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Alipour-Khezri E, Skurnik M, Zarrini G. Pseudomonas aeruginosa Bacteriophages and Their Clinical Applications. Viruses 2024; 16:1051. [PMID: 39066214 PMCID: PMC11281547 DOI: 10.3390/v16071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Antimicrobial resistance poses a serious risk to contemporary healthcare since it reduces the number of bacterial illnesses that may be treated with antibiotics, particularly for patients with long-term conditions like cystic fibrosis (CF). People with a genetic predisposition to CF often have recurrent bacterial infections in their lungs due to a buildup of sticky mucus, necessitating long-term antibiotic treatment. Pseudomonas aeruginosa infections are a major cause of CF lung illness, and P. aeruginosa airway isolates are frequently resistant to many antibiotics. Bacteriophages (also known as phages), viruses that infect bacteria, are a viable substitute for antimicrobials to treat P. aeruginosa infections in individuals with CF. Here, we reviewed the utilization of P. aeruginosa bacteriophages both in vivo and in vitro, as well as in the treatment of illnesses and diseases, and the outcomes of the latter.
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Affiliation(s)
- Elaheh Alipour-Khezri
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 51368, Iran;
| | - Mikael Skurnik
- Human Microbiome Research Program, and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Gholamreza Zarrini
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 51368, Iran;
- Microbial Biotechnology Research Group, University of Tabriz, Tabriz 51368, Iran
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2
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Rabiey M, Grace ER, Pawlos P, Bihi M, Ahmed H, Hampson GE, Al Riyami A, Alharbi L, Sanchez‐Lucas R, Korotania N, Ciusa ML, Mosley O, Hulin MT, Baxter L, Dhaouadi S, Vinchira‐Villarraga D, Jackson RW. Coevolutionary analysis of Pseudomonas syringae-phage interactions to help with rational design of phage treatments. Microb Biotechnol 2024; 17:e14489. [PMID: 38864499 PMCID: PMC11167607 DOI: 10.1111/1751-7915.14489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Treating plant bacterial diseases is notoriously difficult because of the lack of available antimicrobials. Pseudomonas syringae pathovar syringae (Pss) is a major pathogen of cherry (Prunus avium) causing bacterial canker of the stem, leaf and fruit, impacting productivity and leading to a loss of trees. In an attempt to find a treatment for this disease, naturally occurring bacteriophage (phage) that specifically target Pss is being investigated as a biocontrol strategy. However, before using them as a biocontrol treatment, it is important to both understand their efficacy in reducing the bacterial population and determine if the bacterial pathogens can evolve resistance to evade phage infection. To investigate this, killing curve assays of five MR phages targeting Pss showed that phage resistance rapidly emerges in vitro, even when using a cocktail of the five phages together. To gain insight to the changes occurring, Pss colonies were collected three times during a 66-h killing curve assay and separately, Pss and phage were also coevolved over 10 generations, enabling the measurement of genomic and fitness changes in bacterial populations. Pss evolved resistance to phages through modifications in lipopolysaccharide (LPS) synthesis pathways. Bacterial fitness (growth) and virulence were affected in only a few mutants. Deletion of LPS-associated genes suggested that LPS was the main target receptor for all five MR phages. Later generations of coevolved phages from the coevolution experiment were more potent at reducing the bacterial density and when used with wild-type phages could reduce the emergence of phage-resistant mutants. This study shows that understanding the genetic mechanisms of bacterial pathogen resistance to phages is important for helping to design a more effective approach to kill the bacteria while minimizing the opportunity for phage resistance to manifest.
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Affiliation(s)
- Mojgan Rabiey
- School of Life Sciences, Gibbet Hill CampusUniversity of WarwickCoventryUK
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Emily R. Grace
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paulina Pawlos
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Muscab Bihi
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Haleem Ahmed
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Georgina E. Hampson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Amna Al Riyami
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Leena Alharbi
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Rosa Sanchez‐Lucas
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Naina Korotania
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Maria Laura Ciusa
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Olivia Mosley
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Michelle T. Hulin
- Department of Plant Soil & Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Laura Baxter
- Bioinformatics Research Technology PlatformUniversity of WarwickCoventryUK
| | - Sabrine Dhaouadi
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Diana Vinchira‐Villarraga
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Robert W. Jackson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
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3
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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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4
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Naknaen A, Samernate T, Saeju P, Nonejuie P, Chaikeeratisak V. Nucleus-forming jumbophage PhiKZ therapeutically outcompetes non-nucleus-forming jumbophage Callisto. iScience 2024; 27:109790. [PMID: 38726363 PMCID: PMC11079468 DOI: 10.1016/j.isci.2024.109790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
With the recent resurgence of phage therapy in modern medicine, jumbophages are currently under the spotlight due to their numerous advantages as anti-infective agents. However, most significant discoveries to date have primarily focused on nucleus-forming jumbophages, not their non-nucleus-forming counterparts. In this study, we compare the biological characteristics exhibited by two genetically diverse jumbophages: 1) the well-studied nucleus-forming jumbophage, PhiKZ; and 2) the newly discovered non-nucleus-forming jumbophage, Callisto. Single-cell infection studies further show that Callisto possesses different replication machinery, resulting in a delay in phage maturation compared to that of PhiKZ. The therapeutic potency of both phages was examined in vitro and in vivo, demonstrating that PhiKZ holds certain superior characteristics over Callisto. This research sheds light on the importance of the subcellular infection machinery and the organized progeny maturation process, which could potentially provide valuable insight in the future development of jumbophage-based therapeutics.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Panida Saeju
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
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5
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Maffei E, Woischnig AK, Burkolter MR, Heyer Y, Humolli D, Thürkauf N, Bock T, Schmidt A, Manfredi P, Egli A, Khanna N, Jenal U, Harms A. Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication. Nat Commun 2024; 15:175. [PMID: 38168031 PMCID: PMC10761892 DOI: 10.1038/s41467-023-44157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly in a slow- or non-growing, dormant state. Here, we show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates ("hibernation"). However, a newly isolated Pseudomonas aeruginosa phage, named Paride, can directly replicate and induce the lysis of deep-dormant hosts. While non-growing bacteria are notoriously tolerant to antibiotic drugs, the combination with Paride enables the carbapenem meropenem to eradicate deep-dormant cultures in vitro and to reduce a resilient bacterial infection of a tissue cage implant in mice. Our work might inspire new treatments for persistent bacterial infections and, more broadly, highlights two viral strategies to infect dormant bacteria (hibernation and direct replication) that will guide future studies on phage-host interactions.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Anne-Kathrin Woischnig
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Marco R Burkolter
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | - Dorentina Humolli
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | | | - Thomas Bock
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Basel, Basel, Switzerland
| | - Nina Khanna
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Harms
- Biozentrum, University of Basel, Basel, Switzerland.
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland.
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6
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da Silva JD, Melo LDR, Santos SB, Kropinski AM, Xisto MF, Dias RS, da Silva Paes I, Vieira MS, Soares JJF, Porcellato D, da Silva Duarte V, de Paula SO. Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage. Appl Microbiol Biotechnol 2023; 107:7231-7250. [PMID: 37741937 PMCID: PMC10638138 DOI: 10.1007/s00253-023-12743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/03/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.
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Affiliation(s)
- Jéssica Duarte da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luís D R Melo
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mariana Fonseca Xisto
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Isabela da Silva Paes
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marcella Silva Vieira
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - José Júnior Ferreira Soares
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Vinícius da Silva Duarte
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
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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] [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.
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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.
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Naknaen A, Samernate T, Wannasrichan W, Surachat K, Nonejuie P, Chaikeeratisak V. Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria. Sci Rep 2023; 13:8921. [PMID: 37264114 DOI: 10.1038/s41598-023-36034-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phage treatment has been used as an alternative to antibiotics since the early 1900s. However, bacteria may acquire phage resistance quickly, limiting the use of phage treatment. The combination of genetically diverse phages displaying distinct replication machinery in phage cocktails has therefore become a novel strategy to improve therapeutic outcomes. Here, we isolated and studied lytic phages (SPA01 and SPA05) that infect a wide range of clinical Pseudomonas aeruginosa isolates. These relatively small myophages have around 93 kbp genomes with no undesirable genes, have a 30-min latent period, and reproduce a relatively high number of progenies, ranging from 218 to 240 PFU per infected cell. Even though both phages lyse their hosts within 4 h, phage-resistant bacteria emerge during the treatment. Considering SPA01-resistant bacteria cross-resist phage SPA05 and vice versa, combining SPA01 and SPA05 for a cocktail would be ineffective. According to the decreased adsorption rate of the phages in the resistant isolates, one of the anti-phage mechanisms may occur through modification of phage receptors on the target cells. All resistant isolates, however, are susceptible to nucleus-forming jumbophages (PhiKZ and PhiPA3), which are genetically distinct from phages SPA01 and SPA05, suggesting that the jumbophages recognize a different receptor during phage entry. The combination of these phages with the jumbophage PhiKZ outperforms other tested combinations in terms of bactericidal activity and effectively suppresses the emergence of phage resistance. This finding reveals the effectiveness of the diverse phage-composed cocktail for reducing bacterial growth and prolonging the evolution of phage resistance.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Wichanan Wannasrichan
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Cell and Biomolecular Imaging Research Unit (CBIRU), Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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9
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Unveil the Secret of the Bacteria and Phage Arms Race. Int J Mol Sci 2023; 24:ijms24054363. [PMID: 36901793 PMCID: PMC10002423 DOI: 10.3390/ijms24054363] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage's nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and other defense systems to interfere with the replication of phage genes in the host; through the quorum sensing (QS) enhancement of phage's resistant effect. At the same time, phages have also evolved a variety of counter-defense strategies, such as degrading extracellular polymeric substances (EPS) that mask receptors or recognize new receptors, thereby regaining the ability to adsorb host cells; modifying its own genes to prevent the R-M systems from recognizing phage genes or evolving proteins that can inhibit the R-M complex; through the gene mutation itself, building nucleus-like compartments or evolving anti-CRISPR (Acr) proteins to resist CRISPR-Cas systems; and by producing antirepressors or blocking the combination of autoinducers (AIs) and its receptors to suppress the QS. The arms race between bacteria and phages is conducive to the coevolution between bacteria and phages. This review details bacterial anti-phage strategies and anti-defense strategies of phages and will provide basic theoretical support for phage therapy while deeply understanding the interaction mechanism between bacteria and phages.
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10
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Warring SL, Malone LM, Jayaraman J, Easingwood RA, Rigano LA, Frampton RA, Visnovsky SB, Addison SM, Hernandez L, Pitman AR, Lopez Acedo E, Kleffmann T, Templeton MD, Bostina M, Fineran PC. A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance. Environ Microbiol 2022; 24:4834-4852. [PMID: 35912527 PMCID: PMC9796965 DOI: 10.1111/1462-2920.16106] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in-depth examination of the genome of ΦPsa374-like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo-electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T = 9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage resistance is overcome by mutations in a tail fibre and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374-like phages that informs their use as antimicrobials against Psa.
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Affiliation(s)
- Suzanne L. Warring
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Lucia M. Malone
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
| | | | - Luciano A. Rigano
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Plant Health & Environment Laboratory, Biosecurity New ZealandMinistry for Primary IndustriesAucklandNew Zealand
| | - Rebekah A. Frampton
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Sandra B. Visnovsky
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Shea M. Addison
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Loreto Hernandez
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Andrew R. Pitman
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand,Foundation for Arable Research (FAR), TempletonChristchurchNew Zealand
| | - Elena Lopez Acedo
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | | | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand,School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Mihnea Bostina
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Otago Centre for Electron MicroscopyUniversity of OtagoDunedinNew Zealand
| | - Peter C. Fineran
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
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11
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Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and MicrobiologyWestmead Institute for Medical ResearchWestmeadNSWAustralia
- Faculty of ScienceSydney School of Veterinary ScienceThe University of SydneySydneyNSWAustralia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and MicrobiologyWestmead Institute for Medical ResearchWestmeadNSWAustralia
- Faculty of Health and MedicineSchool of MedicineSydney Medical SchoolThe University of SydneySydneyNSWAustralia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and MicrobiologyWestmead Institute for Medical ResearchWestmeadNSWAustralia
- Faculty of Health and MedicineSchool of MedicineSydney Medical SchoolThe University of SydneySydneyNSWAustralia
| | - Stefanie Barbirz
- Department of MedicineScience FacultyMSB Medical School BerlinBerlinGermany
| | - Jonathan Iredell
- Centre for Infectious Diseases and MicrobiologyWestmead Institute for Medical ResearchWestmeadNSWAustralia
- Faculty of Health and MedicineSchool of MedicineSydney Medical SchoolThe University of SydneySydneyNSWAustralia
- Westmead HospitalWestern Sydney Local Health DistrictWestmeadNSWAustralia
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12
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Pires DP, Meneses L, Brandão AC, Azeredo J. An overview of the current state of phage therapy for the treatment of biofilm-related infections. Curr Opin Virol 2022; 53:101209. [PMID: 35240424 DOI: 10.1016/j.coviro.2022.101209] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/27/2021] [Accepted: 01/22/2022] [Indexed: 12/19/2022]
Abstract
Bacterial biofilms are involved in many chronic and difficult-to-treat infections. Phage therapy against infectious biofilms is becoming a promising strategy, as suggested by the increasing number of publications demonstrating the efficacy of phages against in vitro formed biofilms. However, the translation between in vitro results to in vivo phage therapy outcome is not straightforward due to the complexity of phage-biofilm interactions in clinical contexts. Here, we provide a critical overview of the in vitro studies of phages for biofilm control of clinical pathogens, followed by the major outcomes and lessons learned from the recently reported case studies (between 2018 and 2021) of phage therapy against biofilm-related infections.
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Affiliation(s)
- Diana P Pires
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Luciana Meneses
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Ana C Brandão
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, 4800-122 Guimarães, Portugal.
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13
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The Antibacterial Effect of PEGylated Carbosilane Dendrimers on P. aeruginosa Alone and in Combination with Phage-Derived Endolysin. Int J Mol Sci 2022; 23:ijms23031873. [PMID: 35163794 PMCID: PMC8836974 DOI: 10.3390/ijms23031873] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
The search for new microbicide compounds is of an urgent need, especially against difficult-to-eradicate biofilm-forming bacteria. One attractive option is the application of cationic multivalent dendrimers as antibacterials and also as carriers of active molecules. These compounds require an adequate hydrophilic/hydrophobic structural balance to maximize the effect. Herein, we evaluated the antimicrobial activity of cationic carbosilane (CBS) dendrimers unmodified or modified with polyethylene glycol (PEG) units, against planktonic and biofilm-forming P. aeruginosa culture. Our study revealed that the presence of PEG destabilized the hydrophilic/hydrophobic balance but reduced the antibacterial activity measured by microbiological cultivation methods, laser interferometry and fluorescence microscopy. On the other hand, the activity can be improved by the combination of the CBS dendrimers with endolysin, a bacteriophage-encoded peptidoglycan hydrolase. This enzyme applied in the absence of the cationic CBS dendrimers is ineffective against Gram-negative bacteria because of the protective outer membrane shield. However, the endolysin-CBS dendrimer mixture enables the penetration through the membrane and then deterioration of the peptidoglycan layer, providing a synergic antimicrobial effect.
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14
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Holtappels D, Fortuna KJ, Moons L, Broeckaert N, Bäcker LE, Venneman S, Rombouts S, Lippens L, Baeyen S, Pollet S, Noben JP, Oechslin F, Vallino M, Aertsen A, Maes M, Van Vaerenbergh J, Lavigne R, Wagemans J. The potential of bacteriophages to control Xanthomonas campestris pv. campestris at different stages of disease development. Microb Biotechnol 2022; 15:1762-1782. [PMID: 35084112 PMCID: PMC9151335 DOI: 10.1111/1751-7915.14004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a vascular pathogen that invades the xylem of Brassica crops. Current chemical and antibiotics‐based control measures for this bacterium are unsustainable and inefficient. After establishing a representative collection of Xcc strains, we isolated and characterized bacteriophages from two clades of phages to assess their potential in phage‐based biocontrol. The most promising phages, FoX2 and FoX6, specifically recognize (lipo) polysaccharides, associated with the wxc gene cluster, on the surface of the bacterial cell wall. Next, we determined and optimized the applicability of FoX2 and FoX6 in an array of complementary bioassays, ranging from seed decontamination to irrigation‐ and spray‐based applications. Here, an irrigation‐based application showed promising results. In a final proof‐of‐concept, a CaCl2‐formulated phage cocktail was shown to control the outbreak of Xcc in the open field. This comprehensive approach illustrates the potential of phage biocontrol of black rot disease in Brassica and serves as a reference for the broader implementation of phage biocontrol in integrated pest management strategies.
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Affiliation(s)
| | | | - Lauren Moons
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | - Léon E Bäcker
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | - Sofie Venneman
- Proefstation voor de groenteteelt, Sint-Katelijne-Waver, Belgium
| | - Sofie Rombouts
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | - Louis Lippens
- Provinciaal Proefcentrum voor de Groenteteelt Oost-Vlaanderen, Kruishoutem, Belgium
| | - Steve Baeyen
- Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | | | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Counsil of Italy, Turin, Italy
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | | | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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15
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A novel method to create efficient phage cocktails via use of phage-resistant bacteria. Appl Environ Microbiol 2022; 88:e0232321. [PMID: 35080902 DOI: 10.1128/aem.02323-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid anti-phage mutation of pathogens is a big challenge often encountered in the application of phages in aquaculture, animal husbandry and human disease prevention. A cocktail composed of phages with different infection strategies can better suppress the anti-phage resistance of pathogens. However, randomly selecting phages with different infection strategies is time-consuming and labor-intensive. Here, we verified that using a resistant pathogen quickly-evolved under single phage infection as the new host can easily obtain phages with different infection strategies. We randomly isolated two lytic phages (i.e., Va1 and Va2) that infect the opportunistic pathogen Vibrio alginolyticus. Whether they were used alone or in combination, the pathogen easily gained resistance. Using a mutated pathogen resistant to Va1 as a new host, a third lytic phage Va3 was isolated. These three phages have a similar infection cycle and lytic ability, but quite different morphologies and genome information. Notably, phage Va3 is a jumbo phage containing a larger and more complex genome (240 kb) than Va1 and Va2. Furthermore, the 34 tRNAs and multiple genes encoding receptor binding proteins and NAD+ synthesis proteins in the Va3 genome implicated its quite different infection strategy compared to Va1 and Va2. Although the wild-type pathogen could still readily evolve resistance under single phage infection by Va3, when Va3 was used in combination with Va1 and Va2, pathogen resistance was strongly suppressed. This study provides a novel approach for rapid isolation of phages with different infection strategies, which will be highly beneficial when designing effective phage cocktails. Importance The rapid anti-phage mutation of pathogens is a big challenge often encountered in phage therapy. Using a cocktail composed of phages with different infection strategies can better overcome this problem. However, randomly selecting phages with different infection strategies is time-consuming and labor-intensive. To address this problem, we developed a method to efficiently obtain phages with disparate infection strategies. The trick is to use the characteristics of the pathogenic bacteria that are prone to develop resistance to single phage infection, to rapidly obtain the anti-phage variant of the pathogen. Using this anti-phage variant as the host results in other phages with different infection strategies being efficiently isolated. We also verified the reliability of this method by demonstrating the ideal phage control effects on two pathogens, and thus revealed its potential importance in the development of phage therapies.
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16
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Abstract
The Pseudomonas aeruginosa is one of the bacteria that cause serious infections due to resistance to many antibiotics can be fatal in severe cases. Antimicrobial resistance is a global public health concern. To solve this problem, interest in phage therapy has revived; some studies are being developed to try to prove the effectiveness of this therapy. Thus, in this opinion article, several historical aspects are addressed as well some applications of phage therapy against P. aeruginosa.
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17
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Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness. ISME JOURNAL 2021; 16:533-542. [PMID: 34465897 PMCID: PMC8776877 DOI: 10.1038/s41396-021-01096-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 01/21/2023]
Abstract
When considering the interactions between bacteriophages and their host, the issue of phage-resistance emergence is a key element in understanding the ecological impact of phages on the bacterial population. It is also an essential parameter for the implementation of phage therapy to combat antibiotic-resistant pathogens. This study investigates the phenotypic and genetic responses of five Pseudomonas aeruginosa strains (PAO1, A5803, AA43, CHA, and PAK) to the infection by seven phages with distinct evolutionary backgrounds and recognised receptors (LPS/T4P). Emerging phage-insensitivity was generally accompanied by self and cross-resistance mechanisms. Significant differences were observed between the reference PAO1 responses compared to other clinical representatives. LPS-dependent phage infections in clinical strains selected for mutations in the "global regulatory" and "other" genes, rather than in the LPS-synthesis clusters detected in PAO1 clones. Reduced fitness, as proxied by the growth rate, was correlated with large deletion (20-500 kbp) and phage carrier state. Multi-phage resistance was significantly correlated with a reduced growth rate but only in the PAO1 population. In addition, we observed that the presence of prophages decreased the lytic phage maintenance seemingly protecting the host against carrier state and occasional lytic phage propagation, thus preventing a significant reduction in bacterial growth rate.
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18
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Figueiredo CM, Malvezzi Karwowski MS, da Silva Ramos RCP, de Oliveira NS, Peña LC, Carneiro E, Freitas de Macedo RE, Rosa EAR. Bacteriophages as tools for biofilm biocontrol in different fields. BIOFOULING 2021; 37:689-709. [PMID: 34304662 DOI: 10.1080/08927014.2021.1955866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Microbial biofilms are difficult to control due to the limited accessibility that antimicrobial drugs and chemicals have to the entrapped inner cells. The extracellular matrix, binds water, contributes to altered cell physiology within biofilms and act as a barrier for most antiproliferative molecules. Thus, new strategies need to be developed to overcome biofilm vitality. In this review, based on 223 documents, the advantages, recommendations, and limitations of using bacteriophages as 'biofilm predators' are presented. The plausibility of using phages (bacteriophages and mycoviruses) to control biofilms grown in different environments is also discussed. The topics covered here include recent historical experiences in biofilm control/eradication using phages in medicine, dentistry, veterinary, and food industries, the pros and cons of their use, and the development of microbial resistance/immunity to such viruses.
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Affiliation(s)
| | | | | | | | - Lorena Caroline Peña
- Xenobiotics Research Unit, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Everdan Carneiro
- Graduate Program in Dentistry, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | | | - Edvaldo Antonio Ribeiro Rosa
- Graduate Program in Dentistry, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
- Graduate Program in Animal Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
- Xenobiotics Research Unit, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
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19
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Abstract
Bacteriophages and bacterial biofilms are widely present in natural environments, a fact that has accelerated the evolution of phages and their bacterial hosts in these particular niches. Phage-host interactions in biofilm communities are rather complex, where phages are not always merely predators but also can establish symbiotic relationships that induce and strengthen biofilms. In this review we provide an overview of the main features affecting phage-biofilm interactions as well as the currently available methods of studying these interactions. In addition, we address the applications of phages for biofilm control in different contexts.
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Affiliation(s)
- Diana P Pires
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
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20
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Gałczyńska K, Rachuna J, Ciepluch K, Kowalska M, Wąsik S, Kosztołowicz T, Lewandowska KD, Semaniak J, Kurdziel K, Arabski M. Experimental and Theoretical Analysis of Metal Complex Diffusion through Cell Monolayer. ENTROPY 2021; 23:e23030360. [PMID: 33802897 PMCID: PMC8002612 DOI: 10.3390/e23030360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/12/2023]
Abstract
The study of drugs diffusion through different biological membranes constitutes an essential step in the development of new pharmaceuticals. In this study, the method based on the monolayer cell culture of CHO-K1 cells has been developed in order to emulate the epithelial cells barrier in permeability studies by laser interferometry. Laser interferometry was employed for the experimental analysis of nickel(II) and cobalt(II) complexes with 1-allylimidazole or their chlorides’ diffusion through eukaryotic cell monolayers. The amount (mol) of nickel(II) and cobalt(II) chlorides transported through the monolayer was greater than that of metals complexed with 1-allylimidazole by 4.34-fold and 1.45-fold, respectively, after 60 min. Thus, laser interferometry can be used for the quantitative analysis of the transport of compounds through eukaryotic cell monolayers, and the resulting parameters can be used to formulate a mathematical description of this process.
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Affiliation(s)
- Katarzyna Gałczyńska
- Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (K.G.); (J.R.); (K.C.); (M.K.)
| | - Jarosław Rachuna
- Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (K.G.); (J.R.); (K.C.); (M.K.)
| | - Karol Ciepluch
- Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (K.G.); (J.R.); (K.C.); (M.K.)
| | - Magdalena Kowalska
- Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (K.G.); (J.R.); (K.C.); (M.K.)
| | - Sławomir Wąsik
- Institute of Physics, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (S.W.); (T.K.); (J.S.)
| | - Tadeusz Kosztołowicz
- Institute of Physics, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (S.W.); (T.K.); (J.S.)
| | - Katarzyna D. Lewandowska
- Department of Radiological Informatics and Statistics, Medical University of Gdańsk, Tuwima 15, 80-210 Gdańsk, Poland;
| | - Jacek Semaniak
- Institute of Physics, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (S.W.); (T.K.); (J.S.)
| | - Krystyna Kurdziel
- Institute of Chemistry, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland;
| | - Michał Arabski
- Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland; (K.G.); (J.R.); (K.C.); (M.K.)
- Correspondence: ; Tel./Fax: +48-41-349-63-31
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21
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Jiang L, Zheng R, Sun Q, Li C. Isolation, characterization, and application of Salmonella paratyphi phage KM16 against Salmonella paratyphi biofilm. BIOFOULING 2021; 37:276-288. [PMID: 33947280 DOI: 10.1080/08927014.2021.1900130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 02/20/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Salmonella biofilm prevention and control is of great importance. This study, investigated the use of the isolated phage KM16 belonging to the family Myoviridae in the order Caudovirales. The phage genome size was 170,126 bp. Almost all phages were adsorbed to the host within 20 min. KM16 had a latent period of 70 min followed by a rise period of 40 min. Phage KM16 had the ability to lytically infect 10 out of the 12 clinical strains of S. paratyphi tested. Phylogenetic analysis indicated that the S. paratyphi 16S rRNA, crispr 1 and fimA genes correlated with the lytic spectrum of phage KM16. The lytic spectrum of phage KM16 correlated with Salmonella pili (fimA), and Salmonella pili were the recognition site for phage adsorption to the host. Phage KM16 (MOI = 0.1) had a better anti-biofilm effect than kanamycin sulfate (10 ug ml-1) in high-concentration Salmonella cultures.
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Affiliation(s)
- Liming Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, PR China
| | - Rui Zheng
- Department of Clinical laboratory, The First People's Hospital of Yunnan Province, Kunming, PR China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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22
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Drulis-Kawa Z, Maciejewska B. Special Issue: "Bacteriophages and Biofilms". Viruses 2021; 13:v13020257. [PMID: 33567515 PMCID: PMC7915279 DOI: 10.3390/v13020257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/28/2022] Open
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23
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Vaitekenas A, Tai AS, Ramsay JP, Stick SM, Kicic A. Pseudomonas aeruginosa Resistance to Bacteriophages and Its Prevention by Strategic Therapeutic Cocktail Formulation. Antibiotics (Basel) 2021; 10:145. [PMID: 33540528 PMCID: PMC7912912 DOI: 10.3390/antibiotics10020145] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance poses a significant threat to modern healthcare as it limits treatment options for bacterial infections, particularly impacting those with chronic conditions such as cystic fibrosis (CF). Viscous mucus accumulation in the lungs of individuals genetically predisposed to CF leads to recurrent bacterial infections, necessitating prolonged antimicrobial chemotherapy. Pseudomonas aeruginosa infections are the predominant driver of CF lung disease, and airway isolates are frequently resistant to multiple antimicrobials. Bacteriophages, or phages, are viruses that specifically infect bacteria and are a promising alternative to antimicrobials for CF P. aeruginosa infections. However, the narrow host range of P. aeruginosa-targeting phages and the rapid evolution of phage resistance could limit the clinical efficacy of phage therapy. A promising approach to overcome these issues is the strategic development of mixtures of phages (cocktails). The aim is to combine phages with broad host ranges and target multiple distinct bacterial receptors to prevent the evolution of phage resistance. However, further research is required to identify and characterize phage resistance mechanisms in CF-derived P. aeruginosa, which differ from their non-CF counterparts. In this review, we consider the mechanisms of P. aeruginosa phage resistance and how these could be overcome by an effective future phage therapy formulation.
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Affiliation(s)
- Andrew Vaitekenas
- Occupation and the Environment, School of Public Health, Curtin University, Perth, WA 6102, Australia
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Crawley, WA 6009, Australia; (A.V.); (S.M.S.)
| | - Anna S. Tai
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA 6009, Australia;
- Institute for Respiratory Health, Perth, WA 6009, Australia
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Joshua P. Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia;
| | - Stephen M. Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Crawley, WA 6009, Australia; (A.V.); (S.M.S.)
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA 6009, Australia
- Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Anthony Kicic
- Occupation and the Environment, School of Public Health, Curtin University, Perth, WA 6102, Australia
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Crawley, WA 6009, Australia; (A.V.); (S.M.S.)
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA 6009, Australia
- Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
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24
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Kwon J, Kim SG, Kim HJ, Giri SS, Kim SW, Lee SB, Park SC. Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04. Viruses 2020; 13:v13010027. [PMID: 33375688 PMCID: PMC7823757 DOI: 10.3390/v13010027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022] Open
Abstract
The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.
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25
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Misol GN, Kokkari C, Katharios P. Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi. Pathogens 2020; 9:E1051. [PMID: 33333990 PMCID: PMC7765460 DOI: 10.3390/pathogens9121051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022] Open
Abstract
Vibrio harveyi is a Gram-negative marine bacterium that causes major disease outbreaks and economic losses in aquaculture. Phage therapy has been considered as a potential alternative to antibiotics however, candidate bacteriophages require comprehensive characterization for a safe and practical phage therapy. In this work, a lytic novel jumbo bacteriophage, vB_VhaM_pir03 belonging to the Myoviridae family was isolated and characterized against V. harveyi type strain DSM19623. It had broad host lytic activity against 31 antibiotic-resistant strains of V. harveyi, V. alginolyticus, V. campbellii and V. owensii. Adsorption time of vB_VhaM_pir03 was determined at 6 min while the latent-phase was at 40 min and burst-size at 75 pfu/mL. vB_VhaM_pir03 was able to lyse several host strains at multiplicity-of-infections (MOI) 0.1 to 10. The genome of vB_VhaM_pir03 consists of 286,284 base pairs with 334 predicted open reading frames (ORFs). No virulence, antibiotic resistance, integrase encoding genes and transducing potential were detected. Phylogenetic and phylogenomic analysis showed that vB_VhaM_pir03 is a novel bacteriophage displaying the highest similarity to another jumbo phage, vB_BONAISHI infecting Vibrio coralliilyticus. Experimental phage therapy trial using brine shrimp, Artemia salina infected with V. harveyi demonstrated that vB_VhaM_pir03 was able to significantly reduce mortality 24 h post infection when administered at MOI 0.1 which suggests that it can be an excellent candidate for phage therapy.
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Affiliation(s)
- Gerald N. Misol
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; (G.N.M.J.); (C.K.)
- Department of Biology, University of Crete, 71003 Heraklion, Crete, Greece
| | - Constantina Kokkari
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; (G.N.M.J.); (C.K.)
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; (G.N.M.J.); (C.K.)
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26
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Modelling experimentally measured of ciprofloxacin antibiotic diffusion in Pseudomonas aeruginosa biofilm formed in artificial sputum medium. PLoS One 2020; 15:e0243003. [PMID: 33270697 PMCID: PMC7714214 DOI: 10.1371/journal.pone.0243003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
We study the experimentally measured ciprofloxacin antibiotic diffusion through a gel-like artificial sputum medium (ASM) mimicking physiological conditions typical for a cystic fibrosis layer, in which regions occupied by Pseudomonas aeruginosa bacteria are present. To quantify the antibiotic diffusion dynamics we employ a phenomenological model using a subdiffusion-absorption equation with a fractional time derivative. This effective equation describes molecular diffusion in a medium structured akin Thompson's plumpudding model; here the 'pudding' background represents the ASM and the 'plums' represent the bacterial biofilm. The pudding is a subdiffusion barrier for antibiotic molecules that can affect bacteria found in plums. For the experimental study we use an interferometric method to determine the time evolution of the amount of antibiotic that has diffused through the biofilm. The theoretical model shows that this function is qualitatively different depending on whether or not absorption of the antibiotic in the biofilm occurs. We show that the process can be divided into three successive stages: (1) only antibiotic subdiffusion with constant biofilm parameters, (2) subdiffusion and absorption of antibiotic molecules with variable biofilm transport parameters, (3) subdiffusion and absorption in the medium but the biofilm parameters are constant again. Stage 2 is interpreted as the appearance of an intensive defence build-up of bacteria against the action of the antibiotic, and in the stage 3 it is likely that the bacteria have been inactivated. Times at which stages change are determined from the experimentally obtained temporal evolution of the amount of antibiotic that has diffused through the ASM with bacteria. Our analysis shows good agreement between experimental and theoretical results and is consistent with the biologically expected biofilm response. We show that an experimental method to study the temporal evolution of the amount of a substance that has diffused through a biofilm is useful in studying the processes occurring in a biofilm. We also show that the complicated biological process of antibiotic diffusion in a biofilm can be described by a fractional subdiffusion-absorption equation with subdiffusion and absorption parameters that change over time.
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27
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Kim SG, Lee SB, Giri SS, Kim HJ, Kim SW, Kwon J, Park J, Roh E, Park SC. Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus. Viruses 2020; 12:E1373. [PMID: 33266226 PMCID: PMC7760394 DOI: 10.3390/v12121373] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Hyoun Joong Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (J.P.); (E.R.)
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (J.P.); (E.R.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
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28
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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] [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.
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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
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Holtappels D, Kerremans A, Busschots Y, Van Vaerenbergh J, Maes M, Lavigne R, Wagemans J. Preparing for the KIL: Receptor Analysis of Pseudomonas syringae pv. porri Phages and Their Impact on Bacterial Virulence. Int J Mol Sci 2020; 21:ijms21082930. [PMID: 32331264 PMCID: PMC7216180 DOI: 10.3390/ijms21082930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 12/20/2022] Open
Abstract
The prevalence of Pseudomonas syringae pv. porri (Pspo) in Belgium continues to increase and sustainable treatments for this pathogen remain unavailable. A potentially attractive biocontrol strategy would be the application of bacteriophages. The ideal application strategy of phages in an agricultural setting remains unclear, especially in a field-based production such as for leek plants in Flanders. Therefore, more insight in bacteria–phage interaction is required, along with the evaluation of different application strategies. In this study, we further characterized the infection strategy of two Pspo phages, KIL3b and KIL5. We found that both phages recognize lipopolysaccharide (LPS) moieties on the surface of the bacterium. LPS is an important pathogenicity factor of Pspo. Our data also suggest that KIL5 requires an additional protein in the bacterial cytoplasmatic membrane to efficiently infect its host. Virulence tests showed that this protein also contributes to Pspo virulence. Furthermore, a cocktail of both phages was applied in a seed bioassay. A combination of KIL3b and KIL5 reduced the bacterial concentration 100-fold. However, in vitro Pspo resistance against phage infection developed quite rapidly. However, the impact of this phage resistance might be mitigated as is suggested by the fact that those resistance mutations preferably occur in genes involved in LPS metabolism, and that the virulence of those mutants is possibly reduced. Our data suggest that the phage cocktail has promising potential to lower the prevalence of Pspo and to be integrated in a pest management strategy. Targeted research is needed to further explore the applicability of the phages in combination with other disease control strategies.
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Affiliation(s)
- Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium; (D.H.); (A.K.); (Y.B.); (R.L.)
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium; (D.H.); (A.K.); (Y.B.); (R.L.)
| | - Yoni Busschots
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium; (D.H.); (A.K.); (Y.B.); (R.L.)
| | - Johan Van Vaerenbergh
- Department of Crop Protection, Institute for Agricultural and Fisheries Research, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium;
| | - Martine Maes
- Independent Researcher, Willem Tellstraat 20, 9000 Ghent, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium; (D.H.); (A.K.); (Y.B.); (R.L.)
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium; (D.H.); (A.K.); (Y.B.); (R.L.)
- Correspondence:
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30
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The Application of Impedance Spectroscopy for Pseudomonas Biofilm Monitoring during Phage Infection. Viruses 2020; 12:v12040407. [PMID: 32272740 PMCID: PMC7232529 DOI: 10.3390/v12040407] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial biofilm prevention and eradication are common treatment problems, hence there is a need for advanced and precise experimental methods for its monitoring. Bacterial resistance to antibiotics has resulted in an interest in using a natural bacterial enemy-bacteriophages. In this study, we present the application of quartz tuning forks (QTF) as impedance sensors to determine in real-time the direct changes in Pseudomonas aeruginosa PAO1 biofilm growth dynamics during Pseudomonas phage LUZ 19 treatment at different multiplicities of infection (MOI). The impedance of the electric equivalent circuit (EEC) allowed us to measure the series resistance (Rs) corresponding to the growth-medium resistance (planktonic culture changes) and the conductance (G) corresponding to the level of QTF sensor surface coverage by bacterial cells and the extracellular polymer structure (EPS) matrix. It was shown that phage impacts on sessile cells (G dynamics) was very similar in the 10-day biofilm development regardless of applied MOI (0.1, 1 or 10). The application of phages at an early stage (at the sixth h) and on three-day biofilm caused a significant slowdown in biofilm dynamics, whereas the two-day biofilm turned out to be insensitive to phage infection. We observed an inhibitory effect of phage infection on the planktonic culture (Rs dynamics) regardless of the MOI applied and the time point of infection. Moreover, the Rs parameter made it possible to detect PAO1 population regrowth at the latest time points of incubation. The number of phage-insensitive forms reached the level of untreated culture at around the sixth day of infection. We conclude that the proposed impedance spectroscopy technique can be used to measure the physiological changes in the biofilm matrix composition, as well as the condition of planktonic cultures in order to evaluate the activity of anti-biofilm compounds.
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