1
|
Khan S, Aziz S, Waqas M, Kakar MA, Ahmad S. Targeted vaccine development against Bilophila wadsworthia to curb colon diseases: A multiepitope approach based on reverse vaccinology and computational analysis. Int J Biol Macromol 2023; 250:126002. [PMID: 37506789 DOI: 10.1016/j.ijbiomac.2023.126002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
The presence of excessive hydrogen sulfide (H2S)-producing bacteria, particularly Bilophila wadsworthia in appendices, is linked to a weaker colonic mucus barrier, inflammatory bowel disease, and colorectal cancer. Thus, targeting this bacterium could reduce sulfide levels and address associated health concerns. Here, we utilized reverse vaccinology and immunoinformatics to design a chimeric vaccine against B. wadsworthia, focusing on membrane-bound and extracellular proteins. Subtractive proteome analysis identified 18 potential vaccine candidates (PVCs), from which six B-cell, eight CD8+ T cell, and six CD4+ T cell epitopes were predicted. Chosen epitopes were assessed for immunological properties and cross-reactivity with human and mouse proteomes. Subsequently, these epitopes were fused with appropriate linkers, PADRE epitope, TAT peptide, and Cholera Toxin B subunit adjuvant to form a robust multi-epitope vaccine (MEV). The MEV's tertiary structure was modelled and validated for reliable analysis. Molecular docking and dynamics simulations demonstrated stable binding of MEV with Toll-like receptor 4. The MEV showed favorable physicochemical characteristics, high expression potential in Escherichia coli, broad population coverage (∼98 %), and cross-protection against different B. wadsworthia strains. Immune simulation suggested induction of strong B and T cell responses, including primary, secondary, and tertiary immune responses. Further experimental studies are necessary to validate these findings.
Collapse
Affiliation(s)
- Sara Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and genetic Engineering, Hazara University, Mansehra 21120, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Oman
| | | | - Sohail Ahmad
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan.
| |
Collapse
|
2
|
Jiang Z, Kang X, Song Y, Zhou X, Yue M. Identification and Evaluation of Novel Antigen Candidates against Salmonella Pullorum Infection Using Reverse Vaccinology. Vaccines (Basel) 2023; 11:vaccines11040865. [PMID: 37112777 PMCID: PMC10143441 DOI: 10.3390/vaccines11040865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Pullorum disease, caused by the Salmonella enterica serovar Gallinarum biovar Pullorum, is a highly contagious disease in the poultry industry, leading to significant economic losses in many developing countries. Due to the emergence of multidrug-resistant (MDR) strains, immediate attention is required to prevent their endemics and global spreading. To mitigate the prevalence of MDR Salmonella Pullorum infections in poultry farms, it is urgent to develop effective vaccines. Reverse vaccinology (RV) is a promising approach using expressed genomic sequences to find new vaccine targets. The present study used the RV approach to identify new antigen candidates against Pullorum disease. Initial epidemiological investigation and virulent assays were conducted to select strain R51 for presentative and general importance. An additional complete genome sequence (4.7 Mb) for R51 was resolved using the Pacbio RS II platform. The proteome of Salmonella Pullorum was analyzed to predict outer membrane and extracellular proteins, and was further selected for evaluating transmembrane domains, protein prevalence, antigenicity, and solubility. Twenty-two high-scored proteins were identified among 4713 proteins, with 18 recombinant proteins successfully expressed and purified. The chick embryo model was used to assess protection efficacy, in which vaccine candidates were injected into 18-day-old chick embryos for in vivo immunogenicity and protective effects. The results showed that the PstS, SinH, LpfB, and SthB vaccine candidates were able to elicit a significant immune response. Particularly, PstS confers a significant protective effect, with a 75% survival rate compared to 31.25% for the PBS control group, confirming that identified antigens can be promising targets against Salmonella Pullorum infection. Thus, we offer RV to discover novel effective antigens in an important veterinary infectious agent with high priority.
Collapse
Affiliation(s)
- Zhijie Jiang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiamei Kang
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Song
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Zhou
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
3
|
Quinn C, Tomás-Cortázar J, Ofioritse O, Cosgrave J, Purcell C, McAloon C, Frost S, McClean S. GlnH, a Novel Antigen That Offers Partial Protection against Verocytotoxigenic Escherichia coli Infection. Vaccines (Basel) 2023; 11:175. [PMID: 36680019 PMCID: PMC9863631 DOI: 10.3390/vaccines11010175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Verotoxin-producing Escherichia coli (VTEC) causes zoonotic infections, with potentially devastating complications, and children under 5 years old are particularly susceptible. Antibiotic treatment is contraindicated, and due to the high proportion of infected children that suffer from severe and life-changing complications, there is an unmet need for a vaccine to prevent VTEC infections. Bacterial adhesins represent promising candidates for the successful development of a vaccine against VTEC. Using a proteomic approach to identify bacterial proteins interacting with human gastrointestinal epithelial Caco-2 and HT-29 cells, we identified eleven proteins by mass spectrometry. These included a glutamine-binding periplasmic protein, GlnH, a member of the ABC transporter family. The glnH gene was identified in 13 of the 15 bovine and all 5 human patient samples tested, suggesting that it is prevalent. We confirmed that GlnH is involved in the host cell attachment of an O157:H7 prototype E. coli strain to gastrointestinal cells in vitro. Recombinant GlnH was expressed and purified prior to the immunisation of mice. When alum was used as an adjuvant, GlnH was highly immunogenic, stimulating strong serological responses in immunised mice, and it resulted in a modest reduction in faecal shedding but did not reduce colonisation. GlnH immunisation with a T-cell-inducing adjuvant (SAS) also showed comparable antibody responses and an IgG1/IgG2a ratio suggestive of a mixed Th1/Th2 response but was partially protective, with a 1.5-log reduction in colonisation of the colon and caecum at 7 days relative to the adjuvant only (p = 0.0280). It is clear that future VTEC vaccine developments should consider the contribution of adjuvants in addition to antigens. Moreover, it is likely that a combined cellular and humoral response may prove more beneficial in providing protective interventions against VTEC.
Collapse
Affiliation(s)
- Conor Quinn
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute, University College Dublin, Belfield, Dublin 24, Ireland
- APC Ltd., Building 11, Cherrywood Business Park, Loughlinstown, D18 DH5 Co. Dublin, Ireland
| | - Julen Tomás-Cortázar
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute, University College Dublin, Belfield, Dublin 24, Ireland
| | - Oritsejolomi Ofioritse
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Joanne Cosgrave
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Claire Purcell
- Children’s Health Ireland (CHI) at Tallaght, Tallaght University Hospital, Tallaght, Dublin 24, Ireland
| | - Catherine McAloon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Susanna Frost
- Children’s Health Ireland (CHI) at Tallaght, Tallaght University Hospital, Tallaght, Dublin 24, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute, University College Dublin, Belfield, Dublin 24, Ireland
| |
Collapse
|
4
|
Yousaf M, Ullah A, Sarosh N, Abbasi SW, Ismail S, Bibi S, Hasan MM, Albadrani GM, Talaat Nouh NA, Abdulhakim JA, Abdel-Daim MM, Bin Emran T. Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach. Vaccines (Basel) 2022; 10:vaccines10081192. [PMID: 36016080 PMCID: PMC9414393 DOI: 10.3390/vaccines10081192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.
Collapse
Affiliation(s)
- Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan; (M.Y.); (N.S.)
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Nida Sarosh
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan; (M.Y.); (N.S.)
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan;
| | - Saba Ismail
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan;
- Correspondence: (S.I.); (S.B.)
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
- Correspondence: (S.I.); (S.B.)
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh;
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Nehal Ahmed Talaat Nouh
- Department of Microbiology, Medicine Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia;
- Inpatient Pharmacy, Mansoura University Hospitals, Mansoura 35516, Egypt
| | - Jawaher A. Abdulhakim
- Medical Laboratory Department, College of Applied Medical Sciences, Taibah University, Yanbu 46522, Saudi Arabia;
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia;
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| |
Collapse
|
5
|
Abbasi BA, Saraf D, Sharma T, Sinha R, Singh S, Sood S, Gupta P, Gupta A, Mishra K, Kumari P, Rawal K. Identification of vaccine targets & design of vaccine against SARS-CoV-2 coronavirus using computational and deep learning-based approaches. PeerJ 2022; 10:e13380. [PMID: 35611169 PMCID: PMC9124463 DOI: 10.7717/peerj.13380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/13/2022] [Indexed: 01/13/2023] Open
Abstract
An unusual pneumonia infection, named COVID-19, was reported on December 2019 in China. It was reported to be caused by a novel coronavirus which has infected approximately 220 million people worldwide with a death toll of 4.5 million as of September 2021. This study is focused on finding potential vaccine candidates and designing an in-silico subunit multi-epitope vaccine candidates using a unique computational pipeline, integrating reverse vaccinology, molecular docking and simulation methods. A protein named spike protein of SARS-CoV-2 with the GenBank ID QHD43416.1 was shortlisted as a potential vaccine candidate and was examined for presence of B-cell and T-cell epitopes. We also investigated antigenicity and interaction with distinct polymorphic alleles of the epitopes. High ranking epitopes such as DLCFTNVY (B cell epitope), KIADYNKL (MHC Class-I) and VKNKCVNFN (MHC class-II) were shortlisted for subsequent analysis. Digestion analysis verified the safety and stability of the shortlisted peptides. Docking study reported a strong binding of proposed peptides with HLA-A*02 and HLA-B7 alleles. We used standard methods to construct vaccine model and this construct was evaluated further for its antigenicity, physicochemical properties, 2D and 3D structure prediction and validation. Further, molecular docking followed by molecular dynamics simulation was performed to evaluate the binding affinity and stability of TLR-4 and vaccine complex. Finally, the vaccine construct was reverse transcribed and adapted for E. coli strain K 12 prior to the insertion within the pET-28-a (+) vector for determining translational and microbial expression followed by conservancy analysis. Also, six multi-epitope subunit vaccines were constructed using different strategies containing immunogenic epitopes, appropriate adjuvants and linker sequences. We propose that our vaccine constructs can be used for downstream investigations using in-vitro and in-vivo studies to design effective and safe vaccine against different strains of COVID-19.
Collapse
|
6
|
Attar R, Alatawi EA, Aba Alkhayl FF, Alharbi KN, Allemailem KS, Almatroudi A. Immunoinformatics and Biophysics Approaches to Design a Novel Multi-Epitopes Vaccine Design against Staphylococcus auricularis. Vaccines (Basel) 2022; 10:vaccines10050637. [PMID: 35632394 PMCID: PMC9146471 DOI: 10.3390/vaccines10050637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
Due to the misuse of antibiotics in our daily lives, antimicrobial resistance (AMR) has become a major health problem. Penicillin, the first antibiotic, was used in the 1930s and led to the emergence of AMR. Due to alterations in the microbe’s genome and the evolution of new resistance mechanisms, antibiotics are losing efficacy against microbes. There are high rates of mortality and morbidity due to antibiotic resistance, so addressing this major health issue requires new approaches. Staphylococcus auricularis is a Gram-positive cocci and is capable of causing opportunistic infections and sepsis. S. auricularis is resistant to several antibiotics and does not currently have a licensed vaccine. In this study, we used bacterial pan-genome analysis (BPGA) to study S. auricularis pan-genome and applied a reverse immunology approach to prioritize vaccine targets against S. auricularis. A total of 15,444 core proteins were identified by BPGA analysis, which were then used to identify good vaccine candidates considering potential vaccine filters. Two vaccine candidates were evaluated for epitope prediction including the superoxide dismutase and gamma-glutamyl transferase protein. The epitope prediction phase involved the prediction of a variety of B-Cell and T-cell epitopes, and the epitopes that met certain criteria, such as antigenicity, immunogenicity, non-allergenicity, and non-toxicity were chosen. A multi-epitopes vaccine construct was then constructed from all the predicted epitopes, and a cholera toxin B-subunit adjuvant was also added to increase vaccine antigenicity. Three-dimensional models of the vaccine were used for downward analyses. Using the best-modeled structure, binding potency was tested with MHC-I, MHC-II and TLR-4 immune cells receptors, proving that the vaccine binds strongly with the receptors. Further, molecular dynamics simulations interpreted strong intermolecular binding between the vaccine and receptors and confirmed the vaccine epitopes exposed to the host immune system. The results support that the vaccine candidate may be capable of eliciting a protective immune response against S. auricularis and may be a promising candidate for experimental in vitro and in vivo studies.
Collapse
Affiliation(s)
- Roba Attar
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah 21959, Saudi Arabia;
| | - Eid A. Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Faris F. Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (K.N.A.); (K.S.A.)
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Dentistry and Pharmacy, Buraydah Colleges, Buraydah 51418, Saudi Arabia
| | - Khloud Nawaf Alharbi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (K.N.A.); (K.S.A.)
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (K.N.A.); (K.S.A.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (K.N.A.); (K.S.A.)
- Correspondence:
| |
Collapse
|
7
|
El-Saadony MT, Salem HM, El-Tahan AM, Abd El-Mageed TA, Soliman SM, Khafaga AF, Swelum AA, Ahmed AE, Alshammari FA, Abd El-Hack ME. The control of poultry salmonellosis using organic agents: an updated overview. Poult Sci 2022; 101:101716. [PMID: 35176704 PMCID: PMC8857471 DOI: 10.1016/j.psj.2022.101716] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Salmonellosis is a severe problem that threatens the poultry sector worldwide right now. Salmonella gallinarium and Salmonella pullorum (Fowl typhoid) are the most pathogenic serovars in avian species leading to systemic infection resulting in severe economic losses in the poultry industry. Nontyphoidal serotypes of Salmonella (Paratyphoid disease) constitute a public health hazard for their involvement in food poisoning problems in addition to their zoonotic importance. Also, Salmonella species distribution is particularly extensive. They resisted environmental conditions that made it difficult to control their spread for a long time. Therefore, the current review aimed to through light on Salmonellosis in poultry with particular references to its pathogenesis, economic importance, immune response to Salmonella, Salmonella antibiotics resistance, possible methods for prevention and control of such problems using promising antibiotics alternatives including probiotics, prebiotics, symbiotics, organic acids, essential oils, cinnamaldehyde, chitosan, nanoparticles, and vaccines.
Collapse
Affiliation(s)
- Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University 12211, Giza, Egypt
| | - Amira M El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Taia A Abd El-Mageed
- Soil and Water Department, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Soliman M Soliman
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University 1221, Giza, Egypt
| | - Asmaa F Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt
| | - Ayman A Swelum
- Department of Animal production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University, Sharkia 44519, Egypt
| | - Ahmed E Ahmed
- Biology Department, College of Science, King Khalid University 61413 Abha, Saudi Arabia; Department of Theriogenology, Faculty of Veterinary Medicine, South Valley University 83523 Qena, Egypt
| | - Fahdah A Alshammari
- Department of Biology, College of Sciences and Literature, Northern Border University, Rafha 76312, Saudi Arabia
| | - Mohamed E Abd El-Hack
- Poultry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt.
| |
Collapse
|
8
|
Abstract
Tuberculosis (TB) is a highly contagious disease that mostly affects the lungs and is caused by a bacterial pathogen, Mycobacterium tuberculosis. The associated mortality rate of TB is much higher compared to any other disease and the situation is more worrisome by the rapid emergence of drug resistant strains. Bacillus Calmette-Guerin (BCG) is the only licensed attenuated vaccine available for use in humans however, many countries have stopped its use as it fails to confer protective immunity. Therefore, urgent efforts are required to identify new and safe vaccine candidates that are not only provide high immune protection but also have broad spectrum applicability. Considering this, herein, I performed an extensive computational vaccine analysis to investigate 200 complete sequenced genomes of M. tuberculosis to identify core vaccine candidates that harbor safe, antigenic, non-toxic, and non-allergic epitopes. To overcome literature reported limitations of epitope-based vaccines, I carried out additional analysis by designing a multi-epitopes vaccine to achieve maximum protective immunity as well as to make experimental follow up studies easy by selecting a vaccine that can be easily analyzed because of its favorable physiochemical profile. Based on these analyses, I identified two potential vaccine proteins that fulfill all required vaccine properties. These two vaccine proteins are diacylglycerol acyltransferase and ESAT-6-like protein. Epitopes: DSGGYNANS from diacylglycerol acyltransferase and AGVQYSRAD, ADEEQQQAL, and VSRADEEQQ from ESAT-6-like protein were found to cover all necessary parameters and thus used in a multi-epitope vaccine construct. The designed vaccine is depicting a high binding affinity for different immune receptors and shows stable dynamics and rigorous van der Waals and electrostatic binding energies. The vaccine also simulates profound primary, secondary, tertiary immunoglobulin production as well as high interleukins and interferons count. In summary, the designed vaccine is ideal to be evaluated experimentally to decipher its real biological efficacy in controlling drug resistant infections of M. tuberculosis.
Collapse
Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia.
| |
Collapse
|
9
|
Allemailem KS. A Comprehensive Computer Aided Vaccine Design Approach to Propose a Multi-Epitopes Subunit Vaccine against Genus Klebsiella Using Pan-Genomics, Reverse Vaccinology, and Biophysical Techniques. Vaccines (Basel) 2021; 9:1087. [PMID: 34696195 PMCID: PMC8540426 DOI: 10.3390/vaccines9101087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
Klebsiella is a genus of nosocomial bacterial pathogens and is placed in the most critical list of World Health Organization (WHO) for development of novel therapeutics. The pathogens of the genus are associated with high mortality and morbidity. Owing to their strong resistance profile against different classes of antibiotics and nonavailability of a licensed vaccine, urgent efforts are required to develop a novel vaccine candidate that can tackle all pathogenic species of the Klebsiella genus. The present study aims to design a broad-spectrum vaccine against all species of the Klebsiella genus with objectives to identify the core proteome of pathogen species, prioritize potential core vaccine proteins, analyze immunoinformatics of the vaccine proteins, construct a multi-epitopes vaccine, and provide its biophysical analysis. Herein, we investigated all reference species of the genus to reveal their core proteome. The core proteins were then subjected to multiple reverse vaccinology checks that are mandatory for the prioritization of potential vaccine candidates. Two proteins (TonB-dependent siderophore receptor and siderophore enterobactin receptor FepA) were found to fulfill all vaccine parameters. Both these proteins harbor several potent B-cell-derived T-cell epitopes that are antigenic, nonallergic, nontoxic, virulent, water soluble, IFN-γ producer, and efficient binder of DRB*0101 allele. The selected epitopes were modeled into a multi-epitope peptide comprising linkers and Cholera Toxin B adjuvant. For docking with innate immune and MHC receptors and afterward molecular dynamics simulations and binding free energy analysis, the vaccine structure was modeled for tertiary structure and refined for structural errors. To assess the binding affinity and presentation of the designed vaccine construct, binding mode and interactions analysis were performed using molecular docking and molecular dynamics simulation techniques. These biophysical approaches illustrated the vaccine as a good binder to the immune receptors and revealed robust interactions energies. The vaccine sequence was further translated to nucleotide sequence and cloned into an appropriate vector for expressing it at high rate in Escherichia coli K12 strain. In addition, the vaccine was illustrated to generate a good level of primary, secondary, and tertiary immune responses, proving good immunogenicity of the vaccine. Based on the reported results, the vaccine can be a good candidate to be evaluated for effectiveness in wet laboratory validation studies.
Collapse
Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| |
Collapse
|
10
|
Rawal K, Sinha R, Abbasi BA, Chaudhary A, Nath SK, Kumari P, Preeti P, Saraf D, Singh S, Mishra K, Gupta P, Mishra A, Sharma T, Gupta S, Singh P, Sood S, Subramani P, Dubey AK, Strych U, Hotez PJ, Bottazzi ME. Identification of vaccine targets in pathogens and design of a vaccine using computational approaches. Sci Rep 2021; 11:17626. [PMID: 34475453 PMCID: PMC8413327 DOI: 10.1038/s41598-021-96863-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
Antigen identification is an important step in the vaccine development process. Computational approaches including deep learning systems can play an important role in the identification of vaccine targets using genomic and proteomic information. Here, we present a new computational system to discover and analyse novel vaccine targets leading to the design of a multi-epitope subunit vaccine candidate. The system incorporates reverse vaccinology and immuno-informatics tools to screen genomic and proteomic datasets of several pathogens such as Trypanosoma cruzi, Plasmodium falciparum, and Vibrio cholerae to identify potential vaccine candidates (PVC). Further, as a case study, we performed a detailed analysis of the genomic and proteomic dataset of T. cruzi (CL Brenner and Y strain) to shortlist eight proteins as possible vaccine antigen candidates using properties such as secretory/surface-exposed nature, low transmembrane helix (< 2), essentiality, virulence, antigenic, and non-homology with host/gut flora proteins. Subsequently, highly antigenic and immunogenic MHC class I, MHC class II and B cell epitopes were extracted from top-ranking vaccine targets. The designed vaccine construct containing 24 epitopes, 3 adjuvants, and 4 linkers was analysed for its physicochemical properties using different tools, including docking analysis. Immunological simulation studies suggested significant levels of T-helper, T-cytotoxic cells, and IgG1 will be elicited upon administration of such a putative multi-epitope vaccine construct. The vaccine construct is predicted to be soluble, stable, non-allergenic, non-toxic, and to offer cross-protection against related Trypanosoma species and strains. Further, studies are required to validate safety and immunogenicity of the vaccine.
Collapse
Affiliation(s)
- Kamal Rawal
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India.
| | - Robin Sinha
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Bilal Ahmed Abbasi
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Amit Chaudhary
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Swarsat Kaushik Nath
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Priya Kumari
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - P Preeti
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Devansh Saraf
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Shachee Singh
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Kartik Mishra
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Pranjay Gupta
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Astha Mishra
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Trapti Sharma
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Srijanee Gupta
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Prashant Singh
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Shriya Sood
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Preeti Subramani
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Aman Kumar Dubey
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Ulrich Strych
- Texas Children's Hospital Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Peter J Hotez
- Texas Children's Hospital Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Biology, Baylor University, Waco, TX, USA
| | - Maria Elena Bottazzi
- Texas Children's Hospital Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Biology, Baylor University, Waco, TX, USA
| |
Collapse
|
11
|
Chatterjee S, Basak AJ, Nair AV, Duraivelan K, Samanta D. Immunoglobulin-fold containing bacterial adhesins: molecular and structural perspectives in host tissue colonization and infection. FEMS Microbiol Lett 2021; 368:6045506. [PMID: 33355339 DOI: 10.1093/femsle/fnaa220] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Immunoglobulin (Ig) domains are one of the most widespread protein domains encoded by the human genome and are present in a large array of proteins with diverse biological functions. These Ig domains possess a central structure, the immunoglobulin-fold, which is a sandwich of two β sheets, each made up of anti-parallel β strands, surrounding a central hydrophobic core. Apart from humans, proteins containing Ig-like domains are also distributed in a vast selection of organisms including vertebrates, invertebrates, plants, viruses and bacteria where they execute a wide array of discrete cellular functions. In this review, we have described the key structural deviations of bacterial Ig-folds when compared to the classical eukaryotic Ig-fold. Further, we have comprehensively grouped all the Ig-domain containing adhesins present in both Gram-negative and Gram-positive bacteria. Additionally, we describe the role of these particular adhesins in host tissue attachment, colonization and subsequent infection by both pathogenic and non-pathogenic Escherichia coli as well as other bacterial species. The structural properties of these Ig-domain containing adhesins, along with their interactions with specific Ig-like and non Ig-like binding partners present on the host cell surface have been discussed in detail.
Collapse
Affiliation(s)
- Shruti Chatterjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Aditya J Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Asha V Nair
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Kheerthana Duraivelan
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| |
Collapse
|
12
|
Ma C, McClean S. Mapping Global Prevalence of Acinetobacter baumannii and Recent Vaccine Development to Tackle It. Vaccines (Basel) 2021; 9:vaccines9060570. [PMID: 34205838 PMCID: PMC8226933 DOI: 10.3390/vaccines9060570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/16/2021] [Accepted: 05/22/2021] [Indexed: 12/23/2022] Open
Abstract
Acinetobacter baumannii is a leading cause of nosocomial infections that severely threaten public health. The formidable adaptability and resistance of this opportunistic pathogen have hampered the development of antimicrobial therapies which consequently leads to very limited treatment options. We mapped the global prevalence of multidrug-resistant A. baumannii and showed that carbapenem-resistant A. baumannii is widespread throughout Asia and the Americas. Moreover, when antimicrobial resistance rates of Acinetobacter spp. exceed a threshold level, the proportion of A. baumannii isolates from clinical samples surges. Therefore, vaccines represent a realistic alternative strategy to tackle this pathogen. Research into anti-A. baumannii vaccines have enhanced in the past decade and multiple antigens have been investigated preclinically with varying results. This review summarises the current knowledge of virulence factors relating to A. baumannii–host interactions and its implication in vaccine design, with a view to understanding the current state of A. baumannii vaccine development and the direction of future efforts.
Collapse
|
13
|
Dar HA, Ismail S, Waheed Y, Ahmad S, Jamil Z, Aziz H, Hetta HF, Muhammad K. Designing a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology. Sci Rep 2021; 11:11197. [PMID: 34045649 PMCID: PMC8159972 DOI: 10.1038/s41598-021-90868-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Mycobacteroides abscessus (Previously Mycobacterium abscessus) is an emerging microorganism of the newly defined genera Mycobacteroides that causes mainly skin and tissue diseases in humans. The recent availability of total 34 fully sequenced genomes of different strains belonging to this species has provided an opportunity to utilize this genomics data to gain novel insights and guide the development of specific antimicrobial therapies. In the present study, we collected collectively 34 complete genome sequences of M. abscessus from the NCBI GenBank database. Pangenome analysis was conducted on these genomes to understand the genetic diversity and to obtain proteins associated with its core genome. These core proteins were then subjected to various subtractive filters to identify potential antigenic targets that were subjected to multi-epitope vaccine design. Our analysis projected the open pangenome of M. abscessus containing 3443 core genes. After applying various stepwise filtration steps on the core proteins, a total of four potential antigenic targets were identified. Utilizing their constituent CD4 and CD8 T-cell epitopes, a multi-epitope based subunit vaccine was computationally designed. Sequence-based analysis as well as structural characterization revealed the immunological effectiveness of this designed vaccine. Further molecular docking, molecular dynamics simulation and binding free energy estimation with Toll-like receptor 2 indicated strong structural associations of the vaccine with the immune receptor. The promising results are encouraging and need to be validated by additional wet laboratory studies for confirmation.
Collapse
Affiliation(s)
- Hamza Arshad Dar
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Saba Ismail
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan.
| | - Sajjad Ahmad
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Zubia Jamil
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Hafsa Aziz
- Nuclear Medicine, Oncology, and Radiotherapy Institute, Islamabad, 44000, Pakistan
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, 71515, Egypt
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates.
| |
Collapse
|
14
|
Wang W, Liu J, Guo S, Liu L, Yuan Q, Guo L, Pan S. Identification of Vibrio parahaemolyticus and Vibrio spp. Specific Outer Membrane Proteins by Reverse Vaccinology and Surface Proteome. Front Microbiol 2021; 11:625315. [PMID: 33633699 PMCID: PMC7901925 DOI: 10.3389/fmicb.2020.625315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022] Open
Abstract
The discovery of outer membrane proteins (OMPs) with desirable specificity and surface availability is a fundamental challenge to develop accurate immunodiagnostic assay and multivalent vaccine of pathogenic Vibrio species in food and aquaculture. Herein 101 OMPs were systemically screened from 4,831 non-redundant proteins of Vibrio parahaemolyticus by bioinformatical predication of signaling peptides, transmembrane (TM) α-helix, and subcellular location. The sequence homology analysis with 32 species of Vibrio spp. and all the non-Vibrio strains revealed that 15 OMPs were conserved in at least 23 Vibrio species, including BamA (VP2310), GspD (VP0133), Tolc (VP0425), OmpK (VP2362), OmpW (VPA0096), LptD (VP0339), Pal (VP1061), flagellar L-ring protein (VP0782), flagellar protein MotY (VP2111), hypothetical protein (VP1713), fimbrial assembly protein (VP2746), VacJ lipoprotein (VP2214), agglutination protein (VP1634), and lipoprotein (VP1267), Chitobiase (VP0755); high adhesion probability of flgH, LptD, OmpK, and OmpW indicated they were potential multivalent Vibrio vaccine candidates. V. parahaemolyticus OMPs were found to share high homology with at least one or two Vibrio species, 19 OMPs including OmpA like protein (VPA073), CsuD (VPA1504), and MtrC (VP1220) were found relatively specific to V. parahaemolyticus. The surface proteomic study by enzymatical shaving the cells showed the capsular polysaccharides most likely limited the protease action, while the glycosidases improved the availability of OMPs to trypsin. The OmpA (VPA1186, VPA0248, VP0764), Omp (VPA0166), OmpU (VP2467), BamA (VP2310), TolC (VP0425), GspD (VP0133), OmpK (VP2362), lpp (VPA1469), Pal (VP1061), agglutination protein (VP1634), and putative iron (III) compound receptor (VPA1435) have better availability on the cell surface.
Collapse
Affiliation(s)
- Wenbin Wang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
| | - Jianxin Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Shanshan Guo
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Lei Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Qianyun Yuan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Lei Guo
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
| | - Saikun Pan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
| |
Collapse
|
15
|
Ali A, Kolenda R, Khan MM, Weinreich J, Li G, Wieler LH, Tedin K, Roggenbuck D, Schierack P. Novel Avian Pathogenic Escherichia coli Genes Responsible for Adhesion to Chicken and Human Cell Lines. Appl Environ Microbiol 2020; 86:e01068-20. [PMID: 32769194 PMCID: PMC7531953 DOI: 10.1128/aem.01068-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/02/2020] [Indexed: 12/13/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is a major bacterial pathogen of commercial poultry contributing to extensive economic losses and contamination of the food chain. One of the initial steps in bacterial infection and successful colonization of the host is adhesion to the host cells. A random transposon mutant library (n = 1,300) of APEC IMT 5155 was screened phenotypically for adhesion to chicken (CHIC-8E11) and human (LoVo) intestinal epithelial cell lines. The detection and quantification of adherent bacteria were performed by a modified APEC-specific antibody staining assay using fluorescence microscopy coupled to automated VideoScan technology. Eleven mutants were found to have significantly altered adhesion to the cell lines examined. Mutated genes in these 11 "adhesion-altered mutants" were identified by arbitrary PCR and DNA sequencing. The genes were amplified from wild-type APEC IMT 5155, cloned, and transformed into the respective adhesion-altered mutants, and complementation was determined in adhesion assays. Here, we report contributions of the fdtA, rluD, yjhB, ecpR, and fdeC genes of APEC in adhesion to chicken and human intestinal cell lines. Identification of the roles of these genes in APEC pathogenesis will contribute to prevention and control of APEC infections.IMPORTANCE Avian pathogenic E. coli is not only pathogenic for commercial poultry but can also cause foodborne infections in humans utilizing the same attachment and virulence mechanisms. Our aim was to identify genes of avian pathogenic E. coli involved in adhesion to chicken and human cells in order to understand the colonization and pathogenesis of these bacteria. In contrast to the recent studies based on genotypic and bioinformatics data, we have used a combination of phenotypic and genotypic approaches for identification of novel genes contributing to adhesion in chicken and human cell lines. Identification of adhesion factors remains important, as antibodies elicited against such factors have shown potential to block colonization and ultimately prevent disease as prophylactic vaccines. Therefore, the data will augment the understanding of disease pathogenesis and ultimately in designing strategies against the infections.
Collapse
Affiliation(s)
- Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
- Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Muhammad Moman Khan
- Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jörg Weinreich
- Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | | | - Karsten Tedin
- Institute for Microbiology and Epizootics, Free University of Berlin, Berlin, Germany
| | - Dirk Roggenbuck
- Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Peter Schierack
- Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| |
Collapse
|
16
|
Ismail S, Ahmad S, Azam SS. Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine. J Mol Liq 2020; 314:113612. [PMID: 32834259 PMCID: PMC7297697 DOI: 10.1016/j.molliq.2020.113612] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/14/2020] [Accepted: 06/14/2020] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health emergency of international concern and thus calling for the development of effective and safe therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for a vaccine, antibodies, and inhibitors development because of the many roles it plays in attachment, fusion and entry into the host cell. In the present investigation, we characterized the SARS-CoV-2 spike glycoprotein by immunoinformatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in aqueous milieu aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel axial frequency distribution (AFD) analytical tool. Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus could be considered in experimental studies.
Collapse
Affiliation(s)
- Saba Ismail
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|
17
|
Ahmad S, Navid A, Farid R, Abbas G, Ahmad F, Zaman N, Parvaiz N, Azam SS. Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics. Eur J Pharm Sci 2020; 151:105387. [PMID: 32454128 PMCID: PMC7245302 DOI: 10.1016/j.ejps.2020.105387] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 01/08/2023]
Abstract
The emergence and rapid expansion of the coronavirus disease (COVID-19) require the development of effective countermeasures especially a vaccine to provide active acquired immunity against the virus. This study presented a comprehensive vaccinomics approach applied to the complete protein data published so far in the National Center for Biotechnological Information (NCBI) coronavirus data hub. We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. Epitopes prediction illustrated both B-cell and T-cell epitopes associated with the mentioned proteins. The shared B and T-cell epitopes: DRDAAMQRK and QARSEDKRA of Nsp8, EDMLNPNYEDL and EFTPFDVVR of 3C-like proteinase, and VNNSYECDIPI of the spike glycoprotein are regions of high potential interest and have a high likelihood of being recognized by the human immune system. The vaccine construct of the epitopes shows stimulation of robust primary immune responses and high level of interferon gamma. Also, the construct has the best conformation with respect to the tested innate immune receptors involving vigorous molecular mechanics and solvation energy. Designing of vaccination strategies that target immune response focusing on these conserved epitopes could generate immunity that not only provide cross protection across Betacoronaviruses but additionally resistant to virus evolution.
Collapse
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Afifa Navid
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rabia Farid
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ghulam Abbas
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan..
| |
Collapse
|
18
|
Loubet P, Ranfaing J, Dinh A, Dunyach-Remy C, Bernard L, Bruyère F, Lavigne JP, Sotto A. Alternative Therapeutic Options to Antibiotics for the Treatment of Urinary Tract Infections. Front Microbiol 2020; 11:1509. [PMID: 32719668 PMCID: PMC7350282 DOI: 10.3389/fmicb.2020.01509] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/10/2020] [Indexed: 12/29/2022] Open
Abstract
Urinary tract infections (UTIs) mainly caused by Uropathogenic Escherichia coli (UPEC), are common bacterial infections. Many individuals suffer from chronically recurring UTIs, sometimes requiring long-term prophylactic antibiotic regimens. The global emergence of multi-drug resistant uropathogens in the last decade underlines the need for alternative non-antibiotic therapeutic and preventative strategies against UTIs. The research on non-antibiotic therapeutic options in UTIs has focused on the following phases of the pathogenesis: colonization, adherence of pathogens to uroepithelial cell receptors and invasion. In this review, we discuss vaccines, small compounds, nutraceuticals, immunomodulating agents, probiotics and bacteriophages, highlighting the challenges each of these approaches face. Most of these treatments show interesting but only preliminary results. Lactobacillus-containing products and cranberry products in conjunction with propolis have shown the most robust results to date and appear to be the most promising new alternative to currently used antibiotics. Larger efficacy clinical trials as well as studies on the interplay between non-antibiotic therapies, uropathogens and the host immune system are warranted.
Collapse
Affiliation(s)
- Paul Loubet
- VBMI, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
| | - Jérémy Ranfaing
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Aurélien Dinh
- Service des Maladies Infectieuses, AP-HP Raymond-Poincaré, Garches, France
| | - Catherine Dunyach-Remy
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Louis Bernard
- PRES Centre Val de Loire, Université François Rabelais de Tours, Tours, France.,Service des Maladies Infectieuses, CHU Tours, Tours, France
| | - Franck Bruyère
- PRES Centre Val de Loire, Université François Rabelais de Tours, Tours, France.,Service d'Urologie, CHU Tours, Tours, France
| | - Jean-Philippe Lavigne
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Albert Sotto
- VBMI, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
| |
Collapse
|
19
|
Yan F, Gao F. A systematic strategy for the investigation of vaccines and drugs targeting bacteria. Comput Struct Biotechnol J 2020; 18:1525-1538. [PMID: 32637049 PMCID: PMC7327267 DOI: 10.1016/j.csbj.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Infectious and epidemic diseases induced by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide. At present, many researchers are working on the discovery of viable drug and vaccine targets for bacteria through multiple methods, including the analyses of comparative subtractive genome, core genome, replication-related proteins, transcriptomics and riboswitches, which plays a significant part in the treatment of infectious and pandemic diseases. The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis. Meanwhile, molecular dynamics (MD) analysis of the constructed drug/epitope-protein complexes is an important standard for testing the suitability of these screened drugs and vaccines. Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria. We hope that this comprehensive strategy will help in the design of high-performance vaccines and drugs.
Collapse
Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| |
Collapse
|
20
|
Back CR, Higman VA, Le Vay K, Patel VV, Parnell AE, Frankel D, Jenkinson HF, Burston SG, Crump MP, Nobbs AH, Race PR. The streptococcal multidomain fibrillar adhesin CshA has an elongated polymeric architecture. J Biol Chem 2020; 295:6689-6699. [PMID: 32229583 PMCID: PMC7212634 DOI: 10.1074/jbc.ra119.011719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/26/2020] [Indexed: 11/06/2022] Open
Abstract
The cell surfaces of many bacteria carry filamentous polypeptides termed adhesins that enable binding to both biotic and abiotic surfaces. Surface adherence is facilitated by the exquisite selectivity of the adhesins for their cognate ligands or receptors and is a key step in niche or host colonization and pathogenicity. Streptococcus gordonii is a primary colonizer of the human oral cavity and an opportunistic pathogen, as well as a leading cause of infective endocarditis in humans. The fibrillar adhesin CshA is an important determinant of S. gordonii adherence, forming peritrichous fibrils on its surface that bind host cells and other microorganisms. CshA possesses a distinctive multidomain architecture comprising an N-terminal target-binding region fused to 17 repeat domains (RDs) that are each ∼100 amino acids long. Here, using structural and biophysical methods, we demonstrate that the intact CshA repeat region (CshA_RD1-17, domains 1-17) forms an extended polymeric monomer in solution. We recombinantly produced a subset of CshA RDs and found that they differ in stability and unfolding behavior. The NMR structure of CshA_RD13 revealed a hitherto unreported all β-fold, flanked by disordered interdomain linkers. These findings, in tandem with complementary hydrodynamic studies of CshA_RD1-17, indicate that this polypeptide possesses a highly unusual dynamic transitory structure characterized by alternating regions of order and disorder. This architecture provides flexibility for the adhesive tip of the CshA fibril to maintain bacterial attachment that withstands shear forces within the human host. It may also help mitigate deleterious folding events between neighboring RDs that share significant structural identity without compromising mechanical stability.
Collapse
Affiliation(s)
- Catherine R Back
- Bristol Dental School, University of Bristol, Bristol BS1 2LY, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Victoria A Higman
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Kristian Le Vay
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- Bristol Centre for Functional Nanomaterials, H. H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Viren V Patel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Alice E Parnell
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Daniel Frankel
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom
| | - Howard F Jenkinson
- Bristol Dental School, University of Bristol, Bristol BS1 2LY, United Kingdom
| | - Steven G Burston
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Matthew P Crump
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol BS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Angela H Nobbs
- Bristol Dental School, University of Bristol, Bristol BS1 2LY, United Kingdom
| | - Paul R Race
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Bristol BS8 1TQ, United Kingdom
| |
Collapse
|
21
|
Ismail S, Ahmad S, Azam SS. Vaccinomics to design a novel single chimeric subunit vaccine for broad-spectrum immunological applications targeting nosocomial Enterobacteriaceae pathogens. Eur J Pharm Sci 2020; 146:105258. [DOI: 10.1016/j.ejps.2020.105258] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 12/21/2022]
|
22
|
Sajjad R, Ahmad S, Azam SS. In silico screening of antigenic B-cell derived T-cell epitopes and designing of a multi-epitope peptide vaccine for Acinetobacter nosocomialis. J Mol Graph Model 2019; 94:107477. [PMID: 31654980 DOI: 10.1016/j.jmgm.2019.107477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/20/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022]
Abstract
Globally, antibiotic-resistant and tolerated bacterial isolates of Acinetobacter species are imposing high financial cost on health care systems and as such, molecular targets with promising immune protection could provide substantive benefits to human healthcare. Here, we performed an in silico based proteome-wide screening for antigenic B-cell derived T-cell epitopes and their following use to design a multi-epitope peptide vaccine that can effectively engage the host immune system against Acinetobacter nosocomialis SSA3 strain. Epitopes of the fimbrial biogenesis outer membrane usher FimD protein: YQQGINNYL and YRTNYTTVG were revealed appropriate for multi-epitope peptide construct designing. This protein has no homology to the host, essential to the pathogen survival and is localized at the pathogen surface. The predicted epitopes have high affinity for the highly expressed DRB*0101 allele in humans based on the lowest IC50 value in MHCPred and have an exo-membrane topology for efficient immune system recognition. The designed multi-epitope peptide vaccine is composed of the mentioned shortlisted antigenic epitopes linked to each other through a GPGPG linker, and an EAAAK linker that joined the multi-epitope peptide to the Cholera B subunit from Vibrio cholera as an adjuvant to increase vaccine construct antigenicity. The vaccine construct was docked and simulated with a transmembrane toll-like receptor (TLR4) that revealed construct stable binding with the TLR4 through the adjuvant, allowing the epitopes exposed to the host immune system essential for generating effective innate and long-lasting adaptive immunity. The designed multi-epitope peptide vaccine may prompt the development of a vaccine to control refractory and deleterious A. nosocomialis infections.
Collapse
Affiliation(s)
- Rida Sajjad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| |
Collapse
|
23
|
Das S, Mohakud NK, Suar M, Sahu BR. Vaccine development for enteric bacterial pathogens: Where do we stand? Pathog Dis 2019; 76:5040763. [PMID: 30052916 DOI: 10.1093/femspd/fty057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/19/2018] [Indexed: 01/06/2023] Open
Abstract
Gut infections triggered by pathogenic bacteria lead to most frequently occurring diarrhea in humans accounting for million deaths annually. Currently, only a few licensed vaccines are available against these pathogens for mostly travelers moving to diarrheal endemic areas. Besides commercialized vaccines, there are many formulations that are either under clinical or pre-clinical stages of development and despite several efforts to improve safety, immunogenicity and efficacy, none of them can confer long-term protective immunity, for which repeated booster doses are always recommended. Further in many countries, financial, social and political constraints have jeopardized vaccine development program against these pathogens that enforce us to gather knowledge on safety, tolerability, immunogenicity and protective efficacy regarding the same. In this review, we analyze safety and efficacy issues of vaccines against five major gut bacteria causing enteric infections. The article also simultaneously describes several barriers for vaccine development and further discusses possible strategies to enhance immunogenicity and efficacy.
Collapse
Affiliation(s)
- Susmita Das
- Infection Biology Lab, KIIT School of Biotechnology, Campus XI, Bhubaneswar 751024, India
| | - Nirmal K Mohakud
- Department of Pediatrics, Kalinga Institute of Medical Sciences, Patia, Bhubaneswar 751024, India
| | - Mrutyunjay Suar
- Infection Biology Lab, KIIT School of Biotechnology, Campus XI, Bhubaneswar 751024, India
| | - Bikash R Sahu
- Infection Biology Lab, KIIT School of Biotechnology, Campus XI, Bhubaneswar 751024, India
| |
Collapse
|
24
|
Abstract
With the rise in novel infectious agents and disease pandemics, a new era of vaccine discovery is necessary. To address this, the new field of immunomics is described, which is synergistically powered by integrating bioinformatics methodologies with technological advances in biology and high-throughput instrumentation. By incorporating biological data from immunology and molecular biology with current genomics and proteomics, immunomics is geared to deliver an insight into immune function, optimal stimulation of immune responses and precise mapping and rational selection of immune targets that cover antigenic diversity. These efforts are expected to contribute towards the development of new generation of vaccines, tailored to both the genetic make-up of the human population and of the pathogen. Vaccine technologies are also being explored for prevention or control of non-communicable diseases.
Collapse
|
25
|
Abstract
BACKGROUND Infections caused by bacteria are a foremost cause of morbidity and mortality in the world. The common strategy of treating bacterial infections is by local or systemic administration of antimicrobial agents. Currently, the increasing antibiotic resistance is a serious and global problem. Since the most important agent for infection is bacteria attaching to host cells, hence, new techniques and attractive approaches that interfere with the ability of the bacteria to adhere to tissues of the host or detach them from the tissues at the early stages of infection are good therapeutic strategies. METHODS All available national and international databanks were searched using the search keywords. Here, we review various approaches to anti-adhesion therapy, including use of receptor and adhesion analogs, dietary constituents, sublethal concentrations of antibiotics, and adhesion-based vaccines. RESULTS Altogether, the findings suggest that interference with bacterial adhesion serves as a new means to fight infectious diseases. CONCLUSION Anti-adhesion-based therapies can be effective in prevention and treatment of bacterial infections, but further work is needed to elucidate underlying mechanisms.
Collapse
Affiliation(s)
- Arezoo Asadi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Malihe Talebi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Gholami
- Department of Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| |
Collapse
|
26
|
Ehsan N, Ahmad S, Azam SS, Rungrotmongkol T, Uddin R. Proteome-wide identification of epitope-based vaccine candidates against multi-drug resistant Proteus mirabilis. Biologicals 2018; 55:27-37. [PMID: 30078661 DOI: 10.1016/j.biologicals.2018.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 07/11/2018] [Accepted: 07/29/2018] [Indexed: 11/19/2022] Open
Abstract
Proteus mirabilis is one of the important pathogens of urinary tract and exhibits resistance to multiple drugs. Development of vaccine tends to be the most promising and cost-effective remedy against the said pathogen. Herein, we implement a combinatorial approach for screening proteins harboring potential broad-spectrum antigenic epitopes in the proteome of P. mirabilis. The targets are host non-homologous, essential and virulent, and have localization in the extracellular and outer membrane. Immuno-informatics revealed antigenic, surface exposed and broad-spectrum B-cell derived T-cell epitopes for three membrane usher family candidates: AtfC, PMI2533 and PMI1466, which could evoke a substantial immune response. Protein-protein interactions of targeted three proteins have shown their involvement in biologically significant pathways indispensable for the growth and survival of the pathogen. The antigenic epitopes are conserved among all completely annotated strains and docked deeply in the binding cavity of the most prevalent allele-DRB1*0101 in human population. Future work is necessary to characterize the shortlisted proteins and epitopes for immune protection in animal models.
Collapse
Affiliation(s)
- Nosheen Ehsan
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| |
Collapse
|
27
|
Ahmad S, Azam SS. A novel approach of virulome based reverse vaccinology for exploring and validating peptide-based vaccine candidates against the most troublesome nosocomial pathogen: Acinetobacter baumannii. J Mol Graph Model 2018; 83:1-11. [PMID: 29753164 DOI: 10.1016/j.jmgm.2018.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022]
Abstract
Acinetobacter baumannii is one of the major cause of nosocomial infections around the globe. The emergence of hyper-virulent strains of the pathogen greatly narrows down therapeutic options for patients infected with this red alert superbug. Development of a peptide-based vaccine can offers an alternative, attractive, and cost-effective remedy for multidrug-resistant A. baumannii associated complications. Herein, we introduced a novel virulome based Reverse Vaccinology for screening peptide based vaccine candidates against A. baumannii and its validation using a negative control. The pipeline screened "FYLNDQPVS" of polysaccharide export outer membrane protein (EpsA) and "LQNNTRRMK" of chaperone-usher pathway protein B (CsuB) as broad-spectrum peptides for induction of targeted immune responses. The 9-mer epitope of both proteins was rendered virulent, antigenic, non-allergen, and highly conserved among thirty-four completely annotated strains. Interactome examination unravels peptides protein direct and indirect interactions with biological significant pathways, essential for A. baumannii pathogenesis and survival. Protein-peptide docking aids in addition by unveiling deep binding of the epitopes in the active site of the most prevalent binding allele in the human population-the DRB1*0101. Both the proteins till to date are not characterized for immunoprotective efficacy and desirable to be deciphered experimentally. The designed series of in silico filters rejected few recently reported peptide and non-peptide vaccine targets and has delivered outcomes, which we believe will enrich the existing knowledge of vaccinology against this life-threatening human pathogen.
Collapse
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan.
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan.
| |
Collapse
|
28
|
Abstract
BACKGROUND Irrigation is one of the key procedures in open fracture management to eliminate pathogens and prevent infection. Metal ion deprivation could inhibit bacterial adhesins and weaken adhesion to the host tissue. EDTA in solution can competitively bind to a metal ion and thus might be able to inhibit bacterial adhesins. QUESTIONS/PURPOSES (1) Is normal saline-EDTA toxic to fibroblasts and endothelial cells? (2) In a contaminated wound rat model, does irrigation with normal saline-EDTA solution decrease the risk of positive bacterial cultures and infection when compared with normal saline and soap solutions? (3) In an infected wound rat model, are fewer surgical débridements and irrigations with normal saline-EDTA solution required to obtain culture-free wounds when compared with normal saline and soap controls? METHODS Normal saline-EDTA solution refers to 1 mmol/L EDTA dissolved in normal saline (pH adjusted to 7.4). Normal saline and soap solutions acted as controls. The toxicity of these solutions to fibroblasts and endothelial cells was assessed in vitro by Annexin V/propidium iodide staining and flow cytometer counting (a well-established method to quantitatively measure the number of dead cells). We established contaminated and infected wound models (bone-exposed or not) with either Staphylococcus aureus or Escherichia coli in rats to investigate the efficacy of normal saline-EDTA solution (n = 30 for the contaminated model and n = 50 for the infected model). For contaminated wounds, the proportion of positive bacterial cultures and infections was compared after irrigation and débridement among the three groups. For infected wounds, we performed irrigation and débridement every 48 hours until the cultures were negative and compared the number of débridements required to achieve a negative culture with survival analysis. RESULTS Normal saline-EDTA showed no additional toxicity to fibroblasts and endothelial cells when compared with normal saline (normal saline [97%] versus EDTA [98%] on fibroblasts, p = 0.654; normal saline [97%] versus EDTA [98%] on endothelial cells, p = 0.711). When bone was exposed in the contaminated models, EDTA irrigation resulted in fewer positive bacterial cultures with S aureus (EDTA: 23%, normal saline: 67%, soap: 40%, p = 0.003) and with E coli (EDTA: 27%, normal saline: 57%, soap: 30%, p = 0.032); however, infection risk was only lower with EDTA irrigation (S aureus with EDTA: 10%, normal saline: 33%, soap: 37%, p = 0.039; E coli with EDTA: 3%, normal saline: 27%, soap: 23%, p = 0.038). In the infected wound model, EDTA irrigation resulted in earlier culture-negative wounds (fewer surgical sessions) compared with normal saline and soap solutions (nonbone-exposed wounds infected by S aureus: p = 0.003, infected by E coli: p = 0.001; bone-exposed wounds infected by S aureus: p = 0.012, infected by E coli: p = 0.022). CONCLUSIONS After in vitro assessment of toxicity and in vivo evaluation of efficacy, we concluded that normal saline-EDTA is superior to normal saline and soap solution in our laboratory models. CLINICAL RELEVANCE The use of normal-saline EDTA as an irrigation solution may reduce the infection rate of wounds. Future studies in large animals and humans might prove our observation in rat models that normal saline-EDTA has an advantage over normal saline as an irrigation solution.
Collapse
Affiliation(s)
- Hongyi Zhu
- Department of Orthopaedic Surgery, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | | | | |
Collapse
|
29
|
Li Q, Zhang Y, Dechao D, Yanfei Y, Zhang W. Characterization and functional analysis of PnuC that is involved in the oxidative stress tolerance and virulence of Streptococcus suis serotype 2. Vet Microbiol 2018; 216:198-206. [DOI: 10.1016/j.vetmic.2018.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
30
|
O'Brien VP, Hannan TJ, Nielsen HV, Hultgren SJ. Drug and Vaccine Development for the Treatment and Prevention of Urinary Tract Infections. Microbiol Spectr 2016; 4. [PMID: 26999391 DOI: 10.1128/microbiolspec.UTI-0013-2012] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Urinary tract infections (UTI) are among the most common bacterial infections in humans, affecting millions of people every year. UTI cause significant morbidity in women throughout their lifespan, in infant boys, in older men, in individuals with underlying urinary tract abnormalities, and in those that require long-term urethral catheterization, such as patients with spinal cord injuries or incapacitated individuals living in nursing homes. Serious sequelae include frequent recurrences, pyelonephritis with sepsis, renal damage in young children, pre-term birth, and complications of frequent antimicrobial use including high-level antibiotic resistance and Clostridium difficile colitis. Uropathogenic E. coli (UPEC) cause the vast majority of UTI, but less common pathogens such as Enterococcus faecalis and other enterococci frequently take advantage of an abnormal or catheterized urinary tract to cause opportunistic infections. While antibiotic therapy has historically been very successful in controlling UTI, the high rate of recurrence remains a major problem, and many individuals suffer from chronically recurring UTI, requiring long-term prophylactic antibiotic regimens to prevent recurrent UTI. Furthermore, the global emergence of multi-drug resistant UPEC in the past ten years spotlights the need for alternative therapeutic and preventative strategies to combat UTI, including anti-infective drug therapies and vaccines. In this chapter, we review recent advances in the field of UTI pathogenesis, with an emphasis on the identification of promising drug and vaccine targets. We then discuss the development of new UTI drugs and vaccines, highlighting the challenges these approaches face and the need for a greater understanding of urinary tract mucosal immunity.
Collapse
|
31
|
Won G, Lee JH. Effectiveness of F18 + Fimbrial Antigens Released by a Novel Autolyzed Salmonella Expression System as a Vaccine Candidate against Lethal F18 + STEC Infection. Front Microbiol 2016; 7:1835. [PMID: 27920758 PMCID: PMC5118419 DOI: 10.3389/fmicb.2016.01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/01/2016] [Indexed: 12/04/2022] Open
Abstract
Porcine edema disease (ED) caused by Shiga toxin 2e producing Escherichia coli expressing F18ab+ fimbriae (F18ab+STEC) frequently occurs in post-weaned piglets, resulting in a significant economic loss in swine industries worldwide. In the present study, we proposed an efficient prevention scheme against ED in which the attenuated Salmonella Typhimurium inactivated by the E-mediated cell lysis to deliver target antigens, FedF and FedA, which function in fimbrial-mediated adhesion and as a major subunit of F18ab+fimbriae, respectively. The co-expression of FedA and FedF protein with outer membrane protein A signal peptide was confirmed in the resultant strains JOL1460 and JOL1464 by immunoblot analysis. Immunization with the candidate strains in mice led to the significant generation of immunoglobulin (Ig) G, specific to both antigens and secretory IgA specific to FedF (P < 0.05). The titers of IgG isotypes, IgG1 and IgG2a, used as markers for T-helpers (Th)-2 and Th-1lymphocytes, respectively, also significantly increased in the immunized group (P < 0.05). The increase in CD3+CD4+ T lymphocyte subpopulation and in vitro proliferative activity was observed in in vivo stimulated splenocytes, which indicated the immunostimulatory effect of the candidate strains. Moreover, the immunized mice were completely protected from a lethal challenge against wild-type F18+STEC whereas 28% of mice died in the non-immunized group. This study demonstrated that the inactivated Salmonella system could efficiently release FedF and FedA and induce robust immune responses specific to the target antigens, which is sufficient to protect the mice from the lethal challenge.
Collapse
Affiliation(s)
- Gayeon Won
- College of Veterinary Medicine, Chonbuk National University Iksan, South Korea
| | - John H Lee
- College of Veterinary Medicine, Chonbuk National University Iksan, South Korea
| |
Collapse
|
32
|
Zakrisson J, Singh B, Svenmarker P, Wiklund K, Zhang H, Hakobyan S, Ramstedt M, Andersson M. Detecting Bacterial Surface Organelles on Single Cells Using Optical Tweezers. Langmuir 2016; 32:4521-9. [PMID: 27088225 DOI: 10.1021/acs.langmuir.5b03845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bacterial cells display a diverse array of surface organelles that are important for a range of processes such as intercellular communication, motility and adhesion leading to biofilm formation, infections, and bacterial spread. More specifically, attachment to host cells by Gram-negative bacteria are mediated by adhesion pili, which are nanometers wide and micrometers long fibrous organelles. Since these pili are significantly thinner than the wavelength of visible light, they cannot be detected using standard light microscopy techniques. At present, there is no fast and simple method available to investigate if a single cell expresses pili while keeping the cell alive for further studies. In this study, we present a method to determine the presence of pili on a single bacterium. The protocol involves imaging the bacterium to measure its size, followed by predicting the fluid drag based on its size using an analytical model, and thereafter oscillating the sample while a single bacterium is trapped by an optical tweezer to measure its effective fluid drag. Comparison between the predicted and the measured fluid drag thereby indicate the presence of pili. Herein, we verify the method using polymer coated silica microspheres and Escherichia coli bacteria expressing adhesion pili. Our protocol can in real time and within seconds assist single cell studies by distinguishing between piliated and nonpiliated bacteria.
Collapse
Affiliation(s)
- Johan Zakrisson
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Bhupender Singh
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Pontus Svenmarker
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Krister Wiklund
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Hanqing Zhang
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Shoghik Hakobyan
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Madeleine Ramstedt
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| | - Magnus Andersson
- Department of Physics, and ‡Department of Chemistry, Umeå University , 901 87 Umeå, Sweden
| |
Collapse
|
33
|
Grossart HP, Wurzbacher C, James TY, Kagami M. Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.06.004] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
34
|
Andreoni F, Amagliani G, Magnani M. Selection of Vaccine Candidates for Fish Pasteurellosis Using Reverse Vaccinology and an In Vitro Screening Approach. Methods Mol Biol 2016; 1404:181-192. [PMID: 27076298 DOI: 10.1007/978-1-4939-3389-1_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The advent of new technologies in recent years has revolutionized the methods by which pathogens are studied and at the same time it has provided new tools to design vaccines against infections for which vaccine development has so far been unsuccessful. The availability of genomic data provides the basis for the reverse vaccinology approach, a biotechnological strategy that uses bioinformatics analysis of microbial genome data for the in silico selection of potential vaccine candidates for the development of protein-based vaccines. The antigens selected by reverse vaccinology can be produced as recombinant proteins and subjected to further in vitro screening assays before in vivo experiments to assess immunogenicity and protection. The reverse vaccinology approach has been applied to several pathogens affecting human health, but also to marine bacteria, including Photobacterium damselae subsp. piscicida causing significant harm in marine aquaculture.
Collapse
Affiliation(s)
- Francesca Andreoni
- Department of Biomolecular Science-Section of Biotechnology, University of Urbino "Carlo Bo", Via Arco d'Augusto 2, Fano, 61032, Italy.
| | - Giulia Amagliani
- Department of Biomolecular Science-Section of Biotechnology, University of Urbino "Carlo Bo", Via Arco d'Augusto 2, Fano, 61032, Italy
| | - Mauro Magnani
- Department of Biomolecular Science-Section of Biotechnology, University of Urbino "Carlo Bo", Via Arco d'Augusto 2, Fano, 61032, Italy
| |
Collapse
|
35
|
Gholamhosseini-Moghaddam T, Rad M, Mousavi SF, Ghazvini K. Detection of lytA, pspC, and rrgA genes in Streptococcus pneumoniae isolated from healthy children. Iran J Microbiol 2015; 7:156-60. [PMID: 26668703 PMCID: PMC4676985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND AND OBJECTIVES Many surface proteins are implicated in nasopharyngeal colonization and pathogenesis of Streptococcus pneumoniae. Some of these factors are candidate antigens for protein based vaccines. New vaccine designs focus on the surface proteins (e. g., pspA and pspC) and also cytolysin, and pneumolysin. In this study, 3 key virulence genes, lytA, pspC, and rrgA, which encoded surface proteins, were detected among S. pneumoniae isolates. MATERIALS AND METHODS A total of 260 nasopharyngeal swabs were collected from healthy children under 6 years old attending day care centers in Mashhad, Iran. Isolates of S. pneumoniae were confirmed by optochin susceptibility and colony appearance and also by PCR for cpsA gene. The presence of lytA, pspC, and rrgA genes were also detected by PCR. RESULTS A total of 59 isolates were confirmed as S. pneumoniae. Among these isolates, 50 (84.74%), 19 (32.20%), and 2 (3.38%) were positive for lytA, rrgA, and pspC genes respectively. The presence of these genes among S.pneumoniae isolates were as follows: 1) rrgA, lytA, pspC (1 isolate), 2) rrgA, lytA(17isolates), 3) pspC (2 isolate), 4) lytA (50 isolates). CONCLUSION cpsA gene was specific for detection of S. pneumoniae isolates which were colonized in nasopharynx. The lytA gene was the most frequent gene among the S. pneumoniae isolates, and combination of rrgA, lytA was the most observed pattern. Thus, it is important for future monitoring of vaccine formulation in our country.
Collapse
Affiliation(s)
| | - Mehrnaz Rad
- Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.,Corresponding author: Mehrnaz Rad, Seyed Fazlollah-Mousavi, E-mail: ,
| | - Seyed Fazlollah Mousavi
- Department of Bacteriology and Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Corresponding author: Mehrnaz Rad, Seyed Fazlollah-Mousavi, E-mail: ,
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Faculty of Madicine, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
36
|
Shippy DC, Eakley NM, Mikheil DM, De La Cotera A, Fadl AA. Characterization of SEN3800-associated virulence of Salmonella enterica serovar Enteritidis phage type 8. ANN MICROBIOL 2015; 65:631-637. [DOI: 10.1007/s13213-014-0898-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
37
|
Musa HH, Zhang W, Tao J, Guan Y, Duan X, Yang Y, Zhu C, Li H, Zhu G. Cloning and expression of FimA-c3d recombinant protein. Journal of Genetic Engineering and Biotechnology 2014; 12:55-9. [DOI: 10.1016/j.jgeb.2014.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
38
|
Musa HH, Zhang WJ, Lv J, Duan XL, Yang Y, Zhu CH, Li HF, Chen KW, Meng X, Zhu GQ. The molecular adjuvant mC3d enhances the immunogenicity of FimA from type I fimbriae of Salmonella enterica serovar Enteritidis. Journal of Microbiology, Immunology and Infection 2014; 47:57-62. [DOI: 10.1016/j.jmii.2012.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/30/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
|
39
|
Ramos PIP, Picão RC, Almeida LGPD, Lima NCB, Girardello R, Vivan ACP, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Médigue C, Vasconcelos ATRD, Gales AC, Nicolás MF. Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms. BMC Genomics 2014; 15:54. [PMID: 24450656 PMCID: PMC3904158 DOI: 10.1186/1471-2164-15-54] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/26/2013] [Indexed: 11/24/2022] Open
Abstract
Background Klebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumoniae genomes, which can constitute extra challenges in the treatment of infections caused by some strains. K. pneumoniae Kp13 is a multidrug-resistant strain responsible for causing a large nosocomial outbreak in a teaching hospital located in Southern Brazil. Kp13 produces K. pneumoniae carbapenemase (KPC-2) but is unrelated to isolates belonging to ST 258 and ST 11, the main clusters associated with the worldwide dissemination of KPC-producing K. pneumoniae. In this report, we perform a genomic comparison between Kp13 and each of the following three K. pneumoniae genomes: MGH 78578, NTUH-K2044 and 342. Results We have completely determined the genome of K. pneumoniae Kp13, which comprises one chromosome (5.3 Mbp) and six plasmids (0.43 Mbp). Several virulence and resistance determinants were identified in strain Kp13. Specifically, we detected genes coding for six beta-lactamases (SHV-12, OXA-9, TEM-1, CTX-M-2, SHV-110 and KPC-2), eight adhesin-related gene clusters, including regions coding for types 1 (fim) and 3 (mrk) fimbrial adhesins. The rmtG plasmidial 16S rRNA methyltransferase gene was also detected, as well as efflux pumps belonging to five different families. Mutations upstream the OmpK35 porin-encoding gene were evidenced, possibly affecting its expression. SNPs analysis relative to the compared strains revealed 141 mutations falling within CDSs related to drug resistance which could also influence the Kp13 lifestyle. Finally, the genetic apparatus for synthesis of the yersiniabactin siderophore was identified within a plasticity region. Chromosomal architectural analysis allowed for the detection of 13 regions of difference in Kp13 relative to the compared strains. Conclusions Our results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens. The general chromosomal structure was somewhat conserved among the compared bacteria, and recombination events with consequent gain/loss of genomic segments appears to be driving the evolution of these strains.
Collapse
|
40
|
Abstract
Bacterial infections are a major cause of morbidity and mortality worldwide and are increasingly problematic to treat due to the rise in antibiotic-resistant strains. It becomes more and more challenging to develop new antimicrobials that are able to withstand the ever-increasing repertoire of bacterial resistance mechanisms. This necessitates the development of alternative approaches to prevent and treat bacterial infections. One of the first steps during bacterial infection is adhesion of the pathogen to host cells. A pathogen’s ability to colonize and invade host tissues strictly depends on this process. Thus, interference with adhesion (anti-adhesion therapy) is an efficient way to prevent or treat bacterial infections. As a basis to present different strategies to interfere with pathogen adhesion, this review briefly introduces general concepts of bacterial attachment to host cells. We further discuss advantages and disadvantages of anti-adhesion treatments and issues that are in need of improvement so as to make anti-adhesion compounds a more broadly applicable alternative to conventional antimicrobials.
Collapse
Affiliation(s)
- Anne Marie Krachler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | |
Collapse
|
41
|
Shippy DC, Eakley NM, Mikheil DM, Fadl AA. Role of the flagellar basal-body protein, FlgC, in the binding of Salmonella enterica serovar Enteritidis to host cells. Curr Microbiol 2014; 68:621-8. [PMID: 24420330 DOI: 10.1007/s00284-014-0521-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/23/2013] [Indexed: 12/29/2022]
Abstract
Salmonella enterica serovar Enteritidis (SE) infection in humans is often associated with the consumption of contaminated poultry products. Binding of the bacterium to the intestinal mucosa is a major pathogenic mechanism of Salmonella in poultry. Transposon mutagenesis identified flgC as a potential binding mutant of SE. Therefore, we hypothesize FlgC which plays a significant role in the binding ability of SE to the intestinal mucosa of poultry. To test our hypothesis, we created a mutant of SE in which flgC was deleted. We then tested the in vitro and in vivo binding ability of ∆flgC when compared to the wild-type SE strain. Our data showed a significant decrease in the binding ability of ∆flgC to intestinal epithelial cells as well as in the small intestine and cecum of poultry. Furthermore, the decrease in binding correlated to a defect in invasion as shown by a cell culture model using intestinal epithelial cells and bacterial recovery from the livers and spleens of chickens. Overall, these studies indicate FlgC is a major factor in the binding ability of Salmonella to the intestinal mucosa of poultry.
Collapse
Affiliation(s)
- Daniel C Shippy
- Department of Animal Sciences, University of Wisconsin-Madison, 1675 Observatory Drive, Madison, WI, 53706, USA
| | | | | | | |
Collapse
|
42
|
Shippy DC, Eakley NM, Mikheil DM, Fadl AA. Role of StdA in adhesion of Salmonella enterica serovar Enteritidis phage type 8 to host intestinal epithelial cells. Gut Pathog 2013; 5:43. [PMID: 24367906 DOI: 10.1186/1757-4749-5-43] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 12/21/2013] [Indexed: 12/31/2022] Open
Abstract
Background Salmonella is often implicated in foodborne outbreaks, and is a major public health concern in the United States and throughout the world. Salmonella enterica serovar Enteritidis (SE) infection in humans is often associated with the consumption of contaminated poultry products. Adhesion to epithelial cells in the intestinal mucosa is a major pathogenic mechanism of Salmonella in poultry. Transposon mutagenesis identified stdA as a potential adhesion mutant of SE. Therefore, we hypothesize StdA plays a significant role in adhesion of SE to the intestinal mucosa of poultry. Methods and results To test our hypothesis, we created a mutant of SE in which stdA was deleted. Growth and motility were assayed along with the in vitro and in vivo adhesion ability of the ∆stdA when compared to the wild-type SE strain. Our data showed a significant decrease in motility in ∆stdA when compared to the wild-type and complemented strain. A decrease in adhesion to intestinal epithelial cells as well as in the small intestine and cecum of poultry was observed in ∆stdA. Furthermore, the lack of adhesion correlated to a defect in invasion as shown by a cell culture model using intestinal epithelial cells and bacterial recovery from the livers and spleens of chickens. Conclusions These studies suggest StdA is a major contributor to the adhesion of Salmonella to the intestinal mucosa of poultry.
Collapse
|
43
|
Jaiswal V, Chanumolu SK, Gupta A, Chauhan RS, Rout C. Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics 2013; 14:211. [PMID: 23815072 PMCID: PMC3701604 DOI: 10.1186/1471-2105-14-211] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 06/20/2013] [Indexed: 11/24/2022] Open
Abstract
Background Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs. Results A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset. Conclusions Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html
Collapse
Affiliation(s)
- Varun Jaiswal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173234, India
| | | | | | | | | |
Collapse
|
44
|
Shivachandra SB, Kumar A, Yogisharadhya R, Ramakrishnan MA, Viswas KN. Carboxyl terminus heterogeneity of type IV fimbrial subunit protein of Pasteurella multocida isolates. Vet Res Commun 2013; 37:269-75. [DOI: 10.1007/s11259-013-9569-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
|
45
|
Abstract
Anti-adhesion therapies for bacterial infections offer an alternative to antibiotics, with those therapies bacteria are not killed but are prevented from causing harm to a host by inhibiting adherence to host cells and tissues, a prerequisite for the majority of infectious diseases. The mechanisms of these potential therapeutic agents include inhibition of adhesins and their host receptors, vaccination with adhesins or analogs, use of probiotics and dietary supplements that interfere with receptor-adhesin interactions, subminimal inhibitory concentrations of antibiotics and manipulation of hydrophobic interactions. Once developed, these drugs will contribute to the arsenal for fighting infectious disease in the future, potentially subverting antibiotic resistance.
Collapse
Affiliation(s)
- Daniel Cozens
- Department of Infection & Immunity, K Floor, Royal Hallamshire Hospital, Sheffield School of Medicine & Biomedical Science, University of Sheffield, Sheffield, S10 3JF, UK
| | | |
Collapse
|
46
|
Yang Y, Wan C, Xu H, Aguilar ZP, Tan Q, Xu F, Lai W, Xiong Y, Wei H. Identification of an outer membrane protein of Salmonella enterica serovar Typhimurium as a potential vaccine candidate for Salmonellosis in mice. Microbes Infect 2013; 15:388-98. [PMID: 23485513 DOI: 10.1016/j.micinf.2013.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 02/10/2013] [Accepted: 02/18/2013] [Indexed: 12/27/2022]
Abstract
We report our investigation of the functions of PagN in Salmonella pathogenesis and its potential as a vaccine candidate. Further investigation conducted in this study indicates that the outer membrane protein PagN is important for Salmonella adhesion/invasion of epithelial cells as well as bacterial virulence. When pagN was deleted from Salmonella enterica serovar Typhimurium (S. Typhimurium), the adhesion and invasion of HT-29 epithelial cells was significantly decreased compared with the wild type strain. Mice infected with the pagN mutant strain exhibited less pathological signs in the intestine and survived longer than the wild-type-infected mice. PagN is widely distributed and conserved among clinical isolates of different Salmonella serovars, making PagN a potential vaccine candidate for Salmonella infection. To elucidate the potential of PagN as a vaccine, we expressed and purified recombinant PagN (rPagN). When rPagN was tested in mice, it provided significant protection against Salmonella infection in vivo. In vitro, anti-PagN serum enhanced clearance of Salmonella, indicating a contribution of PagN-specific antibodies to the killing process. This correlates well with the observed protection of mice immunized with rPagN. Our preliminary results indicate more functions of PagN in S. Typhimurium virulence as well as its potential as a protective vaccine.
Collapse
Affiliation(s)
- Youjun Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang 330047, PR China
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Lo AW, Moonens K, Remaut H. Chemical attenuation of pilus function and assembly in Gram-negative bacteria. Curr Opin Microbiol 2013; 16:85-92. [DOI: 10.1016/j.mib.2013.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 01/30/2013] [Accepted: 02/03/2013] [Indexed: 10/27/2022]
|
48
|
Lima SS, Ching ATC, Fávaro RD, Da Silva JB, Oliveira MLS, Carvalho E, Abreu PAE, Vasconcellos SA, Ho PL. Adhesin activity of Leptospira interrogans lipoprotein identified by in vivo and in vitro shotgun phage display. Biochem Biophys Res Commun 2013; 431:342-7. [PMID: 23291183 DOI: 10.1016/j.bbrc.2012.12.095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 12/22/2012] [Indexed: 11/19/2022]
Abstract
Leptospira interrogans causes leptospirosis, one of the most common zoonotic diseases in the world. This pathogenic spirochete is able to bind to extracellular matrix, to express virulent factors and to cause host death. Until now, there is no effective human vaccine for the disease. Shotgun phage display genomic libraries of L. interrogans were constructed and used for in vivo biopanning in hamsters and screened for ligands able to bind to LLC-PK1 epithelial cells. In both panning procedures, clones coding for the putative lipoprotein LIC12976 were identified and, in order to confirm its adhesin activity, a recombinant protein was produced in Escherichia coli and showed to interact with A31 fibroblasts, LLC-PK1 and Vero epithelial cells in vitro. Moreover, rLIC12976 was shown to bind to laminin, indicating an adhesin function. This protein was also detected in extracts of L. interrogans from different serovars and it was found to be conserved among pathogenic leptospires. Further, the protein was tested as vaccine candidate and immunization of hamsters with LIC12976 did not confer protection against a lethal challenge with the homologous L. interrogans serovar Copenhageni. Nevertheless, LIC12976 seems to act as an adhesin, and may be important for the host-pathogen interaction, so that its study can contribute to the understanding of the virulence mechanisms in pathogenic leptospires.
Collapse
|
49
|
Andreoni F, Boiani R, Serafini G, Amagliani G, Dominici S, Riccioni G, Zaccone R, Mancuso M, Scapigliati G, Magnani M. Isolation of a novel gene from Photobacterium damselae subsp. piscicida and analysis of the recombinant antigen as promising vaccine candidate. Vaccine 2013; 31:820-6. [DOI: 10.1016/j.vaccine.2012.11.064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 10/19/2012] [Accepted: 11/22/2012] [Indexed: 11/30/2022]
|
50
|
Arenas AF, Salcedo GE, Moncada DM, Erazo DA, Osorio JF, Gomez-Marin JE. Cluster analysis identifies aminoacid compositional features that indicate Toxoplasma gondii adhesin proteins. Bioinformation 2012; 8:916-23. [PMID: 23144551 PMCID: PMC3488833 DOI: 10.6026/97320630008916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/03/2012] [Indexed: 11/23/2022] Open
Abstract
Toxoplasma gondii invade host cells using a multi-step process that depends on the regulated secretion of adhesions. To identify key primary sequence features of adhesins in this parasite, we analyze the relative frequency of individual amino acids, their dipeptide frequencies, and the polarity, polarizability and Van der Waals volume of the individual amino acids by using cluster analysis. This method identified cysteine as a key amino acid in the Toxoplasma adhesin group. The best vector algorithm of non-concatenated features was for 2 attributes: the single amino acid relative frequency and the dipeptide frequency. Polarity, polarizability and Van der Waals volume were not good classificatory attributes. Single amino acid attributes clustered unambiguously 67 apicomplexan hypothetical adhesins. This algorithm was also useful for clustering hypothetical Toxoplasma target host receptors. All of the cluster performances had over 70% sensitivity and 80% specificity. Compositional aminoacid data can be useful for improving machine learning-based prediction software when homology and structural data are not sufficient.
Collapse
Affiliation(s)
- Ailan F Arenas
- Grupo de Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Gladys E Salcedo
- Grupo de Investigación y Asesoría en Estadística, Universidad del Quindío, Armenia, Colombia
| | - Diego M Moncada
- Grupo de Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Diego A Erazo
- Grupo de Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Juan F Osorio
- Grupo de Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Jorge E Gomez-Marin
- Grupo de Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| |
Collapse
|