Abstract
Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality in children. The ability of healthcare providers to diagnose and prognose LRTIs in the pediatric population remains a challenge, as children can present with similar clinical features regardless of the underlying pathogen or ultimate severity. Metabolomics, the large-scale analysis of metabolites and metabolic pathways offers new tools and insights that may aid in diagnosing and predicting the outcomes of LRTIs in children. This review highlights the latest literature on the clinical utility of metabolomics in providing care for children with bronchiolitis, pneumonia, COVID-19, and sepsis.
Impact
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This article summarizes current metabolomics approaches to diagnosing and predicting the course of pediatric lower respiratory infections.
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This article highlights the limitations to current metabolomics research and highlights future directions for the field.
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Data sharing is not applicable to this article as no datasets were generated or analyzed for this review.
References
Troeger, C. et al. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the global burden of disease study 2015. Lancet Infect. Dis. 17, 1133–1161 (2017).
Boloursaz, M. R. et al. Epidemiology of lower respiratory tract infections in children. J. Compr. Pediatr. 4, 93–98 (2013).
Elliott, S. P. & Ray, C. G. Viral infections of the lower respiratory tract. Pediatr. Respir. Med. 481–489 (2008).
Elemraid, M. A. et al. Accuracy of the interpretation of chest radiographs for the diagnosis of paediatric pneumonia. PLoS ONE 9, e106051 (2014).
Edwards, G. et al. Predicting poor outcomes in children aged 1–12 with respiratory tract infections: a systematic review. PLoS ONE 16, e0249533 (2021).
Emwas, A.-H. M. The strengths and weaknesses in NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. Metabonomics Methods Mol. Biol. 1277, 161–193 (2015).
Dieterle, F. et al. NMR and MS methods for metabonomics. Methods Mol. Biol. 691, 385–415 (2011).
Dunn, W. B., Broadhurst, D. I., Atherton, H. J., Goodacre, R. & Griffin, J. L. Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem. Soc. Rev. 40, 387–426 (2011).
Gowda, G. A. & Djukovic, D. Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol. Biol. 1198, 3–12 (2014).
Nakayama, Y., Tamada, Y., Tsugawa, H., Bamba, T. & Fukusaki, E. Novel strategy for non-targeted isotope-assisted metabolomics by means of metabolic turnover and multivariate analysis. Metabolites 4, 722–739 (2014).
Courant, F., Antignac, J. P., Dervilly-Pinel, G., & Le Bizec, B. Basics of mass spectrometry based metabolomics. Proteomics 14, 21–22 (2014).
Slupsky, C. M. et al. Streptococcus pneumoniae and Staphylococcus aureus pneumonia induce distinct metabolic responses. J. Proteome Res. 8, 3029–3036 (2009).
Kaddurah-Daouk, R., Kristal, B. S. & Weinshilboum, R. M. Metabolomics: a global biochemical approach to drug response and disease. Annu. Rev. Pharmacol. Toxicol. 48, 653–683 (2008).
Atzei, A. et al. Metabolomics in paediatric respiratory diseases and bronchiolitis. J. Matern. Fetal Neonatal Med. 24(Suppl 2), 59–62 (2011).
Han, Y. Y. et al. Early reversal of pediatric-neonatal septic shock by community physicians is associated with improved outcome. Pediatrics 112, 793–799 (2003).
Dessi, A. et al. New diagnostic possibilities in systemic neonatal infections: metabolomics. Early Hum. Dev. 90(Suppl 1), S19–S21 (2014).
Delanghe, J. R. & Speeckaert, M. M. Translational research and biomarkers in neonatal sepsis. Clin. Chim. Acta 451, 46–64 (2015).
Ng, S. et al. Precision medicine for neonatal sepsis. Front. Mol. Biosci. 5, 70 (2018).
Hasegawa, K., Tsugawa, Y., Brown, D. F., Mansbach, J. M. & Camargo, C. A. Jr Trends in bronchiolitis hospitalizations in the United States, 2000-2009. Pediatrics 132, 28–36 (2013).
Mansbach, J. M. et al. Prospective multicenter study of viral etiology and hospital length of stay in children with severe bronchiolitis. Arch. Pediatr. Adolesc. Med. 166, 700–706 (2012).
Calvo, C. et al. Detection of new respiratory viruses in hospitalized infants with bronchiolitis: a three-year prospective study. Acta Paediatr. 99, 883–887 (2010).
Voets, S., van Berlaer, G. & Hachimi-Idrissi, S. Clinical predictors of the severity of bronchiolitis. Eur. J. Emerg. Med. 13, 134–138 (2006).
Sigurs, N., Bjarnason, R., Sigurbergsson, F., Kjellman, B. & Björkstén, B. Asthma and immunoglobulin E antibodies after respiratory syncytial virus bronchiolitis: a prospective cohort study with matched controls. Pediatrics 95, 500–505 (1995).
Sigurs, N. et al. Asthma and allergy patterns over 18 years after severe RSV bronchiolitis in the first year of life. Thorax 65, 1045–1052 (2010).
Adamko, D. J., Saude, E., Bear, M., Regush, S. & Robinson, J. L. Urine metabolomic profiling of children with respiratory tract infections in the emergency department: a pilot study. BMC Infect. Dis. 16, 439 (2016).
Jackson, D. J. et al. Wheezing rhinovirus illnesses in early life predict asthma development in high-risk children. Am. J. Respir. Crit. Care Med. 178, 667–672 (2008).
Turi, K. N. et al. Using urine metabolomics to understand the pathogenesis of infant respiratory syncytial virus (RSV) infection and its role in childhood wheezing. Metabolomics 14, 135 (2018).
Stewart, C. J. et al. Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways. J. Infect. Dis. 217, 1160–1169 (2018).
Stewart, C. J. et al. Associations of nasopharyngeal metabolome and microbiome with severity among infants with bronchiolitis. A multiomic analysis. Am. J. Respir. Crit. Care Med. 196, 882–891 (2017).
Stewart, C. J. et al. Serum metabolome is associated with the nasopharyngeal microbiota and disease severity among infants with bronchiolitis. J. Infect. Dis. 219, 2005–2014 (2019).
Golan-Tripto, I. et al. Vitamin D deficiency in children with acute bronchiolitis: a prospective cross-sectional case- control study. BMC Pediatr. 21, 211 (2021).
Alakaş, Y., Celiloğlu, C., Tolunay, O. & Matyar, S. The relationship between bronchiolitis severity and vitamin D status. J. Trop. Pediatr. 67, fmab081 (2021).
Hasegawa, K. et al. Circulating 25-hydroxyvitamin D, nasopharyngeal airway metabolome, and bronchiolitis severity. Allergy 73, 1135–1140 (2018).
Hasegawa, K. et al. Serum 25-hydroxyvitamin D, metabolome, and bronchiolitis severity among infants-a multicenter cohort study. Pediatr. Allergy Immunol. 29, 441–445 (2018).
Zhang, X. et al. Serum metabolomic profiling reveals important difference between infants with and without subsequent recurrent wheezing in later childhood after RSV bronchiolitis. APMIS 129, 128–137 (2021).
Barlotta, A. et al. Metabolomic profiling of infants with recurrent wheezing after bronchiolitis. J. Infect. Dis. 219, 1216–1223 (2019).
Zhu, Z. et al. Metabolome subtyping of severe bronchiolitis in infancy and risk of childhood asthma. J. Allergy Clin. Immunol. 149, 102–112 (2021).
Castro-Rodriguez, J. A., Cifuentes, L. & Martinez, F. D. Predicting asthma using clinical indexes. Front. Pediatr. 7, 320–320 (2019).
Fujiogi, M. et al. Respiratory viruses are associated with serum metabolome among infants hospitalized for bronchiolitis: a multicenter study. Pediatr. Allergy Immunol. 31, 755–766 (2020).
Fujiogi, M. et al. Integrated associations of nasopharyngeal and serum metabolome with bronchiolitis severity and asthma: a multicenter prospective cohort study. Pediatr. Allergy Immunol. 32, 905–916 (2021).
Ghidoni, R., Caretti, A. & Signorelli, P. Role of sphingolipids in the pathobiology of lung inflammation. Mediators Inflamm. 2015, 487508–487508 (2015).
North, M. L., Khanna, N., Marsden, P. A., Grasemann, H. & Scott, J. A. Functionally important role for arginase 1 in the airway hyperresponsiveness of asthma. Am. J. Physiol. Lung Cell Mol. Physiol. 296, L911–L920 (2009).
Lara, A. et al. Alterations of the arginine metabolome in asthma. Am. J. Respir. Crit. Care Med. 178, 673–681 (2008).
Liu, L. et al. Global, regional, and national causes of child mortality in 2000-13, with projections to inform post-2015 priorities: an updated systematic analysis. Lancet 385, 430–440 (2015).
Torres, A. et al. Pneumonia. Nat. Rev. Dis. Prim. 7, 25 (2021).
Shah, S. N., Bachur, R. G., Simel, D. L. & Neuman, M. I. Does this child have pneumonia?: the rational clinical examination systematic review. JAMA 318, 462–471 (2017).
Florin, T. A. et al. Biomarkers and disease severity in children with community-acquired pneumonia. Pediatrics 145, e20193728 (2020).
Thomas, J., Pociute, A., Kevalas, R., Malinauskas, M. & Jankauskaite, L. Blood biomarkers differentiating viral versus bacterial pneumonia aetiology: a literature review. Ital. J. Pediatr. 46, 4 (2020).
Laiakis, E. C., Morris, G. A., Fornace, A. J. & Howie, S. R. Metabolomic analysis in severe childhood pneumonia in the Gambia, West Africa: findings from a pilot study. PLoS ONE 5, e12655 (2010).
Hersh, A. L., Shapiro, D. J., Pavia, A. T. & Shah, S. S. Antibiotic prescribing in ambulatory pediatrics in the United States. Pediatrics 128, 1053–1061 (2011).
Del Borrello, G. et al. New insights into pediatric community-acquired pneumonia gained from untargeted metabolomics: a preliminary study. Pediatr. Pulmonol. 55, 418–425 (2020).
Hasegawa, K. et al. Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis. Eur. Respir. J. 48, 1329–1339 (2016).
Fletcher, M. A., Schmitt, H. J., Syrochkina, M. & Sylvester, G. Pneumococcal empyema and complicated pneumonias: global trends in incidence, prevalence, and serotype epidemiology. Eur. J. Clin. Microbiol. Infect. Dis. 33, 879–910 (2014).
Light, R. W. Parapneumonic effusions and empyema. Proc. Am. Thorac. Soc. 3, 75–80 (2006).
Chung, C. L., Chen, C. H., Sheu, J. R., Chen, Y. C. & Chang, S. C. Proinflammatory cytokines, transforming growth factor-beta1, and fibrinolytic enzymes in loculated and free-flowing pleural exudates. Chest 128, 690–697 (2005).
Gayretli-Aydın, Z. G. et al. Evaluation of complicated and uncomplicated parapneumonic effusion in children. Turk. J. Pediatr. 58, 623–631 (2016).
Chiu, C. Y. et al. Metabolomic profiling of infectious parapneumonic effusions reveals biomarkers for guiding management of children with streptococcus pneumoniae pneumonia. Sci. Rep. 6, 24930 (2016).
Chiu, C. Y. et al. Metabolomics reveals anaerobic bacterial fermentation and hypoxanthine accumulation for fibrinous pleural effusions in children with pneumonia. J. Proteome Res. 18, 1248–1254 (2019).
Bridy-Pappas, A. E., Margolis, M. B., Center, K. J. & Isaacman, D. J. Streptococcus pneumoniae: description of the pathogen, disease epidemiology, treatment, and prevention. Pharmacotherapy 25, 1193–1212 (2005).
Hartman, M. E., Linde-Zwirble, W. T., Angus, D. C. & Watson, R. S. Trends in the epidemiology of pediatric severe sepsis. Pediatr. Crit. Care Med. 14, 686–693 (2013).
Weiss, S. L. et al. Surviving sepsis campaign international guidelines for the management of septic shock and sepsis-associated organ dysfunction in children. Pediatr. Crit. Care Med. 21, e52–e106 (2020).
Patel, K. & McElvania, E. Diagnostic challenges and laboratory considerations for pediatric sepsis. J. Appl. Lab. Med. 3, 587–600 (2019).
Hazwani, T. R. et al. Association between culture-negative versus culture-positive sepsis and outcomes of patients admitted to the pediatric intensive care unit. Cureus 12, e9981 (2020).
Mickiewicz, B., Vogel, H. J., Wong, H. R. & Winston, B. W. Metabolomics as a novel approach for early diagnosis of pediatric septic shock and its mortality. Am. J. Respir. Crit. Care Med. 187, 967–976 (2013).
Ambroggio, L. et al. Emerging biomarkers of illness severity: urinary metabolites associated with sepsis and necrotizing methicillin-resistant Staphylococcus aureus pneumonia. Pharmacotherapy 37, 1033–1042 (2017).
Mickiewicz, B. et al. Development of metabolic and inflammatory mediator biomarker phenotyping for early diagnosis and triage of pediatric sepsis. Crit. Care 19, 320 (2015).
Mickiewicz, B. et al. Biomarker phenotype for early diagnosis and triage of sepsis to the pediatric intensive care unit. Sci. Rep. 8, 16606 (2018).
Grauslys, A. et al. Title NMR-based metabolic profiling provides diagnostic and prognostic information in critically ill children with suspected infection. Sci. Rep. 10, 20198 (2020).
Li, G.-B. et al. Plasma metabolic profiling of pediatric sepsis in a chinese cohort. Front. Cell Dev. Biol. 9, 643979 (2021).
World Health Organization. WHO coronavirus (Covid-19) dashboard. https://covid19.who.int (2022).
de Souza, T. H., Nadal, J. A., Nogueira, R. J. N., Pereira, R. M. & Brandão, M. B. Clinical manifestations of children with COVID-19: a systematic review. Pediatr. Pulmonol. 55, 1892–1899 (2020).
Rabinowicz, S., Leshem, E. & Pessach, I. M. COVID-19 in the pediatric population-review and current evidence. Curr. Infect. Dis. Rep. 22, 29 (2020).
Wang, C. et al. Multi-omic profiling of plasma reveals molecular alterations in children with COVID-19. Theranostics 11, 8008–8026 (2021).
Wu, D. et al. Plasma metabolomic and lipidomic alterations associated with COVID-19. Natl Sci. Rev. 7, 1157–1168 (2020).
Shu, T. et al. Plasma proteomics identify biomarkers and pathogenesis of COVID-19. Immunity 53, 1108.e5–1122.e5 (2020).
Rist, M. J. et al. Influence of freezing and storage procedure on human urine samples in nmr-based metabolomics. Metabolites 3, 243–258 (2013).
Kamlage, B. et al. Quality markers addressing preanalytical variations of blood and plasma processing identified by broad and targeted metabolite profiling. Clin. Chem. 60, 399–412 (2014).
Ang, J. E. et al. Identification of human plasma metabolites exhibiting time-of-day variation using an untargeted liquid chromatography-mass spectrometry metabolomic approach. Chronobiol. Int. 29, 868–881 (2012).
Kastenmüller, G., Raffler, J., Gieger, C. & Suhre, K. Genetics of human metabolism: an update. Hum. Mol. Genet. 24, R93–R101 (2015).
Pinu, F. R., Goldansaz, S. A. & Jaine, J. Translational metabolomics: current challenges and future opportunities. Metabolites 9, 108 (2019).
Annese, V. F. et al. A monolithic single-chip point-of-care platform for metabolomic prostate cancer detection. Microsyst. Nanoeng. 7, 21 (2021).
McAllister, D. A. et al. Global, regional, and national estimates of pneumonia morbidity and mortality in children younger than 5 years between 2000 and 2015: a systematic analysis. Lancet Glob. Health 7, e47–e57 (2019).
Acknowledgements
The authors thank Nicole Dunnewold, MLIS and Diane Lorenzetti MLS, Ph.D. from the Health Sciences Library at the University of Calgary for their assistance with this review.
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E.W. drafted the manuscript, collected the data, performed data analysis and data interpretation, revised the manuscript, and approved the final version of the manuscript to be published. B.M. conceptualized and designed the study, performed data interpretation, revised and critically reviewed the manuscript for important intellectual content, and approved the final version of the manuscript to be published. H.J.V. participated in data interpretation, revised and critically reviewed the manuscript for important intellectual content, and approved the final version of the manuscript to be published. G.C.T. conceptualized and designed the study, supervised data collection and data interpretation, revised and critically reviewed the manuscript for important intellectual content, and approved the final version of the manuscript to be published. All authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work.
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B.M. and H.J.V. hold patent US 8969017 “Metabolite biomarkers for diagnosis and prognosis of pediatric septic shock.”
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Wildman, E., Mickiewicz, B., Vogel, H.J. et al. Metabolomics in pediatric lower respiratory tract infections and sepsis: a literature review. Pediatr Res 93, 492–502 (2023). https://doi.org/10.1038/s41390-022-02162-0
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DOI: https://doi.org/10.1038/s41390-022-02162-0


