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Antibiotics
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Phage Diversity for Research and Application
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Phage Diversity for Research and Application

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Bacteriophages".

Deadline for manuscript submissions: closed (1 June 2020) | Viewed by 49362

Special Issue Editors

Dr. Christine Rohde

E-Mail Website
Guest Editor
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
Interests: support of political and regulative strategies to foster phage therapy implementation in Germany and Europe; networking with policy-makers and with the national licensing authority; cooperation with medical doctors
Dr. Johannes Wittmann

E-Mail Website
Guest Editor
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
Interests: phage genomics; phages diversity; taxonomy; application

Special Issue Information

Dear Colleagues,

Since we entered the post-antibiotic era, bacteriophages have resurfaced as one promising alternative to antibiotics and are now the focus of interest for application and general research again.

Bacteriophages are the most abundant biological entities on earth, with an estimated number of 4.8 × 1031 phage particles in the whole biosphere. Several sequencing projects analyzing the metagenomes of different habitats have revealed that the diversity of bacterial viruses is huge, and there is always something new to discover, with a lot of habitats and bacterial species still underrepresented in terms of phage research. Phages are probably the main drivers of evolution and powerfully contribute to biodiversity in the microbe world, including human and animal microbiomes, plants, and the rhizosphere or marine habitats.

In addition to their impact on ecology and evolution, they have also played an important role in the development of modern molecular biology, and research is still going on to find new ways to use phage diversity for different applications. Phages are a success story of nature and have served as appreciated model systems, including for human disease.

The Special Issue "Phage Diversity for Research and Application" will give phage researchers the opportunity to share their findings and discussion with the scientific community in the life sciences and will encourage them to initiate new thinktanks towards promoting infrastructures and funding bodies. General phage diversity and different aspects of phage biology should be addressed and various submission types, including original research papers, short communications, reviews, and perspectives are welcome, such as:

  • Phage diversity studies
  • Phages of fastidious host bacteria or in underexplored habitats
  • Phages as tools
  • Phages for different applications apart from phage therapy
  • Phage lysis mechanisms and kinetics
  • Phage host interactions and receptor studies
  • Phages in the One Health context

Dr. Christine Rohde
Dr. Johannes Wittmann
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review, Other

5 pages, 186 KiB  
Editorial
Phage Diversity for Research and Application
by Christine Rohde and Johannes Wittmann
Antibiotics 2020, 9(11), 734; https://doi.org/10.3390/antibiotics9110734 - 26 Oct 2020
Cited by 6 | Viewed by 2094
Abstract
Bacteriophages (in short, phages) are viruses that specifically recognize and infect bacteria; they are the most abundant forms of life in the biosphere outnumbering bacteria by an estimated factor of one order of magnitude [...] Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)

Research

Jump to: Editorial, Review, Other

13 pages, 2528 KiB  
Article
Application of Bacteriophages to Control Vibrio alginolyticus Contamination in Oyster (Saccostrea glomerata) Larvae
by Tuan Son Le, Paul C. Southgate, Wayne O’Connor, Sang V. Vu and D. İpek Kurtböke
Antibiotics 2020, 9(7), 415; https://doi.org/10.3390/antibiotics9070415 - 16 Jul 2020
Cited by 29 | Viewed by 4820
Abstract
Mortalities of bivalve larvae and spat linked with Vibrio spp. infection have been described in hatcheries since 1959, causing potential development of resistant bacteria. A reliable and sustainable solution to this problem is yet to be developed. Potential treatment of bacterial infection with [...] Read more.
Mortalities of bivalve larvae and spat linked with Vibrio spp. infection have been described in hatcheries since 1959, causing potential development of resistant bacteria. A reliable and sustainable solution to this problem is yet to be developed. Potential treatment of bacterial infection with bacteriophages is gaining interest in aquaculture as a more sustainable option for managing Vibrio spp. infection. This study assessed the effectiveness of bacteriophages (Φ-5, Φ-6, and Φ-7) against pathogenic Vibrio isolates (USC-26004 and USC-26005). These phage isolates were found to belong to the Myoviridae viral family. A total of 212 ORFs of Φ-5 were identified and annotated. The genome of this phage contained putative thymidine kinase and lysin enzyme. During infections with phages, the OD values of the isolates USC-26005 and USC-26004 remained stable at a much lower reading compared to the control after 9 h of incubation. Mortality rate of oyster (Saccostrea glomerata) larvae was 28.2 ± 3.5% in the bacteriophage treatment group, compared to 77.9 ± 9.1% in the bacterial treatment group after 24 h incubation. Findings of this study indicate that lytic phages might be utilized as potential bio-control agents of luminescent bacterial disease in oyster hatcheries. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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15 pages, 1515 KiB  
Article
Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of Klebsiella pneumoniae Indicates Phage Synergy
by Holger Loessner, Insea Schlattmeier, Marie Anders-Maurer, Isabelle Bekeredjian-Ding, Christine Rohde, Johannes Wittmann, Cornelia Pokalyuk, Oleg Krut and Christel Kamp
Antibiotics 2020, 9(7), 408; https://doi.org/10.3390/antibiotics9070408 - 14 Jul 2020
Cited by 5 | Viewed by 3648
Abstract
The specific temporal evolution of bacterial and phage population sizes, in particular bacterial depletion and the emergence of a resistant bacterial population, can be seen as a kinetic fingerprint that depends on the manifold interactions of the specific phage–host pair during the course [...] Read more.
The specific temporal evolution of bacterial and phage population sizes, in particular bacterial depletion and the emergence of a resistant bacterial population, can be seen as a kinetic fingerprint that depends on the manifold interactions of the specific phage–host pair during the course of infection. We have elaborated such a kinetic fingerprint for a human urinary tract Klebsiella pneumoniae isolate and its phage vB_KpnP_Lessing by a modeling approach based on data from in vitro co-culture. We found a faster depletion of the initially sensitive bacterial population than expected from simple mass action kinetics. A possible explanation for the rapid decline of the bacterial population is a synergistic interaction of phages which can be a favorable feature for phage therapies. In addition to this interaction characteristic, analysis of the kinetic fingerprint of this bacteria and phage combination revealed several relevant aspects of their population dynamics: A reduction of the bacterial concentration can be achieved only at high multiplicity of infection whereas bacterial extinction is hardly accomplished. Furthermore the binding affinity of the phage to bacteria is identified as one of the most crucial parameters for the reduction of the bacterial population size. Thus, kinetic fingerprinting can be used to infer phage–host interactions and to explore emergent dynamics which facilitates a rational design of phage therapies. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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14 pages, 2285 KiB  
Article
Tackling Intrinsic Antibiotic Resistance in Serratia marcescens with a Combination of Ampicillin/Sulbactam and Phage SALSA
by Lorenz Weber, Mathias Jansen, Alex Krüttgen, Eva Miriam Buhl and Hans-Peter Horz
Antibiotics 2020, 9(7), 371; https://doi.org/10.3390/antibiotics9070371 - 1 Jul 2020
Cited by 8 | Viewed by 5036
Abstract
During the antibiotic crisis, bacteriophages (briefly phages) are increasingly considered as potential antimicrobial pillars for the treatment of infectious diseases. Apart from acquired drug resistance, treatment options are additionally hampered by intrinsic, chromosomal-encoded resistance. For instance, the chromosomal ampC gene encoding for the [...] Read more.
During the antibiotic crisis, bacteriophages (briefly phages) are increasingly considered as potential antimicrobial pillars for the treatment of infectious diseases. Apart from acquired drug resistance, treatment options are additionally hampered by intrinsic, chromosomal-encoded resistance. For instance, the chromosomal ampC gene encoding for the AmpC-type β-lactamases is typically present in a number of nosocomial pathogens, including S. marcescens. In this study, phage SALSA (vB_SmaP-SALSA), with lytic activity against clinical isolates of S. marcescens, was isolated from effluent. Besides phage characterization, the aim of this study was to evaluate whether a synergistic effect between the antibiotic ampicillin/sulbactam (SAM) and phage can be achieved despite intrinsic drug resistance. Phage SALSA belongs to the Podoviridae family and genome-wide treeing analysis groups this phage within the phylogenetic radiation of T7-like viruses. The genome of Phage SALSA consists of 39,933 bp, which encode for 49 open reading frames. Phage SALSA was able to productively lyse 5 out of 20 clinical isolates (25%). A bacterial challenge with phage alone in liquid medium revealed that an initial strong bacterial decline was followed by bacterial re-growth, indicating the emergence of phage resistance. In contrast, the combination of SAM and phage, together at various concentrations, caused a complete bacterial eradication, confirmed by absorbance measurements and the absence of colony forming units after plating. The data show that it is principally possible to tackle the axiomatic condition of intrinsic drug resistance with a dual antimicrobial approach, which could be extended to other clinically relevant bacteria. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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24 pages, 6739 KiB  
Article
Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
by Colin Buttimer, Caoimhe Lynch, Hanne Hendrix, Horst Neve, Jean-Paul Noben, Rob Lavigne and Aidan Coffey
Antibiotics 2020, 9(6), 352; https://doi.org/10.3390/antibiotics9060352 - 21 Jun 2020
Cited by 23 | Viewed by 5300
Abstract
To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects [...] Read more.
To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins—20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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21 pages, 2093 KiB  
Article
The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa
by Christine Pourcel, Cédric Midoux, Gilles Vergnaud and Libera Latino
Antibiotics 2020, 9(6), 339; https://doi.org/10.3390/antibiotics9060339 - 18 Jun 2020
Cited by 12 | Viewed by 4941
Abstract
Pseudomonas aeruginosa is responsible for long-term infections and is particularly resistant to treatments when hiding inside the extracellular matrix or biofilms. Phage therapy might represent an alternative to antibiotic treatment, but up to 10% of clinical strains appear to resist multiple phages. We [...] Read more.
Pseudomonas aeruginosa is responsible for long-term infections and is particularly resistant to treatments when hiding inside the extracellular matrix or biofilms. Phage therapy might represent an alternative to antibiotic treatment, but up to 10% of clinical strains appear to resist multiple phages. We investigated the characteristics of P. aeruginosa clinical strains naturally resistant to phages and compared them to highly susceptible strains. The phage-resistant strains were defective in lipopolysaccharide (LPS) biosynthesis, were nonmotile and displayed an important degree of autolysis, releasing phages and pyocins. Complete genome sequencing of three resistant strains showed the existence of a large accessory genome made of multiple insertion elements, genomic islands, pyocins and prophages, including two phages performing lateral transduction. Mutations were found in genes responsible for the synthesis of LPS and/or type IV pilus, the major receptors for most phages. CRISPR-Cas systems appeared to be absent or inactive in phage-resistant strains, confirming that they do not play a role in the resistance to lytic phages but control the insertion of exogenous sequences. We show that, despite their apparent weakness, the multiphage-resistant strains described in this study displayed selective advantages through the possession of various functions, including weapons to eliminate other strains of the same or closely related species. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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20 pages, 831 KiB  
Article
Antimicrobial Resistance Determinants Circulating among Thermophilic Campylobacter Isolates Recovered from Broilers in Ireland Over a One-Year Period
by Caoimhe T. Lynch, Helen Lynch, Sarah Burke, Kayleigh Hawkins, Colin Buttimer, Conor Mc Carthy, John Egan, Paul Whyte, Declan Bolton, Aidan Coffey and Brigid Lucey
Antibiotics 2020, 9(6), 308; https://doi.org/10.3390/antibiotics9060308 - 8 Jun 2020
Cited by 16 | Viewed by 4667
Abstract
Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, [...] Read more.
Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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Review

Jump to: Editorial, Research, Other

17 pages, 332 KiB  
Review
Bacteriophages and the One Health Approach to Combat Multidrug Resistance: Is This the Way?
by Mary Garvey
Antibiotics 2020, 9(7), 414; https://doi.org/10.3390/antibiotics9070414 - 16 Jul 2020
Cited by 41 | Viewed by 5119
Abstract
Antimicrobial resistance necessitates action to reduce and eliminate infectious disease, ensure animal and human health, and combat emerging diseases. Species such as Acinetobacter baumanniii, vancomycin resistant Enterococcus, methicillin resistance Staphylococcus aureus, and Pseudomonas aeruginosa, as well as other WHO [...] Read more.
Antimicrobial resistance necessitates action to reduce and eliminate infectious disease, ensure animal and human health, and combat emerging diseases. Species such as Acinetobacter baumanniii, vancomycin resistant Enterococcus, methicillin resistance Staphylococcus aureus, and Pseudomonas aeruginosa, as well as other WHO priority pathogens, are becoming extremely difficult to treat. In 2017, the EU adopted the “One Health” approach to combat antibiotic resistance in animal and human medicine and to prevent the transmission of zoonotic disease. As the current therapeutic agents become increasingly inadequate, there is a dire need to establish novel methods of treatment under this One Health Framework. Bacteriophages (phages), viruses infecting bacterial species, demonstrate clear antimicrobial activity against an array of resistant species, with high levels of specificity and potency. Bacteriophages play key roles in bacterial evolution and are essential components of all ecosystems, including the human microbiome. Factors such are their specificity, potency, biocompatibility, and bactericidal activity make them desirable options as therapeutics. Issues remain, however, relating to their large-scale production, formulation, stability, and bacterial resistance, limiting their implementation globally. Phages used in therapy must be virulent, purified, and well characterized before administration. Clinical studies are warranted to assess the in vivo pharmacokinetics and pharmacodynamic characteristics of phages to fully establish their therapeutic potential. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)

Other

12 pages, 1731 KiB  
Brief Report
From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses
by Johannes Wittmann, Dann Turner, Andrew D. Millard, Padmanabhan Mahadevan, Andrew M. Kropinski and Evelien M. Adriaenssens
Antibiotics 2020, 9(10), 663; https://doi.org/10.3390/antibiotics9100663 - 30 Sep 2020
Cited by 38 | Viewed by 5950
Abstract
Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new [...] Read more.
Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family “Schitoviridae”, including eight subfamilies and numerous new genera. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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8 pages, 232 KiB  
Opinion
Prophage in Phage Manufacturing: Is the Risk Overrated Compared to Other Therapies or Food?
by Gabard Jérôme
Antibiotics 2020, 9(8), 435; https://doi.org/10.3390/antibiotics9080435 - 22 Jul 2020
Cited by 6 | Viewed by 2618
Abstract
The rehabilitation of lytic bacteriophages, as living and replicative biological therapeutic agents, is only 2 decades old in western countries, compared to other therapeutic approaches using chemicals and inactivated or alive biologicals. This paper attempts to provide arguments to address prophage content issues [...] Read more.
The rehabilitation of lytic bacteriophages, as living and replicative biological therapeutic agents, is only 2 decades old in western countries, compared to other therapeutic approaches using chemicals and inactivated or alive biologicals. This paper attempts to provide arguments to address prophage content issues in phage pharmaceutical preparations from a regulatory perspective. The author rebalances the risk associated with the presence of prophages in their pharmaceutical preparations in comparison (i) to lysogenic phages and prophages contained in various therapeutic anti-infective treatments, as well as in food or probiotics, (ii) to adventitious whole retroviruses or fragments contained in vaccines, and (iii) to the massive release of lysogenic phages and prophages induced by antibiotics usage. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
8 pages, 214 KiB  
Perspective
Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist
by Philip Serwer
Antibiotics 2020, 9(5), 255; https://doi.org/10.3390/antibiotics9050255 - 15 May 2020
Cited by 4 | Viewed by 4255
Abstract
Recently, the research community has had a real-world look at reasons for improving vaccine responses to emerging RNA viruses. Here, a vaccine non-specialist suggests how this might be done. I propose two alternative options and compare the primary alternative option with current practice. [...] Read more.
Recently, the research community has had a real-world look at reasons for improving vaccine responses to emerging RNA viruses. Here, a vaccine non-specialist suggests how this might be done. I propose two alternative options and compare the primary alternative option with current practice. The basis of comparison is feasibility in achieving what we need: a safe, mass-produced, emerging virus-targeted vaccine on 2–4 week notice. The primary option is the following. (1) Start with a platform based on live viruses that infect bacteria, but not humans (bacteriophages, or phages). (2) Isolate phages (to be called pathogen homologs) that resemble and provide antigenic context for membrane-covered, pathogenic RNA viruses; coronavirus-phage homologs will probably be found if the search is correctly done. (3) Upon isolating a viral pathogen, evolve its phage homolog to bind antibodies neutralizing for the viral pathogen. Vaccinate with the evolved phage homolog by generating a local, non-hazardous infection with the phage host and then curing the infection by propagating the phage in the artificially infecting bacterial host. I discuss how this alternative option has the potential to provide what is needed after appropriate platforms are built. Full article
(This article belongs to the Special Issue Phage Diversity for Research and Application)
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