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Bacteriophages and Their Components as Promising and Alternative Tools for...
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Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 77041

Special Issue Editor

Dr. Marco Maria D'Andrea

E-Mail Website
Guest Editor
Department of Biology, University of “Tor Vergata”, Rome, Italy
Interests: antibiotic resistance mechanisms; genetic bases for the diffusion of antibiotic resistance genes; microbial bioinformatics; new antimicrobial drugs; bacteriophages; bacteriophages as tools for phage therapy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The dissemination of bacterial pathogens, which often display complex antibiotic resistance phenotypes, constitutes a major global problem affecting human health at several diverse levels. These include, but are not limited to, hospital settings, agriculture and animal breeding. The appearance and wide dissemination of antibiotic-resistant bacteria observed over the last few decades could in fact lead to the establishment in all these settings of antibiotic-resistant “bad bugs”, which could possibly bring us back to a “pre-antibiotic era” in the near future. Therefore, fast and effective actions need to be taken to avoid this scenario. The slow pace of the classical antibiotic development pipeline and the rapid emergence of resistance to novel compounds frequently observed soon after their clinical use have led to renewed interest in Felix d’Herelle’s old idea of phage therapy. This option, already being successfully used mainly in Eastern European countries, has recently received attention at a world-wide scale, with several excellent examples that have proved its promising efficacy at clinical level.    

The scope of this Special Issue is to collect original contributions on the use of bacteriophages or their selected components for fighting bacterial pathogens. It is expected that this Special Issue will collect research articles on new phage components with antimicrobial activity, to be used alone or in combination with conventional antibiotics, and reports on the use of bacteriophages for phage therapy. Detailed characterizations of newly discovered bacteriophages active against multidrug-resistant pathogens and with potential use as therapeutics are also welcomed. It is my pleasure to invite you to also submit review articles or short communications related to these topics.

Dr. Marco Maria D'Andrea
Guest Editor

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. Microorganisms 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 2700 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.

Keywords

  • bacteriophage
  • phage therapy
  • antibiotic resistance
  • multidrug-resistant bacteria
  • bacterial infection
  • novel antimicrobial approach
  • lysin
  • depolymerase.

Published Papers (21 papers)

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Editorial

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4 pages, 211 KiB  
Editorial
Application of Bacteriophages for Human Health: An Old Approach against Contemporary “Bad Bugs”
by Lucia Henrici De Angelis, Greta Ponsecchi, Maurizio Fraziano and Marco Maria D’Andrea
Microorganisms 2022, 10(3), 485; https://doi.org/10.3390/microorganisms10030485 - 22 Feb 2022
Cited by 2 | Viewed by 1391
Abstract
The breadth of the antimicrobial resistance (AMR) problem exposes humankind to serious threats, which could lead, in the near future, to a worrisome raising of mortality and morbidity rates due to infections by “bad bugs” [...] Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)

Research

Jump to: Editorial, Review, Other

18 pages, 2703 KiB  
Article
APTC-EC-2A: A Lytic Phage Targeting Multidrug Resistant E. coli Planktonic Cells and Biofilms
by Karen Hon, Sha Liu, Sophie Camens, George Spyro Bouras, Alkis James Psaltis, Peter-John Wormald and Sarah Vreugde
Microorganisms 2022, 10(1), 102; https://doi.org/10.3390/microorganisms10010102 - 04 Jan 2022
Cited by 6 | Viewed by 2554
Abstract
Escherichia coli (E. coli) are common bacteria that colonize the human and animal gastrointestinal tract, where they help maintain a balanced microbiome. However, some E. coli strains are pathogenic and can cause serious infectious diseases and life-threatening complications. Due to the [...] Read more.
Escherichia coli (E. coli) are common bacteria that colonize the human and animal gastrointestinal tract, where they help maintain a balanced microbiome. However, some E. coli strains are pathogenic and can cause serious infectious diseases and life-threatening complications. Due to the overuse of antibiotics and limited development of novel antibiotics, the emergence of antibiotic-resistant strains has threatened modern medicine, whereby common infections can become lethal. Phage therapy has once again attracted interest in recent years as an alternative treatment option to antibiotics for severe infections with antibiotic-resistant strains. The aim of this study was to isolate and characterize phage against multi-drug resistant E. coli isolated from clinical samples and hospital wastewater. For phage isolation, wastewater samples were collected from The Queen Elizabeth Hospital (Adelaide, SA, Australia) followed by phage enrichment as required. Microbiological assays, electron microscopy and genomic sequencing were carried out to characterize the phage. From the 10 isolated E. coli phages, E. coli phage APTC-EC-2A was the most promising and could lyse 6/7 E. coli clinical isolates. APTC-EC-2A was stable at a broad pH range (3–11) and could lyse the host E. coli at temperatures ranging between 30–50 °C. Furthermore, APTC-EC-2A could kill E. coli in planktonic and biofilm form. Electron microscopy and genomic sequencing indicated the phage to be from the Myoviridae family and of lytic nature. In conclusion, the newly isolated phage APTC-EC-2A has the desired properties that support its potential for development as a therapeutic agent against therapy refractory E. coli infections. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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16 pages, 5150 KiB  
Article
Preclinical Development of a Bacteriophage Cocktail for Treating Multidrug Resistant Pseudomonas aeruginosa Infections
by Sophie Camens, Sha Liu, Karen Hon, George Spyro Bouras, Alkis James Psaltis, Peter-John Wormald and Sarah Vreugde
Microorganisms 2021, 9(9), 2001; https://doi.org/10.3390/microorganisms9092001 - 21 Sep 2021
Cited by 10 | Viewed by 3603
Abstract
A Pseudomonas aeruginosa (P. aeruginosa) airway infection is one of the predominant causes contributing to the high morbidity and mortality rates in cystic fibrosis (CF) patients. The emergence of antibiotic resistant P. aeruginosa strains has led to an urgent need for [...] Read more.
A Pseudomonas aeruginosa (P. aeruginosa) airway infection is one of the predominant causes contributing to the high morbidity and mortality rates in cystic fibrosis (CF) patients. The emergence of antibiotic resistant P. aeruginosa strains has led to an urgent need for new therapeutic approaches. Bacteriophages (phages) are viruses that can infect and lyse specific bacteria, providing a potential alternative approach in targeting antibiotic-resistant strains. We aim to isolate and characterise novel P. aeruginosa phages for combination in a cocktail to kill P. aeruginosa. One particular phage, PA4, could lyse 14/20 clinical isolates as observed through spot assays. This phage could significantly reduce the growth of bacteria in vitro, as determined through planktonic adsorption and inhibition assays as well as crystal violet- and LIVE/DEAD-stained biofilm assays. A morphological and genomic analysis revealed that PA4 belongs to the Myoviridae family and contained 66,450 bp. The broad infectivity profile, good stability in various pH and temperature conditions, lytic ability and the absence of the absences of antibiotic resistance, toxic and lysogenic genes suggest that PA4 is a good candidate for clinical grade use. Overall, phage therapy represents a promising alternative treatment option to antibiotics when treating a P. aeruginosa infection. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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10 pages, 1502 KiB  
Communication
Phage Resistance Is Associated with Decreased Virulence in KPC-Producing Klebsiella pneumoniae of the Clonal Group 258 Clade II Lineage
by Lucia Henrici De Angelis, Noemi Poerio, Vincenzo Di Pilato, Federica De Santis, Alberto Antonelli, Maria Cristina Thaller, Maurizio Fraziano, Gian Maria Rossolini and Marco Maria D’Andrea
Microorganisms 2021, 9(4), 762; https://doi.org/10.3390/microorganisms9040762 - 06 Apr 2021
Cited by 10 | Viewed by 2354
Abstract
Phage therapy is now reconsidered with interest in the treatment of bacterial infections. A major piece of information for this application is the definition of the molecular targets exploited by phages to infect bacteria. Here, the genetic basis of resistance to the lytic [...] Read more.
Phage therapy is now reconsidered with interest in the treatment of bacterial infections. A major piece of information for this application is the definition of the molecular targets exploited by phages to infect bacteria. Here, the genetic basis of resistance to the lytic phage φBO1E by its susceptible host Klebsiella pneumoniae KKBO-1 has been investigated. KKBO-1 phage-resistant mutants were obtained by infection at high multiplicity. One mutant, designated BO-FR-1, was selected for subsequent experiments, including virulence assessment in a Galleria mellonella infection model and characterization by whole-genome sequencing. Infection with BO-FR-1 was associated with a significantly lower mortality when compared to that of the parental strain. The BO-FR-1 genome differed from KKBO-1 by a single nonsense mutation into the wbaP gene, which encodes a glycosyltransferase involved in the first step of the biosynthesis of the capsular polysaccharide (CPS). Phage susceptibility was restored when BO-FR-1 was complemented with the constitutive wbaP gene. Our results demonstrated that φBO1E infects KKBO-1 targeting the bacterial CPS. Interestingly, BO-FR-1 was less virulent than the parental strain, suggesting that in the context of the interplay among phage, bacterial pathogen and host, the emergence of phage resistance may be beneficial for the host. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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9 pages, 1807 KiB  
Communication
Characterization and In Vitro Efficacy against Listeria monocytogenes of a Newly Isolated Bacteriophage, ΦIZSAM-1
by Silvia Scattolini, Daniela D’Angelantonio, Arianna Boni, Iolanda Mangone, Maurilia Marcacci, Noemi Battistelli, Krizia D’Agostino, Francesco Pomilio, Cesare Camma, Giacomo Migliorati and Giuseppe Aprea
Microorganisms 2021, 9(4), 731; https://doi.org/10.3390/microorganisms9040731 - 31 Mar 2021
Cited by 5 | Viewed by 2066
Abstract
Listeria monocytogenes is a bacterial pathogen responsible of listeriosis, a disease that in humans is often related to the contamination of ready-to-eat foods. Phages are candidate biodecontaminants of pathogenic bacteria thanks to their ability to lyse prokaryotes while being safe for eukaryotic cells. [...] Read more.
Listeria monocytogenes is a bacterial pathogen responsible of listeriosis, a disease that in humans is often related to the contamination of ready-to-eat foods. Phages are candidate biodecontaminants of pathogenic bacteria thanks to their ability to lyse prokaryotes while being safe for eukaryotic cells. In this study, ΦIZSAM-1 was isolated from the drain-waters of an Italian blue cheese plant and showed lytic activity against antimicrobial resistant Listeria monocytogenes strains. This phage was subjected to purification and in vitro efficacy tests. The results showed that at multiplicities of infection (MOIs) ≤ 1, phages were able to keep Listeria monocytogenes at low optical density values up to 8 h, with bacterial counts ranging from 1.02 to 3.96 log10 units lower than the control. Besides, ΦIZSAM-1 was further characterized, showing 25 principal proteins (sodium dodecyl sulfate polyacrylamide gel electrophoresis profile) and a genome of approximately 50 kilo base pairs. Moreover, this study describes a new approach to phage isolation for applications in Listeriamonocytogenes biocontrol in food production. In particular, the authors believe that the selection of phages from the same environments where pathogens live could represent a new approach to successfully integrating the control measures in an innovative, cost effective, safe and environmentally friendly way. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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15 pages, 4272 KiB  
Article
Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus
by Emilija Žukauskienė, Monika Šimoliūnienė, Lidija Truncaitė, Martynas Skapas, Algirdas Kaupinis, Mindaugas Valius, Rolandas Meškys and Eugenijus Šimoliūnas
Microorganisms 2021, 9(3), 668; https://doi.org/10.3390/microorganisms9030668 - 23 Mar 2021
Cited by 5 | Viewed by 2363
Abstract
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed [...] Read more.
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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12 pages, 1061 KiB  
Article
Variability in Bacteriophage and Antibiotic Sensitivity in Serial Pseudomonas aeruginosa Isolates from Cystic Fibrosis Airway Cultures over 12 Months
by Isaac Martin, Dervla T. D. Kenna, Sandra Morales, Eric W. F. W. Alton and Jane C. Davies
Microorganisms 2021, 9(3), 660; https://doi.org/10.3390/microorganisms9030660 - 22 Mar 2021
Cited by 6 | Viewed by 2455
Abstract
Antibiotic treatment for Pseudomonas aeruginosa (Pa) in cystic fibrosis is limited in efficacy and may lead to multi-drug resistance (MDR). Alternatives such as bacteriophages are being explored but well designed, and controlled trials are crucial. The rational selection of patients with bacteriophage susceptible [...] Read more.
Antibiotic treatment for Pseudomonas aeruginosa (Pa) in cystic fibrosis is limited in efficacy and may lead to multi-drug resistance (MDR). Alternatives such as bacteriophages are being explored but well designed, and controlled trials are crucial. The rational selection of patients with bacteriophage susceptible infections is required for both safety and efficacy monitoring. We questioned whether bacteriophage susceptibility profiles were constant or variable over time, variability having been reported with antibiotics. Serial Pa isolates (n = 102) from 24 chronically infected cystic fibrosis (CF) patients over one year were investigated with plaque and antibiotic disc diffusion assays. Variable number tandem repeat (VNTR) analysis identified those patients with >1 isolate. A median (range) of 4 (3–6) isolates/patient were studied. Twenty-one (87.5%) individuals had a single VNTR type; three (12.5%) had two VNTR types at different times. Seventy-five percent of isolates were sensitive to bacteriophage at ≥ 1 concentration; 50% of isolates were antibiotic multidrug resistant. Serial isolates, even when representing a single VNTR type, varied in sensitivity to both bacteriophages and antibiotics. The rates of sensitivity to bacteriophage supports the development of this therapy; however, the variability in response has implications for the selection of patients in future trials which must be on the basis of current, not past, isolate testing. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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20 pages, 4202 KiB  
Article
Isolation and Characterization of a Novel Lytic Bacteriophage against the K2 Capsule-Expressing Hypervirulent Klebsiella pneumoniae Strain 52145, and Identification of Its Functional Depolymerase
by Botond Zsombor Pertics, Alysia Cox, Adrienn Nyúl, Nóra Szamek, Tamás Kovács and György Schneider
Microorganisms 2021, 9(3), 650; https://doi.org/10.3390/microorganisms9030650 - 21 Mar 2021
Cited by 29 | Viewed by 3797
Abstract
Klebsiella pneumoniae is among the leading bacteria that cause nosocomial infections. The capsule of this Gram-negative bacterium is a dominant virulence factor, with a prominent role in defense and biofilm formation. Bacteriophages, which are specific for one bacterial strain and its capsule type, [...] Read more.
Klebsiella pneumoniae is among the leading bacteria that cause nosocomial infections. The capsule of this Gram-negative bacterium is a dominant virulence factor, with a prominent role in defense and biofilm formation. Bacteriophages, which are specific for one bacterial strain and its capsule type, can evoke the lysis of bacterial cells, aided by polysaccharide depolymerase enzymes. In this study, we isolated and characterized a bacteriophage against the nosocomial K. pneumoniae 52145 strain with K2 capsular serotype. The phage showed a narrow host range and stable lytic activity, even when exposed to different temperatures or detergents. Preventive effect of the phage in a nasal colonization model was investigated in vivo. Phlyogenetic analysis showed that the newly isolated Klebsiella phage B1 belongs to the Webervirus genus in Drexlerviridae family. We identified the location of the capsule depolymerase gene of the new phage, which was amplified, cloned, expressed, and purified. The efficacy of the recombinant B1dep depolymerase was tested by spotting on K. pneumoniae strains and it was confirmed that the extract lowers the thickness of the bacterium lawn as it degrades the protective capsule on bacterial cells. As K. pneumoniae strains possessing the K2 serotype have epidemiological importance, the B1 phage and its depolymerase are promising candidates for use as possible antimicrobial agents. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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11 pages, 964 KiB  
Article
Efficacy of Bacteriophage Cocktail to Control E. coli O157:H7 Contamination on Baby Spinach Leaves in the Presence or Absence of Organic Load
by Badrinath Vengarai Jagannathan, Steven Kitchens, Paul Priyesh Vijayakumar, Stuart Price and Melissa Morgan
Microorganisms 2021, 9(3), 544; https://doi.org/10.3390/microorganisms9030544 - 06 Mar 2021
Cited by 15 | Viewed by 2977
Abstract
Fruits and vegetables are high in nutrients that are essential for a healthy lifestyle. However, they also harbor an extensive array of microorganisms such as bacteria, which can be beneficial, neutral, or pathogenic. Foodborne pathogens can contaminate produce at any stage from the [...] Read more.
Fruits and vegetables are high in nutrients that are essential for a healthy lifestyle. However, they also harbor an extensive array of microorganisms such as bacteria, which can be beneficial, neutral, or pathogenic. Foodborne pathogens can contaminate produce at any stage from the farm to the consumer’s table. Appropriate washing techniques using sanitizers can reduce the risk of pathogen contamination. Issues related to maintaining concentration, efficacy, and other problems have been a challenge for the food industry and, when left unresolved, have led to different outbreaks of foodborne illnesses. In this study, the efficacy of a lytic bacteriophage cocktail was examined for its ability to infect and reduce the contamination of Escherichia coli O157:H7 (E. coli O157:H7), in media with a high organic load, using a microplate technique. The study was conducted for 3 h to determine if the bacteriophage cocktail could reduce the pathogen in the presence of a high organic load. A significant (p < 0.05) reduction in the population of E. coli O157:H7 was observed, representing a 99.99% pathogen reduction at the end of 3 h. Fresh spinach leaves were washed in sterile potable or organic water (~9000 ppm organic load) containing E. coli O157:H7 and a bacteriophage cocktail to study the effectiveness of bacteriophages against the foodborne pathogen. Results indicated that the bacteriophage significantly (p < 0.05) reduced the contamination of E. coli O157:H7 in both situations. The study also demonstrated the bacteriophages’ ability to infect and reduce the pathogen in an organic-rich environment. This characteristic differs from commercially available sanitizers that have demonstrated a tendency to bind with the available organic load. Thus, these studies highlight the advantage of employing bacteriophages during produce wash to eliminate foodborne pathogen contamination on fruits and vegetables. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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19 pages, 3010 KiB  
Article
Bacteriophages to Control Multi-Drug Resistant Enterococcus faecalis Infection of Dental Root Canals
by Mohamed El-Telbany, Gamal El-Didamony, Ahmed Askora, Eman Ariny, Dalia Abdallah, Ian F. Connerton and Ayman El-Shibiny
Microorganisms 2021, 9(3), 517; https://doi.org/10.3390/microorganisms9030517 - 03 Mar 2021
Cited by 21 | Viewed by 4095
Abstract
Phage therapy is an alternative treatment to antibiotics that can overcome multi-drug resistant bacteria. In this study, we aimed to isolate and characterize lytic bacteriophages targeted against Enterococcus faecalis isolated from root canal infections obtained from clinics at the Faculty of Dentistry, Ismalia, [...] Read more.
Phage therapy is an alternative treatment to antibiotics that can overcome multi-drug resistant bacteria. In this study, we aimed to isolate and characterize lytic bacteriophages targeted against Enterococcus faecalis isolated from root canal infections obtained from clinics at the Faculty of Dentistry, Ismalia, Egypt. Bacteriophage, vB_ZEFP, was isolated from concentrated wastewater collected from hospital sewage. Morphological and genomic analysis revealed that the phage belongs to the Podoviridae family with a linear double-stranded DNA genome, consisting of 18,454, with a G + C content of 32.8%. Host range analysis revealed the phage could infect 10 of 13 E. faecalis isolates exhibiting a range of antibiotic resistances recovered from infected root canals with efficiency of plating values above 0.5. One-step growth curves of this phage showed that it has a burst size of 110 PFU per infected cell, with a latent period of 10 min. The lytic activity of this phage against E. faecalis biofilms showed that the phage was able to control the growth of E. faecalis in vitro. Phage vB_ZEFP could also prevent ex-vivo E. faecalis root canal infection. These results suggest that phage vB_ZEFP has potential for application in phage therapy and specifically in the prevention of infection after root canal treatment. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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12 pages, 1759 KiB  
Article
An Engineered Reporter Phage for the Fluorometric Detection of Escherichia coli in Ground Beef
by Anqi Chen, Danhui Wang, Sam R. Nugen and Juhong Chen
Microorganisms 2021, 9(2), 436; https://doi.org/10.3390/microorganisms9020436 - 19 Feb 2021
Cited by 11 | Viewed by 3306
Abstract
Despite enhanced sanitation implementations, foodborne bacterial pathogens still remain a major threat to public health and generate high costs for the food industry. Reporter bacteriophage (phage) systems have been regarded as a powerful technology for diagnostic assays for their extraordinary specificity to target [...] Read more.
Despite enhanced sanitation implementations, foodborne bacterial pathogens still remain a major threat to public health and generate high costs for the food industry. Reporter bacteriophage (phage) systems have been regarded as a powerful technology for diagnostic assays for their extraordinary specificity to target cells and cost-effectiveness. Our study introduced an enzyme-based fluorescent assay for detecting the presence of E. coli using the T7 phage engineered with the lacZ operon which encodes beta-galactosidase (β-gal). Both endogenous and overexpressed β-gal expression was monitored using a fluorescent-based method with 4-methylumbelliferyl β-d-galactopyranoside (MUG) as the substrate. The infection of E. coli with engineered phages resulted in a detection limit of 10 CFU/mL in ground beef juice after 7 h of incubation. In this study, we demonstrated that the overexpression of β-gal coupled with a fluorogenic substrate can provide a straightforward and sensitive approach to detect the potential biological contamination in food samples. The results also suggested that this system can be applied to detect E. coli strains isolated from environmental samples, indicating a broader range of bacterial detection. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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12 pages, 3324 KiB  
Article
In Vitro and In Vivo Evaluation of Three Newly Isolated Bacteriophage Candidates, phiEF7H, phiEF14H1, phiEF19G, for Treatment of Enterococcus faecalis Endophthalmitis
by Tatsuma Kishimoto, Waka Ishida, Tadahiro Nasukawa, Takako Ujihara, Isana Nakajima, Takashi Suzuki, Jumpei Uchiyama, Daisuke Todokoro, Masanori Daibata, Atsuki Fukushima, Shigenobu Matsuzaki and Ken Fukuda
Microorganisms 2021, 9(2), 212; https://doi.org/10.3390/microorganisms9020212 - 20 Jan 2021
Cited by 7 | Viewed by 2379
Abstract
Post-operative endophthalmitis caused by Enterococcus spp. progresses rapidly and often results in substantial and irreversible vision loss. Therefore, novel alternative treatments that are effective against enterococcal endophthalmitis are required. Bacteriophage therapy has the potential to be an optional therapy for infectious diseases. Therefore, [...] Read more.
Post-operative endophthalmitis caused by Enterococcus spp. progresses rapidly and often results in substantial and irreversible vision loss. Therefore, novel alternative treatments that are effective against enterococcal endophthalmitis are required. Bacteriophage therapy has the potential to be an optional therapy for infectious diseases. Therefore, we investigated the therapeutic potential of three newly isolated enterococcal phages, phiEF7H, phiEF14H1, and phiEF19G, in E. faecalis-induced endophthalmitis. These phages could lyse the broad-range E. faecalis, including strains derived from endophthalmitis and vancomycin-resistant E. faecalis in vitro, as determined by the streak test. Morphological and genomic analyses revealed that these phages were classified into the Herelleviridae genus Kochikohdavirus. The whole genomes of these phages contained 143,399, 143,280, and 143,400 bp, respectively. Endophthalmitis was induced in mice by injection of three strains of E. faecalis derived from post-operative endophthalmitis or vancomycin-resistant strains into the vitreous body. The number of viable bacteria and infiltration of neutrophils in the eye were both decreased by intravitreous injection of phiEF7H, phiEF14H1, and phiEF19G 6 h after injection of all E. faecalis strains. Thus, these results suggest that these newly isolated phages may serve as promising candidates for phage therapy against endophthalmitis. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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17 pages, 2307 KiB  
Article
First Report of Filamentous Phages Isolated from Tunisian Orchards to Control Erwinia amylovora
by Ismahen Akremi, Dominique Holtappels, Wided Brabra, Mouna Jlidi, Adel Hadj Ibrahim, Manel Ben Ali, Kiandro Fortuna, Mohammed Ahmed, Bart Van Meerbeek, Ali Rhouma, Rob Lavigne, Mamdouh Ben Ali and Jeroen Wagemans
Microorganisms 2020, 8(11), 1762; https://doi.org/10.3390/microorganisms8111762 - 10 Nov 2020
Cited by 15 | Viewed by 3163
Abstract
Newly discovered Erwinia amylovora phages PEar1, PEar2, PEar4 and PEar6 were isolated from three different orchards in North Tunisia to study their potential as biocontrol agents. Illumina sequencing revealed that the PEar viruses carry a single-strand DNA genome between 6608 and 6801 nucleotides [...] Read more.
Newly discovered Erwinia amylovora phages PEar1, PEar2, PEar4 and PEar6 were isolated from three different orchards in North Tunisia to study their potential as biocontrol agents. Illumina sequencing revealed that the PEar viruses carry a single-strand DNA genome between 6608 and 6801 nucleotides and belong to the Inoviridae, making them the first described filamentous phages of E. amylovora. Interestingly, phage-infected cells show a decreased swimming and swarming motility and a cocktail of the four phages can significantly reduce infection of E. amylovora in a pear bioassay, potentially making them suitable candidates for phage biocontrol. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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22 pages, 4336 KiB  
Article
Isolation and Characterization of Bacillus cereus Phage vB_BceP-DLc1 Reveals the Largest Member of the Φ29-Like Phages
by Chun Li, Xiaoming Yuan, Na Li, Juan Wang, Shubo Yu, Haiyan Zeng, Jumei Zhang, Qingping Wu and Yu Ding
Microorganisms 2020, 8(11), 1750; https://doi.org/10.3390/microorganisms8111750 - 07 Nov 2020
Cited by 17 | Viewed by 3796
Abstract
Bacillus phage φ29 and its relatives have been considered as one of the most important model organisms for DNA replication, transcription, morphogenesis, DNA packaging studies, and nanotechnology applications. Here, we isolated and characterized a new member of the φ29-like phage, named Bacillus cereus [...] Read more.
Bacillus phage φ29 and its relatives have been considered as one of the most important model organisms for DNA replication, transcription, morphogenesis, DNA packaging studies, and nanotechnology applications. Here, we isolated and characterized a new member of the φ29-like phage, named Bacillus cereus phage vB_BceP-DLc1. This phage, with a unique inserted gene cluster, has the largest genome among known φ29-like phages. DLc1 can use the surface carbohydrate structures of the host cell as receptors and only infects the most related B. cereus strains, showing high host-specificity. The adsorption rate constant and life cycle of DLc1 under experimental conditions were also determined. Not only stable under temperatures below 55 °C and pH range from 5 to 11, the new phage also showed tolerance to high concentrations of NaCl, 75% ethanol, chloroform, and mechanical vortex, which is preferable for practical use in the food and pharmaceutical industries. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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20 pages, 3581 KiB  
Article
Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
by María A. Núñez-Sánchez, Joan Colom, Lauren Walsh, Colin Buttimer, Andrei Sorin Bolocan, Rory Pang, Cormac G. M. Gahan and Colin Hill
Microorganisms 2020, 8(9), 1374; https://doi.org/10.3390/microorganisms8091374 - 07 Sep 2020
Cited by 11 | Viewed by 4184
Abstract
An intestinal epithelium model able to produce mucus was developed to provide an environment suitable for testing the therapeutic activity of gut bacteriophages. We show that Enterococcus faecalis adheres more effectively in the presence of mucus, can invade the intestinal epithelia and is [...] Read more.
An intestinal epithelium model able to produce mucus was developed to provide an environment suitable for testing the therapeutic activity of gut bacteriophages. We show that Enterococcus faecalis adheres more effectively in the presence of mucus, can invade the intestinal epithelia and is able to translocate after damaging tight junctions. Furthermore, Enterococcus phage vB_EfaM_A2 (a member of Herelleviridae that possesses virion associated immunoglobin domains) was found to translocate through the epithelium in the presence and absence of its host bacteria. Phage A2 protected eukaryotic cells by reducing mortality and maintaining the structure of the cell layer structure. We suggest the mammalian cell model utilized within this study as an adaptable in vitro model that can be employed to enable a better understanding of phage–bacteria interactions and the protective impact of phage therapy relating to the intestinal epithelium. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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13 pages, 2554 KiB  
Article
An Innovative Approach to Control H. pylori-Induced Persistent Inflammation and Colonization
by Paola Cuomo, Marina Papaianni, Andrea Fulgione, Fabrizia Guerra, Rosanna Capparelli and Chiara Medaglia
Microorganisms 2020, 8(8), 1214; https://doi.org/10.3390/microorganisms8081214 - 10 Aug 2020
Cited by 19 | Viewed by 3307
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative bacterium which colonizes the human stomach. The ability of H. pylori to evade the host defense system and the emergence of antibiotic resistant strains result in bacteria persistence and chronic inflammation, which leads to [...] Read more.
Helicobacter pylori (H. pylori) is a Gram-negative bacterium which colonizes the human stomach. The ability of H. pylori to evade the host defense system and the emergence of antibiotic resistant strains result in bacteria persistence and chronic inflammation, which leads to both severe gastric and extra-gastric diseases. Consequently, innovative approaches able to overcome H. pylori clinical outcomes are needed. In this work, we develop a novel non-toxic therapy based on the synergistic action of H. pylori phage and lactoferrin adsorbed on hydroxyapatite nanoparticles, which effectively impairs bacteria colonization and minimizes the damage of the host pro-inflammatory response. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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Review

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14 pages, 1650 KiB  
Review
Bacteriophages as a Potential 360-Degree Pathogen Control Strategy
by Maria D’Accolti, Irene Soffritti, Sante Mazzacane and Elisabetta Caselli
Microorganisms 2021, 9(2), 261; https://doi.org/10.3390/microorganisms9020261 - 27 Jan 2021
Cited by 38 | Viewed by 5176
Abstract
Bacteriophages are viruses that exclusively kill bacteria and are the most ubiquitous organisms on the planet. Since their discovery, bacteriophages have been considered an important weapon to fight human and animal infections of bacterial origin due to their specific ability to attack the [...] Read more.
Bacteriophages are viruses that exclusively kill bacteria and are the most ubiquitous organisms on the planet. Since their discovery, bacteriophages have been considered an important weapon to fight human and animal infections of bacterial origin due to their specific ability to attack the associated target bacteria. With the discovery of antibiotics, phage treatment was progressively abandoned in Western countries. However, due to the recent emergence of growing antimicrobial resistance (AMR) to antibiotics, interest in phage use in human therapy has once again grown. Similarly, at the environmental level, the extensive use of disinfectants based on chemicals, including biocides in agriculture, has been associated with the emergence of resistance against disinfectants themselves, besides having a high environmental impact. Due to these issues, the applications of phages with biocontrol purposes have become an interesting option in several fields, including farms, food industry, agriculture, aquaculture and wastewater plants. Notably, phage action is maintained even when the target bacteria are multidrug resistant (MDR), rendering this option extremely interesting in counteracting AMR emergence both for therapeutical and decontamination purposes. Based on this, bacteriophages have been interestingly proposed as environmental routine sanitizers in hospitals, to counteract the spread of the pathogenic MDR bacteria that persistently contaminate hard surfaces. This review summarizes the studies aimed at evaluating the potential use of phages as decontaminants, with a special focus on hospital sanitation. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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15 pages, 615 KiB  
Review
Animal Models in the Evaluation of the Effectiveness of Phage Therapy for Infections Caused by Gram-Negative Bacteria from the ESKAPE Group and the Reliability of Its Use in Humans
by Martyna Cieślik, Natalia Bagińska, Andrzej Górski and Ewa Jończyk-Matysiak
Microorganisms 2021, 9(2), 206; https://doi.org/10.3390/microorganisms9020206 - 20 Jan 2021
Cited by 23 | Viewed by 5025
Abstract
The authors emphasize how extremely important it is to highlight the role played by animal models in an attempt to determine possible phage interactions with the organism into which it was introduced as well as to determine the safety and effectiveness of phage [...] Read more.
The authors emphasize how extremely important it is to highlight the role played by animal models in an attempt to determine possible phage interactions with the organism into which it was introduced as well as to determine the safety and effectiveness of phage therapy in vivo taking into account the individual conditions of a given organism and its physiology. Animal models in which phages are used make it possible, among other things, to evaluate the effective therapeutic dose and to choose the possible route of phage administration depending on the type of infection developed. These results cannot be applied in detail to the human body, but the knowledge gained from animal experiments is invaluable and very helpful. We would like to highlight how useful animal models may be for the possible effectiveness evaluation of phage therapy in the case of infections caused by gram-negative bacteria from the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species) group of pathogens. In this review, we focus specifically on the data from the last few years. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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15 pages, 325 KiB  
Review
Phage Prevalence in the Human Urinary Tract—Current Knowledge and Therapeutic Implications
by Maciej Żaczek, Beata Weber-Dąbrowska, Ryszard Międzybrodzki and Andrzej Górski
Microorganisms 2020, 8(11), 1802; https://doi.org/10.3390/microorganisms8111802 - 17 Nov 2020
Cited by 18 | Viewed by 2496
Abstract
Recent metagenomic analyses imply an immense abundance of phages in the human body. Samples collected from different sites (lungs, skin, oral cavity, intestines, ascitic fluid, and urine) reveal a generally greater number of phage particles than that of eukaryotic viruses. The presence of [...] Read more.
Recent metagenomic analyses imply an immense abundance of phages in the human body. Samples collected from different sites (lungs, skin, oral cavity, intestines, ascitic fluid, and urine) reveal a generally greater number of phage particles than that of eukaryotic viruses. The presence of phages in those tissues and fluids reflects the paths they must overcome in the human body, but may also relate to the health statuses of individuals. Besides shaping bacterial metabolism and community structure, the role of phages circulating in body fluids has not been fully understood yet. The lack of relevant reports is especially visible with regard to the human urobiome. Certainly, phage presence and the role they have to fulfill in the human urinary tract raises questions on potential therapeutic connotations. Urinary tract infections (UTIs) are among the most common bacterial infections in humans and their treatment poses a difficult therapeutic dilemma. Despite effective antibiotic therapy, these infections tend to recur. In this review, we summarized the recent data on phage presence in the human urinary tract and its possible implications for health and disease. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
20 pages, 294 KiB  
Review
Effectiveness of Phage-Based Inhibition of Listeria monocytogenes in Food Products and Food Processing Environments
by Iwona Kawacka, Agnieszka Olejnik-Schmidt, Marcin Schmidt and Anna Sip
Microorganisms 2020, 8(11), 1764; https://doi.org/10.3390/microorganisms8111764 - 10 Nov 2020
Cited by 43 | Viewed by 9650
Abstract
Providing safe products and compliance of legal requirements is still a great challenge for food manufacturers regarding microbiological safety, especially in the context of Listeria monocytogenes food contamination. L. monocytogenes is a human pathogen, which, due to the ability of survival and proliferation [...] Read more.
Providing safe products and compliance of legal requirements is still a great challenge for food manufacturers regarding microbiological safety, especially in the context of Listeria monocytogenes food contamination. L. monocytogenes is a human pathogen, which, due to the ability of survival and proliferation in preservation conditions such as high salinity, acidity and refrigeration temperatures, is a significant threat to the food industry. Novel methods of elimination of the bacterial pathogen in food products and food processing environments are required. Among emerging technologies, one of the very promising solutions is using bacteriophages as natural control agents. This review focus on the major aspects of phage-based inhibition of L. monocytogenes in aspects of food safety. We describe an overview of foods and technological factors influencing the efficacy of phage use in biocontrol of L. monocytogenes. The most noteworthy are food matrix properties, phage concentration and stability, the time of phage application and product storage temperature. The combined methods, phage immobilization (active packing), pathogen resistance to phages and legislation aspects of antilisterial bacteriophage use in the food industry are also discussed. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)

Other

11 pages, 1850 KiB  
Perspective
Indirect Selection against Antibiotic Resistance via Specialized Plasmid-Dependent Bacteriophages
by Reetta Penttinen, Cindy Given and Matti Jalasvuori
Microorganisms 2021, 9(2), 280; https://doi.org/10.3390/microorganisms9020280 - 29 Jan 2021
Cited by 6 | Viewed by 4697
Abstract
Antibiotic resistance genes of important Gram-negative bacterial pathogens are residing in mobile genetic elements such as conjugative plasmids. These elements rapidly disperse between cells when antibiotics are present and hence our continuous use of antimicrobials selects for elements that often harbor multiple resistance [...] Read more.
Antibiotic resistance genes of important Gram-negative bacterial pathogens are residing in mobile genetic elements such as conjugative plasmids. These elements rapidly disperse between cells when antibiotics are present and hence our continuous use of antimicrobials selects for elements that often harbor multiple resistance genes. Plasmid-dependent (or male-specific or, in some cases, pilus-dependent) bacteriophages are bacterial viruses that infect specifically bacteria that carry certain plasmids. The introduction of these specialized phages into a plasmid-abundant bacterial community has many beneficial effects from an anthropocentric viewpoint: the majority of the plasmids are lost while the remaining plasmids acquire mutations that make them untransferable between pathogens. Recently, bacteriophage-based therapies have become a more acceptable choice to treat multi-resistant bacterial infections. Accordingly, there is a possibility to utilize these specialized phages, which are not dependent on any particular pathogenic species or strain but rather on the resistance-providing elements, in order to improve or enlengthen the lifespan of conventional antibiotic approaches. Here, we take a snapshot of the current knowledge of plasmid-dependent bacteriophages. Full article
(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)
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