Comparative genomic analysis of novel bacteriophages infecting Vibrio parahaemolyticus isolated from western and southern coastal areas of Korea

Isolation and characterization of a novel lytic bacteriophage Pv27 with biocontrol potential against Vibrio parahaemolyticus infections in shrimp

Background

Vibrio parahaemolyticus is a major disease-causing species of Vibrio that is pathogenic to both farmed shrimp and humans. With the increasing spread of antibiotic-resistant V. parahaemolyticus strains, bacteriophages (or phages) are considered potential agents for biocontrol as an alternative to antibiotics. In this study, a bacteriophage capable of lysing V. parahaemolyticus, named Pv27, was isolated, characterized, and evaluated for its potential to control Vibrio infections as a natural therapy.

Methods

Phage Pv27 was isolated using the double-layer agar technique and its morphology was characterized by transmission electron microscopy (TEM). We further assessed the host range specificity, optimal multiplicity of infection (MOI), one-step growth kinetics, and environmental stability of Pv27 under various pH and temperature conditions. The inhibitory activity of Pv27 against V. parahaemolyticus was evaluated in vitro. Finally, genomic analysis of Pv27 was conducted through whole-genome sequencing, followed by functional annotation of open reading frames (ORFs) and phylogenetic analysis.

Results

Phage Pv27 exhibited a Myovirus-like morphology, characterized by an icosahedral head (92.7 ± 2 nm) and a contractile tail (103 ± 11 nm), and belongs to the class Caudoviricetes. Pv27 demonstrated high lytic activity against its host cells, with a short latent period of approximately 25 minutes and a large burst size of 112 plaque-forming units (PFU) per infected cell. The phage displayed significant tolerance to a wide pH range (from 3 to 11) and remained heat-stable at temperatures up to 60 °C for 90 min. Genetically, Pv27 possesses a circular double-stranded DNA genome spanning 191,395 base pairs, with a G + C content of 35% and comprising 355 open reading frames (ORFs). Remarkably, up to 23 tRNA genes were identified in its genome, while no genes associated with antibiotic resistance, virulence, or lysogeny were detected, suggesting its potential as a valuable biocontrol agent. Results from the VIRIDIC, Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses revealed that Pv27 is closely related to the two known Vibrio phages, phiKT1024 and phiTY18. Several genes associated with enhanced environmental competitiveness were also identified in the Pv27 genome, including those encoding a PhoH-like phosphate starvation-inducible protein and endolysin. Phage Pv27 effectively lyses V. parahaemolyticus highlighting its potential as a biocontrol agent.

Complete genome sequence of Vibrio diabolicus bacteriophage vB_Vc_SrVc2 and its efficacy as prophylactic phage therapy

Vibrio diabolicus is widely distributed in the marine environment and is an important pathogen of aquatic organisms such as shrimp, fish, and mollusks. The emergence of multi-drug resistance among these bacteria has resulted in a global public health problem, which requires alternative treatment approaches, such as phage therapy. In the present study, we isolated the phage vB_Vc_SrVc2 from the hepatopancreas of white shrimp showing symptoms of acute hepatopancreatic necrosis disease (AHPND) and evaluated the efficacy of this phage in preventing the mortality associated with V. diabolicus presence in shrimp culture. Phage vB_Vc_SrVc2 belongs to the genus Maculvirus within the family Autographiviridae and demonstrates high lytic ability against Vibrio isolates. It exhibits substantial resilience across a broad range of temperatures, salinity levels, UV radiation and chloroform exposure. The phage genome size is 43,157 bp, with a GC content of 49.2%, that encodes 49 putative ORFs, and no tRNAs. Compared to phage vB_Vc_SrVc9, it shows three single nucleotide polymorphisms, two small deletions, and one nucleotide insertion, which result in slightly different infectivity profiles. No lysogeny-related genes were detected in the vB_Vc_SrVc2 genome. In vivo trials revealed that the phage offered protection against V. diabolicus infection by delaying mortality onset by at least 40 h post-infection (hpi). Although phage vB_Vc_SrVc2 alone significantly reduced mortality associated with V. diabolicus infection, this capacity could be enhanced with multiple doses and/or the use of phage cocktails or probiotics. Overall, phage vB_Vc_SrVc2 shows promising potential for therapeutic application in the aquaculture industry against V. diabolicus infections.

Characterization and genomic analysis of a broad-spectrum lytic phage PG288: A potential natural therapy candidate for Vibrio infections

Vibrio parahaemolyticus, an important zoonotic pathogen, can cause severe diseases and even death in aquatic animals and humans. As the widespread use of antibiotics gradually diminishes their effectiveness, phages, which can selectively lyse bacteria, are garnering increased attention as a valuable alternative antibacterial strategy. This study characterized PG288, a lytic phage utilizing V. parahaemolyticus strain G855 as its host. Morphologically, the phage features a polyhedral head and a long, non-retractable tail. Bactericidal assays revealed that phage PG288 exhibited a strong lytic ability against V. parahaemolyticus strain G855 and demonstrated a broad host range, as evidenced by the ability to infect several distinct Vibrio species. The one-step growth curve indicated a latent period of approximately 50 min for phage PG288, with a burst size of roughly 92 PFU per cell. Additionally, phage PG288 exhibited remarkable stability within a temperature range of 20-50°C and a pH range of 4-10. Genomic analysis unveiled 105 ORFs within phage PG288, notably devoid of genes associated with antibiotic resistance, virulence, and lysogenic activity. Phylogenetic analysis conclusively identified it as a new member of the genus Mardecavirus within the class Caudoviricetes. In summary, this study contributes valuable insights to the phage database, presenting phage PG288 as a promising candidate for phage therapies against Vibrio infections.

Role of Bacteriophages in the Evolution of Pathogenic Vibrios and Lessons for Phage Therapy

Viruses of bacteria, i.e., bacteriophages (or phages for short), were discovered over a century ago and have played a major role as a model system for the establishment of the fields of microbial genetics and molecular biology. Despite the relative simplicity of phages, microbiologists are continually discovering new aspects of their biology including mechanisms for battling host defenses. In turn, novel mechanisms of host defense against phages are being discovered at a rapid clip. A deeper understanding of the arms race between bacteria and phages will continue to reveal novel molecular mechanisms and will be important for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections, respectively. Here we delve into the molecular interactions of Vibrio species and phages.

Characterization and Genomic Analysis of Novel Vibrio parahaemolyticus Phage vB_VpaP_DE10

In the present study, a novel lytic Vibrio parahaemolyticus phage, vB_VpaP_DE10, was isolated from sewage samples collected in Guangzhou city, China. Transmission electron microscopy revealed that phage vB_VpaP_DE10 has an icosahedral head (52.4 ± 2.5 nm) and a short non-contracted tail (21.9 ± 1.0 nm). Phage vB_VpaP_DE10 lysed approximately 31% (8/26) of the antibiotic-resistant V. parahaemolyticus strains tested. A one-step growth curve showed that phage vB_VpaP_DE10 has a relatively long latency time of 25 min and a burst size of ~19 PFU per cell. The genome of phage vB_VpaP_DE10 is a 42,871-bp-long dsDNA molecule with a G + C content of 49.19% and is predicted to contain 46 open reading frames, 26 of which are predicted to be related to functions such as phage structure, packaging, host lysis, and DNA metabolism. Sequence comparisons suggested that vB_VpaP_DE10 is a member of the genus Maculvirus within the family Autographiviridae. Morphological and genomic analysis indicated that vB_VpaP_DE10 is a novel V. parahaemolyticus phage.

Isolation and Characterization of a Lytic Vibrio parahaemolyticus Phage vB_VpaP_GHSM17 from Sewage Samples

Vibrio parahaemolyticus is a major foodborne pathogen and the main cause of diarrheal diseases transmitted by seafood such as fish, shrimp, and shellfish. In the current study, a novel lytic phage infecting V. parahaemolyticus, vB_VpaP_GHSM17, was isolated from the sewage of a seafood market, Huangsha, Guangzhou, and its morphology, biochemistry, and taxonomy features were identified. Morphological observation revealed that GHSM17 had an icosahedral head with a short, non-contractile tail. The double-stranded DNA genome of GHSM17 consisted of 43,228 bp with a GC content of 49.42%. In total, 45 putative ORFs were identified in the GHSM17 genome. Taxonomic analysis indicated GHSM17 belonging to genus Maculvirus, family Autographiviridae. In addition, GHSM17 was stable over a wide range of temperatures (20-60 °C) and pH (5-11) and was completely inactivated after 70 min of ultraviolet irradiation. The bacterial inhibition assay revealed that GHSM17 could inhibit the growth of V. parahaemolyticus within 8 h. The results support that phage GHSM17 may be a potential candidate in the biological control of V. parahaemolyticus contamination in aquaculture.

Isolation and Characterization of a Lytic Vibriophage OY1 and Its Biocontrol Effects Against Vibrio spp

Vibrio species are important pathogens of marine animals and aquaculture populations and some of them can cause serious infections in humans through consumption of contaminated seafood and aquaculture products. Lytic bacteriophages can potentially alleviate Vibrio contamination in the aquaculture organisms and in the processing of aquatic products and have gained significant scientific attention in recent years. In the present study, bacteriophages were isolated from sewage of local aquatic products markets and grown using Vibrio mimicus CICC 21613 as host cells. The lytic vibriophage OY1 belonging to the newly proposed family Autographiviridae and the genus Maculvirus was identified by observation under electron microscope and comparative genomic analysis. The phage OY1 showed lytic activity against 24 among 32 tested strains belonging to eight Vibrio species. The complete phage OY1 genome consists of a single circular double-stranded DNA of 43,479 bp with a total GC content of 49.27% and was predicted to encode 40 open reading frames (ORFs). To evaluate its potential against vibrios, the one-step growth curve, thermal and pH stability, host range, and lytic activity of the OY1 phage against Vibrio species were evaluated. The results showed that phage OY1 had a range of thermal and pH tolerance, and exhibited a significant inhibitory effect on the growth of tested Vibrio species. Bacterial growth in the fish muscle extract juice (FMEJ) inoculated with Vibrio mimicus CICC 21613, Vibrio parahaemolyticus CICC 21617, Vibrio alginolyticus VJ14, and the mixed bacterial culture was reduced by 2.65 log CFU/ml, 2.42 log CFU/ml, 1.93 log CFU/ml, and 2.01 log CFU/ml, respectively, by incubation with phage OY1 at 25°C for 36 h. Phage OY1 also showed a strong ability to prevent biofilm formation and destroy formed Vibrio species biofilms. These results indicate that phage OY1 is a potential biocontrol agent against Vibrio species in the aquaculture industry and in food safety control.

Isolation and characterization of vibriophage vB_Vc_SrVc9: an effective agent in preventing Vibrio campbellii infections in brine shrimp nauplii (Artemia franciscana)

AIMS

This study describes the physicochemical and genomic characterization of phage vB_Vc_SrVc9 and its potential for phage therapy application against a pathogenic Vibrio campbellii strain.

METHODS AND RESULTS

A lytic phage vB_Vc_SrVc9 against V. campbellii was isolated from shrimp farm sediment, and characterized physicochemical and genomically. The use of vB_Vc_SrVc9 phage increased the survival in brine shrimp Artemia franciscana and reduced presumptive V. campbellii to nondetectable numbers. Genomic analysis showed a genome with a single contig of 43·15 kb, with 49 predicted genes and no tRNAs, capable of recognizing and generating complete inhibition zones of three Vibrio sp.

CONCLUSIONS

To our knowledge vB_Vc_SrVc9 is a lytic phage that could be used against Vibrio infections, reducing vibrio presence without any apparent impact over the natural microbiota at the family level in 28 libraries tested.

SIGNIFICANCE AND IMPACT OF THE STUDY

vB_Vc_SrVC9 is a novel phage and ecofriendly alternative for therapeutic applications and biotechnological purposes because is stable at different environmental conditions, has the potential to eliminate several strains, and has a short latent period with a good burst size. Therefore, the use of phages, which are natural killers of bacteria, represents a promising strategy to reduce the mortality of farmed organisms caused by pathogenic bacteria.

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

The gut microbiome harbors a ‘silent reservoir’ of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through horizontal gene transfer (HGT). To counteract the spread of AR, it is paramount to know which organisms harbor mobile AR genes and which organisms engage in HGT. Despite methods that characterize the overall abundance of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) encoding AR genes. Here, we apply Hi-C, a high-throughput, culture-independent method, to surveil the bacterial carriage of MGEs. We compare two healthy individuals with seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics, and are acutely vulnerable to the threat of multidrug-resistant infections. We find distinct networks of HGT across individuals, though AR and mobile genes are associated with more diverse taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT occurs frequently over a several-week period in both cohorts. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process.

Linking antibiotic resistance (AR) in the gut microbiome with their bacterial hosts remains challenging. Here, the authors apply bacterial Hi-C to map mobile genetic elements in metagenomes, and illustrate that genes are present in more diverse taxa in neutropenic patients than healthy subjects.