Abstract
Despite global control efforts, tuberculosis remains the leading infectious cause of death, with rising incidence, pediatric cases, and drug-resistant strains posing major public health challenges. Mycobacteria, including Mycobacterium tuberculosis, possess a lipid-rich, dual-membrane cell envelope that contributes to their impermeability, drug resistance, and unique pathogenic mechanisms. Some lipids play key roles in modulating host immune responses, enabling survival within macrophages, and promoting granuloma formation. Since it is known that lipid remodeling of the cell envelope is correlated with the antibiotics tolerance in mycobacteria we used liquid chromatography coupled to mass spectrometry to analyze the lipid profiles of M. tuberculosis clinical isolates with diverse drug-resistance characteristics in order to investigate if there is any link between Mtb lipids composition, its drugs susceptibility and the antimycobacterial activity of natural small molecules used in combination with first line antibiotics. The results showed that among cross combinations of antibiotics and natural products (piperine and thymoquinone) the potentiation of antimycobacterial activity was obtained in all strains only for rifampicin. Drug-resistant isolates presented the shift in glycerophospholipids building the inner membrane towards molecules with shorter acyl chains, but the decreased membrane hydrophobic thickness was compensated in some strains by increased membrane rigidity. The pXDR/XDR isolates accumulated mycobactins loaded iron and showed dysregulation in the production of phthiocerol/phthiodiolone dimycocerosates and triacylglycerols. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41967-5.