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Ragab S, Gouda SM, Abdelmoteleb M, El-Shibiny A. The role of identified and characterized bacteriophage ZCEC13 in controlling pathogenic and multidrug-resistant Escherichia coli in wastewater: in vitro study. ENVIRONMENTAL TECHNOLOGY 2024; 45:3544-3558. [PMID: 37255221 DOI: 10.1080/09593330.2023.2220886] [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: 11/20/2022] [Accepted: 05/20/2023] [Indexed: 06/01/2023]
Abstract
The spread and development of Multi-Drug Resistant (MDR) bacteria in wastewater became beyond control and a global public health concern. The conventional disinfectants used in wastewater treatment methods have been becoming increasingly ineffective against a range of pathogenic and MDR bacteria. Bacteriophages are considered a novel approach to microbial control. Therefore, this study aims to explore the possibility of using phages against pathogenic and MDR Escherichia coli strains isolated from wastewater treatment plants. The wastewater samples were collected from two different treatment plants for E. coli isolation. The antibiotic sensitivity profile and occurrence of virulence and resistant genes were tested in 28 E. coli isolates. Phage ZCEC13 was selected based on its promising activity and host range to undergo identification and characterization. ZCEC13 was evaluated by transmission electron microscopy, genomic sequencing, in vitro lytic activity and tested for its stability under different conditions such as pH, Ultraviolet light exposure, and temperature. The results reported that ZCEC13 belongs to the Caudoviricetes class, with a high antibacterial dynamic. Phage ZCEC13 displayed high stability at different pH values ranging from 2 to 12, good tolerance to temperatures from -4 to 65°C, and high stability at UV exposure for 120 min. Respectively, the findings showed stability of the phage under several conditions and high efficiency in killing MDR bacteria isolated from the treatment plants. Further studies are encouraged to analyse the efficacy of phages as a microbial control agent in wastewater treatment plants.
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Affiliation(s)
- Samar Ragab
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Shrouk Mohamed Gouda
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | | | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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Lewis JM, Williams J, Sagona AP. Making the leap from technique to treatment - genetic engineering is paving the way for more efficient phage therapy. Biochem Soc Trans 2024; 52:1373-1384. [PMID: 38716972 DOI: 10.1042/bst20231289] [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: 01/16/2024] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Bacteriophages (phages) are viruses specific to bacteria that target them with great efficiency and specificity. Phages were first studied for their antibacterial potential in the early twentieth century; however, their use was largely eclipsed by the popularity of antibiotics. Given the surge of antimicrobial-resistant strains worldwide, there has been a renaissance in harnessing phages as therapeutics once more. One of the key advantages of phages is their amenability to modification, allowing the generation of numerous derivatives optimised for specific functions depending on the modification. These enhanced derivatives could display higher infectivity, expanded host range or greater affinity to human tissues, where some bacterial species exert their pathogenesis. Despite this, there has been a noticeable discrepancy between the generation of derivatives in vitro and their clinical application in vivo. In most instances, phage therapy is only used on a compassionate-use basis, where all other treatment options have been exhausted. A lack of clinical trials and numerous regulatory hurdles hamper the progress of phage therapy and in turn, the engineered variants, in becoming widely used in the clinic. In this review, we outline the various types of modifications enacted upon phages and how these modifications contribute to their enhanced bactericidal function compared with wild-type phages. We also discuss the nascent progress of genetically modified phages in clinical trials along with the current issues these are confronted with, to validate it as a therapy in the clinic.
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Affiliation(s)
- Jessica M Lewis
- School of Life Sciences, University of Warwick, Coventry, U.K
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, U.K
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3
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Guzel M, Yucefaydali A, Yetiskin S, Deniz A, Yaşar Tel O, Akçelik M, Soyer Y. Genomic analysis of Salmonella bacteriophages revealed multiple endolysin ORFs and importance of ligand-binding site of receptor-binding protein. FEMS Microbiol Ecol 2024; 100:fiae079. [PMID: 38816206 PMCID: PMC11180984 DOI: 10.1093/femsec/fiae079] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024] Open
Abstract
Salmonella is a prevalent foodborne pathogen causing millions of global cases annually. Antimicrobial resistance is a growing public health concern, leading to search for alternatives like bacteriophages. A total of 97 bacteriophages, isolated from cattle farms (n = 48), poultry farms (n = 37), and wastewater (n = 5) samples in Türkiye, were subjected to host-range analysis using 36 Salmonella isolates with 18 different serotypes. The broadest host range belonged to an Infantis phage (MET P1-091), lysing 28 hosts. A total of 10 phages with the widest host range underwent further analysis, revealing seven unique genomes (32-243 kb), including a jumbophage (>200 kb). Except for one with lysogenic properties, none of them harbored virulence or antibiotic resistance genes, making them potential Salmonella reducers in different environments. Examining open reading frames (ORFs) of endolysin enzymes revealed surprising findings: five of seven unique genomes contained multiple endolysin ORFs. Despite sharing same endolysin sequences, phages exhibited significant differences in host range. Detailed analysis unveiled diverse receptor-binding protein sequences, with similar structures but distinct ligand-binding sites. These findings emphasize the importance of ligand-binding sites of receptor-binding proteins. Additionally, bacterial reduction curve and virulence index revealed that Enteritidis phages inhibit bacterial growth even at low concentrations, unlike Infantis and Kentucky phages.
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Affiliation(s)
- Mustafa Guzel
- Department of Biotechnology, Middle East Technical University, Ankara 06800, Türkiye
- Department of Food Engineering, Hitit University, Corum 19030, Türkiye
| | - Aysenur Yucefaydali
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Segah Yetiskin
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Aysu Deniz
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Osman Yaşar Tel
- Faculty of Veterinary Medicine, Harran University, Şanlıurfa 63300, Türkiye
| | - Mustafa Akçelik
- Department of Biology, Ankara University, Ankara 06100, Türkiye
| | - Yeşim Soyer
- Department of Biotechnology, Middle East Technical University, Ankara 06800, Türkiye
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
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Bernabéu-Gimeno M, Pardo-Freire M, Chan BK, Turner PE, Gil-Brusola A, Pérez-Tarazona S, Carrasco-Hernández L, Quintana-Gallego E, Domingo-Calap P. Neutralizing antibodies after nebulized phage therapy in cystic fibrosis patients. MED 2024:S2666-6340(24)00221-6. [PMID: 38917792 DOI: 10.1016/j.medj.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/02/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) patients are prone to recurrent multi-drug-resistant (MDR) bacterial lung infections. Under this scenario, phage therapy has been proposed as a promising tool. However, the limited number of reported cases hampers the understanding of clinical outcomes. Anti-phage immune responses have often been overlooked and only described following invasive routes of administration. METHODS Three monophage treatments against Staphylococcus aureus and/or Pseudomonas aeruginosa lung infections were conducted in cystic fibrosis patients. In-house phage preparations were nebulized over 10 days with standard-of-care antibiotics. Clinical indicators, bacterial counts, phage and antibiotic susceptibility, phage detection, and immune responses were monitored. FINDINGS Bacterial load was reduced by 3-6 log in two of the treatments. No adverse events were described. Phages remained in sputum up to 33 days after completion of the treatment. In all cases, phage-neutralizing antibodies were detected in serum from 10 to 42 days post treatment, with this being the first report of anti-phage antibodies after nebulized therapy. CONCLUSIONS Nebulized phage therapy reduced bacterial load, improving quality of life even without bacterial eradication. The emergence of antibodies emphasizes the importance of long-term monitoring to better understand clinical outcomes. These findings encourage the use of personalized monophage therapies in contrast to ready-to-use cocktails, which might induce undesirable antibody generation. FUNDING This study was supported by the Spanish Ministry of Science, Innovation and Universities; Generalitat Valenciana; and a crowdfunding in collaboration with the Spanish Cystic Fibrosis Foundation.
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Affiliation(s)
- Mireia Bernabéu-Gimeno
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain
| | - Marco Pardo-Freire
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Phage Biology and Therapy, Yale University, New Haven, CT 06520, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Phage Biology and Therapy, Yale University, New Haven, CT 06520, USA; Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ana Gil-Brusola
- Microbiology Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; Severe Infection Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Santiago Pérez-Tarazona
- Pediatric Pulmonology Unit, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
| | - Laura Carrasco-Hernández
- Medical-Surgical Unit of Respiratory Diseases, Virgen del Rocío University Hospital, 41013 Sevilla, Spain; CIBER Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Esther Quintana-Gallego
- Medical-Surgical Unit of Respiratory Diseases, Virgen del Rocío University Hospital, 41013 Sevilla, Spain; CIBER Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain.
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Michelle JiaMin L, Karthikeyan P, Kumaresan R, Millard A, Parimannan S, Rajandas H. Complete genome sequence of Enterococcus faecalis phage EF_RCK. Microbiol Resour Announc 2024; 13:e0010924. [PMID: 38651923 DOI: 10.1128/mra.00109-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
A lytic bacteriophage EF_RCK infecting Enterococcus faecalis was isolated from a water sample collected in a raw cockle storage container at Taman Ria market, Sungai Petani, Malaysia. The phage has a 57,848-bp double-stranded DNA genome harboring 107 protein-encoding genes and shares 90.9% nucleotide similarity with Enterococcus phage EFKL (Saphexavirus genus).
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Affiliation(s)
- Loh Michelle JiaMin
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | | | | | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Ridgway R, Lu H, Blower TR, Evans NJ, Ainsworth S. Genomic and taxonomic evaluation of 38 Treponema prophage sequences. BMC Genomics 2024; 25:549. [PMID: 38824509 PMCID: PMC11144348 DOI: 10.1186/s12864-024-10461-5] [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: 11/01/2023] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage. RESULTS We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes. CONCLUSIONS In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.
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Affiliation(s)
- Rachel Ridgway
- Department of Infection Biology and Microbiomes, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire, CH64 7TE, UK.
| | - Hanshuo Lu
- Department of Infection Biology and Microbiomes, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Nicholas James Evans
- Department of Infection Biology and Microbiomes, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire, CH64 7TE, UK
| | - Stuart Ainsworth
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool Science Park IC2, 146 Brownlow Hill, Liverpool, L3 5RF, UK
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Sevilla-Navarro S, Torres-Boncompte J, Garcia-Llorens J, Bernabéu-Gimeno M, Domingo-Calap P, Catalá-Gregori P. Fighting Salmonella Infantis: bacteriophage-driven cleaning and disinfection strategies for broiler farms. Front Microbiol 2024; 15:1401479. [PMID: 38812676 PMCID: PMC11134195 DOI: 10.3389/fmicb.2024.1401479] [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: 03/15/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Salmonella is a bacterium that can cause food-borne infections and is responsible for the most common gastrointestinal illnesses. The emergence of multi-drug resistant (MDR) strains worldwide is a major threat, representing a major challenge in public health. To reduce its incidence, the One Health approach is required, and the development of new biocontrol protocols will help prevent or eliminate the spread of Salmonella. Prevention measures, such as on-farm cleaning and disinfection protocols, are a crucial step in reducing infection to new flocks and eliminating bacteria that remain in the facilities. However, MDR Salmonella species, such as S. Infantis, are highly resistant to conventional cleaning and disinfection protocols, with an increased ability to persist in the broiler farm environment. The need for alternative biocontrol methods has led to the use of bacteriophages or phages, viruses that target bacteria, as promising tools. Thus, the aim of this study was to evaluate the efficacy of phages as a biocide against S. Infantis isolates in combination with cleaning and disinfection protocols in 10 commercial poultry farms. Methods All commercial farms selected in this study had persistent Salmonella, even after the routinely used cleaning and disinfection procedures. In addition, Salmonella isolated before treatment were phenotypically characterized by antimicrobial resistance patterns. Results The results showed that 100% of S. Infantis were resistant to at least one antibiotic, and > 70% were MDR. Phages were then isolated against the in-farm bacteria, purified, and multiplied for each poultry farm. The cleaning and disinfection protocols included the application of the lytic phages (vB_Si_CECAV_FGS009; vB_Si_CECAV_FGS017; vB_Si_CECAV_FGS029 and vB_Si_CECAV _FGS030) twice at 24-h intervals between cleaning and disinfection. Following the cleaning and disinfection procedures, Salmonella detection was reduced from 100% after cleaning to 36% after applying the phages and dropped to 0% after the final step of disinfection, thus eliminating Salmonella from the farm facilities. Discussion This study demonstrates that bacteriophage application after cleaning and before disinfection enhances the removal of MDR Salmonella Infantis in commercial broiler farms, suggesting their use as biocontrol agents to reduce Salmonella, a major public health concern.
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Affiliation(s)
- Sandra Sevilla-Navarro
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Jan Torres-Boncompte
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Josep Garcia-Llorens
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Mireia Bernabéu-Gimeno
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pablo Catalá-Gregori
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
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Manley R, Fitch C, Francis V, Temperton I, Turner D, Fletcher J, Phil M, Michell S, Temperton B. Resistance to bacteriophage incurs a cost to virulence in drug-resistant Acinetobacter baumannii. J Med Microbiol 2024; 73:001829. [PMID: 38743467 PMCID: PMC11170128 DOI: 10.1099/jmm.0.001829] [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: 10/25/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction . Acinetobacter baumannii is a critical priority pathogen for novel antimicrobials (World Health Organization) because of the rise in nosocomial infections and its ability to evolve resistance to last resort antibiotics. A. baumannii is thus a priority target for phage therapeutics. Two strains of a novel, virulent bacteriophage (LemonAid and Tonic) able to infect carbapenem-resistant A. baumannii (strain NCTC 13420), were isolated from environmental water samples collected through a citizen science programme.Gap statement. Phage-host coevolution can lead to emergence of host resistance, with a concomitant reduction in the virulence of host bacteria; a potential benefit to phage therapy applications.Methodology. In vitro and in vivo assays, genomics and microscopy techniques were used to characterize the phages; determine mechanisms and impact of phage resistance on host virulence, and the efficacy of the phages against A. baumannii.Results. A. baumannii developed resistance to both viruses, LemonAid and Tonic. Resistance came at a cost to virulence, with the resistant variants causing significantly reduced mortality in a Galleria mellonella larval in vivo model. A replicated 8 bp insertion increased in frequency (~40 % higher frequency than in the wild-type) within phage-resistant A. baumannii mutants, putatively resulting in early truncation of a protein of unknown function. Evidence from comparative genomics and an adsorption assay suggests this protein acts as a novel phage receptor site in A. baumannii. We find no evidence linking resistance to changes in capsule structure, a known virulence factor. LemonAid efficiently suppressed growth of A. baumanni in vitro across a wide range of titres. However, in vivo, while survival of A. baumannii infected larvae significantly increased with both remedial and prophylactic treatment with LemonAid (107 p.f.u. ml-1), the effect was weak and not sufficient to save larvae from morbidity and mortality.Conclusion. While LemonAid and Tonic did not prove effective as a treatment in a Galleria larvae model, there is potential to harness their ability to attenuate virulence in drug-resistant A. baumannii.
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Affiliation(s)
- Robyn Manley
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
| | - Christian Fitch
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
| | - Vanessa Francis
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
| | - Isaac Temperton
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Julie Fletcher
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
| | - Mitchelmore Phil
- University of Exeter, College of Medicine and Health, Department of Respiratory Medicine, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Steve Michell
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
| | - Ben Temperton
- University of Exeter, Health and Life Sciences, Streatham Campus, Exeter, EX4 4QD, UK
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Fletcher J, Manley R, Fitch C, Bugert C, Moore K, Farbos A, Michelsen M, Alathari S, Senior N, Mills A, Whitehead N, Soothill J, Michell S, Temperton B. The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK. Microorganisms 2024; 12:253. [PMID: 38399657 PMCID: PMC10893117 DOI: 10.3390/microorganisms12020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.
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Affiliation(s)
- Julie Fletcher
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Robyn Manley
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christian Fitch
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christina Bugert
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Audrey Farbos
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Michelle Michelsen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Shayma Alathari
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Nicola Senior
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Alice Mills
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - Natalie Whitehead
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - James Soothill
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
| | - Stephen Michell
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Ben Temperton
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
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Ali SF, Teh SH, Yang HH, Tsai YC, Chao HJ, Peng SS, Chen SC, Lin LC, Lin NT. Therapeutic Potential of a Novel Lytic Phage, vB_EclM_ECLFM1, against Carbapenem-Resistant Enterobacter cloacae. Int J Mol Sci 2024; 25:854. [PMID: 38255926 PMCID: PMC10815064 DOI: 10.3390/ijms25020854] [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: 11/22/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The global rise of multidrug-resistant Enterobacter cloacae strains, especially those that are resistant to carbapenems and produce metallo-β-lactamases, poses a critical challenge in clinical settings owing to limited treatment options. While bacteriophages show promise in treating these infections, their use is hindered by scarce resources and insufficient genomic data. In this study, we isolated ECLFM1, a novel E. cloacae phage, from sewage water using a carbapenem-resistant clinical strain as the host. ECLFM1 exhibited rapid adsorption and a 15-min latent period, with a burst size of approximately 75 PFU/infected cell. Its genome, spanning 172,036 bp, was characterized and identified as a member of Karamvirus. In therapeutic applications, owing to a high multiplicity of infection, ECLFM1 showed increased survival in zebrafish infected with E. cloacae. This study highlights ECLFM1's potential as a candidate for controlling clinical E. cloacae infections, which would help address challenges in treating multidrug-resistant strains and contribute to the development of alternative treatments.
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Affiliation(s)
- Saieeda Fabia Ali
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
| | - 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 97002, Taiwan;
| | - Hsueh-Hui Yang
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97002, Taiwan;
| | - Yun-Chan Tsai
- Department of Life Sciences, College of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
| | - Huei-Jen Chao
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97002, Taiwan; (H.-J.C.); (S.-S.P.); (S.-C.C.)
| | - Si-Shiuan Peng
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97002, Taiwan; (H.-J.C.); (S.-S.P.); (S.-C.C.)
| | - Shu-Chen Chen
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97002, Taiwan; (H.-J.C.); (S.-S.P.); (S.-C.C.)
| | - Ling-Chun Lin
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
| | - Nien-Tsung Lin
- Master Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan;
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11
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Montso PK, Kropinski AM, Mokoena F, Pierneef RE, Mlambo V, Ateba CN. Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces. Sci Rep 2023; 13:21426. [PMID: 38052835 PMCID: PMC10698182 DOI: 10.1038/s41598-023-48788-w] [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: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
The increasing prevalence of antimicrobial-resistant (AMR) pathogens has become a major global health concern. To address this challenge, innovative strategies such as bacteriophage therapy must be optimised. Genomic characterisation is a crucial step in identifying suitable phage candidates for combating AMR pathogens. The aim of this study was to characterise seven phages that infect the Escherichia coli O177 strain using a whole genome sequencing. The analysis of genome sequences revealed that these phages had linear dsDNA, with genome sizes spanning from 136, 483 to 166,791 bp and GC content varying from 35.39 to 43.63%. Taxonomically, the phages were classified under three different subfamilies (Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae) and three genera (Phapecoctavirus, Tequatrovirus, and Vequintavirus) within the class Caudoviricetes. In silico PhageAI analysis predicted that all the phages were virulent, with confidence levels between 96.07 and 97.26%. The phage genomes contained between 66 and 82 ORFs, which encode hypothetical and putative functional proteins. In addition, the phage genomes contained core genes associated with molecular processes such as DNA replication, transcription modulation, nucleotide metabolism, phage structure (capsid and tail), and lysis. None of the genomes carried genes associated with undesirable traits such as integrase, antimicrobial resistance, virulence, and toxins. The study revealed high genome and proteome homology among E. coli O177 phages and other known Escherichia phages. The results suggest that the seven phages are new members of the genera Phapecoctavirus, Tequatrovirus, and Vequintavirus under the subfamilies Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae, respectively.
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Affiliation(s)
- Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| | - Andrew M Kropinski
- Department Food Science, and Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa
- SARChI Chair: Marine Microbiomics, Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Victor Mlambo
- Faculty of Agriculture and Natural Sciences, School of Agricultural Sciences, University of Mpumalanga, Mbombela, 1200, South Africa
| | - Collins Njie Ateba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
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12
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Nada MAL, Ancla JB, Yadao NMR, de Paz VP, Manalaysay JG, Samante FLD, Bigol UG. Isolation and genome sequencing of five lytic bacteriophages from hospital wastewater in the Philippines. Microbiol Resour Announc 2023; 12:e0031123. [PMID: 37526448 PMCID: PMC10508110 DOI: 10.1128/mra.00311-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/17/2023] [Indexed: 08/02/2023] Open
Abstract
Here, we report the genome sequences of five bacteriophages isolated from hospital wastewater, including two new species and two candidates for therapeutic application. No virulence, temperate marker and antibiotic resistance genes were found in the genomes of Escherichia phage vB_VIPECOOM03 and Klebsiella phage vB_VIPKPNUMC01, making them suitable candidate for therapy.
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Affiliation(s)
- Michael Angelou L. Nada
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
| | - Joseph B. Ancla
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
| | - Nikka Mae R. Yadao
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
| | - Virgilio P. de Paz
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
| | - Jessica G. Manalaysay
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
| | - Fred Lawrence D. Samante
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
| | - Ursela G. Bigol
- Department of Science and Technology, Industrial Technology Development Institute, Taguig City, Philippines
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13
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Balasubramaniam HM, Tze Yan F, Michelle JiaMin L, Parimannan S, Mutusamy P, Jaya Jothi S, Rajandas H. Genome characterization of Dickeya solani bacteriophage W2B. Microbiol Resour Announc 2023; 12:e0045223. [PMID: 37540022 PMCID: PMC10508119 DOI: 10.1128/mra.00452-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/02/2023] [Indexed: 08/05/2023] Open
Abstract
We have successfully characterized the complete genome sequence of the lytic Dickeya solani bacteriophage W2B, isolated from the Bunus Sewage Treatment Plant. The lytic phage from the Ningirsuvirus family has a 40,385-bp linear double-stranded DNA genome containing 51 coding sequences (CDSs).
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Affiliation(s)
| | - Fong Tze Yan
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
| | - Loh Michelle JiaMin
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
| | - Sivachandran Parimannan
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Prasanna Mutusamy
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
| | | | - Heera Rajandas
- Center of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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14
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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] [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.
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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
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15
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Romero-Calle DX, Pedrosa-Silva F, Ribeiro Tomé LM, Fonseca V, Guimarães Benevides R, de Oliveira Santos LTS, de Oliveira T, da Costa MM, Alcantara LCJ, de Carvalho Azevedo VA, Brenig B, Venancio TM, Billington C, Góes-Neto A. Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil. Microorganisms 2023; 11:1837. [PMID: 37513009 PMCID: PMC10384808 DOI: 10.3390/microorganisms11071837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthropological activities. The phage genome sequence was determined by Oxford Nanopore Technologies (ONT) MinION and Illumina HiSeq sequencing, and assembly was carried out by Racon (MinION) and Unicycler (Illumina, Illumina + MinION). The genome was annotated and compared to other Salmonella phages using various bioinformatics approaches. MinION DNA sequencing combined with Racon assembly gave the best complete genome sequence. Phylogenetic analysis revealed that Wara is a member of the Tequintavirus genus. A lack of lysogeny genes, antimicrobial resistance, and virulence genes indicated that Wara has therapeutic and biocontrol potential against Salmonella species in healthcare and agriculture.
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Affiliation(s)
- Danitza Xiomara Romero-Calle
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratory of Chemistry, Function of Proteins and Peptides, Center for Biosciences and Biotechnology, Darcy Ribeiro North Fluminense State University (UENF), Campos dos Goytacazes 28013-602, Brazil
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vagner Fonseca
- General Coordination of Public Health Laboratories/Secretariat of Health Surveillance, Ministry of Health, Brasília 70800-400, Brazil
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Raquel Guimarães Benevides
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mateus Matiuzzi da Costa
- Department of Biological Sciences, Federal University of the São Francisco Valley, Petrolina 56304-917, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
- Flavivirus Laboratory, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, 37073 Göttingen, Germany
| | - Thiago M Venancio
- Laboratory of Chemistry, Function of Proteins and Peptides, Center for Biosciences and Biotechnology, Darcy Ribeiro North Fluminense State University (UENF), Campos dos Goytacazes 28013-602, Brazil
| | - Craig Billington
- Health & Environment Group, Institute of Environmental Sciences and Research, Christchurch 8540, New Zealand
| | - Aristóteles Góes-Neto
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
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16
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Opperman CJ, Wojno J, Goosen W, Warren R. Phages for the treatment of Mycobacterium species. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:41-92. [PMID: 37770176 DOI: 10.1016/bs.pmbts.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Highly drug-resistant strains are not uncommon among the Mycobacterium genus, with patients requiring lengthy antibiotic treatment regimens with multiple drugs and harmful side effects. This alarming increase in antibiotic resistance globally has renewed the interest in mycobacteriophage therapy for both Mycobacterium tuberculosis complex and non-tuberculosis mycobacteria. With the increasing number of genetically well-characterized mycobacteriophages and robust engineering tools to convert temperate phages to obligate lytic phages, the phage cache against extensive drug-resistant mycobacteria is constantly expanding. Synergistic effects between phages and TB drugs are also a promising avenue to research, with mycobacteriophages having several additional advantages compared to traditional antibiotics due to their different modes of action. These advantages include less side effects, a narrow host spectrum, biofilm penetration, self-replication at the site of infection and the potential to be manufactured on a large scale. In addition, mycobacteriophage enzymes, not yet in clinical use, warrant further studies with their additional benefits for rupturing host bacteria thereby limiting resistance development as well as showing promise in vitro to act synergistically with TB drugs. Before mycobacteriophage therapy can be envisioned as part of routine care, several obstacles must be overcome to translate in vitro work into clinical practice. Strategies to target intracellular bacteria and selecting phage cocktails to limit cross-resistance remain important avenues to explore. However, insight into pathophysiological host-phage interactions on a molecular level and innovative solutions to transcend mycobacteriophage therapy impediments, offer sufficient encouragement to explore phage therapy. Recently, the first successful clinical studies were performed using a mycobacteriophage-constructed cocktail to treat non-tuberculosis mycobacteria, providing substantial insight into lessons learned and potential pitfalls to avoid in order to ensure favorable outcomes. However, due to mycobacterium strain variation, mycobacteriophage therapy remains personalized, only being utilized in compassionate care cases until there is further regulatory approval. Therefore, identifying the determinants that influence clinical outcomes that can expand the repertoire of mycobacteriophages for therapeutic benefit, remains key for their future application.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa; Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.
| | - Justyna Wojno
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa; Lancet Laboratories, Cape Town, South Africa
| | - Wynand Goosen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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17
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Sattar S, Bailie M, Yaqoob A, Khanum S, Fatima K, Altaf AURB, Ahmed I, Shah STA, Munawar J, Zehra QA, Daud S, Arshad A, Imdad K, Javed S, Tariq A, Bostan N, Altermann E. Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential. Sci Rep 2023; 13:10043. [PMID: 37340022 DOI: 10.1038/s41598-023-37176-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.
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Affiliation(s)
- Sadia Sattar
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan.
| | - Marc Bailie
- AgResearch, Palmerston North, 4410, New Zealand
| | - Akasha Yaqoob
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | | | - Kaniz Fatima
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Anees Ur Rehman Bin Altaf
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, 45710, Pakistan
| | - Syed Tahir Abbas Shah
- Functional Genomics Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Javeria Munawar
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Quaratul Ain Zehra
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Sajeela Daud
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Ayesha Arshad
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Kaleem Imdad
- Microbiology and Immunology Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Sundus Javed
- Microbiology and Immunology Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Amira Tariq
- Microbiology and Immunology Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Nazish Bostan
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Eric Altermann
- School of Veterinary Science Massey University Centre for Bioparticle Applications, Massey University, Palmerston North, 4472, New Zealand
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18
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Serian D, Churin Y, Hammerl JA, Rohde M, Jung A, Müller A, Yue M, Kehrenberg C. Characterization of Temperate LPS-Binding Bordetella avium Phages That Lack Superinfection Immunity. Microbiol Spectr 2023; 11:e0370222. [PMID: 37125905 PMCID: PMC10269795 DOI: 10.1128/spectrum.03702-22] [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: 09/13/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Bordetella avium causes a highly infectious upper respiratory tract disease in turkeys and other poultry with high economic losses. Considering the antimicrobial resistance crisis, bacteriophages (phages) may be an alternative approach for treating bacterial infections such as bordetellosis. Here, we describe seven B. avium phages, isolated from drinking water and feces from chicken and turkey farms. They showed strong bacteriolytic activity with a broad host range and used lipopolysaccharides (LPS) as a host receptor for their adsorption. All phages are myoviruses based on their structure observed by transmission electron microscopy. Genome sequence analyses revealed genome assembly sizes ranging from 39,087 to 43,144 bp. Their permutated genomes were organized colinearly, with a conserved module order, and were packed according to a predicted headful packing strategy. Notably, they contained genes encoding putative markers of lysogeny, indicative of temperate phages, despite their lytic phenotype. Further investigation revealed that the phages could indeed undergo a lysogenic life cycle with varying frequency. However, the lysogenic bacteria were still susceptible to superinfection with the same phages. This lack of stable superinfection immunity after lysogenization appears to be a characteristic feature of B. avium phages, which is favorable in terms of a potential therapeutic use of phages for the treatment of avian bordetellosis. IMPORTANCE To maintain the effectiveness of antibiotics over the long term, alternatives to treat infectious diseases are urgently needed. Therefore, phages have recently come back into focus as they can specifically infect and lyse bacteria and are naturally occurring. However, there is little information on phages that can infect pathogenic bacteria from animals, such as the causative agent of bordetellosis of poultry, B. avium. Therefore, in this study, B. avium phages were isolated and comprehensively characterized, including whole-genome analysis. Although phenotypically the phages were thought to undergo a lytic cycle, we demonstrated that they undergo a lysogenic phase, but that infection does not confer stable host superinfection immunity. These findings provide important information that could be relevant for potential biocontrol of avian bordetellosis by using phage therapy.
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Affiliation(s)
- Dorothee Serian
- Institute for Veterinary Food Science, Justus Liebig University Giessen, Giessen, Germany
| | - Yury Churin
- Institute for Veterinary Food Science, Justus Liebig University Giessen, Giessen, Germany
| | - Jens André Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research GmbH, Braunschweig, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Anja Müller
- Institute for Veterinary Food Science, Justus Liebig University Giessen, Giessen, Germany
| | - Min Yue
- Institute of Preventive Veterinary Science and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus Liebig University Giessen, Giessen, Germany
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19
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Ioannou P, Baliou S, Samonis G. Bacteriophages in Infectious Diseases and Beyond-A Narrative Review. Antibiotics (Basel) 2023; 12:1012. [PMID: 37370331 DOI: 10.3390/antibiotics12061012] [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: 04/09/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The discovery of antibiotics has revolutionized medicine and has changed medical practice, enabling successful fighting of infection. However, quickly after the start of the antibiotic era, therapeutics for infectious diseases started having limitations due to the development of antimicrobial resistance. Since the antibiotic pipeline has largely slowed down, with few new compounds being produced in the last decades and with most of them belonging to already-existing classes, the discovery of new ways to treat pathogens that are resistant to antibiotics is becoming an urgent need. To that end, bacteriophages (phages), which are already used in some countries in agriculture, aquaculture, food safety, and wastewater plant treatments, could be also used in clinical practice against bacterial pathogens. Their discovery one century ago was followed by some clinical studies that showed optimistic results that were limited, however, by some notable obstacles. However, the rise of antibiotics during the next decades left phage research in an inactive status. In the last decades, new studies on phages have shown encouraging results in animals. Hence, further studies in humans are needed to confirm their potential for effective and safe treatment in cases where there are few or no other viable therapeutic options. This study reviews the biology and applications of phages for medical and non-medical uses in a narrative manner.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- Internal Medicine Department, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Stella Baliou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George Samonis
- School of Medicine, University of Crete, 71003 Heraklion, Greece
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Fayez MS, Hakim TA, Zaki BM, Makky S, Abdelmoteleb M, Essam K, Safwat A, Abdelsattar AS, El-Shibiny A. Morphological, biological, and genomic characterization of Klebsiella pneumoniae phage vB_Kpn_ZC2. Virol J 2023; 20:86. [PMID: 37138257 PMCID: PMC10158348 DOI: 10.1186/s12985-023-02034-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/07/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Bacteriophages (phages) are one of the most promising alternatives to traditional antibiotic therapies, especially against multidrug-resistant bacteria. Klebsiella pneumoniae is considered to be an opportunistic pathogen that can cause life-threatening infections. Thus, this study aims at the characterization of a novel isolated phage vB_Kpn_ZC2 (ZCKP2, for short). METHODS The phage ZCKP2 was isolated from sewage water by using the clinical isolate KP/08 as a host strain. The isolated bacteriophage was purified and amplified, followed by testing of its molecular weight using Pulse-Field Gel Electrophoresis (PFGE), transmission electron microscopy, antibacterial activity against a panel of other Klebsiella pneumoniae hosts, stability studies, and whole genome sequencing. RESULTS Phage ZCKP2 belongs morphologically to siphoviruses as indicated from the Transmission Electron Microscopy microgram. The Pulsed Field Gel Electrophoresis and the phage sequencing estimated the phage genome size of 48.2 kbp. Moreover, the absence of lysogeny-related genes, antibiotic resistance genes, and virulence genes in the annotated genome suggests that phage ZCKP2 is safe for therapeutic use. Genome-based taxonomic analysis indicates that phage ZCKP2 represents a new family that has not been formally rated yet. In addition, phage ZCKP2 preserved high stability at different temperatures and pH values (-20 - 70 °C and pH 4 - 9). For the antibacterial activity, phage ZCKP2 maintained consistent clear zones on KP/08 bacteria along with other hosts, in addition to effective bacterial killing over time at different MOIs (0.1, 1, and 10). Also, the genome annotation predicted antibacterial lytic enzymes. Furthermore, the topology of class II holins was predicted in some putative proteins with dual transmembrane domains that contribute significantly to antibacterial activity. Phage ZCKP2 characterization demonstrates safety and efficiency against multidrug-resistant K. pneumoniae, hence ZCKP2 is a good candidate for further in vivo and phage therapy clinical applications.
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Affiliation(s)
- Mohamed S Fayez
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Toka A Hakim
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, 11787, Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Mohamed Abdelmoteleb
- Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, 12578, Egypt.
- Faculty of Environmental Agricultural Sciences, Arish University, Arish, 45511, Egypt.
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Michelle JiaMin L, Mutusamy P, Karthikeyan P, Kumaresan R, Millard A, Parimannan S, Rajandas H. Genome Characterization of Enterococcus faecalis Bacteriophage EFKL. Microbiol Resour Announc 2023:e0016023. [PMID: 37133380 DOI: 10.1128/mra.00160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.
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Affiliation(s)
- Loh Michelle JiaMin
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Prasanna Mutusamy
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | | | | | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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22
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Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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23
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Abdelsattar AS, Eita MA, Hammouda ZK, Gouda SM, Hakim TA, Yakoup AY, Safwat A, El-Shibiny A. The Lytic Activity of Bacteriophage ZCSE9 against Salmonella enterica and Its Synergistic Effects with Kanamycin. Viruses 2023; 15:v15040912. [PMID: 37112892 PMCID: PMC10142335 DOI: 10.3390/v15040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Salmonella, the causative agent of several diseases in humans and animals, including salmonellosis, septicemia, typhoid fever, and fowl typhoid, poses a serious threat to global public health and food safety. Globally, reports of therapeutic failures are increasing because of the increase in bacterial antibiotic resistance. Thus, this work highlights the combined phage–antibiotic therapy as a promising approach to combating bacterial resistance. In this manner, the phage ZCSE9 was isolated, and the morphology, host infectivity, killing curve, combination with kanamycin, and genome analysis of this phage were all examined. Morphologically, phage ZCSE9 is a siphovirus with a relatively broad host range. In addition, the phage can tolerate high temperatures until 80 °C with one log reduction and a basic environment (pH 11) without a significant decline. Furthermore, the phage prevents bacterial growth in the planktonic state, according to the results of the time-killing curve. Moreover, using the phage at MOI 0.1 with kanamycin against five different Salmonella serotypes reduces the required antibiotics to inhibit the growth of the bacteria. Comparative genomics and phylogenetic analysis suggested that phage ZCSE9, along with its close relatives Salmonella phages vB_SenS_AG11 and wksl3, belongs to the genus Jerseyvirus. In conclusion, phage ZCSE9 and kanamycin form a robust heterologous antibacterial combination that enhances the effectiveness of a phage-only approach for combating Salmonella.
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Affiliation(s)
- Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Mohamed Atef Eita
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Zainab K. Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 11787, Egypt
| | - Shrouk Mohamed Gouda
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Toka A. Hakim
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Aghapy Yermans Yakoup
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
- Faculty of Environmental Agricultural Sciences, Arish University, Arish 45511, Egypt
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Cebeci A, Türe M, Alemdağ M, Altinok I. Whole Genome Sequence of a Novel Bacteriophage APT65 Infecting Aeromonas hydrophila. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:46-50. [PMID: 37214649 PMCID: PMC10196078 DOI: 10.1089/phage.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Aeromonas hydrophila is a prevalent pathogenic bacterium in aquaculture that causes economic loss around the world. Antimicrobials are used to control and prevent the incidence of bacterial pathogens in aquaculture. However, they lead to the emergence of antimicrobial resistance strains and the accumulation of antibiotic residues in fish tissue. To address these issues, bacteriophages may be promising alternatives to many antibiotics in combating bacterial infections in aquaculture. Materials and Methods The phage specific to A. hydrophila was isolated from domestic wastewater. The morphology of phages was analyzed using transmission electron microscopy. The genomic DNA of the Aeromonas phage T65 strain (APT65) phage was sequenced with a paired-end read length of 2 × 150 bp. The genome sequence was assembled and annotated. The tRNAs were predicted, and antimicrobial resistance and virulence genes were screened. A representation of the APT65 genome was constructed. Results The genome of APT65 is linear double-stranded DNA with 85188 base pairs having 116 open reading frames (ORFs) and a G + C content of 39.41%. The 32 ORFs were predicted to encode proteins with known phage functions. No virulence factors, antibiotic resistance genes, or temperate lifestyle genes were found. The phage is icosahedral and measures 60 nm in diameter. Based on the whole genome sequence, APT65 belongs to Lahexavirus. Conclusions The taxonomic analysis of the phage with a genome length of 85,188 bp revealed that it is a new species of the genus Lahexavirus. We announce the whole genome sequence of APT65, which should be named Lahexavirus APT65, as well as the absence of antimicrobial resistance and virulence factors from its genome. Based on our results, the Lahexavirus APT65 phage may have potential as a therapeutic agent to tackle antimicrobial resistance in aquaculture.
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Affiliation(s)
- Ayşe Cebeci
- Fish Health Department, Central Fisheries Research Institute, Trabzon, Turkey
| | - Mustafa Türe
- Fish Health Department, Central Fisheries Research Institute, Trabzon, Turkey
| | - Melike Alemdağ
- Fish Health Department, Central Fisheries Research Institute, Trabzon, Turkey
| | - Ilhan Altinok
- Aquatic Animal Health and Molecular Genetics Laboratory, Faculty of Marine Sciences, Karadeniz Technical University, Trabzon, Turkey
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25
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Phenotypic Characterization and Comparative Genomic Analysis of Novel Salmonella Bacteriophages Isolated from a Tropical Rainforest. Int J Mol Sci 2023; 24:ijms24043678. [PMID: 36835084 PMCID: PMC9963771 DOI: 10.3390/ijms24043678] [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: 12/10/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Salmonella infections across the globe are becoming more challenging to control due to the emergence of multidrug-resistant (MDR) strains. Lytic phages may be suitable alternatives for treating these multidrug-resistant Salmonella infections. Most Salmonella phages to date were collected from human-impacted environments. To further explore the Salmonella phage space, and to potentially identify phages with novel characteristics, we characterized Salmonella-specific phages isolated from the Penang National Park, a conserved rainforest. Four phages with a broad lytic spectrum (kills >5 Salmonella serovars) were further characterized; they have isometric heads and cone-shaped tails, and genomes of ~39,900 bp, encoding 49 CDSs. As the genomes share a <95% sequence similarity to known genomes, the phages were classified as a new species within the genus Kayfunavirus. Interestingly, the phages displayed obvious differences in their lytic spectrum and pH stability, despite having a high sequence similarity (~99% ANI). Subsequent analysis revealed that the phages differed in the nucleotide sequence in the tail spike proteins, tail tubular proteins, and portal proteins, suggesting that the SNPs were responsible for their differing phenotypes. Our findings highlight the diversity of novel Salmonella bacteriophages from rainforest regions, which can be explored as an antimicrobial agent against MDR-Salmonella strains.
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26
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Srisangthong I, Sangseedum C, Chaichanit N, Surachat K, Suanyuk N, Mittraparp-arthorn P. Characterization and Genome Analysis of Vibrio campbellii Lytic Bacteriophage OPA17. Microbiol Spectr 2023; 11:e0162322. [PMID: 36719217 PMCID: PMC10101143 DOI: 10.1128/spectrum.01623-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
Vibrio campbellii is a marine bacterium that is associated with luminous vibriosis, especially in the hatchery and nursery stages of penaeid shrimp cultivation worldwide, which has led to low survival rates of shrimp during aquaculture. Phage therapy has been reported as an alternative biocontrol agent which can reduce or replace the use of antibiotics and other chemicals. This study characterized a lytic V. campbellii bacteriophage, OPA17, originally isolated from bloody clams and investigated its biocontrol efficacy against V. campbellii infection in a model system, Artemia franciscana. Phage OPA17 lysed 83.89% of V. campbellii strains tested (n = 118) with clear plaque morphology. Some strains of Vibrio parahaemolyticus and Vibrio vulnificus were also infected by phage OPA17. Transmission electron microscopy and genetic features indicated that OPA17 belongs to the Siphoviridae family. The latent period and burst size of OPA17 were approximately 50 min and 123 PFU/cell, respectively. Moreover, it survived in artificial seawater throughout the 2-month study period and effectively destroyed Vibrio campbellii biofilms after 4 h of incubation. The addition of OPA17 significantly increased the survival of A. franciscana nauplii infected with V. campbellii. The genome sequence of OPA17 showed that it does not carry genes unsuitable for phage therapy. The phylogenetic tree analysis showed that OPA17 was closely related to the V. vulnificus lytic phage SSP002 (98.90% similarity), which was previously reported as a potential biocontrol agent. Accordingly, the results of this study provide valuable information regarding the potential biocontrol application of phage OPA17 against V. campbellii. IMPORTANCE V. campbellii is an emerging luminous pathogen associated with vibriosis, especially in marine shrimp hatcheries. Several strategies, including pond management and use of natural antimicrobials and probiotics, have been studied for control of this organism. Phage therapy is considered one of the effective biocontrol strategies against bacterial infections in aquaculture. However, there has been limited study of V. campbellii bacteriophages. In this study, V. campbellii-specific bacteriophage OPA17 was isolated, characterized, and investigated for its biocontrol efficacy against V. campbellii infection in an Artemia nauplii model. Phage OPA17 belongs to the Siphoviridae family and shares significant genome similarity to phage SSP002, a potential biocontrol agent against V. vulnificus infection in a murine model. However, the host range of OPA17 was broader than that of SSP002. Overall, we discuss the potential of OPA17 for phage therapy application in shrimp hatcheries.
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Affiliation(s)
- Intraporn Srisangthong
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Chadtida Sangseedum
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Netnapa Chaichanit
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Naraid Suanyuk
- Aquatic Science and Innovative Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Pradal I, Casado A, del Rio B, Rodriguez-Lucas C, Fernandez M, Alvarez MA, Ladero V. Enterococcus faecium Bacteriophage vB_EfaH_163, a New Member of the Herelleviridae Family, Reduces the Mortality Associated with an E. faecium vanR Clinical Isolate in a Galleria mellonella Animal Model. Viruses 2023; 15:179. [PMID: 36680219 PMCID: PMC9860891 DOI: 10.3390/v15010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
The rise of antimicrobial resistant (AMR) bacteria is a major health concern, especially with regard to members of the ESKAPE group, to which vancomycin-resistant (VRE) Enterococcus faecium belongs. Phage therapy has emerged as a novel alternative for the treatment of AMR infections. This, however, relies on the isolation and characterisation of a large collection of phages. This work describes the exploration of human faeces as a source of new E. faecium-infecting phages. Phage vB_EfaH_163 was isolated and characterised at the microbiological, genomic, and functional levels. vB_EfaH_163 phage, a new member of Herelleviridae, subfamily Brockvirinae, has a dsDNA genome of 150,836 bp that does not harbour any virulence factors or antibiotic resistance genes. It infects a wide range of E. faecium strains of different origins, including VRE strains. Interestingly, it can also infect Enterococcus faecalis strains, even some that are linezolid-resistant. Its capacity to control the growth of a clinical VRE isolate was shown in broth culture and in a Galleria mellonella animal model. The discovery and characterisation of vB_EfaH_163 increases the number of phages that might be used therapeutically against AMR bacteria.
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Affiliation(s)
- Inés Pradal
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA-CSIC, 33300 Villaviciosa, Spain
| | - Angel Casado
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA-CSIC, 33300 Villaviciosa, Spain
| | - Beatriz del Rio
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA-CSIC, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Rodriguez-Lucas
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Microbiology Laboratory, Hospital el Bierzo, 24404 Ponferrada, Spain
- Microbiology Laboratory, Hospital Universitario de Cabueñes, 33394 Gijón, Spain
| | - Maria Fernandez
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA-CSIC, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Miguel A. Alvarez
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA-CSIC, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Victor Ladero
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA-CSIC, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 130] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
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Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
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Complete Genome Sequence of Dickeya chrysanthemi Bacteriophage DchS19. Microbiol Resour Announc 2022; 11:e0080022. [PMID: 36102644 PMCID: PMC9583810 DOI: 10.1128/mra.00800-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the complete genome of a lytic Dickeya chrysanthemi bacteriophage, DchS19, which was isolated from a soil sample in Sungai Petani, Kedah, Malaysia. The phage, from the Autographviridae family, has a 39,149-bp double-stranded DNA genome containing 49 protein-coding genes and shares 94.65% average nucleotide identity with Erwinia phage pEp_SNUABM_12.
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30
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Vill AC, Delesalle VA, Tomko BE, Lichty KB, Strine MS, Guffey AA, Burton EA, Tanke NT, Krukonis GP. Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:171-178. [PMID: 36793550 PMCID: PMC9917325 DOI: 10.1089/phage.2022.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background Despite their importance to microbial dynamics involving Bacillus subtilis, we have a limited understanding of the diversity of phages that can lyse this model organism. Materials and Methods Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild B. subtilis strain. Their genomes were assembled, characterized, and bioinformatically compared. Results Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes. Conclusions A comparative approach provides insights into phage evolution, including the role of indels in protein folding.
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Affiliation(s)
- Albert C. Vill
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | | | - Brianne E. Tomko
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | | | - Madison S. Strine
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | | | | | - Natalie T. Tanke
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Greg P. Krukonis
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
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31
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Identification of Phage Receptor-Binding Protein Sequences with Hidden Markov Models and an Extreme Gradient Boosting Classifier. Viruses 2022; 14:v14061329. [PMID: 35746800 PMCID: PMC9230537 DOI: 10.3390/v14061329] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
Receptor-binding proteins (RBPs) of bacteriophages initiate the infection of their corresponding bacterial host and act as the primary determinant for host specificity. The ever-increasing amount of sequence data enables the development of predictive models for the automated identification of RBP sequences. However, the development of such models is challenged by the inconsistent or missing annotation of many phage proteins. Recently developed tools have started to bridge this gap but are not specifically focused on RBP sequences, for which many different annotations are available. We have developed two parallel approaches to alleviate the complex identification of RBP sequences in phage genomic data. The first combines known RBP-related hidden Markov models (HMMs) from the Pfam database with custom-built HMMs to identify phage RBPs based on protein domains. The second approach consists of training an extreme gradient boosting classifier that can accurately discriminate between RBPs and other phage proteins. We explained how these complementary approaches can reinforce each other in identifying RBP sequences. In addition, we benchmarked our methods against the recently developed PhANNs tool. Our best performing model reached a precision-recall area-under-the-curve of 93.8% and outperformed PhANNs on an independent test set, reaching an F1-score of 84.0% compared to 69.8%.
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