Method for bacteriophage isolation against target Campylobacter strains

Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis

Rivers are critical ecosystems that support biodiversity and local livelihoods. This study aimed to evaluate the effects of metal contamination and anthropogenic activities on microbial and phage community dynamics within major Indian river ecosystems, focusing on the Ganga, Narmada, Cauvery, and Gomti rivers -using metagenomic techniques, Biolog, and ICP-MS analysis. Significant variations in microbial communities were observed both within each river and across the four systems, influenced by ecological factors like geography and hydrology, as well as anthropogenic pressures. Downstream sites consistently exhibited higher microbial diversity, with prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae dominating, while Proteobacteria and Bacteroides declined. The Ganga River showed a higher abundance of bacteriophages compared to other rivers, which gradually reduced with the increment of anthropogenic impact. Functional gene analysis revealed correlations between carbon utilization and metal resistance in contaminated sites. ICP-MS analysis indicates elevated chromium and lead levels in downstream sites of all rivers compared to upstream sites. Interestingly, pristine upstream sites in the Ganga had higher trace element levels than those in Narmada and Cauvery, likely due to its Himalayan origin. Both the Ganga and Cauvery rivers contained numerous metal resistance genes. The Alaknanda was identified as the primary source of microbial communities, bacteriophages, trace elements, and heavy metals in the Ganga. These findings offer new insights into anthropogenic influences on river microbial dynamics and highlight the need for targeted monitoring and management strategies to preserve river health.

Phage cocktails - an emerging approach for the control of bacterial infection with major emphasis on foodborne pathogens

Phage therapy has recently attracted a great deal of attention to counteract the rapid emergence of antibiotic-resistant bacteria. In comparison to monophage therapy, phage cocktails are typically used to treat individual and/or multi-bacterial infections since the bacterial agents are unlikely to become resistant as a result of exposure to multiple phages simultaneously. The bacteriolytic effect of phage cocktails may produce efficient killing effect in comparison to individual phage. However, multiple use of phages (complex cocktails) may lead to undesirable side effects such as dysbiosis, horizontal gene transfer, phage resistance, cross resistance, and/or higher cost of production. Cocktail formulation, therefore, representa compromise between limiting the complexity of the cocktail and achieving substantial bacterial load reduction towards the targeted host organisms. Despite some constraints, the applications of monophage therapy have been well documented in the literature. However, phage cocktails-based approaches and their role for the control of pathogens have not been well investigated. In this review, we discuss the principle of phage cocktail formulations, their optimization strategies, major phage cocktail preparations, and their efficacy in inactivating various food borne bacterial pathogens.

More's the Same-Multiple Hosts Do Not Select for Broader Host Range Phages

Bacteriophage host range is a result of the interactions between phages and their hosts. For phage therapy, phages with a broader host range are desired so that a phage can infect and kill the broadest range of pathogen strains or related species possible. A common, but not well-tested, belief is that using multiple hosts during the phage isolation will make the isolation of broader host range phage more likely. Using a Bacillus cereus group system, we compared the host ranges of phages isolated on one or four hosts and found that there was no difference in the breadth of host ranges of the isolated phages. Both narrow and broader host range phage were also equally likely to be isolated from either isolation procedure. While there are methods that reliably isolate broader host range phages, such as sequential host isolation, and there are other reasons to use multiple hosts during isolation, multiple hosts are not a consistent way to obtain broader host range phages.

Application and challenge of bacteriophage in the food protection

In recent years, foodborne diseases caused by pathogens have been increasing. Therefore, it is essential to control the growth and transmission of pathogens. Bacteriophages (phages) have the potential to play an important role in the biological prevention, control, and treatment of these foodborne diseases due to their favorable advantages. Phages not only effectively inhibit pathogenic bacteria and prolong the shelf life of food, but also possess the advantages of specificity and an absence of chemical residues. Currently, there are many cases of phage applications in agriculture, animal disease prevention and control, food safety, and the treatment of drug-resistant disease. In this review, we summarize the recent research progress on phages against foodborne pathogenic bacteria, including Escherichia coli, Salmonella, Campylobacter, Listeria monocytogenes, Shigella, Vibrio parahaemolyticus, and Staphylococcus aureus. We also discuss the main issues and their corresponding solutions in the application of phages in the food industry. In recent years, although researchers have discovered more phages with potential applications in the food industry, most researchers use these phages based on their host spectrum, and the application environment is mostly in the laboratory. Therefore, the practical application of these phages in different aspects of the food industry may be unsatisfactory and even have some negative effects. Thus, we suggest that before using these phages, it is necessary to identify their specific receptors. Using their specific receptors as the selection basis for their application and combining phages with other phages or phages with traditional antibacterial agents may further improve their safety and application efficiency. Collectively, this review provides a theoretical reference for the basic research and application of phages in the food industry.

Removal of MS2 and fr Bacteriophages Using MgAl2O4-Modified, Al2O3-Stabilized Porous Ceramic Granules for Drinking Water Treatment

Point-of-use ceramic filters are one of the strategies to address problems associated with waterborne diseases to remove harmful microorganisms in water sources prior to its consumption. In this study, development of adsorption-based ceramic depth filters composed of alumina platelets was achieved using spray granulation (calcined at 800 °C). Their virus retention performance was assessed using cartridges containing granular material (4 g) with two virus surrogates: MS2 and fr bacteriophages. Both materials showed complete removal, with a 7 log10 reduction value (LRV) of MS2 up to 1 L. MgAl2O4-modified Al2O3 granules possessed a higher MS2 retention capacity, contrary to the shortcomings of retention limits in pure Al2O3 granules. No significant decline in the retention of fr occurred during filtration tests up to 2 L. The phase composition and morphology of the materials were preserved during filtration, with no magnesium or aluminum leakage during filtration, as confirmed by X-ray diffractograms, electron micrographs, and inductively coupled plasma-optical emission spectrometry. The proposed MgAl2O4-modified Al2O3 granular ceramic filter materials offer high virus retention, achieving the criterion for virus filtration as required by the World Health Organization (LRV ≥ 4). Owing to their high thermal and chemical stability, the developed materials are thus suitable for thermal and chemical-free regeneration treatments.

Identification of Novel Phage Resistance Mechanisms in Campylobacter jejuni by Comparative Genomics

Phages infecting Campylobacter jejuni are considered a promising intervention strategy at broiler farms, yet phage sensitivity of naturally occurring poultry isolates is not well studied. Here, we investigated phage sensitivity and identified resistance mechanisms of C. jejuni strains originating from Danish broilers belonging to the most prevalent MLST (ST) types. Determining plaque formation of 51 phages belonging to Fletchervirus or Firehammervirus showed that 21 out of 31 C. jejuni strains were susceptible to at least one phage. While C. jejuni ST-21 strains encoded the common phase variable O-methyl phosphoramidate (MeOPN) receptor of the Fletchervirus and were only infected by these phages, ST-45 strains did not encode this receptor and were exclusively infected by Firehammervirus phages. To identify internal phage resistance mechanism in ST-21 strains, we performed comparative genomics of two strains, CAMSA2002 sensitive to almost all Fletchervirus phages and CAMSA2038, resistant to all 51 phages. The strains encoded diverse clustered regularly interspaced short palindromic repeats (CRISPR) spacers but none matched the tested phages. Sequence divergence was also observed in a predicted SspE homolog and putative restriction modification systems including a methyl-specific McrBC endonuclease. Furthermore, when mcrB was deleted, CAMSA2038 became sensitive to 17 out of 43 phages, three being Firehammervirus phages that otherwise did not infect any ST-21 strains. Yet, 16 phages demonstrated significantly lower efficiencies of plating on the mcrB mutant suggesting additional resistance mechanism still restricting phage propagation in CAMSA2038. Thus, our work demonstrates that C. jejuni isolates originating from broilers may have acquired several resistance mechanisms to successfully prevent phage infection in their natural habitat.

Phage susceptibility testing and infectious titer determination through wide-field lensless monitoring of phage plaque growth

The growing number of drug-resistant bacterial infections worldwide is driving renewed interest in phage therapy. Based on the use of a personalized cocktail composed of highly specific bacterial viruses, this therapy relies on a range of tests on agar media to determine the most active phage on a given bacterial target (phage susceptibility testing), or to isolate new lytic phages from an environmental sample (enrichment of phage banks). However, these culture-based techniques are still solely interpreted through direct visual detection of plaques. The main objective of this work is to investigate computer-assisted methods in order to ease and accelerate diagnosis in phage therapy but also to study phage plaque growth kinetics. For this purpose, we designed a custom wide-field lensless imaging device, which allows continuous monitoring over a very large area sensor (3.3 cm2). Here we report bacterial susceptibility to Staphylococcus aureus phage in 3 hr and estimation of infectious titer in 8 hr 20 min. These are much shorter time-to-results than the 12 to 24 hours traditionally needed, since naked eye observation and counting of phage plaques is still the most widely used technique for susceptibility testing prior to phage therapy. Moreover, the continuous monitoring of the samples enables the study of plaque growth kinetics, which enables a deeper understanding of the interaction between phage and bacteria. Finally, thanks to the 4.3 μm resolution, we detect phage-resistant bacterial microcolonies of Klebsiella pneumoniae inside the boundaries of phage plaques and thus show that our prototype is also a suitable device to track phage resistance. Lensless imaging is therefore an all-in-one method that could easily be implemented in cost-effective and compact devices in phage laboratories to help with phage therapy diagnosis.

Phage Biocontrol of Campylobacter: A One Health Approach

Human infections by Campylobacter species are among the most reported bacterial gastrointestinal diseases in the European Union and worldwide with severe outcomes in rare cases. Considering the transmission routes and farm animal reservoirs of these zoonotic pathogens, a comprehensive One Health approach will be necessary to reduce human infection rates. Bacteriophages are viruses that specifically infect certain bacterial genera, species, strains or isolates. Multiple studies have demonstrated the general capacity of phage treatments to reduce Campylobacter loads in the chicken intestine. However, phage treatments are not yet approved for extensive use in the agro-food industry in Europe. Technical inconvenience is mainly related to the efficacy of phages, depending on the optimal choice of phages and their combination, as well as application route, concentration and timing. Additionally, regulatory uncertainties have been a major concern for investment in commercial phage-based products. This review addresses the question as to how phages can be put into practice and can help to solve the issue of human campylobacteriosis in a sustainable One Health approach. By compiling the reported findings from the literature in a standardized manner, we enabled inter-experimental comparisons to increase our understanding of phage infection in Campylobacter spp. and practical on-farm studies. Further, we address some of the hurdles that still must be overcome before this new methodology can be adapted on an industrial scale. We envisage that phage treatment can become an integrated and standardized part of a multi-hurdle anti-bacterial strategy in food production. The last part of this chapter deals with some of the issues raised by legal authorities, bringing together current knowledge on Campylobacter-specific phages and the biosafety requirements for approval of phage treatment in the food industry.

Isolation, host specificity and genetic characterization of Campylobacter specific bacteriophages from poultry and swine sources

The isolation and characterization of 304 Campylobacter specific bacteriophage isolates from broiler and swine sources is reported in this study. Genome size characterization determined by PFGE classified these isolates,called CAM1-CAM304, within the campylophages group II (n = 18) and group III (n = 286). Host range analyses showed a high host specificity and similar lytic spectrum among isolates of the same group. Campylophages of group II infected C. jejuni, C. coli and even a C. fetus strain whereas those of group III only infected C. jejuni strains. The most promising 59 campylophage candidates were selected according to their lytic activity and their genetic diversity was analyzed by RFLP using SmiI and HhaI endonucleases for group II and III campylophages, respectively. Moreover, RAPD-PCR technique was for the first time assessed in the genetic characterization of campylophages and it was shown to be effective only for those of group II. Bacteriophage isolates grouped in a same genotype displayed different host ranges, therefore, 13 campylophages of group II and eight of group III were differentiated considering all the approaches assayed. An in-depth analysis of these bacteriophages will be performed to confirm their promising potential for the biocontrol of Campylobacter within the farm to fork process.

Bacteriophages to Control Campylobacter in Commercially Farmed Broiler Chickens, in Australia

This study describes the development and use of bacteriophage cocktails to control Campylobacter in broiler chickens, in a commercial setting, in Queensland Australia, following the birds from farm to the processing plant. The components of the bacteriophage cocktails were selected to be effective against the maximum number of Campylobacter jejuni and Campylobacter coli isolates encountered on SE Queensland farms. Farms were identified that had suitable Campylobacter target populations and phage were undetectable 1 week prior to the intended treatment. Cocktails of phages were administered at 47 days of age. Groups of study birds were slaughtered the following day, on-farm, at the end of flock transport to the plant, and at processing (approximately 28 h post-treatment). On Farm A, the phage treatment significantly reduced Campylobacter levels in the ceca at the farm in the range of 1-3 log10 CFU/g (p = 0.007), compared to mock treated controls. However, individual birds sampled on farm (1/10) or following transport (2/10) exhibited high cecal Campylobacter counts with low phage titers, suggesting that treatment periods > 24 h may be required to ensure phage replication for effective biocontrol in vivo. At the time of the trial the control birds in Farm B were phage positive despite having been negative one week earlier. There was no significant difference in the cecal Campylobacter counts between the treatment and control groups following treatment but a fall of 1.7 log10 CFU/g was observed from that determined from birds collected the previous week (p = 0.0004). Campylobacter isolates from both farms retained sensitivity to the treatment phages. These trials demonstrated bacteriophages sourced from Queensland farms have the potential to reduce intestinal Campylobacter levels in market ready broiler chickens.

Efficient isolation of Campylobacter bacteriophages from chicken skin, analysis of several isolation protocols

The application of Campylobacter specific bacteriophages appears as a promising food safety tool for the biocontrol of this pathogen in the poultry meat production chain. However, their isolation is a complicated challenge since their occurrence appears to be low. This work assessed the efficiency of seven protocols for recovering Campylobacter phages from chicken skin samples inoculated at phage loads from 5.0 × 10¹ to 5.0 × 10⁶ PFU/g. The enrichment of chicken skin in selective Bolton broth containing target isolates was the most efficient procedure, showing a low detection limit of 5.0 × 10¹ PFU/g and high recovery rates of up to 560%. This method's effectiveness increased as phage concentration decreased, showing its suitability for phage isolation. When this method was applied to isolate new Campylobacter phages from retail chicken skin, a total of 280 phages were recovered achieving an isolation success rate of 257%. From the 109 samples 68 resulted phage positive (62%). Chicken skin could be, therefore, considered a rich source in Campylobacter phages. This method is a simple, reproducible and efficient approach for the successful isolation of both group II and III Campylobacter specific bacteriophages, which could be helpful for the enhancement of food safety by reducing this pathogen contamination in broiler meat.

Self-cleansing properties of Ganga during mass ritualistic bathing on Maha-Kumbh

The deterioration of water quality of river Ganga is a huge concern for Govt. of India. Apart from various pollution sources, the religious and ritualistic activities also have a good share in deteriorating Ganga water quality. Thus, the aim of the present study was to evaluate the changes in physico-chemical properties, microbial diversity and role of bacteriophages in controlling bacterial population of Ganga water during mass ritualistic bathing on the occasion of Maha-Kumbh in 2013. The BOD, COD, hardness, TDS and level of various ions significantly increased, while DO decreased in Ganga water during Maha-Kumbh. Ganga water was more affluent in trace elements than Yamuna and their levels further increased during Maha-Kumbh, which was correlated with decreased level of trace elements in the sediment. The bacterial diversity and evenness were increased and correlated with the number of devotees taking a dip at various events. Despite enormous increase in bacterial diversity during mass ritualistic bathing, the core bacterial species found in pre-Kumbh Ganga water were present in all the samples taken during Kumbh and post-Kumbh. In addition, the alteration in bacterial population during mass bathing was well under 2 log units which can be considered negligible. The study of bacteriophages at different bathing events revealed that Ganga was richer with the presence of bacteriophages in comparison with Yamuna against seven common bacteria found during the Maha-Kumbh. These bacteriophages have played a role in controlling bacterial growth and thus preventing putrefaction of Ganga water. Further, the abundance of trace elements in Ganga water might also be a reason for suppression of bacterial growth. Thus, the current study showed that Ganga has characteristic water quality in terms of physico-chemical property and microbial diversity that might have a role in the reported self-cleansing property of Ganga; however, the increased pollution load has surpassed its self-cleansing properties. Since water has been celebrated in all cultures, the outcome of the current study will not only be useful for the policy maker of cleaning and conservation of Ganga but also for restoration of other polluted rivers all over the world.

Gene Transfer Agents in Symbiotic Microbes

Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.

Inhibitory effect of a combination with novel jumbo bacteriophages ΦMV-1 and ΦMV-4 on Morganella morganii subsp. morganii growth and histamine accumulation

Histamine (scombroid) poisoning is a foodborne illness caused by ingestion of histamine-contaminated seafood; therefore, inhibition of the growth of histamine-producing bacteria is key for it prevention. Infection of pathogenic bacteria by bacteriophages (phages) is being developed to prevent multiple foodborne illnesses. Here, we describe the inhibitory effect of a phage mixture on growth and histamine accumulation of Morganella morganii subsp. morganii, the primary causative agent of histamine poisoning in fish meat. We isolated novel two phages, ΦMV-1 and ΦMV-4, which infected M. morganii subsp. morganii strains tested in this study. ΦMV-1 and ΦMV-4 belong to family Myoviridae. Pulsed-field gel electrophoresis revealed that these phages are jumbo bacteriophages with large genomes. The latent period, rise period and burst size of ΦMV-1 were 30 min, 60 min, and 224 PFU per infected cell, respectively, and those of ΦMV-4 were 60 min, 50 min, and 62 PFU per infected cell, respectively. A mixture of ΦMV-1 and ΦMV-4 effectively prevented regrowth of M. morganii subsp. morganii after phage treatment, suggesting that the phage mixture treatment is more effective for inhibition of growth and histamine accumulation by M. morganii subsp. morganii than single phage treatment. Treatment with phage mixture inhibited growth and histamine accumulation by M. morganii subsp. morganii in canned and fresh tuna. The phage mixture might be an effective way to prevent growth of the histamine producer and accumulation of histamine in seafood.

Campylobacter spp. and bacteriophages from broiler chickens: Characterization of antibiotic susceptibility profiles and lytic bacteriophages

Bacteria of the genus Campylobacter are the most common pathogens causing zoonotic diseases in humans. Therefore, the aim of the study was to isolate Campylobacter bacteria from broiler chickens and evaluate their susceptibility to selected antibiotics by determining minimum inhibitory concentrations (MIC), followed by isolation and characterization of bacteriophages specific for Campylobacter spp. The material for the study consisted of field isolates of Campylobacter spp. obtained from the gut (cecum) of broiler chickens directly after slaughter in slaughterhouses, and bacteriophages specific for these strains. We isolated 48 strains from poultry (140 broiler chickens): 31 strains of Campylobacter jejuni and 17 of Campylobacter coli. Identification of the strains was confirmed by multiplex PCR and MALDI-TOF mass spectrometry. Over 83% of Campylobacter strains were resistant to ciprofloxacin, and over half the isolates were resistant to erythromycin, gentamicin, and tetracycline. Resistance to three or more antibiotics was observed in 91.6% of all strains. Four bacteriophages were obtained, and on the basis of their morphological structure, they were assigned to two families of the order Caudovirales: Myoviridae and Siphoviridae. A high percentage of the Campylobacter strains were resistant to at least three of the antibiotic groups tested. All of the phages exhibited lytic activity against the Campylobacter spp. isolates, but the antibacterial effect of the phages was not observed for all strains.

Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth

For a bacteriophage to be useful for phage therapy it must be both isolated from the environment and shown to have certain characteristics beyond just killing strains of the target bacterial pathogen. These include desirable characteristics such as a relatively broad host range and a lack of other characteristics such as carrying toxin genes and the ability to form a lysogen. While phages are commonly isolated first and subsequently characterized, it is possible to alter isolation procedures to bias the isolation toward phages with desirable characteristics. Some of these variations are regularly used by some groups while others have only been shown in a few publications. In this review I will describe (1) isolation procedures and variations that are designed to isolate phages with broader host ranges, (2) characterization procedures used to show that a phage may have utility in phage therapy, including some of the limits of such characterization, and (3) results of a survey and discussion with phage researchers in industry and academia on the practice of characterization of phages.

Inhibition of Clostridium perfringens using Bacteriophages and Bacteriocin Producing Strains

In this study, we isolated and characterized a bacteriocin-producing strain and two bacteriophages (P4, A3), showing antimicrobial effects against Clostridium perfringens, from chicken and swine feces by the spot-on-the lawn antagonism method. The selected strain was identified as Streptococcus hyointestinalis by 16S rRNA gene sequencing. The bacteriocin from the isolated strain exhibited strong inhibitory activity against four strains of C. perfringens and all the tested strains of Listeria monocytogenes, and the bacteriocin were highly heat- and pH-stable even at pH 2, pH 10 and 121℃ for 15 min. We also evaluated the combined effects of the isolated bacteriocin and phages. Combining the phage treatments and bacteriocin resulted in a synergetic effect compared with the phage or the bacteriocin alone. In addition, during the probiotic test, the bacteriocin-producing S. hyointestinalis B19 strain reduced the population of C. perfringens significantly. Treatment with S. hyointestinalis B19 and a cocktail of lytic bacteriophages eradicated the C. perfringens KCTC 3269^T, completely. Consequently, the isolated bacteriocin and bacteriophages represent candidates for effective biocontrol of C. perfringens, and bacteriocin-producing S. hyointestinalis B19 is a potential probiotic candidate for use in domestic animals.

Isolation and Characterization of Listeria phages for Control of Growth of Listeria monocytogenes in Milk

In this study, two Listeria bacteriophages, LMP1 and LMP7, were isolated from chicken feces as a means of biocontrol of L. monocytogenes. Both bacteriophages had a lytic effect on L. monocytogenes ATCC 7644, 15313, 19114, and 19115. Phages LMP1 and LMP7 were able to inhibit the growth of L. monocytogenes ATCC 7644 and 19114 in tryptic soy broth at 10°C and 30°C. Nevertheless, LMP1 was more effective than LMP7 at inhibiting L. monocytogenes ATCC 19114. On the contrary, LMP7 was more effective than LMP1 at inhibiting L. monocytogenes ATCC 7644. The morphology of LMP1 and LMP7 resembled that of members of the Siphoviridae family. The growth of L. monocytogenes ATCC 7644 was inhibited by both LMP1 and LMP7 in milk; however, the growth of L. monocytogenes ATCC 19114 was only inhibited by LMP1 at 30°C. The lytic activity of bacteriophages was also evaluated at 4°C in milk in order to investigate the potential use of these phages in refrigerated products. In conclusion, these two bacteriophages exhibit different host specificities and characteristics, suggesting that they can be used as a component of a phage cocktail to control L. monocytogenes in the food industry.

Methods for Isolation, Purification, and Propagation of Bacteriophages of Campylobacter jejuni

Here, we describe the methods for isolation, purification, and propagation of Campylobacter jejuni bacteriophages from samples expected to contain high number of phages such as chicken feces. The overall steps are (1) liberation of phages from the sample material; (2) observation of plaque-forming units on C. jejuni lawns using a spot assay; (3) isolation of single plaques; (4) consecutive purification procedures; and (5) propagation of purified phages from a plate lysate to prepare master stocks.

Primary isolation strain determines both phage type and receptors recognised by Campylobacter jejuni bacteriophages

In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated using NCTC12662 as the indicator strain, which may have biased the selection of phages. A large group of C. jejuni phages rely on the highly diverse capsular polysaccharide (CPS) for infection and recent work identified the O-methyl phosphoramidate modification (MeOPN) of CPS as a phage receptor. We therefore chose seven C. jejuni strains each expressing different CPS structures as indicator strains in a large screening for phages in samples collected from free-range poultry farms. Forty-three phages were isolated using C. jejuni NCTC12658, NCTC12662 and RM1221 as host strains and 20 distinct phages were identified based on host range analysis and genome restriction profiles. Most phages were isolated using C. jejuni strains NCTC12662 and RM1221 and interestingly phage genome size (140 kb vs. 190 kb), host range and morphological appearance correlated with the isolation strain. Thus, according to C. jejuni phage grouping, NCTC12662 and NCTC12658 selected for CP81-type phages, while RM1221 selected for CP220-type phages. Furthermore, using acapsular ∆kpsM mutants we demonstrated that phages isolated on NCTC12658 and NCTC12662 were dependent on the capsule for infection. In contrast, CP220-type phages isolated on RM1221 were unable to infect non-motile ∆motA mutants, hence requiring motility for successful infection. Hence, the primary phage isolation strain determines both phage type (CP81 or CP220) as well as receptors (CPS or flagella) recognised by the isolated phages.

Use of phages to control Campylobacter spp

The use of phages to control pathogenic bacteria has been investigated since they were first discovered in the beginning of the 1900s. Over the last century we have slowly gained an in-depth understanding of phage biology including which phage properties are desirable when considering phage as biocontrol agents and which phage characteristics to potentially avoid. Campylobacter infections are amongst the most frequently encountered foodborne bacterial infections around the world. Handling and consumption of raw or undercooked poultry products have been determined to be the main route of transmission. The ability to use phages to target these bacteria has been studied for more than a decade and although we have made progress towards deciphering how best to use phages to control Campylobacter associated with poultry production, there is still much work to be done. This review outlines methods to improve the isolation of these elusive phages, as well as methods to identify desirable characteristics needed for a successful outcome. It also highlights the body of research undertaken so far and what criteria to consider when doing in-vivo studies, especially because some in-vitro studies have not been found to translate into to phage efficacy in-vivo.

The genome and proteome of a Campylobacter coli bacteriophage vB_CcoM-IBB_35 reveal unusual features

Background

Campylobacter is the leading cause of foodborne diseases worldwide. Bacteriophages (phages) are naturally occurring predators of bacteria, ubiquitous in the environment, with high host specificity and thus considered an appealing option to control bacterial pathogens. Nevertheless for an effective use of phages as antimicrobial agents, it is important to understand phage biology which renders crucial the analysis of phage genomes and proteomes. The lack of sequence data from Campylobacter phages adds further importance to these studies.

Methods

vB_CcoM-IBB_35 is a broad lytic spectrum Myoviridae Campylobacter phage with high potential for therapeutic use. The genome of this phage was obtained by pyrosequencing and the sequence data was further analyzed. The proteomic analysis was performed by SDS-PAGE and Mass spectrometry.

Results and conclusions

The DNA sequence data of vB_CcoM-IBB_35 consists of five contigs for a total of 172,065 bp with an average GC content of 27%. Attempts to close the gaps between contigs were unsuccessful since the DNA preparations appear to contain substances that inhibited Taq and ϕ29 polymerases. From the 210 identified ORFs, around 60% represent proteins that were not functionally assigned. Homology exists with members of the Teequatrovirinae namely for T4 proteins involved in morphogenesis, nucleotide metabolism, transcription, DNA replication and recombination. Tandem mass spectrometric analysis revealed 38 structural proteins as part of the mature phage particle.

Conclusions

Genes encoding proteins involved in the carbohydrate metabolism along with several incidences of gene duplications, split genes with inteins and introns have been rarely found in other phage genomes yet are found in this phage. We identified the genes encoding for tail fibres and for the lytic cassette, this later, expressing enzymes for bacterial capsular polysaccharides (CPS) degradation, which has not been reported before for Campylobacter phages.

Campylobacter bacteriophages and bacteriophage therapy

Members of the genus Campylobacter are frequently responsible for human enteric disease with occasionally very serious outcomes. Much of this disease burden is thought to arise from consumption of contaminated poultry products. More than 80% of poultry in the UK harbour Campylobacter as a part of their intestinal flora. To address this unacceptably high prevalence, various interventions have been suggested and evaluated. Among these is the novel approach of using Campylobacter-specific bacteriophages, which are natural predators of the pathogen. To optimize their use as therapeutic agents, it is important to have a comprehensive understanding of the bacteriophages that infect Campylobacter, and how they can affect their host bacteria. This review will focus on many aspects of Campylobacter-specific bacteriophages including: their first isolation in the 1960s, their use in bacteriophage typing schemes, their isolation from the different biological sources and genomic characterization. As well as their use as therapeutic agents to reduce Campylobacter in poultry their future potential, including their use in bio-sanitization of food, will be explored. The evolutionary consequences of naturally occurring bacteriophage infection that have come to light through investigations of bacteriophages in the poultry ecosystem will also be discussed.

Bacteriophages as biocontrol agents of food pathogens

Bacteriophages have long been recognized for their potential as biotherapeutic agents. The recent approval for the use of phages of Listeria monocytogenes for food safety purposes has increased the impetus of phage research to uncover phage-mediated applications with activity against other food pathogens. Areas of emerging and growing significance, such as predictive modelling and genomics, have shown their potential and impact on the development of new technologies to combat food pathogens. This review will highlight recent advances in the research of phages that target food pathogens and that promote their use in biosanitation, while it will also discuss its limitations.

The in vivo efficacy of two administration routes of a phage cocktail to reduce numbers of Campylobacter coli and Campylobacter jejuni in chickens

BACKGROUND

Poultry meat is one of the most important sources of human campylobacteriosis, an acute bacterial enteritis which is a major problem worldwide. Campylobacter coli and Campylobacter jejuni are the most common Campylobacter species associated with this disease. These pathogens live in the intestinal tract of most avian species and under commercial conditions they spread rapidly to infect a high proportion of the flock, which makes their treatment and prevention very difficult. Bacteriophages (phages) are naturally occurring predators of bacteria with high specificity and also the capacity to evolve to overcome bacterial resistance. Therefore phage therapy is a promising alternative to antibiotics in animal production. This study tested the efficacy of a phage cocktail composed of three phages for the control of poultry infected with C. coli and C. jejuni. Moreover, it evaluated the effectiveness of two routes of phage administration (by oral gavage and in feed) in order to provide additional information regarding their future use in a poultry unit.

RESULTS

The results indicate that experimental colonisation of chicks was successful and that the birds showed no signs of disease even at the highest dose of Campylobacter administered. The phage cocktail was able to reduce the titre of both C. coli and C. jejuni in faeces by approximately 2 log10 cfu/g when administered by oral gavage and in feed. This reduction persisted throughout the experimental period and neither pathogen regained their former numbers. The reduction in Campylobacter titre was achieved earlier (2 days post-phage administration) when the phage cocktail was incorporated in the birds' feed. Campylobacter strains resistant to phage infection were recovered from phage-treated chickens at a frequency of 13%. These resistant phenotypes did not exhibit a reduced ability to colonize the chicken guts and did not revert to sensitive types.

CONCLUSIONS

Our findings provide further evidence of the efficacy of phage therapy for the control of Campylobacter in poultry. The broad host range of the novel phage cocktail enabled it to target both C. jejuni and C. coli strains. Moreover the reduction of Campylobacter by approximately 2 log10cfu/g, as occurred in our study, could lead to a 30-fold reduction in the incidence of campylobacteriosis associated with consumption of chicken meals (according to mathematical models). To our knowledge this is the first report of phage being administered in feed to Campylobacter-infected chicks and our results show that it lead to an earlier and more sustainable reduction of Campylobacter than administration by oral gavage. Therefore the present study is of extreme importance as it has shown that administering phages to poultry via the food could be successful on a commercial scale.