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ORIGINAL ARTICLE
Year : 2021  |  Volume : 10  |  Issue : 4  |  Page : 421-427

The espD full gene as a potential biomarker in active pulmonary tuberculosis


1 Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga; Department of Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
2 Department of Microbiology, Faculty of Medicine, Universitas Ciputra, Surabaya, Indonesia; Department of Bacteriology School of Medicine, Niigata University, Niigata, Japan
3 Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
4 Department of Health, Faculty of Vocational Studies, Universitas Airlangga; Department of Proteomic Laboratory, University CoE Research Center for Bio Molecule Engineering, Universitas Airlangga, Surabaya, Indonesia
5 Department of Proteomic Laboratory, University CoE Research Center for Bio Molecule Engineering, Universitas Airlangga; Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
6 Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
7 Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia; Department of Bacteriology School of Medicine, Niigata University, Niigata, Japan

Correspondence Address:
Ni Made Mertaniasih
Jl. Mayjen Prof. Dr. Moestopo No. 47 Surabaya 60131
Indonesia
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/ijmy.ijmy_198_21

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Background: Pulmonary tuberculosis (PTB) is still a major health problem worldwide. The espD has a potential to be a new biomarker because it is important for the espA, espC, and ESX-1 protein secretion system that are actively expressed in active multiplication of Mycobacterium tuberculosis complex. Methods: A total of 55 sputum samples and 41 culture isolates from newly diagnosed PTB patients at Dr. Soetomo Academic Hospital were collected from September 2016 to April 2019. The tested samples using polymerase chain reaction targeted 555 bp of espD gene and sequencing. Clone Manager Version 6 and NCBI BLAST were used to align the gene sequence against wild-type M. tuberculosis. The prediction of T-cell epitope in espD gene was detected by GENETYX. The three-dimensional (3D) structure of espD was modeled by SWISS-MODEL and I-TASSER and was visualized with PyMOL. Results: From 55 sputum samples, 43 (78.18%) showed positive results, and all culture isolates showed positive results. In addition, all sequenced samples showed 100% homolog with M. tuberculosis H37Rv gene without detected variant or mutation. There were four T-cell epitopes that could be obtained. The 3D model had a I-TASSER confidence score of 3.91 with estimated RMSD of approximately 14.5 Å. The structure consists of a main fold of a three-stranded antiparallel β-sheet and a long α-helix surrounded by several minor secondary structures. Conclusions: This study provides a brief information about the sequence, epitope prediction, and 3D structure of EspD protein from M. tuberculosis strains in Indonesia.


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