TB or not TB? Improving the understanding and diagnosis of tuberculosis through metabolomics

Mass spectrometry-based metabolomics for the investigation of antibiotic-bacterial interactions

With the development of analytical technologies especially mass spectrometry, metabolomics is becoming increasingly hot in the field of studying antibiotic-bacterial interactions. On the one hand, metabolomics can reveal metabolic perturbations in bacteria in the presence of antibiotics and expose metabolic mechanisms. On the other hand, through in-depth analysis of bacterial metabolic profiles, biomarkers and bioactive secondary metabolites with great potential as drug precursors can be discovered. This review focuses on the experimental workflow of bacterial metabolomics and its application to study the interaction between bacteria and antibiotics. Metabolomics improves the understanding of antibiotic lethality, reveals metabolic perturbations in antibiotic-resistant bacteria, guides the diagnosis and antibiotic treatment of infectious diseases, and aids in the exploration of antibacterial metabolites in nature. Furthermore, current limitations and directions for future developments in this area are discussed.

Cost-Effective Whole Transcriptome Sequencing Landscape and Diagnostic Potential Biomarkers in Active Tuberculosis

Tuberculosis (TB) is a prevalent and severe infectious disease that poses a significant threat to human health. However, it is frequently disregarded as there are not enough quick and accurate ways to diagnose tuberculosis. Here, we develop a strategy for tuberculosis detection to address the challenges, including an experimental strategy, namely, Double Adapter Directional Capture sequencing (DADCSeq), an easily operated and low-cost whole transcriptome sequencing method, and a computational method to identify hub differentially expressed genes as well as the diagnosis of TB based on whole transcriptome data using DADCSeq on peripheral blood mononuclear cells (PBMCs) from active TB and latent TB or healthy control. Applying our approach to create a robust and stable TB multi-mRNA risk probability model (TBMMRP) that can accurately distinguish active and latent TB patients, including active TB and healthy controls in clinical cohorts, this diagnostic biomarker was successfully validated by several independent cross-platform cohorts with favorable performance in differentiating active TB from latent TB or active TB from healthy controls and further demonstrated superior or similar diagnostic accuracy compared to previous diagnostic markers. Overall, we develop a low-cost and effective strategy for tuberculosis diagnosis; as the clinical cohort increases, we can expand to different disease kinds and learn new features through our disease diagnosis strategy.

Potential anti-TB investigational compounds and drugs with repurposing potential in TB therapy: a conspectus

The latest WHO report estimates about 1.6 million global deaths annually from TB, which is further exacerbated by drug-resistant (DR) TB and comorbidities with diabetes and HIV. Exiguous dosing, incomplete treatment course, and the ability of the tuberculosis bacilli to tolerate and survive current first-line and second-line anti-TB drugs, in either their latent state or active state, has resulted in an increased prevalence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and totally drug-resistant TB (TDR-TB). Although a better understanding of the TB microanatomy, genome, transcriptome, proteome, and metabolome, has resulted in the discovery of a few novel promising anti-TB drug targets and diagnostic biomarkers of late, no new anti-TB drug candidates have been approved for routine therapy in over 50 years, with only bedaquiline, delamanid, and pretomanid recently receiving tentative regulatory approval. Considering this, alternative approaches for identifying possible new anti-TB drug candidates, for effectively eradicating both replicating and non-replicating Mycobacterium tuberculosis, are still urgently required. Subsequently, several antibiotic and non-antibiotic drugs with known treatment indications (TB targeted and non-TB targeted) are now being repurposed and/or derivatized as novel antibiotics for possible use in TB therapy. Insights gathered here reveal that more studies focused on drug-drug interactions between licensed and potential lead anti-TB drug candidates need to be prioritized. This write-up encapsulates the most recent findings regarding investigational compounds with promising anti-TB potential and drugs with repurposing potential in TB therapy.

Identification of serum biomarkers for active pulmonary tuberculosis using a targeted metabolomics approach

Although tuberculosis (TB) is a severe health problem worldwide, the current diagnostic methods are far from optimal. Metabolomics is increasingly being used in the study of infectious diseases. We performed metabolome profiling to identify potential biomarkers in patients with active TB. Serum samples from 21 patients with active pulmonary TB, 20 subjects with latent TB infection (LTBI), and 28 healthy controls were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by multivariate and univariate analyses. Metabolic profiles indicated higher serum levels of glutamate, sulfoxy methionine, and aspartate and lower serum levels of glutamine, methionine, and asparagine in active TB patients than in LTBI subjects or healthy controls. The ratios between metabolically related partners (glutamate/glutamine, sulfoxy methionine/methionine, and aspartate/asparagine) were also elevated in the active TB group. There was no significant difference in the serum concentration of these metabolites according to the disease extent or risk of relapse in active TB patients. Novel serum biomarkers such as glutamate, sulfoxy methionine, aspartate, glutamine, methionine, and asparagine are potentially useful for adjunctive, rapid, and noninvasive pulmonary TB diagnosis.

Use of Liquid Chromatography-Mass Spectrometry-Based Metabolomics to Identify Biomarkers of Tuberculosis

Liquid chromatography-mass spectrometry (LC-MS) based metabolomics has proven to be a powerful analytical tool for biomarker screening. Here we describe two workflows which employ untargeted metabolomics to study serum biomarkers in tuberculosis patients. Expression profiles for samples of hydrophilic metabolites and hydrophobic metabolites (lipids) may be obtained by this method.

Metabolomics biomarkers for tuberculosis diagnostics: current status and future objectives

Numerous studies have contributed to our current understanding of the complex biology of pulmonary tuberculosis and subsequently provided solutions to its control or eradication. Metabolomics, a newcomer to the Omics research domain, has significantly contributed to this understanding by identifying biomarkers originating from the disease-associated metabolome adaptations of both the microbe and host. These biomarkers have shed light on previously unknown disease mechanisms, many of which have been implemented toward the development of improved diagnostic strategies. In this review, we will discuss the role that metabolomics has played in tuberculosis research to date, with a specific focus on new biomarker identification, and how these have contributed to improved disease characterization and diagnostics, and their potential clinical applications.