In vitro and in vivo bacteriolytic activities of Escherichia coli phages: implications for phage therapy

Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh

The genomic diversity of 99 T4-like coliphages was investigated by sequencing an equimolar mixture with Illumina technology and screening them against different databases for horizontal gene transfer and undesired genes. A 9-phage cocktail was given to 15 healthy adults from Bangladesh at a dose of 3×10(9) and 3×10(7) plaque-forming units and placebo respectively. Phages were detected in 64% of the stool samples when subjects were treated with higher titer phage, compared to 30% and 28% with lower-titer phage and placebo, respectively. No Escherichia coli was present in initial stool samples, and no amplification of phage was observed. One percent of the administered oral phage was recovered from the feces. No adverse events were observed by self-report, clinical examination, or from laboratory tests for liver, kidney, and hematology function. No impact of oral phage was seen on the fecal microbiota composition with respect to bacterial 16S rRNA from stool.

Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine

In vivo bacteriophage targeting of enteroaggregative Escherichia coli (EAEC) was assessed using a mouse intestinal model of colonization with the O104:H4 55989Str strain and a cocktail of three virulent bacteriophages. The colonization model was shown to mimic asymptomatic intestinal carriage found in humans. The addition of the cocktail to drinking water for 24 h strongly decreased ileal and weakly decreased fecal 55989Str concentrations in a dose-dependent manner. These decreases in ileal and fecal bacterial concentrations were only transient, since 55989Str concentrations returned to their original levels 3 days later. These transient decreases were independent of the mouse microbiota, as similar results were obtained with axenic mice. We studied the infectivity of each bacteriophage in the ileal and fecal environments and found that 55989Str bacteria in the mouse ileum were permissive to all three bacteriophages, whereas those in the feces were permissive to only one bacteriophage. Our results provide the first demonstration that bacterial permissivity to infection with virulent bacteriophages is not uniform throughout the gut; this highlights the need for a detailed characterization of the interactions between bacteria and bacteriophages in vivo for the further development of phage therapy targeting intestinal pathogens found in the gut of asymptomatic human carriers.

Bacteriophage vB_EcoM_FV3: a new member of "rV5-like viruses"

A proposed new genus of the family Myoviridae, "rV5-like viruses", includes two lytic bacteriophages: Escherichia coli O157: H7-specific bacteriophage rV5 and Salmonella phage PVP-SE1. Here, we present basic properties and genomic characterization of a novel rV5-like phage, vB_EcoM_FV3, which infects E. coli K-12-derived laboratory strains and replicates at high temperature (up to 47 °C). The 136,947-bp genome of vB_EcoM_FV3 contains 218 open reading frames and encodes 5 tRNAs. The genomic content and organization of vB_EcoM_FV3 is more similar to that of rV5 than to PVP-SE1, but all three phages share similar morphological characteristics and form a homogeneous phage group.

Going viral: next-generation sequencing applied to phage populations in the human gut

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.

Modulation of antibiotic resistance in bacterial pathogens by oleanolic acid and ursolic acid

Antibiotic resistance among bacterial pathogens is a serious problem for human and veterinary medicine, which necessitates the development of novel therapeutics and antimicrobial strategies. Some plant-derived compounds, e.g. pentacyclic triterpenoids such as oleanolic acid (OA) and ursolic acid (UA), have potential as a new class of antibacterial agents as they are active against many bacterial species, both Gram-positive and Gram-negative, and specifically target the cell envelope. The aim of the present study was to investigate the influence of OA and UA on the susceptibility of four bacterial pathogens (Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus and Staphylococcus epidermidis) to the β-lactam antibiotics ampicillin (Ap) and oxacillin (Ox). Antimicrobial assays were conducted with bacteria growing in liquid suspension cultures (planktonic cells) or as biofilms. Using FICI value estimation and the time-kill method it was demonstrated that in some combinations, the tested compounds acted in synergy to lower the susceptibility of S. aureus, S. epidermidis and L. monocytogenes to ampicillin and oxacillin, but no synergy was observed for P. aeruginosa. These results indicate that OA and UA may be useful when administered in combination with β-lactam antibiotics to combat bacterial infections caused by some Gram-positive pathogens.

Efficacy of bacteriophage therapy in experimental sepsis and meningitis caused by a clone O25b:H4-ST131 Escherichia coli strain producing CTX-M-15

We evaluated phage therapy in experimental infections due to S242, a fatal neonatal meningitis Escherichia coli strain belonging to the worldwide-distributed O25b:H4-ST131 clone that produces extended-spectrum beta-lactamase CTX-M-15. A lytic phage, EC200(PP), active against S242, was isolated from environmental water. After determining in vitro and ex vivo stabilities and pharmacokinetic properties of EC200(PP) in rat pups, we assessed the therapeutic efficacy of a single dose of 10(8) PFU using models of sepsis and meningitis in which fatality was 100%. EC200(PP) was partially neutralized by human serum. In contrast to the high concentration of phage in the spleen and the kidney, low titers in urine and the central nervous system were observed. Nevertheless, in the sepsis model, EC200(PP) administered 7 h or 24 h postinfection resulted in 100% and 50% pup survival, respectively. In the meningitis model, EC200(PP) administered 1 h or 7 h postinfection rescued 100% of the animals. The most delayed treatments were associated with the selection of phage-resistant S242 mutants. However, a representative mutant was highly sensitive to killing serum activity and avirulent in an animal model. EC200(PP) is a potential therapeutic agent for sepsis and meningitis caused by the widespread E. coli O25:H4-ST131 multidrug-resistant clone.

Introducing yesterday’s phage therapy in today’s medicine

The worldwide emergence of ‘superbugs’ and a dry antibiotic pipeline threaten modern society with a return to the preantibiotic era. Phages – the viruses of bacteria – could help fight antibiotic-resistant bacteria. Phage therapy was first attempted in 1919 by Felix d’Herelle and was commercially developed in the 1930s before being replaced by antibiotics in most of the western world. The current antibiotic crisis fueled a worldwide renaissance of phage therapy. The inherent potential of phages as natural biological bacterium controllers can only be put to use if the potential of the coevolutionary aspect of the couplet phage–bacterium is fully acknowledged and understood, including potential negative consequences. We must learn from past mistakes and set up credible studies to gather the urgently required data with regard to the efficacy of phage therapy and the evolutionary consequences of its (unlimited) use. Unfortunately, our current pharmaceutical economic model, implying costly and time-consuming medicinal product development and marketing, and requiring strong intellectual property protection, is not compatible with traditional sustainable phage therapy. A specific framework with realistic production and documentation requirements, which allows a timely (rapid) supply of safe, tailor-made, natural bacteriophages to patients, should be developed. Ultimately, economic models should be radically reshaped to cater for more sustainable approaches such as phage therapy. This is one of the biggest challenges faced by modern medicine and society as a whole.

Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice

Bacteriophages have been known to be present in the gut for many years, but studies of relationships between these viruses and their hosts in the intestine are still in their infancy. We isolated three bacteriophages specific for an enteroaggregative O104:H4 Escherichia coli (EAEC) strain responsible for diarrhoeal diseases in humans. We studied the replication of these bacteriophages in vitro and in vivo in a mouse model of gut colonization. Each bacteriophage was able to replicate in vitro in both aerobic and anaerobic conditions. Each bacteriophage individually reduced biofilms formed on plastic pegs and a cocktail of the three bacteriophages was found to be more efficient. The cocktail was also able to infect bacterial aggregates formed on the surface of epithelial cells. In the mouse intestine, bacteriophages replicated for at least 3 weeks, provided the host was present, with no change in host levels in the faeces. This model of stable and continuous viral replication provides opportunities for studying the long-term coevolution of virulent bacteriophages with their hosts within a mammalian polymicrobial ecosystem.

Characterization of induced Staphylococcus aureus bacteriophage SAP-26 and its anti-biofilm activity with rifampicin

Lytic bacteriophages (phages) have been investigated as treatments for bacterial infectious diseases. An induced phage, SAP-26, was isolated from a clinical isolate of Staphylococcus aureus. It belongs to the family Siphoviridae and its genome consists of double-stranded 41,207 bp DNA coding for 63 open reading frames. The phage SAP-26 showed a wide spectrum of lytic activity against both methicillin-resistant S. aureus and methicillin-susceptible S.aureus. Furthermore, combined treatment with a phage and antimicrobial agents showed a strong biofilm removal effect which induced structural changes in the biofilm matrix and a substantial decrease in the number of bacteria. Such a broad host range in S. aureus and biofilm removal activity of the phage SAP-26 suggests the possibility of its use as a therapeutic phage in combination with appropriate antimicrobial agent(s). Among the three antimicrobial agents combined with phage, the combination of rifampicin showed the best biofilm removal effect. To the authors' knowledge, this study showed for the first time that S. aureus biofilm could be efficiently eradicated with the mixture of phage and an antimicrobial agent, especially rifampicin.

Staphylococcus epidermidis bacteriophages from the anterior nares of humans

The role of virulent bacteriophages in staphylococcal colonization of the human anterior nares is not known. This report of lytic bacteriophages against Staphylococcus epidermidis in the anterior nares of 5.5% of human subjects (n = 202) suggests their potential role in modulating staphylococcal colonization in this ecological niche.

Recent advances in bacteriophage therapy: how delivery routes, formulation, concentration and timing influence the success of phage therapy

Objectives

Bacteriophages are bacteria-specific viruses that infect and, in the case of obligately lytic phages, destroy their host bacteria. Phage therapy has been used therapeutically to combat bacterial infections since their discovery. This paper reviewed recent in-vivo phage therapy studies, with a distinct focus on the effect of delivery routes, phage concentration and timing of administration on the success of the therapy.

Key findings

It was found that the most successful route of administration for the treatment of systemic infections was via the parenteral route. Oral delivery is mainly used to treat gastrointestinal infections. However, in some cases phages can also reach the systemic circulation. Local delivery (skin, ears, teeth) has proved extremely successful in the treatment of topical infections, as has the inhalation of phages for the treatment of lung infections. The ability of phages to prevent biofilm formation on medical devices has received much attention, mainly in the area of catheter coatings. This review also highlights areas in which phage therapy needs substantial development. Many papers were lacking in formulation details, with crude phage stocks being used in most cases. No phage stability data were included in any of the papers.

Summary

The review concluded that although phage therapy is an excellent alternative for the treatment of bacterial infections, optimisation of formulations and long-term stability data is required before it can be widely used within a clinical setting.

Prevalence of Staphylococcus aureus and lack of its lytic bacteriophages in the anterior nares of patients and healthcare workers at a rural clinic

BACKGROUND

Nearly 30% of people in the United States are colonized with Staphylococcus aureus and 1% to 2% with methicillin-resistant Staphylococcus aureus (MRSA) in the anterior nares. However, it is not known if lytic bacteriophages against S. aureus are present in the anterior nares, and if they are, what the prevalence rate is, or if they interfere with S. aureus colonization. The aim of this study was to determine the prevalence of nasal carriage of S. aureus and MRSA and to screen for S. aureus lytic bacteriophages in healthcare environment workers and ambulatory patients.

METHODS

We enrolled 202 individuals into this study. The anterior nares were swabbed to isolate S. aureus, MRSA, and any lytic S. aureus bacteriophages that may be present. Putative S. aureus colonies on blood agar plates were identified using gram stain, catalase and coagulase tests, and confirmed by S. aureus-specific PCR. Presence of staphylococcal lytic bacteriophages were screened by a plaque assay technique using a methicillin-sensitive reference S. aureus strain ATCC 29213.

RESULTS

Of the 49 (24%) individuals who screened positive for S. aureus, two (1%) were positive for MRSA. None of the samples were positive for lytic bacteriophages against S. aureus. Subgroup analysis found no significant difference in the prevalence of S. aureus in the house staff compared to other healthcare environment workers or ambulatory patients of the clinic. Similarly, no significant difference in colonization was noted across the population with respect to age, sex, body mass index, or presence of diabetes mellitus.

CONCLUSION

The prevalence of nasal carriage of S. aureus and MRSA in the studied population was 24% and 1%, respectively, similar to the rate of prevalence in the United States. The study also showed that the anterior nares do not seem to harbor lytic bacteriophages against S. aureus.

Isolation and selection of coliphages as potential biocontrol agents of enterohemorrhagic and Shiga toxin-producing E. coli (EHEC and STEC) in cattle

AIMS

To isolate, characterize and select phages as potential biocontrol agents of enterohemorrhagic and Shiga toxin-producing Escherichia coli (EHEC and STEC) in cattle.

METHODS AND RESULTS

Sixteen STEC and EHEC coliphages were isolated from bovine minced meat and stool samples and characterized with respect to their host range against STEC, EHEC and other Gram-negative pathogens; their morphology by electron microscopy; the presence of the stx1, stx2 and cI genes by means of PCR; RAPD and rep-PCR profiles; plaque formation; and acid resistance. Six isolates belonged to the Myoviridae and 10 to the Podoviridae families. The phages negative for stx and cI that formed large, well-defined plaques were all isolated using EHEC O157:H7 as host. Among them, only CA911 was a myophage and, together with CA933P, had the broadest host range for STEC and EHEC; the latter phage also infected Shigella and Pseudomonas. Isolates CA911, MFA933P and MFA45D differed in particle morphology and amplification patterns by RAPD and rep-PCR and showed the highest acidity tolerance.

CONCLUSIONS

Myophage CA911 and podophages CA933P, MFA933P and MFA45D were chosen as the best candidates for biocontrol of STEC and EHEC in cattle.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work employs steps for a rational selection and characterization of bacteriophages as therapeutic agents. This report constitutes the first documentation of STEC and EHEC phages isolated in Argentina and proposes for the first time the use of rep-PCR as a complement of RAPD on DNA fingerprinting of phages.

Decreasing Enterobacter sakazakii (Cronobacter spp.) food contamination level with bacteriophages: prospects and problems

Enterobacter sakazakii (Cronobacter spp.) is an opportunistic pathogen, which can cause rare, but life-threatening infections in neonates and infants through feeding of a contaminated milk formula. We isolated 67 phages from environmental samples and tested their lytic host range on a representative collection of 40 E. sakazakii strains. A cocktail of five phages prevented the outgrowth of 35 out of 40 test strains in artificially contaminated infant formula. Two E. sakazakii phages represented prolate head Myoviridae. Molecular tests identified them as close relatives of Escherichia coli phage T4. The remaining three phages represented isometric head Myoviridae with large genome size of 140 and 200 kb, respectively, which belonged to two different DNA hybridization groups. A high dose of 10(8) pfu ml(-1) of phage could effectively sterilize a broth contaminated with both high and low pathogen counts (10(6) and 10(2) cfu ml(-1)). In contrast, broth inoculated with 10(4) phage and 10(2) bacteria per ml first showed normal bacterial growth until reaching a cell titre of 10(5) cfu ml(-1). Only when crossing this threshold, phage replication started, but it could not reduce the contamination level below 100 cfu ml(-1). Phages could be produced with titres of 10(10) pfu ml(-1) in broth culture, but they were not stable upon freeze-drying. Addition of trehalose or milk formula stabilized the phage preparation, which then showed excellent storage stability even at elevated temperature.

Bacteriophages as twenty-first century antibacterial tools for food and medicine

Antibiotic-resistant bacteria are an increasing source of concern in all environments in which these drugs have been used. More stringent regulations have led to a slow but sure decrease in antibiotic use in the food industry worldwide, but have also stimulated the search for alternative antibacterial agents. In medicine, the number of people infected with pan-resistant bacteria is driving research to develop new treatments. Within these contexts, studies on the use of bacteriophages in both medicine and the food industry have recently flourished. This renewed interest has coincided with the demonstration that these viruses are involved in geochemical cycles, revolutionizing our vision of their ecological role on our planet. Bacteriophages have co-evolved with bacteria for billions of years and retain the ability to infect bacteria efficiently. They are undoubtedly one of the best potential sources of new solutions for the management of undesirable bacteria.

Phage treatment of human infections

Phages as bactericidal agents have been employed for 90 years as a means of treating bacterial infections in humans as well as other species, a process known as phage therapy. In this review we explore both the early historical and more modern use of phages to treat human infections. We discuss in particular the little-reviewed French early work, along with the Polish, US, Georgian and Russian historical experiences. We also cover other, more modern examples of phage therapy of humans as differentiated in terms of disease. In addition, we provide discussions of phage safety, other aspects of phage therapy pharmacology, and the idea of phage use as probiotics.

Characterization of a T5-like coliphage, SPC35, and differential development of resistance to SPC35 in Salmonella enterica serovar typhimurium and Escherichia coli

The potential of bacteriophage as an alternative biocontrol agent has recently been revisited due to the widespread occurrence of antibiotic-resistant bacteria. We isolated a virulent bacteriophage, SPC35, that can infect both Salmonella enterica serovar Typhimurium and Escherichia coli. Morphological analysis by transmission electron microscopy and analysis of its 118,351-bp genome revealed that SPC35 is a T5 group phage belonging to the family Siphoviridae. BtuB, the outer membrane protein for vitamin B(12) uptake, was found to be a host receptor for SPC35. Interestingly, resistant mutants of both E. coli and S. Typhimurium developed faster than our expectation when the cultures were infected with SPC35. Investigation of the btuB gene revealed that it was disrupted by the IS2 insertion sequence element in most of the resistant E. coli isolates. In contrast, we could not detect any btuB gene mutations in the resistant S. Typhimurium isolates; these isolates easily regained sensitivity to SPC35 in its absence, suggesting phase-variable phage resistance/sensitivity. These results indicate that a cocktail of phages that target different receptors on the pathogen should be more effective for successful biocontrol.

Experimental phage therapy in treating Klebsiella pneumoniae-mediated liver abscesses and bacteremia in mice

Intragastric inoculation of mice with Klebsiella pneumoniae can cause liver abscesses, necrosis of liver tissues, and bacteremia. A newly isolated phage (φNK5) with lytic activity for K. pneumoniae was used to treat K. pneumoniae infection in an intragastric model. Both intraperitoneal and intragastric administration of a single dose of φNK5 lower than 2 × 10(8) PFU at 30 min after K. pneumoniae infection was able to protect mice from death in a dose-dependent manner, but the efficacy achieved with a low dose of φNK5 by intragastric treatment provided the more significant protection. Phage φNK5 administered as late as 24 h after K. pneumoniae inoculation was still protective, while intraperitoneal treatment with phage was more efficient than intragastric treatment as a result of the dissemination of bacteria into the circulation at 24 h postinfection. Surveys of bacterial counts for mice treated with φNK5 by the intraperitoneal route revealed that the bacteria were eliminated effectively from both blood and liver tissue. K. pneumoniae-induced liver injury, such as liver necrosis, as well as blood levels of aspartate aminotransferase and alanine aminotransferase and inflammatory cytokine production, was significantly inhibited by φNK5 treatment. These data suggest that a low dose of φNK5 is a potential therapeutic agent for K. pneumoniae-induced liver infection.

Antibacterial activity of oleanolic and ursolic acids and their derivatives

Bacterial resistance to antibiotics is increasing at an alarming rate and many commonly used antibiotics are no longer effective. Thus, there is considerable interest in investigating novel antibacterial compounds, such as the plant-derived pentacyclic triterpenoids, including oleanolic acid (OA), ursolic acid (UA) and their derivatives. These compounds can be isolated from many medicinal and crop plants and their antibacterial, antiviral, antiulcer and anti-inflammatory effects are well documented. OA and UA are active against many bacterial species, particularly Gram-positive species, including mycobacteria. They inhibit bacterial growth and survival, and the spectrum of minimal inhibitory concentration (MIC) values is very broad. In addition, OA, UA and their derivatives display potent antimutagenic activity. Studies to identify the cellular targets and molecular mechanisms of OA and UA action were initiated a few years ago and it has already been demonstrated that both acids influence bacterial gene expression, the formation and maintenance of biofilms, cell autolysis and peptidoglycan turnover. Before these compounds can be used clinically as antimicrobial agents, further extensive studies are required to determine their cytotoxicity and the optimum mode of their application.

Phenotypic characterization and genomic analysis of the Shigella sonnei bacteriophage SP18

A novel bacteriophage that infects Shigella sonnei was isolated from the Gap River in Korea, and its phenotypic and genomic characteristics were investigated. The virus, called SP18, showed morphology characteristic of the family Myoviridae, and phylogenetic analysis of major capsid gene (gp23) sequences classified it as a T4-like phage. Based on host spectrum analysis, it is lytic to S. sonnei, but not to Shigella flexneri, Shigella boydii or members of the genera Escherichia and Salmonella. Pyrosequencing of the SP18 bacteriophage genome revealed a 170-kb length sequence. In total, 286 ORFs and 3 tRNA genes were identified, and 259 ORFs showed similarity (BLASTP e-value<0.001) to genes of other bacteriophages. The results from comparative genomic analysis indicated that the enterophage JS98, isolated from human stool, is the closest relative of SP18. Based on phylogenetic analysis of gp23 protein-coding sequences, dot plot comparison and BLASTP analysis of genomes, SP18 and JS98 appear to be closely related to T4-even phages. However, several insertions, deletions, and duplications indicate differences between SP18 and JS98. Comparison of duplicated gp24 genes and the soc gene showed that duplication events are responsible for the differentiation and evolution of T4-like bacteriophages.

Ecological basis for rational phage therapy

Understanding the mutual interactions of bacterial and phage populations in the environment of a human or animal body is essential in any attempt to influence these complex processes, particularly for rational phage therapy. Current knowledge on the impact of naturally occurring bacteriophages on the populations of their host bacteria, and their role in the homeostasis maintenance of a macro host, is still sketchy. The existing data suggest that different mechanisms stabilize phage-bacteria coexistence in different animal species or different body sites. The defining set of parameters governing phage infection includes specific physical, chemical, and biological conditions, such as pH, nutrient densities, host prevalence, relation to mucosa and other surfaces, the presence of phage inhibiting substances, etc. Phage therapy is also an ecological process that always implies three components that form a complex pattern of interactions: populations of the pathogen, the bacteriophages used as antibacterial agents, and the macroorganism. We present a review of contemporary data on natural bacteriophages occuring in human- and animal-body associated microbial communities, and analyze ecological and physiological considerations that determine the success of phage therapy in mammals.

In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli

The gut transit of T4 phages was studied in axenic mice mono-colonized with the non-pathogenic Escherichia coli strain K-12. Thirty minutes, 1 and 2 h after phage feeding, T4 phage had reached the jejunum, ileum and cecum, respectively. Phage was found in the lumen and was also associated with the mucosa. One day later no phage was detected in the feces. Compared to germ-free control animals, oral T4 phage led to a 300-fold higher fecal phage titer in mice mono-colonized with E. coli strain WG-5. The in vivo T4 phage replication was transient and reached peak fecal titers about 8 h after oral phage application followed by a rapid titer decrease over two days. Similar data were obtained in mice colonized with E. coli strain Nissle. In contrast, orally applied T7 phage experienced a massive and sustained in vivo replication in mice mono-colonized with E. coli strain WG-5 irrespective whether phage or E. coli host was applied first. T7 phage replication occurred mainly in the large intestine. High titers of T7 phage and high E. coli cell counts coexisted in the feces. The observation of only 20% T7 phage-resistant fecal E. coli colonies suggests a refuge model where phage-sensitive E. coli cells are physically or physiologically protected from phage infection in the gut. The difference between T7 and T4 with respect to gut replication might partly reflect their distinct in vitro capacity to replicate on slowly growing cells.

Bacteriophage and their lysins for elimination of infectious bacteria

When phages were originally identified, the possibility of using them as antibacterial agents against pathogens was immediately recognized and put into practise based on the knowledge available at the time. However, with the advent of antibiotics a decline in the use of phage as therapeutics followed. Phages did, however, become more useful in the study of fundamental aspects of molecular biology and in the diagnostic laboratory for the identification of pathogenic bacteria. More recently, the original application of phage as therapeutics to treat human and animal infections has been rekindled, particularly in an era where antibiotic resistance has become so problematic/commonplace. Phage lysins have also been studied and utilized in their own right as potential therapeutics for the treatment of bacterial infections. Indeed the past decade has seen a considerable amount of research worldwide focused on the engineering of phages as antibacterial agents in a wide range of applications. Furthermore, the US Food and Drug Administration and/or the US Department of Agriculture have recently approved commercial phage preparations to prevent bacterial contamination of livestock, food crops, meat and other foods. Such developments have prompted this review into the status of phage research as it pertains to the control of infectious bacteria.

Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials

We describe the small-scale, laboratory-based, production and quality control of a cocktail, consisting of exclusively lytic bacteriophages, designed for the treatment of Pseudomonas aeruginosa and Staphylococcus aureus infections in burn wound patients. Based on succesive selection rounds three bacteriophages were retained from an initial pool of 82 P. aeruginosa and 8 S. aureus bacteriophages, specific for prevalent P. aeruginosa and S. aureus strains in the Burn Centre of the Queen Astrid Military Hospital in Brussels, Belgium. This cocktail, consisting of P. aeruginosa phages 14/1 (Myoviridae) and PNM (Podoviridae) and S. aureus phage ISP (Myoviridae) was produced and purified of endotoxin. Quality control included Stability (shelf life), determination of pyrogenicity, sterility and cytotoxicity, confirmation of the absence of temperate bacteriophages and transmission electron microscopy-based confirmation of the presence of the expected virion morphologic particles as well as of their specific interaction with the target bacteria. Bacteriophage genome and proteome analysis confirmed the lytic nature of the bacteriophages, the absence of toxin-coding genes and showed that the selected phages 14/1, PNM and ISP are close relatives of respectively F8, φKMV and phage G1. The bacteriophage cocktail is currently being evaluated in a pilot clinical study cleared by a leading Medical Ethical Committee.

Using bacteriophages to modulate Salmonella colonization of the chicken's gastrointestinal tract: lessons learned from in silico and in vivo modeling

An increasing prevalence of antibiotic-resistant foodborne infections has resulted in considerable concern about how antimicrobials are used in meat and poultry production. Because many foodborne bacterial pathogens are commonly found among the intestinal bacterial community of poultry, new methods of prevention are being considered. Bacteriophage therapy is one such alternative method that has not been well developed in the United States; however, bacteriophages have been shown to be effective in modulating bacterial numbers in acute infection models. In this study we evaluated whether bacteriophages could theoretically reduce Salmonella colonization of the gastrointestinal tract of chickens. Using computer simulations, we studied bacteriophage and bacterial replication dynamics in a mathematical model based on parameters expected to occur in the intestinal environment. In addition, we performed in vivo experiments by administering SP6 bacteriophage and Salmonella orally to young chickens and compared the levels of phage and Salmonella shed in the feces to the models of replication dynamics. SP6 is an ideal candidate bacteriophage because its genome and target receptor are known. Although SP6 did not reduce the levels of Salmonella shed by treated birds, most of the isolates recovered from treated birds were not resistant to the bacteriophage. These results suggest that phage resistance may not be the primary limiting parameter of phage prophylaxis for modulating colonization of the intestine. Our findings that this phage could be replicated in vivo supports the attractiveness of phage use, because unlike antibiotics they may be amplified in vivo if given a suitable host on which to replicate. If successful, this approach to modulating bacterial colonization of the intestinal tract could have a tremendous effect on the meat and poultry industry by reducing the use of antimicrobial drugs and increasing the use of biological therapeutics.

The bacteriophages in human- and animal body-associated microbial communities

Felix d'Herelle first demonstrated, about 90 years ago, the presence of bacteriophages in human and animal body microbiota. Our comprehension of the impact of naturally occurring bacteriophages on symbiotic bacteria, and of their role in general homeostasis of macro-organism, nevertheless remains quite fragmentary. Analysis of data in various human- and animal body-associated microbial systems on phage occurrence, diversity, host specificity and dynamics, as well as host occurrence, specificity and dynamics, suggests that mechanisms which stabilize phage-bacteria coexistence are not identical for either different species or different body sites. Regulation by phage infection instead probably depends on specific physical, chemical and biological conditions, e.g. pH, nutrient densities, host prevalence, relation to mucosa and other surfaces and presence of phage inhibiting substances. In some animal species intestinal bacteriophages thus appear to exert significant selective pressure over at least some resident bacterial populations, resulting in phages playing important roles in the self-regulation of these microbial systems while at the same time contributing to maintenance of bacterial diversity (i.e. 'killing the winner'). Emerging data additionally suggest that bacteriophage particles could play roles in regulating the immune reactions of the macro-organism. Alternatively, for many systems links between phages and community characteristics have not been established.

Microencapsulation of bacteriophage felix O1 into chitosan-alginate microspheres for oral delivery

This paper reports the development of microencapsulated bacteriophage Felix O1 for oral delivery using a chitosan-alginate-CaCl(2) system. In vitro studies were used to determine the effects of simulated gastric fluid (SGF) and bile salts on the viability of free and encapsulated phage. Free phage Felix O1 was found to be extremely sensitive to acidic environments and was not detectable after a 5-min exposure to pHs below 3.7. In contrast, the number of microencapsulated phage decreased by 0.67 log units only, even at pH 2.4, for the same period of incubation. The viable count of microencapsulated phage decreased only 2.58 log units during a 1-h exposure to SGF with pepsin at pH 2.4. After 3 h of incubation in 1 and 2% bile solutions, the free phage count decreased by 1.29 and 1.67 log units, respectively, while the viability of encapsulated phage was fully maintained. Encapsulated phage was completely released from the microspheres upon exposure to simulated intestinal fluid (pH 6.8) within 6 h. The encapsulated phage in wet microspheres retained full viability when stored at 4 degrees C for the duration of the testing period (6 weeks). With the use of trehalose as a stabilizing agent, the microencapsulated phage in dried form had a 12.6% survival rate after storage for 6 weeks. The current encapsulation technique enables a large proportion of bacteriophage Felix O1 to remain bioactive in a simulated gastrointestinal tract environment, which indicates that these microspheres may facilitate delivery of therapeutic phage to the gut.

Comparison of fecal versus rectoanal mucosal swab sampling for detecting Escherichia coli O157:H7 in experimentally inoculated cattle used in assessing bacteriophage as a mitigation strategy

This study was conducted to compare fecal grab (FEC) and rectoanal mucosal swab (RAMS) techniques as sampling methods for surveillance of Escherichia coli O157:H7 in conjunction with administration of a mitigation therapy. The study was nested within a larger experiment that investigated bacteriophage as a preharvest strategy for controlling E. coli O157:H7 in feedlot steers. Samples (FEC and RAMS) were collected from 16 of the 32 feedlot steers (control and oral bacteriophage treatment; n = 8) involved in the mitigation study. All steers had been inoculated on day 0 with 10(10) CFU of nalidixic acid-resistant E. coli O157:H7, and samples were collected on 16 occasions over the next 83 days. FEC samples were assessed by direct plating of serial dilutions in PBS, plus a 6-h enrichment and immunomagnetic separation when E. coli O157:H7 concentrations were below limits detectable by direct plating (i.e., <1 log CFU/g). All RAMS samples were assessed by enrichment and immunomagnetic separation. E. coli O157:H7 was detected more frequently (P < 0.01) by FEC than by RAMS. Overall, 213 of 256 samples were positive either by FEC or RAMS. Discrepancies between sampling techniques were observed in 63 of the 213 positive samples; FEC missed 11 samples that were positive by RAMS, and RAMS missed 52 of those positive by FEC (miss rates of 5.16 and 24.41%, respectively). Kappa values (0.36 to 0.45) indicated only fair to moderate agreement between FEC and RAMS results, but this agreement was higher at lower levels of E. coli O157:H7 shedding (later in the experimental period). Selection of sampling procedure could significantly influence the assessed merit during testing of potential strategies for controlling E. coli O157:H7 on the farm.

Purification and concentration of bacteriophage T4 using monolithic chromatographic supports

Phages are gaining importance due to their wide usage. In this work strong anion exchange monolithic chromatographic column was used for single step phage purification. Most of the proteins and DNA were removed and recovery of approximately 70% of infective virus was reproducibly achieved. 30 ml of phage sample was purified in around 10 min.

European regulatory conundrum of phage therapy

The treatment of infectious diseases with antibiotics is becoming increasingly challenging. Very few new antimicrobials are in the pharmaceutical industry pipeline. One of the potential alternatives for antibiotics is phage therapy. Major obstacles for the clinical application of bacteriophages are a false perception of viruses as 'enemies of life' and the lack of a specific frame for phage therapy in the current Medicinal Product Regulation. Short-term borderline solutions under the responsibility of a Medical Ethical Committee and/or under the umbrella of the Declaration of Helsinki are emerging. As a long-term solution, however, we suggest the creation of a specific section for phage therapy under the Advanced Therapy Medicinal Product Regulation.

Bovine whey proteins inhibit the interaction of Staphylococcus aureus and bacteriophage K

AIMS

To understand the potential use of bacteriophage K to treat bovine Staphylococcus aureus mastitis, we studied the role of whey proteins in the inhibition of the phage-pathogen interaction in vitro.

METHODS AND RESULTS

The interaction of bacteriophage K and S. aureus strain Newbould 305 was studied in raw bovine whey and serum. Incubation of S. aureus with phage in whey showed that the bacteria are more resistant to phage lysis when grown in whey and also bovine serum. Whey collected from 23 animals showed a wide variation in the level of phage-binding inhibition. The role of the protein component of milk whey in this inhibition was established; treatment of the whey by heat, proteases and ultrafiltration removed the inhibitory activity. Brief exposure of S. aureus cells to whey, followed by resuspension in broth, also reduced phage binding. Microscopy showed the adhesion of extracellular material to the S. aureus cell surface following exposure to whey. Chromatographic fractionation of the whey demonstrated that the inhibitory proteins were present in the high molecular weight fraction.

CONCLUSIONS

The adsorption of whey proteins to the S. aureus cell surface appeared to inhibit phage attachment and thereby hindered lysis. The inhibitory whey proteins are of high molecular weight in their native form and may sterically block phage attachment sites on the cell surface.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings have implications for any future use of phage therapy in the treatment of mastitis, and other diseases, caused by S. aureus. This pathogen is predicted to be much more resistant to phage treatment in vivo than would be expected from in vitro broth culture experiments.

Biotechnological exploitation of bacteriophage research

The experimentally amenable nature of phage and their use in testing fundamental biological questions have meant that phage research has had a profound effect on modern molecular biology. Phage research has also fuelled multiple biotechnological developments. For example, phage display has recently been harnessed in a multidisciplinary approach for the generation of novel nanotechnologies. In addition, with the emerging threat of antibiotic-resistant bacterial infections, phage have begun to provide technologies to combat these problems. Finally, recent data acquired from genome sequencing and advances in phage biology research have aided the development of phage-derived bacterial detection and treatment strategies in addition to methods to control the detrimental effects of phage in industry. Here, we examine the promising uses of phage in these important areas of biotechnology.

The newly isolated lytic bacteriophages st104a and st104b are highly virulent against Salmonella enterica

AIMS

To screen Irish faecal samples from a variety of sources with a view to isolating novel anti-Salmonella phages and to subsequently evaluate their lytic capability.

METHODS AND RESULTS

Two novel anti-Salmonella phages st104a and st104b were isolated from a screening programme based on their lytic capability. The phages produced significantly larger plaques (2 mm) on the chosen indicator Salmonella enterica strain, DPC6046, when compared with the well-known control phage, Felix 01 (0.5 mm). Both phages st104a and st104b were found to have a broad host range within the Salm. enterica species. During in vitro trials, both phages (st104a and st104b) reduced Salm. enterica numbers more than 99% within 1 h. In vivo studies, involving the addition of the phage to porcine gastric juice (pH 2.5) demonstrated that phage st104a and phage Felix 01 were capable of surviving (10 and 30% survival respectively) the acidic conditions, unlike st104b, which was undetectable after 2 h exposure.

CONCLUSIONS

Two novel lytic anti-Salmonella phages were isolated and characterized.

SIGNIFICANCE AND IMPACT OF THE STUDY

With the exception of phage Felix 01, there has been relatively little phage therapy work performed using lytic Salmonella phage. In this study, the lytic phages st104a and st104b were isolated as a result of a faecal screening programme. Subsequently, phage st104a was found to have potential for biocontrol of Salm. enterica numbers if administered orally to pigs given their survival in porcine gastric juice, whereas, phage st104b may have potential in reducing cell numbers if applied by alternative approaches.

Phage Therapy - Everything Old is New Again

The study of bacterial viruses (bacteriophages or phages) proved pivotal in the nascence of the disciplines of molecular biology and microbial genetics, providing important information on the central processes of the bacterial cell (DNA replication, transcription and translation) and on how DNA can be transferred from one cell to another. As a result of the pioneering genetics studies and modern genomics, it is now known that phages have contributed to the evolution of the microbial cell and to its pathogenic potential. Because of their ability to transmit genes, phages have been exploited to develop cloning vector systems. They also provide a plethora of enzymes for the modern molecular biologist. Until the introduction of antibiotics, phages were used to treat bacterial infections (with variable success). Western science is now having to re-evaluate the application of phage therapy - a therapeutic modality that never went out of vogue in Eastern Europe - because of the emergence of an alarming number of antibiotic-resistant bacteria. The present article introduces the reader to phage biology, and the benefits and pitfalls of phage therapy in humans and animals.

Phage therapy: Facts and fiction

Recent examples of the use of bacteriophages in controlling bacterial infections are presented, some of which show therapeutic promise. The therapeutic use of bacteriophages, possibly in combination with antibiotics, may be a valuable approach. However, it is also quite clear that the safe and controlled use of phage therapy will require detailed information on the properties and behavior of specific phage-bacterium systems, both in vitro and especially in vivo. In vivo susceptibility of bacterial pathogens to bacteriophages is still largely poorly understood and future research on more phage-bacterium systems has to be undertaken to define the requirements for successful phage treatments.

Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases

Bacteriophage (phage) therapy involves using phages or their products as bioagents for the treatment or prophylaxis of bacterial infectious diseases. Much evidence in support of the effectiveness of phage therapy against bacterial infectious diseases has accumulated since 1980 from animal model studies conducted in Western countries. Reports indicate that appropriate administration of living phages can be used to treat lethal infectious diseases caused by gram-negative bacteria, such as Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, Vibrio vulnificus, and Salmonella spp., and gram-positive bacteria, such as Enterococcus faecium and Staphylococcus aureus. The phage display system and genetically modified nonreplicating phages are also effective for treatment of Helicobacter pylori and P. aeruginosa, respectively. In addition to phage particles per se, purified phage-encoded peptidoglycan hydrolase (lysin) is also reported to be effective for the treatment of bacterial infectious diseases caused by gram-positive bacteria such as Streptococcus pyogenes, S. pneumoniae, Bacillus anthracis, and group B streptococci. All phage lysins that have been studied to date exhibit immediate and strong bacteriolytic activity when applied exogenously. Furthermore, phage-coded inhibitors of peptidoglycan synthesis (protein antibiotics), search methods for novel antibacterial agents using phage genome informatics, and vaccines utilizing phages or their products are being developed. Phage therapy will compensate for unavoidable complications of chemotherapy such as the appearance of multidrug resistance or substituted microbism.

Bacteriophage P100 for control of Listeria monocytogenes in foods: Genome sequence, bioinformatic analyses, oral toxicity study, and application

Listeria monocytogenes is an opportunistic foodborne pathogen responsible for Listeriosis, a frequently fatal infection. This investigation represents a comprehensive approach to characterize and evaluate the broad host range, strictly virulent phage P100, which can infect and kill a majority of Listeria monocytogenes strains. First, the complete nucleotide sequence (131,384 basepairs) of the genome of P100 was determined, predicted to encode 174 gene products and 18 tRNAs. Bioinformatic analyses revealed that none of the putative phage proteins has any homologies to genes or proteins of Listeria or any other bacteria which are known or suspected to be toxins, pathogenicity factors, antibiotic resistance determinants, or any known allergens. Next, a repeated dose oral toxicity study in rats was conducted, which did not produce any abnormal histological changes, morbidity or mortality. Therefore, no indications for any potential risk associated with using P100 as a food additive were found. As proof of concept, and to determine the parameters for application of P100 to foods sensitive to Listeria contamination, surface-ripened red-smear soft cheese was produced. Cheeses were contaminated with low concentrations of L. monocytogenes at the beginning of the ripening period, and P100 was applied to the surface during the rind washings. Depending on the time points, frequency and dose of phage applications, we were able to obtain a significant reduction (at least 3.5 logs) or a complete eradication of Listeria viable counts, respectively. We found no evidence for phage resistance in the Listeria isolates recovered from samples. Taken together, our results indicate that P100 can provide an effective and safe measure for the control of Listeria contamination in foods and production equipment.

Phage therapy: the Escherichia coli experience

Phages have been proposed as natural antimicrobial agents to fight bacterial infections in humans, in animals or in crops of agricultural importance. Phages have also been discussed as hygiene measures in food production facilities and hospitals. These proposals have a long history, but are currently going through a kind of renaissance as documented by a spate of recent reviews. This review discusses the potential of phage therapy with a specific example, namely Escherichia coli.

Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy

To reveal the factors influencing architecture of protein-coding genes in staphylococcal phages, relative synonymous codon usage variation has been investigated in 920 protein-coding genes of 16 staphylococcal phages. As expected for AT rich genomes, there are predominantly A and T ending codons in all 16 phages. Both Nc plot and correspondence analysis on relative synonymous codon usage indicates that mutation bias influences codon usage variation in the 16 phages. Correspondence analysis also suggests that translational selection and gene length also influence the codon usage variation in the phages to some extent and codon usage in staphylococcal phages is phage-specific but not S. aureus-specific. Further analysis indicates that among 16 staphylococcal phages, 44AHJD, P68 and K may be extremely virulent in nature as most of their genes have high translation efficiency. If this is true, then above three phages may be useful for curing staphylococcal infections.

Human volunteers receiving Escherichia coli phage T4 orally: a safety test of phage therapy

Fifteen healthy adult volunteers received in their drinking water a lower Escherichia coli phage T4 dose (10(3) PFU/ml), a higher phage dose (10(5) PFU/ml), and placebo. Fecal coliphage was detected in a dose-dependent way in volunteers orally exposed to phage. All volunteers receiving the higher phage dose showed fecal phage 1 day after exposure; this prevalence was only 50% in subjects receiving the lower phage dose. No fecal phage was detectable a week after a 2-day course of oral phage application. Oral phage application did not cause a decrease in total fecal E. coli counts. In addition, no substantial phage T4 replication on the commensal E. coli population was observed. No adverse events related to phage application were reported. Serum transaminase levels remained in the normal range, and neither T4 phage nor T4-specific antibodies were observed in the serum of the subjects at the end of the study. This is, to our knowledge, the first safety test in the recent English literature which has measured the bioavailability of oral phage in humans and is thus a first step to the rational evaluation of phage therapy for diarrheal diseases.

Studies of the efficacy of Enterocoliticin, a phage-tail like bacteriocin, as antimicrobial agent against Yersinia enterocolitica serotype O3 in a cell culture system and in mice

The efficacy of enterocoliticin, a phage tail-like bacteriocin, as antimicrobial compound against infections with pathogenic Yersinia enterocolitica serotype O3 strains was assessed. In cell cultures, which were infected with the Y. enterocolitica strains 13 169 or 6471/76, bactericidal activity of enterocoliticin was found for bacteria adhering to the surface of eukaryotic cells, whereas bacteria, which had invaded the eukaryotic cells, were not accessible to the bacteriocin. The interaction of enterocoliticin with Y. enterocolitica was further examined in animals. Female BALB/c mice were experimentally infected with the two Y. enterocolitica strains and enterocoliticin was applied as antimicrobial compound by the oral route. Experimental variations concerning the infectious doses of the Y. enterocolitica strains and the time points of application of the bacteriocin were investigated. The increase of the Yersinia CFU titre in animals was retarded at time points shortly after the application of enterocoliticin indicating that the particles were effective on recently introduced Yersinia. The repeated application of enterocoliticin, however, did not prevent the colonization of the gastrointestinal tract by Yersinia.

The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages

Bacteriophages are the most abundant life forms in the biosphere. They play important roles in bacterial ecology, evolution, adaptation to new environments, and pathogenesis of human bacterial infections. Here, we report the complete genomic sequences, and predicted proteins of 27 bacteriophages of the Gram-positive bacterium Staphylococcus aureus. Comparative nucleotide and protein sequence analysis indicates that these phages are a remarkable source of untapped genetic diversity, encoding 2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated for structure or function, and 522 are proteins with no similarity to other phage or bacterial sequences. Based on their genome size, organization of their gene map and comparative nucleotide and protein sequence analysis, the S. aureus phages can be organized into three groups. Comparison of their gene maps reveals extensive genome mosaicism, hinting to a large reservoir of unidentified S. aureus phage genes. Among the phages in the largest size class (178-214 kbp) that we characterized is phage Twort, the first discovered bacteriophage (responsible for the Twort-D'Herelle effect). These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity.

Bacteriophages as biocontrol agents in food

Bacteriophages possess attributes that appear to be attractive to those searching for novel ways to control foodborne pathogens and spoilage organisms. These phages have a history of safe use, can be highly host specific, and replicate in the presence of a host. Campylobacter, Salmonella, and Listeria monocytogenes and various spoilage organisms have responded to phage control on some foods. However, the use of phages as biocontrol agents is complicated by factors such as an apparent requirement for a threshold level of host before replication can proceed and by suboptimal performance, at best, at temperatures beneath the optimum for the host. This review is a summary of the information on these issues and includes brief descriptions of alternative phage-based strategies for control of foodborne pathogens.

Isolation of Escherichia coli bacteriophages from the stool of pediatric diarrhea patients in Bangladesh

A 3-week coliphage survey was conducted in stool samples from 140 Bangladeshi children hospitalized with severe diarrhea. On the Escherichia coli indicator strain K803, all but one phage isolate had 170-kb genomes and the morphology of T4 phage. In spot tests, the individual T4-like phages infected up to 27 out of 40 diarrhea-associated E. coli, representing 22 O serotypes and various virulence factors; only five of them were not infected by any of these new phages. A combination of diagnostic PCR based on g32 (DNA binding) and g23 (major capsid protein) and Southern hybridization revealed that half were T-even phages sensu strictu, while the other half were pseudo-T-even or even more distantly related T4-like phages that failed to cross-hybridize with T4 or between each other. Nineteen percent of the acute stool samples yielded T4-like phages, and the prevalence was lower in convalescent stool samples. T4-like phages were also isolated from environmental and sewage water, but with low frequency and low titers. On the enteropathogenic E. coli strain O127:K63, 14% of the patients yielded phage, all of which were members of the phage family Siphoviridae with 50-kb genomes, showing the morphology of Jersey- and beta-4 like phages and narrow lytic patterns on E. coli O serotypes. Three siphovirus types could be differentiated by lack of cross-hybridization. Only a few stool samples were positive on both indicator strains. Phages with closely related restriction patterns and, in the case of T4-like phages, identical g23 gene sequences were isolated from different patients, suggesting epidemiological links between the patients.