Eating oysters without risk of vibriosis: Application of a bacteriophage against Vibrio parahaemolyticus in oysters

Pulsed ultraviolet (PUV) disinfection of artificially contaminated seawater seeded with high levels of pathogen disease indicators as an alternative for the shellfish industry depuration systems

The increase in pathogen levels in seawater threatens the safety of entire aquatic ecosystems. Foodborne pathogens can potentially accumulate in shellfish, especially in filter feeders such as bivalves, requiring an efficient depuration process before consumption. Alternative approaches to promote a cost-efficient purge at depuration plants are urgently needed. A small prototype pulsed ultraviolet (PUV) light recirculation system was designed, and its depuration potential was tested in a seawater matrix artificially contaminated with high levels of microbial pathogens Escherichia coli, Staphylococcus aureus, Salmonella typhimurium, Bacillus cereus and Candida albicans. The analysis of treatment parameters including voltage, number of pulses and duration of treatment was performed to ensure the highest reduction in contaminant levels. Optimal PUV disinfection was attained at 60 pulses/min at 1 kV for 10 min (a UV output of 12.9 J/cm²). All reductions were statistically significant, and the greatest was observed for S. aureus (5.63 log₁₀), followed by C. albicans (5.15 log₁₀), S. typhimurium (5 log₁₀), B. cereus (4.59 log₁₀) and E. coli (4.55 log₁₀). PUV treatment disrupted the pathogen DNA with the result that S. aureus, C. albicans and S. typhimurium were not detectable by PCR. Regulations were reviewed to address the applicability of PUV treatment as a promising alternative to assist in the reduction of microbial pathogens at depuration plants due to its high efficiency, short treatment period, high UV dose and recirculation system as currently employed in shellfish depuration plants.

Isolation, characterization, and complete genome sequence of vibrio phage KIT04, a novel lytic phage of the subfamily ermolyevavirinae

Vibrio phage KIT04 was isolated from muscle tissue samples collected from a local market in Vietnam. KIT04 is a lytic phage that is specific to Vibrio parahaemolyticus. The one-step growth curve determined the burst size and latent period of 0.01 multiplicity of infection KIT04 in V. parahaemolyticus as approximately 156 plaque-forming units/bacterium and 45 min, respectively. Vibrio phage KIT04 has an approximately 76.4 ± 4.5 nm diameter icosahedral head and a tail length of approximately 159.5 ± 16.6 nm long tail. KIT04 significantly reduced V. parahaemolyticus ATCC 17802 in vitro. Complete genome analysis showed that KIT04 had a 114,933 bp dsDNA genome with 40.24% G + C content and 160 open reading frames (ORFs). However, the phage genome contained 24 tRNAs and no lysogeny-related genes. Moreover, five of the 160 ORFs encoded unique hypothetical proteins, indicating that KIT04 is a novel phage. Genomic comparison indicated that KIT04 is closely related to the Vibrio phages pVp-1 and VPT02. Further, phylogenetic analysis of the major tail proteins and whole genome supported the KIT04 classification into the subfamily Ermolyevavirinae. Our study describes a new candidate phage that could be used as a bioagent for controlling Vibrio pathogens.

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.

Characterization and Genomic Analysis of a Bacteriophage with Potential in Lysing Vibrio alginolyticus

Vibrio alginolyticus is one of the major pathogens causing vibriosis to a variety of aquatic animals as well as bringing about severe food safety concerns. Nowadays, phage therapy has received increasing attention as an alternative to the antibiotics that have being limited for use in aquaculture industries. In this work, a potent bacteriophage, vB_ValM_PVA23 (PVA23), which efficiently infects pathogenic strains of V. alginolyticus, was isolated from sewage water and characterized by microbiological and genomic analyses. Based on the transmission electronic observation, the phage was characterized to be the Myoviridae family. It has a latent period of 10 min and a burst size of 203 PFUs/infected bacterium, and was stable over a broad pH range (5.0−11.0) and a wide temperature span (−80 °C to 60 °C), respectively. Genome sequencing results show that PVA23 has a 246,962-bp double-stranded DNA with a G + C content of 41.25%. The lab and plant shrimp farming trials demonstrated that phage preparation derived from PVA23 out-performed the chemical disinfectant iodine treatment in the prevention of V. alginolyticus propagation, and the phage application could rapidly yet significantly reduce the level of V. alginolyticus in the pond within 12 h, with negligible rebound observed. These results suggests that phage PVA23 has the potential to be used as an anti-V. alginolyticus agent in aquaculture industries.

Tracking the phage trends: A comprehensive review of applications in therapy and food production

In the present scenario, the challenge of emerging antimicrobial resistance is affecting human health globally. The increasing incidences of multidrug-resistant infections have become harder to treat, causing high morbidity, and mortality, and are posing extensive financial loss. Limited discovery of new antibiotic molecules has further complicated the situation and has forced researchers to think and explore alternatives to antibiotics. This has led to the resurgence of the bacteriophages as an effective alternative as they have a proven history in the Eastern world where lytic bacteriophages have been used since their first implementation over a century ago. To help researchers and clinicians towards strengthening bacteriophages as a more effective, safe, and economical therapeutic alternative, the present review provides an elaborate narrative about the important aspects of bacteriophages. It abridges the prerequisite essential requirements of phage therapy, the role of phage biobank, and the details of immune responses reported while using bacteriophages in the clinical trials/compassionate grounds by examining the up-to-date case reports and their effects on the human gut microbiome. This review also discusses the potential of bacteriophages as a biocontrol agent against food-borne diseases in the food industry and aquaculture, in addition to clinical therapy. It finishes with a discussion of the major challenges, as well as phage therapy and phage-mediated biocontrols future prospects.

Antibiofilm Efficacy of Quercetin against Vibrio parahaemolyticus Biofilm on Food-Contact Surfaces in the Food Industry

Vibrio parahaemolyticus, one of the most common foodborne pathogenic bacteria that forms biofilms, is a persistent source of concern for the food industry. The food production chain employs a variety of methods to control biofilms, although none are completely successful. This study aims to evaluate the effectiveness of quercetin as a food additive in reducing V. parahaemolyticus biofilm formation on stainless-steel coupons (SS) and hand gloves (HG) as well as testing its antimicrobial activities. With a minimum inhibitory concentration (MIC) of 220 µg/mL, the tested quercetin exhibited the lowest bactericidal action without visible growth. In contrast, during various experiments in this work, the inhibitory efficacy of quercetin at sub-MICs levels (1/2, 1/4, and 1/8 MIC) against V. parahaemolyticus was examined. Control group was not added with quercetin. With increasing quercetin concentration, swarming and swimming motility, biofilm formation, and expression levels of target genes linked to flagellar motility (flaA, flgL), biofilm formation (vp0952, vp0962), virulence (VopQ, vp0450), and quorum-sensing (aphA, luxS) were all dramatically suppressed. Quercetin (0−110 μg/mL) was investigated on SS and HG surfaces, the inhibitory effect were 0.10−2.17 and 0.26−2.31 log CFU/cm2, respectively (p < 0.05). Field emission scanning electron microscopy (FE-SEM) corroborated the findings because quercetin prevented the development of biofilms by severing cell-to-cell contacts and inducing cell lysis, which resulted in the loss of normal cell shape. Additionally, there was a significant difference between the treated and control groups in terms of motility (swimming and swarming). According to our research, quercetin produced from plants should be employed as an antibiofilm agent in the food sector to prevent the growth of V. parahaemolyticus biofilms. These results indicate that throughout the entire food production chain, bacterial targets are of interest for biofilm reduction with alternative natural food agents in the seafood industry.

Functional characterization of Vibrio alginolyticus T3SS regulator ExsA and evaluation of its mutant as a live attenuated vaccine candidate in zebrafish (Danio rerio) model

Vibrio alginolyticus, a Gram-negative bacterium, is an opportunistic pathogen of both marine animals and humans, resulting in significant losses in the aquaculture industry. Type III secretion system (T3SS) is a crucial virulence mechanism of V. alginolyticus. In this study, the T3SS regulatory gene exsA, which was cloned from V. alginolyticus wild-type strain HY9901, is 861 bp encoding a protein of 286 amino acids. The ΔexsA was constructed by homologous recombination and Overlap-PCR. Although there was no difference in growth between HY9901 and ΔexsA, the ΔexsA exhibited significantly decreased extracellular protease activity and biofilm formation. Besides, the ΔexsA showed a weakened swarming phenotype and an ~100-fold decrease in virulence to zebrafish. Antibiotic susceptibility testing showed the HY9901ΔexsA was more sensitive to kanamycin, minocycline, tetracycline, gentamicin, doxycycline and neomycin. Compared to HY9901 there were 541 up-regulated genes and 663 down-regulated genes in ΔexsA, screened by transcriptome sequencing. qRT-PCR and β-galactosidase reporter assays were used to analyze the transcription levels of hop gene revealing that exsA gene could facilitate the expression of hop gene. Finally, Danio rerio, vaccinated with ΔexsA through intramuscular injection, induced a relative percent survival (RPS) value of 66.7% after challenging with HY9901 wild type strain. qRT-PCR assays showed that vaccination with ΔexsA increased the expression of immune-related genes, including GATA-1, IL6, IgM, and TNF-α in zebrafish. In summary, these results demonstrate the importance of exsA in V. alginolyticus and provide a basis for further investigations into the virulence and infection mechanism.

Tackling Vibrio parahaemolyticus in ready-to-eat raw fish flesh slices using lytic phage VPT02 isolated from market oyster

The opportunistic pathogen V. parahaemolyticus is a major causative agent for seafood-borne illness worldwide. It also causes severe vibriosis in aquaculture animals, affecting seafood production with huge economic loss. These issues are getting worse due to the current global warming in oceans, spread of antibiotic resistance, and changes in consumer preference toward ready-to-eat (RTE) food items including seafood. To answer the urgent need for sustainable biocontrol agents against V. parahaemolyticus, we isolated and characterized a novel lytic bacteriophage VPT02 from market oyster. VPT02 lysed antibiotic resistant V. parahaemolyticus strains including FORC_023. Moreover, it exhibited notable properties as a biocontrol agent suitable for seafood-related settings, like short eclipse/latent periods, high burst size, broad thermal and pH stability, and no toxin/antibiotic resistance genes in the genome. Further comparative genomic analysis with the previously reported homologue phage pVp-1 revealed that VPT02 additionally possesses genes related to the nucleotide scavenging pathway, presumably enabling the phage to propagate quickly. Consistent with its strong in vitro bacteriolytic activity, treatment of only a small quantity of VPT02 (multiplicity of infection of 10) significantly increased the survival rate of V. parahaemolyticus-infected brine shrimp (from 16.7% to 46.7%). When applied to RTE raw fish flesh slices, the same quantity of VPT02 achieved up to 3.9 log reduction of spiked V. parahaemolyticus compared with the phage untreated control. Taken together, these results suggest that VPT02 may be a sustainable anti-V. parahaemolyticus agent useful in seafood-related settings including for RTE items.

Phage Therapy as a Focused Management Strategy in Aquaculture

Therapeutic bacteriophages, commonly called as phages, are a promising potential alternative to antibiotics in the management of bacterial infections of a wide range of organisms including cultured fish. Their natural immunogenicity often induces the modulation of a variated collection of immune responses within several types of immunocytes while promoting specific mechanisms of bacterial clearance. However, to achieve standardized treatments at the practical level and avoid possible side effects in cultivated fish, several improvements in the understanding of their biology and the associated genomes are required. Interestingly, a particular feature with therapeutic potential among all phages is the production of lytic enzymes. The use of such enzymes against human and livestock pathogens has already provided in vitro and in vivo promissory results. So far, the best-understood phages utilized to fight against either Gram-negative or Gram-positive bacterial species in fish culture are mainly restricted to the Myoviridae and Podoviridae, and the Siphoviridae, respectively. However, the current functional use of phages against bacterial pathogens of cultured fish is still in its infancy. Based on the available data, in this review, we summarize the current knowledge about phage, identify gaps, and provide insights into the possible bacterial control strategies they might represent for managing aquaculture-related bacterial diseases.

Screening of a Plesiomonas shigelloides phage and study of the activity of its lysis system

Plesiomonas shigelloides is an important fish pathogen that causes significant losses in aquaculture. Phage therapy is a new approach to overcome the problem of multidrug-resistant bacteria. Herein, a virulent phage of P. shigelloides was isolated from the intestines of grass carp. This phage belongs to the Siphoviridae family and was designated PSP01. The optimal multiplicity of infection of PSP01 was 1 with a latent period of 30 min and a lytic period of 140 min. Good activity was observed over a wide range of temperatures (-20 °C-50 °C), pH values (3-12), and NaCl concentrations (0.1-3.5%). The phage PSP01 lysis cassette is composed of 3 genes, HolPSP, LysPSP-1 and LysPSP-2. Expression of HolPSP or LysPSP-2 in Escherichia coli resulted in bacterial lysis, and a synergistic effect was observed when the HolPSP and LysPSP-1 proteins were co-expressed. In-frame deletion uncovered an important role of the transmembrane domain (TMD) in HolPSP and the signal peptide (SP) in LysPSP-2 for bacterial lysis function. The protective effects of phage PSP01 were investigated by intraperitoneal injection into grass carp infected with P. shigelloides, showing a 33.3% increase in the survival rate of the infected grass carp. Pathological analysis of the spleens from the infected grass carp revealed alleviation of the pathological symptoms. In conclusion, isolation and bacterial lysis investigations of phage PSP01 provide a new tool for the control of fish pathogens and possesses potential for aquaculture applications.

Phages in Food Industry Biocontrol and Bioremediation

Bacteriophages are ubiquitous in nature and their use is a current promising alternative in biological control. Multidrug resistant (MDR) bacterial strains are present in the livestock industry and phages are attractive candidates to eliminate them and their biofilms. This alternative therapy also reduces the non-desirable effects produced by chemicals on food. The World Health Organization (WHO) estimates that around 420,000 people die due to a foodborne illness annually, suggesting that an improvement in food biocontrol is desirable. This review summarizes relevant studies of phage use in biocontrol focusing on treatments in live animals, plants, surfaces, foods, wastewaters and bioremediation.

Phages in Food Industry Biocontrol and Bioremediation

Bacteriophages are ubiquitous in nature and their use is a current promising alternative in biological control. Multidrug resistant (MDR) bacterial strains are present in the livestock industry and phages are attractive candidates to eliminate them and their biofilms. This alternative therapy also reduces the non-desirable effects produced by chemicals on food. The World Health Organization (WHO) estimates that around 420,000 people die due to a foodborne illness annually, suggesting that an improvement in food biocontrol is desirable. This review summarizes relevant studies of phage use in biocontrol focusing on treatments in live animals, plants, surfaces, foods, wastewaters and bioremediation.

Bacteriophages with Potential to Inactivate Aeromonas hydrophila in Cockles: In Vitro and In Vivo Preliminary Studies

The recurrent emergence of infection outbreaks associated with shellfish consumption is of extreme importance for public health. The present study investigated the potential application of phages AH-1, AH-4, and AH-5 to inactivate Aeromonas hydrophila, a causative agent of infections in humans associated with bivalve shellfish consumption. The inactivation of A. hydrophila was assessed in vitro, using a liquid culture medium, and in vivo, using artificially contaminated cockles with A. hydrophila ATCC 7966. In the in vitro experiments, all phages were effective against A. hydrophila, but phage AH-1 (with a maximum reduction of 7.7 log colonies forming units CFU/mL) was more effective than phages AH-4 and AH-5 (with reductions of 4.9 and 4.5 log CFU/mL, respectively). The cocktails AH-1/AH-4, AH-1/AH-5, AH-4/AH-5, and AH-1/AH-4/AH-5 were slightly more effective than the single phage suspensions. The phages presented a low emergence rate of phage-resistant mutants. When artificially contaminated cockles were treated in static seawater with phage AH-1, around 44% of the added A. hydrophila (1.0 log CFU/g) was inactivated. The results of this study suggest that phage therapy can be an effective alternative to control human pathogenic bacteria during depuration.

Isolation and characterization of a podovirus infecting the opportunist pathogen Vibrio alginolyticus and Vibrio parahaemolyticus

Bacterial infections have a negative impact on both animal husbandry industry and medicine, and increasing bacterial drug resistance exacerbates this adverse impact. Phages show promise as an alternative to drugs against drug-resistant bacteria. In this study, a novel virulent bacteriophage (phage) vB_ValP_IME234 against Vibrio alginolyticus and Vibrio parahaemolyticus was isolated from freshwater in Beijing, China. Phage vB_ValP_IME234 had an isometric head (59 nm in diameter) and a short tail (10 nm long), belonging to Podoviridae family. Its complete genome is liner double-stranded DNA (dsDNA) with a GC content of 41.6% while encoding 61 putative proteins. Three transfer RNA (tRNA) and no lysogenic gene was detected. vB_ValP_IME234 had a polyvalent infectivity, a burst of 390 PFU/cell, and is stable under different temperatures (4 °C to 50 °C) and pH (6.0 to 10.0) values. Host range test showed that vB_ValP_IME234 has the ability to infect seven strains of Vibrio in total. Phylogenetic analyses based on terminase and capsid suggested that this phage had a close relationship with Vibrio phages. These results indicate that vB_ValP_IME234 could be used as a potential biocontrol agent against V. alginolyticus strains.

Motility, biofilm formation and associated gene expression in Vibrio parahaemolyticus impaired by co-culture with live Ulva fasciata

AIMS

Vibrio parahaemolyticus is one of the most frequently occurred pathogens in mariculture. This study aimed to explore the mechanism of the impact of Ulva fasciata on the motility and biofilm formation of V. parahaemolyticus.

METHODS AND RESULTS

The inhibitory effect of U. fasciata on a V. parahaemolyticus, isolated from clam maricultural sediment, was examined by co-culture of them. The live U. fasciata significantly inhibited the swimming behaviour, twitching behaviour and biofilm formation of V. parahaemolyticus JF, with inhibition rates range of 2.48%-20.26%, 1.59%-39.18% and 28.3%-94.7% under different nitrate and phosphate levels, respectively. The results of transcriptome sequencing showed that 210 significantly differentially expressed genes (DEGs) were found in strain JF between the presence and absence of U. fasciata, including 90 upregulated genes and 120 downregulated genes. According to GO (Gene Ontology) function enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis, the downregulated genes of JF were partially enriched in flagella assembly (fliC, fliK, fliG, fliN, fliH, fliI, fliJ and fliA), bacterial chemotaxis (mCP, cheB, cheW and cheY) and biofilm formation (fliA/σ²⁸ and eps), which explained the suppressed motility and biofilm formation of V. parahaemolyticus JF under U. fasciata stress.

CONCLUSIONS

Live U. fasciata significantly impaired the motility and biofilm formation of V. parahaemolyticus, which could occur in niches with either sufficient or inadequate nutrient (nitrate and phosphate) concentrations. The DEGs of V. parahaemolyticus modulated by U. fasciata were enriched mainly in the flagellar assembly, bacterial chemotaxis and biofilm pathways.

SIGNIFICANCE AND IMPACT OF THE STUDY

New information on how V. parahaemolyticus respond to U. fasciata regarding motility and adhesion behaviours, and the mechanism of that was firstly explored in this study. The results suggested that the seaweed U. fasciata has promising prospects as an environmentally friendly preventive measure to treat vibriosis in mariculture.

Isolation and Characterization of Bacteriophages from Inland Saline Aquaculture Environments to Control Vibrio parahaemolyticus Contamination in Shrimp

Among the various bacterial pathogens associated with the aquaculture environment, Vibrio parahaemolyticus the important one from shrimp and human health aspects. Though having been around for several decades, phage-based control of bacterial pathogens (phage therapy) has recently re-emerged as an attractive alternative due to the availability of modern phage characterization tools and the global emergence of antibiotic-resistant bacteria. In the present study, a total of 12 V. parahaemolyticus specific phages were isolated from 264 water samples collected from inland saline shrimp culture farms. During the host range analysis against standard/field isolates of V. parahaemolyticus and other bacterial species, lytic activity was observed against 2.3-45.5% of tested V. parahaemolyticus isolates. No lytic activity was observed against other bacterial species. For genomic characterization, high-quality phage nucleic acid with concentrations ranging from 7.66 to 220 ng/µl was isolated from 9 phages. After digestion treatments with DNase, RNase and S1 nuclease, the nature of phage nucleic acid was determined as ssDNA and dsDNA for 7 and 2 phages respectively. During transmission electron microscopy analysis of phage V5, it was found to have a filamentous shape making it a member of the family Inoviridae. During efficacy study of phage against V. parahaemolyticus in shrimp, 78.1% reduction in bacterial counts was observed within 1 h of phage application. These results indicate the potential of phage therapy for the control of V. parahaemoyticus in shrimp.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-021-00934-6.

Identification of a novel bacterial receptor that binds tail tubular proteins and mediates phage infection of Vibrio parahaemolyticus

The adsorption of phages to hosts is the first step of phage infection. Studies have shown that tailed phages use tail fibres or spikes to recognize bacterial receptors and mediate adsorption. However, whether other phage tail components can also recognize host receptors is unknown. To identify potential receptors, we screened a transposon mutagenesis library of the marine pathogen Vibrio parahaemolyticus and discovered that a vp0980 mutant (vp0980 encodes a predicted transmembrane protein) could not be lysed by phage OWB. Complementation of this mutant with wild-type vp0980 in trans restored phage-mediated lysis. Phage adsorption and confocal microscopy assays demonstrated that phage OWB had dramatically reduced adsorption to the vp0980 mutant compared to that to the wild type. Pulldown assays showed that phage tail tubular proteins A and B (TTPA and TTPB) interact with Vp0980, suggesting that Vp0980 is a TTPA and TTPB receptor. Vp0980 lacking the outer membrane region (aa 114–127) could not bind to TTPA and TTPB, resulting in reduced phage adsorption. These results strongly indicated that TTPA and TTPB binding with their receptor Vp0980 mediates phage adsorption and subsequent bacterial lysis. To the best of our knowledge, this study is the first report of a bacterial receptor for phage tail tubular proteins.

Phage therapy as a potential approach in the biocontrol of pathogenic bacteria associated with shellfish consumption

Infectious human diseases acquired from bivalve shellfish consumption constitute a public health threat. These health threats are largely related to the filter-feeding phenomenon, by which bivalve organisms retain and concentrate pathogenic bacteria from their surrounding waters. Even after depuration, bivalve shellfish are still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new and efficient strategies to control transmission of shellfish infection. Bacteriophage (or phage) therapy represents a promising, tailor-made approach to control human pathogens in bivalves, but its success depends on a deep understanding of several factors that include the bacterial communities present in the harvesting waters, the appropriate selection of phage particles, the multiplicity of infection that produces the best bacterial inactivation, chemical and physical factors, the emergence of phage-resistant bacterial mutants and the life cycle of bivalves. This review discusses the need to advance phage therapy research for bivalve decontamination, highlighting their efficiency as an antimicrobial strategy and identifying critical aspects to successfully apply this therapy to control human pathogens associated with bivalve consumption.

Phages as a Cohesive Prophylactic and Therapeutic Approach in Aquaculture Systems

Facing antibiotic resistance has provoked a continuously growing focus on phage therapy. Although the greatest emphasis has always been placed on phage treatment in humans, behind phage application lies a complex approach that can be usefully adopted by the food industry, from hatcheries and croplands to ready-to-eat products. Such diverse businesses require an efficient method for combating highly pathogenic bacteria since antibiotic resistance concerns every aspect of human life. Despite the vast abundance of phages on Earth, the aquatic environment has been considered their most natural habitat. Water favors multidirectional Brownian motion and increases the possibility of contact between phage particles and their bacterial hosts. As the global production of aquatic organisms has rapidly grown over the past decades, phage treatment of bacterial infections seems to be an obvious and promising solution in this market sector. Pathogenic bacteria, such as Aeromonas and Vibrio, have already proved to be responsible for mass mortalities in aquatic systems, resulting in economic losses. The main objective of this work is to summarize, from a scientific and industry perspective, the recent data regarding phage application in the form of targeted probiotics and therapeutic agents in aquaculture niches.

A Hundred Years of Bacteriophages: Can Phages Replace Antibiotics in Agriculture and Aquaculture?

Agriculture, together with aquaculture, supplies most of the foodstuffs required by the world human population to survive. Hence, bacterial diseases affecting either agricultural crops, fish, or shellfish not only cause large economic losses to producers but can even create food shortages, resulting in malnutrition, or even famine, in vulnerable populations. Years of antibiotic use in the prevention and the treatment of these infections have greatly contributed to the emergence and the proliferation of multidrug-resistant bacteria. This review addresses the urgent need for alternative strategies for the use of antibiotics, focusing on the use of bacteriophages (phages) as biocontrol agents. Phages are viruses that specifically infect bacteria; they are highly host-specific and represent an environmentally-friendly alternative to antibiotics to control and kill pathogenic bacteria. The information evaluated here highlights the effectiveness of phages in the control of numerous major pathogens that affect both agriculture and aquaculture, with special emphasis on scientific and technological aspects still requiring further development to establish phagotherapy as a real universal alternative to antibiotic treatment.

Current and future perspectives for controlling Vibrio biofilms in the seafood industry: a comprehensive review

The contamination of seafood with Vibrio species can have severe repercussions in the seafood industry. Vibrio species can form mature biofilms and persist on the surface of several seafoods such as crabs, oysters, mussels, and shrimp, for extended duration. Several conventional approaches have been employed to inhibit the growth of planktonic cells and prevent the formation of Vibrio biofilms. Since Vibrio biofilms are mostly resistant to these control measures, novel alternative methods need to be urgently developed. In this review, we propose environmentally friendly approaches to suppress Vibrio biofilm formation using a hypothesized mechanism of action.

Complementary Methods to Improve the Depuration of Bivalves: A Review

Bivalves are filter feeders that can accumulate and concentrate waterborne contaminants present in the water in which they live. Biotoxins, pathogenic bacteria, viruses, and heavy metals present in the aquaculture environment constitute the main hazards for human health. The most common method employed for combating waterborne pollutants in bivalves is depuration with purified seawater. Although this method is effective at increasing the microbiological quality of bivalves, in most cases, it is ineffective at eliminating other risks, such as, for example, viruses or heavy metals. Biological (bacteriocins and bacteriophages), physical (UV light, ozone, and gamma-irradiation), chemical (metallothioneins and chitosan), and other industrial processing methods have been found to be useful for eliminating some contaminants from seawater. The aim of this work was to provide a review of academic articles concerning the use of treatments complementary to conventional depuration, aiming to improve depuration process efficiency by reducing depuration times and decreasing the levels of the most difficult-to-erase contaminants. We conclude that there are different lab-tested strategies that can reduce depuration times and increase the food safety of bivalve produce, with possible short- and long-term industrial applications that could improve the competitivity of the aquaculture industry.

Yersinia Phages and Food Safety

One of the human- and animal-pathogenic species in genus Yersinia is Yersinia enterocolitica, a food-borne zoonotic pathogen that causes enteric infections, mesenteric lymphadenitis, and sometimes sequelae such as reactive arthritis and erythema nodosum. Y. enterocolitica is able to proliferate at 4 C, making it dangerous if contaminated food products are stored under refrigeration. The most common source of Y. enterocolitica is raw pork meat. Microbiological detection of the bacteria from food products is hampered by its slow growth rate as other bacteria overgrow it. Bacteriophages can be exploited in several ways to increase food safety with regards to contamination by Y. enterocolitica. For example, Yersinia phages could be useful in keeping the contamination of food products under control, or, alternatively, the specificity of the phages could be exploited in developing rapid and sensitive diagnostic tools for the identification of the bacteria in food products. In this review, we will discuss the present state of the research on these topics.

Biocontrol of Salmonella Typhimurium in Raw Salmon Fillets and Scallop Adductors by Using Bacteriophage SLMP1

The aim of this study was to evaluate the effectiveness of bacteriophage (phage) SLMP1 to reduce Salmonella Typhimurium on contaminated raw salmon fillets and scallop adductors as a function of Salmonella inoculum level, phage dose, storage temperature, and storage time. Samples were inoculated with 10² and 10⁴ CFU/g Salmonella and then treated with different concentrations of phage SLMP1, followed by incubation at 4, 15, and 25°C, respectively. The results showed that 10⁸ PFU/g was the optimal concentration of phage for the control of Salmonella, which was applied in the following storage experiments over a 7-day period at 4°C, a 4-day period at 15°C, and a 2-day period at 25°C. For the salmon fillets samples, 10² CFU/g Salmonella could be reduced below the detection limit at all three temperatures, whereas 10⁴ CFU/g Salmonella was first decreased and then increased at 15 and 25°C. For the scallop adductors samples, 10² CFU/g Salmonella could be reduced below the detection limit first and then increased after a certain period at 15 and 25°C. The variation trends of 10⁴ CFU/g Salmonella in scallop adductors were similar to those in salmon fillets. The results also showed that the Salmonella counts of both inoculum levels on samples could be reduced below the detection limit or maintained at a low level by phage SLMP1 during storage at 4°C. Phage SLMP1 remained stable on raw salmon fillets and scallop adductors. This study indicated that phage SLMP1 has potential effectiveness as a biocontrol agent of Salmonella in seafood.

Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions

Seafood comprising of both vertebrate and invertebrate aquatic organisms are nutritious, rich in omega-3 fatty acids, essential vitamins, proteins, minerals and form part of healthy diet. However, despite the health and nutritional benefits, seafood is highly perishable. Spoilage of seafood could be as a result of microbial activity, autolysis or chemical oxidation. Microbial activity constitutes more spoilage than others. Spoilage bacteria are commonly Gram negative and produce off odours and flavours in seafood as a result of their metabolic activities. Storage temperature, handling and packaging conditions affect microbial growth and thus the shelf-life of seafood. Due to the complexity of the microbial communities in seafood, culture dependent methods of detection may not be useful, hence the need for culture independent methods are necessary to understand the diversity of microbiota and spoilage process. Similarly, the volatile organic compounds released by spoilage bacteria are not fully understood in some seafood. This review therefore highlights current knowledge and understanding of seafood spoilage microbiota, volatile organic compounds, effects of storage temperature and packaging conditions on quality of seafood.

Phage Application for the Protection from Acute Hepatopancreatic Necrosis Disease (AHPND) in Penaeus vannamei

Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus has been one of the most problematic diseases in marine shrimp aquaculture throughout Southeast Asia and Latin America. To evaluate the effectiveness of a bacteriophage (phage) treatment for AHPND, a series of bioassays were carried out in a marine shrimp (Penaeus vannamei) model using an AHPND-V. parahaemolyticus strain that is highly pathogenic to shrimp. We monitored the mortality and histopathological changes during phage treatment. Shrimps treated with phage prophylaxis and phage therapy displayed significant protection from AHPND and survived a lethal bacterial challenge.

The Use of Electrochemical Biosensors in Food Analysis

Rapid and accurate analysis of food produce is essential to screen for species that may cause significant health risks like bacteria, pesticides and other toxins. Considerable developments in analytical techniques and instrumentation, for example chromatography, have enabled the analyses and quantitation of these contaminants. However, these traditional technologies are constrained by high cost, delayed analysis times, expensive and laborious sample preparation stages and the need for highly-trained personnel. Therefore, emerging, alternative technologies, for example biosensors may provide viable alternatives. Rapid advances in electrochemical biosensors have enabled significant gains in quantitative detection and screening and show incredible potential as a means of countering such limitations. Apart from demonstrating high specificity towards the analyte, these biosensors also address the challenge of the multifactorial food industry of providing high analytical accuracy amidst complex food matrices, while also overcoming differing densities, pH and temperatures. This (public and Industry) demand for faster, reliable and cost-efficient analysis of food samples, has driven investment into biosensor design. Here, we discuss some of the recent work in this area and critique the role and contributions biosensors play in the food industry. We also appraise the challenges we believe biosensors need to overcome to become the industry standard.

Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures

Bacteriophages encode anti-CRISPR suppressors to counteract the CRISPR/Cas immunity of their bacterial hosts, thus facilitating their survival and replication. Previous studies have shown that two phage-encoded anti-CRISPR proteins, AcrF1 and AcrF2, suppress the type I-F CRISPR/Cas system of Pseudomonas aeruginosa by preventing target DNA recognition by the Csy surveillance complex, but the precise underlying mechanism was unknown. Here we present the structure of AcrF1/2 bound to the Csy complex determined by cryo-EM single-particle reconstruction. By structural analysis, we found that AcrF1 inhibits target DNA recognition of the Csy complex by interfering with base pairing between the DNA target strand and crRNA spacer. In addition, multiple copies of AcrF1 bind to the Csy complex with different modes when working individually or cooperating with AcrF2, which might exclude target DNA binding through different mechanisms. Together with previous reports, we provide a comprehensive working scenario for the two anti-CRISPR suppressors, AcrF1 and AcrF2, which silence CRISPR/Cas immunity by targeting the Csy surveillance complex.

Application of phage therapy during bivalve depuration improves Escherichia coli decontamination

The present study investigated the potential application of the bacteriophage (or phage) phT4A, ECA2 and the phage cocktail phT4A/ECA2 to decrease the concentration of Escherichia coli during the depuration of natural and artificially contaminated cockles. Depuration in static seawater at multiplicity of infection (MOI) of 1 with single phage suspensions of phT4A and ECA2 was the best condition, as it decreased by ∼2.0 log CFU/g the concentration of E. coli in artificially contaminated cockles after a 4 h of treatment. When naturally contaminated cockles were treated in static seawater with single phage suspensions and the phage cocktail, similar decreases in the concentration of E. coli (∼0.7 log CFU/g) were achieved. However, when employing the phage cocktail, a longer treatment time was required to obtain comparable results to those achieved when using single phage suspensions. When naturally contaminated cockles were depurated with phage phT4A in a recirculated seawater system (mimicking industrial depuration conditions), a 0.6 log CFU/g reduction of E. coli was achieved after a 2 h of treatment. When the depuration process was performed without phage addition, a 4 h treatment was necessary to obtain a similar decrease. By combining phage therapy and depuration procedures, a reduction in bivalves depuration period can be achieved for, thus decreasing the cost associated with this procedure and even enhance the quality and safety of depurated bivalves destined for human consumption.

Insights into Bacteriophage Application in Controlling Vibrio Species

Bacterial infections from various organisms including Vibrio sp. pose a serious hazard to humans in many forms from clinical infection to affecting the yield of agriculture and aquaculture via infection of livestock. Vibrio sp. is one of the main foodborne pathogens causing human infection and is also a common cause of losses in the aquaculture industry. Prophylactic and therapeutic usage of antibiotics has become the mainstay of managing this problem, however, this in turn led to the emergence of multidrug resistant strains of bacteria in the environment; which has raised awareness of the critical need for alternative non-antibiotic based methods of preventing and treating bacterial infections. Bacteriophages - viruses that infect and result in the death of bacteria - are currently of great interest as a highly viable alternative to antibiotics. This article provides an insight into bacteriophage application in controlling Vibrio species as well underlining the advantages and drawbacks of phage therapy.

A Nonautochthonous U.S. Strain of Vibrio parahaemolyticus Isolated from Chesapeake Bay Oysters Caused the Outbreak in Maryland in 2010

In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to the consumption of oysters. Strains isolated from both stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). However, the oysters contained other potentially pathogenic V. parahaemolyticus strains exhibiting different PFGE patterns. In order to assess the identity, genetic makeup, relatedness, and potential pathogenicity of the V. parahaemolyticus strains, we sequenced 11 such strains (2 clinical strains and 9 oyster strains). We analyzed these genomes by in silico multilocus sequence typing (MLST) and determined their phylogeny using a whole-genome MLST (wgMLST) analysis. Our in silico MLST analysis identified six different sequence types (STs) (ST8, ST676, ST810, ST811, ST34, and ST768), with both of the clinical and four of the oyster strains being identified as belonging to ST8. Using wgMLST, we showed that the ST8 strains from clinical and oyster samples were nearly indistinguishable and belonged to the same outbreak, confirming that local oysters were the source of the infections. The remaining oyster strains were genetically diverse, differing in >3,000 loci from the Maryland ST8 strains. eBURST analysis comparing these strains with strains of other STs available at the V. parahaemolyticus MLST website showed that the Maryland ST8 strains belonged to a clonal complex endemic to Asia. This indicates that the ST8 isolates from clinical and oyster sources were likely not endemic to Maryland. Finally, this study demonstrates the utility of whole-genome sequencing (WGS) and associated analyses for source-tracking investigations.

IMPORTANCE

Vibrio parahaemolyticus is an important foodborne pathogen and the leading cause of bacterial infections in the United States associated with the consumption of seafood. In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to oyster consumption. Strains isolated from stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). The oysters also contained other potentially pathogenic V. parahaemolyticus strains with different PFGE patterns. Since their identity, genetic makeup, relatedness, and potential pathogenicity were unknown, their genomes were determined by using next-generation sequencing. Whole-genome sequencing (WGS) analysis by whole-genome multilocus sequence typing (wgMLST) allowed (i) identification of clinical and oyster strains with matching PFGE profiles as belonging to ST8, (ii) determination of oyster strain diversity, and (iii) identification of the clinical strains as belonging to a clonal complex (CC) described only in Asia. Finally, WGS and associated analyses demonstrated their utility for trace-back investigations.

Biocontrol and Rapid Detection of Food-Borne Pathogens Using Bacteriophages and Endolysins

Bacteriophages have been suggested as natural food preservatives as well as rapid detection materials for food-borne pathogens in various foods. Since Listeria monocytogenes-targeting phage cocktail (ListShield) was approved for applications in foods, numerous phages have been screened and experimentally characterized for phage applications in foods. A single phage and phage cocktail treatments to various foods contaminated with food-borne pathogens including E. coli O157:H7, Salmonella enterica, Campylobacter jejuni, Listeria monocytogenes, Staphylococcus aureus, Cronobacter sakazakii, and Vibrio spp. revealed that they have great potential to control various food-borne pathogens and may be alternative for conventional food preservatives. In addition, phage-derived endolysins with high host specificity and host lysis activities may be preferred to food applications rather than phages. For rapid detection of food-borne pathogens, cell-wall binding domains (CBDs) from endolysins have been suggested due to their high host-specific binding. Fluorescence-tagged CBDs have been successfully evaluated and suggested to be alternative materials of expensive antibodies for various detection applications. Most recently, reporter phage systems have been developed and tested to confirm their usability and accuracy for specific detection. These systems revealed some advantages like rapid detection of only viable pathogenic cells without interference by food components in a very short reaction time, suggesting that these systems may be suitable for monitoring of pathogens in foods. Consequently, phage is the next-generation biocontrol agent as well as rapid detection tool to confirm and even identify the food-borne pathogens present in various foods.

Emerging Seafood Preservation Techniques to Extend Freshness and Minimize Vibrio Contamination

Globally, the popularity of seafood consumption is increasing exponentially. To meet the demands of a growing market, the seafood industry has increasingly been innovating ways to keep their products fresh and safe while increasing production. Marine environments harbor several species of indigenous microorganisms, some of which, including Vibrio spp., may be harmful to humans, and all of which are part of the natural microbiota of the seafood. After harvest, seafood products are often shipped over large geographic distances, sometimes for prolonged periods, during which the food must stay fresh and pathogen proliferation must be minimized. Upon arrival there is often a strong desire, arising from both culinary and nutritional considerations, to consume seafood products raw, or minimally cooked. This supply chain along with popular preferences have increased challenges for the seafood industry. This has resulted in a desire to develop methodologies that reduce pathogenic and spoilage organisms in seafood items to comply with regulations and result in minimal changes to the taste, texture, and nutritional content of the final product. This mini-review discusses and compares several emerging technologies, such as treatment with plant derived natural compounds, phage lysis, high-pressure processing, and irradiation for their ability to control pathogenic vibrios, limit the growth of spoilage organisms, and keep the desired organoleptic properties of the seafood product intact.

Isolation and Comparative Genomic Analysis of T1-Like Shigella Bacteriophage pSf-2

The increasing prevalence of antibiotic-resistant Shigella sp. emphasizes that alternatives to conventional antibiotics are needed. Siphoviridae bacteriophage (phage), pSf-2, infecting S. flexneri ATCC(®) 12022 was isolated from Geolpocheon stream in Korea. Morphological analysis by transmission electron microscopy revealed that pSf-2 has a head of about 57 ± 4 nm in diameter with a long tail of 136 ± 3 nm in length and 15 ± 2 nm in width. One-step growth analysis revealed that pSf-2 has latent period of 30 min and burst size of 16 PFU/infected cell. The DNA genome of pSf-2 is composed of 50,109 bp with a G+C content of 45.44 %. The genome encodes 83 putative ORFs, 19 putative promoters, and 23 transcriptional terminator regions. Genome sequence analysis of pSf-2 and comparative analysis with the homologous T1-like Shigella phages, Shfl1 and pSf-1, revealed that pSf-2 is a novel T1-like Shigella phage. These results showed that pSf-2 might have a high potential as a biocontrol agent to control shigellosis. Also, the genomic information may lead to further understanding of phage biodiversity, especially T1-like phages.

Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece

Vibrio parahaemolyticus is an important foodborne pathogen responsible for gastroenteritis outbreaks globally. It has also been identified as an important pathogen in aquatic organisms. Here, we report a draft genome sequence of V. parahaemolyticus, strain VH3, isolated from farmed juvenile greater amberjack, Seriola dumerili, in Greece.