Complete genome sequence of new bacteriophage phiE142, which causes simultaneously lysis of multidrug-resistant Escherichia coli O157:H7 and Salmonella enterica

Biocontrol Approaches against Escherichia coli O157:H7 in Foods

Shiga-toxin-producing Escherichia coli O157:H7 is a well-known water- and food-borne zoonotic pathogen that can cause gastroenteritis in humans. It threatens the health of millions of people each year; several outbreaks of E. coli O157:H7 infections have been linked to the consumption of contaminated plant foods (e.g., lettuce, spinach, tomato, and fresh fruits) and beef-based products. To control E. coli O157:H7 in foods, several physical (e.g., irradiation, pasteurization, pulsed electric field, and high-pressure processing) and chemical (e.g., using peroxyacetic acid; chlorine dioxide; sodium hypochlorite; and organic acids, such as acetic, lactic, and citric) methods have been widely used. Although the methods are quite effective, they are not applicable to all foods and carry intrinsic disadvantages (alteration of sensory properties, toxicity, etc.). Therefore, the development of safe and effective alternative methods has gained increased attention recently. Biocontrol agents, including bacteriophages, probiotics, antagonistic bacteria, plant-derived natural compounds, bacteriocins, endolysins, and enzymes, are rapidly emerging as effective, selective, relatively safe for human consumption, and environmentally friendly alternatives. This paper summarizes advances in the application of biocontrol agents for E. coli O157:H7 control in foods.

Investigation of Phages Infecting Escherichia coli Strains B and C, and Enterobacter cloacae in Sewage and Ebrié Lagoon, Côte d'Ivoire

Background: Bacteriophages are a promising biotechnological against bacterial pathogens. Currently, phage research is garnering interest in sub-Saharan countries as bacterial resistance to antibiotics becomes widespread. They are sought in all environments as they offer the possibility of a sustainable alternative to antibiotics. Materials and Methods: Altogether 30 water samples from urban sewage and environmental water were screened for the presence of bacteriophages able to infect Escherichia coli and Enterobacter cloacae. Their genomic diversity was determined by random amplification of polymorphic DNA (RAPD)-PCR fingerprinting. Results: We isolated 35 phages including 9 polyvalent phages that infect simultaneously E. coli and E. cloacae. This study allowed first isolation of E. cloacae-specific phages in Côte d'Ivoire. All phages were distinct based on their RAPD band patterns. Conclusions: Sewage systems of Yopougon and the environmental water of Ebrié lagoon were a rich source of phages. The phage collection could be useful for phage application in Côte d'Ivoire.

A Novel Polyvalent Bacteriophage vB_EcoM_swi3 Infects Pathogenic Escherichia coli and Salmonella enteritidis

A novel virulent bacteriophage vB_EcoM_swi3 (swi3), isolated from swine feces, lyzed 9% (6/65) of Escherichia coli and isolates 54% (39/72) of Salmonella enteritidis isolates, which were all clinically pathogenic multidrug-resistant strains. Morphological observation showed that phage swi3 belonged to the Myoviridae family with an icosahedral head (80 nm in diameter) and a contractile sheathed tail (120 nm in length). At the optimal multiplicity of infection of 1, the one-step growth analysis of swi3 showed a 25-min latent period with a burst size of 25-plaque-forming units (PFU)/infected cell. Phage swi3 remained stable both at pH 6.0–8.0 and at less than 50°C for at least 1 h. Genomic sequencing and bioinformatics analysis based on genomic sequences and the terminase large subunit showed that phage swi3 was a novel member that was most closely related to Salmonella phages and belonged to the Rosemountvirus genus. Phage swi3 harbored a 52-kb double-stranded DNA genome with 46.02% GC content. Seventy-two potential open reading frames were identified and annotated, only 15 of which had been assigned to functional genes. No gene associated with pathogenicity and virulence was identified. The effects of phage swi3 in treating pathologic E. coli infections in vivo were evaluated using a mouse model. The administration of a single intraperitoneal injection of swi3 (10⁶ PFU) at 2 h after challenge with the E. coli strain (serotype K88) (10⁸ colony-forming units) sufficiently protected all mice without toxic side effects. This finding highlighted that phage swi3 might be used as an effective antibacterial agent to prevent E. coli and S. enteritidis infection.

How Broad Is Enough: The Host Range of Bacteriophages and Its Impact on the Agri-Food Sector

Novel bacteriophages (phages) possessing a broad host range are consistently and routinely reported, yet there is presently no consensus on the definition of “broad host range.” As phages are increasingly being used in the development of methods for the detection and biocontrol of human pathogens, it is important to address the limitations associated with the host range. For instance, unanticipated host range breadth may result in the detection of nonpathogenic targets, thereby increasing the false-positive rate. Moreover, a broad host range is generally favored in biocontrol applications despite the risk of undesirable ancillary effects against nontarget species. Here, we discuss the research progress, applications, and implications of broad host range phages with a focus on tailed broad host range phages infecting human pathogens of concern in the Agri-Food sector.

Systemic Expression, Purification, and Initial Structural Characterization of Bacteriophage T4 Proteins Without Known Structure Homologs

Bacteriophage T4 of Escherichia coli is one of the most studied phages. Research into it has led to numerous contributions to phage biology and biochemistry. Coding about 300 gene products, this double-stranded DNA virus is the best-understood model in phage study and modern genomics and proteomics. Ranging from viral RNA polymerase, commonly found in phages, to thymidylate synthase, whose mRNA requires eukaryotic-like self-splicing, its gene products provide a pool of fine examples for phage research. However, there are still up to 130 gene products that remain poorly characterized despite being one of the most-studied model phages. With the recent advancement of cryo-electron microscopy, we have a glimpse of the virion and the structural proteins that present in the final assembly. Unfortunately, proteins participating in other stages of phage development are absent. Here, we report our systemic analysis on 22 of these structurally uncharacterized proteins, of which none has a known homologous structure due to the low sequence homology to published structures and does not belong to the category of viral structural protein. Using NMR spectroscopy and cryo-EM, we provided a set of preliminary structural information for some of these proteins including NMR backbone assignment for Cef. Our findings pave the way for structural determination for the phage proteins, whose sequences are mainly conserved among phages. While this work provides the foundation for structural determinations of proteins like Gp57B, Cef, Y04L, and Mrh, other in vitro studies would also benefit from the high yield expression of these proteins.

The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains

Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.

Bacteriophage-mediated manipulation of the gut microbiome – promises and presents limitations

Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.

Riding the wave of genomics to investigate aquatic coliphage diversity and activity

Bacteriophages infecting Escherichia coli (coliphages) have been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that is present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterized coliphages from three coastal locations in the United Kingdom and Poland. Comparative genomics and phylogenetic analysis of phage isolates facilitated the identification of putative new species within the genera Rb69virus and T5virus and a putative new genus within the subfamily Tunavirinae. Furthermore, genomic and proteomic analysis combined with host range analysis allowed the identification of a putative tail fibre that is likely responsible for the observed differences in host range of phages vB_Eco_mar003J3 and vB_Eco_mar004NP2.

The dawn of phage therapy

Bacteriophages or phages, being the most abundant entities on earth, represent a potential solution to a diverse range of problems. Phages are successful antibacterial agents whose use in therapeutics was hindered by the discovery of antibiotics. Eventually, because of the development and spread of antibiotic resistance among most bacterial species, interest in phage as therapeutic entities has returned, because their noninfectious nature to humans should make them safe for human nanomedicine. This review highlights the most recent advances and progress in phage therapy and bacterial hosts against which phage research is currently being conducted with respect to food, human, and marine pathogens. Bacterial immunity against phages and tactics of phage revenge to defeat bacterial defense systems are also summarized. We have also discussed approved phage-based products (whole phage-based products and phage proteins) and shed light on their influence on the eukaryotic host with respect to host safety and induction of immune response against phage preparations. Moreover, creation of phages with desirable qualities and their uses in cancer treatment, vaccine production, and other therapies are also reviewed to bring together evidence from the scientific literature about the potentials and possible utility of phage and phage encoded proteins in the field of therapeutics and industrial biotechnology.

Bacteriophage cocktail for biocontrol of Escherichia coli O157:H7: Stability and potential allergenicity study

Escherichia coli O157:H7 has become a global public health and a food safety problem. Despite the implementation of control strategies that guarantee the safety in various products, outbreaks persist and new alternatives are necessary to reduce this pathogen along the food chain. Recently, our group isolated and characterised lytic bacteriophages against E. coli O157:H7 with potential to be used as biocontrol agents in food. To this end, phages need certain requirements to allow their manufacture and application. The aim of this study was to determine the physical stability and allergenic potential of free and microencapsulated (ME) bacteriophage cocktails against E. coli O157:H7. In vitro and in vivo studies were performed to determine phage survival under different pH, gastrointestinal conditions, temperature and UV light intensities. Results showed that the stability of ME phages was significantly (P<0.05) higher than free phages after ultraviolet irradiation, pH conditions between 3 to 7, and exposure to temperatures between at -80°C and 70°C. Both formulations were highly sensitive to very low pH in simulated gastric fluid, but stable in bile salts. In vivo studies in mice confirmed these phages passed through the gastrointestinal tract and were excreted in faeces. In silico, full-length alignment analysis showed that all phage proteins were negative for allergenic potential, but different predicting criteria classified seven phage proteins with a very low probability to be an allergen. In conclusion, these data demonstrated that microencapsulation provided a greater stability to phage formulation under stress conditions and assure a more suitable commercial formulation for the biological control of E. coli O157:H7.

Isolation and identification of Salmonella pullorum bacteriophage YSP2 and its use as a therapy for chicken diarrhea

Salmonella pullorum is the major pathogen that is harmful to the poultry industry in developing countries, and the treatment of chicken diarrhea caused by S. pullorum has become increasingly difficult. In this study, a virulent bacteriophage YSP2, which was able to specifically infect Salmonella, was isolated and characterized. Phage YSP2 was classified in the Siphoviridae family and had a short latent period of 10 min. No bacterial virulence- or lysogenesis-related ORF is present in the YSP2 genome, making it eligible for use in phage therapy. Experiments in vivo investigated the potential use of phages as a therapy against diarrhea in chickens caused by S. pullorum in a chicken diarrhea model, demonstrating that a single oral administration of YSP2 (1 × 10¹⁰ PFU/mL, 80 μL/chicken) 2 h after S. pullorum oral administration at a double median lethal dose was sufficient to protect chickens against diarrhea. Gross inspection showed that YSP2 can effectively reduce organ damage and significantly relieve hemorrhage in the intestine and liver tissue. Moreover, YSP2 can maintain a high curative effect when diluted to 10⁸ PFU/mL. In light of its therapeutic effect on chicken diarrhea, YSP2 may serve as an alternative treatment strategy for infections caused by S. pullorum.