Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia
Background: Tuberculosis (TB) is the second concern of a fatal infectious disease in the world caused by Mycobacterium tuberculosis (MTB). Indonesia has many regions that is known as a hotspot region for MTB cases, one of the most cities high newly case detected in 5 years was Surabaya. In 2022, Sur...
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| Format: | Article |
| Language: | English |
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Wolters Kluwer Medknow Publications
2025-04-01
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| Series: | International Journal of Mycobacteriology |
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| Online Access: | https://journals.lww.com/10.4103/ijmy.ijmy_54_25 |
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| author | Ni Made Mertaniasih Muhamad Frendy Setyawan Ummi Amaliatush Sholichah Putri Merdekawati Nurul Wiqoyah Deby Kusumaningrum Irfan Arif Ikhwani Sohkichi Matsumoto |
| author_facet | Ni Made Mertaniasih Muhamad Frendy Setyawan Ummi Amaliatush Sholichah Putri Merdekawati Nurul Wiqoyah Deby Kusumaningrum Irfan Arif Ikhwani Sohkichi Matsumoto |
| author_sort | Ni Made Mertaniasih |
| collection | DOAJ |
| description | Background:
Tuberculosis (TB) is the second concern of a fatal infectious disease in the world caused by Mycobacterium tuberculosis (MTB). Indonesia has many regions that is known as a hotspot region for MTB cases, one of the most cities high newly case detected in 5 years was Surabaya. In 2022, Surabaya reported a higher pulmonary TB (PTB) prevalence rate of 0.35%. This study aimed to investigate the genomic and phylogenetic characteristics of MTB from isolates of rifampicin-sensitive PTB patients in Surabaya using whole genome sequencing (WGS).
Methods:
This study is a cross-sectional study to descriptively analyses WGS data using bioinformatics. Out of 8 enrolled drug-sensitive PTB patients; however, only three cultured isolates successfully grew on MB 7H11/OADC agar and subjected for WGS analysis.
Results:
Whole genome analysis revealed that all the samples were drug sensitive. The identified samples were majority belonged to lineage 4.4.1 (Euro-American [S-type]) and we found a novel strain in East Java region known as Lineage 4.10 (Euro-American [Uganda 1]). In addition, we identified a novel SNVs predicted to be associated with genomic adaptation in fgd1, embC, embA, and rv0565c under antibiotic pressures.
Conclusion:
WGS predicts that all the samples from pulmonary rifampicin-sensitive TB patients in this study were drug sensitive. We report the first discovery of a novel L4.10 strain, classified as Uganda 1, in Surabaya, Indonesia. |
| format | Article |
| id | doaj-art-c4601b0430f5414a9956c15e6a37e19f |
| institution | Matheson Library |
| issn | 2212-5531 2212-554X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Wolters Kluwer Medknow Publications |
| record_format | Article |
| series | International Journal of Mycobacteriology |
| spelling | doaj-art-c4601b0430f5414a9956c15e6a37e19f2025-07-04T07:41:48ZengWolters Kluwer Medknow PublicationsInternational Journal of Mycobacteriology2212-55312212-554X2025-04-0114215316310.4103/ijmy.ijmy_54_25Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, IndonesiaNi Made MertaniasihMuhamad Frendy SetyawanUmmi Amaliatush Sholichah Putri MerdekawatiNurul WiqoyahDeby KusumaningrumIrfan Arif IkhwaniSohkichi MatsumotoBackground: Tuberculosis (TB) is the second concern of a fatal infectious disease in the world caused by Mycobacterium tuberculosis (MTB). Indonesia has many regions that is known as a hotspot region for MTB cases, one of the most cities high newly case detected in 5 years was Surabaya. In 2022, Surabaya reported a higher pulmonary TB (PTB) prevalence rate of 0.35%. This study aimed to investigate the genomic and phylogenetic characteristics of MTB from isolates of rifampicin-sensitive PTB patients in Surabaya using whole genome sequencing (WGS). Methods: This study is a cross-sectional study to descriptively analyses WGS data using bioinformatics. Out of 8 enrolled drug-sensitive PTB patients; however, only three cultured isolates successfully grew on MB 7H11/OADC agar and subjected for WGS analysis. Results: Whole genome analysis revealed that all the samples were drug sensitive. The identified samples were majority belonged to lineage 4.4.1 (Euro-American [S-type]) and we found a novel strain in East Java region known as Lineage 4.10 (Euro-American [Uganda 1]). In addition, we identified a novel SNVs predicted to be associated with genomic adaptation in fgd1, embC, embA, and rv0565c under antibiotic pressures. Conclusion: WGS predicts that all the samples from pulmonary rifampicin-sensitive TB patients in this study were drug sensitive. We report the first discovery of a novel L4.10 strain, classified as Uganda 1, in Surabaya, Indonesia.https://journals.lww.com/10.4103/ijmy.ijmy_54_25genomicmycobacterium tuberculosis/mycobacterium tuberculosis complexsingle nucleotide polymorphismsurveillancewhole genome sequencing |
| spellingShingle | Ni Made Mertaniasih Muhamad Frendy Setyawan Ummi Amaliatush Sholichah Putri Merdekawati Nurul Wiqoyah Deby Kusumaningrum Irfan Arif Ikhwani Sohkichi Matsumoto Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia International Journal of Mycobacteriology genomic mycobacterium tuberculosis/mycobacterium tuberculosis complex single nucleotide polymorphism surveillance whole genome sequencing |
| title | Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia |
| title_full | Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia |
| title_fullStr | Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia |
| title_full_unstemmed | Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia |
| title_short | Potential Role of Whole Genome Sequencing to Predict the Virulence, Anti-TB Resistance, and Variants of Mycobacterium tuberculosis Strains from Rifampicin-sensitive Pulmonary Tuberculosis Patients in Surabaya, East Java, Indonesia |
| title_sort | potential role of whole genome sequencing to predict the virulence anti tb resistance and variants of mycobacterium tuberculosis strains from rifampicin sensitive pulmonary tuberculosis patients in surabaya east java indonesia |
| topic | genomic mycobacterium tuberculosis/mycobacterium tuberculosis complex single nucleotide polymorphism surveillance whole genome sequencing |
| url | https://journals.lww.com/10.4103/ijmy.ijmy_54_25 |
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