1
|
Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
Collapse
Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
| |
Collapse
|
2
|
Pourcel C, Essoh C, Ouldali M, Tavares P. Acinetobacter baumannii satellite phage Aci01-2-Phanie depends on a helper myophage for its multiplication. J Virol 2024; 98:e0066724. [PMID: 38829140 PMCID: PMC11264900 DOI: 10.1128/jvi.00667-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024] Open
Abstract
We report the discovery of a satellite-helper phage system with a novel type of dependence on a tail donor. The Acinetobacter baumannii satellite podovirus Aci01-2-Phanie (short name Phanie) uses a phage phi29-like DNA replication and packaging mode. Its linear 11,885 bp dsDNA genome bears 171 bp inverted terminal repeats (ITR). Phanie is related to phage DU-PP-III from Pectobacterium and to members of the Astrithrvirus from Salmonella enterica. Together, they form a new clade of phages with 27% to 30% identity over the whole genome. Detailed 3D protein structure prediction and mass spectrometry analyses demonstrate that Phanie encodes its capsid structural genes and genes necessary to form a short tail. However, our study reveals that Phanie virions are non-infectious unless they associate with the contractile tail of an unrelated phage, Aci01-1, to produce chimeric myoviruses. Following the coinfection of Phanie with myovirus Aci01-1, hybrid viral particles composed of Phanie capsids and Aci01-1 contractile tails are assembled together with Phanie and Aci01-1 particles.IMPORTANCEThere are few reported cases of satellite-helper phage interactions but many more may be yet undiscovered. Here we describe a new mode of satellite phage dependence on a helper phage. Phanie, like phage phi29, replicates its linear dsDNA by a protein primed-mechanism and protects it inside podovirus-like particles. However, these particles are defective, requiring the acquisition of the tail from a myovirus helper for production of infectious virions. The formation of chimeras between a phi29-like podovirus and a helper contractile tail reveals an unexpected association between very different bacterial viruses.
Collapse
Affiliation(s)
- Christine Pourcel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christiane Essoh
- Department of Biochemistry-Genetic, School of Biological Sciences, Université Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Malika Ouldali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [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: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
Collapse
Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
| |
Collapse
|
5
|
Fortaleza JAG, Ong CJN, De Jesus R. Efficacy and clinical potential of phage therapy in treating methicillin-resistant Staphylococcus aureus (MRSA) infections: A review. Eur J Microbiol Immunol (Bp) 2024; 14:13-25. [PMID: 38305804 PMCID: PMC10895361 DOI: 10.1556/1886.2023.00064] [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: 12/27/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
Staphylococcus aureus infections have already presented a substantial public health challenge, encompassing different clinical manifestations, ranging from bacteremia to sepsis and multi-organ failures. Among these infections, methicillin-resistant S. aureus (MRSA) is particularly alarming due to its well-documented resistance to multiple classes of antibiotics, contributing significantly to global mortality rates. Consequently, the urgent need for effective treatment options has prompted a growing interest in exploring phage therapy as a potential non-antibiotic treatment against MRSA infections. Phages represent a class of highly specific bacterial viruses known for their ability to infect certain bacterial strains. This review paper explores the clinical potential of phages as a treatment for MRSA infections due to their low toxicity and auto-dosing capabilities. The paper also discusses the synergistic effect of phage-antibiotic combination (PAC) and the promising results from in vitro and animal model studies, which could lead to extensive human clinical trials. However, clinicians need to establish and adhere to standard protocols governing phage administration and implementation. Prominent clinical trials are needed to develop and advance phage therapy as a non-antibiotic therapy intervention, meeting regulatory guidelines, logistical requirements, and ethical considerations, potentially revolutionizing the treatment of MRSA infections.
Collapse
Affiliation(s)
- Jamil Allen G Fortaleza
- 1Senior High School Department, NU Fairview Incorporated, Quezon City, 1118, Philippines
- 2National University, Philippines, Sampaloc, Manila, 1008, Philippines
| | | | - Rener De Jesus
- 4Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| |
Collapse
|
6
|
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.
Collapse
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.)
| |
Collapse
|
7
|
Thammatinna K, Sinprasertporn A, Naknaen A, Samernate T, Nuanpirom J, Chanwong P, Somboonwiwat K, Pogliano J, Sathapondecha P, Thawonsuwan J, Nonejuie P, Chaikeeratisak V. Nucleus-forming vibriophage cocktail reduces shrimp mortality in the presence of pathogenic bacteria. Sci Rep 2023; 13:17844. [PMID: 37857653 PMCID: PMC10587174 DOI: 10.1038/s41598-023-44840-x] [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: 07/22/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
The global aquaculture industry has suffered significant losses due to the outbreak of Acute Hepatopancreatic Necrosis Disease (AHPND) caused by Vibrio parahaemolyticus. Since the use of antibiotics as control agents has not been shown to be effective, an alternative anti-infective regimen, such as phage therapy, has been proposed. Here, we employed high-throughput screening for potential phages from 98 seawater samples and obtained 14 phages exhibiting diverse host specificity patterns against pathogenic VPAHPND strains. Among others, two Chimallinviridae phages, designated Eric and Ariel, exhibited the widest host spectrum against vibrios. In vitro and in vivo studies revealed that a cocktail derived from these two nucleus-forming vibriophages prolonged the bacterial regrowth of various pathogenic VPAHPND strains and reduced shrimp mortality from VPAHPND infection. This research highlights the use of high-throughput phage screening that leads to the formulation of a nucleus-forming phage cocktail applicable for bacterial infection treatment in aquaculture.
Collapse
Affiliation(s)
- Khrongkhwan Thammatinna
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ammara Sinprasertporn
- Songkhla Aquatic Animal Health Research and Development Center (SAAHRDC), Department of Fisheries, Songkhla, Thailand
| | - Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Jiratchaya Nuanpirom
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Parinda Chanwong
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jumroensri Thawonsuwan
- Songkhla Aquatic Animal Health Research and Development Center (SAAHRDC), Department of Fisheries, Songkhla, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| |
Collapse
|
8
|
Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
Collapse
Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
9
|
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: 2] [Impact Index Per Article: 2.0] [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.
Collapse
Affiliation(s)
- Nikoline S Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Peter Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, US
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| |
Collapse
|
10
|
Elek CKA, Brown TL, Le Viet T, Evans R, Baker DJ, Telatin A, Tiwari SK, Al-Khanaq H, Thilliez G, Kingsley RA, Hall LJ, Webber MA, Adriaenssens EM. A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses. Microb Genom 2023; 9:mgen001065. [PMID: 37463032 PMCID: PMC10438801 DOI: 10.1099/mgen.0.001065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/17/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.
Collapse
Affiliation(s)
- Claire K. A. Elek
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Teagan L. Brown
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - David J. Baker
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Sumeet K. Tiwari
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Haider Al-Khanaq
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Gaëtan Thilliez
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL—Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mark A. Webber
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | | |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Four novel Curtobacterium phages isolated from environmental samples. Arch Virol 2023; 168:89. [PMID: 36786922 DOI: 10.1007/s00705-023-05706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/20/2022] [Indexed: 02/15/2023]
Abstract
Despite Curtobacterium spp. often being associated with the plant phyllosphere, i.e., the areal region of different plant species, only one phage targeting a member of the genus Curtobacterium has been isolated so far. In this study, we isolated four novel plaque-forming Curtobacterium phages, Reje, Penoan, Parvaparticeps, and Pize, with two novel Curtobacterium strains as propagation hosts. Based on the low nucleotide intergenomic similarity (<32.4%) between these four phages and any phage with a genome sequence in the NCBI database, we propose the establishment of the four genera, "Rejevirus", "Pizevirus", "Penoanvirus", and "Parvaparticepsvirus", all in the class of Caudoviricetes.
Collapse
|
13
|
A Flexible and Efficient Microfluidics Platform for the Characterization and Isolation of Novel Bacteriophages. Appl Environ Microbiol 2023; 89:e0159622. [PMID: 36602353 PMCID: PMC9888219 DOI: 10.1128/aem.01596-22] [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] [Indexed: 01/06/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria. This property makes them highly suitable for varied uses in industry or in the development of the treatment of bacterial infections. However, the conventional methods that are used to isolate and analyze these bacteriophages from the environment are generally cumbersome and time consuming. Here, we adapted a high-throughput microfluidic setup for long-term analysis of bacteriophage-bacteria interaction and demonstrate isolation of phages from environmental samples. IMPORTANCE Bacteriophages are gaining increased attention for their potential application as agents to combat antibiotic-resistant infections. However, isolation and characterization of new phages are time consuming and limited by currently used methods. The microfluidics platform presented here allows the isolation and long-term analysis of phages and their effect on host cells with fluorescent light microscopy imaging. Furthermore, this new workflow allows high-throughput characterization of environmental samples for the identification of phages alongside gaining detailed insight into the host response. Taken together, this microfluidics platform will be a valuable tool for phage research, enabling faster and more efficient screening and characterization of host-phage interactions.
Collapse
|
14
|
Alanin KWS, Olsen NS, Djurhuus AM, Carstens AB, Nielsen TK, Wagner N, Lametsch R, Bak F, Hennessy RC, Nicolaisen MH, Kot W, Hansen LH. Three novel Erwinia billingiae phages isolated from organic waste represent three new genera. Arch Virol 2023; 168:71. [PMID: 36658443 DOI: 10.1007/s00705-023-05700-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/19/2022] [Indexed: 01/21/2023]
Abstract
Despite the ecological significance of viral communities, phages remain insufficiently studied. Current genomic databases lack high-quality phage genome sequences linked to specific bacteria. Bacteria of the genus Erwinia are known to colonize the phyllosphere of plants, both as commensals and as pathogens. We isolated three Erwinia billingiae phages-Zoomie, Pecta, and Snitter-from organic household waste. Based on sequence similarity to their closest relatives, we propose that they represent three new genera: "Pectavirus" within the family Zobellviridae, "Snittervirus" in the subfamily Tempevirinae, family Drexlerviridae, and "Zoomievirus" within the family Autographiviridae, which, together with the genus Limelightvirus, may constitute a new subfamily.
Collapse
Affiliation(s)
- Katrine Wacenius Skov Alanin
- Department for Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Nikoline S Olsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Natalia Wagner
- Institute for Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Rosanna Catherine Hennessy
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Witold Kot
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| |
Collapse
|
15
|
Glonti T, Pirnay JP. In Vitro Techniques and Measurements of Phage Characteristics That Are Important for Phage Therapy Success. Viruses 2022; 14:1490. [PMID: 35891470 PMCID: PMC9323186 DOI: 10.3390/v14071490] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023] Open
Abstract
Validated methods for phage selection, host range expansion, and lytic activity determination are indispensable for maximizing phage therapy outcomes. In this review, we describe some relevant methods, highlighting their advantages and disadvantages, and categorize them as preliminary or confirmatory methods where appropriate. Experimental conditions, such as the composition and consistency of culture media, have an impact on bacterial growth and, consequently, phage propagation and the selection of phage-resistant mutants. The phages require different experimental conditions to be tested to fully reveal their characteristics and phage therapy potential in view of their future use in therapy. Phage lytic activity or virulence should be considered as a result of the phage, its host, and intracellular/environmental factors, including the ability of a phage to recognize receptors on the bacterial cell surface. In vitro quantitative and qualitative measurements of phage characteristics, further validated by in vivo experiments, could be incorporated into one system or mathematical model/formula, which could predict a potential successful outcome of clinical applications.
Collapse
Affiliation(s)
- Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, B-1120 Brussels, Belgium;
| | | |
Collapse
|
16
|
Khan A, Joshi H. Simple Two-step, High Yield Protocol for Isolation and Amplification of Bacteriophages Against Methicillin-resistant Staphylococcus Aureus (MRSA). Curr Protoc 2022; 2:e395. [PMID: 35259286 DOI: 10.1002/cpz1.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacteriophages are bacteria-targeting viruses that may prove useful as therapeutic agents against multidrug-resistant bacterial strains. Though phage therapy is a century-old concept, there is very limited progress on its therapeutic application due to the rapid expansion of antibiotics portfolios in the last few decades. However, the emergence of multidrug-resistant organisms has brought our attention back to bacteriophages. The first step towards developing effective phage therapy against multidrug-resistant bacteria is isolation, amplification, and purification of specific bacteriophages. There are many reported protocols for isolating host-specific bacteriophages from the environment. However, most of them are complex, multistep, low-yielding, resource-intensive protocols, requiring elaborate laboratory setup. We have demonstrated a simple two-step, high-yielding protocol for isolating and amplifying bacteriophages against methicillin-resistant Staphylococcus aureus (MRSA). We have shown that mixing various environmental samples (i.e., sample pooling) and phage amplification at two different temperatures significantly enhance the yield of MRSA phages. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of water sample filtrate for isolation of bacteriophages Basic Protocol 2: Bacterial strain and culture conditions Basic Protocol 3: Native bacteriophage count in water sample filtrate Basic Protocol 4: Isolation and enrichment of MRSA-specific bacteriophages Basic Protocol 5: Quantification of bacteriophages by drop cast method Basic Protocol 6: Effect of incubation temperature and heat shock on bacteriophage yield.
Collapse
Affiliation(s)
- Atif Khan
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, BARC Facilities, Kalpakkam, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Hiren Joshi
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, BARC Facilities, Kalpakkam, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| |
Collapse
|
17
|
Lood C, Boeckaerts D, Stock M, De Baets B, Lavigne R, van Noort V, Briers Y. Digital phagograms: predicting phage infectivity through a multilayer machine learning approach. Curr Opin Virol 2021; 52:174-181. [PMID: 34952265 DOI: 10.1016/j.coviro.2021.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/26/2021] [Accepted: 12/04/2021] [Indexed: 12/19/2022]
Abstract
Machine learning has been broadly implemented to investigate biological systems. In this regard, the field of phage biology has embraced machine learning to elucidate and predict phage-host interactions, based on receptor-binding proteins, (anti-)defense systems, prophage detection, and life cycle recognition. Here, we highlight the enormous potential of integrating information from omics data with insights from systems biology to better understand phage-host interactions. We conceptualize and discuss the potential of a multilayer model that mirrors the phage infection process, integrating adsorption, bacterial pan-immune components and hijacking of the bacterial metabolism to predict phage infectivity. In the future, this model can offer insights into the underlying mechanisms of the infection process, and digital phagograms can support phage cocktail design and phage engineering.
Collapse
Affiliation(s)
- Cédric Lood
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium; Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Dimitri Boeckaerts
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium; KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium; BIOBIX, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium; Institute of Biology, Leiden University, Leiden, The Netherlands.
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
| |
Collapse
|
18
|
Maffei E, Shaidullina A, Burkolter M, Heyer Y, Estermann F, Druelle V, Sauer P, Willi L, Michaelis S, Hilbi H, Thaler DS, Harms A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol 2021; 19:e3001424. [PMID: 34784345 PMCID: PMC8594841 DOI: 10.1371/journal.pbio.3001424] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
Collapse
Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Luc Willi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - David S. Thaler
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, Rockefeller University, New York City, New York, United States of America
| | | |
Collapse
|
19
|
Ng RN, Grey LJ, Vaitekenas A, McLean SA, Rudrum JD, Laucirica DR, Poh MWP, Hillas J, Winslow SG, Iszatt JJ, Iosifidis T, Tai AS, Agudelo-Romero P, Chang BJ, Stick SM, Kicic A. Development and validation of a miniaturized bacteriophage host range screening assay against antibiotic resistant Pseudomonas aeruginosa. J Microbiol Methods 2021; 190:106346. [PMID: 34637818 DOI: 10.1016/j.mimet.2021.106346] [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: 08/01/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 10/20/2022]
Abstract
Antimicrobial resistance is a current global health crisis, and the increasing emergence of multidrug resistant infections has led to the resurgent interest in bacteriophages as an alternative treatment. Prior to clinical application, phage suitability is assessed, via susceptibility testing and breadth of host range to bacteriophage, however, these are both large-scale manual processes and labor-intensive. The aim of the study was to establish and validate a scaled down methodology for high-throughput screening to reduce procedural footprint. In this paper, we describe a scaled-down adapted methodology that can successfully screen bacteriophages, isolated and purified from wastewater samples. Furthermore, we describe a miniaturized host range assay against clinical Pseudomonas aeruginosa isolates using a spot test (2 μL/ drop) that was found to be both sensitive (94.6%) and specific (94.7%). It also demonstrated a positive predictive value (PPV) of 86.4% and negative predictive value (NPV) of 98%. The breadth of host range of bacteriophages that exhibited lytic activity on P. aeruginosa isolates was corroborated using the scaled down assay. The high correlation achieved in this study confirms miniaturization as the first step in future automation that could test phage diversity and efficacy as antimicrobials.
Collapse
Affiliation(s)
- Renee Nicole Ng
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia; Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Lucinda Jane Grey
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia; Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Andrew Vaitekenas
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Occupation, Environment and Safety, School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Samantha Abagail McLean
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Jack Dylan Rudrum
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia; Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Daniel Rodolfo Laucirica
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Matthew Wee-Peng Poh
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Jessica Hillas
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Scott Glenn Winslow
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Joshua James Iszatt
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Occupation, Environment and Safety, School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Thomas Iosifidis
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Occupation, Environment and Safety, School of Population Health, Curtin University, Perth, Western Australia, Australia; Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Anna Sze Tai
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia; Institute for Respiratory Health, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Barbara Jane Chang
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Stephen Michael Stick
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, Western Australia, Australia; Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Occupation, Environment and Safety, School of Population Health, Curtin University, Perth, Western Australia, Australia; Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, Western Australia, Australia; Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.
| | -
- Wal-Yan Respiratory Research Center, Telethon Kids Institute, Perth, Western Australia, Australia; Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, Western Australia, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
20
|
Knezevic P, Petrovic Fabijan A, Gavric D, Pejic J, Doffkay Z, Rakhely G. Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case. Viruses 2021; 13:1965. [PMID: 34696396 PMCID: PMC8540360 DOI: 10.3390/v13101965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10-4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.
Collapse
Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Aleksandra Petrovic Fabijan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Jovana Pejic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Zsolt Doffkay
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| |
Collapse
|
21
|
Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
Collapse
Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
| |
Collapse
|
22
|
Buchholz HH, Michelsen ML, Bolaños LM, Browne E, Allen MJ, Temperton B. Efficient dilution-to-extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. THE ISME JOURNAL 2021; 15:1585-1598. [PMID: 33495565 PMCID: PMC8163748 DOI: 10.1038/s41396-020-00872-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
Abstract
Microbes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus-host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages, including the first known siphophage-infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host ranges. Similar to the abundant human-associated phage ɸCrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes, or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus-host systems in culture collections and genomic databases will improve both our understanding of virus-host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.
Collapse
Affiliation(s)
| | | | | | - Emily Browne
- School of Biosciences, University of Exeter, Exeter, UK
| | - Michael J Allen
- School of Biosciences, University of Exeter, Exeter, UK
- Plymouth Marine Laboratory, Plymouth, UK
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
| |
Collapse
|
23
|
Alanin KWS, Junco LMF, Jørgensen JB, Nielsen TK, Rasmussen MA, Kot W, Hansen LH. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay. Viruses 2021; 13:959. [PMID: 34064231 PMCID: PMC8224292 DOI: 10.3390/v13060959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.
Collapse
Affiliation(s)
- Katrine Wacenius Skov Alanin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Laura Milena Forero Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Jacob Bruun Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Morten Arendt Rasmussen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark;
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| |
Collapse
|
24
|
Abdelsattar AS, Dawoud A, Makky S, Nofal R, Aziz RK, El-Shibiny A. Bacteriophages: from isolation to application. Curr Pharm Biotechnol 2021; 23:337-360. [PMID: 33902418 DOI: 10.2174/1389201022666210426092002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Bacteriophages are considered as a potential alternative to fight pathogenic bacteria during the antibiotic resistance era. With their high specificity, they are being widely used in various applications: medicine, food industry, agriculture, animal farms, biotechnology, diagnosis, etc. Many techniques have been designed by different researchers for phage isolation, purification, and amplification, each of which has strengths and weaknesses. However, all aim at having a reasonably pure phage sample that can be further characterized. Phages can be characterized based on their physiological, morphological or inactivation tests. Microscopy, in particular, has opened a wide gate not only for visualizing phage morphological structure, but also for monitoring biochemistry and behavior. Meanwhile, computational analysis of phage genomes provides more details about phage history, lifestyle, and potential for toxigenic or lysogenic conversion, which translate to safety in biocontrol and phage therapy applications. This review summarizes phage application pipelines at different levels and addresses specific restrictions and knowledge gaps in the field. Recently developed computational approaches, which are used in phage genome analysis, are critically assessed. We hope that this assessment provides researchers with useful insights for selection of suitable approaches for Phage-related research aims and applications.
Collapse
Affiliation(s)
- Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Rana Nofal
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, Cairo. Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| |
Collapse
|