The emergence of new mutations causing resistance to drugs used for rifampicin-resistant TB is of great concern in TB control. The development of resistance to Both LZD and DLM poses a significant threat to disease management, precluding the use of the WHO-recommended BPaLM regimen. The identification of previously unreported mutations highlights the dynamic nature of MTB resistance. It highlights the importance of understanding the selection pressures, raising concerns about their potential global spread and associated health implications. Comprehensive knowledge of the spectrum of mutations conferring resistance to these drugs in MTB and the resultant mutant phenotypes is critical for timely and accurate diagnosis and the design of optimal treatment, promoting the safe and effective use of these drugs in clinical settings.
The observed resistance may be due to novel mutations that have not yet been reported in global databases (like the WHO catalog of mutations). This is particularly relevant in geographically isolated settings or in cases of de novo acquisition of resistance under specific treatment pressures. Given the prior context of an inadequate initial regimen (due to false RR and true INH resistance), there could have been a strong selective pressure for the bacterium to adapt. This could have driven the selection of rare or novel resistance mechanisms.
Previous studies have described the spontaneous high-level resistance of M. tuberculosis (MTB) to the nitroimidazole prodrugs DLM and PMD through mutations that occur in one of the five genes previously associated with nitroimidazole activation and resistance, including the fbiC gene [8]. Their classification in the WHO catalog v2 [12] may vary. Still, they are categorized as group 2 mutations for DLM and PMD. They are associated with reduced susceptibility to both drugs and mutations affecting the biosynthesis of coenzyme F420, the target of PMD and DLM. While resistance to LZD is linked with mutations in the rplC gene, these mutations may be classified as Category I or II mutations in the WHO catalogue, indicating varying levels of resistance to LZD. They can be associated with increased MIC values for LZD and mutations in the ribosomal protein L3, the target of LZD [12].
It is unknown whether higher doses of nitroimidazoles and LZD may overcome resistance to achieve the desired therapeutic effect without excess toxicity associated with especially LZD use [3]. Higher doses could lead to alterations in the metabolism of DLM and LZD within the bacterial cell, potentially impacting the ability of these drugs to target and inhibit specific enzymes or pathways involved in bacterial growth and survival [3].
Xpert provided a RR result at the start, while pDST and WGS yielded a discordant result. The discrepancies observed between Xpert MTB/RIF and the pDST and WGS in rifampicin resistance detection were predominantly driven by delayed probe binding by Xpert MTB/RIF, in this case in sample with low bacillary load. Probe dropout or significantly delayed probe hybridization (indicated by elevated ΔCt values exceeding the recommended threshold of 4 cycles) can falsely indicate rifampicin resistance even in the absence of true mutations [13–15]. Other studies have found that the accuracy of the Xpert in detecting RR can be influenced by the amount of bacteria present in the sample. When there are very few bacteria (paucibacillary samples), the test may occasionally yield incorrect results indicating resistance [16].
This case report highlights the need for an active, ongoing surveillance and monitoring of emerging drug resistance in MTB, also in low resource settings, where limited access to healthcare, poverty and social determinants of health, and high burden of HIV/AIDS have been identified as key factors contributing to the rise of DR-TB [16]. Additionally, the lack of access to universal DST in resource-limited areas with a high prevalence of DR-TB poses a significant barrier to timely diagnosis, further exacerbating the spread of DR-TB within these communities. Moreover, the high burden of DR-TB in these regions underscores the importance of prioritizing resources and conducting targeted studies to understand the local drivers of DR-TB emergence and transmission [17]. By addressing these challenges and implementing comprehensive strategies, it is possible to mitigate the impact of DR-TB and improve treatment outcomes in these vulnerable populations.
In conclusion, the lengthy diagnostic journey outlined in the case study highlights the challenges in diagnosing drug resistance, and in supporting patients to take the full treatment course. As shown here, multiple diagnostic modalities are necessary to accurately characterize drug resistance profiles in MTB strains. The identification of baseline resistance to second-line drugs DLM and LZD emphasizes the evolving landscape of drug resistance in tuberculosis and the challenges in managing DR-TB.