Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection

Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages

Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages-ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.2 Kbp)-when infecting the same Cellulophaga baltica strain #18 (Cba18), of the class Flavobacteriia. Phage phi18:4 belongs to a new family of ssDNA phages, has an internal lipid membrane, and its genome encodes primarily structural proteins, as well as a DNA replication protein common to ssDNA phages and a unique lysis protein. Phage phi18:1 is a siphovirus that encodes several virulence genes, despite not having a known temperate lifestyle, a CAZy enzyme likely for regulatory purposes, and four DNA methyltransferases dispersed throughout the genome that suggest both host modulation and phage DNA protection against host restriction. Physiologically, ssDNA phage phi18:4 has a shorter latent period and smaller burst size than dsDNA phage phi18:1, and both phages efficiently infect this host. These results help augment the diversity of characterized environmental phage-host model systems by studying infections of genomically diverse phages (ssDNA vs. dsDNA) on the same host.

Isolation, characterization, and receptor-binding protein specificity of phages PAS7, PAS59 and PAS61 infecting Shiga toxin-producing Escherichia coli O103 and O146

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen with 6,534 annual reported cases in the EU in 2021. This pathotype generally contains strains with smooth LPS with O-antigen serogroup O157 being the predominant serogroup in the US. However, non-O157 STEC serogroups are becoming increasingly prevalent. Here we announce the complete genomes of three newly isolated phages that infect STEC serogroups O103 and O146, namely Escherichia phages vB_EcoP_PAS7, vB_EcoP_PAS59 and vB_EcoP_PAS61. The genome sequences revealed that they belong to three distinct genera, namely the newly proposed genus Cepavirus within the Slopekvirinae subfamily, the genus Suseptimavirus and the genus Uetakevirus, respectively. We identified the tailspikes of phages PAS7 and PAS61 as a primary specificity determinant for the O-antigens O103 and O146, respectively, and predicted their active site in silico.

Selective bacteriophages reduce the emergence of resistant bacteria in bacteriophage-antibiotic combination therapy

Escherichia coli O157:H7 is a globally important foodborne pathogen with implications for food safety. Antibiotic treatment for O157 may potentially contribute to the exacerbation of hemolytic uremic syndrome, and the increasing prevalence of antibiotic-resistant strains necessitates the development of new treatment strategies. In this study, the bactericidal effects and resistance development of antibiotic and bacteriophage monotherapy were compared with those of combination therapy against O157. Experiments involving continuous exposure of O157 to phages and antibiotics, along with genetic deletion studies, revealed that the deletion of glpT and uhpT significantly increased resistance to fosfomycin. Furthermore, we found that OmpC functions as a receptor for the PP01 phage, which infects O157, and FhuA functions as a receptor for the newly isolated SP15 phage, targeting O157. In the glpT and uhpT deletion mutants, additional deletion in ompC, the receptor for the PP01 phage, increased resistance to fosfomycin. These findings suggest that specific phages may contribute to antibiotic resistance by selecting the emergence of gene mutations responsible for both phage and antibiotic resistance. While combination therapy with phages and antibiotics holds promise for the treatment of bacterial infections, careful consideration of phage selection is necessary.IMPORTANCEThe combination treatment of fosfomycin and bacteriophages against Escherichia coli O157 demonstrated superior bactericidal efficacy compared to monotherapy, effectively suppressing the emergence of resistance. However, mutations selected by phage PP01 led to enhanced resistance not only to the phage but also to fosfomycin. These findings underscore the importance of exercising caution in selecting phages for combination therapy, as resistance selected by specific phages may increase the risk of developing antibiotic resistance.

Detection of hemolytic Shiga toxin-producing Escherichia coli in fresh vegetables and efficiency of phytogenically synthesized silver nanoparticles by Syzygium aromaticum extract and gamma radiation against isolated pathogens

BACKGROUND

Shiga toxin-producing E. coli (STEC) is a major cause of foodborne diseases accompanied by several clinical illnesses in humans. This research aimed to isolate, identify, and combat STEC using novel alternative treatments, researchers have lately investigated using plant extract to produce nanoparticles in an environmentally acceptable way. At various gamma-ray doses, gamma irradiation is used to optimize the conditions for the biogenically synthesized silver nanoparticles (Ag NPs) using an aqueous extract of clove as a reducing and stabilizing agent.

METHODS

On a specific medium, 120 vegetable samples were screened to isolate STEC and molecularly identified using real-time PCR. Moreover, the antibacterial and antibiofilm activities of biogenically synthesized Ag NPs against the isolated STEC were examined.

RESULTS

Twenty-five out of 120 samples of eight types of fresh vegetables tested positive for E. coli, as confirmed by 16S rRNA, of which three were positive for the presence of Stx-coding genes, and six were partially hemolytic. Seven antibiotic disks were used to determine antibiotic susceptibility; the results indicated that isolate STX2EC had the highest antibiotic resistance. The results demonstrated that Ag NPs were highly effective against the STEC isolates, particularly the isolate with the highest drug resistance, with inhibition zones recorded as 19 mm for STX2EC, 11 mm for STX1EC1, and 10 mm for STX1EC2 at a concentration of 108 µg/mL. MICs of the isolates STX1EC1, and STX1EC2 were 13.5 µg/mL whereas it was detected as 6.75 µg/mL for STX2EC. The percentages of biofilm inhibition for STX1EC2, STX1EC1, and STX2EC, were 78.7%, 76.9%, and 71.19%, respectively.

CONCLUSION

These findings suggest that the biogenic Ag NPs can be utilized as a new promising antibacterial agent to combat biofouling on surfaces.

Phages for treatment of Escherichia coli infections

Diseases due to infections by pathogenic Escherichia coli strains are on the rise and with the growing antimicrobial resistance among bacterial pathogens, including this group. Thus, alternative therapeutic options are actively investigated. Among these alternatives is phage therapy. In the case of E. coli, the combination of the well understood biology of this species and its bacteriophages represents a good guiding example for the establishment of phage therapy principles against this and other pathogenic bacteria. In this chapter, the procedures toward the development of phage therapy against pathogenic E. coli with the use of T-even group of phages are discussed. These steps involve the isolation, purification, characterisation and large-scale production of these phages, with formulation of phage cocktails for in vitro and in vivo studies. The main emphasis is made on phage therapy of enteropathogenic E. coli O157:H, which is one of the prominent human pathogens but persists as a commensal bacterium in many food animals. The implementation of phage therapy against E. coli O157:H within the One Health framework in carrier animals and for treatment of meat, vegetables, fruits and other agricultural produce thus would allow controlling and interrupting the transmission routes of this pathogen to the human food chain and preventing human disease. Examples of successful control and elimination of E. coli O157:H are given, while the problems encountered in phage treatment of this pathogen are also discussed.

An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota

Lytic bacteriophages are considered safe for human consumption as biocontrol agents against foodborne pathogens, in particular in ready-to-eat foodstuffs. Phages could, however, evolve to infect different hosts when passing through the gastrointestinal tract (GIT). This underlines the importance of understanding the impact of phages towards colonic microbiota, particularly towards bacterial families usually found in the colon such as the Enterobacteriaceae. Here we propose in vitro batch fermentation as model for initial safety screening of lytic phages targeting Shiga toxin-producing Escherichia coli (STEC). As inoculum we used faecal material of three healthy donors. To assess phage safety, we monitored fermentation parameters, including short chain fatty acid production and gas production/intake by colonic microbiota. We performed shotgun metagenomic analysis to evaluate the outcome of phage interference with colonic microbiota composition and functional potential. During the 24 h incubation, concentrations of phage and its host were also evaluated. We found the phage used in this study, named E. coli phage vB_EcoS_Ace (Ace), to be safe towards human colonic microbiota, independently of the donors’ faecal content used. This suggests that individuality of donor faecal microbiota did not interfere with phage effect on the fermentations. However, the model revealed that the attenuated STEC strain used as phage host perturbed the faecal microbiota as based on metagenomic analysis, with potential differences in metabolic output. We conclude that the in vitro batch fermentation model used in this study is a reliable safety screening for lytic phages intended to be used as biocontrol agents.

Synergistic Effects of Bacteriophage vB_Eco4-M7 and Selected Antibiotics on the Biofilm Formed by Shiga Toxin-Producing Escherichia coli

Apart from antibiotic resistance of pathogenic bacteria, the formation of biofilms is a feature that makes bacterial infections especially difficulty to treat. Shiga toxin-producing Escherichia coli (STEC) strains are dangerous pathogens, causing severe infections in humans, and capable of biofilm production. We have reported previously the identification and characterization of the vB_Eco4-M7 bacteriophage, infecting various STEC strains. It was suggested that this phage might be potentially used in phage therapy against these bacteria. Here, we tested the effects of vB_Eco4-M7 alone or in a phage cocktail with another STEC-infecting phage, and/or in a combination with different antibiotics (ciprofloxacin and rifampicin) on biofilm formed by a model STEC strain, named E. coli O157:H7 (ST2-8624). The vB_Eco4-M7 phage appeared effective in anti-biofilm action in all these experimental conditions (2–3-fold reduction of the biofilm density, and 2–3 orders of magnitude reduction of the number of bacterial cells). However, the highest efficiency in reducing a biofilm’s density and number of bacterial cells was observed when phage infection preceded antibiotic treatment (6-fold reduction of the biofilm density, and 5–6 orders of magnitude reduction of the number of bacterial cells). Previous reports indicated that the use of antibiotics to treat STEC-caused infections might be dangerous due to the induction of Shiga toxin-converting prophages from bacterial genomes under stress conditions caused by antibacterial agents. We found that ciprofloxacin was almost as efficient in inducing prophages from the E. coli O15:H7 (ST2-8624) genome as a classical inducer, mitomycin C, while no detectable prophage induction could be observed in rifampicin-treated STEC cells. Therefore, we conclude the latter antibiotic or similarly acting compounds might be candidate(s) as effective and safe drug(s) when used in combination with phage therapy to combat STEC-mediated infections.

AB5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins

Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB₅ toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB₅ and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.

The interactions of bacteriophage Ace and Shiga toxin-producing Escherichia coli during biocontrol

Strictly lytic phages are considered powerful tools for biocontrol of foodborne pathogens. Safety issues needed to be addressed for the biocontrol of Shiga toxin-producing Escherichia coli (STEC) include: lysogenic conversion, Shiga toxin production through phage induction, and emergence/proliferation of bacteriophage insensitive mutants (BIMs). To address these issues, two new lytic phages, vB_EcoS_Ace (Ace) and vB_EcoM_Shy (Shy), were isolated and characterized for life cycle, genome sequence and annotation, pH stability and efficacy at controlling STEC growth. Ace was efficient in controlling host planktonic cells and did not stimulate the production of the Stx prophage or Shiga toxin. A single dose of phage did not lead to the selection of BIMs. However, when reintroduced, BIMs were detected after 24 h of incubation. The gain of resistance was associated with lower virulence, as a subset of BIMs failed to agglutinate with O157-specific antibody and were more sensitive to human serum complement. BIM's biofilm formation capacity and susceptibility to disinfectants was equal to that of the wild-type strain. Overall, this work demonstrated that phage Ace is a safe biocontrol agent against STEC contamination and that the burden of BIM emergence did not represent a greater risk in environmental persistence and human pathogenicity.

Revisiting the rules of life for viruses of microorganisms

Viruses that infect microbial hosts have traditionally been studied in laboratory settings with a focus on either obligate lysis or persistent lysogeny. In the environment, these infection archetypes are part of a continuum that spans antagonistic to beneficial modes. In this Review, we advance a framework to accommodate the context-dependent nature of virus-microorganism interactions in ecological communities by synthesizing knowledge from decades of virology research, eco-evolutionary theory and recent technological advances. We discuss that nuanced outcomes, rather than the extremes of the continuum, are particularly likely in natural communities given variability in abiotic factors, the availability of suboptimal hosts and the relevance of multitrophic partnerships. We revisit the 'rules of life' in terms of how long-term infections shape the fate of viruses and microbial cells, populations and ecosystems.

Phage-specific metabolic reprogramming of virocells

Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.

Anti-biofilm and Antibacterial Activity of Allium sativum Against Drug Resistant Shiga-Toxin Producing Escherichia coli (STEC) Isolates from Patient Samples and Food Sources

Escherichia coli (E. coli) colonizes human intestinal tract and is usually harmless to the host. However, several strains of E. coli have acquired virulent genes and could cause enteric diseases, urinary tract and even brain infections. Shiga toxin producing Escherichia coli (STEC) is an enterohaemorrhagic E. coli (EHEC) which can result in bloody diarrhoea and could potentially lead to deadly heamolytic uremic syndrome (HUS). STEC is one of the important food borne pathogens that causes food poisoning leading to diarrhoea and number of STEC outbreaks have occurred across the world. The use of standard antibiotics to treat STEC infection is not recommended as it increases the production of shiga toxin which could lead to HUS. Therefore, use of alternative approaches which include use of plant products to treat STEC infections have been gaining attention. The objective of this study was to evaluate the antibacterial and anti-biofilm activity of garlic (Allium sativum) against STEC strains isolated from various patient and food samples using in vitro assays. The microbiological isolation of STEC from various patient and food samples resulted in eight STEC isolates of which seven strains were multidrug resistant. Antibacterial assay results indicated that all the strains exhibited dose dependent sensitivity towards garlic with zone of inhibition diameters ranging from 7 to 24 mm with 15 µl of fresh garlic extract (FGE). Minimum inhibitory  concentration (MIC) of FGE for isolates ranged from 30 to 140 µl/ml. Interestingly, the biofilm formation of all isolates in presence of 4% of FGE decreased by 35 to 59%. FTIR analysis indicated that treatment with 1% FGE results in compositional and content changes in the biofilm. In addition, the total carbohydrate content of biofilm was reduced by 40% upon 1% FGE treatment. The results of the present study report for the first time the antibacterial and anti-biofilm activity of garlic against STEC. The findings will enable development of novel garlic organosulfide based drugs for the prevention and treatment of STEC infections.

Complete Genome Sequences of Escherichia coli Phages vB_EcoM-EP75 and vB_EcoP-EP335

Phages vB_EcoM-EP75 (EP75) and vB_EcoP-EP335 (EP335) specifically infect Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 strains. EP75 has a genome size of 158,143 bp and belongs to the genus Vi1virus.

Phages vB_EcoM-EP75 (EP75) and vB_EcoP-EP335 (EP335) specifically infect Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 strains. EP75 has a genome size of 158,143 bp and belongs to the genus Vi1virus. The genome size of EP335 is 76,622 bp, and it belongs to the genus Phieco32virus.