Morphological, host range, and genetic characterization of two coliphages

Guidelines to Compose an Ideal Bacteriophage Cocktail

Properly designed bacteriophage therapeutics are the cornerstone for a successful outcome of bacteriophage therapy. Here we present an overview of the different strategies and steps that can be taken to develop a bacteriophage cocktail that complies with relevant quality and safety requirements. It is based on empirical bacteriophage therapy knowledge from over a century of experience, more recently performed studies, and emerging technologies. We emphasize the selection of adequate bacteriophages and describe a modified Appelmans' method to improve the overall performance of therapeutic bacteriophages individually and collectively in the cocktail. We present two versions of the method, which differ from each other by the employed techniques to evaluate phage activity and synergy: photometric assessment of bacterial growth versus measurement of bacterial respiration via the Omnilog® system.

Combined Effect of Isolated Bacteriophage and Neem Extract on Isolated Multiple Drug-Resistant Pathogenic Escherichia coli E1 From Well Water

Multiple drug-resistant Escherichia coli (E. coli) is a serious cause of concern, and they can be observed in hospital settings, natural environment, and animals. Dissemination of multiple drug-resistant (MDR) E. coli can pose a high risk to public health. Moreover, they are hard to control with commercial antibiotics, since they have acquired resistance against most of them. Therefore, to control multiple drug-resistant bacteria, alternative strategies have been adopted such as phage therapy, herbal remedies, nanoparticles etc. In the current study, the combined application of neem leaf extract and bacteriophage is used to control an isolated multiple drug-resistant E. coli E1. We have applied 0.1 mg/ml concentration of neem extract in combination with an isolated phage vB_EcoM_C2 of 10¹¹ titer and found that the combinatorial treatment approach significantly controls the growth of E. coli E1 as compared to a single non-combinatorial treatment. In this study, every E. coli cell is targeted by 2 antimicrobials (phage and neem extract) at the same time, which is more effective as compared to the sole treatment. Implementation of the neem extract with phage opens a new alternative approach to the chemotherapeutics for the control of multiple drug-resistant bacterial pathogens. This approach may be effective, economical, and eco-friendly to combat MDR.

CAM-21, a novel lytic phage with high specificity towards Escherichia coli O157:H7 in food products

Escherichia coli O157:H7 is a foodborne pathogen that has become a serious global concern for food safety. Despite the application of different traditional biocontrol methods in the food industry, food borne disease outbreaks linked to this organism remain. Due to their high specificity, lytic bacteriophages are promising antimicrobial agents that could be utilized to control pathogens in foods. In this study, a novel Escherichia phage, CAM-21, was isolated from a dairy farm environment. CAM-21 showed targeted host specificity towards various serotypes of Shiga toxin-producing E. coli, including O157:H7, O26, O103, and O145. Morphological analyses revealed that CAM-21 has a polyhedron capsid and a contractile tail with a diameter of about 92.83 nm, and length of about 129.75 nm, respectively. CAM-21 showed a strong inhibitory effect on the growth of E. coli O157:H7, even at a multiplicity of infection (MOI) of as low as 0.001. Phage adsorption and one-step growth analysis indicated that the target pathogen was rapidly lysed by CAM-21 that exhibited a short latent time (20 min). Electron microscopic and genomic DNA analyses suggested that CAM-21 is a lytic phage, classified as a new species in the Tequatrovirus genus of the Myoviridae Family. Based on whole genome sequencing, CAM-21 has a double-stranded DNA with 166,962 bp, 265 open reading frames and 11 tRNA. The genome of CAM-21 did not encode toxins, virulence factors, antibiotic resistance, lysogeny or allergens. Phylogenetic and genomic comparative analyses suggested that CAM-21 is a T4-like phage species. The growth of E. coli O157:H7 was effectively controlled in milk, ground beef and baby spinach at MOIs of 1000 and 10,000. CAM-21 significantly (P ≤ 0.05) reduced the bacterial counts of the treated foods, ranging from 1.4-2.0 log CFU/mL in milk to 1.3-1.4 log CFU/g in ground beef and baby spinach. These findings suggest that the lytic phage, CAM-21, is a potential candidate for controlling E. coli O157:H7 contamination in foods.

Prevalence and Characterization of CRISPR Locus 2.1 Spacers in Escherichia coli Isolates Obtained from Feces of Animals and Humans

The clustered regularly interspaced short palindromic repeat (CRISPR) has been studied as an immune system in prokaryotes for the survival of bacteriophages. The CRISPR system in prokaryotes records the invasion of bacteriophages or other genetic materials in CRISPR loci. Accordingly, CRISPR loci can reveal a history of infection records of bacteriophages and other genetic materials. Therefore, identification of the CRISPR array may help trace the events that bacteria have undergone. In this study, we characterized and identified the spacers of the CRISPR loci in Escherichia coli isolates obtained from the feces of animals and humans. Most CRISPR spacers were found to stem from phages. Although we did not find any patterns in CRISPR spacers according to sources, our results showed that phage-derived spacers mainly originated from the families Inoviridae, Myoviridae, Podoviridae, and Siphoviridae and the order Caudovirales, whereas plasmid-derived CRISPR spacers were mainly from the Enterobacteriaceae family. In addition, it is worth noting that the isolates from each animal and human source harbored source-specific spacers. Considering that some of these taxa are likely found in the gut of mammalian animals, CRISPR spacers identified in these E. coli isolates were likely derived from the bacteriophageome and microbiome in closed gut environments. Although the bacteriophageome database limits the characterization of CRISPR arrays, the present study showed that some spacers were specifically found in both animal and human sources. Thus, this finding may suggest the possible use of E. coli CRISPR spacers as a microbial source tracking tool. IMPORTANCE We characterized spacers of CRISPR locus 2.1 in E. coli isolates obtained from the feces of various sources. Phage-derived CRISPR spacers are mainly acquired from the order Caudovirales, and plasmid-derived CRISPR spacers are mostly from the Enterobacteriaceae family. This is thought to reflect the microbiome and phageome of the gut environment of the sources. Hence, spacers may help track the encounter of bacterial cells with bacterial cells, viruses, or other genetic materials. Interestingly, source-specific spacers are also observed. The identification of source-specific spacers is thought to help develop the methodology of microbial source tracking and understanding the interactions between viruses and bacteria. However, very few spacers have been uncovered to track where they originate. The accumulation of genome sequences can help identify the hosts of spacers and can be applied for microbial source tracking.

Coliphages as viral indicators of sanitary significance for drinking water

Coliphages are virus that infect coliform bacteria and are used in aquatic systems for risk assessment for human enteric viruses. This mini-review appraises the types and sources of coliphage and their fate and behavior in source waters and engineered drinking water treatment systems. Somatic (cell wall infection) and F+ (male specific) coliphages are abundant in drinking water sources and are used as indicators of fecal contamination. Coliphage abundances do not consistently correlate to human enteric virus abundance, but they suitably reflect the risks of exposure to human enteric viruses. Coliphages have highly variable surface characteristics with respect to morphology, size, charge, isoelectric point, and hydrophobicity which together interact to govern partitioning and removal characteristics during water treatment. The groups somatic and F+ coliphages are valuable for investigating the virus elimination during water treatment steps and as indicators for viral water quality assessment. Strain level analyses (e.g., Qβ or GA-like) provide more information about specific sources of viral pollution but are impractical for routine monitoring. Consistent links between rapid online monitoring tools (e.g., turbidity, particle counters, and flow cytometry) and phages in drinking water have yet to be established but are recommended as a future area of research activity. This could enable the real-time monitoring of virus and improve the process understanding during transient operational events. Exciting future prospects for the use of coliphages in aquatic microbiology are also discussed based on current scientific evidence and practical needs.

Isolation and characterization of Escherichia coli O157: H7 novel bacteriophage for controlling this food-borne pathogen

Escherichia coli O157: H7 is known as a high-risk food-born pathogen, and its removal is vital for maintaining food safety. The increasing trend of food-borne diseases caused by this bacterium and other pathogens indicates the low efficiency of the methods to remove pathogens from foodstuffs. One of the new and effective methods is to use of a bio-control agent called bacteriophage, which has shown good function in eliminating and reducing pathogens. In this study, a novel bacteriophage was isolated and identified from the slaughterhouse wastewater to control E. coli O157: H7. This bacteriophage belonged to the Myoviridae family. Two bacterial genera including E. coli and Salmonella, were allocated to determine the bacteriophage host range; the result showed that the anti- Salmonella effect of phage was low. The phage was stable at high temperature (80°C) and caused an acceptable reduction in the E. coli O157: H7 (4.18 log CFU / mL for 10 hours). The isolated bacteriophage was corroborated to be completely safe based on the whole genome sequencing and lack of any virulence factor from the host bacteria. Considering the characteristics of this phage and its function in vitro, this bacteriophage may be used as an effective bio-control agent in foods with the possible E. coli O157: H7 -induced contamination.

Morphogenesis and Genetic Diversity of Some Virulent Phages Specific for Bacillus velezensis

<b>Background and Objective:</b> Phosphorus (P) is one of the most limiting nutrients for plant growth. Phosphorus deficiency is limiting crop production in many agricultural soils worldwide. The application of phosphorus solubilizing bacteria (PSB) to soils can replace or partially reduce using of inorganic P fertilizers. A bacteriophage, or phage, is a virus that infects a bacterial cell, taking over the host cell's genetic material. The four phages were propagated, purified, studied for the morphological properties, finally studying the genetic diversity. <b>Materials and Methods:</b> Obtained, examined the efficiency and identification of bacteria for solubilizing phosphorus. Isolation, studying the properties and studying genetic diversity. <b>Results:</b> Four virulent phages (Bv<sub>1</sub>, Bv<sub>2</sub>, Bv<sub>3</sub> and Bv<sub>4</sub>) specific for <i>Bacillus velezensis</i> were isolated from the Egyptian soil. The <i>Bacillus</i> phages were purified by alternative low and high-speed centrifugation methods. Electron micrographs showed that phages appeared to be a member of the <i>Siphoviridae </i>family based on their structure and particle morphology (the particles have a head and long non-contractile tail). Sodium Dodecyl Sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) technique was performed to determine the properties of viral proteins. It was found that the Bv<sub>1</sub> virus had five structural proteins, while Bv<sub>2</sub> and Bv<sub>3</sub> virus had eight structural proteins and finally, the Bv<sub>4</sub> virus had ten structural proteins. The purity and quantity of isolated DNAs were determined spectrophotometrically. Data showed that the concentration of Bv<sub>1</sub> DNA was 0.75 μg, Bv<sub>2</sub> DNA and Bv<sub>3</sub> DNA was 0.60 μg and finally Bv<sub>4</sub> DNA 0.55 μg μL<sup></sup><sup>1</sup>. The analysis of genetic material of <i>B. velezensis</i> phages was determined based on both the ISSR-PCR technique and the effect of restriction enzymes. Data showed different amplification patterns with all phages. <b>Conclusion:</b> The bacteriophages of <i>B. velezensis</i> were isolated from soil, propagated, purified, study some of its properties.

Isolation, characterization, and genomic analysis of the novel T4-like bacteriophage ΦCJ20

Pathogenic Escherichia coli infections have been consistently reported annually. The basic characteristics and genome of the newly isolated ΦCJ20 from swine feces was analyzed. To determine basic characteristics, dotting assays and double-layer agar assays were conducted. Bacteriophage particles were analyzed via transmission electron microscopy. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was performed to determine the sizes of major structural proteins. The complete genome of the phage was analyzed. Bacteriophage particles were identified as Myoviridae, with a head measuring 110.57 ± 1.89 nm and a contractile tail measuring 107.97 ± 3.20 nm and were found to infect E. coli. Major structural proteins of ΦCJ20 showed two well-pronounced bands of approximately 53.6 and 70.9 kDa. The genome size of ΦCJ20 was 169,884 bp, and 118 of 307 open reading frames were annotated. This study provides a baseline for the development of E. coli infection treatment strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-021-00906-y.

T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors

The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50-80 min with burst sizes of 44-65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84-92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal β-helices connecting loops.

Klebsiella virus UPM2146 lyses multiple drug-resistant Klebsiella pneumoniae in vitro and in vivo

Klebsiella pneumoniae are opportunistic bacteria found in the gut. In recent years they have been associated with nosocomial infections. The increased incidence of multiple drug-resistant K. pneumoniae makes it necessary to find new alternatives to treat the disease. In this study, phage UPM2146 was isolated from a polluted lake which can lyse its host K. pneumoniae ATCC BAA-2146. Observation from TEM shows that UPM2146 belongs to Caudoviriales (Order) based on morphological appearance. Whole genome analysis of UPM2146 showed that its genome comprises 160,795 bp encoding for 214 putative open reading frames (ORFs). Phylogenetic analysis revealed that the phage belongs to Ackermannviridae (Family) under the Caudoviriales. UPM2146 produces clear plaques with high titers of 1010 PFU/ml. The phage has an adsorption period of 4 min, latent period of 20 min, rise period of 5 min, and releases approximately 20 PFU/ bacteria at Multiplicity of Infection (MOI) of 0.001. UPM2146 has a narrow host-range and can lyse 5 out of 22 K. pneumoniae isolates (22.72%) based on spot test and efficiency of plating (EOP). The zebrafish larvae model was used to test the efficacy of UPM2146 in lysing its host. Based on colony forming unit counts, UPM2146 was able to completely lyse its host at 10 hours onwards. Moreover, we show that the phage is safe to be used in the treatment against K. pneumoniae infections in the zebrafish model.

Antiviral, Antioxidant, and Antihemolytic Effect of Annona muricata L. Leaves Extracts

Annona muricata L. is a tropical tree that is used in traditional medicine around the world. The high content of flavonoid, alkaloid, acetogenin, phenolic and lipophilic compounds of this tropical tree forms the basis of its traditional medical uses. Our objective was to study soursop leaf extracts to support their use as antiviral therapies and investigate their protective effects against oxidative damage. The aqueous extract (AE) and acidified ethanolic extract (AEE) of soursop leaves were characterized by ultra performance liquid chromatography (UPLC), and their effects on human erythrocytes and in vitro antioxidant capacity, as evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assays, were investigated. The antiviral effects were evaluated using a bacteriophage surrogate. AEE showed the highest phenolic content, with rutin as the predominant compound. This extract showed higher values in the DPPH and ABTS assays, with 23.61 ± 0.42 and 24.91 ± 0.16 mmol of Trolox equivalent per gram, respectively. Inhibition of hemolysis was 34% and 51% for AE and AEE, respectively. AEE was selected for the antiviral study because of its higher antioxidant activity. The viral reduction ranged from 5-6 log10 plaque-forming units/volume (PFU) at contact times of 15-360 min. Soursop leaves have a positive effect on reducing oxidative stress in human erythrocytes and viral infections.

Antiviral effects of Brazilian green and red propolis extracts on Enterovirus surrogates

Propolis is a natural product of bees with biological activities that are mainly associated with bee type and geographic origin. Propolis extract has been proposed with several applications in environmental health. The ethanol extracts have shown good antimicrobial activity. The association of this technique with ultrasound-assisted extraction has been studied to improve the characteristics of the obtained extracts. Thus, the objective of this work is to verify the antiviral action against two strains of bacteriophages of two extracts of Brazilian propolis (green and red) obtained by conventional extraction and ultrasonic extraction. The activities of the propolis red and green extracts were confirmed by the significant ~3 and ~4.5 Log 10 PFU/mL reduction in the concentrations of the MS2 and Av-08 bacteriophages, respectively. It was found that ultrasound-assisted extraction is comparable to the maceration process and demonstrated the best antiviral activities. Brazilian red propolis was more effective than green propolis in viral reduction in all treatments.

Use of Bacteriophages to Control Vibrio Contamination of Microalgae Used as a Food Source for Oyster Larvae During Hatchery Culture

Cultured microalgae are the primary food source for oyster larvae during hatchery culture and are a potential vector for Vibrio spp. infection of larval cultures. Bacteriophages have shown potential for controlling contamination of Vibrio spp. in aquaculture systems and their application could be an effective biological control method to eliminate such bacterial contamination of microalgae. This study investigated whether Vibrio-free microalgae sources could be ensured via the application of Vibrio specific phages. As a first step, four different Vibrio bacteriophages (belonging to the Myoviridae viral family) were isolated from marine waters in Queensland, Australia and used in challenge tests against a Vibrio host species, previously isolated from New South Wales oyster hatchery and found to be closely related to V. alginolyticus (ATCC 17749). The genome sequence of one of the four isolated bacteriophages, Vibrio Φ-2, that displayed strongest virulence against the host was determined. The 242446 bp genome of this bacteriophage was predicted to encode 217 proteins with an average GC content of 43.91%, containing putative thymidine kinases and a lysin enzyme. Application of these bacteriophages to pathogenic Vibrio spp. contaminating microalgae suspensions resulted in significant decreases in their numbers within 2 h. Findings indicated that direct application of bacteriophages to microalgae suspensions could be an effective method of reducing the occurrence of vibriosis in oyster hatcheries.

Isolation, characterization and application of a polyvalent phage capable of controlling Salmonella and Escherichia coli O157:H7 in different food matrices

Salmonella Enteritidis, Salmonella Typhimurium, and Escherichia coli O157:H7 are the most important foodborne pathogens, causing serious food poisoning outbreaks worldwide. Bacteriophages are increasingly considered as novel antibacterial agents to control foodborne pathogens. In this study, 8 Salmonella phages and 10 E. coli O157:H7 phages were isolated from chicken products. A polyvalent phage PS5 capable of infecting S. Enteritidis, S. Typhimurium, and E. coli O157:H7 was further characterized and its efficacy in reducing these foodborne pathogens was evaluated in in vitro and in foods. Morphology, one-step growth, and stability assay showed that phage PS5 was a myovirus, with relatively short latent periods, large burst sizes, and high stability. Genome sequencing analysis revealed that the genome of PS5 does not contain any genes associated to antibiotic resistance, toxins, lysogeny, and virulence factors. In broth, phage PS5 significantly decreased the viable counts of all the three bacterial hosts by more than 1.3 log CFU/mL compared to controls after 2 h of incubation at 4 °C and 24 °C. In foods, treatment with PS5 also resulted in significant reductions of viable counts of all the three bacterial hosts compared to controls at temperatures tested. This is the first report on single phage capable of simultaneously controlling S. Enteritidis, S. Typhimurium and E. coli O157:H7 in both in vitro and in foods.

Genome sequence analysis of Vibrio parahaemolyticus lytic phage Vp_R1 with a C3 morphotype

Phage Vp_R1 belongs to the family Podoviridae and has a C3 morphotype, with an elongated head with a diameter of 190 ± 1.1 nm and an ultrashort tail with a length of 9 ± 1.2 nm. The double-stranded DNA genome is 112.1 kb long, has a mol% G + C content of 40.3, contains 129 ORFs, and encodes four tRNAs. Phylogenetic analysis suggests that phage Vp_R1 is a novel member of the genus Kuravirus.

Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil

Bacteriophages are ubiquitously distributed prokaryotic viruses that are more abundant than bacteria. As a consequence of their life cycle, phages can kidnap part of their host's genetic material, including antibiotic resistance genes (ARGs), which released phage particles transfer in a process called transduction. The spread of ARGs among pathogenic bacteria currently constitutes a serious global health problem. In this study, fresh vegetables (lettuce, spinach and cucumber), and cropland soil were screened by qPCR for ten ARGs (bla_TEM, bla_CTX-M-1 group, bla_CTX-M-9 group, bla_OXA-48, bla_VIM, mecA, sul1, qnrA, qnrS and armA) in their viral DNA fraction. The presence of ARGs in the phage DNA was analyzed before and after propagation experiments in an Escherichia coli host strain to evaluate the ability of the phage particles to infect a host. ARGs were found in the phage DNA fraction of all matrices, although with heterogeneous values. ARG prevalence was significantly higher in lettuce and soil, and the most common overall were β-lactamases. After propagation experiments, an increase in ARG densities in phage particles was observed in samples of all four matrices, confirming that part of the isolated phage particles were infectious. This study reveals the abundance of free, replicative ARG-containing phage particles in vegetable matrices and cropland soil. The particles are proposed as vehicles for resistance transfer in these environments, where they can persist for a long time, with the possibility of generating new resistant bacterial strains. Ingestion of these mobile genetic elements may also favor the emergence of new resistances, a risk not previously considered.

Liposome Entrapment of Bacteriophages Improves Wound Healing in a Diabetic Mouse MRSA Infection

Diabetic populations are more prone to developing wound infections which results in poor and delayed wound healing. Infection with drug resistant organisms further worsen the situation, driving searches for alternative treatment approaches such as phage therapy. Major drawback of phage therapy, however, is low phage persistence in situ, suggesting further refinement of the approach. In the present work we address this issue by employing liposomes as delivery vehicles. A liposome entrapped phage cocktail was evaluated for its ability to resolve a Staphylococcus aureus-induced diabetic excission wound infection. Two characterized S. aureus specific lytic phages, MR-5 and MR-10 alone, in combination (cocktail), or entrapped in liposomes (versus as free phages) were assesed for their therapeutic efficacy in resolving diabetic wound infection. Mice treated with free phage cocktail showed significant reduction in wound bioburden, greater wound contraction and faster tissue healing than with free monophage therapy. However, to further enhance the availability of viable phages the encapsulation of phage cocktail in the liposomes was done. Results of in vitro stability studies and in vivo phage titer determination, suggests that liposomal entrapment of phage cocktail can lead to better phage persistence at the wound site. A 2 log increase in phage titre, however, was observed at the wound site with liposome entrapped as compared to the free phage cocktail, and this was associaed with increased rates of infection resolution and wound healing. Entrapment of phage cocktails within liposomes thus could represent an attractive approach for treatment of bacterial infections, not responding to antibiotis as increased phage persistence in vitro and in vivo at the wound site was observed.

Protective Effects of Bacteriophages against Aeromonas hydrophila Species Causing Motile Aeromonas Septicemia (MAS) in Striped Catfish

To determine the effectivity of bacteriophages in controlling the mass mortality of striped catfish (Pangasianodon hypophthalmus) due to infections caused by Aeromonas spp. in Vietnamese fish farms, bacteriophages against pathogenic Aeromonas hydrophila were isolated. A. hydrophila-phage 2 and A. hydrophila-phage 5 were successfully isolated from water samples from the Saigon River of Ho Chi Minh City, Vietnam. These phages, belonging to the Myoviridae family, were found to have broad activity spectra, even against the tested multiple-antibiotic-resistant Aeromonas isolates. The latent periods and burst size of phage 2 were 10 min and 213 PFU per infected host cell, respectively. The bacteriophages proved to be effective in inhibiting the growth of the Aeromonas spp. under laboratory conditions. Phage treatments applied to the pathogenic strains during infestation of catfish resulted in a significant improvement in the survival rates of the tested fishes, with up to 100% survival with MOI 100, compared to 18.3% survival observed in control experiments. These findings illustrate the potential for using phages as an effective bio-treatment method to control Motile Aeromonas Septicemia (MAS) in fish farms. This study provides further evidence towards the use of bacteriophages to effectively control disease in aquaculture operations.

Guidelines to Compose an Ideal Bacteriophage Cocktail

Correctly designed bacteriophage therapeutics are the cornerstone for a successful outcome of bacteriophage therapy. Here we overview strategies on how to choose bacteriophages and their bacterial hosts at different steps of a bacteriophage cocktail development in order to comply with all quality and safety requirements based on the already existing essentially empirical experience in bacteriophage therapy and current accomplishments in modern biomedical sciences. A modification of the classic Appelmans' method (1922) to assess stability of bacteriophage activity in liquid media is presented in order to improve the overall performance of therapeutic bacteriophages individually and collectively in the cocktail.

Isolation and Physiomorphological Characterization of Escherichia coli O157:H7-Infecting Bacteriophages Recovered from Beef Cattle Operations

Bacteriophages, recovered from beef cattle environment and specifically targeting Escherichia coli O157:H7, were examined for their physiological and morphological characteristics. Degree of bacterial lysis and host range of isolated bacteriophages was determined against 55 isolates of E. coli O157:H7. Morphology of phages was examined under transmission electron microscope. Phage growth parameters, particularly rate of adsorption, rise period, latent period, and burst size were also determined. The stability of isolated phages was tested at acidic and alkaline pH, at high temperatures, and in cold storage. A total of 7 phages were isolated which showed lytic activity against 50 out of 55 isolates of E. coli O157:H7. Based on the morphology, phages were classified into Myoviridae or Siphoviridae family. Phages had a rise period between 19 and 40 min, a short latent period between 12 and 30 min, and a large burst size (89-631 virions per infected cell), indicating high lytic activity. Phages remained stable for 24 h at a wide pH (1-11) and temperature range (40-60°C) and for 90 d in cold storage. Characterization of bacteriophages, with a diverse host range of E. coli O157:H7, could aid in the development of effective biocontrol strategies for this pathogen in the food industry.

Transfersomal Phage Cocktail Is an Effective Treatment against Methicillin-Resistant Staphylococcus aureus-Mediated Skin and Soft Tissue Infections

The emergence of drug resistance has rekindled interest in phage therapy as an alternative treatment option; its potency, safety, and proven efficacy are worth noting. However, phage therapy still suffers from issues of poor stability, narrow spectra, and poor pharmacokinetic profiles. Therefore, it is essential to look into the use of drug delivery systems for efficient delivery of lytic phages in vivo The present study evaluated the use of nanostructured lipid-based carriers, i.e., transfersomes, as transdermal delivery systems for encapsulating a methicillin-resistant Staphylococcus aureus (MRSA) phage cocktail. Furthermore, the therapeutic potential of the encapsulated phage cocktail in resolving experimental soft tissue infections in rats was studied. Results from in vitro stability and in vivo phage titer experiments indicated that the transfersome-entrapped phage cocktail showed better persistence and stability than did free phages. Rats treated with the transfersome-entrapped phage cocktail resolved the experimental thigh infections within a period of 7 days, unlike the 20-day period required for untreated animals. The findings of the present study support the use of transfersomes as delivery agents to enhance the stability and in vivo persistence of the encapsulated phages. In addition, this study highlights the advantages offered by transfersome-encapsulated phages in providing better therapeutic options than free phages for treating skin and soft tissue infections. The transfersome-entrapped phage cocktail was able to protect all test animals (with no deaths) even when administered with a delay of 12 h postinfection, unlike free phages, thus making this treatment option more suitable for clinical settings.

Isolation and Characterization of phiLLS, a Novel Phage with Potential Biocontrol Agent against Multidrug-Resistant Escherichia coli

Foodborne diseases are a serious and growing problem, and the incidence and prevalence of antimicrobial resistance among foodborne pathogens is reported to have increased. The emergence of antibiotic-resistant bacterial strains demands novel strategies to counteract this epidemic. In this regard, lytic bacteriophages have reemerged as an alternative for the control of pathogenic bacteria. However, the effective use of phages relies on appropriate biological and genomic characterization. In this study, we present the isolation and characterization of a novel bacteriophage named phiLLS, which has shown strong lytic activity against generic and multidrug-resistant Escherichia coli strains. Transmission electron microscopy of phiLLS morphology revealed that it belongs to the Siphoviridae family. Furthermore, this phage exhibited a relatively large burst size of 176 plaque-forming units per infected cell. Phage phiLLS significantly reduced the growth of E. coli under laboratory conditions. Analyses of restriction profiles showed the presence of submolar fragments, confirming that phiLLS is a pac-type phage. Phylogenetic analysis based on the amino acid sequence of large terminase subunits confirmed that this phage uses a headful packaging strategy to package their genome. Genomic sequencing and bioinformatic analysis showed that phiLLS is a novel bacteriophage that is most closely related to T5-like phages. In silico analysis indicated that the phiLLS genome consists of 107,263 bp (39.0 % GC content) encoding 160 putative ORFs, 16 tRNAs, several potential promoters and transcriptional terminators. Genome analysis suggests that the phage phiLLS is strictly lytic without carrying genes associated with virulence factors and/or potential immunoreactive allergen proteins. The bacteriophage isolated in this study has shown promising results in the biocontrol of bacterial growth under in vitro conditions, suggesting that it may prove useful as an alternative agent for the control of foodborne pathogens. However, further oral toxicity testing is needed to ensure the safety of phage use.

A minireview on the in vitro and in vivo experiments with anti-Escherichia coli O157:H7 phages as potential biocontrol and phage therapy agents

Phage therapy is an old method of combating bacterial pathogens that has recently been taken into consideration due to the alarming spread of antibiotic resistance. Escherichia coli O157:H7 is a foodborne pathogen that causes hemorrhagic colitis and life-threatening Hemolytic Uremic Syndrome (HUS). There are several studies on isolation of specific phages against E. coli O157:H7 and more than 60 specific phages have been published so far. Although in vitro experiments have been successful in elimination or reduction of E. coli O157:H7numbers, in vivo experiments have not been as promising. This may be due to escape of bacteria to locations where phages have difficulties to enter or due to the adverse conditions in the gastrointestinal tract that affect phage viability and proliferation. To get around the latter obstacle, an alternative phage delivery method such as polymer microencapsulation should be tried. While the present time results are not very encouraging the work should be continued as more efficient phage treatment regimens might be found in future.

In vivo efficacy of single phage versus phage cocktail in resolving burn wound infection in BALB/c mice

Klebsiella pneumoniae is one of the most predominant pathogens associated with burn wound infections, causing considerable morbidity and mortality. The indiscriminate usage of antibiotics has led to the development of resistant strains, which have contributed towards the inefficacy of antibiotics. Phage therapy is a promising alternative to hinder the progression of pathogenic bacteria. However, phage bacterial resistance is already well known but the use of phage cocktails can overcome this drawback. The aim of the study was to evaluate the therapeutic efficacy of monophage (Kpn1, Kpn2, Kpn3, Kpn4 and Kpn5) in comparison to phage cocktail in resolving the course of burn wound infection in mice. Although, animals receiving monophage therapy exhibited efficacy in resolving the course of infection but phage cocktail was highly effective in arresting the entire infection process (bacterial load, wound contraction, skin myeloperoxidase activity, collagen formation and histopathological analysis). In comparison to untreated control mice, a significant reduction in bacterial load to 4.32, 4.64, 4.42, 4.11 and 4.27 log CFU/ml in Kpn1, Kpn2, Kpn3 Kpn4 and Kpn5 treated animals was obtained respectively was on peak day (3rd day). However, the group receiving phage cocktail (group 7) showed maximum reduction in bacterial load in the skin tissue. The bacterial load was significantly reduced to 3.01 log CFU/ml on peak day. This accounts for a significant reduction of 6 log cycles (p < 0.01) as compared to that of untreated control animals where a peak of 8.81 log CFU/ml was seen followed by steady decrease thereafter. Thus, phage cocktail gave maximum protection against burn wound infection by K. pneumoniae B5055. Compared to any single phage, phage cocktail significantly checked the emergence of resistant mutants. Hence this approach can serve as an effective strategy in treating Klebsiella mediated burn wound infections in individuals who do not respond to conventional antibiotic therapy.

Bacteriophages: biosensing tools for multi-drug resistant pathogens

Pathogen detection is of utmost importance in many sectors, such as in the food industry, environmental quality control, clinical diagnostics, bio-defence and counter-terrorism. Failure to appropriately, and specifically, detect pathogenic bacteria can lead to serious consequences, and may ultimately be lethal. Public safety, new legislation, recent outbreaks in food contamination, and the ever-increasing prevalence of multidrug-resistant infections have fostered a worldwide research effort targeting novel biosensing strategies. This review concerns phage-based analytical and biosensing methods targeted towards theranostic applications. We discuss and review phage-based assays, notably phage amplification, reporter phage, phage lysis, and bioluminescence assays for the detection of bacterial species, as well as phage-based biosensors, including optical (comprising SPR sensors and fiber optic assays), electrochemical (comprising amperometric, potentiometric, and impedimetric sensors), acoustic wave and magnetoelastic sensors.

Functional characterization of a novel lytic phage EcSw isolated from Sus scrofa domesticus and its potential for phage therapy

In this study, multi-drug resistant Escherichia coli Sw1 (E. coli Sw1) and active lytic phage EcSw was isolated from feces samples of Sus scrofa domesticus (piglet) suffering from diarrhea. Transmission electron microscopy (TEM) indicated that isolated EcSw belongs to the Myoviridae family with an icosahedral head (80 ± 4) and a long tail (180 ± 5 nm). The EcSw phage genome size was estimated to be approximately 75 Kb of double-stranded DNA (dsDNA). Phage dynamic studies show that the latent period and burst size of EcSw were approximately 20 min and 28 PFU per cell, respectively. Interestingly, the EcSw phage can tolerate a wide range of environmental conditions, such as temperature, pH and ions (Ca(2+) and Mg(2+)). Furthermore, genome sequence analysis revealed that the lytic genes of the EcSw phage are notably similar to those of enterobacteria phages. In addition, phage-antibiotic synergy has notable effects compared with the effects of phages or antibiotics alone. Inhibition of E. coli Sw1 and 0157:H7 strains showed that the limitations of host specificity and infectivity of EcSw. Even though, it has considerable potential for phage therapy for handling the problem of the emergence of multidrug resistant pathogens.

Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea

Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.

Bacteriophage therapy for safeguarding animal and human health: a review

Since the discovery of bacteriophages at the beginning of the 19th century their contribution to bacterial evolution and ecology and use in a variety of applications in biotechnology and medicine has been recognized and understood. Bacteriophages are natural bacterial killers, proven as best biocontrol agents due to their ability to lyse host bacterial cells specifically thereby helping in disease prevention and control. The requirement of such therapeutic approach is straight away required in view of the global emergence of Multidrug Resistant (MDR) strains of bacteria and rapidly developing resistance to antibiotics in both animals and humans along with increasing food safety concerns including of residual antibiotic toxicities. Phage typing is a popular tool to differentiate bacterial isolates and to identify and characterize outbreak-associated strains of Salmonella, Campylobacter, Escherichia and Listeria. Numerous methods viz. plaque morphology, ultracentrifugation in the density gradient of CsCl2, and random amplified polymorphic DNA (RAPD) have been found to be effective in detection of various phages. Bacteriophages have been isolated and recovered from samples of animal waste products of different livestock farms. High titer cocktails of broad spectrum lytic bacteriophages are usually used for clinical trial for assessing their therapeutic efficacy against antibiotic unresponsive infections in different animals. Bacteriophage therapy also helps to fight various bacterial infections of poultry viz. colibacillosis, salmonellosis and listeriosis. Moreover, the utility of phages concerning biosafety has raised the importance to explore and popularize the therapeutic dimension of this promising novel therapy which forms the topic of discussion of the present review.

Tradeoffs in bacteriophage life histories

Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories-replication, persistence, host range, and adsorption-are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses' life histories have potential importance for viral evolution, ecology, and pathogenesis.

Phage biocontrol of enteropathogenic and shiga toxin-producing Escherichia coli in meat products

Ten bacteriophages were isolated from faeces and their lytic effects assayed on 103 pathogenic and non-pathogenic Enterobacteriaceae. Two phages (DT1 and DT6) were selected based on their host ranges, and their lytic effects on pathogenic E. coli strains inoculated on pieces of beef were determined. We evaluated the reductions of viable cells of Escherichia coli O157:H7 and non-O157 Shiga toxigenic E. coli strains on meat after exposure to DT6 at 5 and 24°C for 3, 6, and 24 h and the effect of both phages against an enteropathogenic E. coli strain. Significant viable cell reductions, compared to controls without phages, at both temperatures were observed, with the greatest decrease taking place within the first hours of the assays. Reductions were also influenced by phage concentration, being the highest concentrations, 1.7 × 10¹⁰ plaque forming units per milliliter (PFU/mL) for DT1 and 1.4 × 10¹⁰ PFU/mL for DT6, the most effective. When enteropathogenic E. coli and Shiga toxigenic E. coli (O157:H7) strains were tested, we obtained viable cell reductions of 0.67 log (p = 0.01) and 0.77 log (p = 0.01) after 3 h incubation and 0.80 log (p = 0.01) and 1.15 log (p = 0.001) after 6 h. In contrast, all nonpathogenic E. coli strains as well as other enterobacteria tested were resistant. In addition, phage cocktail was evaluated on two strains and further reductions were observed. However, E. coli bacteriophage insensitive mutants (BIMs) emerged in meat assays. BIMs isolated from meat along with those isolated by using the secondary culture method were tested to evaluate resistance phenotype stability and reversion. They presented low emergence frequencies (6.5 × 10⁻⁷–1.8 × 10⁻⁶) and variable stability and reversion. Results indicate that isolated phages were stable on storage, negative for all the virulence factors assayed, presented lytic activity for different E. coli virotypes and could be useful in reducing Shiga toxigenic E. coli and enteropathogenic E. coli viable cells in meat products.

Bacteriophages for managing Shigella in various clinical and non-clinical settings

The control of shigellosis in humans enjoys a prominent position in the history of bacteriophage therapy. d’Herelle first demonstrated the efficacy of phage therapy by curing 4 patients of shigellosis, and several subsequent studies confirmed the ability of phages to reduce Shigella based infection. Shigella spp continue to cause millions of illnesses and deaths each year and the use of phages to control the disease in humans and the spread of the bacteria within food and water could point the way forward to the effective management of an infectious disease with global influence.

Co-therapy using lytic bacteriophage and linezolid: effective treatment in eliminating methicillin resistant Staphylococcus aureus (MRSA) from diabetic foot infections

BACKGROUND

Staphylococcus aureus remains the predominant pathogen in diabetic foot infections and prevalence of methicillin resistant S.aureus (MRSA) strains further complicates the situation. The incidence of MRSA in infected foot ulcers is 15-30% and there is an alarming trend for its increase in many countries. Diabetes acts as an immunosuppressive state decreasing the overall immune functioning of body and to worsen the situation, wounds inflicted with drug resistant strains represent a morbid combination in diabetic patients. Foot infections caused by MRSA are associated with an increased risk of amputations, increased hospital stay, increased expenses and higher infection-related mortality. Hence, newer, safer and effective treatment strategies are required for treating MRSA mediated diabetic foot infections. The present study focuses on the use of lytic bacteriophage in combination with linezolid as an effective treatment strategy against foot infection in diabetic population.

METHODOLOGY

Acute hindpaw infection with S.aureus ATCC 43300 was established in alloxan induced diabetic BALB/c mice. Therapeutic efficacy of a well characterized broad host range lytic bacteriophage, MR-10 was evaluated alone as well as in combination with linezolid in resolving the course of hindpaw foot infection in diabetic mice. The process of wound healing was also investigated.

RESULTS AND CONCLUSIONS

A single administration of phage exhibited efficacy similar to linezolid in resolving the course of hindpaw infection in diabetic animals. However, combination therapy using both the agents was much more effective in arresting the entire infection process (bacterial load, lesion score, foot myeloperoxidase activity and histopathological analysis). The entire process of tissue healing was also hastened. Use of combined agents has been known to decrease the frequency of emergence of resistant mutants, hence this approach can serve as an effective strategy in treating MRSA mediated foot infections in diabetic individuals who do not respond to conventional antibiotic therapy.

wksl3, a New biocontrol agent for Salmonella enterica serovars enteritidis and typhimurium in foods: characterization, application, sequence analysis, and oral acute toxicity study

Of the Salmonella enterica serovars, S. Enteritidis and S. Typhimurium are responsible for most of the Salmonella outbreaks implicated in the consumption of contaminated foods in the Republic of Korea. Because of the widespread occurrence of antimicrobial-resistant Salmonella in foods and food processing environments, bacteriophages have recently surfaced as an alternative biocontrol tool. In this study, we isolated a virulent bacteriophage (wksl3) that could specifically infect S. Enteritidis, S. Typhimurium, and several additional serovars. Transmission electron microscopy revealed that phage wksl3 belongs to the family Siphoviridae. Complete genome sequence analysis and bioinformatic analysis revealed that the DNA of phage wksl3 is composed of 42,766 bp with 64 open reading frames. Since it does not encode any phage lysogeny factors, toxins, pathogen-related genes, or food-borne allergens, phage wksl3 may be considered a virulent phage with no side effects. Analysis of genetic similarities between phage wksl3 and four of its relatives (SS3e, vB_SenS-Ent1, SE2, and SETP3) allowed wksl3 to be categorized as a SETP3-like phage. A single-dose test of oral toxicity with BALB/c mice resulted in no abnormal clinical observations. Moreover, phage application to chicken skin at 8°C resulted in an about 2.5-log reduction in the number of Salmonella bacteria during the test period. The strong, stable lytic activity, the significant reduction of the number of S. Enteritidis bacteria after application to food, and the lack of clinical symptoms of this phage suggest that wksl3 may be a useful agent for the protection of foods against S. Enteritidis and S. Typhimurium contamination.

Methicillin-resistant Staphylococcus aureus phage plaque size enhancement using sublethal concentrations of antibiotics

Phage therapy presents an alternative approach against the emerging methicillin-resistant Staphylococcus aureus (MRSA) threat. Some of the problems encountered during isolation of MRSA phages include the high prevalence of enteric phages in natural sources, nonspecific absorption of viable phage, and the formation of pinpoint or tiny plaques. The phage isolated in this study, MR-5, also formed tiny plaques against its host S. aureus ATCC 43300 (MRSA), making its detection and enumeration difficult. An improved method of increasing the plaque size of MRSA phage by incorporating sublethal concentrations of three different classes of antibiotics (inhibitors of protein synthesis) in the classical double-layer agar (DLA) method was investigated. The β-lactam and quinolone antibiotics commonly employed in earlier studies for increasing the plaque size did not show any significant effect on the plaque size of isolated MR-5 phage. Linezolid (oxazolidinone class), tetracycline, and ketolide antibiotics brought significant enhancements (3 times the original size) in the plaque size of MR-5 phage. Prior treatment with these antibiotics resulted in significant reductions in the time of adsorption and the latent period of MR-5 phage. To rule out whether the action of linezolid (which brought the maximum increase in plaque size) was specific for a single phage only, its effect on the plaque size of seven other S. aureus-specific phages was also assessed. Significant enhancements in the plaque size of these phages were observed. These results indicate that this modification can therefore safely be incorporated in the traditional DLA overlay method to search for new MRSA-virulent phages.

Bacteriophages with the ability to degrade uropathogenic Escherichia coli biofilms

Escherichia coli-associated urinary tract infections (UTIs) are among the most common bacterial infections in humans. UTIs are usually managed with antibiotic therapy, but over the years, antibiotic-resistant strains of uropathogenic E. coli (UPEC) have emerged. The formation of biofilms further complicates the treatment of these infections by making them resistant to killing by the host immune system as well as by antibiotics. This has encouraged research into therapy using bacteriophages (phages) as a supplement or substitute for antibiotics. In this study we characterized 253 UPEC in terms of their biofilm-forming capabilities, serotype, and antimicrobial resistance. Three phages were then isolated (vB_EcoP_ACG-C91, vB_EcoM_ACG-C40 and vB_EcoS_ACG-M12) which were able to lyse 80.5% of a subset (42) of the UPEC strains able to form biofilms. Correlation was established between phage sensitivity and specific serotypes of the UPEC strains. The phages' genome sequences were determined and resulted in classification of vB_EcoP_ACG-C91 as a SP6likevirus, vB_EcoM_ACG-C40 as a T4likevirus and vB_EcoS_ACG-M12 as T1likevirus. We assessed the ability of the three phages to eradicate the established biofilm of one of the UPEC strains used in the study. All phages significantly reduced the biofilm within 2-12 h of incubation.

Characterization and comparative genomic analysis of a novel bacteriophage, SFP10, simultaneously inhibiting both Salmonella enterica and Escherichia coli O157:H7

Salmonella enterica and Escherichia coli O157:H7 are major food-borne pathogens causing serious illness. Phage SFP10, which revealed effective infection of both S. enterica and E. coli O157:H7, was isolated and characterized. SFP10 contains a 158-kb double-stranded DNA genome belonging to the Vi01 phage-like family Myoviridae. In vitro adsorption assays showed that the adsorption constant rates to both Salmonella enterica serovar Typhimurium and E. coli O157:H7 were 2.50 × 10⁻⁸ ml/min and 1.91 × 10⁻⁸ ml/min, respectively. One-step growth analysis revealed that SFP10 has a shorter latent period (25 min) and a larger burst size (>200 PFU) than ordinary Myoviridae phages, suggesting effective host infection and lytic activity. However, differential development of resistance to SFP10 in S. Typhimurium and E. coli O157:H7 was observed; bacteriophage-insensitive mutant (BIM) frequencies of 1.19 × 10⁻² CFU/ml for S. Typhimurium and 4.58 × 10⁻⁵ CFU/ml for E. coli O157:H7 were found, indicating that SFP10 should be active and stable for control of E. coli O157:H7 with minimal emergence of SFP10-resistant pathogens but may not be for S. Typhimurium. Specific mutation of rfaL in S. Typhimurium and E. coli O157:H7 revealed the O antigen as an SFP10 receptor for both bacteria. Genome sequence analysis of SFP10 and its comparative analysis with homologous Salmonella Vi01 and Shigella phiSboM-AG3 phages revealed that their tail fiber and tail spike genes share low sequence identity, implying that the genes are major host specificity determinants. This is the first report identifying specific infection and inhibition of Salmonella Typhimurium and E. coli O157:H7 by a single bacteriophage.