Evidence map›Paper›PMID 42635856›Full record

ArticleMolecular biology reports2026

Comparative whole genome analysis of Mycobacterium tuberculosis isolated from BPaLM and individualized regimen treated patients at Dr. Soetomo Hospital, Indonesia.

Muhamad Frendy Setyawan, Amina K Shaban, Hayato Takihara, Yoshitaka Tateishi, Akihito Nishiyama, Yuriko Ozeki, Zakiyathun Nuha, Ni Made Mertaniasih, Shujiro Okuda, Soedarsono Soedarsono and 5 more

Abstract readComparative Study
PubMed Publisher
In one paragraph

Article in Molecular biology reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Muhamad Frendy SetyawanCellular and Molecular Mechanisms in Biological Systems (CEMBIOS) Research Group, Department of Biology, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok, West Java, Indonesia. m.frendy@sci.ui.ac.id.ORCID http://orcid.org/0000-0002-3159-9226
Amina K ShabanDepartment of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0001-6306-1298
Hayato TakiharaMedical AI Center, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0001-6884-8292
Yoshitaka TateishiDepartment of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0003-1200-0000
Akihito NishiyamaDepartment of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0003-4416-7710
Yuriko OzekiDepartment of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0003-0672-1039
Zakiyathun NuhaDepartment of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0001-8652-0469
Ni Made MertaniasihDepartment of Clinical Microbiology, Faculty of Medicine, Airlangga University, Surabaya, Indonesia. ni-made-m@fk.unair.ac.id.ORCID http://orcid.org/0009-0008-4094-6585
Shujiro OkudaMedical AI Center, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0002-7704-8104
Soedarsono SoedarsonoSub-pulmonology Department of Internal Medicine, Faculty of Medicine, Hang Tuah University, Surabaya, Indonesia.ORCID http://orcid.org/0000-0001-7317-5619
Maryam OmraniEmerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.ORCID http://orcid.org/0000-0002-0056-109X
Yuni RukminiatiNational Health Biology Laboratory, Ministry of Health, Surabaya, Indonesia.ORCID http://orcid.org/0000-0002-9935-7143
Ummi Amaliatush Sholichah Putri MerdekawatiLaboratory of Tuberculosis, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.ORCID http://orcid.org/0009-0009-9234-1163
Wayan Tunas ArtamaResearch Center for Biotechnology, Graduate School, Gadjah Mada University, Yogyakarta, Indonesia.ORCID http://orcid.org/0000-0002-8504-7558
Sohkichi MatsumotoDepartment of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0002-6106-7538

Funding

Directorate General of Higher Education and Culture, Ministry of Education and Culture under the "PMDSU and PKPI scholarship" 106.3/E4.4/KU/2023
6 · The paper itself

Abstract

backgroundThe World Health Organization (WHO) recommends whole genome sequencing (WGS) to support the detection of drug-resistant tuberculosis and the use of the new regimen BPaLM (Bedaquiline-Pretomanid-Linezolid-Moxifloxacin) to treat drug-resistant tuberculosis (TB). Genomic profiles of Mycobacterium tuberculosis (MTB) are needed to understand the regimen's future impact comprehensively.

methodsIn this study, we performed WGS to Mycobacterium tuberculosis isolates from rifampicin resistant tuberculosis patients at Dr. Soetomo Hospital. A total of 15 samples consisting of 14 clinical isolate samples (8 BPaLM and 6 Individualized treated patients) and one laboratory H37Rv reference strain were sequenced using the Illumina MiSeq platform and analyzed using Galaxy, TBProfiler, Mykrobe, and ResFinder.

resultsLineage analysis revealed that L2.2 was the predominant strain (48%), followed by L4, L4.3, L2.1, and L1.2. Most rifampicin-resistant and multidrug-resistant strains were associated with the East Asian Beijing lineage, with a smaller proportion linked to Euro-American lineages. The TBProfiler and Mykrobe demonstrated higher sensitivity than ResFinder (86% versus 79%), while all tools showed high specificity. Resistance associated mutations were primarily identified in rpoB, katG, embB, and pncA, with single nucleotide variants being the most common. This study has a limited number of representative clinical isolates, thus representing further study with a greater number of population sample of both groups.

conclusionsBeijing lineage strains predominated and were associated with increased drug resistance. Variants in efflux regulatory genes may contribute to the emergence of multidrug-resistant strains. The Mann-Whitney U test revealed no statistically significant difference between the two groups, with a p-value of 0.4136 (p > 0.05). Furthermore, genomic analysis revealed that the BPALM group exhibited a lower burden of single nucleotide polymorphisms (SNPs) and fewer unique cumulative genetic variants than the Individualized treatment group.

Indexed as

Mycobacterium tuberculosisTuberculosis, Multidrug-ResistantAntitubercular AgentsBacterial ProteinsDiarylquinolinesDrug Resistance, Multiple, BacterialGenome, BacterialHumansIndonesiaMicrobial Sensitivity TestsMoxifloxacinPolymorphism, Single NucleotideRifampinWhole Genome SequencingAntitubercular AgentsBacterial ProteinsbedaquilineDiarylquinolinesMoxifloxacinRifampinBPaLMMultidrug resistant tuberculosis (RR/MDR-TB)Single nucleotide polymorphisms (SNPs)TuberculosisWhole genome sequencing (WGS)

Identifiers

PMID42635856

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