Phage Biocontrol of Campylobacter jejuni in Chickens Does Not Produce Collateral Effects on the Gut Microbiota

Identification of novel small molecule inhibitors of twin arginine translocation (Tat) pathway and their effect on the control of Campylobacter jejuni in chickens

Introduction

Control of Campylobacter from farm to fork is challenging due to the frequent emergence of antimicrobial-resistant isolates. Furthermore, poultry production systems are known reservoirs of Campylobacter. The twin-arginine translocation (Tat) pathway is a crucial bacterial secretion system that allows Campylobacter to colonize the host intestinal tract by using formate as the main source of energy. However, Tat pathway is also a major contributing factor for resistance to copper sulfate (CuSO4).

Methods

Since mammals and chickens do not have proteins or receptors that are homologous to bacterial Tat proteins, identification of small molecule (SM) inhibitors targeting the Tat system would allow the development of safe and effective control methods to mitigate Campylobacter in infected or colonized hosts in both pre-harvest and post-harvest. In this study, we screened 11 commercial libraries (n = 50,917 SM) for increased susceptibility to CuSO4 (1 mM) in C. jejuni 81-176, a human isolate which is widely studied.

Results

Furthermore, we evaluated 177 SM hits (2.5 μg/mL and above) that increased the susceptibility to CuSO4 for the inhibition of formate dehydrogenase (Fdh) activity, a Tat-dependent substrate. Eight Tat-dependent inhibitors (T1-T8) were selected for further studies. These selected eight Tat inhibitors cleared all tested Campylobacter strains (n = 12) at >10 ng/mL in the presence of 0.5 mM CuSO4in vitro. These selected SMs were non-toxic to colon epithelial (Caco-2) cells when treated with 50 μg/mL for 24 h and completely cleared intracellular C. jejuni cells when treated with 0.63 μg/mL of SM for 24 h in the presence of 0.5 mM of CuSO4. Furthermore, 3 and 5-week-old chicks treated with SM candidates for 5 days had significantly decreased cecal colonization (up to 1.2 log; p < 0.01) with minimal disruption of microbiota. In silico analyses predicted that T7 has better drug-like properties than T2 inhibitor and might target a key amino acid residue (glutamine 165), which is located in the hydrophobic core of TatC protein.

Discussion

Thus, we have identified novel SM inhibitors of the Tat pathway, which represent a potential strategy to control C. jejuni spread on farms.

Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers

Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C. jejuni is critical as they may confer bacterial resistance to bacteriophage treatment. Therefore, in this study, we explored the distribution of the CRISPR arrays from 178 C. jejuni isolated from chicken livers between January and July 2018. Genomic DNA of C. jejuni isolates was extracted, and CRISPR type 1 sequences were amplified by PCR. Amplicons were purified and sequenced by the Sanger dideoxy sequencing method. Direct repeats (DRs) and spacers of CRISPR sequences were identified using the CRISPRFinder program. Further, spacer sequences were submitted to the CRISPRTarget to identify potential homology to bacteriophage types. Even though CRISPR-Cas is reportedly not an active system in Campylobacter, a total of 155 (87%) C. jejuni isolates were found to harbor CRISPR sequences; one type of DR was identified in all 155 isolates. The CRISPR loci lengths ranged from 97 to 431 nucleotides. The numbers of spacers ranged from one to six. A total of 371 spacer sequences were identified in the 155 isolates that could be grouped into 51 distinctive individual sequences. Further comparison of these 51 spacer sequences with those in databases showed that most spacer sequences were homologous to Campylobacter bacteriophage DA10. The results of our study provide important information relative to the development of an effective bacteriophage treatment to mitigate Campylobacter during poultry production.

Broiler farming practices using new or re-used bedding, inclusive of free-range, have no impact on Campylobacter levels, species diversity, Campylobacter community profiles and Campylobacter bacteriophages

A multi-stage option to address food-safety can be produced by a clearer understanding of Campylobacter's persistence through the broiler production chain, its environmental niche and its interaction with bacteriophages. This study addressed Campylobacter levels, species, genotype, bacteriophage composition/ levels in caeca, litter, soil and carcasses across commercial broiler farming practices to inform on-farm management, including interventions. Broilers were sequentially collected as per company slaughter schedules over two-years from 17 farms, which represented four commercially adopted farming practices, prior to the final bird removal (days 39-53). The practices were conventional full clean-out, conventional litter re-use, free-range-full cleanout and free-range-litter re-use. Caeca, litter and soil collected on-farm, and representative carcases collected at the processing plant, were tested for Campylobacter levels, species dominance and Campylobacter bacteriophages. General community profiling via denaturing gradient gel electrophoresis of the flaA gene was used to establish the population relationships between various farming practices on representative Campylobacter isolates. The farming practice choices did not influence the high caeca Campylobacter levels (log 7.5 to log 8.5 CFU/g), the carcass levels (log 2.5 to log 3.2 CFU/carcass), the C. jejuni/C. coli dominance and the on-farm bacteriophage presence/levels. A principal coordinate analysis of the flaA distribution for farm and litter practices showed strong separation but no obvious farming practice related grouping of Campylobacter. Bacteriophages originated from select farms, were not practice-dependent, and were detected in the environment (litter) only if present in the birds (caeca). This multifaceted study showed no influence of farming practices on on-farm Campylobacter dynamics. The significance of this study means that a unified on-farm risk-management could be adopted irrespective of commercial practice choices to collectively address caeca Campylobacter levels, as well as the potential to include Campylobacter bacteriophage biocontrol. The impact of this study means that there are no constraints in re-using bedding or adopting free-range farming, thus contributing to environmentally sustainable (re-use) and emerging (free-range) broiler farming choices.

Bacteriophages: Status quo and emerging trends toward one health approach

The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.

Phage-Based Biosanitation Strategies for Minimizing Persistent Salmonella and Campylobacter Bacteria in Poultry

Control strategies to minimize pathogenic bacteria in food animal production are one of the key components in ensuring safer food for consumers. The most significant challenges confronting the food industry, particularly in the major poultry and swine sectors, are antibiotic resistance and resistance to cleaning and disinfection in zoonotic bacteria. In this context, bacteriophages have emerged as a promising tool for zoonotic bacteria control in the food industry, from animals and farm facilities to the final product. Phages are viruses that infect bacteria, with several advantages as a biocontrol agent such as high specificity, self-replication, self-limitation, continuous adaptation, low inherent toxicity and easy isolation. Their development as a biocontrol agent is of particular interest, as it would allow the application of a promising and even necessary "green" technology to combat pathogenic bacteria in the environment. However, bacteriophage applications have limitations, including selecting appropriate phages, legal restrictions, purification, dosage determination and bacterial resistance. Overcoming these limitations is crucial to enhance phage therapy's effectiveness against zoonotic bacteria in poultry. Thus, this review aims to provide a comprehensive view of the phage-biosanitation strategies for minimizing persistent Salmonella and Campylobacter bacteria in poultry.

Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection

Excessive usage of antibiotics threatens the bacterial diversity in the microbiota of animals. An alternative to antibiotics that has been suggested to not disturb the microbiota is (bacterio)phage therapy. In this study, we challenged germ-free and microbially colonized yolk sac fry of Atlantic salmon with Flavobacterium columnare and observed that the mere presence of a microbiota protected the fish against lethal infection. We then investigated the effect of phage- or oxytetracycline treatment on fish survival and rearing water bacterial community characteristics using 16S rRNA gene amplicon sequencing. Phage treatment led to an increased survival of F. columnare-challenged fish and reduced the relative amounts of the pathogen in the water microbiota. In the absence of F. columnare, phage treatment did not affect the composition or the α-diversity of the rearing water microbiota. In the presence of the phage's host, phage treatment induced minor changes to the bacterial community composition, without affecting the α-diversity. Surprisingly, oxytetracycline treatment had no observable effect on the water microbiota and did not reduce the relative abundance of F. columnare in the water. In conclusion, we showed that phage treatment prevents mortality while not negatively affecting the rearing water microbiota, thus suggesting that phage treatment may be a suitable alternative to antibiotics. We also demonstrated a protective effect of the microbiota in Atlantic salmon yolk sac fry.

Oral phage therapy with microencapsulated phage A221 against Escherichia coli infections in weaned piglets

BACKGROUND

Escherichia coli (E. coli) is a common pathogen that often causes diarrhea in piglets. Since bacteria are becoming more and more resistant to antibiotics, phages have become a promising alternative therapy. However, the therapy of oral phage often fails to achieve the desired effect. A novel phage named A221 was isolated by using E. coli GXXW-1103 as host strain, characterized by electron microscopy, genomic sequencing and analyzed by measuring lysis ability in vitro.

RESULTS

Phage A221 was identified as a member of Ackermannviridae, Aglimvirinae, Agtrevirus with 153297 bp genome and effectively inhibited bacterial growth in vitro for 16 h. This study was conducted to evaluate the therapeutic effect of oral microencapsulated phage A221 on E. coli GXXW-1103 infections in weaned piglets. The protective effect of phage was evaluated by body weight analysis, bacterial load and histopathological changes. The results showed that with the treatment of phage A221, the body weight of piglets increased, the percentage of Enterobacteriaceae in duodenum decreased to 0.64%, the lesions in cecum and duodenum were alleviated, and the bacterial load in the jejunal lymph nodes, cecum and spleen were also significantly different with infected group (P < 0.001).

CONCLUSIONS

The results showed that phage A221 significantly increased the daily weight gain of piglets, reduced the bacterial load of tissues and the intestinal lesions, achieved the same therapeutic effect as antibiotic Florfenicol. Taken together, oral microencapsulated phage A221 has a good therapeutic effect on bacterial diarrhea of weaned piglets, which provides guidance for the clinical application of phage therapy in the future.

Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review

Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.

Bacteriophage cocktail application for Campylobacter mitigation - from in vitro to in vivo

BACKGROUND

Effective strategies are urgently needed to control Campylobacteriosis, one of the most important foodborne gastrointestinal diseases worldwide. Administering bacteriophages (phages) is under evaluation as a possible intervention strategy in primary poultry production to reduce the public health risk of human infection. A major challenge is the translation of results from small-scale animal studies to large broiler flocks. In this study, the in vitro lytic activity of 18 Campylobacter-specific group II phages and 19 group III phages were examined singly, and in different combinations from the same group and from both groups using a planktonic killing assay. Based on these results, a combination of phage NCTC 12,673 (group III) and vB_CcM-LmqsCPL1/1 (group II) was selected for in vivo application in a seeder bird model to study its effectiveness under conditions as close as possible to field conditions. One hundred eighty Ross 308 broiler chickens were divided into a control and a treatment group. Ten days post hatch, seeder birds were orally inoculated with the C. jejuni target strain. Phages were administered via drinking water at a total concentration of 107 PFU/mL four, three, and two days before necropsy.

RESULTS

Combining group II and group III phages resulted in significantly higher in vitro growth inhibition against the C. jejuni target strain BfR-CA-14,430 than single application or combinations of phages from the same group. The results of the animal trial showed that the application of the two phages significantly reduced Campylobacter counts in cloacal swabs. At necropsy, Campylobacter counts in colonic content of the treatment group were significantly reduced by 2 log10 units compared to the control group.

CONCLUSIONS

We demonstrated that combining phages of groups II and III results in significantly increased lytic activities. The in vitro results were successfully translated into practical application in a study design close to field conditions, providing new data to apply phages in conventional broiler flocks in the future. Phage application reduced the fecal Campylobacter excretion and Campylobacter concentrations in the colon of broilers.

Bacteriophages for the Targeted Control of Foodborne Pathogens

Foodborne illness is exacerbated by novel and emerging pathotypes, persistent contamination, antimicrobial resistance, an ever-changing environment, and the complexity of food production systems. Sporadic and outbreak events of common foodborne pathogens like Shiga toxigenic E. coli (STEC), Salmonella, Campylobacter, and Listeria monocytogenes are increasingly identified. Methods of controlling human infections linked with food products are essential to improve food safety and public health and to avoid economic losses associated with contaminated food product recalls and litigations. Bacteriophages (phages) are an attractive additional weapon in the ongoing search for preventative measures to improve food safety and public health. However, like all other antimicrobial interventions that are being employed in food production systems, phages are not a panacea to all food safety challenges. Therefore, while phage-based biocontrol can be promising in combating foodborne pathogens, their antibacterial spectrum is generally narrower than most antibiotics. The emergence of phage-insensitive single-cell variants and the formulation of effective cocktails are some of the challenges faced by phage-based biocontrol methods. This review examines phage-based applications at critical control points in food production systems with an emphasis on when and where they can be successfully applied at production and processing levels. Shortcomings associated with phage-based control measures are outlined together with strategies that can be applied to improve phage utility for current and future applications in food safety.

Advances in enteropathogen control throughout the meat chicken production chain

Enteropathogens, namely Salmonella and Campylobacter, are a concern in global public health and have been attributed in numerous risk assessments to a poultry source. During the last decade, a large body of research addressing this problem has been published. The literature reviewed contains review articles on certain aspects of poultry production chain; however, in the past decade there has not been a review on the entire chain-farm to fork-of poultry production. For this review, a pool of 514 articles were selected for relevance via a systematic screening process (from >7500 original search articles). These studies identified a diversity of management and intervention strategies for the elimination or reduction of enteropathogens in poultry production. Many studies were laboratory or limited field trials with implementation in true commercial operations being problematic. Entities considering using commercial antienteropathogen products and interventions are advised to perform an internal validation and fit-for-purpose trial as Salmonella and Campylobacter serovars and biovars may have regional diversity. Future research should focus on nonchemical application within the processing plant and how a combination of synergisticinterventions through the production chain may contribute to reducing the overall carcass burden of enteropathogens, coupled with increased consumer education on safe handling and cooking of poultry.

Application of the lytic bacteriophage Rostam to control Salmonella enteritidis in eggs

Foodborne Salmonella enteritidis infections place human health at risk, driven by regular outbreaks and individual cases by different contaminated food materials. This study was conducted to characterize and employ a single bacteriophage as a potential biocontrol agent. Phage Rostam was isolated, characterized and then applied as biocontrol agent against S. enteritidis in liquid whole eggs and eggshell. Rostam is a novel myovirus belonging to the Rosemountvirus genus and active against Escherichia coli and Salmonella spp. Rostam is stable in a pH range from 4 to 10, a salt concentration of 1-9 %, whereas UV radiation gradually reduces phage stability, and its 53 kb genome sequence indicates this phage does not contain known toxins or lysogeny-associated genes. Its latent period is short with a burst size of 151 PFU/cell, under standard growth conditions. Killing curves indicate that at higher multiplicities of infection (MOI), the reduction in S. enteritidis count is more pronounced. Phage Rostam (MOI 10,000) reduces S. enteritidis growth to below the detection limit at 4 °C in both liquid whole eggs and on the eggshell within 24 h. Due to its high lytic activity and stability in relevant conditions, Rostam has the potential to be an efficient biopreservative for egg and egg products.

Current and future interventions for improving poultry health and poultry food safety and security: A comprehensive review

Poultry is thriving across the globe. Chicken meat is the most preferred poultry worldwide, and its popularity is increasing. However, poultry also threatens human hygiene, especially as a fomite of infectious diseases caused by the major foodborne pathogens (Campylobacter, Salmonella, and Listeria). Preventing pathogenic bacterial biofilm is crucial in the chicken industry due to increasing food safety hazards caused by recurring contamination and the rapid degradation of meat, as well as the increased resistance of bacteria to cleaning and disinfection procedures commonly used in chicken processing plants. To address this, various innovative and promising strategies to combat bacterial resistance and biofilm are emerging to improve food safety and quality and extend shelf-life. In particular, natural compounds are attractive because of their potential antimicrobial activities. Natural compounds can also boost the immune system and improve poultry health and performance. In addition to phytochemicals, bacteriophages, nanoparticles, coatings, enzymes, and probiotics represent unique and environmentally friendly strategies in the poultry processing industry to prevent foodborne pathogens from reaching the consumer. Lactoferrin, bacteriocin, antimicrobial peptides, cell-free supernatants, and biosurfactants are also of considerable interest for their prospective application as natural antimicrobials for improving the safety of raw poultry meat. This review aims to describe the feasibility of these proposed strategies and provide an overview of recent published evidences to control microorganisms in the poultry industry, considering the human health, food safety, and economic aspects of poultry production.

Natural Killers: Opportunities and Challenges for the Use of Bacteriophages in Microbial Food Safety from the One Health Perspective

Ingestion of food or water contaminated with pathogenic bacteria may cause serious diseases. The One Health approach may help to ensure food safety by anticipating, preventing, detecting, and controlling diseases that spread between animals, humans, and the environment. This concept pays special attention to the increasing spread and dissemination of antibiotic-resistant bacteria, which are considered one of the most important environment-related human and animal health hazards. In this context, the development of innovative, versatile, and effective alternatives to control bacterial infections in order to assure comprehensive food microbial safety is becoming an urgent issue. Bacteriophages (phages), viruses of bacteria, have gained significance in the last years due to the request for new effective antimicrobials for the treatment of bacterial diseases, along with many other applications, including biotechnology and food safety. This manuscript reviews the application of phages in order to prevent food- and water-borne diseases from a One Health perspective. Regarding the necessary decrease in the use of antibiotics, results taken from the literature indicate that phages are also promising tools to help to address this issue. To assist future phage-based real applications, the pending issues and main challenges to be addressed shortly by future studies are also taken into account.

The rise of antibiotic resistance in Campylobacter

PURPOSE OF REVIEW

Campylobacter is a major foodborne pathogen that infects the human intestinal tract. This review discusses the current status of antibiotic resistance, transmission of antibiotic resistance genes, and strategies to combat the global Campylobacter epidemic.

RECENT FINDINGS

Over the past 18 months, articles on Campylobacter antibiotic resistance have been published in ∼39 countries. Antibiotic-resistant Campylobacter have been detected in humans, livestock, poultry, wild animals, the environment, and food. Campylobacter spp. are resistant to a wide spectrum of antimicrobial agents, including the antibiotics quinolones, macrolides, tetracyclines, aminoglycosides, and chloramphenicols. Multidrug resistance is a globally emerging problem. Continuous antibiotic pressure promotes the spread of drug-resistant Campylobacter spp. Additionally, Campylobacter is well adapted to acquiring foreign drug resistance genes, including ermB, optrA, fexA, and cfrC, which are usually acquired from gram-positive bacteria.

SUMMARY

The widespread use of antibiotics has caused a global epidemic of drug-resistant Campylobacter infections. Many countries are actively reducing the use of antibiotics and adopting alternatives in the livestock and poultry industries to control the spread of drug-resistant Campylobacter spp.

An overview of the use of bacteriophages in the poultry industry: Successes, challenges, and possibilities for overcoming breakdowns

The primary contaminants in poultry are Salmonella enterica, Campylobacter jejuni, Escherichia coli, and Staphylococcus aureus. Their pathogenicity together with the widespread of these bacteria, contributes to many economic losses and poses a threat to public health. With the increasing prevalence of bacterial pathogens being resistant to most conventional antibiotics, scientists have rekindled interest in using bacteriophages as antimicrobial agents. Bacteriophage treatments have also been investigated as an alternative to antibiotics in the poultry industry. Bacteriophages' high specificity may allow them only to target a specific bacterial pathogen in the infected animal. However, a tailor-made sophisticated cocktail of different bacteriophages could broaden their antibacterial activity in typical situations with multiple clinical strains infections. Bacteriophages may not only be used in terms of reducing bacterial contamination in animals but also, under industrial conditions, they can be used as safe disinfectants to reduce contamination on food-contact surfaces or poultry carcasses. Nevertheless, bacteriophage therapies have not been developed sufficiently for widespread use. Problems with resistance, safety, specificity, and long-term stability must be addressed in particular. This review highlights the benefits, challenges, and current limitations of bacteriophage applications in the poultry industry.

Role of Bacteriophages for Optimized Health and Production of Poultry

The poultry sector is facing infections from Salmonella, Campylobacter, Listeria and Staphylococcus spp., and Escherichia coli, that have developed multidrug resistance aptitude. Antibiotics cause disturbances in the balance of normal microbiota leading to dysbiosis, immunosuppression, and the development of secondary infections. Bacteriophages have been reported to lower the colonization of Salmonella and Campylobacter in poultry. The specificity of bacteriophages is greater than that of antibiotics and can be used as a cocktail for enhanced antibacterial activity. Specie-specific phages have been prepared, e.g., Staphylophage (used against Staphylococcus bacteria) that specifically eliminate bacterial pathogens. Bacteriophage products, e.g., BacWash^TM and Ecolicide PX have been developed as antiseptics and disinfectants for effective biosecurity and biosafety measures. The success of phage therapy is influenced by time to use, the amount used, the delivery mechanism, and combination therapy with other therapeutics. It is a need of time to build a comprehensive understanding of the use of bacteriophages in poultry production. The current review thus focuses on mechanisms of bacteriophages against poultry pathogens, their applications in various therapeutics, impacts on the economy, and current challenges.

Antimicrobial effect of a drinking water additive comprising four organic acids on Campylobacter load in broilers and monitoring of bacterial susceptibility

Application of organic acids via feed or drinking water is under discussion as a possible intervention strategy to reduce Campylobacter (C.) load in primary poultry production. A previous in vitro study showed that reduced concentrations of sorbic acid, benzoic acid, propionic acid, and acetic acid were required for antibacterial activity against Campylobacter when using a mixture of these 4 acids compared to when using the single acids. The present study aimed at determining the antibacterial efficiency of this combination in vivo as a drinking water additive for reducing shedding and intestinal C. jejuni colonization in broilers. Furthermore, we assessed whether the inoculated C. jejuni strain BfR-CA-14430 adapted in vivo to the applied organic acids. Results of this study showed that adding the organic acids consistently reduced Campylobacter loads in cloacal swabs. While significant reductions were observed within the entire study period, a maximum 2 log reduction occurred at an age of 18 d. However, after dissection at the end of the trial, no significant differences were detected in Campylobacter loads of cecal and colon contents compared to the control group. Susceptibility testing of re-isolates from cloacal swabs and cecal content revealed equal minimum inhibitory concentration (MIC) values compared to the inoculated test strain, suggesting that C. jejuni remained susceptible throughout the trial.

Examining the effects of Salmonella phage on the caecal microbiota and metabolome features in Salmonella-free broilers

Bacteriophages selectively infect and kill their target bacterial host, being a promising approach to controlling zoonotic bacteria in poultry production. To ensure confidence in its use, fundamental questions of safety and toxicity monitoring of phage therapy should be raised. Due to its high specificity, a minimal impact on the gut ecology is expected; however, more in-depth research into key parameters that influence the success of phage interventions has been needed to reach a consensus on the impact of bacteriophage therapy in the gut. In this context, this study aimed to investigate the interaction of phages with animals; more specifically, we compared the caecum microbiome and metabolome after a Salmonella phage challenge in Salmonella-free broilers, evaluating the role of the phage administration route. To this end, we employed 45 caecum content samples from a previous study where Salmonella phages were administered via drinking water or feed for 24 h from 4, 5 to 6-weeks-old broilers. High-throughput 16S rRNA gene sequencing showed a high level of similarity (beta diversity) but revealed a significant change in alpha diversity between broilers with Salmonella-phage administered in the drinking water and control. Our results showed that the phages affected only a few genera of the microbiota's structure, regardless of the administration route. Among these, we found a significant increase in Streptococcus and Sellimonas in the drinking water and Lactobacillus, Anaeroplasma and Clostridia_vadinBB60_group in the feed. Nevertheless, the LC-HRMS-based metabolomics analyses revealed that despite few genera were significantly affected, a substantial number of metabolites, especially in the phage administered in the drinking water were significantly altered (64 and 14 in the drinking water and feed groups, respectively). Overall, our study shows that preventive therapy with bacteriophages minimally alters the caecal microbiota but significantly impacts their metabolites, regardless of the route of administration.

Recent Advances in the Application of Bacteriophages against Common Foodborne Pathogens

Bacteriophage potential in combating bacterial pathogens has been recognized nearly since the moment of discovery of these viruses at the beginning of the 20th century. Interest in phage application, which initially focused on medical treatments, rapidly spread throughout different biotechnological and industrial fields. This includes the food safety sector in which the presence of pathogens poses an explicit threat to consumers. This is also the field in which commercialization of phage-based products shows the greatest progress. Application of bacteriophages has gained special attention particularly in recent years, presumably due to the potential of conventional antibacterial strategies being exhausted. In this review, we present recent findings regarding phage application in fighting major foodborne pathogens, including Salmonella spp., Escherichia coli, Yersinia spp., Campylobacter jejuni and Listeria monocytogenes. We also discuss advantages of bacteriophage use and challenges facing phage-based antibacterial strategies, particularly in the context of their widespread application in food safety.

Recent Progress in Phage Therapy to Modulate Multidrug-Resistant Acinetobacter baumannii, including in Human and Poultry

Acinetobacter baumannii is a multidrug-resistant and invasive pathogen associated with the etiopathology of both an increasing number of nosocomial infections and is of relevance to poultry production systems. Multidrug-resistant Acinetobacter baumannii has been reported in connection to severe challenges to clinical treatment, mostly due to an increased rate of resistance to carbapenems. Amid the possible strategies aiming to reduce the insurgence of antimicrobial resistance, phage therapy has gained particular importance for the treatment of bacterial infections. This review summarizes the different phage-therapy approaches currently in use for multiple-drug resistant Acinetobacter baumannii, including single phage therapy, phage cocktails, phage-antibiotic combination therapy, phage-derived enzymes active on Acinetobacter baumannii and some novel technologies based on phage interventions. Although phage therapy represents a potential treatment solution for multidrug-resistant Acinetobacter baumannii, further research is needed to unravel some unanswered questions, especially in regard to its in vivo applications, before possible routine clinical use.

From Farm to Fork: Streptococcus suis as a Model for the Development of Novel Phage-Based Biocontrol Agents

Bacterial infections of livestock threaten the sustainability of agriculture and public health through production losses and contamination of food products. While prophylactic and therapeutic application of antibiotics has been successful in managing such infections, the evolution and spread of antibiotic-resistant strains along the food chain and in the environment necessitates the development of alternative or adjunct preventive and/or therapeutic strategies. Additionally, the growing consumer preference for "greener" antibiotic-free food products has reinforced the need for novel and safer approaches to controlling bacterial infections. The use of bacteriophages (phages), which can target and kill bacteria, are increasingly considered as a suitable measure to reduce bacterial infections and contamination in the food industry. This review primarily elaborates on the recent veterinary applications of phages and discusses their merits and limitations. Furthermore, using Streptococcus suis as a model, we describe the prevalence of prophages and the anti-viral defence arsenal in the genome of the pathogen as a means to define the genetic building blocks that are available for the (synthetic) development of phage-based treatments. The data and approach described herein may provide a framework for the development of therapeutics against an array of bacterial pathogens.

Potential Substitutes of Antibiotics for Swine and Poultry Production

Early of the last century, it was detected that antibiotics added to the animal feeds at low doses and for a long time can improve technical performances such as average daily gain and gain-to-feed ratio. Since then, the antibiotics have been used worldwide as feed additives for many decades. At the end of the twentieth century, the consequences of the uses of antibiotics in animal feeds as growth promoters were informed. Since then, many research studies have been done to find other solutions to replace partly or fully to antibiotic as growth promoters (AGPs). Many achievements in finding alternatives to AGPs in which probiotics and direct-fed microorganism, prebiotics, organic acids and their salts, feed enzymes, bacteriophages, herbs, spices, and other plant extractives (phytogenics), mineral and essential oils are included.

Salmonella Phages Affect the Intestinal Barrier in Chicks by Altering the Composition of Early Intestinal Flora: Association With Time of Phage Use

Phages show promise in replacing antibiotics to treat or prevent bacterial diseases in the chicken breeding industry. Chicks are easily affected by their environment during early growth. Thus, this study investigated whether oral phages could affect the intestinal barrier function of chicks with a focus on the cecal microbiome. In a two-week trial, forty one-day-old hens were randomly divided into four groups: (1) NC, negative control; (2) Phage 1, 10⁹ PFU phage/day (days 3–5); (3) Phage 2, 10⁹ PFU phage/day (days 8–10); and (4) AMX, 1 mg/mL amoxicillin/day (days 8–10). High-throughput sequencing results of cecal contents showed that oral administration of phages significantly affected microbial community structure and community composition, and increased the relative abundance of Enterococcus. The number of different species in the Phage 1 group was much higher than that in the Phage 2 group, and differences in alpha and beta diversity also indicated that the magnitude of changes in the composition of the cecal microbiota correlated with the time of phage use. Particularly in the first stage of cecal microbiota development, oral administration of bacteriophages targeting Salmonella may cause substantial changes in chicks, as evidenced by the results of the PICRUSt2 software function prediction, reminding us to be cautious about the time of phage use in chicks and to avoid high oral doses of phages during the first stage. Additionally, the Phage 2 samples not only showed a significant increase in the relative abundance of Bifidobacterium and Subdoligranulum, but also improved the intestinal morphology (jejunum) and increased the mRNA expression level of occludin and ZO-1. We concluded that phages do not directly interact with eukaryotic cells. The enhancement of intestinal barrier function by phages in chicks may be related to changes in the intestinal flora induced by phages. This implies that phages may affect intestinal health by regulating the intestinal flora. This study provides new ideas for phage prevention of intestinal bacterial infections and promotes large-scale application of phages in the poultry industry.

Insights in the Development and Uses of Alternatives to Antibiotic Growth Promoters in Poultry and Swine Production

The overuse and misuse of antibiotics has contributed to the rise and spread of multidrug-resistant bacteria. To address this global public health threat, many countries have restricted the use of antibiotics as growth promoters and promoted the development of alternatives to antibiotics in human and veterinary medicine and animal farming. In food-animal production, acidifiers, bacteriophages, enzymes, phytochemicals, probiotics, prebiotics, and antimicrobial peptides have shown hallmarks as alternatives to antibiotics. This review reports the current state of these alternatives as growth-promoting factors for poultry and swine production and describes their mode of action. Recent findings on their usefulness and the factors that presently hinder their broader use in animal food production are identified by SWOT (strength, weakness, opportunity, and threat) analysis. The potential for resistance development as well as co- and cross-resistance with currently used antibiotics is also discussed. Using predetermined keywords, we searched specialized databases including Scopus, Web of Science, and Google Scholar. Antibiotic resistance cannot be stopped, but its spreading can certainly be hindered or delayed with the development of more alternatives with innovative modes of action and a wise and careful use of antimicrobials in a One Health approach.

The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies

In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.

Campylobacter Bacteriophage Cocktail Design Based on an Advanced Selection Scheme

Campylobacteriosis is a worldwide-occurring disease and has been the most commonly reported zoonotic gastrointestinal infection in the European Union in recent years. The development of successful phage-based intervention strategies will require a better understanding of phage-bacteria interactions to facilitate advances in phage cocktail design. Therefore, this study aimed to investigate the effects of newly isolated group II and group III phages and their combinations on current Campylobacter field strains. A continuous workflow for host range and efficiency of plating (EOP) value determination was combined with a qPCR-based phage group identification and a liquid-based planktonic killing assay (PKA). An advanced analysis scheme allowed us to evaluate phage cocktails by their efficacy in inhibiting bacterial population growth and the resulting phage concentrations. The results of this study indicate that data obtained from PKAs are more accurate than host range data based on plaque formation (EOP). Planktonic killing assays with Campylobacter appear to be a useful tool for a straightforward cocktail design. Results show that a group II phage vB_CcM-LmqsCP218-2c2 and group III phage vB_CjM-LmqsCP1-1 mixture would be most promising for practical applications against Campylobacter coli and Campylobacter jejuni.

Application of Bacteriophages to Limit Campylobacter in Poultry Production

Campylobacter is a major foodborne pathogen with over a million United States cases a year and is typically acquired through the consumption of poultry products. The common occurrence of Campylobacter as a member of the poultry gastrointestinal tract microbial community remains a challenge for optimizing intervention strategies. Simultaneously, increasing demand for antibiotic-free products has led to the development of several alternative control measures both at the farm and in processing operations. Bacteriophages administered to reduce foodborne pathogens are one of the alternatives that have received renewed interest. Campylobacter phages have been isolated from both conventionally and organically raised poultry. Isolated and cultivated Campylobacter bacteriophages have been used as an intervention in live birds to target colonized Campylobacter in the gastrointestinal tract. Application of Campylobacter phages to poultry carcasses has also been explored as a strategy to reduce Campylobacter levels during poultry processing. This review will focus on the biology and ecology of Campylobacter bacteriophages in poultry production followed by discussion on current and potential applications as an intervention strategy to reduce Campylobacter occurrence in poultry production.

Biocontrol of Escherichia coli and Salmonella in poultry meat using phage cocktail

BACKGROUND

Despite advances in food management techniques, foodborne illness remains a major concern. Contamination of Salmonell a and Escherichia coli pathogens, especially in the poultry sector, is responsible for salmonellosis and other gastrointestinal illness, leading to millions of deaths worldwide. Overuse of antibiotics and other chemical treatments have further increased the emergence of antibiotic resistant bacteria.

AIMS

This study aimed to study the efficacy of phages cocktail to reduce the load of E. coli and Samlonella spiked on poultry meat.

METHODS

In this study, a broad spectrum cocktail of phages was used to lyse E. coli and Salmonella spiked on chicken meat.

RESULTS

Based on the result of the CFU drop assay, phages like E. coli 153T 3ii and Salmonella 191(3) were selected. Phage concentration of 0.01 MOI showed a reduction in E. coli and Salmonella count to 6 h and 2 h, respectively. Further, phages were tested on the surface of chicken meat. E. coli showed a 90% reduction up to 4 h, whereas Salmonella showed a 90% reduction up to 6 h. When phages were treated in combination, a significant reduction of up to 12 h was found with Salmonella phage, showing better antimicrobial activity.

CONCLUSION

The suitable concentration of a specific phage or phage cocktail can significantly reduce the bacterial count on chicken meat. Phage mediated biocontrol can be used as an alternative approach to eliminate enteric pathogens in the poultry industry.

Isolation and Characterization of Group III Campylobacter jejuni-Specific Bacteriophages From Germany and Their Suitability for Use in Food Production

Campylobacter spp. are a major cause of bacterial foodborne diarrhea worldwide. While thermophilic Campylobacter species asymptomatically colonize the intestines of chickens, most human infections in industrial countries have been attributed to consumption of chicken meat or cross-contaminated products. Bacteriophages (phages) are natural predators of bacteria and their use at different stages of the food production chain has been shown to reduce the public health burden of human campylobacteriosis. However, regarding regulatory issues, the use of lytic phages in food is still under discussion and evaluation. This study aims to identify lytic phages suitable for reducing Campylobacter bacteria along the food production chain. Therefore, four of 19 recently recovered phages were further characterized in detail for their lytic efficacy against different Campylobacter field strains and their suitability under food production settings at different temperatures and pH values. Based on the results of this study, the phages vB_CjM-LmqsCP1-4 and vB_CjM-LmqsCP1-5 appear to be promising candidates for the reduction of Campylobacter jejuni in food production settings.

A systematic review from basics to omics on bacteriophage applications in poultry production and processing

The growing human population is currently facing an unprecedented challenge on global food production and sustainability. Despite recognizing poultry as one of the most successful and rapidly growing food industries to address this challenge; poultry health and safety remain major issues that entail immediate attention. Bacterial diseases including colibacillosis, salmonellosis, and necrotic enteritis have become increasingly prevalent during poultry production. Likewise, outbreaks caused by consumption of undercooked poultry products contaminated with zoonotic bacterial pathogens such as Salmonella, Campylobacter and Listeria, are a serious public health concern. With antimicrobial resistance problem and restricted use of antibiotics in food producing animals, bacteriophages are increasingly recognized as an attractive natural antibacterial alternative. Bacteriophages have recently shown promising results to treat diseases in poultry, reduce contamination of carcasses, and enhance the safety of poultry products. Omics technologies have been successfully employed to accurately characterize bacteriophages and their genes/proteins important for interaction with bacterial hosts. In this review, the potential of using lytic bacteriophages to mitigate the risk of major poultry-associated bacterial pathogens are explored. This study also explores challenges associated with the adoption of this technology by industries. Furthermore, the impact of omics approaches on studying bacteriophages, their host interaction and applications is discussed.

Genome Mining of Three Plant Growth-Promoting Bacillus Species from Maize Rhizosphere

Bacillus species genomes are rich in plant growth-promoting genetic elements. Bacillus subtilis and Bacillus velezensis are important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using ten Bacillus species. From the analysis, pan-genome of Bacillus subtilis and Bacillus velezensis are still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

Bacteriophage mediated control of necrotic enteritis caused by C. perfringens in broiler chickens

In Egypt, little attention has been paid to the isolation and application of C. perfringens phages for treating necrotic enteritis at the farm level. This study aims to evaluate the efficiency of the podovirus C. perfringens phage in treating necrotic enteritis in broiler chickens. Accordingly, C. perfringens phage was isolated from cecal samples of apparently healthy chickens and characterized by transmission electron microscopy, thermal stability test, and pH stability test. Commercial 14-day-old Arbor Acres broiler chickens were allocated to three groups: group Ӏ received BHI broth and assigned as a negative control, group П served as a positive control group that was challenged with C. perfringens via oral gavage for four successive days, and group Ш was administrated six phage doses on several occasions after oral gavage challenge with C. perfringens. Daily clinical symptoms and mortality were recorded. At three-time intervals, necrotic enteritis lesions were scored. Cecal samples were examined for re-isolation and counting of C. perfringens. The isolated C. perfringens phage was a podovirus with an icosahedral head diameter of 78.7 nm and a short non-contractile tail length of 22.2 nm. It remained stable for 60 min at 30 °C and 50 °C at pH values of 2, 4, 8, and 10. The phage-treated group (Ш) showed mild gross lesions with a lower mortality rate and reduced colony-forming units than the positive control group (П). The findings revealed that the isolated C. perfringens phage effectively treated experimental necrotic enteritis in broiler chickens.

Phage and phage lysins: New era of bio-preservatives and food safety agents

There has been an increase in the search and application of new antimicrobial agents as alternatives to use of chemical preservatives and antibiotic-like compounds by the food industry. The massive use of antibiotic has created a reservoir of antibiotic-resistant bacteria that find their way from farm to humans. Thus, there exists an imperative need to explore new antibacterial options and bacteriophages perfectly fit into the class of safe and potent antimicrobials. Phage bio-control has come a long way owing to advances with use of phage cocktails, recombinant phages, and phage lysins; however, there still exists unmet challenges that restrict the number of phage-based products reaching the market. Hence, further studies are required to explore for more efficient phage-based bio-control strategies that can become an integral part of food safety protocols. This review thus aims to highlight the recent developments made in the application of phages and phage enzymes covering pre-harvest as well as post-harvest usage. It further focuses on the major issues in both phage and phage lysin research hindering their optimum use while detailing out the advances made by researchers lately in this direction for full exploitation of phages and phage lysins in the food sector.

Bacteriophage Therapy to Reduce Colonization of Campylobacter jejuni in Broiler Chickens before Slaughter

Campylobacteriosis is the most commonly reported gastrointestinal disease in humans. Campybacter jejuni is the main cause of the infection, and bacterial colonization in broiler chickens is widespread and difficult to prevent, leading to high risk of occurrence in broiler meat. Phage therapy represents an alternative strategy to control Campylobacter in poultry. The aim of this work was to assess the efficacy of two field-isolated bacteriophages against experimental infections with an anti-microbial resistant (AMR) Campylobacter jejuni strain. A two-step phage application was tested according to a specific combination between chickens’ rearing time and specific multiplicities of infections (MOIs), in order to reduce the Campylobacter load in the animals at slaughtering and to limit the development of phage-resistant mutants. In particular, 75 broilers were divided into three groups (A, B and C), and phages were administered to animals of groups B and C at day 38 (Φ 16-izsam) and 39 (Φ 7-izsam) at MOI 0.1 (group B) and 1 (group C). All broilers were euthanized at day 40, and Campylobacter jejuni was enumerated in cecal contents. Reductions in Campylobacter counts were statistically significant in both group B (1 log₁₀ colony forming units (cfu)/gram (gr)) and group C (2 log₁₀ cfu/gr), compared to the control group. Our findings provide evidence about the ability of phage therapy to reduce the Campylobacter load in poultry before slaughtering, also associated with anti-microbial resistance pattern.

Application of a novel phage vB_SalS-LPSTLL for the biological control of Salmonella in foods

Salmonella is one of the most common foodborne pathogens around the world. Phages are envisioned as a new strategy to control foodborne pathogenic bacteria and food safety. A Salmonella specific lytic phage vB_SalS-LPSTLL (LPSTLL) was selected for food applications on the basis of lytic range, lytic efficiency, functional stability and characteristics. Phage LPSTLL was able to lyse 11 Salmonella serotypes, which represents the broadest range reported Salmonella phages, and was able to suppress the growth of Salmonella enterica in liquid culture over nine hours. LPSTLL exhibited rapid reproductive activity with a short latent period and a large burst size in one-step growth experiment. LPSTLL remained active over a pH range of 3.0 to 12.0, and at incubation temperatures up to 60 °C for 60 min, indicating wide applicability for food processing and storage. Significant reductions of viable Salmonella were observed in diverse foods (milk, apple juice, chicken and lettuce) with reductions up to 2.8 log CFU/mL recorded for milk. Sensory evaluation indicated that treatment with phage LPSTLL did not alter the visual or tactile quality of food matrices. Genome analysis of LPSTLL indicated the absence of any virulence or antimicrobial resistance genes. Genomic comparisons suggest phage LPSTLL constitutes a novel member of a new genus, the LPSTLLvirus with the potential for Salmonella biocontrol in the food industry.

Unveiling the Impact of Antibiotics and Alternative Methods for Animal Husbandry: A Review

Since the 1950s, antibiotics have been used in the field of animal husbandry for growth promotion, therapy and disease prophylaxis. It is estimated that up to 80% of the antibiotics produced by the pharmaceutical industries are used in food production. Most of the antibiotics are used as feed additives at sub-therapeutic levels to promote growth. However, studies show the indiscriminate use of antibiotics has led to the emergence of multidrug-resistant pathogens that threaten both animal health and human health, including vancomycin-resistant Enterococcus (VRE), Methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae (CRE). This scenario is further complicated by the slow progress in achieving scientific breakthroughs in uncovering novel antibiotics following the 1960s. Most of the pharmaceutical industries have long diverted research funds away from the field of antibiotic discovery to more lucrative areas of drug development. If this situation is allowed to continue, humans will return to the pre-antibiotics era and potentially succumb to huge health and economic consequences. Fortunately, studies investigating various alternatives to antibiotics use in livestock show promising results. These alternatives include the application of bacteriophages and phage derived peptidoglycan degrading enzymes, engineered peptides, egg yolk antibodies, probiotics, prebiotics and synbiotics, as well as quorum quenching molecules. Therefore, this review aims to discuss the use of growth-promoting antibiotics and their impact on livestock and provide insights on the alternative approaches for animal husbandry.

Phage Therapy in Veterinary Medicine

To overcome the obstacle of antimicrobial resistance, researchers are investigating the use of phage therapy as an alternative and/or supplementation to antibiotics to treat and prevent infections both in humans and in animals. In the first part of this review, we describe the unique biological characteristics of bacteriophages and the crucial aspects influencing the success of phage therapy. However, despite their efficacy and safety, there is still no specific legislation that regulates their use. In the second part of this review, we describe the comprehensive research done in the past and recent years to address the use of phage therapy for the treatment and prevention of bacterial disease affecting domestic animals as an alternative to antibiotic treatments. While in farm animals, phage therapy efficacy perspectives have been widely studied in vitro and in vivo, especially for zoonoses and diseases linked to economic losses (such as mastitis), in pets, studies are still few and rather recent.

Applied Microbiology—An Open Access Journal

Welcome to Applied Microbiology, a new Open Access MDPI journal that will report original studies and reviews on the growing numbers of applications for microorganisms and their associated technologies [...]

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.

Developing Innolysins Against Campylobacter jejuni Using a Novel Prophage Receptor-Binding Protein

Campylobacter contaminated poultry remains the major cause of foodborne gastroenteritis worldwide, calling for novel antibacterials. We previously developed the concept of Innolysin composed of an endolysin fused to a phage receptor binding protein (RBP) and provided the proof-of-concept that Innolysins exert bactericidal activity against Escherichia coli. Here, we have expanded the Innolysin concept to target Campylobacter jejuni. As no C. jejuni phage RBP had been identified so far, we first showed that the H-fiber originating from a CJIE1-like prophage of C. jejuni CAMSA2147 functions as a novel RBP. By fusing this H-fiber to phage T5 endolysin, we constructed Innolysins targeting C. jejuni (Innolysins Cj). Innolysin Cj1 exerts antibacterial activity against diverse C. jejuni strains after in vitro exposure for 45 min at 20°C, reaching up to 1.30 ± 0.21 log reduction in CAMSA2147 cell counts. Screening of a library of Innolysins Cj composed of distinct endolysins for growth inhibition, allowed us to select Innolysin Cj5 as an additional promising antibacterial candidate. Application of either Innolysin Cj1 or Innolysin Cj5 on chicken skin refrigerated to 5°C and contaminated with C. jejuni CAMSA2147 led to 1.63 ± 0.46 and 1.18 ± 0.10 log reduction of cells, respectively, confirming that Innolysins Cj can kill C. jejuni in situ. The receptor of Innolysins Cj remains to be identified, however, the RBP component (H-fiber) recognizes a novel receptor compared to lytic phages binding to capsular polysaccharide or flagella. Identification of other unexplored Campylobacter phage RBPs may further increase the repertoire of new Innolysins Cj targeting distinct receptors and working as antibacterials against Campylobacter.

The Data Behind Risk Analysis of Campylobacter Jejuni and Campylobacter Coli Infections

Campylobacter jejuni and Campylobacter coli are major causes of food-borne enteritis in humans. Poultry meat is known to be responsible for a large proportion of cases of human campylobacteriosis. However, other food-borne, environmental and animal sources are frequently associated with the disease in humans as well. Human campylobacteriosis causes gastroenteritis that in most cases is self-limiting. Nevertheless, the burden of the disease is relatively large compared with other food-borne diseases, which is mostly due to rare but long-lasting symptoms related to immunological sequelae. In order to pave the way to improved surveillance and control of human campylobacteriosis, we review here the data that is typically used for risk analysis to quantify the risk and disease burden, identify specific surveillance strategies and assist in choosing the most effective control strategies. Such data are mostly collected from the literature, and their nature is discussed here, for each of the three processes that are essential for a complete risk analysis procedure: risk assessment, risk management and risk communication. Of these, the first, risk assessment, is most dependent on data, and this process is subdivided into the steps of hazard identification, hazard characterization, exposure assessment and risk characterization. For each of these steps of risk assessment, information from published material that is typically collected will be summarized here. In addition, surveillance data are highly valuable for risk assessments. Different surveillance systems are employed in different countries, which can make international comparison of data challenging. Risk analysis typically results in targeted control strategies, and these again differ between countries. The applied control strategies are as yet not sufficient to eradicate human campylobacteriosis. The surveillance tools of Campylobacter in humans and exposure sources in place in different countries are briefly reviewed to better understand the Campylobacter dynamics and guide control strategies. Finally, the available control measures on different risk factors and exposure sources are presented.

Last Call for Replacement of Antimicrobials in Animal Production: Modern Challenges, Opportunities, and Potential Solutions

The constant market demand for easily available and cheap food of animal origin necessitates an increasing use of antibiotics in animal production. The alarming data provided by organizations monitoring drug resistance in indicator and pathogenic bacteria isolated from humans and animals indicate a possible risk of a return to the preantibiotic era. For this reason, it seems that both preventive and therapeutic measures, taken as an alternative to antimicrobials, seem not only advisable but also necessary. Nevertheless, the results of various studies and market analyses, as well as difficulties in the implementation of alternative substances into veterinary medicine, do not guarantee that the selected alternatives will completely replace antimicrobials in veterinary medicine and animal production on a global scale. This publication is a brief overview of the drug resistance phenomenon and its determinants, the steps taken to solve the problem, including the introduction of alternatives to antimicrobials, and the evaluation of some factors influencing the potential implementation of alternatives in animal production. The review also presents two groups of alternatives, which, given their mechanism of action and spectrum, are most comparable to the effectiveness of antibiotics, as emphasized by the authors.