogenic Pseudomonas sp. NS1 had intermediate numbers. Potential bacteriophage resistance mechanisms were identified in all three strains, but only P. agarici NCPPB 2472 was observed to have a single Type I-F CRISPR/Cas system predicted to be involved in phage resistance. Three novel bacteriophages, NV1, ϕNV3, and NV6, were isolated from environmental samples. Bacteriophage NV1 and ϕNV3 had a narrow host range for specific mushroom pathogens, whereas phage NV6 was able to infect both mushroom pathogens. ϕNV3 and NV6 genomes were almost identical and differentiated within their T7-like tail fiber protein, indicating this is likely the major host specificity determinant. Our findings provide the foundations for future comparative analyses to study mushroom disease and phage resistance.
Collapse
Affiliation(s)
- Nathaniel Storey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
| | - Mojgan Rabiey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Benjamin W. Neuman
- Biology Department, College of Arts, Sciences and Education, TAMUT, Texarkana, TX 75503, USA;
| | - Robert W. Jackson
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Geraldine Mulley
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
| |
Collapse
|
40
|
Ceyssens PJ, De Smet J, Wagemans J, Akulenko N, Klimuk E, Hedge S, Voet M, Hendrix H, Paeshuyse J, Landuyt B, Xu H, Blanchard J, Severinov K, Lavigne R. The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit. Viruses 2020; 12:v12090976. [PMID: 32887488 PMCID: PMC7552054 DOI: 10.3390/v12090976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/20/2022] Open
Abstract
In this study, we describe the biological function of the phage-encoded protein RNA polymerase alpha subunit cleavage protein (Rac), a predicted Gcn5-related acetyltransferase encoded by phiKMV-like viruses. These phages encode a single-subunit RNA polymerase for transcription of their late (structure- and lysis-associated) genes, whereas the bacterial RNA polymerase is used at the earlier stages of infection. Rac mediates the inactivation of bacterial transcription by introducing a specific cleavage in the α subunit of the bacterial RNA polymerase. This cleavage occurs within the flexible linker sequence and disconnects the C-terminal domain, required for transcription initiation from most highly active cellular promoters. To achieve this, Rac likely taps into a novel post-translational modification (PTM) mechanism within the host Pseudomonas aeruginosa. From an evolutionary perspective, this novel phage-encoded regulation mechanism confirms the importance of PTMs in the prokaryotic metabolism and represents a new way by which phages can hijack the bacterial host metabolism.
Collapse
Affiliation(s)
- Pieter-Jan Ceyssens
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen De Smet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Evgeny Klimuk
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Subray Hedge
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Marleen Voet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Hanne Hendrix
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jan Paeshuyse
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Bart Landuyt
- Department of Biology, KU Leuven, 3000 Leuven, Belgium;
| | - Hua Xu
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - John Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
- Correspondence: ; Tel.: +32-16-379-524
| |
Collapse
|
41
|
Wen L, Chen L, Yuan S, Tian L, Yan T, Zhang H, Tan Y, Yu Y, Wen H, Ma Y, Wei T, Huang S. Complete genome analysis of PaGz-1 and PaZq-1, two novel phages belonging to the genus Pakpunavirus. Arch Virol 2020; 165:2393-2396. [PMID: 32719957 DOI: 10.1007/s00705-020-04745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/22/2020] [Indexed: 11/26/2022]
Abstract
Pseudomonas phages PaGz-1 and PaZq-1, two new phages infecting Pseudomonas aeruginosa, were isolated from fresh water in Guangdong province, China. The genomes of these two phages consist of 93,975 bp and 94,315 bp and contain 175 and 172 open reading frames (ORFs), respectively. The genome sequences of PaGz-1 and PaZq-1 share 95.8% identity with a query coverage of 94%, suggesting that these two phages belong to two different species. Based on results of nucleotide sequence alignment, gene annotation, and phylogenetic analysis, we propose PaGz-1 and PaZq-1 as representative isolates of two species in the genus Pakpunavirus within the family Myoviridae.
Collapse
Affiliation(s)
- Lingling Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shengjian Yuan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linyu Tian
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Tingwei Yan
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Haoran Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yue Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hui Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yingfei Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ting Wei
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| |
Collapse
|
42
|
Evseev P, Sykilinda N, Gorshkova A, Kurochkina L, Ziganshin R, Drucker V, Miroshnikov K. Pseudomonas Phage PaBG-A Jumbo Member of an Old Parasite Family. Viruses 2020; 12:E721. [PMID: 32635178 PMCID: PMC7412058 DOI: 10.3390/v12070721] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteriophage PaBG is a jumbo Myoviridae phage isolated from water of Lake Baikal. This phage has limited diffusion ability and thermal stability and infects a narrow range of Pseudomonas aeruginosa strains. Therefore, it is hardly suitable for phage therapy applications. However, the analysis of the genome of PaBG presents a number of insights into the evolutionary history of this phage and jumbo phages in general. We suggest that PaBG represents an ancient group distantly related to all known classified families of phages.
Collapse
Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Nina Sykilinda
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia; (A.G.); (V.D.)
| | - Lidia Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Rustam Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia; (A.G.); (V.D.)
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| |
Collapse
|
43
|
Lood C, Danis‐Wlodarczyk K, Blasdel BG, Jang HB, Vandenheuvel D, Briers Y, Noben J, van Noort V, Drulis‐Kawa Z, Lavigne R. Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages. Environ Microbiol 2020; 22:2165-2181. [PMID: 32154616 PMCID: PMC7318152 DOI: 10.1111/1462-2920.14979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 03/06/2020] [Indexed: 11/28/2022]
Abstract
Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms.
Collapse
Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
| | - Katarzyna Danis‐Wlodarczyk
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Bob G. Blasdel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Ho Bin Jang
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Dieter Vandenheuvel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Yves Briers
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Jean‐Paul Noben
- Biomedical Research Institute and Transnational University LimburgHasselt UniversityDiepenbeekBelgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| |
Collapse
|
44
|
Shi X, Zhao F, Sun H, Yu X, Zhang C, Liu W, Pan Q, Ren H. Characterization and Complete Genome Analysis of Pseudomonas aeruginosa Bacteriophage vB_PaeP_LP14 Belonging to Genus Litunavirus. Curr Microbiol 2020; 77:2465-2474. [PMID: 32367280 DOI: 10.1007/s00284-020-02011-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022]
Abstract
A lytic Pseudomonas aeruginosa phage vB_PaeP_LP14 belonging to the family Podoviridae was isolated from infected mink. The microbiological characterization revealed that LP14 was stable at 40 to 50 °C and stable over a broad range of pH (5 to 12). The latent period was 5 min, and the burst size was 785 pfu/infected cell. The whole-genome sequencing showed that LP14 was a dsDNA virus and has a genome of 73,080 bp. The genome contained 93 predicted open reading frames (ORFs), 17 of which have known functions including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. No tRNA genes were identified. BLASTn analysis revealed that phage LP14 had a high-sequence identity (96%) with P. aeruginosa phage YH6. Both morphological characterization and genome annotation indicate that phage LP14 is a memberof the family Podoviridae genus Litunavirus. The study of phage LP14 will provide basic information for further research on treatment of P. aeruginosa infections.
Collapse
Affiliation(s)
- Xiaojie Shi
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Xiaoyan Yu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
| |
Collapse
|
45
|
Olszak T, Danis-Wlodarczyk K, Arabski M, Gula G, Maciejewska B, Wasik S, Lood C, Higgins G, Harvey BJ, Lavigne R, Drulis-Kawa Z. Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence. Viruses 2019; 11:E1089. [PMID: 31771160 PMCID: PMC6950013 DOI: 10.3390/v11121089] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.
Collapse
Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Katarzyna Danis-Wlodarczyk
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Michal Arabski
- Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Slawomir Wasik
- Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Cédric Lood
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Gerard Higgins
- National Children Research Centre, Our Lady’s Children’s Hospital, Crumlin, 12 Dublin, Ireland;
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Brian J. Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| |
Collapse
|
46
|
Chaikeeratisak V, Khanna K, Nguyen KT, Sugie J, Egan ME, Erb ML, Vavilina A, Nonejuie P, Nieweglowska E, Pogliano K, Agard DA, Villa E, Pogliano J. Viral Capsid Trafficking along Treadmilling Tubulin Filaments in Bacteria. Cell 2019; 177:1771-1780.e12. [PMID: 31199917 PMCID: PMC7301877 DOI: 10.1016/j.cell.2019.05.032] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 01/24/2019] [Accepted: 05/17/2019] [Indexed: 12/13/2022]
Abstract
Cargo trafficking along microtubules is exploited by eukaryotic viruses, but no such examples have been reported in bacteria. Several large Pseudomonas phages assemble a dynamic, tubulin-based (PhuZ) spindle that centers replicating phage DNA sequestered within a nucleus-like structure. Here, we show that capsids assemble on the membrane and then move rapidly along PhuZ filaments toward the phage nucleus for DNA packaging. The spindle rotates the phage nucleus, distributing capsids around its surface. PhuZ filaments treadmill toward the nucleus at a constant rate similar to the rate of capsid movement and the linear velocity of nucleus rotation. Capsids become trapped along mutant static PhuZ filaments that are defective in GTP hydrolysis. Our results suggest a transport and distribution mechanism in which capsids attached to the sides of filaments are trafficked to the nucleus by PhuZ polymerization at the poles, demonstrating that the phage cytoskeleton evolved cargo-trafficking capabilities in bacteria.
Collapse
Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA; Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Katrina T Nguyen
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Marcella L Erb
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Anastasia Vavilina
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Eliza Nieweglowska
- Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - David A Agard
- Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA.
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA.
| |
Collapse
|
47
|
Burrowes BH, Molineux IJ, Fralick JA. Directed in Vitro Evolution of Therapeutic Bacteriophages: The Appelmans Protocol. Viruses 2019; 11:v11030241. [PMID: 30862096 PMCID: PMC6466182 DOI: 10.3390/v11030241] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/27/2019] [Accepted: 03/08/2019] [Indexed: 01/07/2023] Open
Abstract
The ‘Appelmans protocol’ is used by Eastern European researchers to generate therapeutic phages with novel lytic host ranges. Phage cocktails are iteratively grown on a suite of mostly refractory bacterial isolates until the evolved cocktail can lyse the phage-resistant strains. To study this process, we developed a modified protocol using a cocktail of three Pseudomonas phages and a suite of eight phage-resistant (including a common laboratory strain) and two phage-sensitive Pseudomona aeruginosa strains. After 30 rounds of selection, phages were isolated from the evolved cocktail with greatly increased host range. Control experiments with individual phages showed little host-range expansion, and genomic analysis of one of the broad-host-range output phages showed its recombinatorial origin, suggesting that the protocol works predominantly via recombination between phages. The Appelmans protocol may be useful for evolving therapeutic phage cocktails as required from well-defined precursor phages.
Collapse
Affiliation(s)
- Ben H Burrowes
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA.
- Roche Molecular Systems, 983 University Avenue B200, Los Gatos, CA 95032, USA.
| | - Ian J Molineux
- Center for Infectious Disease, Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA.
| | - Joe A Fralick
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA.
| |
Collapse
|
48
|
Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA. Temperature-Responsive Competitive Inhibition of CRISPR-Cas9. Mol Cell 2019; 73:601-610.e5. [PMID: 30595438 PMCID: PMC6480404 DOI: 10.1016/j.molcel.2018.11.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/23/2018] [Accepted: 11/14/2018] [Indexed: 01/17/2023]
Abstract
CRISPR-Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory "anti-CRISPR" (Acr) proteins, including six inhibitors (AcrIIA1-AcrIIA6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here that AcrIIA2 and its more potent homolog, AcrIIA2b, prevent Cas9 binding to DNA by occluding protein residues required for DNA binding. Cryo-EM-determined structures of AcrIIA2 or AcrIIA2b bound to S. pyogenes Cas9 reveal a mode of competitive inhibition of DNA binding that is distinct from other known Acrs. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arise from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. These findings expand the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially, and conditionally.
Collapse
Affiliation(s)
- Fuguo Jiang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jun-Jie Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Beatriz A Osuna
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joel D Berry
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin J Rauch
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Berkeley; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA; Howard Hughes Medical Institute, Berkeley; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA.
| |
Collapse
|
49
|
Watkins SC, Sible E, Putonti C. Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages. Viruses 2018; 10:v10060331. [PMID: 29914169 PMCID: PMC6024596 DOI: 10.3390/v10060331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 02/07/2023] Open
Abstract
Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.
Collapse
Affiliation(s)
- Siobhan C Watkins
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| | - Emily Sible
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
- Department of Computer Science, Loyola University Chicago, Chicago, IL 60660, USA.
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA.
| |
Collapse
|
50
|
Abstract
We isolated a Pseudomonas phage infecting Pseudomonas fluorescens SA1 separated from a soil sample collected in Sichuan Province, China. This phage, which we named PPSC2, has a genome that is composed of a 97,330-bp-long linear double-stranded DNA with 47.51% G+C content and 168 putative protein-coding genes. We identified 20 tRNA genes in the genome of PPSC2, and the tRNA GC content ranged from 44.2% to 58.4%. Phylogenetic and BLASTn analysis revealed that the Pseudomonas phage PPSC2 should be considered a new member of the family Myoviridae.
Collapse
Affiliation(s)
- Xiang Wu
- College of Architecture and Environment, Sichuan University, No. 24, south section of 1st Ring Road, Chengdu, 610065, China
- Soil and Fertilizer institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Yongfeng Wu
- Sichuan Provincial Transport Department Highway Planning, Survey, Design and Research Institute, Chengdu, 610041, China
| | - Ya Tang
- College of Architecture and Environment, Sichuan University, No. 24, south section of 1st Ring Road, Chengdu, 610065, China.
| | - Bingcheng Gan
- Soil and Fertilizer institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| |
Collapse
|