Mycobacterium tuberculosis: Diagnostics, Drug Resistance and Molecular Epidemiology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 2174

Special Issue Editor


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Guest Editor
Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo 01246-000, Brazil
Interests: tuberculosis diagnostics; drug-resistant tuberculosis; public health

Special Issue Information

Dear Colleagues,

Mycobacterium tuberculosis remains a major global health threat, responsible for significant morbidity and mortality, particularly in low- and middle-income countries. The emergence and spread of drug-resistant forms, including multidrug-resistant (MDR) and extensively drug-resistant tuberculosis (XDR-TB), pose serious challenges to TB elimination efforts. Timely and accurate diagnosis, coupled with reliable detection of drug resistance, is essential to guide appropriate therapy and reduce transmission.

In recent years, advances in molecular diagnostics—such as line probe assays, real-time PCR platforms, and whole-genome sequencing—have transformed TB detection and drug susceptibility testing, offering faster and more precise results compared to conventional methods. Furthermore, molecular epidemiology studies provide critical insights into transmission dynamics, outbreaks, and the evolution of resistance-associated mutations.

This Special Issue aims to gather original research and reviews focusing on innovative diagnostic approaches, mechanisms of drug resistance, molecular surveillance, and epidemiological studies of M. tuberculosis. Contributions addressing challenges in implementation, novel biomarkers, and applications of genomic technologies in clinical or public health settings are particularly welcome.

I look forward to hearing from you.

Dr. Juliana Maíra Watanabe Pinhata
Guest Editor

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Keywords

  • Mycobacterium tuberculosis
  • tuberculosis diagnostics
  • drug-resistant tuberculosis
  • multidrug-resistant tuberculosis (MDR-TB)
  • molecular epidemiology
  • whole-genome sequencing
  • tuberculosis molecular typing

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Published Papers (2 papers)

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Research

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13 pages, 782 KB  
Article
Fluoroquinolone and Second-Line Injectable Resistance Among Rifampicin- and Isoniazid-Resistant Mycobacterium tuberculosis Clinical Isolates: A Molecular Study from a High-Burden Setting
by Rosângela Siqueira Oliveira, Angela Pires Brandao, Fabiane Maria de Almeida Ferreira, Sonia Maria da Costa, Vera Lucia Maria Silva, Lucilaine Ferrazoli, Erica Chimara and Juliana Maira Watanabe Pinhata
Microorganisms 2025, 13(11), 2470; https://doi.org/10.3390/microorganisms13112470 - 29 Oct 2025
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Abstract
Drug-resistant tuberculosis (DR-TB) threatens global TB control. We investigated the prevalence and molecular characteristics of second-line drug resistance among rifampicin (RIF)- and/or isoniazid (INH)-resistant Mycobacterium tuberculosis complex (MTBC) isolates in São Paulo, Brazil, using the MTBDRsl v. 2.0 line-probe assay. MTBC isolates [...] Read more.
Drug-resistant tuberculosis (DR-TB) threatens global TB control. We investigated the prevalence and molecular characteristics of second-line drug resistance among rifampicin (RIF)- and/or isoniazid (INH)-resistant Mycobacterium tuberculosis complex (MTBC) isolates in São Paulo, Brazil, using the MTBDRsl v. 2.0 line-probe assay. MTBC isolates RIF- and/or INH-resistant by GenoType MTBDRplus or phenotypic testing (2019–2021) were subsequently tested by MTBDRsl for fluoroquinolone (FQ) and injectable drugs (capreomycin, amikacin, kanamycin) resistance. Isolates with inferred mutations underwent Sanger sequencing. Of 13,557 isolates, 728 (5.4%) were RIF- and/or INH-resistant (297 INH-R, 235 RIF-R, 196 MDR). Among them, 623 (85.6%) were tested by MTBDRsl; 582 (93.4%) showed no additional resistance, while 41 (6.6%) carried mutations. FQ resistance was detected in 38 isolates (92.7%), mostly in gyrA (n = 35). Three isolates with gyrB mutations were wild-type by sequencing. Two MDR isolates harbored the rrs a1401g mutation, and one also harbored gyrA D94G. Sequencing confirmed resistance in 38 of 41 isolates. Most MDR strains with second-line mutations (n = 32/33; 97%) were pre-XDR. Affected patients were predominantly male (68.4%), with pulmonary TB (92.1%), and unfavorable outcomes (39.5%). Second-line resistance prevalence was low overall, but FQ resistance was high among MDR isolates. Findings support integrating molecular and sequencing-based tools for accurate detection and management of DR-TB. Full article
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Review

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28 pages, 797 KB  
Review
Molecular Epidemiology of Mycobacterium tuberculosis in Mexico
by Luis M. Rodríguez-Martínez, Jose L. Chavelas-Reyes, Carlo F. Medina-Ramírez, Eli Fuentes-Chávez, Zurisaday S. Muñoz-Troncoso, Ángeles G. Estrada-Vega, Enrique Rodríguez-Díaz, Diego Torres-Morales, María G. Moreno-Treviño and Josefina G. Rodríguez-González
Microorganisms 2025, 13(11), 2453; https://doi.org/10.3390/microorganisms13112453 - 25 Oct 2025
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Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, continues to be a leading cause of morbidity and mortality in Mexico, with more than 20,000 new cases annually and a rising proportion of drug-resistant strains. This work addresses the molecular epidemiology of TB in the [...] Read more.
Tuberculosis (TB), caused by Mycobacterium tuberculosis, continues to be a leading cause of morbidity and mortality in Mexico, with more than 20,000 new cases annually and a rising proportion of drug-resistant strains. This work addresses the molecular epidemiology of TB in the Mexican context, emphasizing its role in understanding transmission, genetic diversity, and resistance mechanisms. To achieve this, we reviewed molecular typing approaches including spoligotyping, Mycobacterial Interspersed Repetitive Unit–Variable Number Tandem Repeat (MIRU-VNTR) analysis, and whole-genome sequencing (WGS), which have been applied to characterize circulating lineages and identify drug-resistance-associated mutations. The results indicate that the Euro-American lineage (L4) predominates across the country, although significant regional variation exists, with Haarlem, LAM, T, and X sub lineages dominating in different states, and occasional detection of Asian (L2) and Indo-Oceanic (L1) lineages. Key resistance mutations were identified in katG, rpoB, pncA, and gyrA, contributing to the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains, particularly in border and marginalized regions. These findings highlight how social factors, such as migration, urban overcrowding, and comorbidities including diabetes and HIV, influence transmission dynamics. We conclude that integrating molecular tools with epidemiological surveillance is crucial for strengthening public health strategies and guiding interventions tailored to Mexico’s heterogeneous TB burden. Full article
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