INTRODUCTION
Drug-resistant tuberculosis (DR-TB) continues to be a global public health concern, requiring rapid and accurate diagnostic strategies to combat its progression and transmission. Among these, the comparison of phenotypic and genotypic methods for drug susceptibility testing (DST) is crucial for understanding their respective strengths and limitations. This study assesses both phenotypic resistance using Löwenstein–Jensen medium and genotypic resistance using the GenoType MTBDRplus assay in Mycobacterium tuberculosis isolates. It evaluates resistance patterns to both first-line and second-line anti-TB drugs, including isoniazid (INH), rifampicin (RIF), streptomycin (STR), ethambutol (EMB), fluoroquinolones, and aminoglycosides. The results emphasize the growing burden of multidrug-resistant (MDR) and extensively drug-resistant tuberculosis (XDR-TB), underscoring the need for diagnostic approaches that combine speed and reliability. While genotypic testing enables rapid detection, certain phenotypically resistant strains remain undetected, suggesting a diagnostic gap. This calls for an integrative diagnostic framework that combines molecular assays and phenotypic methods for robust MDR-TB detection and management.
DRUG RESISTANCE PATTERNS IN TUBERCULOSIS
Understanding drug resistance patterns in M. tuberculosis is vital for tailoring effective treatment regimens. This study identified high levels of resistance to INH (84.85%) and significant resistance to RIF (46.97%), which are two cornerstone drugs in first-line TB therapy. Notably, nearly half of the isolates also showed resistance to STR (48.48%) and EMB (30.30%). These resistance rates illustrate the ongoing challenge of treating TB with standard regimens and highlight the urgent need for routine susceptibility testing, especially in regions with a high burden of MDR-TB. Such data not only inform clinicians but also shape public health strategies for TB control.
GENOTYPIC VERSUS PHENOTYPIC TESTING
Genotypic methods such as the GenoType MTBDRplus offer speed and specificity in detecting mutations associated with drug resistance, particularly for INH and RIF. This study found high concordance between genotypic and phenotypic results—95.16% for INH and 94.74% for RIF. However, discordant cases underscore a limitation of molecular methods, especially when resistance is due to novel or uncommon mutations not covered by the assay. Phenotypic testing remains essential for detecting such cases. Therefore, the integration of both testing modalities enhances diagnostic precision and ensures that resistant strains are not missed, thus supporting more effective treatment planning.
CHARACTERIZATION OF MDR AND XDR-TB STRAINS
Multidrug-resistant tuberculosis is defined by resistance to both INH and RIF, while extensively drug-resistant TB includes additional resistance to fluoroquinolones and aminoglycosides. In this study, 29 MDR-TB isolates were identified, of which 41.37% were resistant to fluoroquinolones and 31.03% to both fluoroquinolones and aminoglycosides—thus meeting XDR-TB criteria. These findings indicate a disturbing trend in the emergence of highly resistant TB strains that are increasingly difficult to treat. Identifying these resistance profiles early is crucial for administering second-line therapies effectively and avoiding therapeutic failure, further emphasizing the need for advanced DST systems.
ROLE OF SEQUENCING IN TB DIAGNOSTICS
While current genotypic assays are effective in detecting common resistance mutations, whole-genome sequencing (WGS) offers a more comprehensive view of resistance mechanisms. Cases in this study where phenotypic resistance was not matched by genotypic results suggest the presence of mutations not targeted by the GenoType MTBDRplus assay. Integrating WGS can help bridge this diagnostic gap by identifying novel mutations and providing insights into the evolutionary pathways of resistance. Sequencing could ultimately become the gold standard for MDR/XDR-TB diagnostics, especially when combined with rapid assays for initial screening.
IMPLICATIONS FOR TB CONTROL STRATEGIES
The findings of this study have significant implications for public health policy and TB management programs. The coexistence of high phenotypic resistance with partial genotypic detection underlines the need for dual diagnostic approaches in TB-endemic regions. Surveillance programs should incorporate both molecular and culture-based methods to improve case detection and reduce transmission. Additionally, routine resistance profiling for all confirmed TB cases will enable early identification of MDR/XDR forms, ensuring timely initiation of appropriate treatment and reducing the likelihood of further drug resistance amplification.
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