Identification of Vibrio parahaemolyticus and Vibrio spp. Specific Outer Membrane Proteins by Reverse Vaccinology and Surface Proteome

Global landscape of Vibrio parahaemolyticus research: a bibliometric analysis

Vibrio parahaemolyticus poses a notable threat to marine ecosystems and can cause infections and disease outbreaks in seafood species, which can affect humans upon consumption. The global impacts of such infections and outbreaks on human and animal health led to a growing number of studies from various countries discussing the prevention, control, treatment, and overall implications of V. parahaemolyticus. Hence, this study aims to retrieve relevant studies on V. parahaemolyticus using a bibliometric analysis to understand current research status, trends, and hotspots regarding this bacteria. Relevant literature was searched across the Scopus database, and the data were subsequently analyzed using Biblioshiny software. In addition, a manual examination was conducted to identify the hosts of V. parahaemolyticus and diseases caused by the bacteria. Overall, 7,096 records were obtained from Scopus from 1963 to 2023. A bibliometric analysis identified 17,220 authors, with China emerging as the global leader. The analysis also highlighted significant keywords such as "Vibrio parahaemolyticus," "Litopenaeus vannamei," and "innate immunity," suggesting a focus on the impact of V. parahaemolyticus on L. vannamei, specifically emphasizing the shrimp's innate immune responses. Host-disease interaction network also uncovered 53 interactions between hosts and diseases involving L. vannamei or Penaeus vannamei as the primary host, with acute hepatopancreas necrosis disease (AHPND) emerging as the most prevalent among them. This study can enhance our understanding of infections caused by V. parahaemolyticus and contribute to the development of effective strategies for their prevention and management.

Proteomic Analysis of the Fish Pathogen Vibrio ordalii Strain Vo-LM-18 and Its Outer Membrane Vesicles

Vibrio ordalii is the causative agent of atypical vibriosis in salmonids cultured in Chile. While extensive research provides insights into V. ordalii through phenotypic, antigenic, and genetic typing, as well as various virulence mechanisms, proteomic characterization remains largely unexplored. This study aimed to advance the proteomic knowledge of Chilean V. ordalii Vo-LM-18 and its OMVs, which have known virulence. Using Nano-UHPLC-LC-MS/MS, we identified 2242 proteins and 1755 proteins in its OMVs. Of these, 644 unique proteins were detected in V. ordalii Vo-LM-18, namely 156 unique proteins in its OMVs and 1596 shared proteins. The major categories for the OMVs were like those in the bacteria (i.e., cytoplasmic and cytoplasmic membrane proteins). Functional annotation identified 37 biological pathways in V. ordalii Vo-LM-18 and 28 in its OMVs. Proteins associated with transport, transcription, and virulence were predominant in both. Evident differences in protein expression were found. OMVs expressed a higher number of virulence-associated proteins, including those related to iron- and heme-uptake mechanisms. Notable pathways in the bacteria included flagellum assembly, heme group-associated proteins, and protein biosynthesis. This proteomic analysis is the first to detect the RTX toxin in a V. ordalii strain (Vo-LM-18) and its vesicles. Our results highlight the crucial role of OMVs in the pathogenesis and adaptation of V. ordalii, suggesting use as potential diagnostic biomarkers and therapeutic targets for bacterial infections.

Comprehensive in silico analyses of fifty-one uncharacterized proteins from Vibrio cholerae

Due to the rise of multidrug-resistant strains of Vibrio cholerae and the recent cholera outbreaks in African and Asian nations, it is imperative to identify novel therapeutic targets and possible vaccine candidates. In this regard, this work primarily aims to identify and characterize new antigenic molecules using comparative RNA sequencing data and label-free proteomics data, carried out with essential GTPase cgtA knockdown and wild-type strain of V. cholerae. We identified hitherto 51 characterized proteins from high-throughput RNA-sequencing and proteomics data. This work involved the assessment of their physicochemical characteristics, subcellular localization, solubility, structures, and functional annotations. In addition, the immunoinformatic and reverse vaccinology technique was used to find new vaccine targets with high antigenicity, low allergenicity, and low toxicity profiles. Among the 51 proteins, 24 were selected based on their immunogenic profiles to identify B/T-cell epitopes. In addition, 20 prospective therapeutic targets were identified using virulence predictions and related investigations. Furthermore, two proteins, UniProt ID- Q9KRD2 and Q9KU58, with molecular weight of 92kDa and 12kDa, respectively, were chosen for cloning and expression towards in vitro biochemical characterization based on their range of expression patterns, high antigenic, low allergenic, and low toxicity properties. In conclusion, we believe that this study will reveal new facets and avenues for drug discovery and put us a step forward toward novel therapeutic interventions against the deadly disease of cholera.

Genome sequencing analysis and validation of infestation-related functional genes of Vibrio parahaemolyticus LG2206 isolated from the hepatopancreas of diseased mud crab (Scylla paramamosain) in South China

Vibrio parahaemolyticus (V. parahaemolyticus) is a major bacterial pathogen found in brackish environments, leading to disease outbreaks and great economic losses in the mud crab industry. This study investigated the molecular mechanism of V. parahaemolyticus infecting mud crabs through genome sequencing analysis, survival experiments, and the expression patterns of related functional genes. A strain of V. parahaemolyticus with high pathogenicity and lethality was isolated from diseased mud crab in South China. The genome sequencing results showed that the genome size of V. parahaemolyticus was a circular chromosome of 3,357,271 bp, with a GC content of 45 %, containing 2985 protein-coding genes, denoted as V. parahaemolyticus LG2206. Genome analysis data revealed that a total of 113 adherence coding genes were obtained, including 120 virulence factor coding genes, 37 type III secretion system (T3SS) coding genes, and 277 sequences of T3SS effectors. Survival experiments showed that the mortality was 20 % within 96 h in the 1 × 104 CFU/mL infection group, 90 % in the 3.2 × 105 CFU/mL treatment group, and 100 % in the 1 × 106 CFU/mL treatment group. The LD50 of V. parahaemolyticus LG2206 was determined as 4.6 × 104 CFU/mL. Six genes of znuA and fliD (flagellin encoding genes), yscE and yscR (T3SS encoding genes), and nfuA and htpX (virulence factor encoding genes) were selected and validated by quantitative real-time PCR analysis after infection with 4.6 × 104 CFU/mL of V. parahaemolyticus LG2206 for 96 h. The expression of the six genes exhibited a significant up-regulation trend at all tested time points. The results indicated that the infestation-related genes screened in the experiment play important roles in the infestation process. This study provides timely and effective information to further analyze the molecular mechanism of V. parahaemolyticus infection and develop comprehensive measures for disease prevention and control.

Maintenance of bacterial outer membrane lipid asymmetry: insight into MlaA

The outer membrane (OM) of Gram-negative bacteria acts as an effective barrier to protect against toxic compounds. By nature, the OM is asymmetric with the highly packed lipopolysaccharide (LPS) at the outer leaflet and glycerophospholipids at the inner leaflet. OM asymmetry is maintained by the Mla system, in which is responsible for the retrograde transport of glycerophospholipids from the OM to the inner membrane. This system is comprised of six Mla proteins, including MlaA, an OM lipoprotein involved in the removal of glycerophospholipids that are mis-localized at the outer leaflet of the OM. Interestingly, MlaA was initially identified - and called VacJ - based on its role in the intracellular spreading of Shigella flexneri.Many open questions remain with respect to the Mla system and the mechanism involved in the translocation of mislocated glycerophospholipids at the outer leaflet of the OM, by MlaA. After summarizing the current knowledge on MlaA, we focus on the impact of mlaA deletion on OM lipid composition and biophysical properties of the OM. How changes in OM lipid composition and biophysical properties can impact the generation of membrane vesicles and membrane permeability is discussed. Finally, we explore whether and how MlaA might be a candidate for improving the activity of antibiotics and as a vaccine candidate.Efforts dedicated to understanding the relationship between the OM lipid composition and the mechanical strength of the bacterial envelope and, in turn, how such properties act against external stress, are needed for the design of new targets or drugs for Gram-negative infections.

BacScan: a novel genome-wide strategy for uncovering broadly immunogenic proteins in bacteria

In response to the global threat posed by bacterial pathogens, which are the second leading cause of death worldwide, vaccine development is challenged by the diversity of bacterial serotypes and the lack of immunoprotection across serotypes. To address this, we introduce BacScan, a novel genome-wide technology for the rapid discovery of conserved highly immunogenic proteins (HIPs) across serotypes. Using bacterial-specific serum, BacScan combines phage display, immunoprecipitation, and next-generation sequencing to comprehensively identify all the HIPs in a single assay, thereby paving the way for the development of universally protective vaccines. Our validation of this technique with Streptococcus suis, a major pathogenic threat, led to the identification of 19 HIPs, eight of which conferred 20-100% protection against S. suis challenge in animal models. Remarkably, HIP 8455 induced complete immunity, making it an exemplary vaccine target. BacScan's adaptability to any bacterial pathogen positions it as a revolutionary tool that can expedite the development of vaccines with broad efficacy, thus playing a critical role in curbing bacterial transmission and slowing the march of antimicrobial resistance.

Transcriptomic Profiles of Vibrio parahaemolyticus During Biofilm Formation

Vibrio parahaemolyticus, the leading cause of bacterial seafood-associated gastroenteritis, can form biofilms. In this work, the gene expression profiles of V. parahaemolyticus during biofilm formation were investigated by transcriptome sequencing. A total of 183, 503, and 729 genes were significantly differentially expressed in the bacterial cells at 12, 24 and 48 h, respectively, compared with that at 6 h. Of these, 92 genes were consistently activated or repressed from 6 to 48 h. The genes involved in polar flagellum, chemotaxis, mannose-sensitive haemagglutinin type IV pili, capsular polysaccharide, type III secretion system 1 (T3SS1), T3SS2, thermostable direct hemolysin (TDH), type VI secretion system 1 (T6SS1) and T6SS2 were downregulated, whereas those involved in V. parahaemolyticus pathogenicity island (Vp-PAI) (except for T3SS2 and TDH) and membrane fusion proteins were upregulated. Three extracellular protease genes (vppC, prtA and VPA1071) and a dozen of outer membrane protein encoding genes were also significantly differentially expressed during biofilm formation. In addition, five putative c-di-GMP metabolism-associated genes were significantly differentially expressed, which may account for the drop in c-di-GMP levels after the beginning of biofilm formation. Moreover, many putative regulatory genes were significantly differentially expressed, and more than 1000 putative small non-coding RNAs were detected, suggesting that biofilm formation was tightly regulated by complex regulatory networks. The data provided a global view of gene expression profiles during biofilm formation, showing that the significantly differentially expressed genes were involved in multiple cellular pathways, including virulence, biofilm formation, metabolism, and regulation.

The Screening of the Protective Antigens of Aeromonas hydrophila Using the Reverse Vaccinology Approach: Potential Candidates for Subunit Vaccine Development

The threat of bacterial septicemia caused by Aeromonas hydrophila infection to aquaculture growth can be prevented through vaccination, but differences among A. hydrophila strains may affect the effectiveness of non-conserved subunit vaccines or non-inactivated A. hydrophila vaccines, making the identification and development of conserved antigens crucial. In this study, a bioinformatics analysis of 4268 protein sequences encoded by the A. hydrophila J-1 strain whole genome was performed based on reverse vaccinology. The specific analysis included signal peptide prediction, transmembrane helical structure prediction, subcellular localization prediction, and antigenicity and adhesion evaluation, as well as interspecific and intraspecific homology comparison, thereby screening the 39 conserved proteins as candidate antigens for A. hydrophila vaccine. The 9 isolated A. hydrophila strains from diseased fish were categorized into 6 different molecular subtypes via enterobacterial repetitive intergenic consensus (ERIC)-PCR technology, and the coding regions of 39 identified candidate proteins were amplified via PCR and sequenced to verify their conservation in different subtypes of A. hydrophila and other Aeromonas species. In this way, conserved proteins were screened out according to the comparison results. Briefly, 16 proteins were highly conserved in different A. hydrophila subtypes, of which 2 proteins were highly conserved in Aeromonas species, which could be selected as candidate antigens for vaccines development, including type IV pilus secretin PilQ (AJE35401.1) and TolC family outer membrane protein (AJE35877.1). The present study screened the conserved antigens of A. hydrophila by using reverse vaccinology, which provided basic foundations for developing broad-spectrum protective vaccines of A. hydrophila.

Recombinant expression and immunogenicity evaluation of a TonB-dependent receptor of Vibrio parahaemolyticus

This study constructed the recombinant plasmid of a TonB-dependent receptor from V. parahaemolyticus and evaluated the immunogenicity of the recombinant protein in mice. The TonB-dependent receptor gene (GI: 28901321) was obtained by PCR amplification and cloned into plasmid pET-32a (+). The recombinant plasmids were transformed into Escherichia coli BL21, and the protein expression was induced by isopropyl-β-d-thiogalactopyranoside (IPTG). The 6 × His-tagged TonB-dependent receptor inclusion bodies were purified by Ni-NTA Agarose column and renatured by gradient urea dialysis. The soluble and inclusion bodies of the TonB-dependent receptor were emulsified with Freund's adjuvant and subcutaneously injected into BALB/c mice. The serum titers with seven V. parahaemolyticus strains, eight Vibrio species, and nine other bacteria were studied by enzyme-linked immunosorbent assay and immunoblotting. The results showed that the serum homogenously bound the target protein in the V. parahaemolyticus cell lysates. The titers against the immunized protein were above 89K, while the titer against whole cells of seven V. parahaemolyticus strains ranged from 4.12K to 12.5K. However, the titers were higher for the soluble TonB-dependent receptor. The serums reacted with E. coli strains but did not cross-react with eight Vibrio species and Photobacterium damselae. These results showed that the TonB-dependent receptor proteins in this study were immunogenic, and the serums showed adequate specificity for V. parahaemolyticus. However, the availability of the TonB-dependent receptor on V. parahaemolyticus cells is probably limited.

Identification of vaccine and drug targets in Shigella dysenteriae sd197 using reverse vaccinology approach

Shigellosis is characterized as diarrheal disease that causes a high mortality rate especially in children, elderly and immunocompromised patients. More recently, the World Health Organization advised safe vaccine designing against shigellosis due to the emergence of Shigella dysenteriae resistant strains. Therefore, the aim of this study is to identify novel drug targets as well as the design of the potential vaccine candidates and chimeric vaccine models against Shigella dysenteriae. A computational based Reverse Vaccinology along with subtractive genomics analysis is one of the robust approaches used for the prioritization of drug targets and vaccine candidates through direct screening of genome sequence assemblies. Herein, a successfully designed peptide-based novel highly antigenic chimeric vaccine candidate against Shigella dysenteriae sd197 strain is proposed. The study resulted in six epitopes from outer membrane WP_000188255.1 (Fe (3+) dicitrate transport protein FecA) that ultimately leads to the construction of twelve vaccine models. Moreover, V9 construct was found to be highly immunogenic, non-toxic, non-allergenic, highly antigenic, and most stable in terms of molecular docking and simulation studies against six HLAs and TLRS/MD complex. So far, this protein and multiepitope have never been characterized as vaccine targets against Shigella dysenteriae. The current study proposed that V9 could be a significant vaccine candidate against shigellosis and to ascertain that further experiments may be applied by the scientific community focused on shigellosis.

Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation

The coronavirus disease 2019 (COVID-19) is an infectious disease that mainly affects the host respiratory system with ~ 80% asymptomatic or mild cases and ~ 5% severe cases. Recent genome-wide association studies (GWAS) have identified several genetic loci associated with the severe COVID-19 symptoms. Delineating the genetic variants and genes is important for better understanding its biological mechanisms. We implemented integrative approaches, including transcriptome-wide association studies (TWAS), colocalization analysis, and functional element prediction analysis, to interpret the genetic risks using two independent GWAS datasets in lung and immune cells. To understand the context-specific molecular alteration, we further performed deep learning-based single-cell transcriptomic analyses on a bronchoalveolar lavage fluid (BALF) dataset from moderate and severe COVID-19 patients. We discovered and replicated the genetically regulated expression of CXCR6 and CCR9 genes. These two genes have a protective effect on lung, and a risk effect on whole blood, respectively. The colocalization analysis of GWAS and cis-expression quantitative trait loci highlighted the regulatory effect on CXCR6 expression in lung and immune cells. In the lung-resident memory CD8⁺ T (T_RM) cells, we found a 2.24-fold decrease of cell proportion among CD8⁺ T cells and lower expression of CXCR6 in the severe patients than moderate patients. Pro-inflammatory transcriptional programs were highlighted in the T_RM cellular trajectory from moderate to severe patients. CXCR6 from the 3p21.31 locus is associated with severe COVID-19. CXCR6 tends to have a lower expression in lung T_RM cells of severe patients, which aligns with the protective effect of CXCR6 from TWAS analysis.