Metabolic Profiles of Clinical Isolates of Drug-Susceptible and Multidrug-Resistant Mycobacterium tuberculosis: A Metabolomics-Based Study

Abstract

Background

Mycobacterium tuberculosis (MTB) is a global and highly deleterious pathogen that creates an enormous pressure on global public health. Although several effective drugs have been used to treat tuberculosis, the emergence of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) has further increased the public health burden. The aim of this study was to describe in depth the metabolic changes in clinical isolates of drug-susceptible Mycobacterium tuberculosis (DS-MTB) and MDR-MTB and to provide clues to the mechanisms of drug resistance based on metabolic pathways.

Methods

Based on the minimum inhibition concentration (MIC) of multiple anti-tuberculosis drugs, two clinical isolates were selected, one DS-MTB isolate (isoniazid MIC=0.06 mg/L, rifampin MIC=0.25 mg/L) and one MDR-MTB isolate (isoniazid MIC=4 mg/L, rifampin MIC=8 mg/L). Through high-throughput metabolomics, the metabolic profiles of the DS-MTB isolate and the MDR-MTB isolate and their cultured supernatants were revealed.

Results

Compared with the DS-MTB isolate, 128 metabolites were significantly altered in the MDR-MTB isolate and 66 metabolites were significantly altered in the cultured supernatant. The differential metabolites were significantly enriched in pyrimidine metabolism, purine metabolism, nicotinate and nicotinamide metabolism, arginine acid metabolism, and phenylalanine metabolism. Furthermore, metabolomics analysis of the bacterial cultured supernatants showed a significant increase in 10 amino acids (L-citrulline, L-glutamic acid, L-aspartic acid, L-norleucine, L-phenylalanine, L-methionine, L-tyrosine, D-tryptophan, valylproline, and D-methionine) and a significant decrease in 2 amino acids (L-lysine and L-arginine) in MDR-MTB isolate.

Conclusion

The present study provided a metabolite alteration profile as well as a cultured supernatant metabolite alteration profile of MDR-MTB clinical isolate, providing clues to the potential metabolic pathways and mechanisms of multidrug resistance.

Keywords:

• Mycobacterium tuberculosis
• multidrug-resistantMycobacterium tuberculosis
• drug-susceptibleMycobacterium tuberculosis
• metabolomics
• metabolic pathway

Abbreviations

TB, Tuberculosis; MTB, Mycobacterium tuberculosis; MDR-MTB, Multidrug-resistant Mycobacterium tuberculosis; DS-MTB, Drug-susceptible Mycobacterium tuberculosis; MIC, Minimum inhibition concentration; MDR-TB, Multidrug-resistant tuberculosis; RR-TB, Rifampicin-resistant tuberculosis; PLS-DA, Partial Least Squares Discrimination Analysis; OPLS-DA, Orthogonal Partial Least Squares Discrimination Analysis; VIP, Variable Importance in the Projection; SCID, Severe combined immunodeficiency.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors declare that they have no conflict of interest.

Additional information

Funding

This study was funded by: Shanghai 2020 “Science and technology innovation action plan” technological innovation fund:Clinical Study on New Short-Course treatment regimens and Host-Directed Therapy for MDR-TB (20Z11900500). Shanghai Clinical Research Center for infectious disease (tuberculosis) (Grant ID:19MC1910800). The three-year action plan for promoting clinical skills and clinical innovation in municipal hospitals of Shanghai Shenkang 2020–2022 (Grant ID: SHDC2020CR6024). National Natural Science Foundation of China (Nos.82102251). Shanghai key clinical specialty construction project - Tuberculosis department (Shslczdzc03001).