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Kant R, Khan MS, Chopra M, Saluja D. Artificial intelligence-driven reverse vaccinology for Neisseria gonorrhoeae vaccine: Prioritizing epitope-based candidates. Front Mol Biosci 2024; 11:1442158. [PMID: 39193221 PMCID: PMC11347834 DOI: 10.3389/fmolb.2024.1442158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
Neisseria gonorrhoeae is the causative agent of the sexually transmitted disease gonorrhea. The increasing prevalence of this disease worldwide, the rise of antibiotic-resistant strains, and the difficulties in treatment necessitate the development of a vaccine, highlighting the significance of preventative measures to control and eradicate the infection. Currently, there is no widely available vaccine, partly due to the bacterium's ability to evade natural immunity and the limited research investment in gonorrhea compared to other diseases. To identify distinct vaccine candidates, we chose to focus on the uncharacterized, hypothetical proteins (HPs) as our initial approach. Using the in silico method, we first carried out a comprehensive assessment of hypothetical proteins of Neisseria gonorrhoeae, encompassing assessments of physicochemical properties, cellular localization, secretary pathways, transmembrane regions, antigenicity, toxicity, and prediction of B-cell and T-cell epitopes, among other analyses. Detailed analysis of all HPs resulted in the functional annotation of twenty proteins with a great degree of confidence. Further, using the immuno-informatics approach, the prediction pipeline identified one CD8+ restricted T-cell epitope, seven linear B-cell epitopes, and seven conformational B-cell epitopes as putative epitope-based peptide vaccine candidates which certainly require further validation in laboratory settings. The study accentuates the promise of functional annotation and immuno-informatics in the systematic design of epitope-based peptide vaccines targeting Neisseria gonorrhoeae.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence (IoE), University of Delhi, Delhi, India
| | - Mohd. Shoaib Khan
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence (IoE), University of Delhi, Delhi, India
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Mondol SM, Islam I, Islam MR, Shakil SK, Rakhi NN, Mustary JF, Amiruzzaman, Gomes DJ, Shahjalal HM, Rahaman MM. Genomic landscape of NDM-1 producing multidrug-resistant Providencia stuartii causing burn wound infections in Bangladesh. Sci Rep 2024; 14:2246. [PMID: 38278862 PMCID: PMC10817959 DOI: 10.1038/s41598-024-51819-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
The increasing antimicrobial resistance in Providencia stuartii (P. stuartii) worldwide, particularly concerning for immunocompromised and burn patients, has raised concern in Bangladesh, where the significance of this infectious opportunistic pathogen had been previously overlooked, prompting a need for investigation. The two strains of P. stuartii (P. stuartii SHNIBPS63 and P. stuartii SHNIBPS71) isolated from wound swab of two critically injured burn patients were found to be multidrug-resistant and P. stuartii SHNIBPS63 showed resistance to all the 22 antibiotics tested as well as revealed the co-existence of blaVEB-6 (Class A), blaNDM-1 (Class B), blaOXA-10 (Class D) beta lactamase genes. Complete resistance to carbapenems through the production of NDM-1, is indicative of an alarming situation as carbapenems are considered to be the last line antibiotic to combat this pathogen. Both isolates displayed strong biofilm-forming abilities and exhibited resistance to copper, zinc, and iron, in addition to carrying multiple genes associated with metal resistance and the formation of biofilms. The study also encompassed a pangenome analysis utilizing a dataset of eighty-six publicly available P. stuartii genomes (n = 86), revealing evidence of an open or expanding pangenome for P. stuartii. Also, an extensive genome-wide analysis of all the P. stuartii genomes revealed a concerning global prevalence of diverse antimicrobial resistance genes, with a particular alarm raised over the abundance of carbapenem resistance gene blaNDM-1. Additionally, this study highlighted the notable genetic diversity within P. stuartii, significant informations about phylogenomic relationships and ancestry, as well as potential for cross-species transmission, raising important implications for public health and microbial adaptation across different environments.
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Affiliation(s)
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shahriar Kabir Shakil
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | | | - Jannatul Ferdous Mustary
- Microbiology Department, Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, 1000, Bangladesh
| | - Amiruzzaman
- Department of Medicine, Sir Salimullah Medical College, Dhaka, 1000, Bangladesh
| | - Donald James Gomes
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Hussain Md Shahjalal
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Mizanur Rahaman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
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