Development of new strategy combining heat treatment and phage cocktail for post-contamination prevention

Surface charge of the C-terminal helix is crucial for antibacterial activity of endolysin against Gram-negative bacteria

BACKGROUNDS

Endolysins are promising alternatives to antibiotics because they can lyse bacterial cells rapidly with a low risk of resistance development, however, their effectiveness against Gram-negative bacteria is hindered by the presence of the outer membrane present in Gram-negative bacteria. Several endolysins with amphipathic helices at the C-terminus have been reported to have intrinsic antibacterial activity against Gram-negative bacteria but their action mechanism is not fully elucidated.

METHODS

The sequence alignment analysis was assessed with the CLC Main workbench 7, and His-tagged endolysins were purified with affinity chromatography. Site-directed mutagenesis was used to generate mutations in the endolysin to make various endolysin mutants. The muralytic activity of the endolysin against Gram-negative bacteria was analyzed using a turbidity reduction assay and the antibacterial activities of the endolysins were assessed through a viable cell counting assay.

RESULTS

We identified two endolysins, LysTS3 and LysTS6, both of which have similar sequences and structures including the amphipathic helices at their C-terminus. LysTS6 exhibited significantly higher antibacterial activity against Gram-negative bacteria compared to LysTS3 even though both enzymes have similar muralytic activity against the outer membrane-permeabilized Gram-negative bacteria. Systematic truncation and bioinformatic analysis of these two endolysins revealed a major difference in the charge on the surface of their C-terminal helices, suggesting the possibility that the charge on this helix can determine the antibacterial activity of the endolysins against Gram-negative bacteria. We could enhance the activity of LysTS3 against Gram-negative bacteria by replacing Ala156 and Glu160 with lysine and alanine, respectively, the amino acid residues at the structurally equivalent positions in LysTS6. A similar activity boost was also seen in LysSPN1S and LysJEP4 when the surface charge of the C-terminal amphipathic helix was altered to be more positive through the modification of the surface-exposed amino acid residues.

CONCLUSIONS

The antibacterial activity of endolysin against Gram-negative bacteria could be enhanced by adjusting the surface charge on the C-terminal amphipathic helix to more positive, suggesting that the positive surface charge on the C-terminal amphipathic helix of endolysin is crucial for its penetration of outer membrane to reach peptidoglycan layer of Gram-negative bacteria.

Can Bacteriophages Be Effectively Utilized for Disinfection in Animal-Derived Food Products? A Systematic Review

Food safety is a paramount public health concern, particularly with the rise of antimicrobial-resistant bacteria. This systematic review explores the efficacy of bacteriophages as a novel and environmentally sustainable approach to controlling multi-resistant and non-resistant bacterial pathogens in animal-derived food products. Following PRISMA guidelines, data from multiple studies were synthesized to evaluate bacteriophage applications across diverse food matrices, including beef, poultry, seafood, and dairy. The findings highlight significant variability in bacteriophage efficacy, influenced by factors such as food matrix properties, bacterial strains, and application methods. Phage cocktails and their combination with thermal treatments consistently demonstrated superior bacterial reduction compared to single-phage applications, which yielded variable results. Interestingly, the absence of a clear dose-response relationship underscores the need for a more detailed understanding of phage-host interactions and environmental influences. This review addresses a critical gap in the literature by advocating for matrix-specific, targeted phage applications over generalized approaches. Additionally, it underscores the transformative potential of bacteriophages as sustainable alternatives to chemical disinfectants in modern food safety practices. These insights provide a framework for future research aimed at optimizing bacteriophage efficacy and scaling their application in real-world food production systems.

Systematic Evaluation of the Impact of a Wide Range of Dietary Habits on Myocardial Infarction: A Two-Sample Mendelian Randomization Analysis

BACKGROUND

Myocardial infarction is a cardiovascular disease that significantly contributes to global morbidity and disability. Given the significant role of diet in the pathogenesis and prevention of cardiovascular diseases, this study rigorously investigates the causal relationship between dietary habits and myocardial infarction.

METHODS AND RESULTS

This study used large-scale genome-wide association studies with pooled UK Biobank data to explore associations between 9 dietary categories (83 types) and myocardial infarction. A 2-sample Mendelian randomization approach was applied to assess these associations, while multivariate Mendelian randomization and mediation analyses investigated the role of lipids in mediating the effects of diet on myocardial infarction. Univariate Mendelian analyses revealed genetic associations among 9 categories of dietary habits (83 types) and myocardial infarction. Notably, robust evidence indicates the "tablespoons of cooked vegetables per day" as the most significant risk factor for myocardial infarction development. "Coffee consumption(cups per day)" and "frequency of adding salt to food" were also identified as supplementary risk factors. In contrast, "overall alcohol intake" showed a protective effect, potentially by increasing high-density lipoprotein cholesterol (4.48% mediation) and reducing triglycerides (6.24% mediation). Cereal category, particularly "cereal consumption (bowls per week)" was associated with reduced myocardial infarction risk, contributing by raising high-density lipoprotein cholesterol (3.69% mediation) and lowering total cholesterol (8.33% mediation). Additionally, "overall cheese consumption" was also protective against myocardial infarction.

CONCLUSIONS

Our findings elucidate the influence of dietary habits on myocardial infarction, showing underlying genetic mechanisms and emphasizing the regulatory role of lipids as an intermediate.

Lytic Spectra of Tailed Bacteriophages: A Systematic Review and Meta-Analysis

As natural predators of bacteria, tailed bacteriophages can be used in biocontrol applications, including antimicrobial therapy. Also, phage lysis is a detrimental factor in technological processes based on bacterial growth and metabolism. The spectrum of bacteria bacteriophages interact with is known as the host range. Phage science produced a vast amount of host range data. However, there has been no attempt to analyse these data from the viewpoint of modern phage and bacterial taxonomy. Here, we performed a meta-analysis of spotting and plaquing host range data obtained on strains of production host species. The main metric of our study was the host range value calculated as a ratio of lysed strains to the number of tested bacterial strains. We found no boundary between narrow and broad host ranges in tailed phages taken as a whole. Family-level groups of strictly lytic bacteriophages had significantly different median plaquing host range values in the range from 0.18 (Drexlerviridae) to 0.70 (Herelleviridae). In Escherichia coli phages, broad host ranges were associated with decreased efficiency of plating. Bacteriophage morphology, genome size, and the number of tRNA-coding genes in phage genomes did not correlate with host range values. From the perspective of bacterial species, median plaquing host ranges varied from 0.04 in bacteriophages infecting Acinetobacter baumannii to 0.73 in Staphylococcus aureus phages. Taken together, our results imply that taxonomy of bacteriophages and their bacterial hosts can be predictive of intraspecies host ranges.

Bacteriophages: Natural antimicrobial bioadditives for food preservation in active packaging

Developing innovative films and coatings is paramount for extending the shelf life of numerous food products and augmenting the barrier and antimicrobial properties of food packaging materials. Many synthetic chemicals used in active packaging and food storage have the potential to leach into food, posing long-term health risks. It is imperative for active packaging materials to inherently possess biological protective properties to ensure food quality and safety throughout its storage. Bacteriophages, or simply phages, are bacteria-eating viruses that serve as promising natural biocontrol agents and antimicrobial bioadditives in food packaging materials, specifically targeting bacterial foodborne pathogens. These phages are generally recognized as safe (GRAS) by regulatory authorities for food safety applications. They exhibit targeted action against various Gram-positive and -negative foodborne pathogens, including Bacillus spp., Campylobacter spp., Escherichia coli, Listeria monocytogenes, Salmonella spp., Shigella spp., and Vibrio spp., associated with foodborne spoilage and illness without affecting the beneficial microbes. Phage cocktails can be applied directly on food surfaces, incorporated into food packaging materials, or utilized during food processing treatments. Unlike chemical agents, phage activity increases proportionally with the rise in pathogenic bacterial populations. Researchers are exploring various packaging materials to deliver phages with broad host range, stability, and viability ensuring their effectiveness in safeguarding various food systems. The effectiveness of phage immobilization or encapsulation on active food packaging materials depends on various factors, including the characteristics of polymers, the choice of solvents, the type of phage, and its loading efficiency. Factors such as the orientation of phage immobilization on substrates, pH, temperature, exposure to carbohydrates and amino acids, exopolysaccharides, lipopolysaccharides, and metals can also influence phage activity. In this review, we comprehensively discuss the various active packaging systems utilizing bacteriophages as natural biocontrols and antimicrobial bioadditives to reduce the incidence of foodborne illness and enhance consumer confidence in the safety of food products.

Isolation, whole genome sequencing and application of a broad-spectrum Salmonella phage

Salmonella is considered as one of the most common zoonotic /foodborne pathogens in the world. The application of bacteriophages as novel antibacterial agents in food substrates has become an emerging strategy. Bacteriophages have the potential to control Salmonella contamination.We have isolated and characterized a broad-spectrum Salmonella phage, SP154, which can lyse 9 serotypes, including S. Enteritidis, S. Typhimurium, S. Pullorum, S. Arizonae, S. Dublin, S. Cholerasuis, S. Chester, S. 1, 4, [5], 12: i: -, and S. Derby, accounting for 81.9% of 144 isolates. SP154 showed a short latent period (40 min) and a high burst size (with the first rapid burst size at 107 PFUs/cell and the second rapid burst size at approximately 40 PFUs/cell). Furthermore, SP154 activity has higher survival rates across various environmental conditions, including pH 4.0-12.0 and temperatures ranging from 4 to 50 °C for 60 min, making it suitable for diverse food processing and storage applications. Significant reductions in live Salmonella were observed in different foods matrices such as milk and chicken meat, with a decrease of up to 1.9 log10 CFU/mL in milk contamination and a 1 log10 CFU/mL reduction in chicken meat. Whole genome sequencing analysis revealed that SP154 belongs to the genus Ithacavirus, subfamily Humphriesvirinae, within the family Schitoviridae. Phylogenetic analysis based on the terminase large subunit supported this classification, although an alternate tree using the tail spike protein gene suggested affiliation with the genus Kuttervirus, underscoring the limitations of relying on a single gene for phylogenetic inference. Importantly, no virulence or antibiotic resistance genes were detected in SP154. Our research highlights the potential of using SP154 for biocontrol of Salmonella in the food industry.

Thermal Inactivation of Escherichia Phage OSYSP and Host Strain Escherichia coli O157:H7 EDL933: A Comparative Kinetic Analysis

Lytic bacteriophages are promising biocontrol agents against pathogenic bacteria for food and therapeutic applications. Investigating the feasibility of combining phage and physical lethal agents, such as heat, as an effective hurdle combination could lead to beneficial applications. The current research was initiated to compare the thermal inactivation kinetics of a lytic phage (Escherichia phage OSYSP) and its host (Shiga toxin-producing Escherichia coli O157:H7 EDL933), considering they have different critical thermal targets in their structures. To provide a basis for comparison, thermal inactivation kinetics were determined on suspensions of these agents in buffered peptone water using a thermally controlled circulating water bath. Results showed that the bacteriophage virions have a remarkable heat resistance (p < 0.05) compared to their host cells. The D-values of the populations of phage (PFU/mL) and EDL933 strain (CFU/mL) were 166.7 and 7.3 min at 55°C, compared to 44.4 and 0.3 min at 60°C, respectively. Additionally, D-values were significantly (p < 0.05) more influenced by temperature changes in the case of E. coli O157:H7 EDL933 (z-value 3.7°C) compared to that for phage OSYSP (z-value 7.7°C). When the phage suspension was heat-treated in a thermal cycler instead of a water bath, no significant differences between the two treatment procedures (p > 0.05) in estimating virus D- and z-values were observed. Based on these findings, it may be feasible to combine phage OSYSP with mild heat during processing of food to selectively inactivate E. coli O157:H7 EDL933 and subsequently maintain product safety during storage by the surviving phage population; however, the feasibility of this application needs to be investigated. Additionally, the relatively heat-resistant phage OSYSP could qualify as a biological indicator to validate thermal treatments of minimally processed foods in which E. coli O157:H7 EDL933 is the pathogen-of-concern.

Evaluation of the biocontrol potential of a collagen peptide/trehalose-based Cronobacter sakazakii phage powder in rehydrated powdered infant formula

Cronobacter sakazakii is a major foodborne pathogen that is mainly transmitted through powdered infant formula (PIF) and has a high mortality rate of up to 80%, particularly in fetuses and neonates. Bacteriophages have emerged as an effective biocontrol agent for antibiotic-resistant bacteria. In this study, lytic phage SG01 was newly characterized and loaded into collagen peptide/trehalose-based powders to develop an antibacterial agent against C. sakazakii contamination in PIF. The phage belongs to the Siphoviridae family, has an icosahedral head and a flexible tail, and showed rapid and persistent antibacterial activity up to 17 h. It was specifically active against C. sakazakii and also exhibited effective anti-biofilm properties. The phage was freeze-dried to a collagen peptide/trehalose-based powder and the phage was tested for viability, storage stability, and antibacterial activity. The optimal composition was 5% (w/v) collagen peptides and 1% (w/v) trehalose, which demonstrated the highest phage viability after freeze-drying. The phage remained stable in the collagen peptide/trehalose-based powder for up to four weeks at 4 °C and 25 °C, indicating that this is a desirable formulation for phage protection. Furthermore, the phage powder showed significant antibacterial efficacy in PIF, with a 4-log CFU/mL reduction within 6 h. Overall, the tested phage powder has the potential to be used as an antimicrobial agent in the food industry, particularly in powdered foods such as PIF.

Application of a novel phage LPCS28 for biological control of Cronobacter sakazakii in milk and reconstituted powdered infant formula

Contamination of infant formula with Cronobacter sakazakii (C. sakazakii) can cause fatal infections in neonates. Phages have emerged as promising antibacterial agents for food safety, but their effectiveness may be limited by thermal processing. In this study, we isolated 27 C. sakazakii phages from environmental water samples and selected LPCS28 due to its broad lysis spectrum. The titer of LPCS28 will not be significantly affected by heating at a temperature of 60 °C for one hour. In both reconstituted powdered infant formula (RPIF) and liquid milk, the pre-added LPCS28, after the thermal processing at 63 °C for 30 min, significantly inhibited the post-contaminated C. sakazakii (103 CFU/mL) and eventually reduced the number of C. sakazakii to below the limit of detection (<10 CFU/mL) within 9 h at 37 °C and significantly delayed the increase of bacterial concentration in the samples at 23 °C. The phylogenetic analysis revealed that LPCS28 belonged to a new genus, we proposed as Nanhuvirus, under the family Straboviridae. These findings suggest that phage LPCS28 is a promising biological control agent for pathogenic C. sakazakii in the dairy industry.

Lytic Escherichia phage OSYSP acts additively and synergistically with gaseous ozone against Escherichia coli O157:H7 on spinach leaves

Bacteriophage and gaseous ozone are evolving as meritorious alternatives to conventional sanitizers in food postharvest applications. Here, we investigated the efficacy of sequential treatments of a lytic bacteriophage and gaseous ozone, during vacuum cooling of fresh produce, against Escherichia coli O157:H7. Spinach leaves were spot-inoculated with 10⁵-10⁷ CFU g^-1 E. coli O157:H7 B6-914 and treated with Escherichia phage OSYSP spray (10⁹ PFU g^-1), gaseous ozone, or their combination. Vacuum cooling, which preceded or followed phage application but ran concomitantly with ozone treatment, was performed in a custom-made vessel at the following process sequence: vacuum to 28.5 in. Hg, vessel pressurization to 10 psig with gas containing 1.5 g ozone/kg gas-mix, holding for 30 min, and vessel depressurization to ambient pressure. Bacteriophage or gaseous ozone inactivated E. coli O157:H7, applied at different initial populations on spinach leaves, by 1.7-2.0 or 1.8-3.5 log CFU g^-1, respectively. At the high inoculum levels tested (7.1 log CFU g^-1), sequential treatments of phage and ozone reduced E. coli O157:H7 population by 4.0 log CFU g^-1, but when treatment order was reversed (i.e., ozone followed by bacteriophage), the combination synergistically decreased pathogen's population on spinach leaves by 5.2 log CFU g^-1. Regardless the antibacterial application order, E. coli O157:H7 populations, applied initially at ~ 10⁵ CFU g^-1, were reduced below the enumeration method's detection level (i.e., < 10¹ CFU g^-1). The study proved that bacteriophage-ozone combination, applied in conjunction with vacuum cooling, is a potent pathogen intervention strategy in fresh produce post-harvest applications.

Synergistic action of phages and lytic proteins with antibiotics: a combination strategy to target bacteria and biofilms

BACKGROUND

Multidrug-resistant bacteria continue to emerge owing to the abuse of antibiotics and have a considerable negative impact on people and the environment. Bacteria can easily form biofilms to improve their survival, which reduces the efficacy of antibacterial drugs. Proteins such as endolysins and holins have been shown to have good antibacterial activity and effectively removal bacterial biofilms and reduce the production of drug-resistant bacteria. Recently, phages and their encoded lytic proteins have attracted attention as potential alternative antimicrobial agents. The aim of the present study was to investigate the sterilising efficacy of phages (SSE1, SGF2, and SGF3) and their encoded lytic proteins (lysozyme and holin), and to further explore their potential in combination with antibiotics. To the ultimate aim is to reduce or replace the use of antibiotics and provide more materials and options for sterilisation.

RESULTS

Phages and their encoded lytic proteins were confirmed to have great advantages in sterilisation, and all exhibited significant potential for reducing bacterial resistance. Previous studies on the host spectrum demonstrated the bactericidal efficacy of three Shigella phages (SSE1, SGF2, and SGF3) and two lytic proteins (LysSSE1 and HolSSE1). In this study, we investigated the bactericidal effects on planktonic bacteria and bacterial biofilms. A combined sterilisation application of antibiotics, phages, and lytic proteins was performed. The results showed that phages and lytic proteins had better sterilisation effects than antibiotics with 1/2 minimum inhibitory concentrations (MIC) and their effect was further improved when used together with antibiotics. The best synergy was shown when combined with β- lactam antibiotics, which might be related to their mechanism of sterilising action. This approach ensures a bactericidal effect at low antibiotic concentrations.

CONCLUSIONS

This study strengthens the idea that phages and lytic proteins can significantly sterilise bacteria in vitro and achieve synergistic sterilisation effects with specific antibiotics. Therefore, a suitable combination strategy may decrease the risk of drug resistance.

A systematic review and modeling of the effect of bacteriophages on Salmonella spp. Reduction in chicken meat

Prevention and control of foodborne pathogens are of vital public health importance, and poultry meat is recognized as a major source of Salmonella infection in humans. Therefore, it is necessary to reduce the presence of salmonella in poultry meat. This article provided a systematic review and modeling to assess the effect of various factors on bacteriophages' function on Salmonella spp. Reduction in poultry meat. Twenty-two studies were included based on the inclusion and exclusion criteria mentioned in the methodology. The results showed that each unit increase in bacterial dose, phage dose, and temperature increases the Salmonella reduction by about 7%, 20%, and 1%, respectively. In addition, wild-type phages were more efficient than commercial-type phages, and this result was statistically significant (β = 1.124; p-value <0.001). This multivariate analysis is a helpful tool to predict the role of various factors in the role of phage in reducing Salmonella in poultry meat.

The application of adaptively evolved thermostable bacteriophage ΦYMFM0293 to control spp. in poultry skin

Bacteriophages, bacterial viruses, are now being re-highlighted as one of the promising alternative antimicrobial agents to control bacterial pathogens in various fields, including the food industry. However, wild-type (WT) phages isolated from nature are vulnerable to external stresses such as heat, limiting the usability of phages in thermal processing. Here, we applied an adaptive laboratory evolution approach to improving the heat stability of newly isolated Salmonella-infecting lytic phage ΦYMFM0293 and examined its application in the poultry scalding process. After 15 cycles of exposure to sub-lethal temperature, the obtained adaptively evolved (AE) phages maintained approximately 3-log more infectious particles at 73 or 74 °C than the WT and non-heat-treated control phages. Missense mutations mainly concentrated in the genes related to the phage tail module were identified from the independently obtained heat-challenged phages, regardless of host Salmonella's heat-shock protein chaperone induction. These results demonstrated the necessity and sufficiency of the phage exposures to heat for thermal adaptation and suggested the involvement of the phage tail in heat stability. No significant physiological or morphological changes except the mutually offsetting phage replication parameters were observed in the AE phages. Accordingly, hot water supplemented with the AE phages significantly reduced the number of artificially contaminated Salmonella cells on chicken and duck skin in the mimicked scalding process. The AE strategy used here could be applied to other WT phages to improve their usability as more feasible antimicrobials for food safety.

Combine thermal processing with polyvalent phage LPEK22 to prevent the Escherichia coli and Salmonella enterica contamination in food

Thermal processing is the most frequently used method to destruct bacteria in food processing. However, insufficient thermal processing may lead to the outbreak of foodborne illness. This study combined thermal processing with thermostable phage to prevent food contamination. The thermostable phages were screened which can retain activity at 70 °C for 1 h. Among them, the polyvalent phage LPEK22 was obtained to lyse Escherichia coli and Salmonella enterica, especially several multi-drug resistant bacteria. In milk (liquid food matrix), LPEK22 significantly reduced the E. coli by 5.00 ± 0.18 log₁₀ CFU/mL and S. enterica by 4.20 ± 0.23 log₁₀ CFU/mL after thermal processing at 63 °C for 30 min. For beef sausage (solid food matrix), LPEK22 significantly reduced the E. coli by 2.34 ± 0.17 log₁₀ CFU/cm² and S. enterica by 1.54 ± 0.13 log₁₀ CFU/cm² after thermal processing at 66 °C for 90 s. Genome analysis revealed that LPEK22 was a novel phage with a unique tail spike protein belonging to the family of Ackermannviridae. LPEK22 did not contain lysogenic, drug-resistant, and virulent genes that may compromise the safety of food application. These results determined that LPEK22, a novel polyvalent Ackermannviridae phage, could combine with thermal processing to prevent drug-resistant E. coli and S. enterica both in vitro and in foods.

Expansion of the Plaquing Host Range and Improvement of the Absorption Rate of a T5-like Salmonella Phage by Altering the Long Tail Fibers

The high host specificity of phages is a real challenge in the therapy applications of the individual phages. This study aimed to edit the long tail fiber proteins (pb1) of a T5-like phage to obtain the engineered phages with expanded plaquing host range. Two T5-like Salmonella phages with high genome sequence homology but different plaquing host ranges, narrow-host range phage vB STyj5-1 (STyj5-1) and wide-host range phage vB BD13 (BD13), were isolated and characterized. The pb1 parts of STyj5-1 were replaced by the corresponding part of BD13 using homologous recombination method to obtain the engineered phages. The alterations of the whole pb1 part or the N-terminal amino acids 1-400 of pb1 of STyj5-1 could expand their plaquing host ranges (from 20 strains to 30 strains) and improve their absorption rates (from 0.28-28.84% to 28.10-99.49%). Besides, the one-step growth curves of these engineered phages with modified pb1 parts were more similar to that of STyj5-1. The burst sizes of phages BD13, STyj5-1 and the engineered phages were 250, 236, 166, and 223 PFU per cell, respectively. The expanded plaquing host range and improved absorption rates of these engineered phages revealed that the pb1 part might be the primary determinant of the host specificities of some T5-like phages. IMPORTANCE Genetic editing can be used to change or expand the host range of phages and have been successfully applied in T2, T4 and other phages to obtain engineered phages. However, there are hardly any similar reports on T5-like phages due to that the determinant regions related to their host ranges have not been completely clarified and the editing of T5-like phages is more difficult compared to other phages. This study attempted and successfully expanded the host range of a narrow-host range T5-like phage (STyj5-1) by exchanging its whole pb1 part or the N-terminal 1-400aa of that part by a broad-host range phage (BD13). These demonstrated the pb1 part might be the primary determinant of the host specificities for some T5-like phages and provided an effective method of extension plaquing host range of these phages.

PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks

BACKGROUND AND OBJECTIVE

Phage therapy is a resurgent strategy used in medicine and the food industry to lyse bacteria that cause damage to health or spoil a food product. Frequently, phage-bacteria infection networks have a large size, making it impossible to manually study all possible phage cocktails. Thus, this article presents an R package called PhageCocktail to automatically design efficient phage cocktails from phage-bacteria infection networks.

METHODS

This R package includes four different methods for designing phage cocktails: ExhaustiveSearch, ExhaustivePhi, ClusteringSearch, and ClusteringPhi. These four methods are explained in detail and are evaluated using 13 empirical phage-bacteria infection networks. More specifically, runtime and expected success (fraction of lysed bacteria) are analyzed.

RESULTS

The four methods have variations in terms of runtime and quality of the results. ExhaustiveSearch always provides the best possible phage cocktail, but its runtime could be long. ExhaustivePhi only focuses on one cocktail size, the one estimated as the best; thus, its runtime is less than ExhaustiveSearch, but it can produce cocktails with more phages than necessary. ClusteringSearch and ClusteringPhi are very fast (generally, less than one millisecond), providing always immediate results due to clustering techniques, but their accuracies can be lower, yielding cocktails with lower expected successes.

CONCLUSIONS

The larger the phage-bacteria infection network is, the more complex its analysis is. Thus, this tool eases this task for scientists and other users while designing phage cocktails of good quality. This R package includes four different methods; therefore, users may choose among them, considering their preferences in speed and accuracy of results.

Bacteriophage and endolysin engineering for biocontrol of food pathogens/pathogens in the food: recent advances and future trends

Despite advances in modern technologies, various foodborne outbreaks have continuously threatened the food safety. The overuse of and abuse/misuse of antibiotics have escalated this threat due to the prevalence of multidrug-resistant (MDR) pathogens. Therefore, the development of new methodologies for controlling microbial contamination is extremely important to ensure the food safety. As an alternative to antibiotics, bacteriophages(phages) and derived endolysins have been proposed as novel, effective, and safe antimicrobial agents and applied for the prevention and/or eradication of bacterial contaminants even in foods and food processing facilities. In this review, we describe recent genetic and protein engineering tools for phages and endolysins. The major aim of engineering is to overcome limitations such as a narrow host range, low antimicrobial activity, and low stability of phages and endolysins. Phage engineering also aims to deter the emergence of phage resistance. In the case of endolysin engineering, enhanced antibacterial ability against Gram-negative and Gram-positive bacteria is another important goal. Here, we summarize the successful studies of phages and endolysins treatment in different types of food. Moreover, this review highlights the recent advances in engineering techniques for phages and endolysins, discusses existing challenges, and suggests technical opportunities for further development, especially in terms of antimicrobial agents in the food industry.