Phages and Enzybiotics in Food Biopreservation

Phage diversity in One Health

One Health aims to bring together human, animal, and environmental research to achieve optimal health for all. Bacteriophages (phages) are viruses that kill bacteria and their utilisation as biocontrol agents in the environment and as therapeutics for animal and human medicine will aid in the achievement of One Health objectives. Here, we assess the diversity of phages used in One Health in the last 5 years and place them in the context of global phage diversity. Our review shows that 98% of phages applied in One Health belong to the class Caudoviricetes, compared to 85% of sequenced phages belonging to this class. Only three RNA phages from the realm Riboviria have been used in environmental biocontrol and human therapy to date. This emphasises the lack in diversity of phages used commercially and for phage therapy, which may be due to biases in the methods used to both isolate phages and select them for applications. The future of phages as biocontrol agents and therapeutics will depend on the ability to isolate genetically novel dsDNA phages, as well as in improving efforts to isolate ssDNA and RNA phages, as their potential is currently undervalued. Phages have the potential to reduce the burden of antimicrobial resistance, however, we are underutilising the vast diversity of phages present in nature. More research into phage genomics and alternative culture methods is required to fully understand the complex relationships between phages, their hosts, and other organisms in the environment to achieve optimal health for all.

Phenotypic Characterization and Genome Analysis of New Broad-Spectrum Virulent Salmophage, Salmonella Phage KKP_3822, for Biocontrol of Multidrug-Resistant Salmonella enterica Strains

Salmonella is one of the main foodborne pathogens. Irrational antibiotic management has led to an increase in the incidence of multidrug-resistant strains. Bacteriophages may be an alternative method of food biopreservation and contribute to reducing the number of food poisonings requiring pharmacotherapy. This study aimed to isolate a bacteriophage (phage) targeting indigenous multidrug-resistant (MDR) Salmonella strains, followed by their biological, morphological, and genomic characterization. In this study we isolated Salmonella phage KKP_3822, targeting MDR Salmonella Manchester strain KKP 1213. Salmonella phage KKP_3822 retained high activity in the temperature range from -20 °C to 40 °C and active acidity from pH 3 to 11. Temperatures of 70 °C and 80 °C and extreme pH values (2 and 12) significantly reduced the phage titer. Its activity decreased proportionally to the time of UV exposure. Genome analysis (linear dsDNA with a length of 114,843 bp) revealed the presence of 27 tRNA genes. Proteins encoded by the vB_Sen-IAFB3822 phage were divided into functional modules related to (i) phage structure/assembly, (ii) DNA replication/modification/regulation, (iii) phage lysis, and (iv) DNA packaging into the capsid. No genes associated with antibiotic resistance or integration into the host genome, markers of temperate bacteriophages, were annotated in the Salmonella phage KKP_3822 genome. Based on morphological features and whole-genome sequence analysis, the newly isolated Salmonella phage KKP_3822 shows the greatest similarity to representatives of tailed phages from the Caudoviricetes class, Demerecviridae family, and Epseptimavirus genus. Genome analysis confirmed the virulent nature of the Salmonella phage KKP_3822, making it a potential candidate for food biocontrol.

Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles' heel to target?

Salmonella is a pathogenic bacterium, being the second most commonly reported foodborne pathogen in Europe, due to the ability of its different serovars to contaminate a wide variety of foods, with differences among countries. Common chemical or physical control methods are not always effective, eco-sustainable and adapted to the diversity of Salmonella serovars. Thus, great attention is given to developing complementary or alternative control methods that can be tailor made for specific situations. One of these methods is biopreservation using lactic acid bacteria, with most studies on their antagonistic activity focused on the production of antimicrobials. Less attention has been given to competition by exploitation of nutrients. This review is thus set to investigate and highlight limiting resources that may be involved in the competitive exclusion of Salmonella in food matrices. To do this the needs for nutrients and microelements and the known homeostatic pathways of Salmonella and lactic acid bacteria are examined. Finally, milk, intended for the manufacture of fermented dairy foods, is pointed out as an example of food to investigate the bioavailable macronutrients, metals and vitamins that could be involved in competition between the different species and serovars, and could be exploited for targeted biopreservation.

Developmental Formulation Principles of Food Preservatives by Nanoencapsulation-Fundamentals, Application, and Challenges

The role of food additives is to preserve food by extending shelf life and limiting harmful microorganism proliferation. They prevent spoilage by enhancing the taste and safety of food by utilizing beneficial microorganisms and their antimicrobial metabolites. Current advances in food preservation and processing utilize green technology principles for green preservative formulation, enhancing nutrition and supplying essential micronutrients safely, while also improving quality, packaging, and food safety. Encapsulation is gaining attention for its potential to protect delicate materials from oxidative degradation and extend their shelf life, thereby ensuring optimal nutrient uptake. Nanoencapsulation of bioactive compounds has significantly improved the food, pharmaceutical, agriculture, and nutraceutical industries by protecting antioxidants, vitamins, minerals, and essential fatty acids by controlling release and ensuring delivery to specific sites in the human body. This emerging area is crucial for future industrial production, improving the sensory properties of foods like color, taste, and texture. Research on encapsulated bioactive compounds like bacteriocins, LAB, natamycin, polylysine, and bacteriophage is crucial for their potential antioxidant and antimicrobial activities in food applications and the food industry. This paper reviews nanomaterials used as food antimicrobial carriers, including nanoemulsions, nanoliposomes, nanoparticles, and nanofibers, to protect natural food antimicrobials from degradation and improve antimicrobial activity. This review discusses nanoencapsulation techniques for biopreservative agents like nisin, poly lysine, and natamycin, focusing on biologically-derived polymeric nanofibers, nanocarriers, nanoliposomes, and polymer-stabilized metallic nanoparticles. Nanomaterials, in general, improve the dispersibility, stability, and availability of bioactive substances, and this study discusses the controlled release of nanoencapsulated biopreservative agents.

Split fluorescent protein-mediated multimerization of cell wall binding domain for highly sensitive and selective bacterial detection

Cell wall peptidoglycan binding domains (CBDs) of cell lytic enzymes, including bacteriocins, autolysins and bacteriophage endolysins, enable highly selective bacterial binding, and thus, have potential as biorecognition molecules for nondestructive bacterial detection. Here, a novel design for a self-complementing split fluorescent protein (FP) complex is proposed, where a multimeric FP chain fused with specific CBDs ((FP-CBD)n) is assembled inside the cell, to improve sensitivity by enhancing the signal generated upon Staphylococcus aureus or Bacillus anthracis binding. Flow cytometry shows enhanced fluorescence on the cell surface with increasing FP stoichiometry and surface plasmon resonance reveals nanomolar binding affinity to isolated peptidoglycan. The breadth of function of these complexes is demonstrated through the use of CBD modularity and the ability to attach enzymatic detection modalities. Horseradish peroxidase-coupled (FP-CBD)n complexes generate a catalytic amplification, with the degree of amplification increasing as a function of FP length, reaching a limit of detection (LOD) of 103 cells/droplet (approximately 0.1 ng S. aureus or B. anthracis) within 15 min on a polystyrene surface. These fusion proteins can be multiplexed for simultaneous detection. Multimeric split FP-CBD fusions enable use as a biorecognition molecule with enhanced signal for use in bacterial biosensing platforms.

Psychrophilic phage phiGM22-3 efficiently controls Pseudomonas fluorescens contamination in cold-stored milk

Pseudomonas fluorescens is a common spoilage causing microbe found in milk. Antibiotic preservatives may cause emergence of multidrug resistance, posing food safety related risks to public health. Phage treatment may be used as an alternative to antibiotics in controlling P. fluorescens contaminations. Here we reported that P. fluorescens phage phiGM22-3 reproduced rapidly over a broad temperature range of 4 through 30°C, and the optimum growth of phiGM22-3 occurred at 10°C, indicating that it was a psychrophilic virus. Genome analysis revealed that phiGM22-3 has a genome of 42,662 bp with an identical terminal direct repeat sequence of 328 bp and encodes 58 predicted proteins. Evidence revealed that phiGM22-3 recognized lipopolysaccharides (LPS) as receptor for infection. Additionally, two phage mutants phiMX2 and phiMX8 with different host ranges were identified in the phiGM22-3 population. Phage killing efficiency of P. fluorescens cells artificially inoculated in milk was evaluated. Phage phiGM22-3 and the cocktails containing phiMX2 and phiMX8 can lyse almost 100% bacterial cells at 4°C within 24 h. Taken together, our data indicated that the psychrophilic virus phiGM22-3 and its two mutants can efficiently inhibit bacteria growth at 4°C, showing a great potential to be used as alternatives to conventional antibiotics against P. fluorescens in refrigerated foods.

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.

Safety Properties of Escherichia coli O157:H7 Specific Bacteriophages: Recent Advances for Food Safety

Shiga-toxin-producing Escherichia coli (STEC) is typically detected on food products mainly due to cross-contamination with faecal matter. The serotype O157:H7 has been of major public health concern due to the severity of illness caused, prevalence, and management. In the food chain, the main methods of controlling contamination by foodborne pathogens often involve the application of antimicrobial agents, which are now becoming less efficient. There is a growing need for the development of new approaches to combat these pathogens, especially those that harbour antimicrobial resistant and virulent determinants. Strategies to also limit their presence on food contact surfaces and food matrices are needed to prevent their transmission. Recent studies have revealed that bacteriophages are useful non-antibiotic options for biocontrol of E. coli O157:H7 in both animals and humans. Phage biocontrol can significantly reduce E. coli O157:H7, thereby improving food safety. However, before being certified as potential biocontrol agents, the safety of the phage candidates must be resolved to satisfy regulatory standards, particularly regarding phage resistance, antigenic properties, and toxigenic properties. In this review, we provide a general description of the main virulence elements of E. coli O157:H7 and present detailed reports that support the proposals that phages infecting E. coli O157:H7 are potential biocontrol agents. This paper also outlines the mechanism of E. coli O157:H7 resistance to phages and the safety concerns associated with the use of phages as a biocontrol.

Control of Escherichia coli in Fresh-Cut Mixed Vegetables Using a Combination of Bacteriophage and Carvacrol

The continual emergence of antibiotic-resistant bacteria and the slow development of new antibiotics has driven the resurgent interest in the potential application of bacteriophages as antimicrobial agents in different medical and industrial sectors. In the present study, the potential of combining phage biocontrol and a natural plant compound (carvacrol) in controlling Escherichia coli on fresh-cut mixed vegetable was evaluated. Four coliphages, designated Escherichia phage SUT_E420, Escherichia phage SUT_E520, Escherichia phage SUT_E1520 and Escherichia phage SUT_E1620, were isolated from raw sewage. Biological characterization revealed that all four phages had a latent period of 20-30 min and a burst size ranging from 116 plaque-forming units (PFU)/colony forming units (CFU) to 441 PFU/CFU. The phages effectively inhibited the growth of respective host bacteria in vitro, especially when used at a high multiplicity of infection (MOI). Based on transmission electron microscopy analysis, all phages were classified as tailed phages in the class of Caudoviricetes. Additionally, next generation sequencing indicated that none of the selected coliphages contained genes encoding virulence or antimicrobial resistance factors, highlighting the suitability of isolated phages as biocontrol agents. When a phage cocktail (~109 PFU/mL) was applied alone onto fresh-cut mixed vegetables artificially contaminated with E. coli, no bacteria were recovered from treated samples on Day 0, followed by a gradual increase in the E. coli population after 24 h of incubation at 8 °C. On the other hand, no significant differences (p < 0.05) were observed between treated and non-treated samples in terms of E. coli viable counts when carvacrol at the minimum inhibitory concentration (MIC) of 6.25 μL/mL was applied alone. When a phage cocktail at an MOI of ~1000 and MIC carvacrol were applied in combination, no E. coli were recovered from treated samples on Day 0 and 1, followed by a slight increase in the E. coli population to approximately 1.2-1.3 log CFU/mL after 48 h of incubation at 8 °C. However, total elimination of E. coli was observed in samples treated with a phage cocktail at a higher MOI of ~2000 and carvacrol at MIC, with a reduction of approximately 4 log CFU/mL observed at the end of Day 3. The results obtained in this study highlight the potential of combined treatment involving phage biocontrol and carvacrol as a new alternative method to reduce E. coli contamination in minimally processed ready-to-eat foods.

Minimal Processing Technologies for Production and Preservation of Tailor-Made Foods§

Tailor-made foods, also known as foods with programmable properties, are specialised systems with unique composition prepared by different methods, using the known mechanisms of action of their bioactive ingredients. The development of tailor-made foods involves the evaluation of individual components, including bioactive substances derived from waste products of other productions, such as essential oils. These components are evaluated both individually and in combination within food compositions to achieve specific functionalities. This review focuses on the application of minimal processing technologies for the production and preservation of tailor-made foods. It examines a range of approaches, including traditional and emerging technologies, as well as novel ingredients such as biomolecules from various sources and microorganisms. These approaches are combined according to the principles of hurdle technology to achieve effective synergistic effects that enhance food safety and extend the shelf life of tailor-made foods, while maintaining their functional properties.

Characterization and application of a lytic jumbo phage ZPAH34 against multidrug-resistant Aeromonas hydrophila

Aeromonas hydrophila is an emerging foodborne pathogen causing human gastroenteritis. Aeromonas species isolated from food such as seafood presented multidrug-resistance (MDR), raising serious concerns regarding food safety and public health. The use of phages to infect bacteria is a defense against drug-resistant pathogens. In this study, phage ZPAH34 isolated from the lake sample exerted lytic activity against MDR A. hydrophila strain ZYAH75 and inhibited the biofilm on different food-contacting surfaces. ZPAH34 has a large dsDNA genome of 234 kb which belongs to a novel jumbo phage. However, its particle size is the smallest of known jumbo phages so far. Based on phylogenetic analysis, ZPAH34 was used to establish a new genus Chaoshanvirus. Biological characterization revealed that ZPAH34 exhibited wide environmental tolerance, and a high rapid adsorb and reproductive capacity. Food biocontrol experiments demonstrated that ZPAH34 reduces the viable count of A. hydrophila on fish fillets (2.31 log) and lettuce (3.28 log) with potential bactericidal effects. This study isolated and characterized jumbo phage ZPAH34 not only enriched the understanding of phage biological entity diversity and evolution because of its minimal virion size with large genome but also was the first usage of jumbo phage in food safety to eliminate A. hydrophila.

Potential Applications of Thermophilic Bacteriophages in One Health

Bacteriophages have a wide range of applications such as combating antibiotic resistance, preventing food contamination for food safety, and as biomarkers to indirectly assess the quality of water. Additionally, bacteriophage components (endolysins and coat proteins) have a lot of applications in food processing, vaccine design, and the delivery of cargo to the body. Therefore, bacteriophages/components have a multitude of applications in human, plant/veterinary, and environmental health (One Health). Despite their versatility, bacteriophage/component use is mostly limited to temperatures within 4-40 °C. This limits their applications (e.g., in food processing conditions, pasteurization, and vaccine design). Advances in thermophilic bacteriophage research have uncovered novel thermophilic endolysins (e.g., ΦGVE2 amidase and MMPphg) that can be used in food processing and in veterinary medicine. The endolysins are thermostable at temperatures > 65 °C and have broad antimicrobial activities. In addition to thermophilic endolysins, enzymes (DNA polymerase and ligases) derived from thermophages have different applications in molecular biology/biotechnology: to generate DNA libraries and develop diagnostics for human and animal pathogens. Furthermore, coat proteins from thermophages are being explored to develop virus-like particle platforms with versatile applications in human and animal health. Overall, bacteriophages, especially those that are thermophilic, have a plethora of applications in One Health.

An Overview of the Public Health Challenges in Diagnosing and Controlling Human Foodborne Pathogens

Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety.

Isolation and characterization of new bacteriophages active against Clostridium tyrobutyricum and their role in preventing the late blowing defect of cheese

Lytic bacteriophages (phages) offer a great potential as biocontrol agents for spoilage Clostridium tyrobutyricum, responsible for butyric acid fermentation in semi-hard and hard ripened cheeses, resulting in late gas blowing defect. With this aim, we have isolated, identified and characterized new lytic phages of C. tyrobutyricum, and have evaluated their efficacy to control cheese late blowing by adding them to manufacture milk. Silage, soil, milk and cheese from dairy farms were screened for anti-clostridial phages, obtaining 96 isolates active against C. tyrobutyricum. According to host range, source and plaque morphology, we obtained 20 phage profiles, 8 of them (represented by phages FA3, FA21, FA29, FA52, FA58, FA67, FA70 and FA88) showing a wider host range and high quality lysis, which were further characterized. Selected isolates showed a non-contractile tail, belonging to the Siphoviridae family, and were grouped into 3 restriction profiles. Viable phages were detected after storage in sodium-magnesium buffer (SM buffer), skim milk and acidified skim milk (pH 5) for 7 d at 4 °C, 12 °C and 37 °C, although a decline in infectivity was observed in some cases. Good phage survival was also detected during semi-hard cheese manufacture and ripening (60 d), and cheese lactococci counts, pH, dry matter values, and volatile compounds were not affected by phage addition. In semi-hard cheese, phage FA67 impaired the early germination of C. tyrobutyricum spores and caused a significant decrease in clostridial vegetative cells counts at 14 d of ripening, delaying by 2 weeks the consumption of lactic acid, formation of butyric acid and appearance of late blowing symptoms, compared to the spoilt control cheese without the phage. This is the first report on the application of phage to control C. tyrobutyricum in cheese.

Broad-Spectrum Salmonella Phages PSE-D1 and PST-H1 Controls Salmonella in Foods

Food contamination by Salmonella can lead to serious foodborne diseases that constantly threaten public health. Innovative and effective strategies are needed to control foodborne pathogenic contamination since the incidence of foodborne diseases has increased gradually. In the present study, two broad-spectrum phages named Salmonella phage PSE-D1 and Salmonella phage PST-H1 were isolated from sewage in China. Phages PSE-D1 and PST-H1 were obtained by enrichment with Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) CVCC1806 and Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) CVCC3384, respectively. They were able to lyse Salmonella, E. coli and K. pneumoniae and exhibited broad host range. Further study demonstrated that PSE-D1 and PST-H1 showed high pH and thermal tolerances. Phage PSE-D1 belongs to the Jiaodavirus genus, Tevenvirinae subfamily, while phage PST-H1 belongs to the Jerseyvirus genus, Guernseyvirinae subfamily according to morphology and phylogeny. The results of genome analysis showed that PSE-D1 and PST-H1 lack virulence and drug-resistance genes. The effects of PSE-D1 and PST-H1 on controlling S. Enteritidis CVCC1806 and S. Typhimurium CVCC3384 contamination in three kinds of foods (eggshells, sausages and milk) were further investigated, respectively. Our results showed that, compared to phage-free groups, PSE-D1 and PST-H1 inhibited the growth of their host strain significantly. A significant reduction of host bacteria titers (1.5 and 1.9 log₁₀ CFU/sample, p < 0.001) on eggshells was observed under PSE-D1 and PST-H1 treatments, respectively. Furthermore, administration of PSE-D1 and PST-H1 decreased the counts of bacteria by 1.1 and 1.2 log₁₀ CFU/cm² (p < 0.001) in sausages as well as 1.5 and 1.8 log₁₀ CFU/mL (p < 0.001) in milk, respectively. Interesting, the bacteriostasis efficacy of both phages exhibited more significantly at 4 °C than that at 28 °C in eggshells and milk and sausages. In sum, the purpose of our research was evaluating the counteracting effect of phage PSE-D1 and PST-H1 on the spread of Salmonella on contaminated foods products. Our results suggested that these two phage-based biocontrol treatments are promising strategies for controlling pathogenic Salmonella contaminated food.

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.

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.

Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples

The recovery of DNA from viromes is a major obstacle in the use of long-read sequencing to study their genomes. For this reason, the use of cellular metagenomes (>0.2-μm size range) emerges as an interesting complementary tool, since they contain large amounts of naturally amplified viral genomes from prelytic replication. We have applied second-generation (Illumina NextSeq; short reads) and third-generation (PacBio Sequel II; long reads) sequencing to compare the diversity and features of the viral community in a marine sample obtained from offshore waters of the western Mediterranean. We found that a major wedge of the expected marine viral diversity was directly recovered by the raw PacBio circular consensus sequencing (CCS) reads. More than 30,000 sequences were detected only in this data set, with no homologues in the long- and short-read assembly, and ca. 26,000 had no homologues in the large data set of the Global Ocean Virome 2 (GOV2), highlighting the information gap created by the assembly bias. At the level of complete viral genomes, the performance was similar in both approaches. However, the hybrid long- and short-read assembly provided the longest average length of the sequences and improved the host assignment. Although no novel major clades of viruses were found, there was an increase in the intraclade genomic diversity recovered by long reads that produced an enriched assessment of the real diversity and allowed the discovery of novel genes with biotechnological potential (e.g., endolysin genes).

IMPORTANCE We explored the vast genetic diversity of environmental viruses by using a combination of cellular metagenome (as opposed to virome) sequencing using high-fidelity long-read sequences (in this case, PacBio CCS). This approach resulted in the recovery of a representative sample of the viral population, and it performed better (more phage contigs, larger average contig size) than Illumina sequencing applied to the same sample. By this approach, the many biases of assembly are avoided, as the CCS reads recovers (typically around 5 kb) complete genes and even operons, resulting in a better discovery of the viral gene diversity based on viral marker proteins. Thus, biotechnologically promising genes, such as endolysin genes, can be very efficiently searched with this approach. In addition, hybrid assembly produces more complete and longer contigs, which is particularly important for studying little-known viral groups such as the nucleocytoplasmic large DNA viruses (NCLDV).

Genomic analysis of a novel active prophage of Hafnia paralvei

Little is known about the prophages in Hafniaceae bacteria. A novel Hafnia phage, yong2, was induced from Hafnia paralvei by treatment with mitomycin C. The phage has an elliptical head with dimensions of approximately 45 × 38 nm and a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546-bp double-stranded DNA with a G+C content of 49.9%, containing 59 open reading frames (ORFs) and having at least one fixed terminus (GGGGCAGCGACA). In phylogenetic analysis, Hafnia phage yong2 clustered with four predicted Hafnia prophages and one predicted Enterobacteriaceae prophage. These prophages and members of the family Drexlerviridae together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and a unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria.

Progress in Alternative Strategies to Combat Antimicrobial Resistance: Focus on Antibiotics

Antibiotic resistance, and, in a broader perspective, antimicrobial resistance (AMR), continues to evolve and spread beyond all boundaries. As a result, infectious diseases have become more challenging or even impossible to treat, leading to an increase in morbidity and mortality. Despite the failure of conventional, traditional antimicrobial therapy, in the past two decades, no novel class of antibiotics has been introduced. Consequently, several novel alternative strategies to combat these (multi-) drug-resistant infectious microorganisms have been identified. The purpose of this review is to gather and consider the strategies that are being applied or proposed as potential alternatives to traditional antibiotics. These strategies include combination therapy, techniques that target the enzymes or proteins responsible for antimicrobial resistance, resistant bacteria, drug delivery systems, physicochemical methods, and unconventional techniques, including the CRISPR-Cas system. These alternative strategies may have the potential to change the treatment of multi-drug-resistant pathogens in human clinical settings.

An Engineered Multimodular Enzybiotic against Methicillin-Resistant Staphylococcus aureus

Development of multidrug antibiotic resistance in bacteria is a predicament encountered worldwide. Researchers are in a constant hunt to develop effective antimicrobial agents to counter these dreadful pathogenic bacteria. Here we describe a chimerically engineered multimodular enzybiotic to treat a clinical isolate of methicillin-resistant Staphylococcus aureus (S. aureus). The cell wall binding domain of phage ϕ11 endolysin was replaced with a truncated and more potent cell wall binding domain from a completely unrelated protein from a different phage. The engineered enzybiotic showed strong activity against clinically relevant methicillin-resistant Staphylococcus aureus. In spite of a multimodular peptidoglycan cleaving catalytic domain, the engineered enzybiotic could not exhibit its activity against a veterinary isolate of S. aureus. Our studies point out that novel antimicrobial proteins can be genetically engineered. Moreover, the cell wall binding domain of the engineered protein is indispensable for a strong binding and stability of the proteins.