Special Issue "Bacteriophages and Biofilms"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Bacterial Viruses".

Deadline for manuscript submissions: closed (15 December 2019).

Special Issue Editors

Prof. Dr. Zuzanna Drulis-Kawa
Website1 Website2
Guest Editor
Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland
Interests: biofilm; phage-host interactions; phage-borne enzymes; alternative antibacterial therapies
Dr. Barbara Maciejewska

Guest Editor
Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, Poland

Special Issue Information

Dear Colleagues,

Biofilms are a community of surface-associated microorganisms embedded within a matrix of extracellular polymeric substances (EPS—extracellular polymeric substances) composed essentially of polysaccharides, eDNA, and proteins. These multicellular communities are characterised by the presence of different cell types in terms of physiology and phenotype.

Persister cells are much more abundant in biofilms compared to planktonic culture; therefore, it is important to understand persister cells interactions with domesticated phages (prophages) as well as with lytic ones. Phages are actively involved in biofilm formation, in two different ways: as promoting or degrading agents. Phages can be equipped with matrix-degrading enzymes and effectively infect biofilm-embedded cells. In this meaning, phages are a natural and helpful weapon against microbial biofilms. On the other hand, prophages regulate phage-mediated cell lysis and eDNA release, an important component of stabilizing the biofilm matrix.

The ability to form biofilms and to modify virulence in response to environmental changes is coordinated by complex bacterial signaling networks such as two-component systems (TCS), secondary messengers involved in quorum sensing (QS), and c-di-GMP networks (diguanylate cyclase systems, DGC). Signal cascades dynamically control the transition from free-living to the sessile mode of growth in response to external environment changes, including viral infection. Therefore, it is interesting to understand the interaction of phages with the bacterial signaling network.

In this Special Issue, we are looking for reports and reviews of the most current findings on the phage role in bacterial biofilms formation, maintenance, and degradation. We welcome the submission of original research, reviews, and mini-reviews covering but not limited to the following topics:

  1. The influence of phages in regulating biofilm initiation, development, function, and dispersal;
  2. Phage-mediated horizontal gene transfer within the sessile community;
  3. Phage-phage interactions and communication in multicellular bacterial communities;
  4. The role of phages in regulating the bacterial signaling network and intercellular interactions;
  5. Phage propagation regulation/preferences during the infection of biofilm-forming bacteria;
  6. Anti-viral infection mechanisms of sessile cells;
  7. Phage influence on the physiology and fitness of biofilm communities;
  8. The development of novel strategies for preventing or controlling biofilm formation based on phage products.

Dr. Zuzanna Drulis-Kawa
Dr. Barbara Maciejewska
Guest Editors

Manuscript Submission Information

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Keywords

  • Biofilm
  • phages
  • phage-sessile cells interactions
  • persister cells
  • lysogeny/pseudolysogeny
  • anti-phage mechanisms of biofilm-living bacteria
  • anti-biofilm treatment
  • phage-based pro-biofilm activity

Published Papers (11 papers)

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Research

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Open AccessArticle
The Protective Effect of Staphylococcus epidermidis Biofilm Matrix against Phage Predation
Viruses 2020, 12(10), 1076; https://doi.org/10.3390/v12101076 - 25 Sep 2020
Abstract
Staphylococcus epidermidis is a major causative agent of nosocomial infections, mainly associated with the use of indwelling devices, on which this bacterium forms structures known as biofilms. Due to biofilms’ high tolerance to antibiotics, virulent bacteriophages were previously tested as novel therapeutic agents. [...] Read more.
Staphylococcus epidermidis is a major causative agent of nosocomial infections, mainly associated with the use of indwelling devices, on which this bacterium forms structures known as biofilms. Due to biofilms’ high tolerance to antibiotics, virulent bacteriophages were previously tested as novel therapeutic agents. However, several staphylococcal bacteriophages were shown to be inefficient against biofilms. In this study, the previously characterized S. epidermidis-specific Sepunavirus phiIBB-SEP1 (SEP1), which has a broad spectrum and high activity against planktonic cells, was evaluated concerning its efficacy against S. epidermidis biofilms. The in vitro biofilm killing assays demonstrated a reduced activity of the phage. To understand the underlying factors impairing SEP1 inefficacy against biofilms, this phage was tested against distinct planktonic and biofilm-derived bacterial populations. Interestingly, SEP1 was able to lyse planktonic cells in different physiological states, suggesting that the inefficacy for biofilm control resulted from the biofilm 3D structure and the protective effect of the matrix. To assess the impact of the biofilm architecture on phage predation, SEP1 was tested in disrupted biofilms resulting in a 2 orders-of-magnitude reduction in the number of viable cells after 6 h of infection. The interaction between SEP1 and the biofilm matrix was further assessed by the addition of matrix to phage particles. Results showed that the matrix did not inactivate phages nor affected phage adsorption. Moreover, confocal laser scanning microscopy data demonstrated that phage infected cells were less predominant in the biofilm regions where the matrix was more abundant. Our results provide compelling evidence indicating that the biofilm matrix can work as a barrier, allowing the bacteria to be hindered from phage infection. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Antibiofilm Activity of a Broad-Range Recombinant Endolysin LysECD7: In Vitro and In Vivo Study
Viruses 2020, 12(5), 545; https://doi.org/10.3390/v12050545 - 15 May 2020
Cited by 3
Abstract
Surfaces of implanted medical devices are highly susceptible to biofilm formation. Bacteria in biofilms are embedded in a self-produced extracellular matrix that inhibits the penetration of antibiotics and significantly contributes to the mechanical stability of the colonizing community which leads to an increase [...] Read more.
Surfaces of implanted medical devices are highly susceptible to biofilm formation. Bacteria in biofilms are embedded in a self-produced extracellular matrix that inhibits the penetration of antibiotics and significantly contributes to the mechanical stability of the colonizing community which leads to an increase in morbidity and mortality rate in clinical settings. Therefore, new antibiofilm approaches and substances are urgently needed. In this paper, we test the efficacy of a broad-range recombinant endolysin of the coliphage LysECD7 against forming and mature biofilms. We used a strong biofilm producer—Klebsiella pneumoniae Ts 141-14 clinical isolate. In vitro investigation of the antibacterial activity was performed using the standard biofilm assay in microtiter plates. We optimized the implantable diffusion chamber approach in order to reach strong biofilm formation in vivo avoiding severe consequences of the pathogen for the animals and to obtain a well-reproducible model of implant-associated infection. Endolysin LysECD7 significantly reduced the biofilm formation and was capable of degrading the preformed biofilm in vitro. The animal trials on the preformed biofilms confirmed these results. Overall, our results show that LysECD7 is a promising substance against clinically relevant biofilms. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
The Application of Impedance Spectroscopy for Pseudomonas Biofilm Monitoring during Phage Infection
Viruses 2020, 12(4), 407; https://doi.org/10.3390/v12040407 - 07 Apr 2020
Cited by 2
Abstract
Bacterial biofilm prevention and eradication are common treatment problems, hence there is a need for advanced and precise experimental methods for its monitoring. Bacterial resistance to antibiotics has resulted in an interest in using a natural bacterial enemy—bacteriophages. In this study, we present [...] Read more.
Bacterial biofilm prevention and eradication are common treatment problems, hence there is a need for advanced and precise experimental methods for its monitoring. Bacterial resistance to antibiotics has resulted in an interest in using a natural bacterial enemy—bacteriophages. In this study, we present the application of quartz tuning forks (QTF) as impedance sensors to determine in real-time the direct changes in Pseudomonas aeruginosa PAO1 biofilm growth dynamics during Pseudomonas phage LUZ 19 treatment at different multiplicities of infection (MOI). The impedance of the electric equivalent circuit (EEC) allowed us to measure the series resistance (Rs) corresponding to the growth-medium resistance (planktonic culture changes) and the conductance (G) corresponding to the level of QTF sensor surface coverage by bacterial cells and the extracellular polymer structure (EPS) matrix. It was shown that phage impacts on sessile cells (G dynamics) was very similar in the 10-day biofilm development regardless of applied MOI (0.1, 1 or 10). The application of phages at an early stage (at the sixth h) and on three-day biofilm caused a significant slowdown in biofilm dynamics, whereas the two-day biofilm turned out to be insensitive to phage infection. We observed an inhibitory effect of phage infection on the planktonic culture (Rs dynamics) regardless of the MOI applied and the time point of infection. Moreover, the Rs parameter made it possible to detect PAO1 population regrowth at the latest time points of incubation. The number of phage-insensitive forms reached the level of untreated culture at around the sixth day of infection. We conclude that the proposed impedance spectroscopy technique can be used to measure the physiological changes in the biofilm matrix composition, as well as the condition of planktonic cultures in order to evaluate the activity of anti-biofilm compounds. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Glycine Cleavage System and cAMP Receptor Protein Co-Regulate CRISPR/cas3 Expression to Resist Bacteriophage
Viruses 2020, 12(1), 90; https://doi.org/10.3390/v12010090 - 13 Jan 2020
Abstract
The CRISPR/Cas system protects bacteria against bacteriophage and plasmids through a sophisticated mechanism where cas operon plays a crucial role consisting of cse1 and cas3. However, comprehensive studies on the regulation of cas3 operon of the Type I-E CRISPR/Cas system are scarce. [...] Read more.
The CRISPR/Cas system protects bacteria against bacteriophage and plasmids through a sophisticated mechanism where cas operon plays a crucial role consisting of cse1 and cas3. However, comprehensive studies on the regulation of cas3 operon of the Type I-E CRISPR/Cas system are scarce. Herein, we investigated the regulation of cas3 in Escherichia coli. The mutation in gcvP or crp reduced the CRISPR/Cas system interference ability and increased bacterial susceptibility to phage, when the casA operon of the CRISPR/Cas system was activated. The silence of the glycine cleavage system (GCS) encoded by gcvTHP operon reduced cas3 expression. Adding N5, N10-methylene tetrahydrofolate (N5, N10-mTHF), which is the product of GCS-catalyzed glycine, was able to activate cas3 expression. In addition, a cAMP receptor protein (CRP) encoded by crp activated cas3 expression via binding to the cas3 promoter in response to cAMP concentration. Since N5, N10-mTHF provides one-carbon unit for purine, we assumed GCS regulates cas3 through associating with CRP. It was evident that the mutation of gcvP failed to further reduce the cas3 expression with the crp deletion. These results illustrated a novel regulatory pathway which GCS and CRP co-regulate cas3 of the CRISPR/Cas system and contribute to the defence against invasive genetic elements, where CRP is indispensable for GCS regulation of cas3 expression. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence
Viruses 2019, 11(12), 1089; https://doi.org/10.3390/v11121089 - 23 Nov 2019
Cited by 7
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides [...] Read more.
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Characterization of Klebsiella pneumoniae ST11 Isolates and Their Interactions with Lytic Phages
Viruses 2019, 11(11), 1080; https://doi.org/10.3390/v11111080 - 19 Nov 2019
Cited by 5
Abstract
The bacterial pathogen Klebsiella pneumoniae causes urinary tract infections in immunocompromised patients. Generally, the overuse of antibiotics contributes to the potential development and the spread of antibiotic resistance. In fact, certain strains of K. pneumoniae are becoming increasingly resistant to antibiotics, making infection [...] Read more.
The bacterial pathogen Klebsiella pneumoniae causes urinary tract infections in immunocompromised patients. Generally, the overuse of antibiotics contributes to the potential development and the spread of antibiotic resistance. In fact, certain strains of K. pneumoniae are becoming increasingly resistant to antibiotics, making infection by these strains more difficult to treat. The use of bacteriophages to control pathogens may offer a non-antibiotic-based approach to treat multidrug-resistant (MDR) infections. However, a detailed understanding of phage–host interactions is crucial in order to explore the potential success of phage-therapy for treatment. In this study, we investigated the molecular epidemiology of nine carbapenemase-producing K. pneumoniae isolates from a local hospital in Shanghai, China. All strain isolates belong to sequence type 11 (ST11) and harbor the blaKPC-2 gene. The S1-PFGE (S1 nuclease pulsed field gel electrophoresis) pattern of the isolates did not show any relationship to the multilocus sequence typing (MLST) profiles. In addition, we characterized phage 117 and phage 31 and assessed the potential application of phage therapy in treating K. pneumoniae infections in vitro. The results of morphological and genomic analyses suggested that both phages are affiliated to the T7 virus genus of the Podoviridae family. We also explored phage–host interactions during growth in both planktonic cells and biofilms. The phages’ heterogeneous lytic capacities against K. pneumoniae strains were demonstrated experimentally. Subsequent culture and urine experiments with phage 117 and host Kp36 initially demonstrated a strong lytic activity of the phages. However, rapid regrowth was observed following the initial lysis which suggests that phage resistant mutants were selected in the host populations. Additionally, a phage cocktail (117 + 31) was prepared and investigated for antimicrobial activity. In Luria Broth (LB) cultures, we observed that the cocktail showed significantly higher antimicrobial activity than phage 117 alone, but this was not observed in urine samples. Together, the results demonstrate the potential therapeutic value of phages in treating K. pneumoniae urinary tract infections. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Eradication of Vancomycin-Resistant Enterococci by Combining Phage and Vancomycin
Viruses 2019, 11(10), 954; https://doi.org/10.3390/v11100954 - 16 Oct 2019
Cited by 10
Abstract
Currently, effective options are needed to fight vancomycin-resistant Enterococcus faecalis (VRE). The present study shows that combinations of phage and vancomycin are highly efficient against VRE, despite being resistant to the antibiotic. Vancomycin-phage EFLK1 (anti-E. faecalis phage) synergy was assessed against VRE [...] Read more.
Currently, effective options are needed to fight vancomycin-resistant Enterococcus faecalis (VRE). The present study shows that combinations of phage and vancomycin are highly efficient against VRE, despite being resistant to the antibiotic. Vancomycin-phage EFLK1 (anti-E. faecalis phage) synergy was assessed against VRE planktonic and biofilm cultures. The effect of the combined treatment on VRE biofilms was determined by evaluating the viable counts and biomass and then visualized using scanning electron microscopy (SEM). The cell wall peptidoglycan was stained after phage treatment, visualized by confocal microscopy and quantified by fluorescence activated cell sorting (FACS) analysis. The combined treatment was synergistically effective compared to treatment with phage or antibiotic alone, both in planktonic and biofilm cultures. Confocal microscopy and FACS analysis showed that fluorescence intensity of phage-treated bacteria increased eight-fold, suggesting a change in the peptidoglycan of the cell wall. Our results indicate that with combined treatment, VRE strains are not more problematic than sensitive strains and thus give hope in the continuous struggle against the current emergence of multidrug resistant pathogens. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Application of a Phage Cocktail for Control of Salmonella in Foods and Reducing Biofilms
Viruses 2019, 11(9), 841; https://doi.org/10.3390/v11090841 - 10 Sep 2019
Cited by 16
Abstract
Salmonella contamination in foods and their formation of biofilms in food processing facility are the primary bacterial cause of a significant number of foodborne outbreaks and infections. Broad lytic phages are promising alternatives to conventional technologies for pathogen biocontrol in food matrices and [...] Read more.
Salmonella contamination in foods and their formation of biofilms in food processing facility are the primary bacterial cause of a significant number of foodborne outbreaks and infections. Broad lytic phages are promising alternatives to conventional technologies for pathogen biocontrol in food matrices and reducing biofilms. In this study, 42 Salmonella phages were isolated from environmentally-sourced water samples. We characterized the host range and lytic capacity of phages LPSTLL, LPST94 and LPST153 against Salmonella spp., and all showed a wide host range and broad lytic activity. Electron microscopy analysis indicated that LPSTLL, LPST94, and LPST153 belonged to the family of Siphoviridae, Ackermannviridae and Podoviridae, respectively. We established a phage cocktail containing three phages (LPSTLL, LPST94 and LPST153) that had broad spectrum to lyse diverse Salmonella serovars. A significant decrease was observed in Salmonella with a viable count of 3 log10 CFU in milk and chicken breast at either 25 °C or 4 °C. It was found that treatment with phage cocktail was able to significantly reduced biofilm on a 96-well microplate (44–63%) and on a stainless steel surface (5.23 to 6.42 log10). These findings demonstrated that the phage cocktail described in this study can be potentially used as a biological control agent against Salmonella in food products and also has the effect to reduce Salmonella formed biofilms. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Therapeutic Potential of an Endolysin Derived from Kayvirus S25-3 for Staphylococcal Impetigo
Viruses 2019, 11(9), 769; https://doi.org/10.3390/v11090769 - 22 Aug 2019
Cited by 7
Abstract
Impetigo is a contagious skin infection predominantly caused by Staphylococcus aureus. Decontamination of S. aureus from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target [...] Read more.
Impetigo is a contagious skin infection predominantly caused by Staphylococcus aureus. Decontamination of S. aureus from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target bacteria without disturbance of the normal microflora. In this study, we investigated the therapeutic potential of a recombinant endolysin derived from kayvirus S25-3 against staphylococcal impetigo in an experimental setting. First, the recombinant S25-3 endolysin required an incubation period of over 15 minutes to exhibit efficient bactericidal effects against S. aureus. Second, topical application of the recombinant S25-3 endolysin decreased the number of intraepidermal staphylococci and the size of pustules in an experimental mouse model of impetigo. Third, treatment with the recombinant S25-3 endolysin increased the diversity of the skin microbiota in the same mice. Finally, we revealed the genus-specific bacteriolytic effect of recombinant S25-3 endolysin against staphylococci, particularly S. aureus, among human skin commensal bacteria. Therefore, topical treatment with recombinant S25-3 endolysin can be a promising disease management procedure for staphylococcal impetigo by efficient bacteriolysis of S. aureus while improving the cutaneous bacterial microflora. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Open AccessArticle
Selection of Bacteriophages to Control In Vitro 24 h Old Biofilm of Pseudomonas aeruginosa Isolated from Drinking and Thermal Water
Viruses 2019, 11(8), 749; https://doi.org/10.3390/v11080749 - 13 Aug 2019
Cited by 1
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes public healthcare issues. In moist environments, this Gram-negative bacterium persists through biofilm-associated contamination on surfaces. Bacteriophages are seen as a promising alternative strategy to chemical biocides. This study evaluates the potential of nine lytic bacteriophages [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen that causes public healthcare issues. In moist environments, this Gram-negative bacterium persists through biofilm-associated contamination on surfaces. Bacteriophages are seen as a promising alternative strategy to chemical biocides. This study evaluates the potential of nine lytic bacteriophages as biocontrol treatments against nine environmental P. aerginosa isolates. The spot test method is preliminarily used to define the host range of each virus and to identify their minimum infectious titer, depending on the strain. Based on these results, newly isolated bacteriophages 14.1, LUZ7, and B1 are selected and assessed on a planktonic cell culture of the most susceptible isolates (strains MLM, D1, ST395E, and PAO1). All liquid infection assays are achieved in a mineral minimum medium that is much more representative of real moist environments than standard culture medium. Phages 14.1 and LUZ7 eliminate up to 90% of the PAO1 and D1 bacterial strains. Hence, their effectiveness is evaluated on the 24 h old biofilms of these strains, established on a stainless steel coupon that is characteristic of materials found in thermal and industrial environments. The results of quantitative PCR viability show a maximum reduction of 1.7 equivalent Log CFU/cm2 in the coupon between treated and untreated surfaces and shed light on the importance of considering the entire virus/host/environment system for optimizing the treatment. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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Review

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Open AccessReview
Bacteriophages for Chronic Wound Treatment: From Traditional to Novel Delivery Systems
Viruses 2020, 12(2), 235; https://doi.org/10.3390/v12020235 - 20 Feb 2020
Cited by 2
Abstract
The treatment and management of chronic wounds presents a massive financial burden for global health care systems, with significant and disturbing consequences for the patients affected. These wounds remain challenging to treat, reduce the patients’ life quality, and are responsible for a high [...] Read more.
The treatment and management of chronic wounds presents a massive financial burden for global health care systems, with significant and disturbing consequences for the patients affected. These wounds remain challenging to treat, reduce the patients’ life quality, and are responsible for a high percentage of limb amputations and many premature deaths. The presence of bacterial biofilms hampers chronic wound therapy due to the high tolerance of biofilm cells to many first- and second-line antibiotics. Due to the appearance of antibiotic-resistant and multidrug-resistant pathogens in these types of wounds, the research for alternative and complementary therapeutic approaches has increased. Bacteriophage (phage) therapy, discovered in the early 1900s, has been revived in the last few decades due to its antibacterial efficacy against antibiotic-resistant clinical isolates. Its use in the treatment of non-healing wounds has shown promising outcomes. In this review, we focus on the societal problems of chronic wounds, describe both the history and ongoing clinical trials of chronic wound-related treatments, and also outline experiments carried out for efficacy evaluation with different phage-host systems using in vitro, ex vivo, and in vivo animal models. We also describe the modern and most recent delivery systems developed for the incorporation of phages for species-targeted antibacterial control while protecting them upon exposure to harsh conditions, increasing the shelf life and facilitating storage of phage-based products. In this review, we also highlight the advances in phage therapy regulation. Full article
(This article belongs to the Special Issue Bacteriophages and Biofilms)
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