Abstract
Antibiotics have been a panacea in animal husbandry as well as in human therapy for decades. The huge amount of antibiotics used to induce the growth and protect the health of farm animals has lead to the evolution of bacteria that are resistant to the drug’s effects. Today, many researchers are working with bacteriophages (phages) as an alternative to antibiotics in the control of pathogens for human therapy as well as prevention, biocontrol, and therapy in animal agriculture. Phage therapy and biocontrol have yet to fulfill their promise or potential, largely due to several key obstacles to their performance. Several suggestions are shared in order to point a direction for overcoming common obstacles in applied phage technology. The key to successful use of phages in modern scientific, farm, food processing and clinical applications is to understand the common obstacles as well as best practices and to develop answers that work in harmony with nature.
Similar content being viewed by others
Avoid common mistakes on your manuscript.
Introduction
Throughout much of the twentieth century, antibiotics have been a primary defense against bacterial disease. Unfortunately, inappropriate and excessive use of antibiotics in animal husbandry is threatening their efficacy.
This review of current issues and causality concerning antibiotic resistance, points out some opportunities and uses for bacteriophage treatment and biocontrol in farm-related applications where the majority of antibiotics at subtherapeutic levels have been used as well as in clinical settings and summarizes some of the stumbling blocks that have emerged during past experimentation. The published work to date on bacteriophage therapy is supplemented with some suggestions for future direction in the field. By following best practices for the use of bacteriophage in farming and processing applications as well as in a potential human therapy and rising from challenges already and yet to be encountered, modern science can avoid a repeat of the resistance phenomenon encountered with antibiotics. A recap of the challenges for using bacteriophages in these varied but related settings along with some potential solutions or best practices is provided to aid future research.
Agricultural antibiotics
Antibiotics are not only used to treat human illness but have also been used in livestock and poultry for more than half a century to control and treat diseases and in sub-therapeutic doses in animal feed, to promote growth and improve production of animal products (Stokstad and Jukes 1949; Page and Gautier 2012). This has resulted in the development of antibiotic-resistant bacteria (Lu 2004); the consequences affect everybody in the world and access to effective treatment for bacterial infections is urgently needed (Laxminarayan et al. 2013). Findings from recent studies using whole genome sequencing have now confirmed animal-to-human transfers of resistance genes (Harrison et al. 2013).
In agricultural industries, anti-microbial treatment in terrestrial animals reared for food production is for enteric and respiratory disorders in young animals and mastitis in dairy cows (Page and Gautier 2012). Anti-infective drugs for livestock now represent one of the largest markets in the world (Page and Gautier 2012). In the U.S. for instance, around 8 billion animals, (7.5 billion chickens, 300 million turkeys, and 100 million cattle) are treated by as many as 10 different antibiotics annually or during their lives (Martin 2004; Page and Gautier 2012). Antibiotics have also been used for prevention via feed or water to animals (Page and Gautier 2012; Laxminarayan et al. 2013). Preventive use can be anything from targeted interventions for controlling the spread of a diagnosed disease in a defined group of animals, to routine treatment of all animals during specific periods of stress such as weaning, after transportation, when combining new animals with a herd or mixing animals from different sources (Laxminarayan et al. 2013). With some exceptions, the antimicrobial classes used in agricultural industries are the same as in human medicine. However, some newer types of antimicrobials, such as carbapenems, oxazolidinones, and glycylcyclines are not used for animals reared for food (Laxminarayan et al. 2013).
Today, subtherapeutic antibiotics are routinely fed to livestock, poultry and fish on industrial farms to promote faster growth and to compensate for the unsanitary conditions in which they are raised (Emanuele 2010). Tetracycline, penicillin, erythromycin, and other antimicrobials that are important in human clinic are used extensively, in the absence of disease, for subtherapeutic purposes in today’s livestock production (Mellon et al. 2001; Page and Gautier 2012). In the US, overall use of antimicrobials for subtherapeutic purposes in animals rose by about 50 % between 1985 and 2001 (Gerber et al. 2007), and approximately 80 % of all antibiotics used in the U.S. are fed to farm animals (US Congress 2011). This was primarily driven by increased use in the poultry industry, where subtherapeutic antibiotic use increased from 2 million to 10.5 million pounds (907,185 kg to 4,762,720 kg) between the 1980s and 2001 which amounted to a dramatic 307 % increase on a per-bird basis (Mellon et al. 2001). In addition, where authorised, antibiotics used for growth promotion can generally be purchased over the counter without veterinary involvement (Khachatourians 1998; Manna et al. 2006; Laxminarayan et al. 2013). These practices have been decreasing the effectiveness of antibiotics in treating common infections, which has quickened in recent years, and the arrival of untreatable strains of carbapenem-resistant Enterobacteriaceae, indicates that the world is marching at the dawn of a post-antibiotic era (CDC 2013).
Additionally, it is estimated that approximately 75 % of all antibiotics given to animals are not fully digested and eventually pass through the body and enter the environment (Chee-Sanford et al. 2009), where they can encounter new bacteria and create additional resistant strains (Horrigan et al. 2002). With huge quantities of manure routinely sprayed onto fields surrounding confined animal feeding operations, antibiotic resistant bacteria can leech into surface and ground water, contaminating drinking wells and endangering the health of people living nearby (Clemans et al. 2011). Bacteria can also be spread by animals, birds and insects that come in contact with animal waste (Graham et al. 2009; Page and Gautier 2012). A considerable amount of pressure is being exerted on the natural microbial environment, including beneficial bacteria, human and animal nutrition and immunity, by the antibiotics provided to humans, animals and plants, as well as the spraying of antibiotics on fruit trees, resulting in dangerous superbugs (Phillips et al. 2004; Yan and Polk 2004; O’Hara and Shanahan 2006; Buffie et al. 2011).
Economic impacts of subtherapeutic use of antibiotics
In 1998, the National Academy of Sciences calculated that increased health care costs associated with antibiotic-resistant bacteria exceed $4 billion each year in the U.S. alone, a figure that reflects the price of pharmaceuticals and longer hospital stays, but does not account for lost workdays, lost productivity or human suffering (Knobler et al. 2003; Westwater et al. 2003; U.S. Congress 2011). In 2009, Cook County Hospital and the Alliance for Prudent Use of Antibiotics estimated that the total health care cost of antibiotic resistant infections in the US was between $16.6 and $26 billion annually (U.S. Congress 2011). The WHO, the American Medical Association and the American Public Health Association have urged a ban on GPAs, arguing that their use leads to increased antibiotic-resistant infections in humans (Graham et al. 2007). Along with expected decreases in health care costs that would stem from reducing the number of drug resistant infections, there is evidence to show that eliminating GPAs would be profitable for both farmers and the public as a whole (U.S. Congress 2011). However, according to a study of Graham et al. (2007), the increased selling price of chickens fed GPAs did not offset the increased cost of the feed, resulting in a higher overall cost to the farmer. The study found that the use of GPAs resulted in an average loss in value per chicken of $0.0093, or about 0.45 % of total cost (Graham et al. 2007).
Today, many animal farmers do not use GPA’s, in large part because they don’t have to compensate for unhealthy conditions associated with confined animal feeding operations (Graham et al. 2007). On these types of farms such as organic poultry farms, Enterococcus faecalis and E. faecium resistance to antibiotics has been found to be significantly lower than on conventional poultry farms (Sapkota et al. 2011). These organic animals are raised in clean environments with adequate space to reduce animal-stress and the likelihood of infections (Graham et al. 2007). These types of farms may use antibiotics to treat acute infections in sick animals (Graham et al. 2007). These results do suggest that completely removing antibiotics from animal agriculture could effectively reduce resistance. In contrast, commercial interests have argued that their removal will have a significant impact on the cost of animal production and is unlikely to affect the risk to humans from antibiotic-resistant infections (Casewell et al. 2003). The economic impact of judicious use or a ban of antibiotics use in animals is difficult to measure, partly because exact figures for employees and profits in feed additives are not available and partly due to this conflicting evidence.
Government intervention
The precise effect of agricultural antibiotic use on resistance levels in the general population is not known, but the evidence points to a link (Ganguly et al. 2011). In 2003, an expert committee convened by the WHO, the United Nations Food and Agriculture Organization and the World Organization for Animal Health concluded there is clear evidence of adverse human health consequences due to resistant organisms resulting from non-human usage of antimicrobials (Ganguly et al. 2011). These consequences include infections that would not have otherwise occurred, increased frequency of treatment failures (in some cases death), and increased severity of infections (FAO/OIE/WHO 2003). Today, governments around the world are taking action to address this issue. The Director-General of the WHO, said in 2011 that ‘The world is on the brink of losing these miracle cures (antibiotics). In the absence of urgent corrective and protective actions, the world is heading towards a post-antibiotic era, in which many common infections will no longer have a cure’ (Liljeqvist et al. 2012).
In Europe, restricted authorisation of antimicrobial types began several decades ago and in 2006 all growth promoting use was abandoned (Laxminarayan et al. 2013). In the US, the FDA has released draft guidelines on judicious use of antimicrobials in the rearing of animals for food production. These recommendations aim to reduce the overall use of medically important anti microbials and include veterinary oversight and consultation. If this guidance is adhered to, a gradual phasing out of growth promoting use is to be expected (Laxminarayan et al. 2013).
The need for an alternative to antibiotics
Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics. At least 23,000 people die annually as a direct result of these infections, while many more die from other conditions that were complicated by an antibiotic-resistant infection (Frieden 2013). Since the 1980s in the US, newly approved antibiotics have steadily declined and despite the increased awareness and redoubled efforts, the current R&D pipeline remains largely dry (Hughes 2011). The underlying economic factors make antibiotic development unprofitable, (Nathan and Goldberg 2005), since it is not commercially viable to develop new drugs if there is a high probability of their becoming ineffective soon after introduction (Liljeqvist et al. 2012). One of the major drawbacks is the inability to discover completely new antibiotics; those discovered over the last few decades have now been modified to produce new generic forms (Jose 2010), which is a disincentive to spending money on R&D.
Antibiotics were used in poultry industries to reduce Salmonella levels at each step of the production in the farms. Yet Salmonella remains the major cause of food-borne diseases worldwide, with chickens known to be the main reservoir for this zoonotic pathogen (FSA 2011; Bardina et al. 2012). It is the second leading cause of bacterial foodborne illness in the US and the great majority of these infections are associated with the consumption of products such as poultry and eggs contaminated with Salmonella (Foley et al. 2008). Salmonella have evolved several virulence and antimicrobial resistance mechanisms that allow for continued challenges to our public health infrastructure (Foley and Lynne 2008).
The emergence of infectious disease caused by drug-resistant bacteria requires alternatives to conventional antibiotics (Barrow and Soothill 1997; Alisky et al. 1998; Carlton 1999; Sulakvelidze et al. 2001). The search for new drugs is becoming critical because of the growing concern over the failing antibiotic drug discovery pipeline. There is a great deal of interest to investigate alternatives and natural antimicrobial agents, which has also increased due to consumer awareness about the use of chemical preservatives in foodstuff and on food processing surfaces.
Bacteriophages
Bacteriophages (phages) are described as viruses that infect bacteria. Application of phages has been investigated extensively, such as in the indicator of fecal contamination (Endley et al. 2003) and against antibiotic resistant bacteria (Yosef et al. 2014).
Lytic phage
When a virulent phage infects a host bacterium, it replicates much faster than the host cell. The whole cycle can be completed in 30–40 min. The phage is a parasite that depends on the host for its propagation, which is influenced by a variety of factors such as temperature, nutrients, light and other environmental forces (Jassim and Limoges 2013). It subverts the host’s biological function and utilizes the host machinery for reproduction. The host cell undergoes lysis and dies, simultaneously liberating a large number of progeny phages, which are each then ready to start another cycle by infecting new neighbouring bacterial cells. This cycle is known a lytic ‘virulent’ cycle.
The lytic cycle or ‘virulent phages’ fit in the class of ‘natural antimicrobial controlling agents’ and are arguably the most abundant biological entities on the planet. These are being exploited in various areas of biotechnology, including rapid bacterial detection (Stewart et al. 1993; McIntyre et al. 1996; Stewart et al. 1998; Favrin et al. 2001, 2003; Jassim and Griffiths 2007; Rees and Loessner 2009; Jassim et al. 2011), food bioprocessing (Jassim et al. 2012) and removal of bacterial biofilm (Hibma et al. 1997; Jassim et al. 2012).
Phages are known to have some advantages associated with human therapy over the use of antibiotics (Sulakvelidze et al. 2001; Sulakvelidze and Kutter 2005; Loc-Carrillo and Abedon 2011). The inexorable rise in the incidence of antibiotic resistance in bacterial pathogens, coupled with the disappointingly low rate of emergence of new, clinically useful antibiotics, has refocused attention on the potential utility of phages for biocontrol and preventing or treating human and animal disease.
Lysogenic phage
Other particles, called lysogenic phages, are ‘temperate’ or dormant phages which may take the form of a ‘prophage’ by integrating with the viral DNA in the host chromosome. They become a part of the host cell and replicate along with the host chromosome for many generations, coexisting as opposed to lysing the host cell (Jassim and Limoges 2013). This phenomenon is called ‘lysogeny’, which also provides immunity against infection by further phage particles of the same type, ensuring that there is only one copy of phage per bacterial cell. The unique characteristics of lysogenic or ‘temperate’ phages and their potential for exploitation have been demonstrated in a system that restores antibiotic efficiency by reversing pathogen resistance to antibiotics (Edgar et al. 2012). These phages are genetically engineered to reverse the pathogens’ drug resistance, thereby restoring their sensitivity to antibiotics. Unlike conventional phage therapy, the system does not rely on the phage’s ability to kill pathogens in the infected host, but instead, on its ability to deliver genetic constructs into the bacteria and thus render them sensitive to antibiotics prior to host infection. The transfer of the sensitizing cassette by the constructed phage will significantly enrich antibiotic-treatable pathogens on hospital surfaces. This may hold key advantages to revive the use of old generation antibiotics leading to the use of phage biotechnology synergistically with antibiotics.
The lysogenic phage or ‘prophage’ will drive the adaptive evolution of bacteria to achieve more powerful virulence factors inherited from previously infected bacteria via transduction, i.e., the transfer of genetic material to a bacterial cell via phage infection (Campbell 1988; Verheust et al. 2010). Lysogenic phages serve as a driving force in bacterial pathogenesis, acting not only in the evolution of bacterial pathogens through gene transfer, but also contributing directly to bacterial pathogenesis at the time of infection (Wagner and Waldor 2002; Verheust et al. 2010). The data of Vojtek et al. (2008) has indicated that horizontal transfer of lysogenic phages among group A Streptococcus can occur across the M-type barrier; these data also provide further support for the hypothesis that toxigenic conversion can occur via lysogeny between species. This mechanism specifically allows more efficient adaptation to changing host challenges, potentially leading to fitter and more virulent clones (Vojtek et al. 2008). Other authors concluded that this may represent a potentially serious hazard to humans, animals and plants (Saunders et al. 2001; Verheust et al. 2010).
In viruses, recombinational repair is most often studied as it is manifested in the phenomenon of phage MR, whereas MR is the process by which viral genomes containing inactivating genomic damage, interact within the infected cell to form a viable genome (Michod et al. 2008). MR was found in many phages that infect E. coli (T1, T2, T5, T6, and phiX174) and Salmonella typhi (Viphage) (Blanco and Devoret 1973; Michod et al. 2008). The genome damage expressed as a lysogenic prophage is an error prone in nature and can be reactivated (Bhattacharyya et al. 1991; Michod et al. 2008). The restoration of impaired biologic activity can be caused by chemical reaction, thermal application, genetic recombination, or helper elements (Duenas and Borrebaeck 1995; Jassim et al. 1995; Maloy and Youderian 1996; Rieder et al. 1996; Maloy and Gardner 1998; O’Sullivan et al. 1998; Gupt 2008; Michod et al. 2008; Jassim et al. 2010).
It is noteworthy that lateral gene transfer virulence factors can also be accomplished through the lysogenic phages, which harbour a multitude of prophages and each phage-encoded virulence or fitness factor makes an incremental contribution to the fitness of the lysogen (Brüssow et al. 2004; Verheust et al. 2010). This will lead eventually to the evolution of pathogenic bacteria (Verheust et al. 2010). However, the phage could become a clinically useful therapy tool through understanding how to control the phage-resistant bacteria (Mizoguchi et al. 2003; Fischer et al. 2004). Subsequent studies revealed that not all phages replicate similarly and that there are important differences in the replication cycles of lytic and lysogenic phages (Sulakvelidze et al. 2001; Jassim et al. 2010).
The emergence of phage-resistant mutants is undesirable and the study of Mizoguchi et al. (2003) employs a continuous culture to investigate sequential mutations of both phage PP01 and its host cells E. coli O157:H7. The phage PP01, previously shown to efficiently and specifically lyse E. coli O157:H7, showed that co-evolution occurred to the phage PP01 reducing the phage lytic activity, therefore they decided to extend their research to find other O157:H7-specific phages. They also concluded that only through understanding and controlling the emergence of phage-resistant bacteria could phage become a clinically useful tool. It seems that broad-range phage O157:H7-PP01 resistance by clonal heterogeneity represents a new class of bacteria–phage interactions (Fischer et al. 2004). Furthermore, S. enteritidis strains did not produce viable phages when grown on particular hosts, which behaved as complexes of phages (Sillankorva et al. 2010). The latter authors have concluded this is most likely because of the presence of inactive phage-related genomes (or their parts) in the bacterial strains which are capable of being reactivated or which can recombine with lytic phages. In fact, some of the failures of phage therapy were due to bacterial mutations leading to resistance to phage infection (Barrow and Soothill 1997; Alisky et al. 1998; Carlton 1999; Sulakvelidze et al. 2001).
Phage in therapy/bio-control (prophylaxis) applications
There are numerous reviews describing both the potential for and caveats associated with the employment of phages to treat bacterial infections, especially in clinical settings (Goodridge and Abedon 2003). Phage therapy is like other methods of biological control with some comfort in the reduction of the use of chemical agents against pathogens (Fujiwara et al. 2011). The advantages associated with phage therapy relative particularly to chemical anti-bacterial agents were also reviewed. (Sulakvelidze and Kutter 2005; Loc-Carrillo and Abedon 2011). Phages can be bactericidal, they can increase in number responding to the incidence of pathogens over the course of treatment, tend to only minimally disrupt normal flora, are equally effective against antibiotic-resistant bacteria, are often easily discovered, seem to be capable of disrupting bacterial biofilms, and can have low inherent toxicities. The exploitation of phages as a realistic approach in the control of pathogens has attracted considerable interest in recent years (Sulakvelidze et al. 2001; Merril et al. 2003; Jassim et al. 2012), because of the emergence of antibiotic-resistant bacteria.
Phage therapeutic applications in various aspects of human therapy and nonclinical settings are reported (Sulakvelidze and Kutter 2005; Brüssow 2007; Górski et al. 2007, 2009; Harper and Kutter 2009; Kutter 2009; Kutter et al. 2010; Abedon et al. 2011; Loc-Carrillo and Abedon 2011). Phage treatment in human eyes, ears and nose via inhalation was used at the Eliava Institute in Tbilisi for decades (Kutter et al. 2010; Abedon et al. 2011). Recently, phages have been suggested to be included in a nebulizer to treat bacterial lung infections in cystic fibrosis patients (Golshahi et al. 2008) or to be sprayed as dried phages in respirable powders for the treatment of pulmonary infections (Matinkhoo et al. 2011). The first controlled clinical trial of a therapeutic phage preparation was conducted in 2009 and showed efficacy and safety in chronic otitis targeting antibiotic-resistant Pseudomonas aeruginosa (Wright et al. 2009). A year later, in an evaluation of a phage treatment for chronic otitis infection in dogs, the results show once more that administration of this topical phage mixture leads to lysis of P. aeruginosa in the ear without apparent toxicity and that it has potential to be a convenient and effective treatment for P. aeruginosa otitis (Hawkins et al. 2010).
In the area of animal biocontrol and agribusiness options, phages have shown a remarkable success (Smith et al. 1987; Biswas et al. 2002; Sulakvelidze and Barrow 2005; Hawkins et al. 2010). Phages have been extremely effective at treating a number of bacterial infections in controlled animal studies, especially as a biocontrol agent in the prevention of food-borne illnesses, due to its target specificity, rapid bacterial killing and ability to self-replicate (Smith et al. 1987; Biswas et al. 2002; Hawkins et al. 2010). Phages have the potential to treat bacterial infections afflicting animals and in particular to prevent fatal Escherichia coli respiratory infections in broiler chickens (Huff et al. 2002a, b, 2003a, b). Aerosol spraying and intramuscular injection have given the best results over using oral delivery of phages via direct administration or addition to drinking water and/or feed (Sillankorva et al. 2012). This is may be due to gastric pH levels preventing the proliferation of phages (Spits 2009). Virulent antigen-specific phages have been used in an attempt to control E. coli O157:H7 in batch culture (Kudva et al. 1999). Loc-Carrillo et al. (2005) and Wagenaar et al. (2005) reported that phage therapy (biocontrol) reduces Campylobacter jejuni colonization of broiler chickens. Several studies have also addressed the use of phages to decrease Campylobacter and Salmonella concentrations on poultry (Goode et al. 2003; Atterbury et al. 2007; Kittler et al. 2013).
Veterinary therapy/biocontrol applications require the appropriate administration targeting specific bacteria, with a strategy that includes a comprehensive methodology, detailing the phage-host interactions, dose optimization and accounting for all chemical and physical factors (Jassim and Limoges 2013). In general, a deep understanding of intrinsic phage properties is critical to designing therapeutic interventions. The reduction of foodborne pathogens requires a comprehensive phage control program at the farm, where the animals are born, hatched or raised, before shipment to processing plants. Potential pre-harvest sources of foodborne pathogen contamination include breeder herds and flocks, hatcheries, contaminated feed and water, along with environmental sources and vectors, such as litter, animal caretakers, and insects (Bailey 1993; Nayak et al. 2003).
Regulatory approval of phage therapy
Classical phage treatments used since the 1920s in the Soviet era is being investigated as another potential strategy (Potera 2013). Since phages are part of both gastrointestinal and environmental ecosystems (Topley and Wilson 1990), bactericidal phages may provide a feasible natural, nontoxic approach for controlling several human pathogens (Alisky et al. 1998). The safety of phages was further assured by Duckworth and Gulig (2002) who stated that there has been no evidence that exposure to phage particles, even those normally associated with disease-causing bacteria, can actually result in the occurrence of human disease. Nevertheless, Borysowski and Górski (2008) examined the safety of phage therapy, especially in immunocompromised individuals. They discussed the possible negative interactions with the immune system and the relative safety of the therapy compared to its effectiveness since phage resistant bacteria and some phage preparations, especially lysates, have been found to exert immunostimulatory activity. This problem is of great importance in phage therapy since immune response-mediated antibacterial activity may be substantially suppressed in immunocompromised patients. In addition, another safety aspect might be taken into consideration, phages replicate at the site of infection or wherever the host bacteria are present, while phages are absent in sterile areas, thus ensuring an optimal self-adjusting dose of phages which is not found in other modes of non-biological antimicrobial agents (Katsunori 2003). These arguments have helped to pave the way for phage therapy/biocontrol to become a broadly relevant technology, including veterinary, agricultural, and food microbiology applications.
It was for the treatment or prevention of human infections that phage therapy first caught the world’s imagination and which today is the primary motivation of the field (Zhukov-Verezhnikov et al. 1978; Biswas et al. 2002; Merril et al. 2006; Hawkins et al. 2010; Kittler et al. 2013). Nevertheless, the regulatory requirements for these types of live drugs, phages are still challenging (Potera 2013) and their uses might not extend to life-threatening infections. The recent USFDA (2006) approval of Listeria-specific phage preparations for food additives has opened the door to new applications of these natural bacterial killers. It is known that phages only infect and lyse bacterial cells and are harmless to mammalians (USFDA 2006). This has eventually led to the development of a phage related product which received regulatory approval from the FDA in 2011, as a natural antimicrobial for use in agro-food industry as GRAS and by US-FSIS as safe for use in animals (Sillankorva et al. 2012; Klumpp and Loessner 2013). In general, although the safety of phages has been strongly suggested by human phage therapy, it should be noted that some phages, notably when in the form of lysogens (prophages), have been recognized as important contributors to bacterial virulence, or as vectors in horizontal gene transfer through transduction (Verheust et al. 2010) as discussed further below.
Current information regarding studies being conducted and/or ongoing trials with the primary purpose of experimental therapy to treat, with the aid of phages, patients with various infections can be obtained from www.clinicaltrial.gov; http://www.clinicaltrial.gov/ct2/results?term=phage+therapy&Search=Search; Parracho et al. (2012). The national and international regulatory compliance and regulations being employed can be obtained from Parracho et al. (2012).
Phage experimental evolution
Replication inside host bacteria by a lytic phage is a complex process consisting of a cascade of events involving several structural and regulatory genes (Sulakvelidze et al. 2001). Some therapeutic phages have unique yet unidentified genes or mechanisms responsible for their ability to effectively lyse their target bacteria. For example, a group of authors from the EIBMV (Adamia et al. 1990) identified and cloned an anti-Salmonella phage gene responsible, at least in part, for the phage’s potent lethal activity against the S. enterica serovar typhimurium host strains. In another study (Andriashvili et al. 1986), a unique mechanism has been described for protecting phage DNA from the restriction-modification defences of Staphylococcus aureus host strain.
Phage gene expression has been studied by many researchers (Gupt 2008). Use of genetic virus design/breeding which is a genetic manipulation of the virus genome has been reported (Duenas and Borrebaeck 1995; Rieder et al. 1996; Barrow and Soothill 1997; Alisky et al. 1998; O’Sullivan et al. 1998). Expression of the ant gene, to determine the lysis-lysogeny decision of phages was also reported (Maloy and Youderian 1996; Maloy and Gardner 1998). This provides a positive selection for and against DNA-binding: repression of ant can be selected by requiring growth of lysogens, and mutants that cannot repress ant can be selected by requiring lytic growth of the phage. The use of genetically engineered nonlytic phage to specifically target and deliver DNA encoding bactericidal proteins to bacteria was reported (Hagens and Bläsi 2003; Westwater et al. 2003). The genetically engineered phage exerted a high killing efficiency while leaving the cells structurally intact. The use of recombinant viral particles in some instances might raise some biosafety concerns by bringing and potentially disseminating new genetic traits among bacterial populations (Verheust et al. 2010).
The identification of bacteriolytic peptides derived from phage could rekindle interest in phage as a source of a new generation of agents for combating multidrug resistant bacteria and offer a starting point for new therapeutic agents that could potentially circumvent such problems (Bernhardt et al. 2001a, b). It was reported that phages produce lysins which break bonds in the bacterial cell-wall peptidoglycan structure just before release of phage progeny and that the lysins enzymes have killed bacteria in vitro within 5 s (Nelson et al. 2001; Schuch et al. 2002). Further work with lysins enzymes may produce an effective bactericide and enhanced rapid diagnostic tools.
The efficiency of the in vivo ‘therapy’ use of lytic phages relies mainly on how robust, rapid and what specific action phages are able to exert before the immune system of the body being treated will reduce them below the level of effectiveness (Abedon et al. 2011). Therefore, it seems that the less robust, un-optimized, phages have less chance to succeed in abolishing in vivo bacterial infection than their robust, optimized counterparts. Moreover, it seems that the in vitro challenge of the attacking phages against host bacteria might be limited by the availability of highly efficient and specific phages for challenging each pathogen successfully.
Modern phage technology: obstacles and indications
Although phage therapy has been practiced for several decades in some of the former Soviet Union countries and Poland, there are still many doubts as to its ability to replace antibiotics (Edgar et al. 2012). They are not yet “magic bullets” and they might not work in certain settings (Sulakvelidze 2011). The development of obligate lytic phages may provide one modality to kill only specific pathogens without harming beneficial flora. There are other issues to address, including the potential in vivo elimination of phages, phage-neutralizing antibodies and phage-resistant mutants (Sulakvelidze 2011).
Human infections caused by pathogens transmitted from fish or the aquatic environments are quite common and depend on the season, as well as patients’ contact with fish and the related environment (Novotny et al. 2004). It is well known that fish and seafood are a potential source of many foodborne pathogens for human beings (Novotny et al. 2004). The effects of phage-host interactions in a commercially important fish pathogen were studied (Laanto et al. 2012). They reported that Flavobacterium columnare has developed resistance to 3 lytic phages associated with a decline in the bacterial virulence. They have hypothesised that this is due to antagonistic co-evolution factors reducing the virulence of bacterial pathogens outside of a host due to the associated costs of defending against lytic phages. This study represents the first report that phage-based therapies can provide a disease management strategy for columnaris disease in aquaculture (Laanto et al. 2012).
The recently discovered, Sputnik virophage is a satellite virus that inhibits replication of its target phage and thus acts as a parasite of that virus in aquatic environments (Jassim and Limoges 2013). These virophages may also coexist as the natural predator of the phages that target foodborne pathogens, perhaps transmitted from their aquatic environments by fish and seafood. Virophages in aquatic environments hijack virus DNA in order to replicate and often deform phage/virus particles, making them less infective (Jassim and Limoges 2013). We have found no published report of their existence or survival outside of aquatic environments, but if confirmed, it may help to explain why, according to the US Center for Science in the Public Interest (CSPI 2008), fish and shellfish are more likely to cause foodborne-illness than any other category of food product. Even if these virophages exist only in aquatic environments, much of their work to hamper the effectiveness of phages is already accomplished prior to the food harvest. These foods are also considered a potential entry source of foodborne pathogens into the home (Scott 2003). It is worthwhile to investigate this postulation and potential association of virophages with aquatic foodborne pathogens in order to aid the understanding of phage ecology and bacterial evolution in greater clarity, assisting in the application of phages in therapy and biocontrol of bacterial infections.
The development of phage resistance by bacteria is an issue facing scientists investigating phage-bacteria interaction. Phage-mediated transduction of bacterial genes likely reflects an infrequent mistake in the assembly of the phage particle, rather than a bacterial adaptation (Michod et al. 2008). The mechanism that caused the spread of antibiotic resistance genes between bacteria occurs most often by the gene transfer process of plasmid mediated conjugation and sometimes by phage-mediated transduction (Michod et al. 2008).
Phage interactions and/or to allow irreversible phage binding to the E. coli O157 antigen was studied (Kudva et al. 1999). It was found that the movement of virions in the LPS layer before DNA injection may involve the release and rebinding of individual tail spikes rather than hydrolysis of the O-antigen (Baxa et al. 1996). This would suggest that effective infection might require normal LPS, thus, phage mutations seem to originate by alternation of LPS structure (Mizoguchi et al. 2003). The importance of LPS of the outer membrane in controlling the fate of phage attachment and the consequent phage infection of the host cell was reported (Mizoguchi et al. 2003). It was inferred that the modification of LPS of the outer membrane of host bacteria may play a key role in controlling the phage-host interaction and consequently control phage infection.
In general, phage host interactions are dependent on the binding of tail proteins to specific bacterial surface receptors (Pelczar et al. 1993). It seems that the development of a successful phage against target bacteria must address the emergence of mutant strains, the phage binding and infection of bacterium not being controlled by a single receptor, and the many factors which contribute to phage resistance including alteration or loss of receptors for the target cell envelope (Heller 1992; Barrow et al. 1998; Biswas et al. 2002; Mizoguchi et al. 2003; Jassim et al. 2010). Thus, the efficient use of phages to control bacterial infections may require isolation of mutant host-specific phages that can adsorb to hosts that make shorter O-side chains (Kudva et al. 1999). Practical application might be hampered by factors such as the lack of broad-host phages and heterogeneity (Kutter 2005). The ecology of both phages and bacteria were also not understood, resistance, failure to neutralize gastric pH prior to oral administration, inactivation of phages by host immune responses and environmental contamination issues are other obstacles (Kutter 2005). It was also suggested that changes of the bacterial hosts used for maintenance of phages must be avoided as these can drastically modify the parameters of the phage preparations, including host range and lytic activity (Sillankorva et al. 2010; Sulakvelidze 2011). The generally poor efficacy of commercial phage preparations led to widespread criticism and disagreement about the effectiveness of phages in treating disease (Atterbury 2009).
Another drawback is the survival and persistence of phages on different surfaces due to the impact of external forces on phage-host interactions in their surrounding environments (Jassim and Limoges 2013). Phage virility is affected by physical and chemical factors associated with the microscopic food matrix and with the conditions of application including environmental factors and the distinct properties of the phage itself (EFSA 2009). All these aspects must be investigated and well characterized before an effective biocontrol agent can be established and marketed (Bardina et al. 2012). The success of phage biocontrol to greatly reduce harmful bacteria entering the food chain at farm level requires the production of virulent phages that can survive in extreme environments and having a broad host range for the target genus, while lacking bacterial virulence genes.
Phage safety and efficacy for therapy
Phage bactericidal activity
Phage biocontrol is applying specific phages to selectively reduce or eliminate susceptible bacteria from selected environments, including human and animal bodies, artificial environments, such as farms, factories, offices, hospitals, or in laboratory (Kurtböke et al. 1992; Grandgirard et al. 2008). The ability of phages to recognize precisely their target hosts, rendered them as favourable antibacterial agents because broad-spectrum antibiotics kill target bacteria along with other beneficial bacteria present in the farm or in the organism body, namely, animal intestinal flora (Merril et al. 2003).
Bacterial resistance to phages will unquestionably develop, although according to some authors (Carlton 1999; Inal 2003; Tanji et al. 2005) the rate of developing resistance to phages is approximately 10-fold lower than that to antibiotics (Sulakvelidze et al. 2001). Furthermore, many earlier studies demonstrated that classical application of phages in bacterial therapy or biocontrol is attainable in theory but in practice were not so successful, due to the lack of full coverage of target bacteria and the rapid emergence of bacterial mutations leading to complete resistance against phage infection (Barrow and Soothill 1997; Alisky et al. 1998; Carlton 1999; Sulakvelidze et al. 2001; Goodridge and Abedon 2003). Therefore, phage therapy or phage biocontrol were unsuccessful and eventually led to replacement of phage therapy with antibiotic treatment (Barrow and Soothill 1997). Scientific methodologies could be developed to deal with antibiotic resistance in bacteria using bacteriophage, however viral proteins would also integrate into human and animal society with unknown effect. Viral based therapy could potentially lead to bacterial development of viral resistance. It would be wise to approach such methodologies with caution in order to avoid repeating mistakes that were made with the improper use of antibiotics. Other authors have refuted these assumptions and concluded that the rate of developing resistance against phages can be partially circumvented by using several phages in one preparation or cocktail (much like using two or more antibiotics simultaneously) (Sulakvelidze et al. 2001). More importantly, unlike using trial and error with antibiotics, when resistance against a given phage occurs, the specialists can rapidly select through testing (in a few days or weeks) a new phage that is effective against the phage-resistant bacteria (Sulakvelidze et al. 2001).
Therapeutic phages have some other advantages over antibiotics (Sulakvelidze et al. 2001; Sulakvelidze and Kutter 2005; Loc-Carrillo and Abedon 2011), and phages have been reported to be more effective than antibiotics in experimentally infected animals (Smith and Huggins 1982). Like bacteria but unlike antibiotics, phages mutate and therefore can also evolve to counter phage-resistant bacteria (Matsuzaki et al. 2005). Because phages attack bacteria by attaching to receptors on the bacterial cell surface, phage-resistant mutants (which lack these receptors) are often less pathogenic than phage-susceptible bacteria (Inal 2003; Santander and Robeson 2007; Capparelli et al. 2010; Friman et al. 2011; Laanto et al. 2012).
Despite the attractions of phage therapy, scientific and logistical challenges remain. Wild-type phage particles are rapidly eliminated by the body’s reticuloendothelial (mononuclear phagocyte) system, so in order to enhance phages’ circulatory time and improve the efficacy of treatment; long-circulating mutants (Merril et al. 1996; Keen 2012) must be selected. Wild-type virion and distribution concerns relating to the scalability of phage therapy have also been discussed (Lu and Koeris 2011). More broadly, for phage therapy to be useful in clinical settings, a patient’s specific etiological agent would need to be rapidly identified and matched to the relevant phage(s) in a comprehensive pre-existing database. Because this scenario is inconsistent with how antibiotics are traditionally employed (Bull et al. 2002), new and interdisciplinary thinking involving bioinformaticists, health care professionals, and phage researchers, among others, would be required to make phage therapy practicable on a large scale.
For oral therapies to be optimized, the phages must be shielded with a non-immunogenic polymer such as polyethylene glycol (Kim et al. 2008). On the other hand, the pharmacokinetics of self-replicating agents such as phages, differ from those of normal drugs (Robert et al. 2000; Brüssow 2005) which needs further investigation. Study of phage-bacterial-host cell interactions such as those carried-out by Cairns et al. (2009) to improve understanding of phages in vivo pharmacokinetics, including relevant inundation, proliferation thresholds, optimisation of formulations and long-term stability data is required before it can be widely used within a clinical setting (Abedon et al. 2011; Ryan et al. 2011; Parracho et al. 2012).
It is also unclear how effective phages would be in treating diseases caused by intracellular pathogens (e.g., Salmonella species), where bacteria multiply primarily inside body cells where they are inaccessible to phages. It is possible that phages will have only limited utility in treating infections caused by intracellular salmonella in children (Kiknadze et al. 1986). 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, and teeth) has proved extremely successful in the treatment of topical infections, as has the inhalation of phages for the treatment of lung infections (Ryan et al. 2011).
In order to ultimately incorporate phage therapy into a larger antibacterial arsenal, a regulatory framework must exist that allows phages to be utilized to their maximum potential. Classical phage therapy is a form of personalized medicine because specific phages (usually multiple phages combined as a multivalent cocktail) are carefully selected to treat a patient’s specific bacterial infection. Success rates from these customized phages are five-to-six fold higher than that of standardized phage products (Zhukov-Verezhnikov et al. 1978), so the use of personalized phage cocktails has historically been crucial for effective treatment. This is most likely because of the presence of inactive phage-related genomes in the host strains which are capable of being reactivated or which can recombine with lytic phages (Sillankorva et al. 2010).
Phage pharmacological study
Despite the large number of publications on phage therapy, there are very few reports in which the pharmacokinetics of therapeutic phage preparations is delineated (Payne et al. 2000; Robert et al. 2000; Payne and Jansen 2003; Levin and Bull 2004; Brüssow 2005; Górski et al. 2006; Gill 2008; Cairns et al. 2009; Abedon and Thomas-Abedon 2010; Gill 2010; Abedon et al. 2011; Parracho et al. 2012). The studies of Bogovazova et al. (1991) and Bogovazova et al. (1992) suggested that phages get into the bloodstream of laboratory animals (after a single oral dose) within 2–4 h and that they are found in the internal organs (liver, spleen, kidney, etc.) in approximately 10 h. Also, data concerning the persistence of administered phages indicate that phages can remain in the body for relatively prolonged periods of time, i.e., up to several days (Babalova et al. 1968). In one study, the time needed for the phage to reduce, eliminate or cure the target bacteria in infected animals was defined as a reduction of Salmonella concentration in the chicken cecum, and obtained when the phage was administered one day before or just after bacterial infection and then again on different days post-infection (Bardina et al. 2012). In comparison, calves and piglets with diarrhea due to experimentally administered pathogenic E. coli were cured within 8 h following phage administration (Smith and Huggins 1983). Hence, elimination of the pathogenic E. coli at the pre-harvest stage could play a significant role in preventing its introduction into the food chain (Tauxe 1997). These results would suggest that due to the phage short-term effect; the application would be optimized according to the type of chronic infection with the length of time before slaughter that is required to control the particular infection for the animals.
Another noteworthy issue regarding pharmacokinetic study is that phage-neutralizing antibodies were reported (Geller et al. 1998). This could be one of the principal reasons phages had failed as a therapeutic, through their supposed inactivation by pre-existing antibodies (Carlton 1999). Phage immune response was also observed in a mice study (Sabah A A Jassim unpublished data). Rats or humans can develop effective immunity against all introduced phages (Merril et al. 2006). It seems the pharmacokinetic aspects of phage therapy pharmacology need considerable research in order to obtain rigorous pharmacological data concerning both lytic and lysogenic phages, including full-scale toxicological studies, before lytic phages can be used therapeutically in humans. Overall, Kutter et al. (2010) has concluded that to provide an overview of the potential of phage therapy as a means of treating or preventing human diseases, there is a need to explore the phage therapy state of the art as currently practiced by physicians in various pockets of phage therapy activity around the world.
Future directions
Phage development and producing preparations as antidotes or as a biocontrol from farm to fork, requires an understanding of the obstacles associated with the use of ‘live drugs’ or phages.
Challenges
There is renewed optimism for phages as possible new ‘live drugs’ with hope to overcome the multi drug resistant bacteria problem. Surprisingly, despite the approval to use phages in food and medical industries by several international agencies FDA, GRAS, US-FSIS (see Regulatory approval of phage therapy), phages have not gained widespread acceptance as compared to commercially proven pharmaceutical antimicrobial agents.
The following summary outlines the key issues in phage biocontrol and treatment that scientists have already encountered both in the literature as well as in the laboratories. These can help to frame a platform from which past mistakes with both phages and antibiotics can be avoided.
Summary of key obstacles to best practices with phage in modern applications
-
Heterogeneity and ecology of both phages and bacteria were not understood.
-
Need to select highly virulent phages against target bacteria in the patient.
-
Single phage preparations used to treat mixtures of different bacteria.
-
Recognition as personalized medicine using a multivalent cocktail carefully selected to treat a patient’s specific bacterial infection(s).
-
Lack of standardized lytic phages that can target only their host cell without using genetic modification.
-
Genetically modified phages changing the composition of colonizing bacterial flora in humans, risk of subsequent development of active infections.
-
Lateral gene transfer virulence factors and antibiotic resistance.
-
Restriction modification degradation of phage DNA upon infection.
-
Resistance mutations in bacterial genes for adsorption, lysogeny and lysogenic conversion. Strict safety standards for human therapies not met.
-
Toxigenic conversion via lysogeny between species allowing more efficient adaptation of host, potentially leading to fitter and more virulent clones.
-
Failure to appropriately characterize or titre phage preparations.
-
Changes in the bacterial cell envelope for example, use of antibiotics in animal production that can cause disruption of microbial cell wall synthesis.
-
Effect of environmental factors which all contribute to the complexity and unpredictability of phage-host interactions in the field such as UV light, chemical disinfectants, nutrients, pollutants etc.
-
The isolation and the cultivation of phages from natural sources are time consuming and problematic for producing large amounts of active inoculums.
-
Failure to characterize phage preparation, i.e., to determine the virulence to the target.
-
Failure to neutralize gastric pH prior to oral administration.
-
Immunogenicity antibodies developed against phage.
-
Presence of endotoxins in phage preparation leading to toxic shock in the patient.
-
Pharmacokinetics of self-replicating agents differs from those of normal drugs.
-
In vivo susceptibility of bacterial pathogens to phages is poorly understood and future research on more phage-host cell interaction needed to define the requirements for successful phage treatments.
-
Many phage experiments done in vitro models need to be extrapolated to in vivo growth.
-
Phages can be reproduced from a commercially available phage preparation, a challenge to commercialization.
-
Intellectual property rights are challenging for the use of phage therapy in modern medicine and these can also trigger ethical discussions.
-
In the healthcare system phage therapy is still seen as a cost and a social program rather than an economic driver.
-
Phage sectors need more time to develop entrepreneurs and innovation in their sector.
Phage reprogramming
Although most phages do not represent a threat to human health (unless they are carrying virulence factors), the use of recombinant viral particles in some instances might raise some biosafety concerns by bringing and potentially disseminating new genetic traits among bacterial populations (Verheust et al. 2010). Jassim et al. (1995) and Jassim et al. (2010) have described novel non-genetically modified phage breeding and design technologies, respectively, for previously resistant bacterial strains. It is of particular importance to determine the host range of the phages that will be used within the complicated animal environments, for example the use of antibiotics in animal production can generate cell wall deficient or cell wall disrupted bacteria. The bacterial cell wall is the most important part of the bacterial structure for the phage attachment, required to initiate bacterial infection. Phage technology was previously developed for cell wall deficient bacteria using non-genetically bred phages by a Jassim research team (Hibma et al. 1997). On the other hand, some phages can infect a number of bacteria strains, while others are more specific and will only infect a particular sub-strain. The evolutionary survival of viruses is attributed to five realities (Jassim et al. 1995; Jassim and Naji 2003; Jassim 2005; Jassim et al. 2010; Jassim and Limoges 2013):
-
Genetic variability,
-
Variety in means of transmission,
-
Efficient replication within host cells,
-
Ability to remain dormant within the host (lysogeny),
-
Environmental or external forces.
Based on the above concepts, phage selectivity cultures (Jassim et al. 1995) and phage design technology (Jassim et al. 2010) were developed to address phage-host interactions and to produce highly lytic phages with no or far less phage-resistant mutants, along with broad host targeting capabilities. These methods do not employ genetic modification, to breed “re-tailored” wild phages on the host cells in order to gain newly bred sub-strains of phages which are able to overcome the host defence mechanisms in order to infect previously resistant bacteria and to play an important role in future applications (Jassim et al. 1995; Hibma et al. 1997). Newer methodologies are used to reprogram phages again without genetic modification, to possess auxiliary mechanisms for phage adherence/binding and uptake that are critical for plaque formation, in order to gain new sub-strains of phages able to infect parent resistant host cells. This non-genetic approach of the technology is environmentally-driven and so mimics natural selection or evolution of the phage by reproducing vast numbers of mixed populations of the most robust wild-type phages. Phage reprogramming technology was developed (Fig. 1) to permit a better selection and adaptation of robust lytic phages for each potential application. This technology is capable of converting naturally occurring wild phages to smart phages with a broader range of host specificity that can overcome a bacterium’s resistive defense mechanisms and completely destroy the target bacterial cell. These findings encourage new optimism and a re-evaluation of the potential for phage therapy.
Discussion
Phages are naturally occurring predators of bacteria. They can be effective antibacterial agents due to their specificity against a particular bacterial species and lack of impact on other microflora. However, the potential problem still exists, that just as bacteria are able to become resistant to antibiotics, they may also be able to develop resistance to phages. Thus during the course of phage treatment, the etiologic agents should be continuously monitored for phage susceptibility and if phage resistance is developed, the subject phages can be replaced with different phages, lytic against the newly emerged, phage-resistant bacteria mutants.
The lysogenic phage contributes by providing axes force in bacterial pathogenesis and contributing in the bacterial pathogens evolution through horizontal gene transfer. Therefore, the development of a successful phage therapeutic against medically important human and animal pathogens must address the emergence of all of these mutant strains. Specialists must focus on modelling phage systems in natural ecosystems to prevent bacterial resistance to the phage, which must be addressed before using phage therapy/biocontrol.
Furthermore, no consensus exists on how quickly phages should produce results to identify patients who really need phage therapy. Should the research need to invest in developing smart phages that can produce results to prevent phage resistance to the host cell? If so, very few researchers have technologies in their pipelines that can meet these requirements. Should a first dose of phages be given and then treatment adjusted on the basis of phage resistant mutants test results? How do the parameters (e.g.; speed, robustness of phages, cost, and user friendliness) fit with the different treatment settings? There is a need to develop phage technology that is able to provide rapid, exceptional viruses that produce less phage-resistant bacteria mutants in the target pathogens.
Figure 2 illustrates the main strands of a possible strategy based on analysis of the literature and reports published in peer reviewed/scholarly journals. The aim is to develop an action plan for safe phage therapy and business management to promote the use of phage therapy in appropriate health care applications.
In parallel there is an equal need for rapid detection methods, also able to detect swiftly any phage-resistant mutants so that corrective therapeutic measures can be taken before putting the patient’s life in danger. The identification of which organisms caused the infection using rapid detection methods is paramount, allowing doctors to know which phages are needed. Knowing which phage-resistant mutants are always expressed in vivo would allow these to also be targeted in the system. Many phage companies are struggling to align their business goals with the technology solutions because these fundamental questions have not been properly addressed by experts in the specialty. The world needs to rethink phage technology and realize that human and animal healthcare with the sharp increase of multi drug resistant bacteria, can be an economic driver that utilizes innovation fostered in the life science sector. Antibiotics are currently being phased out of animal production in many countries. Researchers are keen to continue to explore the science behind phage therapy uses, however, it remains unclear if phage therapy will indeed save lives on a significant scale or if it will ultimately fail to fulfil its promise. One thing seems clear though, if phage therapy is to move out of the twentieth century and into the twenty-first, so too must the regulatory models that govern it (Keen 2012). Obviously classical phage therapy did not produce consistently favourable results leaving antibiotics the preferred treatment. Though many believe that phages will not replace antibiotics right away or maybe ever, there is definite potential for their use in conjunction with antibiotics (Clark and March 2006).
Conclusion
Phages are presenting solutions that will help to replace, curb, or promote judicious use of antibiotics in farm animals. Phage therapeutic approaches are also appropriate as adjunctive therapies to increase the efficacy of antibiotic treatment while simultaneously supporting probiotic supplements and useful microflora. As yet phage clinical therapy is in a progressive and scientific cumulative stage. To move into the pharmaceutical stage, it needs competencies, best practices and data that can support pharmaceutical industries to develop phage therapy ‘live drugs’. Innovative phage treatments will benefit from a new understanding of the phage-host–pathogen and environmental interactions. These are long-term solutions to the challenge of antibiotic resistance, driven by the urgent and growing need for new treatments.
Abbreviations
- CDC:
-
Centres for Disease Control and Prevention
- EFSA:
-
European Food Safety Authority
- FAO:
-
Food and Agriculture Organization of the United Nations
- FDA:
-
Food and Drug Administration
- FSA:
-
Food Standards Agency
- GPAs:
-
Growth promoting antibiotics
- GRAS:
-
Generally recognized as safe
- LPS:
-
Lipopolysaccharide
- MR:
-
Multiplicity reactivation
- OIE:
-
World Organization for Animal Health
- R&D:
-
Research and Development
- US-FSIS:
-
US-Food Safety and Inspection Service
- WHO:
-
World Health Organization
References
Abedon ST, Thomas-Abedon C (2010) Phage therapy pharmacology. Curr Pharm Biotechnol 11:28–47
Abedon ST, Kuhl SJ, Blasdel BG, Kutter EM (2011) Phage treatment of human infections. Bacteriophage 1(2):66–85
Adamia RS, Matitashvili EA, Kvachadze LI, Korinteli VI et al (1990) The virulent bacteriophage IRA of Salmonella typhimurium: cloning of phage genes which are potentially lethal for the host cell. J Basic Microbiol 10:707–716
Alisky J, Iczkowski K, Rapoport A, Troitsky N (1998) Bacteriophages show promise as antimicrobial agents. J Infect 36:5–15
Andriashvili IA, Kvachadze LI, Vashakidze RP, Adamia RS, Chanishvili TG (1986) Molecular mechanisms of DNA protection from restriction endonucleases in Staphylococcus aureus cells. Mol Gen Mikrobiol Virusolol 8:43–45
Atterbury RJ (2009) Bacteriophage biocontrol in animals and meat products. Microbial Biotechnol 2(6):601–612
Atterbury RJ, Van Bergen MAP, Ortiz F, Lovell MA et al (2007) Bacteriophage therapy to reduce Salmonella colonisation of broiler chickens. Appl Environ Microbiol 73:4543–4549
Babalova EG, Katsitadze KT, Sakvarelidze LA, Imnaishvili NS et al (1968) Preventive value of dried dysentery bacteriophage. Zh Mikrobiol Epidemiol Immunobiol 2:143–145
Bailey JS (1993) Control of Salmonella and campylobacter in poultry production. A summary of work at Russell Research Center. Poult Sci 72:1169–1173
Bardina C, Spricigo DA, Cortés P, Llagostera M (2012) Significance of the bacteriophage treatment schedule in reducing salmonella colonization of poultry. Appl Environ Microbiol 78(18):6600–6607
Barrow PA, Soothill JS (1997) Bacteriophage therapy and prophylaxis: rediscovery and renewed assessment of potential. Trends Genet 5:268–271
Barrow P, Lovell MA, Berchieri A Jr (1998) Use of lytic bacteriophage for control of experimental Escherichia coli septicemia and meningitis in chickens and calves. Clin Diagn Lab Immunol 5:294–298
Baxa U, Steinbacher S, Miller S, Weintraub A et al (1996) Interactions of phage P22 tails with their cellular receptor, Salmonella O-antigen polysaccharide. Biophys J 71:2040–2048
Bernhardt TG, Struck DK, Young R (2001a) The lysis protein E of φX174 is a specific inhibitor of the mraY-catalyzed step in peptidoglycan synthesis. J Biol Chem 276:6093–6097
Bernhardt TG, Wang I-N, Struck DK, Young R (2001b) A protein antibiotic in the phage Qβ virion: diversity in lysis targets. Science 292(5525):2326–2329
Bhattacharyya SC, Samad SA, Mandal JC, Chatterjee SN (1991) X-ray inactivation, weigle reactivation, and weigle mutagenesis of the lysogenic vibrio kappa phage. Can J Microbiol 37(4):265–269
Biswas B, Adhya S, Washart P, Paul B et al (2002) Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun 70:204–210
Blanco M, Devoret R (1973) Repair mechanisms involved in prophage reactivation and UV reactivation of UV-irradiated phage lambda. Mutat Res 17(3):293–305
Bogovazova GG, Voroshilova NN, Bondarenko VM (1991) The efficacy of Klebsiella pneumoniae bacteriophage in the therapy of experimental Klebsiella infection. Zh Mikrobiol Epidemiol Immunobiol 4:5–8
Bogovazova GG, Voroshilova NN, Bondarenko VM, Gorbatkova GA et al (1992) Immunobiological properties and therapeutic effectiveness of preparations from Klebsiella bacteriophages. Zh Mikrobiol Epidemiol Immunobiol 3:30–33
Borysowski J, Górski A (2008) Is phage therapy acceptable in the immunocompromised host? Int J Infect Dis 12(5):466–471. doi:10.1016/j.ijid.2008.01.006
Brüssow H (2005) Phage therapy: the Escherichia coli experience. Microbiol 151:2133–2140
Brüssow H (2007) Phage therapy: the western perspective. In: McGrath S, van Sinderen D (eds) Bacteriophage: genetics and microbiology. Caister Academic Press, Norfolk, pp 159–192
Brüssow H, Canchaya C, Hardt W-D (2004) Phages and the evolution of bacterial pathogens: from enomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rew 68(3):560–602
Buffie C, Jarchum I, Equinda M, Lipuma L et al (2011) Profound alterations of intestinal microbiata following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun 80:62–73
Bull J, Levin B, DeRouin T, Walker N, Bloch C (2002) Dynamics of success and failure in phage and antibiotic therapy in experimental infections. BMC Microbiol 2:35
Cairns BJ, Timms AR, Jansen VAA, Connerton IF, Payne RJH (2009) Quantitative models of in vitro bacteriophage–host dynamics and their application to phage therapy. PLoS Pathog 5(1):e1000253
Campbell A (1988) Phage evolution and speciation. In: Calendar R (ed) The bacteriophages. Plenum Press, New York 1:1–14
Capparelli R, Nocerino N, Lanzetta R, Silipo A et al (2010) Bacteriophage-resistant Staphylococcus aureus mutant confers broad immunity against Staphylococcal infection in mice. PLoS ONE 5(7):e11720. doi:10.1371/journal.pone.0011720
Carlton RM (1999) Phage therapy: past history and future prospects. Arch Immunol Ther Exp 47(5):267–274
Casewell M, Friis C, Marco E, McMullin P, Phillips I (2003) The European ban on growth-promoting antibiotics and emerging consequences for human and animal health. J Antimicrob Chemother 52:159–161
CDC (2013) Vital signs: carbapenem-resistant Enterobacteriaceae. Morb Mortal Wkly Rep 62(9):165–170
Chee-Sanford JC, Mackie RI, Koike S, Krapac IG et al (2009) Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. J Environ Qual 38(3):1086–1108
Clark JR, March JB (2006) Bacteriophages and biotechnology: vaccines, gene therapy and antibacterials. Trends Biotechnol 24(5):212–218
Clemans D, Francoeur S, Liggit P, West B (2011) Antibiotic resistance, gene transfer, and water quality patterns observed in waterways near CAFO farms and wastewater treatment facilities. Water Air Soil Pollut 217(1–4):473–489
CSPI (2008) Fish and shellfish cause most foodborne illness outbreaks. CSPI Publishing Web http://www.foodproductiondaily.com/Safety-Regulation/Fish-and-shellfish-cause-most-foodborne-illness-outbreaks-CSPI. Accessed 26 November 2008
Duckworth DH, Gulig PA (2002) Bacteriophages: potential treatment for bacterial infections. BioDrugs 16:57–62
Duenas M, Borrebaeck CAK (1995) Novel helper phage design: intergenic region affects the assembly of bacteriophages and the size of antibody libraries. FEMS Microbiol Lett 125:317–321
Edgar R, Friedman N, Molshanski-Mor S, Qimron U (2012) Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl Environ Microbiol 78(3):744–751
EFSA (2009) The use and mode of action of bacteriophages in food production. EFSA J. 2009:1076 doi:10.2903/j.efsa.2009.1076. http://www.efsa.europa.eu/en/scdocs/doc/1076.pdf
Emanuele P (2010) Antibiotic resistance. AAOHN J 58(9):363–365. doi:10.3928/08910162-20100826-03
Endley S, Lu L, Vega E et al (2003) Male-specific coliphages as an additional fecal contamination indicator for screening fresh carrots. J Food Prot 66:88–93
FAO/OIE/WHO (2003) Expert workshop non-human antimicrobial usage and antimicrobial resistance. Geneva, December 1–5, 2003. WHO Publishing Web http://www.who.int/foodsafety/publications/micro/en/amr.pdf. Accessed 1-5 December 2003
Favrin SJ, Jassim SAA, Griffiths MW (2001) Development and optimization of a novel immunomagnetic separation–bacteriophage assay for the detection of Salmonella enterica Serovar enteritidis in broth. Appl Environ Microbiol 67(1):217–224
Favrin SJ, Jassim SAA, Griffiths MW (2003) Application of a novel immunomagnetic separation-bacteriophage assay for the detection of Salmonella enteritidis and Escherichia coli O157:H7 in food. Int J Food Microbiol 85:63–71
Fischer CR, Yoichi M, Unno H, Tanji Y (2004) The coexistence of Escherichia coli serotype O157:H7 and its specific bacteriophage in continuous culture. FEMS Microbiol Lett 241:171–177
Foley SL, Lynne AM (2008) Food animal-associated Salmonella challenges: pathogenicity and antimicrobial resistance. J Anim Sci 86(14):E173–E187
Foley SL, Lynne AM, Nayak R (2008) Salmonella challenges: prevalence in swine and poultry and potential pathogenicity of such isolates. J Anim Sci 86(14):E149–E162
Frieden T (2013) Antibiotics resistance threats in the United States. CDC Publishing Web http://www.cdc.gov/drugresistance/threat-report-2013/pdf/ar-threats-2013-508.pdf. Accessed 23 April 2013
Friman VP, Hiltunen T, Jalasvuori M, Lindstedt C et al (2011) High temperature and bacteriophages can indirectly select for bacterial pathogenicity in environmental reservoirs. PLoS ONE 6(3):e17651. doi:10.1371/journal.pone.0017651
FSA (2011) Foodborne disease strategy 2010–15: an FSA programme for the reduction of foodborne disease in the UK. Version 1.0. FDS Publishing Web http://www.food.gov.uk/multimedia/pdfs/fds2015.pdf. Accessed May 2011
Fujiwara A, Fujisawa M, Hamasaki R, Kawasaki T et al (2011) Biocontrol of Ralstonia solanacearum by treatment with lytic bacteriophages. Appl Environ Microbiol 77(12):4155–4162
Ganguly NK, Arora NK, Chandy SJ, Fairoze MN et al (2011) Rationalizing antibiotic use to limit antibiotic resistance in India. Indian J Med Res 134(3):281–294
Geller BL, Kraus J, Schell MD, Hornsby MJ (1998) High titer, phage-neutralizing antibodies in bovine colostrum that prevent lytic infection of Lactococcus lactis in fermentations of phage-contaminated milk. J Dairy Sci 81(4):895–900
Gerber P, Opio C, Steinfeld H (2007) Poultry production and the environment—a review. FAO publishing Web. http://www.fao.org/ag/againfo/home/events/bangkok2007/docs/part2/2_2.pdf
Gill JJ (2008) Modeling of bacteriophage therapy. In: Abedon ST (ed) Bacteriophage ecology: population growth, evolution, and impact of bacterial viruses. Cambridge University Press, Cambridge, pp 439–464
Gill JJ (2010) Practical and theoretical considerations for the use of bacteriophages in food systems. In: Sabour PM, Griffiths MW (eds) Bacteriophages in the control of food- and waterborne pathogens. ASM Press, Washington, pp 217–235
Golshahi L, Seed KD, Dennis JJ, Finlay WH (2008) Toward modern inhalational bacteriophage therapy: nebulization of bacteriophages of Burkholderia cepacia. J Aerosol Med Pulm Drug Deliv 21(4):351–360
Goode D, Allen VM, Barrow PA (2003) Reduction of experimental Salmonella and Campylobacter contamination of chicken skin by application of lytic bacteriophages. Appl Environ Microbiol 69(8):5032–5036
Goodridge L, Abedon ST (2003) Bacteriophage biocontrol and bioprocessing: application of phage therapy to industry. SIM News 53(6):254–262
Górski A, Wazna E, Dabrowska BW, Switala-Jelén K, Miedzybrodzki R (2006) Bacteriophage translocation. FEMS Immunol Med Microbiol 46:313–319. doi:10.1111/j.1574-695X.2006.00044.x
Górski A, Borysowski J, Miedzybrodzki R, Weber-Dabrowska B (2007) Bacteriophages in medicine. In: McGrath S, van Sinderen D (eds) Bacteriophage: genetics and molecular biology. Caister Academic Press, Norfolk, pp 125–158
Górski A, Miedzybrodzki R, Borysowski J, Weber-Dabrowska B et al (2009) Bacteriophage therapy for the treatment of infections. Curr Opin Investig Drugs 10:766–774
Graham JP, Boland JJ, Silbergeld EK (2007) Growth promoting antibiotics in food animal production: an economic analysis. Public Health Rep 122(1):79–87
Graham JP, Price LB, Evans SL, Graczyk TK, Silbergeld EK (2009) Antibiotic resistant enterococci and staphylococci isolated from flies collected near confined poultry feeding operations. Sci Total Environ 407(8):2701–2710
Grandgirard D, Loeffler JM, Fischetti VA, Leib SL (2008) Phage lytic enzyme Cpl-1 for antibacterial therapy in experimental pneumococcal meningitis. J Infect Dis 197:1519–1522
Gupt PK (2008) Regulation of gene expression in phage lambda. In: Gupt PK (ed) Molecular biology and genetic engineering. Rastogi Publisher, pp 236–244. ISBN 81-7133-719-8
Hagens S, Bläsi U (2003) Genetically modified filamentous phage as bactericidal agents: a pilot study. Lett Appl Microbiol 37(4):318–323
Harper DR, Kutter E (2009) Bacteriophage: therapeutic uses. Encyclopedia of life sciences. Wiley, Hoboken, pp 1–7
Harrison EM, Paterson GK, Holden MT et al (2013) Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Mol Med 5:509–515
Hawkins C, Harper D, Burch D, Anggård E, Soothill J (2010) Topical treatment of Pseudomonas aeruginosa otitis of dogs with a bacteriophage mixture: a before/after clinical trial. Vet Microbiol 146(3–4):309–313
Heller KJ (1992) Molecular interaction between bacteriophage and the Gram-negative cell envelope. Arch Microbiol 158:235–248
Hibma AM, Jassim SAA, Griffiths MW (1997) Infection and removal of L-forms of Listeria monocytogenes with bred bacteriophage. Int J Food Microbiol 34:197–207
Horrigan L, Lawrence RS, Walker P (2002) How sustainable agriculture can address the environmental and human health harms of industrial agriculture. Environ Health Perspect 110(5):445–456
Huff WE, Huff GR, Rath NC, Balog JM, Donoghue AM (2002a) Prevention of Escherichia coli infection in broiler chickens with a bacteriophage aerosol spray. Poult Sci 81(10):1486–1491
Huff WE, Huff GR, Rath NC, Balog JM et al (2002b) Prevention of Escherichia coli respiratory infection in broiler chickens with bacteriophage (SPR02). Poult Sci 81(4):437–441
Huff WE, Huff GR, Rath NC, Balog JM, Donoghue AM (2003a) Evaluation of aerosol spray and intramuscular injection of bacteriophage to treat an Escherichia coli respiratory infection. Poult Sci 82(7):1108–1112
Huff WE, Huff GR, Rath NC, Balog JM, Donoghue AM (2003b) Bacteriophage treatment of a severe Escherichia coli respiratory infection in broiler chickens. Avian Dis 47:1399–1405
Hughes J (2011) Preserving the lifesaving power of anti-microbial agents. JAMA 305:1027–1028
Inal JM (2003) Phage therapy: a reappraisal of bacteriophages as antibiotics. Arch Immunol Ther Exp 51:237–244
Jassim SAA (2005) Novel phyto-anti-HIV drugs: a cause for optimism. Biologist 52(5):268–272
Jassim SAA, Griffiths MW (2007) Evaluation of a rapid microbial detection method via phage lytic amplification assay coupled with Live/Dead fluorochromic stains. Lett Appl Microbiol 44:673–678
Jassim SAA, Limoges RG (2013) Impact of external forces on cyanophage–host interactions in aquatic ecosystems. World J Microbiol Biotechnol 29(10):1751–1762
Jassim SAA, Naji MA (2003) Novel antiviral agents: a medicinal plant perspective. J Appl Microbiol 95(3):412–427
Jassim SAA, Denyer SP, Stewart GSAB (1995) Selective virus culture. WO/1995/023848. http://patentscope.wipo.int/search/en/WO1995023848
Jassim SAA, Abdulamir AS, Abu Bakar F (2010) Methods for bacteriophage design. WO/2010/064044. http://www.wipo.int/pctdb/en/wo.jsp?WO=2010064044
Jassim SAA, Abdulamir AS, Abu Bakar F (2011) Phage-based limulus amoebocyte lysate assay for rapid detection of bacteria. WO2011/098820A1. http://www.sumobrain.com/patents/wipo/Phage-based-limulus-amoebocyte-lysate/WO2011098820A1.pdf
Jassim SAA, Abdulamir AS, Abu Bakar F (2012) Novel phage-based bio-processing of pathogenic Escherichia coli and its biofilms. World J Microbiol Biotechnol 28:47–60
Jose S (2010) Antibiotics: a global strategic business report. Global Industry Analysts, Inc. PrWeb http://www.prweb.com/releases/antibiotics/anti_infectives/prweb4688824.htm. Accessed 25 October 2010
Katsunori M (2003) Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture. Appl Environ Microbiol 69:170–176
Keen EC (2012) Phage therapy: concept to cure. Front Microbiol 3:238
Khachatourians GG (1998) Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria. Can Med Assoc J 159:1129–1136
Kiknadze GP, Gadua MM, Tsereteli EV, Mchedlidze LS, Birkadze TV (1986) Efficiency of preventive treatment by phage preparations of children’s hospital salmonellosis. In: Kiknadze GP (ed) Intestinal infections. Sovetskaya Meditsina, Tbilisi, pp 41–44
Kim K, Cha J, Jang E, Klumpp J et al (2008) PEGylation of bacteriophages increases blood circulation time and reduces T-helper type 1 immune response. Microb Biotechnol 1(3):247–257
Kittler S, Fischer S, Abdulmawjood A, Glünder G, Klein G (2013) Effect of bacteriophage application on Campylobacter jejuni loads in commercial broiler flocks. Appl Environ Microbiol 79(23):7525–7533
Klumpp J, Loessner MJ (2013) Listeria phages genomes, evolution, and application. Bacteriophage 3(3):e26861. https://www.landesbioscience.com/journals/bacteriophage/2013BACTERIOPHAGE0033R.pdf
Knobler SL, Lemon SM, Najafi M, Burroughs T (2003) The resistance phenomenon in microbes and infectious disease vectors: implications for human health and strategies for containment-workshop summary. National Academies Press, Washington, pp 44–106
Kudva IT, Jelacic S, Tarr PI, Youderian P, Hovde CJ (1999) Bio-control of Escherichia coli O157 with O157-specific bacteriophages. Appl Environ Microbiol 65:3767–3773
Kurtböke DI, Chen CF, Williams ST (1992) Use of polyvalent phage for reduction of streptomycetes on soil dilution plates. J Appl Bacteriol 72:103–111
Kutter EM (2005) Phage therapy: bacteriophages as natural, self-limiting antibiotics. In: Pizzorno JE, Murray MT (eds) Textbook of natural medicine. Churchill Livingstone, London, pp 1147–1161
Kutter E (2009) Bacteriophage therapy: past and present. In: Schaecter M (ed) Encyclopedia of microbiology. Elsevier, Oxford, pp 258–266
Kutter E, De Vos D, Gvasalia G, Alavidze Z et al (2010) Phage therapy in clinical practice: treatment of human infections. Curr Pharm Biotechnol 11(1):69–86
Laanto E, Bamford JKH, Laakso J, Sundberg L-R (2012) Phage-driven loss of virulence in a fish pathogenic bacterium. PLoS ONE 7(12):e53157. doi:10.1371/journal.pone.0053157
Laxminarayan R, Duse A, Wattal C, Zaidi AKM et al (2013) Antibiotic resistance- the need for global solutions. Lancet Infect Dis 13(12):1057–1098
Levin BR, Bull JJ (2004) Population and evolutionary dynamics of phage therapy. Nat Rev Microbiol 2:166–173. doi:10.1038/nrmicro822
Liljeqvist T, Andresen D, Zuo Y, Weston C (2012) Antibiotic resistance: moving forward to the past. NSW Public Health Bull 23(1–2):37
Loc-Carrillo C, Abedon ST (2011) Pros and cons of phage therapy. Bacteriophage 1:111–114. doi:10.4161/bact.1.2.14590
Loc-Carrillo C, Atterbury RJ, El-Shibiny A, Connerton PL et al (2005) Bacteriophage therapy to reduce Campylobacter jejuni colonization of broiler chickens. Appl Environ Microbiol 71(11):6554–6563
Lu L (2004). Autoinducer 2-based quorum sensing response of Escherichia coli to subtherapeutic tetracycline exposure. http://repository.tamu.edu/bitstream/handle/1969.1/4198/etd-tamu-2004B-FSTC-Lu.pdf?sequence=1
Lu T, Koeris M (2011) The next generation of bacteriophage therapy. Curr Opin Microbiol 14:524–531
Maloy S, Gardner J (1998) Use of P22 challenge phage to identify protein-nucleic acid binding sites. Tech Tips Online 3(1):111–119
Maloy S, Youderian P (1996) Genetic approaches for dissecting DNA-protein interactions in vivo. Am Biotechnol Lab 14:14–16
Manna SK, Brahmane MP, Manna C, Batabyal K, Das R (2006) Occurrence, virulence characteristics and antimicrobial resistance of Escherichia coli O157 in slaughtered cattle and diarrhoeic calves in West Bengal, India. Lett Appl Microbiol 43:405–409
Martin R (2004) How ravenous soviet viruses will save the world. Wired Publishing Web http://www.wired.com/wired/archive/11.10/phages_pr.html
Matinkhoo S, Lynch KH, Dennis JJ, Finlay WH, Vehring R (2011) Spray-dried respirable powders containing bacteriophages for the treatment of pulmonary infections. J Pharm Sci 100(12):5197–5205
Matsuzaki S, Rashel M, Uchiyama J, Sakurai S et al (2005) Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. J Infect Chemother 11:211–219
McIntyre L, Jassim SAA, Griffiths MW (1996) Development of a bacteriophage-mediated ATP bioluminescence detection system for Listeria monocytogenes. In: Abstract of the 83rd annual meeting of IAMFES. June 30-July 3, 1996, Seattle, WA, pp 70
Mellon M, Benbrook C, Benbrook KL (2001) Hogging it: estimates of antimicrobial abuse in livestock. Publishing UCS Web. http://www.ucsusa.org/assets/documents/food_and_agriculture/hog_front.pdf. Accessed 4 July 2004
Merril CR, Biswas B, Carlton R, Jensen NC et al (1996) Long-circulating bacteriophage as antibacterial agents. Proc Natl Acad Sci USA 93:3188–3192
Merril CR, Scholl D, Adhya SL (2003) The prospect for bacteriophage therapy in Western medicine. Nat Rev Drug Discov 2:489–497
Merril CR, Scholl D, Adhya SL (2006) Phage therapy. In: Calendar R (ed) The bacteriophage. Oxford University Press, Oxford, pp 725–746
Michod RE, Bernstein H, Nedelcu AM (2008) Adaptive value of sex in microbial pathogens. Infect Genet Evol 8(3):267–285
Mizoguchi K, Morita M, Fischer CY, Yoichi M et al (2003) Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture. Appl Environ Microbiol 69:170–176
Nathan C, Goldberg F (2005) The profit problem in antibiotic R&D. Nat Rev Drug Discov 4:887–891
Nayak R, Kenney PB, Keswani J, Ritz C (2003) Isolation and characterisation of Salmonella in a turkey production facility. Br Poult Sci 44:192–202
Nelson D, Loomis L, Fischetti VA (2001) Prevention and elimination of upper respiratory colonization of mice by group A streptococci by using a bacteriophage lytic enzyme. Proc Natl Acad Sci USA 98(7):4107–4112
Novotny L, Dvorska L, Lorencova A, Beran V, Pavlik I (2004) Fish: a potential source of bacterial pathogens for human beings. Vet Med- Czech 49(9):343–358
O’Hara A, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693
O’Sullivan D, Coffey A, Fitzgerald GF, Hill C, Ross RP (1998) Design of a phage-insensitive lactococcal dairy starter via sequential transfer of naturally occurring conjugative pPlasmids. Appl Environ Microbiol 64:4618–4622
Page SW, Gautier P (2012) Use of antimicrobial agents in livestock. Rev Sci Tech Off Int Epiz 31(1):145–188
Parracho HM, Burrowes BH, Enright MC, McConville ML, Harper DR (2012) The role of regulated clinical trials in the development of bacteriophage therapeutics. J Mol Genet Med 6:279–286
Payne RJH, Jansen VAA (2003) Pharmacokinetic principles of bacteriophage therapy. Clin Pharmacokinet 42:315–325. doi:10.2165/00003088-200342040-00002
Payne RJH, Phil D, Jansen VAA (2000) Phage therapy: the peculiar kinetics of self-replicating pharmaceuticals. Clin Pharmacol Ther 68:225–230. doi:10.1067/mcp.2000.109520
Pelczar MJ, Chan ECS, Krieg NR, Edwards DD, Pelczar MF (1993) Viruses: morphology, classification, replication. In: Pelczar MJ (ed) Microbiology concepts and applications. Mcgraw-Hill College, NY, pp 401–435
Phillips I, Casewell M, Cox T, Groot BD et al (2004) Does the use of antibiotics in food animals pose a risk to human health? a critical review of the published data. J Antimicrob Chemother 53:28–52
Potera C (2013) Phage renaissance: new hope against antibiotic resistance. Environ Health Perspect 121:48–53
Rees CE, Loessner MJ (2009) Phage identification of bacteria. In: Goldman E, Green LH (eds) Practical handbook of microbiology. CRC Press, Boca Raton, pp 85–94
Rieder E, Berinstein A, Baxt B, Kangt A, Mason PW (1996) Propagation of an attenuated virus by design: engineering a novel receptor for a noninfectious foot-and-mouth disease virus. Proc Natl Acad Sci USA 93:10428–10433
Robert JH, Phil PD, Jansen VAA (2000) Phage therapy: the peculiar kinetics of self-replicating pharmaceuticals. Clin Pharmacol Ther 68(3):225–230
Ryan EM, Gorman SP, Donnelly RF, Gilmore BF (2011) Recent advanced in bacteriophage therapy: how delivery routes, formulation, concentration and timing influence the success of phage therapy. J Pharm Pharmacol 63(10):1253–1264
Santander J, Robeson J (2007) Phage-resistance of Salmonella enterica serovar Enteritidis and pathogenesis in Caenorhabditis elegans is mediated by the lipopolysaccharide. Electron J Biotechnol 10(4):627–632. doi:10.1098/rspb.2001.1945
Sapkota AR, Hulet M, Zhang G, McDermott P (2011) Lower prevalence of antibiotic-resistant enterococci on U.S. conventional poultry farms that transitioned to organic practices. Environ Health Perspect 119:1622–1628
Saunders JR, Allison H, James CE, McCarthy AJ, Sharp R (2001) Phage-mediated transfer of virulence genes. J Chem Technol Biotechnol 76(7):662–666
Schuch R, Nelson D, Fischetti VA (2002) A bacteriolytic agent that detects and kills Bacillus anthracis. Nature 418(6900):884–889
Scott E (2003) Food safety and foodborne disease in 21st century homes. Can J Infect Dis 14(5):277–280
Sillankorva S, Pleteneva E, Shaburova O, Santos S (2010) Salmonella enteritidis bacteriophage candidates for phage therapy of poultry. J Appl Microbiol 108(4):1175–1186
Sillankorva SM, Oliveira H, Azeredo J (2012) Bacteriophages and their role in food safety. Int J Microbiol 2012: Article ID 863945. doi:10.1155/2012/863945
Smith HW, Huggins MB (1982) Successful treatment of experimental Escherichia coli infections in mice using phages: its general superiority over antibiotics. J Gen Microbiol 128:307–318
Smith HW, Huggins MB (1983) Effectiveness of phages in treating experimental Escherichia coli diarrhoea in calves, piglets and lambs. J Gen Microbiol 129:2659–2675
Smith HW, Huggins MB, Shaw KM (1987) The control of experimental Escherichia coli diarrhoea in calves by means of bacteriophages. J Gen Microbiol 133(5):1111–1126
Spits HB (2009) Bacteriophages for improvement of intestinal health in pigs and poultry. Master thesis, Faculty of Medicine, University of Utrecht. http://dspace.library.uu.nl/handle/1874/36365
Stewart GSAB, Jassim SAA, Denyer SP (1993) Engineering microbial bioluminescence and biosensor applications. In: Rapley R, Walker MR (eds) Molecular diagnostics. Blackwell Scientific Publications, Oxford, chap. 27, pp 403–423
Stewart GSAB, Jassim SAA, Denyer SP, Newby SP et al (1998) The specific and sensitive detection of bacterial pathogens within 4 h using bacteriophage amplification. J Appl Microbiol 84(5):777–783
Stokstad ELR, Jukes TH (1949) Further observations on the animal protein factor. Proc Soc Biol Exp Med 73:523–528
Sulakvelidze A (2011) Safety by nature: potential bacteriophage applications. Microbe 6(3):122–126
Sulakvelidze A, Barrow P (2005) Phage therapy in animals and agribusiness. In: Kutter E, Sulakvelidze A (eds) Bacteriophages: biology and application. CRC Press, Boca Raton, pp 335–380
Sulakvelidze A, Kutter E (2005) Bacteriophage therapy in humans. In: Kutter E, Sulakvelidze A (eds) Bacteriophages: biology and application. CRC Press, Boca Raton, pp 381–436
Sulakvelidze A, Alavidze Z, Morris JG Jr (2001) Bacteriophage therapy. Antimicrob Agents Chemother 45(3):649–659
Tanji Y, Shimada T, Fukudomi H, Miyanaga K et al (2005) Therapeutic use of phage for controlling Escherichia coli O157:H7 in gastrointestinal tract of mice. J Biosci Bioeng 100:280–287
Tauxe RV (1997) Emerging foodborne diseases: an evolving public health challenge. Emerg Infect Dis 3:425–434
Topley WWC, Wilson GS (1990) Principles of bacteriology, virology and immunity. B.C. Decker Publisher, London, pp 427–480
US Congress (2011) H.R.965 (112th): Preservation of antibiotics for medical treatment act of 2011. 112th Congress, 2011–2013. Publishing Govtrack Web. https://www.govtrack.us/congress/bills/112/hr965/text. Accessed 9 March 2011
USFDA (2006) Food additives permitted for direct addition to food for human consumption; bacteriophage preparation. FDA, Washington, DC. Publishing FDA Web. http://www.fda.gov/OHRMS/DOCKETS/98fr/cf0559.pdf. Accessed 3 August 2006
Verheust C, Pauwels K, Mahillon J, Helinski DR, Herman P (2010) Contained use of bacteriophages: risk assessment and biosafety recommendations. Appl Biosaf 15(1):32–44
Vojtek I, Pirzada ZA, Henriques-Normark B, Mastny M et al (2008) Lysogenic transfer of group A Streptococcus superantigen gene among streptococci. J Infect Dis 197(2):225–234
Wagenaar JA, Van Bergen MA, Mueller MA, Wassenaar TM, Carlton RM (2005) Phage therapy reduces Campylobacter jejuni colonization in broilers. Vet Microbiol 109(3–4):275–283
Wagner PW, Waldor MK (2002) Bacteriophage control of bacterial virulence. Infect Immun 70(8):3985–3993
Westwater C, Kasman LM, Schofield DA, Werner PA et al (2003) Use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections. Antimicrob Agents Chemother 47(4):1301–1307
Wright A, Hawkins CH, Änggård EE, Harper DR (2009) A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Clin Otolaryngol 34(4):349–357
Yan F, Polk B (2004) Commensal bacteria in the gut: learning who our friends are. Curr Opin Gastroenterol 20:565–571
Yosef I, Kiro R, Molshanski-Mor S et al (2014) Different approaches for using bacteriophages against antibiotic-resistant bacteria. Bacteriophage 4:e28491
Zhukov-Verezhnikov N, Peremitina L, Berillo E, Komissarov V et al (1978) A study of the therapeutic effect of bacteriophage agents in a complex treatment of supportive surgical diseases. Sov Med 23:64–66
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
About this article
Cite this article
Jassim, S.A.A., Limoges, R.G. Natural solution to antibiotic resistance: bacteriophages ‘The Living Drugs’. World J Microbiol Biotechnol 30, 2153–2170 (2014). https://doi.org/10.1007/s11274-014-1655-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11274-014-1655-7