Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study
Introduction: Enterococcus faecalis (E. faecalis) belongs to Group D Streptococci and causes recalcitrant infections such as urinary tract infections, wound infections, intra-abdominal and pelvic infections, bacteraemia, and endocarditis. The emergence of multiple drug resistance, including to the l...
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JCDR Research and Publications Private Limited
2025-01-01
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| author | Dev Arora AS Smiline Girija J Vijayashree Priyadharsini |
| author_facet | Dev Arora AS Smiline Girija J Vijayashree Priyadharsini |
| author_sort | Dev Arora |
| collection | DOAJ |
| description | Introduction: Enterococcus faecalis (E. faecalis) belongs to Group D Streptococci and causes recalcitrant infections such as urinary tract infections, wound infections, intra-abdominal and pelvic infections, bacteraemia, and endocarditis. The emergence of multiple drug resistance, including to the last-resort drug vancomycin, is a major concern with E. faecalis infections. Therefore, it is necessary to implement alternative strategies to combat E. faecalis infections in dental settings. An immuno-informatics approach is one such strategy that can predict and assess the immunodominant B-cell and T-cell epitopes. Thus, there is a need to identify novel vaccine candidates as immunodominant epitope peptides from the Enterococcal Fibronectin Binding Protein-A (EfbA) protein for E. faecalis.
Aim: To predict the immunodominant B-cell and T-cell epitopes from the EfbA protein of E. faecalis.
Materials and Methods: An in-vitro and in-silico pilot study was conducted in the Department of Microbiology at Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, India. Total of 20 carious scrapings were collected from patients with root caries and were phenotypically characterised for E. faecalis and the EfbA genetic determinant by Polymerase Chain Reaction (PCR) amplification. The EfbA protein was retrieved from the National Center for Biotechnology Information (NCBI) database, after which prediction of antigenicity and allergenicity was performed via the VaXiJen and Algpred servers, respectively. The prediction of T-cell epitopes was carried out with the help of the EpiDOCK server, and B-cell predictions were made using the Kolaskar and Tongaonkar tool. Docking of the epitopes with reference to Human Leukocyte Antigens (HLA) alleles was assessed using the ClusPro server, and the results were evaluated for the T-cell dominant epitopes.
Results: Among the 20 samples, E. faecalis was characterised in 5 (25%) patients, with three strains exhibiting Multidrug Resistant (MDR) traits. Among the three MDR strains, two strains showed the presence of the EfbA gene by PCR. In-silico analysis of the EfbA protein yielded a total of 17 epitopes, and based on the assessments, a final selection of two epitopes (IRAKGKNHK and LLLSAHPSY) was made, showing promising docking scores with HLA alleles and TLR2.
Conclusion: Among the two epitopes, LLLSAHPSY was identified as the most significant immune-dominant epitope predicted, which needs to be further evaluated for vaccine synthesis and experimentation. |
| format | Article |
| id | doaj-art-45d37c59569f489ebd68c284312b599e |
| institution | Kabale University |
| issn | 2249-782X 0973-709X |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-45d37c59569f489ebd68c284312b599e2025-01-28T11:08:59ZengJCDR Research and Publications Private LimitedJournal of Clinical and Diagnostic Research2249-782X0973-709X2025-01-011901101410.7860/JCDR/2025/72668.20545Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico StudyDev Arora0AS Smiline Girija1J Vijayashree Priyadharsini2Undergraduate Student, Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Institute (SIMATS), Chennai, Tamil Nadu, India.Professor and Head, Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Institute (SIMATS), Chennai, Tamil Nadu, India.Associate Professor, Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Institute (SIMATS), Chennai, Tamil Nadu, India.Introduction: Enterococcus faecalis (E. faecalis) belongs to Group D Streptococci and causes recalcitrant infections such as urinary tract infections, wound infections, intra-abdominal and pelvic infections, bacteraemia, and endocarditis. The emergence of multiple drug resistance, including to the last-resort drug vancomycin, is a major concern with E. faecalis infections. Therefore, it is necessary to implement alternative strategies to combat E. faecalis infections in dental settings. An immuno-informatics approach is one such strategy that can predict and assess the immunodominant B-cell and T-cell epitopes. Thus, there is a need to identify novel vaccine candidates as immunodominant epitope peptides from the Enterococcal Fibronectin Binding Protein-A (EfbA) protein for E. faecalis. Aim: To predict the immunodominant B-cell and T-cell epitopes from the EfbA protein of E. faecalis. Materials and Methods: An in-vitro and in-silico pilot study was conducted in the Department of Microbiology at Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, India. Total of 20 carious scrapings were collected from patients with root caries and were phenotypically characterised for E. faecalis and the EfbA genetic determinant by Polymerase Chain Reaction (PCR) amplification. The EfbA protein was retrieved from the National Center for Biotechnology Information (NCBI) database, after which prediction of antigenicity and allergenicity was performed via the VaXiJen and Algpred servers, respectively. The prediction of T-cell epitopes was carried out with the help of the EpiDOCK server, and B-cell predictions were made using the Kolaskar and Tongaonkar tool. Docking of the epitopes with reference to Human Leukocyte Antigens (HLA) alleles was assessed using the ClusPro server, and the results were evaluated for the T-cell dominant epitopes. Results: Among the 20 samples, E. faecalis was characterised in 5 (25%) patients, with three strains exhibiting Multidrug Resistant (MDR) traits. Among the three MDR strains, two strains showed the presence of the EfbA gene by PCR. In-silico analysis of the EfbA protein yielded a total of 17 epitopes, and based on the assessments, a final selection of two epitopes (IRAKGKNHK and LLLSAHPSY) was made, showing promising docking scores with HLA alleles and TLR2. Conclusion: Among the two epitopes, LLLSAHPSY was identified as the most significant immune-dominant epitope predicted, which needs to be further evaluated for vaccine synthesis and experimentation.https://www.jcdr.net/articles/PDF/20545/72668_CE(Ra1)_F(Sh)_QC(PS_IS)_PF1(AG_IS)_PFA(IS)_PB(AG_IS)_PN(IS).pdforal healthroot cariesvirulence |
| spellingShingle | Dev Arora AS Smiline Girija J Vijayashree Priyadharsini Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study Journal of Clinical and Diagnostic Research oral health root caries virulence |
| title | Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study |
| title_full | Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study |
| title_fullStr | Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study |
| title_full_unstemmed | Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study |
| title_short | Characterisation of EfbA from the Endodontic Pathogen Enterococcus faecalis and Prediction of Immunodominant EfbA Epitope Peptides: An In-vitro and In-silico Study |
| title_sort | characterisation of efba from the endodontic pathogen enterococcus faecalis and prediction of immunodominant efba epitope peptides an in vitro and in silico study |
| topic | oral health root caries virulence |
| url | https://www.jcdr.net/articles/PDF/20545/72668_CE(Ra1)_F(Sh)_QC(PS_IS)_PF1(AG_IS)_PFA(IS)_PB(AG_IS)_PN(IS).pdf |
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