viruses Review Framing the Future with Bacteriophages in Agriculture Antonet Svircev 1,*, Dwayne Roach 2 and Alan Castle 3 1 Agriculture and Agri-Food Canada, Vineland Station, ON L0R 2E0, Canada 2 Department of Microbiology, Pasteur Institute, 75015 Paris, France; dwayne.roach@pasteur.fr 3 Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada; acastle@brocku.ca * Correspondence: Antonet.Svircev@agr.gc.ca; Tel.: +905-562-2018 Received: 27 March 2018; Accepted: 22 April 2018; Published: 25 April 2018 ���������� ������� Abstract: The ability of agriculture to continually provide food to a growing world population is of crucial importance. Bacterial diseases of plants and animals have continually reduced production since the advent of crop cultivation and animal husbandry practices. Antibiotics have been used extensively to mitigate these losses. The rise of antimicrobial resistant (AMR) bacteria, however, together with consumers’ calls for antibiotic-free products, presents problems that threaten sustainable agriculture. Bacteriophages (phages) are proposed as bacterial population control alternatives to antibiotics. Their unique properties make them highly promising but challenging antimicrobials. The use of phages in agriculture also presents a number of unique challenges. This mini-review summarizes recent development and perspectives of phages used as antimicrobial agents in plant and animal agriculture at the farm level. The main pathogens and their adjoining phage therapies are discussed. Keywords: bacteriophage; phage therapy; sustainable agriculture; zoonosis; antibiotic resistance 1. Introduction The goal of sustainable agriculture is to implement practices that will attain healthy disease-free plants and animals, provide safe food for a growing global population, and minimize the impact of agricultural practices on the environment [1–3]. Conversely, agricultural practices are impacted by economic and disease pressures, consumer preferences, geographic location, weather conditions, and government regulations. Following the Second World War, antibiotics have been incorporated into animal husbandry [4,5] and for the control of plant pathogens [6–10]. Important strides in phage therapy were overshadowed by the widespread usage of antibiotics to treat diseases in humans, animal husbandry, and the control of bacterial plant pathogens. The overuse in medicine and animal husbandry has contributed to the rise of worldwide antimicrobial resistant (AMR) bacteria. Using Erwinia amylovora as an example, antimicrobial resistance is present in a number of geographic locations where antibiotics have been overused in apple and pear orchards [6–8,10]. The debate and scientific discussion on the impact and consequences of the presence of streptomycin resistant E. amylovora in orchards still continues in scientific literature [11]. Most antibiotics are non-specific, acting not only against the target pathogen, but also against other bacteria naturally present in the environment or plant and animal microflora. Drug-resistant infections result in millions of people being affected from drug-resistant bacteria each year, with an estimated 700,000 deaths worldwide each year, a number that could increase to 10 million by 2050 if the drug resistance trend continues [12]. Imprudent use of antimicrobials in agriculture may result in reduced efficacy of antibiotics due to facilitated emergence of antibiotic resistant human pathogens, increased human morbidity and mortality, increased healthcare costs, and increased potential for carriage and Viruses 2018, 10, 218; doi:10.3390/v10050218 www.mdpi.com/journal/viruses http://www.mdpi.com/journal/viruses http://www.mdpi.com http://www.mdpi.com/1999-4915/10/5/218?type=check_update&version=1 http://www.mdpi.com/journal/viruses http://dx.doi.org/10.3390/v10050218 Viruses 2018, 10, 218 2 of 13 dissemination of pathogens. Together with consumers’ calls for antibiotic-free products, popularity of organic products and the removal of antibiotics for agricultural use in certain jurisdictions have led to the search for alternatives. Use of phages, which infect and destroy bacteria, could significantly reduce the environmental impact of antibiotic use in agriculture, while potentially increasing profitability by lowering crop loss or animal mortality in early stages of the breeding process. 2. Phages in Agriculture “What is the impact of phages on agricultural environments where sustainable agriculture is being practiced?” becomes an important and intriguing question. Phages are inherently highly specific towards bacterial hosts. This characteristic has both negative and positive aspects in that it is beneficial in terms of avoiding negative effects on the host microbiota and a hindrance when it comes to detection and elimination of the target pathogen. This mini-review will focus primarily on the progress of phage-based biocontrol in food production systems covering the past 10 years. Phage-based laboratory studies that include phage isolation, host range determination, molecular characterization, genomic and proteomics analyses are well described in the recent review articles on plant and animal-associated phage therapy [13–17]. The development of phages as antimicrobial agents in animal and plant production systems follows a similar path in the initial discovery stage however the processes become divergent in the implementation processes. In the following sections we discuss the progress made in the use of phages in plant and animal farming, focusing on the challenges and success stories reported in scientific literature. 3. Bacteriophages in Food Animal Production By volume, the vast majority of antibiotics consumed worldwide are for veterinary purposes, predominantly in intensive and large-scale animal production systems, such as dairy, livestock, poultry, and aquaculture [18,19]. Animal husbandry practices widely use antibiotics therapeutically to treat infectious diseases, as well as non-therapeutically to prevent the spread of disease (prophylaxis) and to promote growth. Controversy, however, surrounds the widespread use of antibiotics for animal production, as their overuse and possible misuse is driving antibiotic microbial resistance. For instance, the practice of prolonged exposure to sub-therapeutic antibiotic doses, the context in which prophylactic and growth-promoting antibiotics are administered, exerts an inestimable amount of selective pressure toward the emergence of AMR [20,21]. Furthermore, AMR bacteria and AMR genes of animal origin can then be transmitted to humans through environmental contamination, food distribution, or direct contact with farm animals [22–24]. Intensive animal production systems necessitate antibiotics to keep animals healthy and maintain productivity, and with rising incomes in transitioning countries expected to boost antibiotic consumption by 67% by 2030 [25], this presents a major health risk to humans and animals. The World Health Organization, the European Commission, the Centers for Disease Control and Prevention, and Health Canada, to name a few, all support immediate antimicrobial stewardship in animal food production, aimed primarily at reducing or eliminating the nontherapeutic use of medically important antibiotics. Eliminating prophylactic antimicrobials outright may not be feasible in intensive animal production systems due to increasing worldwide demand for protein, the potential compromise in animal welfare and health, and in human health and food safety. Phages instead of antibiotics are a promising option in food animal production to maintain animal health and limit the transfer of AMR and zoonotic pathogens that may be harmful to consumers. This section will focus only on application of phages as alternatives to antibiotic growth promoters, prophylaxis, and zoonotic pathogen animal decolonization at the farm level. 3.1. Phages as Growth Promoters Antibiotics in subtherapeutic doses have played important roles in the promotion of growth, enhancement of feed efficiency and improvement of the quality of animal products [20]. To combat the Viruses 2018, 10, 218 3 of 13 increased rate of mortality and morbidity due to reduction of in-feed antibiotics, phages have been proposed as the replacement, particularly in the early stages when vaccination is not possible and the maintenance of the bacterial ecosystem is crucial [26]. The studies reviewed in this subsection highlight the addition of phages in feed rather than for clinical treatment. The distinction between growth promotion and prevention or treatment of diseases is subtle and further work is needed to see if phages do offer growth promotion effects other than simply reducing disease incidence. Clostridium perfringens is a major problem for the poultry industry, resulting in both clinical and subclinical infections. A cocktail of five phages could effectively control necrotic enteritis in chicken broilers and thus improve feed conversion ratios and weight gain [27]. This efficacy was independent of whether the phages were administered in feed or in drinking water. Dietary supplementation with phages has also been shown to improve on growth performance in pigs [28]. Feed supplemented with a commercial phage product, which contained a mixture of phages targeting several pathogens, including Salmonella spp., Escherichia coli, Staphylococcus aureus, and C. perfringens, improved different aspects of grower pig’s performance, such as average daily feed intake [28]. It was determined that barrow gut health improved with a higher abundance of commensal bacterial and lower pathogen load in pig faeces. However, the success of phages against pathogenic bacteria could be related to the method of its addition. Administering phages in drinking water may be disease and/or pathogen dependent. Huff et al. [29] found that phage administered in drinking water could not cure experimental E. coli respiratory infections in broilers. Phages were only effective in reducing respiratory bacterial load when they were administered via direct intratracheal administration [30]. For dairy herds, mastitis is the most important disease worldwide [31]. S. aureus, one of the etiological agents for mastitis, which has a propensity to recur chronically, causes a potentially fatal inflammatory response in gland tissues. In an experimental model, lactating mice intramammarily infected with a clinical bovine S. aureus strain showed significant improvement in mammary gland pathology and a 4-log reduction in bacterial load after phage treatment [32]. However, compared to the antibiotic cefalonium, the phage treatment was far less effective. Gill et al. [33] also found that multiday high-titre intramammary infusions of phage K did not lead to a reduction in S. aureus load in the utter of lactating cows with pre-existing subclinical mastitis [34]. In this latter study, the adsorption of milk whey proteins to the S. aureus cell surface inhibited phage infection in vitro, suggesting this was the cause for treatment failure [33]. It should be noted that antibiotic treatment success is also highly variable with mastitis cure rates as low as 4% [35]. Phages have the potential to be a viable and eco-friendly alternative to antibiotics in aquaculture. Aquaculture is the fastest growing food production sector, providing over fifty percent of the world’s supply of fish and seafood. Antibiotics in feed are commonly used as prophylactics to decrease the corresponding heavy economic losses due to bacterial diseases worldwide. Vibriosis is one of the most prevalent diseases of marine and estuarine fish in both natural and commercial production [36–38]. Vibrio anguillarum is the etiologic agent of vibriosis, a fatal haemorrhagic septicaemia that affects more than 50 fresh- and salt-water fish species including several important food species, such as the Atlantic salmon, rainbow trout, turbot, sea bass, and sea bream [36]. A single phage treatment protected 100% of Atlantic salmon against experimentally induced V. anguillarum infection [39]. Vibriosis also causes high mortality rates in fish larvae. Phages administered in culture water of zebrafish larvae experimentally infected with V. anguillarum significantly lowered larvae mortality [38]. Likewise, phages added to culture water of shrimp larvae improved survival after experimental infection with Vibrio harveyi [40]. Thus, directly supplying phages to the culture water could be an effective and economical approach toward reducing the negative impact of vibriosis in aquaculture, in particular when vaccines are not an option to protect larvae. Other experimental aquaculture models have also shown promising phage efficacy. For instance, phages in-feed has been shown to protect against water-borne Pseudomonas plecoglossicida infection, the etiological agent of bacterial haemorrhagic ascites in freshwater fish, including ayu, pejerrey, rainbow trout, and large yellow croaker [41]. In a field trial, phage-impregnated feed was added to the Viruses 2018, 10, 218 4 of 13 fishpond where P. plecoglossicida was naturally present and daily ayu mortality of fish decreased by 30% after multiple weeks of prophylaxis. Moreover, neither phage-resistant bacteria nor phage-neutralizing antibodies were detected in infected or cured fish [42]. 3.2. Phages that Combat Zoonotic Pathogens Phages offer a non-antibiotic method to improve food safety as a preharvest intervention to reduce zoonotic pathogens from the food supply. For instance, contaminated poultry, pork, beef, and fish have led to food poisoning and food-related disease. Often, food-borne pathogen contamination of meat products occurs during processing when carcasses are exposed to infected animal faeces. Campylobacteriosis caused by Campylobacter jejuni, is the most frequent food-borne human enteritis in developed countries, the major source being tainted poultry meat. Loc Carrillo et al. [43] showed that an antacid solution containing phages given orally could effectively decolonize the gut of birds experimentally colonized with C. jejuni. Under commercial conditions, however, phage decontamination success was highly variable. When a phage cocktail was added to the drinking water at three commercial farms with broilers confirmed to be colonized with Campylobacter spp., only one farm experienced a reduction in bacterial load (<50 CFU/g) in faecal samples [44]. For the other two farms, no significant reduction occurred for undetermined reasons. Salmonellosis is another common cause of gastroenteritis in humans. Pigs can become colonized with Salmonella spp. from contaminated trailers and holding pens, resulting in increased pathogen shedding just prior to processing. Wall et al. [19] showed that administration of a phage cocktail at the time of experimental inoculation with Salmonella enterica serovar Typhimurium reduced bacterial load to almost undetectable limits in the tonsils, ileum, and cecum of infected small pigs. A phage cocktail significantly reduced cecal and ileal Salmonella concentrations by up to 95% after being in a highly contaminated holding pen. S. enteritidis is also a prevalent foodborne pathogen, its main reservoir being the eggshell. Use of a mixture of three different Salmonella-specific phages to reduce S. enteritidis colonization in the ceca of laying hens resulted in a significant decrease in bacterial prevalence of incidence of up to 80% [45]. E. coli is typically a commensal member of human and animal microbiota. However, certain strains can cause a variety of human diseases, including urinary tract infections, haemorrhagic colitis, appendicitis and septicaemia. The most notorious zoonotic strains are those referred to as Vero-Toxigenic E. coli (VTEC). The most common member of this group is strain O157:H7 and the natural reservoir is the cattle gut. A cocktail of phages isolated from cattle faeces was able to reduce O157:H7 populations in the gut of experimentally inoculated sheep, with a 1:1 ratio of phage to bacteria found to be more effective than higher phage ratios [46]. Upon necropsy, E. coli populations were found to be reduced in both the cecum and colon, while ruminal load was not significantly changed, likely due to a relatively low starting population [46]. 4. Bacteriophages in Crop Production The discovery research on phages and plant pathogens took place nine years following the highly disputed discovery of phages by Frederic Twort in 1915 and Felix D’Herelle in 1917 [47]. The first experimental evidence that phages may be associated with plant pathogenic bacteria occurred when it was demonstrated that a filtrate obtained from decomposing cabbage was able to inhibit cabbage-rot caused by Xanthomonas campestris pv. campestris [48]. The following year, Kotila and Coons [49] demonstrated that the exposure of Pectobacterium atrosepticum to phages prevented the development of soft rot in potatoes. The first recorded field trial occurred in 1935, when Stewart’s wilt disease of corn, caused by Pantoea stewartii, was reduced by pre-treatment of seeds by phages [50]. In a 2012 survey, bacterial pathologists that read the Journal Molecular Plant Pathology were asked to list three important plant pathogens [51]. The top 10 plant pathogens listed in descending order were Pseudomonas syringae, Ralstonia solanacearum, Agrobacterium tumefaciens, Xanthomonas spp., Erwinia amylovora, Xylella fastidiosa, Dickeya spp., and Pectobacterium spp. Lack of chemical control Viruses 2018, 10, 218 5 of 13 options and development of antibiotic resistance in many plant pathogens combined with consumers’ preference for organic and antibiotic free products has led to a phage therapy renaissance in agriculture. 4.1. Soft Rot, Bacterial Wilt, and Blight Dickeya solani and Pectobacterium spp. are pathogens associated with potato tuber soft rot in storage and blackleg disease in the field [52,53]. Adriaenssens [52] used two Dickeya sp. Myoviridae phages as biological control agents for the control of soft rot/blackleg in potato. Potato tubers were vacuum infiltrated with the pathogen and the phages were sprayed (nebulised) at MOI of 10 and/or 100 over the infested tubers. Treated tubers were planted in the field and the disease progression was monitored through the growing season. There was no significant difference between the treated control, untreated controls, and the phage/bacteria treatments. To study the ability of the phage mixtures to control multiple pathogen species associated with bacterial soft rot, two broad host range phages [53] and 9 phage mixtures [14] were tested on potato slices but not in the field. Czajkowski [14] provides in a recent review a detailed summary on the advances in research on the phages of the soft rot bacteria. Pre-treatment with a Podoviridae phage PE204 under growth chamber conditions did not achieve control of R. solanacearum, the cause of bacterial wilt of tomato [54]. Single phage and/or cocktails composed of commercial phage mixtures were applied as a soil drench with an attenuated Xanthomonas perforans isolate. Phage populations were followed in the treatments in the root zone and the inside of plants. Partial translocation of phages occurred into the lower portions of the tomato plant and greenhouse and field trials demonstrated that in the presence of X. perforans mutant phage populations increased on leaf surfaces and in the soil [55]. Pseudomonas syringae pathovars are responsible for a large number of plant diseases in agriculture [51,56]. The recent serious global outbreak of P. syringae pv. actinidae in kiwifruit production and the lack of control options has re-focused research onto phages [57,58]. To date, this research has focused on phage characterization by host range and genomic studies. Two parallel field trials in three locations were conducted for the control of P. syringae pv. porri, bacterial blight of leek [59]. The treatments involved a 6-phage cocktail and plants that were either pre-treated with phage and then infected by the pathogen or treated with pathogen followed by the phage cocktail at 109 pfu/ml. Statistically significant difference between treatment and control were not obtained and the results were highly variable between the locations. 4.2. Citrus Bacterial Canker and Spot Balogh (2008) studied phage-mediated control of Xanthomonas axonopodis pv. citri, Asiatic citrus canker (ACC) and X. axonopodis pv. citrumelo, citrus bacterial spot (CBS). Treatments without skim milk, used to stabilise the phage, additive significantly reduced ACC disease severity. In nursery trials, the ability of phage mixtures, copper-mancozeb, and the combination of phage-copper-mancozeb to control CBS and ACC were tested. Phages reduced ACC disease significantly but were not as effective as the copper-macozeb treatment alone. The phage-copper-mancozeb combined treatment failed. Similar results were seen for CBS, where phage control was significantly different from the control in Valencia oranges but not in grapefruit under low disease pressures [60]. Ibrahim et al. [61] obtained successful control of Asiatic citrus canker in greenhouse and field trials, by combing a compound which induced the plants systemic acquired resistance and phage mixtures formulated in skim milk and sugar. 4.3. Pierce’s Disease of Grape Xylella fastidiosa is a pathogen of a number of plants but it has the greatest economic impact in grapes. Disease control options are limited and challenging since the pathogen is limited to the xylem of the grape [62]. Recently, two lytic phages of X. fastidiosa subsp. fastidiosa have been isolated and Viruses 2018, 10, 218 6 of 13 fully characterised [63]. Phage cocktails in grape using therapeutic and prophylactic treatments were able to significantly control the pathogen and symptom development in greenhouse trials. 4.4. Fire Blight in Apples and Pears The causal organism of fire blight, Ewinia amylovora, is a major pathogen in commercially grown apples and pears. The pathogen can exist in asymptomatic tissue or as an epiphyte in the orchard ecosystem [9]. All commercially desirable apple and pear cultivars are moderately to highly susceptible to this pathogen and resistant germplasm is not available. In Canada and the US, streptomycin and kasugamycin are applied during open bloom to obtain control of the fire blight pathogen [6,11]. In growing regions where streptomycin resistance is present and/or organic fruit is grown, the use of antibiotics is prohibited and alternative control strategies for integrated pest management practices are urgently needed. Phages combined with Pantoea agglomerans, non-pathogenic host, belonging to the Myoviridae and Podoviridae have been tested under greenhouse [64] and field conditions [16,65] for their ability to control the pathogen during open bloom. The highly variable seasonal variation in biological control is not uncommon and it serves as one of the biggest challenges to the commercial development of phages in agriculture. 4.5. Impact of Host Exopolysaccharides and Phage Family on Efficacy E. amylovora pathogenicity is largely determined by the presence of amylovoran, a capsular exopolysaccharide (EPS), while virulence is associated with levan, a secondary component of the bacterial capsule [66]. Roach et al. [67] showed that the structure of the host cell surface plays a very important role in phage pathogenesis. Isolates of E. amylovora characterised as producing relatively large amounts of EPS, were called high EPS producers (HEPs) and low producers were labelled low EPS producers (LEPs). Phages in the Myoviridae grew better on LEPs than HEPs. In contrast, most but not all Podoviridae phages exhibited improved replication on HEPs hosts as measured by efficiency of plating. Deletion of genes required for the production of amylovoran and levan provided further insight into the function of the cell surface in phage growth. Deletion of the rcsB gene, which prevented synthesis of the EPS component amylovoran, resulted in almost complete resistance to most podoviruses tested. The effect of this deletion on myoviruses was variable with one phage showing a reduction in the efficiency of plating (EOP) and two others showing an increase, suggesting that amylovoran is likely not a significant contributor to phage pathogenesis for these phages. In contrast, deletion of the levansucrase gene, lsc, had little impact on the pathogenesis of podoviruses but resulted in a reduction of EOP by one to two orders of magnitude for myoviruses. These observations have three important implications on the impact of the use of these phages in a program to control E. amylovora. First, phages in the Podoviridae will likely have little to no impact on other bacterial epiphytes in the orchard because amylovoran synthesis is limited to E. amylovora. This prediction has been validated by tests on P. agglomerans. This epiphytic species does not produce amylovoran and the majority of the isolates do not support the growth of E. amylovora podoviruses). Second, one of the likely mechanisms by which E. amylovora could become resistant would be through a mutation that prevents amylovoran production. This would result in an avirulent bacterium that would greatly reduce the chance of survival. Thus, podoviruses should be included in any biocontrol formulation with the goal of reducing fire blight. Third, myoviruses should also be included in the formulation to increase the probability of inhibiting growth of all E. amylovora strains, including the LEPs. 5. Potential Problems with Phages as Biocontrol Agents The development of phage resistance in the bacterial host is a major concern in phage therapy. Just as bacteria may become resistant to antibiotics they may also become resistant to phages by a variety of mechanisms. These include modification of the phage surface receptors on the bacterial cell such as conversion to mucoidy [68], integration of the phage genome into the bacterial Viruses 2018, 10, 218 7 of 13 chromosome [57,69], restriction/modification systems [70], CRISPR/Cas systems [71,72], BREX [73], DISARM [74], and up to 9 new defense systems [75]. To prevent the development of bacterial resistance to phages the standard adopted practice has been to use a mixtures or cocktails that may contain combinations of phages with host ranges that are narrow, wide and/or composed of host range mutants [27,53,59,60,76]. One intriguing possible outcome of the use of a phage mixture is bacteria that are resistant to a particular phage can still be lysed by that phage through the acquisition of phage receptors from lysed sensitive cells. This effect has been observed during infection of Bacillus subtilis with phage SPP1 [77]. It will be important to investigate if the transfer of receptors is a phenomenon that extends well beyond this one example. Another potential hurdle with the use of phages as biological agents is the production of lysogens or pseudolysogens. Persistence of the phage genome in the host cell would provide superinfection immunity that would negate the efficacy of the biological and possibly impart novel characteristics to the target bacterium. For example, ΦRSS1, a phage that exists in a persistent infective state in R. solanacearum increases virulence of the bacterial host on tomato [78]. Although this risk clearly exists, the scope of the problem remains poorly understood. Roach et al. [69] examined the prevalence of lysogens of myoviruses and podoviruses in 161 isolates of E. amylovora and 82 of P. agglomerans. None was detected. Use of phages to recover bacteriophage insensitive mutants (BIMs), however, showed that lysogeny was possible with the recovery of one stable lysogen. In addition, PCR analysis indicated that phage DNAs could be detected in subcultures of numerous BIMs for up to a year after selection although the association of phage and host was unstable. The authors concluded that though lysogeny could occur, it was likely to be selected against in the resource rich environment of the apple or pear blossom. As such, the risks associated with lysogeny were low. Nonetheless, this possibility should be considered for any application of phages for biocontrol. A third potential hurdle is that phages could serve as vectors for mobile genetic elements, including antibiotic resistance genes [79,80]. Colavecchio et al. [81] recently reviewed the literature on the role of phages in the spread of AMR genes amongst members of the Enterobacteriaceae. These genes could certainly be transferred horizontally by transducing phage particles. The contribution of transduction to AMR spread, however, may be low as compared to conjugation or transformation. This issue is currently unresolved and deserves further attention. Many bacterial pathogens form biofilms, which in turn impact phage therapy. In E. amylovora, amylovoran and levan contribute to the formation of a biofilm [82], yet phage efficacy bioassays continue to be carried out in liquid cultures. Today, models of phage–host interactions should take into consideration that biofilms form a spatial environment where resources are concentrated and bacterial materials and debris build up as cell numbers increase [83]. All these factors will influence the ability of the phage to adsorb and kill the bacterial host. Laboratory studies that use liquid cultures to study phage-host interactions are poor indicators of phage efficacy under greenhouse and/or field conditions. In a recent publication, Abedon [84] provides an excellent treatise on how phage therapy can be improved by incorporating important standards such as the Poisson distribution curve when reporting on the infection of host cells by phage and the avoidance of the commonly used MOIs to report phage dosages. 6. Discussion Present-day research indicates that phages have the potential as an alternative control mechanism for eliminating pathogens posing a threat to animals and plants (Table 1), particularly with the increased risk of AMR and regulatory restrictions on the use of antibiotics in agriculture. Phages developed for the control of plant and animal pathogenic, zoonotic, and problematic bacteria exploit the multiple and complex host–microbe interactions to significantly reduce disease, reduce economic losses, and minimize the effect on the environment and on non-target microorganisms. In animal production, the focus of using phages as antimicrobial agents has been on controlling human and zoonotic pathogens. Viruses 2018, 10, 218 8 of 13 Table 1. Experimental studies using bacteriophages to control bacterial pathogens. Target Species Disease/Issue Animal/Plant Study Clostridium perfringens necrotic enteritis poultry [27] C. perfringens, E. coli, S. aureus weight gain swine [28] Escherichia coli respiratory infection poultry [29,30] Staphylococcus aureus mastitis bovine [32,33] Vibrio anguillarum vibriosis fish [38,39] Vibrio harveyi vibriosis shrimp [40] Pseudomonas plecoglossicida haemorrhagic ascites fish [41,42] Campylobacter jejuni zoonotic poultry [43,44] Salmonella enterica serovar Typhimurium zoonotic swine [19] Salmonella enteriditis zoonotic poultry [45] Escherichia coli colitis sheep [46] Xanthomonas campestris pv. campestris cabbage rot cabbage [48] Pectobacterium atrosepticum soft rot potato [49,52] Pantoea stewartii Stewart’s wilt corn [50] Dickeya solani, Pectobacterium spp. soft rot/blackleg potato [52,53] Ralstonia solanacearum bacterial wilt tomato [54] Pseudomonas syringae pv. actinidae canker kiwifruit [57,58] Pseudomonas syringae pv. porri bacterial blight leak [59] Xanthomonas axonopodis pv. citrumelo bacterial spot citrus [60] Xanthomonas axonopodis pv. citri canker citrus [61] Xylella fastidiosa Pierce’s disease grape [63] Erwinia amylovora fire blight apple/pear [16,64,65] In plant agriculture, control with phages has been difficult to implement due to a number of challenges. These include development of formulations to effectively treat hectares of plants grown in monoculture and/or in greenhouse conditions, assessing susceptible hosts including both bacterial pathogen and plant interactions as well as phage–bacterium matches, persistent pathogen presence, transmission of the pathogen by wind, rain, and insects, modern day farming practices that rely on chemical pesticides that may be deleterious to the phage, and unpredictable weather patterns within and between growing seasons. Timing of the biocontrol delivery is crucially important. Therapeutic treatments may involve phage application to reduce a pre-existing pathogen population or an application timed to the expected arrival of the pathogen [52,55,59,64,85]. For prophylactic treatment, phages are introduced prior to the anticipated appearance of the pathogen [59,85]. Efficacy of both options should be evaluated as part of a biocontrol development program. Aerial phage applications require formulations that will ensure the survival of the phage in the environment [60,61,76,86]. The alternative application methodology is to utilize a living bacterial cell delivery system that ensures survival and continued replication of the phages prior to the arrival of the pathogen [16,65]. For example, live cells of an attenuated bacterial strain of Xanthomonas perforans were used to improve the persistence of the phage populations in and on the soil [55]. In animal production, much of the focus of using phages as antimicrobial agents has been on controlling bacterial infection. The benefits of antibiotics in animal feed have added benefits in production. For instance, Thomke and Elwinger [87] hypothesize that cytokines released during the immune response may also stimulate the release of catabolic hormones, which reduce muscle mass. In addition, there is evidence that antibiotics suppress microbial fermentation in the gastrointestinal tract improving feed conversion by up to 6% (Jensen, 1998). Recent studies showed that a sub-therapeutic antibiotic correlates with the decreased activity of bile salt hydrolase, an intestinal bacteria-produced enzyme that exerts negative impact on host fat digestion and utilization [88]. Regardless of the mechanism of action, the use of animal growth promoters can improve daily growth rates between 1% and 10% resulting in meat of better quality with less fat and increased protein content. It will be important to explore whether phages provide similar growth enhancing effects beyond the benefits of controlling infectious diseases. Phages can also be used in post-slaughter or later processing systems as decontaminants, including the FDA approved commercial products ListShield™ (Intralytix, Baltimore, MD, USA) and PhageGuard L™ (formerly Listex™) (Micreos Food Safety B.V., Wageningen, Netherlands) as food additives for prevention of meat contamination with Listeria monocytogenes [89]. Viruses 2018, 10, 218 9 of 13 EcoShield™ (Intralytixs) for E. coli and SalmoFresh™ (Intralytix) for Salmonella spp. are also FDA approved to decontaminate ready-to-eat meat and poultry, fish and seafood, and dairy products. Plant and animal phage development systems in food agriculture have their own distinct and specialised processes, protocols, and challenges. Regardless of the agricultural application, the process itself should be better defined, organized, and laid out. The science innovation chain for the development of biologicals or biopesticides was developed by Boyetchko [90]. This model defines and designates specific steps and processes that workers should address in the developed of phage biologicals (synonym in agriculture biopesticide). The project deliverables, arranged in continuous and ascending order, include acquisition of scientific knowledge, greenhouse/field/animal efficacy trials, fermentation/formulation, defining of markets, license agreements, large scale field test, manufacturing/process engineering, production of phage product, and product sales/client adoption. Concurrent with the deliverables and in the same ascending order, a series of stages and/or gates include discovery and selection of phages, proof of concept that the therapy works, technology development, market identification, technology transfer, commercial scale up, registration/regulatory processes, and technology adaptation by end users. This type of a model takes into consideration work beyond the laboratory and basic science and provides basic guidelines to the processes and decision points that need to be addressed during the development of a phage biological that can be successfully used in agriculture. Author Contributions: Antonet Svircev, Dwayne Roach and Alan Castle contributed equally to the concept and writing of the mini-review. Darlene Nesbitt (Agriculture Agri-Food Canada) edited the manuscript. Funding: Dwayne Roach was supported by a European Respiratory Society Fellowship (RESPIRE2-2015-8416). Alan Castle is funded by the RGPIN-2016-05590 Natural Sciences and Engineering Research Council of Canada. Antonet Svircev was supported by Agriculture and Agri-Food Canada Growing Forward II grant. Conflicts of Interest: The authors declare no conflict of interest. References 1. Ramankutty, N.; Mehrabi, Z.; Waha, K.; Jarvis, L.; Kremen, C.; Herreo, M.; Rieseberg, L.H. Trends in global agriculturl land use: Implications for environmental health and food safety. Ann. Rev. Plant Biol. 2018, 69. [CrossRef] [PubMed] 2. Muller, A.; Schader, C.; El-Hage Scialabba, N.; Bruggemann, J.; Isensee, A.; Erb, K.H.; Smith, P.; Klocke, P.; Leiber, F.; Stolze, M.; et al. Strategies for feeding the world more sustainably with organic agriculture. Nat. Commun. 2017, 8, 1290. [CrossRef] [PubMed] 3. Pingali, P.L. Green revolution: Impacts, limits, and the path ahead. Proc. Natl. Acad. Sci. USA 2012, 109, 12302–12308. [CrossRef] [PubMed] 4. Moore, P.; Evenson, A.; Luckey, T.; McCoy, E.; Elvehjem, C.; Hart, E. Studies with the chick streptomycin in nutritional streptothricin, and use of sulfasuxidine. J. Biol. Chem. 1946, 165, 437–441. [PubMed] 5. Cheng, G.; Hao, H.; Xie, S.; Wang, X.; Dai, M.; Huang, L.; Yuan, Z. Antibiotic alternatives: The substitution of antibiotics in animal husbandry? Front. Microbiol. 2014, 5, 217. [CrossRef] [PubMed] 6. McManus, P.S.; Stockwell, V.O.; Sundin, G.W.; Jones, A.L. Antibiotic use in plant agriculture. Annu. Rev. Phytopathol. 2002, 40, 443–465. [CrossRef] [PubMed] 7. Sholberg, P.L.; Bedford, K.E.; Haag, P.; Randall, P. Survey of Erwinia amylovora isolates from British Columbia for resistance to bactericides and virulence on apple. Can. J. Plant Pathol. 2001, 23, 60–67. [CrossRef] 8. Förster, H.; McGhee, G.C.; Sundin, G.W.; Adaskaveg, J.E. Characterization of streptomycin resistance in isolates of Erwinia amylovora in California. Phytopathology 2015, 105, 1302–1310. [CrossRef] [PubMed] 9. Tancos, K.A.; Borejsza-Wysocka, E.; Kuehne, S.; Breth, D.; Cox, K.D. Fire blight symptomatic shoots and the presence of Erwinia amylovora in asymptomatic apple budwood. Plant Dis. 2017, 101, 186–191. [CrossRef] 10. Tancos, K.A.; Villani, S.; Kuehne, S.; Borejsza-Wysocka, E.; Breth, D.; Carol, J.; Aldwinckle, H.S.; Cox, K.D. Prevalence of streptomycin-resistant Erwinia amylovora in New York apple orchards. Plant Dis. 2016, 100, 802–809. [CrossRef] 11. McManus, P.S. Does a drop in the bucket make a splash? Assessing the impact of antibiotic use on plants. Curr. Opin. Microbiol. 2014, 19, 76–82. [CrossRef] [PubMed] http://dx.doi.org/10.1146/annurev-arplant-042817-040256 http://www.ncbi.nlm.nih.gov/pubmed/29489395 http://dx.doi.org/10.1038/s41467-017-01410-w http://www.ncbi.nlm.nih.gov/pubmed/29138387 http://dx.doi.org/10.1073/pnas.0912953109 http://www.ncbi.nlm.nih.gov/pubmed/22826253 http://www.ncbi.nlm.nih.gov/pubmed/20276107 http://dx.doi.org/10.3389/fmicb.2014.00217 http://www.ncbi.nlm.nih.gov/pubmed/24860564 http://dx.doi.org/10.1146/annurev.phyto.40.120301.093927 http://www.ncbi.nlm.nih.gov/pubmed/12147767 http://dx.doi.org/10.1080/07060660109506910 http://dx.doi.org/10.1094/PHYTO-03-15-0078-R http://www.ncbi.nlm.nih.gov/pubmed/26413887 http://dx.doi.org/10.1094/PDIS-06-16-0892-RE http://dx.doi.org/10.1094/PDIS-09-15-0960-RE http://dx.doi.org/10.1016/j.mib.2014.05.013 http://www.ncbi.nlm.nih.gov/pubmed/25006016 Viruses 2018, 10, 218 10 of 13 12. O’Neil, J. Tracking a Global Health Crisis: Initial Steps, 2015th ed.; Review of Antimicrobial Resitance; Welcome Trist and UK Government: London, UK, 2015. 13. Buttimer, C.; McAuliffe, O.; Ross, R.P.; Hill, C.; O’Mahony, J.; Coffey, A. Bacteriophages and bacterial plant diseases. Front. Microbiol. 2017, 8, 34. [CrossRef] [PubMed] 14. Czajkowski, R. Bacteriophages of Soft Rot Enterobacteriaceae—A minireview. FEMS Microbiol. Lett. 2016, 363. [CrossRef] [PubMed] 15. Nagy, J.K.; Király, L.; Schwarczinger, I. Phage therapy for plant disease control with a focus on fire blight. Cent. Eur. J. Biol. 2012, 7, 1–12. [CrossRef] 16. Svircev, A.M.; Castle, A.J.; Lehman, S.M. Bacteriophages for control of phytopathogens in food production systems. In Bacteriophages in the Control of Food- and Waterborne Pathogens; Sabour, P.M., Griffiths, M.W., Eds.; ASM Press: Washington, DC, USA, 2010; pp. 79–102. 17. Wittebole, X.; de Roock, S.; Opal, S.M. A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens. Virulence 2014, 5, 226–235. [CrossRef] [PubMed] 18. Aarestrup, F. Get pigs off antibiotics. Nature 2012, 486, 465–466. [CrossRef] [PubMed] 19. Wall, S.K.; Zhang, J.; Rostagno, M.H.; Ebner, P.D. Phage therapy to reduce preprocessing Salmonella infections in market-weight swine. Appl. Environ. Microbiol. 2010, 76, 48–53. [CrossRef] [PubMed] 20. Nosanchuk, J.D.; Lin, J.; Hunter, R.P.; Aminov, R.I. Low-dose antibiotics: current status and outlook for the future. Front. Microbiol. 2014, 5, 478. [CrossRef] [PubMed] 21. Goneau, L.W.; Hannan, T.J.; MacPhee, R.A.; Schwartz, D.J.; Macklaim, J.M.; Gloor, G.B.; Razvi, H.; Reid, G.; Hultgren, S.J.; Burton, J.P. Subinhibitory antibiotic therapy alters recurrent urinary tract infection pathogenesis through modulation of bacterial virulence and host immunity. mBio 2015, 6, e00356-15. [CrossRef] [PubMed] 22. Graham, J.P.; Evans, S.L.; Price, L.B.; Silbergeld, E.K. Fate of antimicrobial-resistant enterococci and staphylococci and resistance determinants in stored poultry litter. Environ. Res. 2009, 109, 682–689. [CrossRef] [PubMed] 23. Robinson, T.P.; Bu, D.P.; Carrique-Mas, J.; Fevre, E.M.; Gilbert, M.; Grace, D.; Hay, S.I.; Jiwakanon, J.; Kakkar, M.; Kariuki, S.; et al. Antibiotic resistance is the quintessential One Health issue. Trans. R. Soc. Trop. Med. Hyg. 2016, 110, 377–380. [CrossRef] [PubMed] 24. Li, D.; Wu, C.; Wang, Y.; Fan, R.; Schwarz, S.; Zhang, S. Identification of multiresistance gene cfr in methicillin-resistant Staphylococcus aureus from pigs: Plasmid location and integration into a staphylococcal cassette chromosome mec complex. Antimicrob. Agents Chemother. 2015, 59, 3641–3644. [CrossRef] [PubMed] 25. Gelband, H.; Miller-Petrie, M.; Pant, S.; Gandra, S.; Levinson, J.; Barter, D.; White, A.; Laxminarayan, R. The state of the world’s antibiotics 2015. Medpharm 2015, 8, 30–34. 26. Seal, B.S.; Lillehoj, H.S.; Donovan, D.M.; Gay, C.G. Alternatives to antibiotics: A symposium on the challenges and solutions for animal production. Anim. Health Res. Rev. 2013, 14, 78–87. [CrossRef] [PubMed] 27. Miller, R.W.; Skinner, E.J.; Sulakvelidze, A.; Mathis, G.F.; Hofacre, C.L. Bacteriophage therapy for control of necrotic enteritis of broiler chickens experimentally infected with Clostridium perfringens. Avian Dis. 2010, 54, 33–40. [CrossRef] [PubMed] 28. Kim, K.H.; Ingale, S.L.; Kim, J.S.; Lee, S.H.; Lee, J.H.; Kwon, I.K.; Chae, B.J. Bacteriophage and probiotics both enhance the performance of growing pigs but bacteriophage are more effective. Anim. Feed Sci. Technol. 2014, 196, 88–95. [CrossRef] 29. Huff, W.E.; Huff, G.R.; Rath, N.C.; Balog, J.M.; Xie, H.; Moore, P.A.; Donoghue, A.M. Prevention of Escherichia coli respiratory infection in broiler chickens with bacteriophage (SPR02). Poult. Sci. 2002, 81, 437–441. [CrossRef] [PubMed] 30. Huff, W.E.; Huff, G.R.; Rath, N.C.; Donoghue, A.M. Method of administration affects the ability of bacteriophage to prevent colibacillosis in 1-day-old broiler chickens. Poult. Sci. 2013, 92, 930–934. [CrossRef] [PubMed] 31. Fessler, A.; Scott, C.; Kadlec, K.; Ehricht, R.; Monecke, S.; Schwarz, S. Characterization of methicillin-resistant Staphylococcus aureus ST398 from cases of bovine mastitis. J. Antimicrob. Chemother. 2010, 65, 619–625. [CrossRef] [PubMed] 32. Breyne, K.; Honaker, R.W.; Hobbs, Z.; Richter, M.; Zaczek, M.; Spangler, T.; Steenbrugge, J.; Lu, R.; Kinkhabwala, A.; Marchon, B.; et al. Efficacy and safety of a bovine-associated Staphylococcus aureus phage cocktail in a murine model of mastitis. Front. Microbiol. 2017, 8, 2348. [CrossRef] [PubMed] http://dx.doi.org/10.3389/fmicb.2017.00034 http://www.ncbi.nlm.nih.gov/pubmed/28163700 http://dx.doi.org/10.1093/femsle/fnv230 http://www.ncbi.nlm.nih.gov/pubmed/26626879 http://dx.doi.org/10.2478/s11535-011-0093-x http://dx.doi.org/10.4161/viru.25991 http://www.ncbi.nlm.nih.gov/pubmed/23973944 http://dx.doi.org/10.1038/486465a http://www.ncbi.nlm.nih.gov/pubmed/22739296 http://dx.doi.org/10.1128/AEM.00785-09 http://www.ncbi.nlm.nih.gov/pubmed/19854929 http://dx.doi.org/10.3389/fmicb.2014.00478 http://www.ncbi.nlm.nih.gov/pubmed/25309518 http://dx.doi.org/10.1128/mBio.00356-15 http://www.ncbi.nlm.nih.gov/pubmed/25827417 http://dx.doi.org/10.1016/j.envres.2009.05.005 http://www.ncbi.nlm.nih.gov/pubmed/19541298 http://dx.doi.org/10.1093/trstmh/trw048 http://www.ncbi.nlm.nih.gov/pubmed/27475987 http://dx.doi.org/10.1128/AAC.00500-15 http://www.ncbi.nlm.nih.gov/pubmed/25824234 http://dx.doi.org/10.1017/S1466252313000030 http://www.ncbi.nlm.nih.gov/pubmed/23702321 http://dx.doi.org/10.1637/8953-060509-Reg.1 http://www.ncbi.nlm.nih.gov/pubmed/20408396 http://dx.doi.org/10.1016/j.anifeedsci.2014.06.012 http://dx.doi.org/10.1093/ps/81.4.437 http://www.ncbi.nlm.nih.gov/pubmed/11998827 http://dx.doi.org/10.3382/ps.2012-02916 http://www.ncbi.nlm.nih.gov/pubmed/23472016 http://dx.doi.org/10.1093/jac/dkq021 http://www.ncbi.nlm.nih.gov/pubmed/20164198 http://dx.doi.org/10.3389/fmicb.2017.02348 http://www.ncbi.nlm.nih.gov/pubmed/29234314 Viruses 2018, 10, 218 11 of 13 33. Gill, J.J.; Sabour, P.M.; Leslie, K.E.; Griffiths, M.W. Bovine whey proteins inhibit the interaction of Staphylococcus aureus and bacteriophage K. J. Appl. Microbiol. 2006, 101, 377–386. [CrossRef] [PubMed] 34. Fernandez, L.; Escobedo, S.; Gutierrez, D.; Portilla, S.; Martinez, B.; Garcia, P.; Rodriguez, A. Bacteriophages in the dairy environment: From enemies to allies. Antibiotics (Basel) 2017, 6, 27. [CrossRef] [PubMed] 35. Barkema, H.; Schukken, Y.; Zadoks, R. Invited review: The role of cow, pathogen, and treatment regimen in the therapeutic success of bovine Staphylococcus aureus mastitis. J. Dairy Sci. 2006, 89, 1877–1895. [CrossRef] 36. Toranzo, A.E.; Magariños, B.; Romalde, J.L. A review of the main bacterial fish diseases in mariculture systems. Aquacul 2005, 246, 37–61. [CrossRef] 37. Rao, B.; Lalitha, K. Bacteriophages for aquaculture: Are they beneficial or inimical. Aquacul 2015, 437, 146–154. 38. Silva, Y.J.; Costa, L.; Pereira, C.; Mateus, C.; Cunha, A.; Calado, R.; Gomes, N.C.; Pardo, M.A.; Hernandez, I.; Almeida, A. Phage therapy as an approach to prevent Vibrio anguillarum infections in fish larvae production. PLoS ONE 2014, 9, e114197. [CrossRef] [PubMed] 39. Higuera, G.; Bastías, R.; Tsertsvadze, G.; Romero, J.; Espejo, R.T. Recently discovered Vibrio anguillarum phages can protect against experimentally induced vibriosis in Atlantic salmon, Salmo salar. Aquaculture 2013, 392–395, 128–133. [CrossRef] 40. Karunasagar, I.; Shivu, M.; Girisha, S.; Krohne, G.; Karunasagar, I. Biocontrol of pathogens in shrimp hatcheries using bacteriophages. Aquacul 2007, 268, 288–292. [CrossRef] 41. Mao, Z.; Li, M.; Chen, J. Draft genome sequence of pseudomonas plecoglossicida strain NB2011, the causative agent of white nodules in large yellow croaker (Larimichthys crocea). Genome Announc. 2013, 1, e00586-13. [CrossRef] [PubMed] 42. Park, S.; Nakai, T. Bacteriophage control of Pseudomonas plecoglossicida infection in ayu Plecoglossus altivelis. Dis. Aquat. Org. 2003, 53, 33–39. [CrossRef] [PubMed] 43. Loc Carrillo, C.; Atterbury, R.J.; El-Shibiny, A.; Connerton, P.L.; Dillon, E.; Scott, A.; Connerton, I.F. Bacteriophage therapy to reduce Campylobacter jejuni colonization of broiler chickens. Appl. Environ. Microbiol. 2005, 71, 6554–6563. [CrossRef] [PubMed] 44. Kittler, S.; Fischer, S.; Abdulmawjood, A.; Glunder, G.; Klein, G. Effect of bacteriophage application on Campylobacter jejuni loads in commercial broiler flocks. Appl. Environ. Microbiol. 2013, 79, 7525–7533. [CrossRef] [PubMed] 45. Borie, C.; Sanchez, M.L.; Navarro, C.; Ramirez, S.; Morales, M.A.; Retamales, J.; Robeson, J. Aerosol spray treatment with bacteriophages and competitive exclusion reduces Salmonella enteritidis infection in chickens. Avian Dis. 2009, 53, 250–254. [CrossRef] [PubMed] 46. Callaway, T.R.; Edrington, T.S.; Brabban, A.D.; Anderson, R.C.; Rossman, M.L.; Mike, J.; Engler, M.J.; Carr, M.A.; Genovese, K.J.; Keen, J.E.; Looper, M.L.; et al. Bacteriophage isolated from feedlot cattle can reduce Escherichia coli O157:H7 populations in ruminant gastrointestinal tracts. Foodborne Pathog. Dis. 2008, 5, 183–191. [CrossRef] [PubMed] 47. Duckworth, D. Who discovered bacteriophage? Bacteriol. Rev. 1976, 40, 793–802. [PubMed] 48. Mallmann, W.; Hemstreet, C. Isolation of an inhibitory substance from plants. Agric. Res. 1924, 28, 599–602. 49. Kotila, J.; Coons, G. Investigations on the Black Leg Disease of Potato; Michigan Agri. Exp. Station Technical Bulletin; Michigan Agricultural College: East Lansing, MI, USA, 1925; Volume 67, pp. 3–29. 50. Thomas, R. A bacteriophage in relationto Stewart’s disease of corn. Phytopathology 1935, 25, 371–372. 51. Mansfield, J.; Genin, S.; Magori, S.; Citovsky, V.; Sriariyanum, M.; Ronald, P.; Dow, M.; Verdier, V.; Beer, S.V.; Machado, M.A.; et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol. Plant Pathol. 2012, 13, 614–629. [CrossRef] [PubMed] 52. Adriaenssens, E.M.; van Vaerenbergh, J.; Vandenheuvel, D.; Dunon, V.; Ceyssens, P.J.; de Proft, M.; Kropinski, A.M.; Noben, J.P.; Maes, M.; Lavigne, R. T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by “Dickeya solani”. PLoS ONE 2012, 7, e33227. [CrossRef] [PubMed] 53. Czajkowski, R.; Ozymko, Z.; de Jager, V.; Siwinska, J.; Smolarska, A.; Ossowicki, A.; Narajczyk, M.; Lojkowska, E. Genomic, proteomic and morphological characterization of two novel broad host lytic bacteriophages PhiPD10.3 and PhiPD23.1 infecting pectinolytic Pectobacterium spp. and Dickeya spp. PLoS ONE 2015, 10, e0119812. [CrossRef] [PubMed] http://dx.doi.org/10.1111/j.1365-2672.2006.02918.x http://www.ncbi.nlm.nih.gov/pubmed/16882145 http://dx.doi.org/10.3390/antibiotics6040027 http://www.ncbi.nlm.nih.gov/pubmed/29117107 http://dx.doi.org/10.3168/jds.S0022-0302(06)72256-1 http://dx.doi.org/10.1016/j.aquaculture.2005.01.002 http://dx.doi.org/10.1371/journal.pone.0114197 http://www.ncbi.nlm.nih.gov/pubmed/25464504 http://dx.doi.org/10.1016/j.aquaculture.2013.02.013 http://dx.doi.org/10.1016/j.aquaculture.2007.04.049 http://dx.doi.org/10.1128/genomeA.00586-13 http://www.ncbi.nlm.nih.gov/pubmed/23929479 http://dx.doi.org/10.3354/dao053033 http://www.ncbi.nlm.nih.gov/pubmed/12608566 http://dx.doi.org/10.1128/AEM.71.11.6554-6563.2005 http://www.ncbi.nlm.nih.gov/pubmed/16269681 http://dx.doi.org/10.1128/AEM.02703-13 http://www.ncbi.nlm.nih.gov/pubmed/24077703 http://dx.doi.org/10.1637/8406-071008-Reg.1 http://www.ncbi.nlm.nih.gov/pubmed/19630232 http://dx.doi.org/10.1089/fpd.2007.0057 http://www.ncbi.nlm.nih.gov/pubmed/18407757 http://www.ncbi.nlm.nih.gov/pubmed/795414 http://dx.doi.org/10.1111/j.1364-3703.2012.00804.x http://www.ncbi.nlm.nih.gov/pubmed/22672649 http://dx.doi.org/10.1371/journal.pone.0033227 http://www.ncbi.nlm.nih.gov/pubmed/22413005 http://dx.doi.org/10.1371/journal.pone.0119812 http://www.ncbi.nlm.nih.gov/pubmed/25803051 Viruses 2018, 10, 218 12 of 13 54. Fujiwara, A.; Fujisawa, M.; Hamasaki, R.; Kawasaki, T.; Fujie, M.; Yamada, T. Biocontrol of Ralstonia solanacearum by treatment with lytic bacteriophages. Appl. Environ. Microbiol. 2011, 77, 4155–4162. [CrossRef] [PubMed] 55. Iriarte, F.B.; Obradovic, A.; Wernsing, M.H.; Jackson, L.E.; Balogh, B.; Hong, J.A.; Momol, M.T.; Jones, J.B.; Vallad, G.E. Soil-based systemic delivery and phyllosphere in vivo propagation of bacteriophages: Two possible strategies for improving bacteriophage persistence for plant disease control. Bacteriophage 2012, 2, 215–224. [CrossRef] [PubMed] 56. Hirano, S.; Upper, C. Population biology and epidemiology of Pseudomonas syringae. Annu. Rev. Phytopathol. 1990, 28, 155–177. [CrossRef] 57. Frampton, R.A.; Taylor, C.; Holguín Moreno, A.V.; Visnovsky, S.B.; Petty, N.K.; Pitman, A.R.; Fineran, P.C. Identification of bacteriophages for biocontrol of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Appl. Environ. Microbiol. 2014, 80, 2216–2228. [CrossRef] [PubMed] 58. Di Lallo, G.; Evangelisti, M.; Mancuso, F.; Ferrante, P.; Marcelletti, S.; Tinari, A.; Superti, F.; Migliore, L.; D’Addabbo, P.; Frezza, D.; et al. Isolation and partial characterization of bacteriophages infecting Pseudomonas syringae pv. actinidiae, causal agent of kiwifruit bacterial canker. J. Basic Microbiol. 2014, 54, 1210–1221. [CrossRef] [PubMed] 59. Rombouts, S.; Volckaert, A.; Venneman, S.; Declercq, B.; Vandenheuvel, D.; Allonsius, C.N.; van Malderghem, C.; Jang, H.B.; Briers, Y.; Noben, J.P.; et al. Characterization of novel bacteriophages for biocontrol of bacterial blight in leek caused by Pseudomonas syringae pv. porri. Front. Microbiol. 2016, 7, 279. [CrossRef] [PubMed] 60. Balogh, B.; Canteros, B.I.; Stall, R.E.; Jones, J.B. Control of citrus canker and citrus bacterial spot with bacteriophages. Plant Dis. 2008, 92, 1048–1052. [CrossRef] 61. Ibrahim, Y.E.; Saleh, A.A.; Al-Saleh, M.A. Management of asiatic citrus canker under field conditions in Saudi Arabia using bacteriophages and acibenzolar-S-methyl. Plant Dis. 2017, 101, 761–765. [CrossRef] 62. Chatterjee, S.; Almeida, R.P.; Lindow, S. Living in two worlds: The plant and insect lifestyles of Xylella fastidiosa. Annu. Rev. Phytopathol. 2008, 46, 243–271. [CrossRef] [PubMed] 63. Ahern, S.J.; Das, M.; Bhowmick, T.S.; Young, R.; Gonzalez, C.F. Characterization of novel virulent broad-host-range phages of Xylella fastidiosa and Xanthomonas. J. Bacteriol. 2014, 196, 459–471. [CrossRef] [PubMed] 64. Boulé, J.; Sholberg, P.L.; Lehman, S.M.; O’Gorman, D.T.; Svircev, A.M. Isolation and characterization of eight bacteriophages infecting Erwinia amylovora and their potential as biological control agents in British Columbia, Canada. Can. J. Plant Pathol. 2011, 33, 308–317. [CrossRef] 65. Lehman, S.M. Development of a Bacteriophage-Based Biopesticide for Fire Blight. Ph.D. Thesis, Brock University, St. Catharines, ON, Canada, 2007. 66. Piqué, N.; Miñana-Galbis, D.; Merino, S.; Tomás, J.M. Virulence factors of Erwinia amylovora: A review. Int. J. Mol. Sci. 2015, 16, 12836–12854. [CrossRef] [PubMed] 67. Roach, D.R.; Sjaarda, D.R.; Castle, A.J.; Svircev, A.M. Host exopolysaccharide quantity and composition impact Erwinia amylovora bacteriophage pathogenesis. Appl. Environ. Microbiol. 2013, 79, 3249–3256. [CrossRef] [PubMed] 68. Scanlan, P.D.; Hall, A.R.; Blackshields, G.; Friman, V.P.; Davis, M.R., Jr.; Goldberg, J.B.; Buckling, A. Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations. Mol. Biol. Evol. 2015, 32, 1425–1435. [CrossRef] [PubMed] 69. Roach, D.R.; Sjaarda, D.R.; Sjaarda, C.P.; Ayala, C.J.; Howcroft, B.; Castle, A.J.; Svircev, A.M. Absence of lysogeny in wild populations of Erwinia amylovora and Pantoea agglomerans. Microb. Biotechnol. 2015, 8, 510–518. [CrossRef] [PubMed] 70. Tock, M.R.; Dryden, D.T. The biology of restriction and anti-restriction. Curr. Opin. Microbiol. 2005, 8, 466–472. [CrossRef] [PubMed] 71. Mojica, F.J.; Diez-Villasenor, C.; Garcia-Martinez, J.; Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 2005, 60, 174–182. [CrossRef] [PubMed] 72. Barrangou, R.; Fremaux, C.; Deveau, H.; Richards, M.; Boyaval, P.; Moineau, S.; Romero, D.A.; Horvath, P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315, 1709–1712. [CrossRef] [PubMed] http://dx.doi.org/10.1128/AEM.02847-10 http://www.ncbi.nlm.nih.gov/pubmed/21498752 http://dx.doi.org/10.4161/bact.23530 http://www.ncbi.nlm.nih.gov/pubmed/23532156 http://dx.doi.org/10.1146/annurev.py.28.090190.001103 http://dx.doi.org/10.1128/AEM.00062-14 http://www.ncbi.nlm.nih.gov/pubmed/24487530 http://dx.doi.org/10.1002/jobm.201300951 http://www.ncbi.nlm.nih.gov/pubmed/24810619 http://dx.doi.org/10.3389/fmicb.2016.00279 http://www.ncbi.nlm.nih.gov/pubmed/27014204 http://dx.doi.org/10.1094/PDIS-92-7-1048 http://dx.doi.org/10.1094/PDIS-08-16-1213-RE http://dx.doi.org/10.1146/annurev.phyto.45.062806.094342 http://www.ncbi.nlm.nih.gov/pubmed/18422428 http://dx.doi.org/10.1128/JB.01080-13 http://www.ncbi.nlm.nih.gov/pubmed/24214944 http://dx.doi.org/10.1080/07060661.2011.588250 http://dx.doi.org/10.3390/ijms160612836 http://www.ncbi.nlm.nih.gov/pubmed/26057748 http://dx.doi.org/10.1128/AEM.00067-13 http://www.ncbi.nlm.nih.gov/pubmed/23503310 http://dx.doi.org/10.1093/molbev/msv032 http://www.ncbi.nlm.nih.gov/pubmed/25681383 http://dx.doi.org/10.1111/1751-7915.12253 http://www.ncbi.nlm.nih.gov/pubmed/25678125 http://dx.doi.org/10.1016/j.mib.2005.06.003 http://www.ncbi.nlm.nih.gov/pubmed/15979932 http://dx.doi.org/10.1007/s00239-004-0046-3 http://www.ncbi.nlm.nih.gov/pubmed/15791728 http://dx.doi.org/10.1126/science.1138140 http://www.ncbi.nlm.nih.gov/pubmed/17379808 Viruses 2018, 10, 218 13 of 13 73. Goldfarb, T.; Sberro, H.; Weinstock, E.; Cohen, O.; Doron, S.; Charpak-Amikam, Y.; Afik, S.; Ofir, G.; Sorek, R. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J. 2015, 34, 169–183. [CrossRef] [PubMed] 74. Ofir, G.; Melamed, S.; Sberro, H.; Mukamel, Z.; Silverman, S.; Yaakov, G.; Doron, S.; Sorek, R. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat. Microbiol. 2018, 3, 90–98. [CrossRef] [PubMed] 75. Doron, S.; Melamed, S.; Ofir, G.; Leavitt, A.; Lopatina, A.; Keren, M.; Amitai, G.; Sorek, R. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 2018, 359. [CrossRef] [PubMed] 76. Jones, J.B.; Jackson, L.E.; Balogh, B.; Obradovic, A.; Iriarte, F.B.; Momol, M.T. Bacteriophages for plant disease control. Annu. Rev. Phytopathol. 2008, 45, 245–262. [CrossRef] [PubMed] 77. Tzipilevich, E.; Habusha, M.; Ben-Yehuda, S. Acquisition of phage sensitivity by bacteria through exchange of phage receptors. Cell 2017, 168, 186–199. [CrossRef] [PubMed] 78. Addy, H.S.; Askora, A.; Kawasaki, T.; Fujie, M.; Yamada, T. Loss of virulence of the phytopathogen Ralstonia solanacearum through infection by ΦRSM filamentous phages. Phytopathology 2012, 102, 469–477. [CrossRef] [PubMed] 79. Muniesa, M.; Colomer-Lluch, M.; Jofre, J. Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations? Mob. Genet. Elem. 2013, 3, e25847. [CrossRef] [PubMed] 80. Muniesa, M.; Colomer-Lluch, M.; Jofre, J. Potential impact of environmental bacteriophages in spreading antibiotic resistance genes. Future Microbiol. 2013, 8, 739–751. [CrossRef] [PubMed] 81. Colavecchio, A.; Cadieux, B.; Lo, A.; Goodridge, L.D. Bacteriophages contribute to the spread of antibiotic resistance genes among foodborne pathogens of the Enterobacteriaceae family—A Review. Front. Microbiol. 2017, 8, 1108. [CrossRef] [PubMed] 82. Koczan, J.M.; Lenneman, B.R.; McGrath, M.J.; Sundin, G.W. Cell surface attachment structures contribute to biofilm formation and xylem colonization by Erwinia amylovora. Appl. Environ. Microbiol. 2011, 77, 7031–7039. [CrossRef] [PubMed] 83. Bull, J.J.; Christensen, K.A.; Scott, C.; Jack, B.R.; Crandall, C.J.; Krone, S.M. Phage-bacterial dynamics with spatial structure: Self organization around phage sinks can promote increased cell densities. Antibiot 2018, 7, 8. [CrossRef] [PubMed] 84. Abedon, S.T. Phage therapy: Various perspectives on how to improve the art. Method Mol. Biol. 2018, 1734, 113–127. 85. Das, M.; Bhowmick, T.S.; Ahern, S.J.; Young, R.; Gonzalez, C.F. Control of Pierce’s disease by phage. PLoS ONE 2015, 10, e0128902. [CrossRef] [PubMed] 86. Born, Y.; Bosshard, L.; Duffy, B.; Loessner, M.J.; Fieseler, L. Protection of Erwinia amylovora bacteriophage Y2 from UV-induced damage by natural compounds. Bacteriophage 2015, 5, e1074330. [CrossRef] [PubMed] 87. Thomke, S.; Elwinger, K. Growth promotants in feeding pigs and poultry. I. Growth and feed efficiency responses to antibiotic growth promotants. Ann. Zootech. 1998, 47, 85–97. [CrossRef] 88. Lin, J. Antibiotic growth promoters enhance animal production by targeting intestinal bile salt hydrolase and its producers. Front. Microbiol. 2014, 5, 33. [CrossRef] [PubMed] 89. Migueis, S.; Saraiva, C.; Esteves, A. Efficacy of LISTEX P100 at different concentrations for reduction of Listeria monocytogenes inoculated in Sashimi. J. Food Prot. 2017, 80, 2094–2098. [CrossRef] [PubMed] 90. Boyetchko, S.; Svircev, A.M. A novel approach for developing microbial biopesticides. In Biological Control Programmes in Canada 2001–2012; Mason, P., Gillespie, D., Eds.; CAB International: Wallingford, UK, 2013; pp. 37–43. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). http://dx.doi.org/10.15252/embj.201489455 http://www.ncbi.nlm.nih.gov/pubmed/25452498 http://dx.doi.org/10.1038/s41564-017-0051-0 http://www.ncbi.nlm.nih.gov/pubmed/29085076 http://dx.doi.org/10.1126/science.aar4120 http://www.ncbi.nlm.nih.gov/pubmed/29371424 http://dx.doi.org/10.1146/annurev.phyto.45.062806.094411 http://www.ncbi.nlm.nih.gov/pubmed/17386003 http://dx.doi.org/10.1016/j.cell.2016.12.003 http://www.ncbi.nlm.nih.gov/pubmed/28041851 http://dx.doi.org/10.1094/PHYTO-11-11-0319-R http://www.ncbi.nlm.nih.gov/pubmed/22352303 http://dx.doi.org/10.4161/mge.25847 http://www.ncbi.nlm.nih.gov/pubmed/24195016 http://dx.doi.org/10.2217/fmb.13.32 http://www.ncbi.nlm.nih.gov/pubmed/23701331 http://dx.doi.org/10.3389/fmicb.2017.01108 http://www.ncbi.nlm.nih.gov/pubmed/28676794 http://dx.doi.org/10.1128/AEM.05138-11 http://www.ncbi.nlm.nih.gov/pubmed/21821744 http://dx.doi.org/10.3390/antibiotics7010008 http://www.ncbi.nlm.nih.gov/pubmed/29382134 http://dx.doi.org/10.1371/journal.pone.0128902 http://www.ncbi.nlm.nih.gov/pubmed/26107261 http://dx.doi.org/10.1080/21597081.2015.1074330 http://www.ncbi.nlm.nih.gov/pubmed/26904378 http://dx.doi.org/10.1051/animres:19980201 http://dx.doi.org/10.3389/fmicb.2014.00033 http://www.ncbi.nlm.nih.gov/pubmed/24575079 http://dx.doi.org/10.4315/0362-028X.JFP-17-098 http://www.ncbi.nlm.nih.gov/pubmed/29166172 http://creativecommons.org/ http://creativecommons.org/licenses/by/4.0/. Introduction Phages in Agriculture Bacteriophages in Food Animal Production Phages as Growth Promoters Phages that Combat Zoonotic Pathogens Bacteriophages in Crop Production Soft Rot, Bacterial Wilt, and Blight Citrus Bacterial Canker and Spot Pierce’s Disease of Grape Fire Blight in Apples and Pears Impact of Host Exopolysaccharides and Phage Family on Efficacy Potential Problems with Phages as Biocontrol Agents Discussion References