Discovering biomarkers for diagnosis, infection stage identification, treatment, and management of pediatric tuberculosis in the era of multi-omics: a narrative review
Introduction
Background
Tuberculosis (TB) is a chronic respiratory infectious disease caused by Mycobacterium tuberculosis (Mtb) infection. The World Health Organization’s 2024 Global tuberculosis Report estimated that there were about 1.30 million new TB cases and 0.19 million deaths in 2023 among children and young adolescents (0–14 years of age), which was regarded as one of the top ten causes of child death (1). Although albeit low in absolute numbers, an increasing trend of pediatric TB cases (aged <15 years) was notified in the European Union/ European Economic Area countries between 2015 and 2023 (2). Compared with adults, children with TB have the characteristics of low bacterial count, increased frequency of latent infection evolving into active TB, and atypical symptoms etc. (3-5).
The integration of clinical, radiographic, and microbiological data is used to diagnose TB [pulmonary TB (PTB), a patient with TB disease involving the lung parenchyma; extrapulmonary TB (EPTB), TB affecting extrapulmonary sites within the body exclusively or in combination with PTB] in children (6,7). The gold standard for diagnosing TB is through microbiological confirmation which supports the diagnosis of confirmed TB (8). Confirmed TB was defined as positive molecular or culture testing for Mtb from at least one respiratory sample. Unconfirmed TB has no microbiological confirmation, but had at least two signs and symptoms of TB (8). However, the sensitivity of microbiological detection methods inevitably correlates with the bacterial burden, especially in the testing for childhood TB. Most affected children have negative smear results, with a culture positivity rate of less than 40% (9). Tuberculin skin test (TST) and interferon gamma release assay (IGRA) are recognized by World Health Organization (WHO) for widespread latent tuberculosis infection (LTBI) screening (9). TST can’t distinguish between latent and active infection and is less sensitive in children (10). The specificity of IGRAs is superior to that of TST, however, IGRAs showed no better performance than TST in low income countries (11). Due to the atypical clinical symptoms of childhood TB, it is prone to misdiagnosis or delayed treatment. Timely and accurate diagnosis will effectively utilize drug resources and avoid inappropriate use of anti-TB drugs.
Rationale and knowledge gap
The development of high-throughput technology (HT) has promoted revolutions in multiple omics disciplines, including proteomics, transcriptomics, metabolomics, lipidomics and genomics. By integrating data from various omics approaches, uncharacterized biological pathways related to specific diseases or conditions can be identified. The accessibility of omics technologies had driven research into novel biomarkers for TB, such as diagnosis, distinguishing different stages of infection, and monitoring treatment responses (12,13). However, most reported omics biomarkers lack multicenter validation and show discrepancy. While previous study provided a general overview of omics technologies for pediatric TB diagnostics, their analysis only focused primarily on proof-of-concept studies and rarely evaluated biomarker reproducibility across populations (14). This review synthesized studies in recent ten years, identifying overlapping biomarkers and future challenges for biomarker validation.
Objectives
This review aimed to summarize existing literature on pediatric TB across omics, which identified overlapping biomarkers and related biological pathways. In addition, we also discussed themes and challenges within clinical and technological contexts in this field (Figure 1). We present this article in accordance with the Narrative Review reporting checklist (available at https://pm.amegroups.com/article/view/10.21037/pm-25-46/rc).
Methods
In this review we searched PubMed for original articles published from 2013.01.01 to 2025.07.20, with the search terms (“pediatric tuberculosis” OR “children”) AND (“proteomics” OR “transcriptomic” OR “metabolomic” OR “lipidomics” OR “radiomic” OR “geonomics”), reporting the biomarkers for pediatric TB in diagnosis, distinguishing different stages of infection, and monitoring treatment responses. Table 1 showed the search strategy summary. The age range of children in the study was 0–14 years and the restriction of language was English.
Table 1
| Items | Specification |
|---|---|
| Date of search | 1/1/2024–20/7/2025 |
| Databases and other sources searched | PubMed |
| Search terms used | (“Pediatric tuberculosis” OR “children”) AND (“proteomics” OR “transcriptomic” OR “metabolomic” OR “lipidomics” OR “radiomic” OR “geonomics”) |
| Timeframe | 2013–2025 |
| Inclusion and exclusion criteria | Includes any reference about omics of pediatric TB, excludes the references of the non-pediatric or non-TB or non-original articles |
| Selection process | The first author selected all the references independently |
TB, tuberculosis.
Discussion
Proteomics
Proteomics encompasses various techniques focused on studying proteins expressed in cells or organisms. It primarily investigates their composition, structure, function, interactions, expression profiles, and modifications. Proteomics is an innovative approach used to identify new biomarkers for diagnosing, prognosing, and understanding the pathophysiological mechanisms related to diseases (15). This methodology can be used to study various biological fluids such as saliva, urine, and blood, with a particular focus on changes in protein abundance that may occur with disease, age, or treatment response. Over the past decade, proteomics technology has been applied in various biomedical contexts, including detecting diagnostic markers, understanding disease mechanisms, tracking variations in proteomic profiles triggered by internal or external signals, and mapping signaling cascades in disease-specific mechanisms (16).
Several different techniques have been used to analyze proteins in biological samples. The enzyme-linked immunosorbent assay (ELISA) method is primarily used for the detection of specific known proteins, widely applied but with limited detection capabilities. With recent advancements in high-throughput proteomics technology, researchers can simultaneously study hundreds to thousands of proteins (17). For non-targeted discovery studies, mass spectrometry (MS) is a critical methodology for protein analysis, capable of identifying and quantifying complex proteomes at the sub-nanogram level. This technology has been widely used to detect biomarkers for TB diagnosis (18,19).
Due to the molecules secreted during the host immune response process after Mtb infection, such as cytokines, which are mainly transmitted through the bloodstream and easily collected, most proteomic biomarker studies for TB diagnosis are based on blood samples. Researchers began to focus on the immune response of the host to Mtb at the beginning of the 21st century, identifying various cytokines involved in Mtb immune responses. Cytokines such as interferon (IFN)-γ and tumor necrosis factor-α (TNF-α) were identified as candidate biomarkers for TB (20-22). Similarly, interferon-gamma-induced protein 10 (IP-10), also known as CXCL10, is an inflammatory-mediating chemokine secreted by various immune cells such as monocytes, neutrophils, macrophages, and endothelial cells. It was upregulated in both proteomics and transcriptomics in pediatric TB which has been widely evaluated as a diagnostic biomarker for active TB (ATB) and LTBI (23-26).
Compared to adults, there is less research on children, mainly aimed at exploring the diagnostic potential of proteomic biomarkers to identify different disease states (active TB versus health, LTBI, or other diseases) and monitor treatment responses for TB (Table 2). These proteins are critically involved in cytokine signaling, complement activation, and innate immunity pathways, such as cytokines, chemokines, and acute phase proteins. Despite significant statistical methodological differences between studies, these proteins are identified relatively frequently, suggesting they are either general markers of infection, interacting with other proteins characteristic of TB, or specific proteins of TB. According to Togun’s study, estimated sensitivity, specificity and area under the curve (AUC) from different logistic discriminant models in the training and test datasets are all between 0.70 and 0.75 (25). Fossati et al. aimed to construct a parsimonious biosignature for pediatric TB disease and finally found the 6-protein model achieved the best performance with 96.7% sensitivity at 70% specificity [95% confidence interval (CI): 0.83–0.99] on test data (27).
Table 2
| Reference | Year published | Country population | Age groups | HIV test | Candidate biomarker | Reported association | Sample size |
|---|---|---|---|---|---|---|---|
| Togun (25) | 2020 | Gambia | 0–14 years | Negative | IL-1ra, IL-7 and IP-10 | TB disease and other respiratory diseases | 104 TB (44 bacteriologically confirmed TB and 60 clinically diagnosed TB), 327 children with other respiratory disease |
| Fossati (27) | 2025 | Gambia, Peru, South Africa, Uganda | 0–14 years | 57 positive, 454 negative | 3-protein model: APOM, HEG1, AMBP. 4-protein model: WARS1, CD44, TNC, APOM. 5-protein model: CD44, TNC, APOM, MMP2, IGHV3-33. 6-protein model: CD44, TNC, APOM, MMP2, FCGR3A, IGKV1D-33 | Unconfirmed TB (negative by sputum-based testing) and confirmed TB | 133 confirmed TB, 120 unconfirmed TB, 231 unlikely TB, 19 healthy control no TB infection, 8 healthy control with latent TB infection |
HIV, human immunodeficiency virus; IL, interleukin; IP-10, interferon γ-induced protein 10; TB, tuberculosis.
IP-10 (CXCL10) is an easily detectable cytokine evaluated as a diagnostic biomarker for ATB. However, the high polymorphism of these proteins in the entire population may limit their widespread application in biological characteristics. From a technical perspective, plasma sampling, sample preparation and data collection need a standardized process to mitigate bias.
Transcriptomic
Transcriptomics focuses on comprehensively analyzing all RNA molecules in cells or tissues under specific spatiotemporal conditions, quantitatively revealing dynamic patterns of gene expression, variable splicing events, and transcriptional regulatory networks through high-throughput sequencing techniques or microarray platforms. It encompasses both coding and non-coding RNA, and gene expression profiles can be used to discover biomarkers, diagnose diseases, predict progression, and monitor responses to treatment (28). Due to improved sample processing methods, whole blood transcriptomics has led the way in the discovery of diagnostic biomarkers for TB, surpassing proteomics and metabolomics. This has resulted in the development of rapid sample input-response multiplex polymerase chain reaction (PCR) platforms (29). In total cellular RNA, 80% consists of ribosomal RNA (rRNA), 15% is transfer RNA (tRNA), leaving only 5% for mRNA and all other forms of RNA. Analysis of host-encoded RNA can be used to study the gene expression patterns throughout the entire disease process and may exhibit different profiles. Non-coding RNA, which does not encode any proteins, is typically associated with regulatory functions and may undergo changes in different disease states.
In addition to discovering biomarkers, interpreting differential expression results based on pathophysiological cascades or regulatory circuitry is a critical outcome of transcriptomic analysis. Studies indicate that blood transcriptome changes can appear before conventional diagnosis of TB (30). Measuring simplified gene expression profiles in clinical settings burdened by TB can aid in diagnosis, prognosis, and treatment decisions in pediatric TB. Sweeney et al. conducted a meta-analysis using 14 publicly available datasets comprising over 2,500 samples from 10 countries. Their findings showed that a composite score (TB score) based on the mRNA levels of three differentially expressed genes in blood (GBP5, DUSP3, and KLF2) can distinguish TB from other diseases (31). A prototype assay kit for Mtb host response (Mtb-HR), based on gene-xpert real-time polymerase chain reaction (RT-PCR) detection, has been developed to quantify relative mRNA levels of three gene markers in whole blood samples from patients (32). Olbrich et al. conducted the first prospective evaluation of pediatric Mtb-HR, using a recommended TB score (GBP5, DUSP3, and KLF2) of 1.5, achieving an AUC of 0.85. The diagnostic accuracy was similar across different age groups and among children with malnutrition, human immunodeficiency virus (HIV), and EPTB (33).
Since 2013, 17 studies have explored transcriptional responses in pediatric TB, identifying diagnostic, prognostic, and treatment response biomarkers through gene expression analysis (Table 3). Several successful studies involved cohorts of hundreds of cases, employing standardized sample processing methods and accurate patient identification. The majority aimed to distinguish ATB from health or other disease states using differential gene expression levels, statistical filters, and hierarchical clustering in training sets [ATB vs. LTBI and healthy controls (HCs)]. These genes are primarily enriched in NF-κB signaling pathways, cytokine-cytokine receptor interactions, and various infection response pathways (including responses to TB).
Table 3
| Reference | Year published | Country population | Age groups | HIV test | Candidate biomarker | Reported association | Sample size | Research type |
|---|---|---|---|---|---|---|---|---|
| Verhagen (34) | 2013 | Venezuela | 1–14 years | Negative | ACOT7, AMPH, CHRM2, GLDC, HBD, PIGC, S100P, SNX17, STYXL1, TAS2R46 | ATB, LTBI and HC | 9 TB, 9 LTBI, 9 HC | Case control st |
| Dhanasekaran (26) | 2013 | India | 0–35 months | Not mentioned | RAB33A, CXCL10, SEC14L1, FOXP3 and TNFRSF1A | ATB, LTBI and HC | 13 TB, 90 LTBI, 107 HC | Case control st |
| Anderson (35) | 2014 | South Africa, Malawi, Kenya | 0–14 years | 166 positive, 180 negative | DEFA1, GBP5, GBP6 | ATB, LTBI and other diseases | 114 PTB, 57 LTBI, 175 with other disease | Case control st |
| Li (36) | 2015 | China | 0–5 years | Negative | IL-9 mRNA | Immune-related markers for childhood TB diagnosis | 39 TB (13 PTB, 26 EPTB), 25 HC | Case control st |
| Wang (37) | 2015 | China | 1–10 years | Not mentioned | miRNA-31 | A diagnostic marker in pediatric TB patients | 65 TB, 60 HC | Case control st |
| Fletcher (38) | 2016 | South Africa | Less than 2 years | Negative | 461 genes | Infants vaccinated with BCG | 26 PTB with culture positive, 20 TB without positive culture, 18 with exposure to TB but negative, 25 HC | Case control st |
| Jenum (39) | 2016 | India | 71–146 months | Positive <1% | (I) CD14, FCGR1A, FPR1, MMP9, RAB24, SEC14L1, TIMP2, BLR1, CD3E, CD8A, IL7R, and TGFBR2. (II) BPI, CD3E, CD14, FPR1, IL4, TGFBR2, TIMP2 and TNFRSF1B | (I) MTB-related pathology and high relevance to a future POC test for pediatric TB. (II) TB with or without asymptomatic siblings | (I) 40 MTB Smear/Culture positive, 48 MTB Smear/Culture negative. (II) 15 with asymptomatic siblings (TST ≥10 mm, TST-positive), 24 with asymptomatic siblings (TST <10 mm, TST-negative) | Case control st |
| Zhou (40) | 2016 | China | 0–14 years | Negative | 29 miRNAs | Diagnosis of TB | 28 TB patients and 24 healthy children | Case control st |
| Gjøen (41) | 2017 | India | 2–216 months | Positive <1% in both settings | 7-transcript signature: MMP9, CD3E, NOD2, GBP5, IFITM1/3, KIF1B and TNIP1 10-transcript signature: IFNG, NLRP1, NLRP3, TGFBR2, TAGAP, NOD2, GBP5, IFITM1/3, KIF1B and TNIP1 | TB-cases and symptomatic non-TB cases | 47 TB cases (19 definite/28 probable) and 36 asymptomatic household controls | Case control st |
| Hemingway (42) | 2017 | South Africa | 0–14 years | Negative | 204 unique transcripts mapped to 165 genes of known function | T cell gene and function in childhood TB | 9 TBM and 9 HC; 13 TBM and 28 PTB | Case control st |
| Rohlwink (43) | 2019 | South Africa | 0.1–12.9 years | Negative | (I) 2,230 genes; (II) 389 significantly different genes | (I) TBM cases and healthy controls. (II) Lumbar and ventricular CSF from TBM | 24 healthy controls and 15 TBM cases | Case control st |
| Tornheim (44) | 2020 | India | 3–14 years | Negative | 71 differentially expressed genes | TB and LTBI | 16 TB, 32 TB-exposed controls | Case control st |
| Dutta (45) | 2020 | India | 0–14 years | Negative | 116 transcripts | Integration of metabolomics and transcriptomics for childhood TB | 16 confirmed TB, 332 controls | Cohort study, case control study |
| Tornheim (46) | 2021 | 0-14 years | Negative | India | IDO-1 | Diagnosis of pediatric TB | 19 bacteriologically confirmed TB, 38 controls | Case control study |
| Bobak (47) | 2023 | South Africa | 0–5 years | Negative | 30 genes | Progression of TB | TB disease (n=10). Tuberculin conversion (n=26) | Cohort study |
| Olbrich (33) | 2024 | South Africa, Tanzania, Mozambique, Malawi, India | 0–14 years | 89/639 (14%) positive | GBP5, DUSP3, and KLF2 | Diagnosis of TB | Confirmed TB (n=202), unconfirmed TB (n=230), unlikely TB (n=207) | Case control study |
| Sweetser (48) | 2025 | The Gambia, Uganda | 0–14 years | 12/91 (13.2%) positive | GBP5, DUSP3, and TBP | Classify TB severity | Severe TB (n=28), non-severe TB (n=78) | Case control study |
ATB, active TB; BCG, Bacillus Calmette-Guérin; CSF, cerebrospinal fluid; EPTB, extrapulmonary TB; HC, healthy controls; HIV, human immunodeficiency virus; LTBI, latent tuberculosis infection; MTB, Mycobacterium tuberculosis; POC, point-of-care; PTB, pulmonary TB; TB, tuberculosis; TBM, tuberculous meningitis; TST, tuberculin skin test.
GBP5 was present in the biomarkers identified by three studies, which was found increased in pediatric TB (33,35,41,48). It was also presented increased in young adults (12–18 years) with TB which supports the importance of type-1 interferon signaling in pediatric TB disease (30). Matrix metalloproteinase-9 (MMP-9) was also significantly upregulated in TB cases compared with HC (39,41). In addition, Azikin et al. found the expression levels of MMP-9 in the group of exposed and Mtb infected children have no differences (49).
The expression of MMP-9 was analysed in many studies in the pathophysiology of TB and its induction is regulated by receptor-mediated signalling pathways (50,51). MMPs exhibit endopeptidase activity, leading to inflammatory tissue damage in TB patients. Scientists are exploring ways to reduce the destruction of Mtb related matrix and reduce the pulmonary inflammation caused by TB by inhibiting the activity of MMP, so as to enhance the treatment of TB (52). On the contrary, CD3E and TGFBR2 were part of a biosignature separating TB cases from asymptomatic HC which showed a decreased likelihood of TB disease (39,41). MicroRNA (miRNA) is a kind of endogenous non coding small RNA molecule with a length of about 18–25 nucleotides, which precisely regulates gene expression through post transcriptional regulation mechanism (53). MiRNAs regulate many important physiological processes, such as cell proliferation and differentiation, organismal metabolism, and host immunity (54,55). Many studies indicate that miRNAs can be identified as biomarkers for the rapid diagnosis of TB (56,57). Some miRNAs actively regulate immune responses to clearMtb, while certain miRNAs are upregulated to inhibit the expression of immune-related genes, preventing TB clearance. This can be suggested that targeting miRNAs could improve immune system function for treating TB (58). MiR-31, conflicting reports (upregulated in Wang-2015 vs. downregulated in Zhou-2016) were presented which may be influenced by disease stage or age differences. It regulates NF-κB and Wnt signaling and modulates T-cell differentiation and macrophage polarization (59).
Further validation in a large multi-center cohort is essential. In addition, an RT-PCR-based validation step is best provided for transcriptomic study due to RNA instability in tropical temperatures.
Future technological advancements may simplify and normalizing, making these signatures such as GBP5 suitable for translation into a point of-care test.
Metabolomic
Metabolomic seeks to comprehensively profile endogenous biochemical entities present in clinical specimens (such as lipids, fatty acids, sugars, amino acids, nucleotides), with surpassing 20,000 distinct metabolic signatures in human samples (60). Nuclear magnetic resonance (NMR) and MS are two primary analytical platforms used to measure metabolite changes, identifying metabolites with characteristic differential expression. These metabolites can serve as biomarkers for diagnosis, disease differentiation, and monitoring drug therapy progress (Table 4). Typical samples studied in metabolomics include biological fluids such as blood, urine, sputum, cerebrospinal fluid (CSF), feces, and bacterial cultures.
Table 4
| Reference | Year published | Age group | HIV test | Country population | Candidate biomarker | Reported association | Sample size | Platform |
|---|---|---|---|---|---|---|---|---|
| Mason (61) | 2016 | Less than 13 years | 3 positive | South Africa | Methylcitric, 2-ketoglutaric, quinolinic and 4-hydroxyhippuric | TBM | 12 TBM, 21 non-TBM, 31 controls (suspected but negative) | GC-MS |
| Sun (62) | 2016 | 0–14 years | Not mentioned | China | L-valine, pyruvic acid and betaine | Diagnosis of pediatric TB | 45 ATB, 38 RTIs group, 30 HC | 1HNMR Spectra |
| Mason (63) | 2017 | 3 months–13 years | 7 positive | South Africa | Alanine, asparagine, glycine, lysine, and proline | Diagnosis of TBM | 33 “definite” and “probable” TBM, 34 suspected of TBM but negative | GC-MS |
| Andreas (64) | 2020 | 0–14 years | Negative | Gambia, Londin | Glutamate, N and O-acetyl glycoproteins (GlycA), phenylalanine, alanine | TB and other diseases | 36 bacteriologically confirmed TB, 55 clinically diagnosed TB, 57 other diseases | 1HNMR spectroscopy. MS |
| Dutta (45) | 2020 | 0–14 years | Negative | India | Gamma glutamylalanine, gamma-glutamylglycine, glutamine, and pyridoxate | Treatment response | 16 ATB, 32 MTB-exposed but uninfected household contacts | UPLC-MS/MS |
| Comella-Del-Barrio (65) | 2021 | 0–14 years | Not mentioned | Haiti | No details | Different diagnostic certainty of TB | 62 TB (6-bacteriologically confirmed TB, 52 unconfirmed TB, 4 unlikely TB); 55 HC | 1HNMR spectra |
| Tornheim (46) | 2022 | 0–14 years | Negative | India | Kynurenine, tryptophan, the K/T ratio, and IDO-1 gene | diagnosis of pediatric TB | 19 bacteriologically confirmed TB, 38 controls | Q-Exactive high resolution/accurate mass spectrometer |
| Samuel (66) | 2024 | 0–12 years | Negative | South Africa | Mannose, arabinose, nonanoic acid and propanoic acid | Discriminate TBM cases from controls | Bacteriologically proven TBM (definite TBM; n=21) and non-meningitis (control; n=25) patients | 1HNMR GCxGC-TOFMS |
| Isaiah (67) | 2024 | 0–13 years | Negative | South Africa | 1-methylnicotinamide, 3-hydroxyisovaleric acid, 5-aminolevulinic acid, N-acetylglutamine and methanol | Diagnose severe TBM | 32 patients with TBM (stratified into stages 1, 2 and 3), 39 controls | 1HNMR |
ATB, active TB; GC-MS, gas chromatography-mass spectrometry; GCxGC-TOFMS, two-dimensional gas chromatography-time of flight mass spectrometry; HC, healthy controls; HIV, human immunodeficiency virus; HNMR, nuclear magnetic resonance spectroscopy of hydrogen; MTB, Mycobacterium tuberculosis; RTI, respiratory tract infections; TB, tuberculosis; TBM, tuberculous meningitis; UPLC-MS/MS, ultra performance liquid chromatography–tandem mass spectrometry.
TB affects multiple metabolic pathways in the host, including those involving nitric oxide, amino acids, glucose, and lipid metabolism (45). The pro-inflammatory and anti-inflammatory responses in ATB and LTBI patients lead to dysregulation of cytokines and related metabolites involved in relevant metabolic pathways. Glutamine, the most abundant amino acid in the bloodstream, is converted to tricarboxylic acid (TCA) cycle metabolites like glutamate through the activity of various enzymes. Some studies have reported significantly reduced levels of Gln in active TB patients, while children infected with Mtb also show lower Gln levels, reflecting the adaptive mechanisms of Mtb and host immune responses (62,68). Dutta et al.’s study indicated that n-acetylneuraminic acid had a potential diagnostic value with an AUC of 0.66. After one month of quinolinic acid ester treatment, the AUC was 0.77, and after successful pyrazinic acid ester treatment, the AUC was 0.87. Ultimately, the treatment response was determined by four metabolites (γ-glutamyl asparagine, γ-glutamyl glycine, glutamine, and pyrazinic acid), yielding an AUC of 0.86 (45). Through analysis, it was found that n-acetylneuraminic acid interacts immunoregulatorily between lymphocytes and non-lymphocytes. Pyrazinic acid salts are associated with metabolic genes regulated by p53 and mitochondrial translation. Additionally, numerous differential metabolites are related to changes in energy metabolism, immune physiology, pathogen cell wall damage, and repair (69).
The well-known association between HIV and TB coinfection in children was not assessed in the metabolomic study. The role of nutrition in driving changes in metabolomic and lipidomic profiles in children with TB has not been clearly explained. In addition, the number of bacteriologically confirmed pediatric TB cases was small. More children with PTB, as well as children with EPTB and immunocompromised children are needed to be included in future research to validate the potential of proposed metabolites as diagnostic biomarkers for pediatric TB.
Lipidomics
Lipidomics is a branch of metabolomics that primarily studies lipid metabolites. Traditional metabolomics focuses on molecules soluble in the cytoplasmic solute, whereas lipidomics primarily examines membrane-bound, water-insoluble molecules. Compared to cytoplasmic metabolites, lipids often contain more hydrocarbons, are larger in size, less polar, and have slower turnover rates (70). Mtb is one of the most complex lipid-coated organisms in nature, forming a barrier between the pathogen and the host. It possesses extensive lipid biosynthetic capabilities within its genome (71). Due to the limited similarity between the lipid structures of Mtb and human lipids, they are potential candidates for diagnostic and therapeutic biomarkers.
High-throughput lipidomics analysis has confirmed that the regulation of toxic lipids in Mtb occurs through metabolic coupling (72). Similarly, lipidomics analysis reveals the relationship between iron acquisition, phospholipid homeostasis, and the virulence of Mtb (73). The virulence factors including mycolic acids, trehalose dimycolates (TDMs), phthiocerol dimycocerosates (PDIMs), and phosphatidylinositol (PI)-based phosphatidylinositol mannosides (PIMs), lipomannan (LM), lipoarabinomannan (LAM), and mannose-capped LAM (ManLAM) are most essential for Mtb’growth and virulence. LAM and its structural variants can be recognized by and activate human CD1b-restricted T cells, and antibodies against LAM can modulate the immune response to Mtb (74). LAM is the only WHO-endorsed TB biomarker that can be detected in urine, an easily collected sample (75). FujiLAM could potentially add value to the rapid diagnosis of TB in children by comparing accuracy of LAM urine tests for diagnosis of PTB in children, with sensitivity of 42–64.9% and specificity of 60–83.8% (76,77). The potential utility of LAM urine testing was also found in HIV-negative children with severe acute malnutrition (SAM) (78). Pal and colleagues conducted lipid analysis of drug-susceptible (DS) and drug-resistant (DR) strains of Mtb, analyzing the lipid composition of clinical isolates. They confirmed that DR Mtb strains have distinct lipid signatures compared to DS strains (79). Lipidomics technology has also elucidated the specific connections between rifampicin resistance and lipid factors, providing targets for diagnosis and treatment (80). Lahiri et al. validate a new organism-wide lipidomic analysis platform for drug-resistant mycobacteria (80). Rifampin resistance mutations lead to altered concentrations of mycobactin siderophores and acylated sulfoglycolipids. Changes in mycobacteria, carboxymybacteriacins, and sulfolipids may be characteristic of mutations at rifampicin binding sites. Enzymes involved in key-steps of FA and cholesterol uptake, catabolism and storage may be feasible targets to treat mycobacterial infections (80).
Shivakoti et al. identified various baseline lipid levels associated with the development of treatment failure in TB. In patients with treatment failure, baseline levels of cholesterol esters, oxylipins, 15,16-dihydroxyeicosatrienoic acid [an oxygenated derivative of α-linolenic acid (ALA)], and certain phosphatidylcholines were lower. Conversely, higher levels were observed in lipid families such as ceramides, diacylglycerols, and various triglycerides. Specific cholesterol esters were highlighted as the best predictive factors for treatment failure in TB (81). Some researches have found that lipid metabolism is related to the occurrence and increase risk of anti-TB drug-induced liver injury (ATB-DILI) (82-84). Wang et al. conducted the first analysis of plasma lipidomics in patients with ATB-DILI. By analyzing the lipid metabolism spectrum, potential lipid biomarkers involved in DILI were identified (85).
Radiomic
Radiomics is defined as extracting and analyzing a large number of high-dimensional imaging features from quantitative medical images. These radiomic parameters describe multi-dimensional features of imaging data, detecting Quantify differences that are not visible to the naked eye (86). Radiomics involves several steps: first, acquiring medical images; next, trained radiologists identify regions of interest (ROIs) and annotate or segment them. Once ROIs are defined, applying imaging informatics and machine learning algorithms can increase efficiency and accuracy. Simultaneously, this non-invasive technology can assist clinicians in making preliminary assessments in cases where disease progression or effective sample collection is challenging.
Currently, radiomics features have been repeatedly used to establish diagnostic, prognostic, and treatment response prediction models for pediatric diseases (87-89). Studies have shown that imaging omics has demonstrated clinical utility in the application of PTB, for example, in adult TB populations, it has been used to differentiate between pulmonary tumors and non-tuberculous mycobacterial pneumonia (90), differentiating between drug-sensitive and drug-resistant PTB (91). According to reports, the non-symptomatic presentations of PTB often share significant phenotypic similarities with pediatric respiratory infections, notably CAP (92). It is one of the most common reasons for pediatric hospitalizations in developed countries and a major cause of death among children in developing countries (6,93,94). Clinical diagnosis of community-acquired pneumonia (CAP) is challenging due to varying symptoms with age, often lacking specificity in young children. Numerous studies indicate that clinical, laboratory, and chest X-ray findings are not reliably distinguishing between bacterial and viral etiologies in children with CAP (95,96). Current pathogen detection methods commonly used suffer from drawbacks such as long detection periods, false positives, false negatives, making it difficult to achieve rapid pathogen diagnosis (97). In terms of imaging, there are many similarities in the radiological manifestations between pediatric TB and CAP, such as consolidations, nodular shadows, and ground-glass opacities (98).
Up to now, only one study on the differential diagnosis of childhood PTB and CAP has been retrieved. Wang et al. (99) extracted lesion characteristics from computed tomography (CT) images of 53 clinically diagnosed pediatric TB patients and 62 CAP patients, 5 and 6 key features respectively were selected to establish radiological characteristics for lung consolidation areas and lymph node areas. Ultimately, these radiological features were combined with clinical factors (duration of fever) to construct a predictive model. The results showed that the classification performance of the combined model (AUC =0.971, 95% CI: 0.912–1) was superior to that of the clinical model alone (AUC =0.832, 95% CI: 0.677–0.987) and the imaging model alone (AUC =0.957, 95% CI: 0.889–1).
Relative to adults, there is a relative lack of imaging omics research in the field of pediatric PTB, limited mainly to studies on differential diagnosis between TB and pneumonia. Several factors contribute to this difference. Firstly, there are significantly fewer pediatric TB cases compared to adults. Secondly, the incidence of pulmonary tumors and non-tuberculous mycobacterial pneumonia is very low in children, resulting in limited and insufficient data available to establish radiological models. Multiple center cases are needed in the future to construct and validate radiomics models to rapid detect pediatric TB.
Genomics
Genomic approaches elucidate pediatric TB through dual lenses: host genetic susceptibility and pathogen variation biomarkers. Several studies identified child-specific susceptibility loci, as shown in Table 5. IL-4 gene SNP rs2243268 and rs2243274 showed a reduced risk of developing EPTB and severe TB in children (100). Toll-like receptor 1 (TLR1) Gene SNP rs5743618 genotypes showed a decreased level of TNF-α and CXCL10 production (101).
Table 5
| Reference | Year published | Country population | Age groups | HIV test | Candidate biomarker | Reported association | Sample size |
|---|---|---|---|---|---|---|---|
| Qi (100) | 2014 | China | 0–14 years | Negative | IL-4: rs2243268, rs2243274 | Reduced risk of developing EPTB and severe TB | 154 PTB, 192 EPTB, 374 HC |
| Qi (101) | 2015 | China | 0–14 years | Negative | TLR1: rs5743618 | Increased risk for TB | 340 TB, 366 HC |
| Li (102) | 2016 | China | 0–14 years | Negative | SFTPA 1: rs1914663 | Increased risk for TB | 342 TB, 365 HC |
| Maruthai (103) | 2022 | India | 0–14 years | Negative | Vitamin D receptor gene and DNA methylation | Increased susceptibility to TB | 43 TB, 33 HC |
EPTB, extrapulmonary TB; HC, healthy controls; HIV, human immunodeficiency virus; PTB, pulmonary TB; TB, tuberculosis.
In the past decade, advancements in routine whole-genome sequencing (WGS) technology have transformed biomedical research. WGS analysis of Mtb is playing an increasingly vital role in diagnosis, predicting drug sensitivity, epidemiological investigations, host-pathogen interactions, pathogenesis, and global epidemiological surveys (104,105). The WGS of the first strain of Mtb (the widely used laboratory strain H37Rv) marked a milestone in TB research (106). Over time, WGS has been used to analyze clinical isolates of Mtb with varying drug susceptibility profiles, as well as laboratory-derived drug-resistant mutants (107-109). Rifampin resistance is conferred by mutation of its target, the subunit of the RNA polymerase (RpoB) (110). Furthermore, using WGS to definitively distinguish between relapse and reinfection, and for testing experimental drug regimens, is of significant importance (111).
Currently, there is limited research on the genetic susceptibility of children with TB which is easily influenced by population and regional distribution. More systematic research were needed about Mtb variation biomarkers in the Tb bacilli isolated from children with TB.
Conclusions
Due to the atypical clinical symptoms of pediatric TB and the similarity between PTB and pneumonia symptoms, it is a longstanding challenge for clinicians to promptly confirm and initiate correct antimicrobial treatment before pathogen detection. Unlike traditional detection methods, biomarkers play a crucial role in accurate diagnosis and prognosis of TB, identification of LTBI, and prediction of the risk of progression to ATB. Additionally, biomarkers can monitor treatment progress, evaluate treatment efficacy, and contribute to understanding drug resistance mechanisms and new drug development. Multi-omics integration can reveal interconnected networks of molecular cross-talk mechanisms, providing a network-based framework to decode pathophysiological cascades in TB and propel biomarker-driven therapeutic optimization.
Through cross-omics integration, we identified these biomarkers recurrently validated across independent cohorts and omics layers. IP-10 (CXCL10) was upregulated in both proteomics and transcriptomics in pediatric TB, involving in chemokine signaling, recruitment of T cells and monocytes. GBP5 was identified in multiple studies as a key diagnostic and prognostic biomarker which was part of the interferon-inducible GTPases, involved in cell-autonomous immunity against intracellular pathogens. MMP-9 was also significantly upregulated in TB cases compared with HC but had no differences in the group of exposed and Mtb infected children. Reducing the inhibition of MMP activity can reduce pulmonary inflammation and enhance the treatment of TB. On the contrary, CD3E and TGFBR2 were part of a biosignature separating TB cases from asymptomatic HC which showed a decreased likelihood of TB disease. Glutamine was consistently reduced in pediatric TB which reflects immune cell metabolic reprogramming (glutaminolysis for energy). It correlates with increased TCA cycle activity and oxidative stress. TB-LAM has good diagnostic value for children with TB, especially in HIV co-infected and severe acute malnutrition (SAM) children.
However, despite extensive research by investigators into pediatric TB across multiple omics disciplines, there was minimal overlap of biomarkers between studies. This is due to several factors including differences in study cohorts, specimen collection, criteria for TB diagnosis, and diversity in data analysis methods. Moving forward, it is imperative to expand sample sets, differentiate more detailed subgroups, and employ advanced machine learning techniques for further validation in prospective studies.
Acknowledgments
None.
Footnote
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References
- WHO. Global Tuberculosis Report 2024. Available online: https://publichealthupdate.com/global-tuberculosis-report-2024/, accessed July 25, 2025.
- Cristea V, Ködmön C, Gomes Dias J, et al. Increase in tuberculosis among children and young adolescents, European Union/European Economic Area, 2015 to 2023. Euro Surveill 2025;30:2500172. [Crossref] [PubMed]
- Gaensbauer J, Broadhurst R. Recent Innovations in Diagnosis and Treatment of Pediatric Tuberculosis. Curr Infect Dis Rep 2019;21:4. [Crossref] [PubMed]
- Tchakounte Youngui B, Tchounga BK, Graham SM, et al. Tuberculosis Infection in Children and Adolescents. Pathogens 2022;11:1512. [Crossref] [PubMed]
- Howard-Jones AR, Marais BJ. Tuberculosis in children: screening, diagnosis and management. Curr Opin Pediatr 2020;32:395-404. [Crossref] [PubMed]
- Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study. Lancet 2019;394:757-79. [Crossref] [PubMed]
- Golden MP, Vikram HR. Extrapulmonary tuberculosis: an overview. Am Fam Physician 2005;72:1761-8.
- Graham SM, Cuevas LE, Jean-Philippe P, et al. Clinical Case Definitions for Classification of Intrathoracic Tuberculosis in Children: An Update. Clin Infect Dis 2015;S179-87. [Crossref] [PubMed]
- Jaganath D, Beaudry J, Salazar-Austin N. Tuberculosis in Children. Infect Dis Clin North Am 2022;36:49-71. [Crossref] [PubMed]
- Mastrolia MV, Sollai S, Totaro C, et al. Utility of tuberculin skin test and IGRA for tuberculosis screening in internationally adopted children: Retrospective analysis from a single center in Florence, Italy. Travel Med Infect Dis 2019;28:64-7. [Crossref] [PubMed]
- Sollai S, Galli L, de Martino M, et al. Systematic review and meta-analysis on the utility of Interferon-gamma release assays for the diagnosis of Mycobacterium tuberculosis infection in children: a 2013 update. BMC Infect Dis 2014;14:S6. [Crossref] [PubMed]
- Martínez-Pérez A, Estévez O, González-Fernández Á. Contribution and Future of High-Throughput Transcriptomics in Battling Tuberculosis. Front Microbiol 2022;13:835620. [Crossref] [PubMed]
- Pitaloka DAE, Syamsunarno MRAAA, Abdulah R, et al. Omics Biomarkers for Monitoring Tuberculosis Treatment: A Mini-Review of Recent Insights and Future Approaches. Infect Drug Resist 2022;15:2703-11. [Crossref] [PubMed]
- Jakhar S, Bitzer AA, Stromberg LR, et al. Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development. Int J Mol Sci 2020;21:6979. [Crossref] [PubMed]
- de Hoog CL, Mann M. Proteomics. Annu Rev Genomics Hum Genet 2004;5:267-93. [Crossref] [PubMed]
- Aslam B, Basit M, Nisar MA, et al. Proteomics: Technologies and Their Applications. J Chromatogr Sci 2017;55:182-96. [Crossref] [PubMed]
- Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. Lab Invest 2022;102:1170-81. [Crossref] [PubMed]
- Mutavhatsindi H, Calder B, McAnda S, et al. Identification of novel salivary candidate protein biomarkers for tuberculosis diagnosis: A preliminary biomarker discovery study. Tuberculosis (Edinb) 2021;130:102118. [Crossref] [PubMed]
- Xu D, Li Y, Li X, et al. Serum protein S100A9, SOD3, and MMP9 as new diagnostic biomarkers for pulmonary tuberculosis by iTRAQ-coupled two-dimensional LC-MS/MS. Proteomics 2015;15:58-67. [Crossref] [PubMed]
- Ribeiro-Rodrigues R. Sputum cytokine levels in patients with pulmonary tuberculosis as early markers of mycobacterial clearance. Clin Diagn Lab Immunol 2002;9:818-23. [Crossref] [PubMed]
- Küpeli E, Karnak D, Beder S, et al. Diagnostic accuracy of cytokine levels (TNF-alpha, IL-2 and IFN-gamma) in bronchoalveolar lavage fluid of smear-negative pulmonary tuberculosis patients. Respiration 2008;75:73-8. [Crossref] [PubMed]
- Peresi E, Silva SM, Calvi SA, et al. Cytokines and acute phase serum proteins as markers of inflammatory regression during the treatment of pulmonary tuberculosis. J Bras Pneumol 2008;34:942-9. [Crossref] [PubMed]
- Qiu X, Xiong T, Su X, et al. Accumulate evidence for IP-10 in diagnosing pulmonary tuberculosis. BMC Infect Dis 2019;19:924. [Crossref] [PubMed]
- Qiu X, Tang Y, Yue Y, et al. Accuracy of interferon-γ-induced protein 10 for diagnosing latent tuberculosis infection: a systematic review and meta-analysis. Clin Microbiol Infect 2019;25:667-72. [Crossref] [PubMed]
- Togun T, Hoggart CJ, Agbla SC, et al. A three-marker protein biosignature distinguishes tuberculosis from other respiratory diseases in Gambian children. EBioMedicine 2020;58:102909. [Crossref] [PubMed]
- Dhanasekaran S, Jenum S, Stavrum R, et al. Identification of biomarkers for Mycobacterium tuberculosis infection and disease in BCG-vaccinated young children in Southern India. Genes Immun 2013;14:356-64. [Crossref] [PubMed]
- Fossati A, Wambi P, Jaganath D, et al. Plasma proteomics for biomarker discovery in childhood tuberculosis. Nat Commun 2025;16:6657. [Crossref] [PubMed]
- Manzoni C, Kia DA, Vandrovcova J, et al. Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. Brief Bioinform 2018;19:286-302. [Crossref] [PubMed]
- McHugh L, Seldon TA, Brandon RA, et al. A Molecular Host Response Assay to Discriminate Between Sepsis and Infection-Negative Systemic Inflammation in Critically Ill Patients: Discovery and Validation in Independent Cohorts. PLoS Med 2015;12:e1001916. [Crossref] [PubMed]
- Zak DE, Penn-Nicholson A, Scriba TJ, et al. A blood RNA signature for tuberculosis disease risk: a prospective cohort study. Lancet 2016;387:2312-22. [Crossref] [PubMed]
- Sweeney TE, Braviak L, Tato CM, et al. Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. Lancet Respir Med 2016;4:213-24. [Crossref] [PubMed]
- Södersten E, Ongarello S, Mantsoki A, et al. Diagnostic Accuracy Study of a Novel Blood-Based Assay for Identification of Tuberculosis in People Living with HIV. J Clin Microbiol 2021;59:e01643-20. [Crossref] [PubMed]
- Olbrich L, Verghese VP, Franckling-Smith Z, et al. Diagnostic accuracy of a three-gene Mycobacterium tuberculosis host response cartridge using fingerstick blood for childhood tuberculosis: a multicentre prospective study in low-income and middle-income countries. Lancet Infect Dis 2024;24:140-9. [Crossref] [PubMed]
- Verhagen LM, Zomer A, Maes M, et al. A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children. BMC Genomics 2013;14:74. [Crossref] [PubMed]
- Anderson ST, Kaforou M, Brent AJ, et al. Diagnosis of childhood tuberculosis and host RNA expression in Africa. N Engl J Med 2014;370:1712-23. [Crossref] [PubMed]
- Li Q, Yu L, Xin T, et al. Increased IL-9 mRNA expression as a biomarker to diagnose childhood tuberculosis in a high burden settings. J Infect 2015;71:273-6. [Crossref] [PubMed]
- Wang JX, Xu J, Han YF, et al. Diagnostic values of microRNA-31 in peripheral blood mononuclear cells for pediatric pulmonary tuberculosis in Chinese patients. Genet Mol Res 2015;14:17235-43. [Crossref] [PubMed]
- Fletcher HA, Filali-Mouhim A, Nemes E, et al. Human newborn bacille Calmette-Guérin vaccination and risk of tuberculosis disease: a case-control study. BMC Med 2016;14:76. [Crossref] [PubMed]
- Jenum S, Dhanasekaran S, Lodha R, et al. Approaching a diagnostic point-of-care test for pediatric tuberculosis through evaluation of immune biomarkers across the clinical disease spectrum. Sci Rep 2016;6:18520. [Crossref] [PubMed]
- Zhou M, Yu G, Yang X, et al. Circulating microRNAs as biomarkers for the early diagnosis of childhood tuberculosis infection. Mol Med Rep 2016;13:4620-6. [Crossref] [PubMed]
- Gjøen JE, Jenum S, Sivakumaran D, et al. Novel transcriptional signatures for sputum-independent diagnostics of tuberculosis in children. Sci Rep 2017;7:5839. [Crossref] [PubMed]
- Hemingway C, Berk M, Anderson ST, et al. Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function. PLoS One 2017;12:e0185973. [Crossref] [PubMed]
- Rohlwink UK, Figaji A, Wilkinson KA, et al. Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity. Nat Commun 2019;10:3767. [Crossref] [PubMed]
- Tornheim JA, Madugundu AK, Paradkar M, et al. Transcriptomic Profiles of Confirmed Pediatric Tuberculosis Patients and Household Contacts Identifies Active Tuberculosis, Infection, and Treatment Response Among Indian Children. J Infect Dis 2020;221:1647-58. [Crossref] [PubMed]
- Dutta NK, Tornheim JA, Fukutani KF, et al. Integration of metabolomics and transcriptomics reveals novel biomarkers in the blood for tuberculosis diagnosis in children. Sci Rep 2020;10:19527. [Crossref] [PubMed]
- Tornheim JA, Paradkar M, Zhao H, et al. The Kynurenine/Tryptophan Ratio Is a Sensitive Biomarker for the Diagnosis of Pediatric Tuberculosis Among Indian Children. Front Immunol 2021;12:774043. [Crossref] [PubMed]
- Bobak CA, Botha M, Workman L, et al. Gene Expression in Cord Blood and Tuberculosis in Early Childhood: A Nested Case-Control Study in a South African Birth Cohort. Clin Infect Dis 2023;77:438-49. [Crossref] [PubMed]
- Sweetser B, Nkereuwem E, Nakafeero J, et al. A Prospective Evaluation of a Three-Gene Host Response Signature to Classify Tuberculosis Severity in Children. J Pediatric Infect Dis Soc 2025;14:piaf041. [Crossref] [PubMed]
- Azikin W, Laompo A, Albar H, et al. Matrix Metalloproteinase-9 (MMP-9) Level in Tuberculosis Exposed and Infected Children. American Journal of Health Research 2017;5:7-10.
- Rivera-Marrero CA, Schuyler W, Roser S, et al. M. tuberculosis induction of matrix metalloproteinase-9: the role of mannose and receptor-mediated mechanisms. Am J Physiol Lung Cell Mol Physiol 2002;282:L546-55. [Crossref] [PubMed]
- Sabir N, Hussain T, Mangi MH, et al. Matrix metalloproteinases: Expression, regulation and role in the immunopathology of tuberculosis. Cell Prolif 2019;52:e12649. [Crossref] [PubMed]
- Jhilta A, Jadhav K, Singh R, et al. Breaking the Cycle: Matrix Metalloproteinase Inhibitors as an Alternative Approach in Managing Tuberculosis Pathogenesis and Progression. ACS Infect Dis 2024;10:2567-83. [Crossref] [PubMed]
- Sinigaglia A, Peta E, Riccetti S, et al. Tuberculosis-Associated MicroRNAs: From Pathogenesis to Disease Biomarkers. Cells 2020;9:2160. [Crossref] [PubMed]
- Guo H, Ingolia NT, Weissman JS, et al. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010;466:835-40. [Crossref] [PubMed]
- Alipoor SD, Adcock IM, Tabarsi P, et al. MiRNAs in tuberculosis: Their decisive role in the fate of TB. Eur J Pharmacol 2020;886:173529. [Crossref] [PubMed]
- Daniel EA, Sathiyamani B, Thiruvengadam K, et al. MicroRNAs as diagnostic biomarkers for Tuberculosis: A systematic review and meta- analysis. Front Immunol 2022;13:954396. [Crossref] [PubMed]
- Gunasekaran H, Sampath P, Thiruvengadam K, et al. A systematic review and meta-analysis of circulating serum and plasma microRNAs in TB diagnosis. BMC Infect Dis 2024;24:402. [Crossref] [PubMed]
- Wang L, Xiong Y, Fu B, et al. MicroRNAs as immune regulators and biomarkers in tuberculosis. Front Immunol 2022;13:1027472. [Crossref] [PubMed]
- Yamagishi M, Nakano K, Miyake A, et al. Polycomb-mediated loss of miR-31 activates NIK-dependent NF-κB pathway in adult T cell leukemia and other cancers. Cancer Cell 2012;21:121-35. [Crossref] [PubMed]
- Wishart DS, Jewison T, Guo AC, et al. HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Res 2013;41:D801-7. [Crossref] [PubMed]
- Mason S, Van Furth AMT, Solomons R, et al. A putative urinary biosignature for diagnosis and follow-up of tuberculous meningitis in children: outcome of a metabolomics study disclosing host–pathogen responses. Metabolomics 2016;12:1-16.
- Sun L, Li JQ, Ren N, et al. Utility of Novel Plasma Metabolic Markers in the Diagnosis of Pediatric Tuberculosis: A Classification and Regression Tree Analysis Approach. J Proteome Res 2016;15:3118-25. [Crossref] [PubMed]
- Mason S, Reinecke CJ, Solomons R. Cerebrospinal Fluid Amino Acid Profiling of Pediatric Cases with Tuberculous Meningitis. Front Neurosci 2017;11:534. [Crossref] [PubMed]
- Andreas NJ, Basu Roy R, Gomez-Romero M, et al. Performance of metabonomic serum analysis for diagnostics in paediatric tuberculosis. Sci Rep 2020;10:7302. [Crossref] [PubMed]
- Comella-Del-Barrio P, Izquierdo-Garcia JL, Gautier J, et al. Urine NMR-based TB metabolic fingerprinting for the diagnosis of TB in children. Sci Rep 2021;11:12006. [Crossref] [PubMed]
- Samuel V, Solomons R, Mason S. Targeted metabolomics investigation of metabolic markers of Mycobacterium tuberculosis in the cerebrospinal fluid of paediatric patients with tuberculous meningitis. PLoS One 2024;19:e0314854. [Crossref] [PubMed]
- Isaiah S, Westerhuis JA, Loots DT, et al. The diagnostic potential of urine in paediatric patients undergoing initial treatment for tuberculous meningitis. Sci Rep 2024;14:19471. [Crossref] [PubMed]
- Magdalena D, Michal S, Marta S, et al. Targeted metabolomics analysis of serum and Mycobacterium tuberculosis antigen-stimulated blood cultures of pediatric patients with active and latent tuberculosis. Sci Rep 2022;12:4131. [Crossref] [PubMed]
- Yu Y, Jiang XX, Li JC. Biomarker discovery for tuberculosis using metabolomics. Front Mol Biosci 2023;10:1099654. [Crossref] [PubMed]
- Layre E, Al-Mubarak R, Belisle JT, et al. Mycobacterial Lipidomics. Microbiol Spectr 2014;
- Brennan PJ. Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2003;83:91-7. [Crossref] [PubMed]
- Jain M, Petzold CJ, Schelle MW, et al. Lipidomics reveals control of Mycobacterium tuberculosis virulence lipids via metabolic coupling. Proc Natl Acad Sci U S A 2007;104:5133-8. [Crossref] [PubMed]
- Madigan CA, Martinot AJ, Wei JR, et al. Lipidomic analysis links mycobactin synthase K to iron uptake and virulence in M. tuberculosis. PLoS Pathog 2015;11:e1004792. [Crossref] [PubMed]
- Correia-Neves M, Sundling C, Cooper A, et al. Lipoarabinomannan in Active and Passive Protection Against Tuberculosis. Front Immunol 2019;10:1968. [Crossref] [PubMed]
- Bulterys MA, Wagner B, Redard-Jacot M, et al. Point-Of-Care Urine LAM Tests for Tuberculosis Diagnosis: A Status Update. J Clin Med 2019;9:111. [Crossref] [PubMed]
- Nkereuwem E, Togun T, Gomez MP, et al. Comparing accuracy of lipoarabinomannan urine tests for diagnosis of pulmonary tuberculosis in children from four African countries: a cross-sectional study. Lancet Infect Dis 2021;21:376-84. [Crossref] [PubMed]
- Nicol MP, Schumacher SG, Workman L, et al. Accuracy of a Novel Urine Test, Fujifilm SILVAMP Tuberculosis Lipoarabinomannan, for the Diagnosis of Pulmonary Tuberculosis in Children. Clin Infect Dis 2021;72:e280-8. [Crossref] [PubMed]
- Schramm B, Nganaboy RC, Uwiragiye P, et al. Potential value of urine lateral-flow lipoarabinomannan (LAM) test for diagnosing tuberculosis among severely acute malnourished children. PLoS One 2021;16:e0250933. [Crossref] [PubMed]
- Pal R, Hameed S, Kumar P, et al. Comparative lipidomics of drug sensitive and resistant Mycobacterium tuberculosis reveals altered lipid imprints. 3 Biotech 2017;7:325.
- Lahiri N, Shah RR, Layre E, et al. Rifampin Resistance Mutations Are Associated with Broad Chemical Remodeling of Mycobacterium tuberculosis. J Biol Chem 2016;291:14248-56. [Crossref] [PubMed]
- Shivakoti R, Newman JW, Hanna LE, et al. Host lipidome and tuberculosis treatment failure. Eur Respir J 2022;59:2004532. [Crossref] [PubMed]
- Liu L, Li X, Huang C, et al. Bile acids, lipid and purine metabolism involved in hepatotoxicity of first-line anti-tuberculosis drugs. Expert Opin Drug Metab Toxicol 2020;16:527-37. [Crossref] [PubMed]
- Pan Y, Tang P, Cao J, et al. Lipid peroxidation aggravates anti-tuberculosis drug-induced liver injury: Evidence of ferroptosis induction. Biochem Biophys Res Commun 2020;533:1512-8. [Crossref] [PubMed]
- Xu S, Chen Y, Ma Y, et al. Lipidomic Profiling Reveals Disruption of Lipid Metabolism in Valproic Acid-Induced Hepatotoxicity. Front Pharmacol 2019;10:819. [Crossref] [PubMed]
- Wang MG, Wu SQ, Zhang MM, et al. Plasma metabolomic and lipidomic alterations associated with anti-tuberculosis drug-induced liver injury. Front Pharmacol 2022;13:1044808. [Crossref] [PubMed]
- Hinzpeter R, Wagner MW, Wurnig MC, et al. Texture analysis of acute myocardial infarction with CT: First experience study. PLoS One 2017;12:e0186876. [Crossref] [PubMed]
- Zhang R, Xu Y, Gao S, et al. Observer- and radiomics model-based computed tomography classification of suppurative versus tuberculous lymphadenitis complicated with nodal necrosis of the neck in children. Pediatr Radiol 2023;53:2586-96. [Crossref] [PubMed]
- Calandrelli R, Boldrini L, Tran HE, et al. CT-based radiomics modeling for skull dysmorphology severity and surgical outcome prediction in children with isolated sagittal synostosis: a hypothesis-generating study. Radiol Med 2022;127:616-26. [Crossref] [PubMed]
- Liu ZM, Zhang H, Ge M, et al. Radiomics signature for the prediction of progression-free survival and radiotherapeutic benefits in pediatric medulloblastoma. Childs Nerv Syst 2022;38:1085-94. [Crossref] [PubMed]
- Yan Q, Zhao W, Kong H, et al. CT based radiomics analysis of consolidation characteristics in differentiating pulmonary disease of non tuberculous mycobacterium from pulmonary tuberculosis. Exp Ther Med 2024;27:112. [Crossref] [PubMed]
- Li Y, Wang B, Wen L, et al. Machine learning and radiomics for the prediction of multidrug resistance in cavitary pulmonary tuberculosis: a multicentre study. Eur Radiol 2023;33:391-400. [Crossref] [PubMed]
- Zar HJ, Workman LJ, Little F, et al. Diagnosis of Pulmonary Tuberculosis in Children: Assessment of the 2012 National Institutes of Health Expert Consensus Criteria. Clin Infect Dis 2015;S173-8. [Crossref] [PubMed]
- Jain S, Williams DJ, Arnold SR, et al. Community-acquired pneumonia requiring hospitalization among U.S. children. N Engl J Med 2015;372:835-45. [Crossref] [PubMed]
- Zar HJ, Barnett W, Stadler A, et al. Aetiology of childhood pneumonia in a well vaccinated South African birth cohort: a nested case-control study of the Drakenstein Child Health Study. Lancet Respir Med 2016;4:463-72. [Crossref] [PubMed]
- Bradley JS, Byington CL, Shah SS, et al. The management of community-acquired pneumonia in infants and children older than 3 months of age: clinical practice guidelines by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. Clin Infect Dis 2011;53:e25-76. [Crossref] [PubMed]
- Harris M, Clark J, Coote N, et al. British Thoracic Society guidelines for the management of community acquired pneumonia in children: update 2011. Thorax 2011;66:ii1-23. [Crossref] [PubMed]
- Wang D, Zhao J, Zhang R, et al. The value of CT radiomic in differentiating mycoplasma pneumoniae pneumonia from streptococcus pneumoniae pneumonia with similar consolidation in children under 5 years. Front Pediatr 2022;10:953399. [Crossref] [PubMed]
- Carlesi E, Orlandi M, Mencarini J, et al. How radiology can help pulmonary tuberculosis diagnosis: analysis of 49 patients. Radiol Med 2019;124:838-45. [Crossref] [PubMed]
- Wang B, Li M, Ma H, et al. Computed tomography-based predictive nomogram for differentiating primary progressive pulmonary tuberculosis from community-acquired pneumonia in children. BMC Med Imaging 2019;19:63. [Crossref] [PubMed]
- Qi H, Sun L, Jin YQ, et al. rs2243268 and rs2243274 of Interleukin-4 (IL-4) gene are associated with reduced risk for extrapulmonary and severe tuberculosis in Chinese Han children. Infect Genet Evol 2014;23:121-8. [Crossref] [PubMed]
- Qi H, Sun L, Wu X, et al. Toll-like receptor 1(TLR1) Gene SNP rs5743618 is associated with increased risk for tuberculosis in Han Chinese children. Tuberculosis (Edinb) 2015;95:197-203. [Crossref] [PubMed]
- Li J, Qi H, Sun L, et al. Rs1914663 of SFTPA 1 gene is associated with pediatric tuberculosis in Han Chinese population. Infect Genet Evol 2016;41:16-20. [Crossref] [PubMed]
- Maruthai K, Sankar S, Subramanian M. Methylation Status of VDR Gene and its Association with Vitamin D Status and VDR Gene Expression in Pediatric Tuberculosis Disease. Immunol Invest 2022;51:73-87. [Crossref] [PubMed]
- Nikolayevskyy V, Niemann S, Anthony R, et al. Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect 2019;25:1377-82. [Crossref] [PubMed]
- Cabibbe AM, Walker TM, Niemann S, et al. Whole genome sequencing of Mycobacterium tuberculosis. Eur Respir J 2018;52:1801163. [Crossref] [PubMed]
- Cole ST, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998;393:537-44. [Crossref] [PubMed]
- Genestet C, Hodille E, Westeel E, et al. Subcultured Mycobacterium tuberculosis isolates on different growth media are fully representative of bacteria within clinical samples. Tuberculosis (Edinb) 2019;116:61-6. [Crossref] [PubMed]
- Chen X, He G, Lin S, et al. Analysis of Serial Multidrug-Resistant Tuberculosis Strains Causing Treatment Failure and Within-Host Evolution by Whole-Genome Sequencing. mSphere 2020;5:e00884-20. [Crossref] [PubMed]
- O'Donnell MR, Larsen MH, Brown TS, et al. Early Detection of Emergent Extensively Drug-Resistant Tuberculosis by Flow Cytometry-Based Phenotyping and Whole-Genome Sequencing. Antimicrob Agents Chemother 2019;63:e01834-18. [Crossref] [PubMed]
- Keshavjee S, Farmer PE. Tuberculosis, drug resistance, and the history of modern medicine. N Engl J Med 2012;367:931-6. [Crossref] [PubMed]
- Bryant JM, Harris SR, Parkhill J, et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med 2013;1:786-92. [Crossref] [PubMed]
Cite this article as: Han C, Fang Y, Guo W. Discovering biomarkers for diagnosis, infection stage identification, treatment, and management of pediatric tuberculosis in the era of multi-omics: a narrative review. Pediatr Med 2026;9:4.
