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Chou H, Godbeer L, Allsworth M, Boyle B, Ball ML. Progress and challenges of developing volatile metabolites from exhaled breath as a biomarker platform. Metabolomics 2024; 20:72. [PMID: 38977623 PMCID: PMC11230972 DOI: 10.1007/s11306-024-02142-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024]
Abstract
BACKGROUND The multitude of metabolites generated by physiological processes in the body can serve as valuable biomarkers for many clinical purposes. They can provide a window into relevant metabolic pathways for health and disease, as well as be candidate therapeutic targets. A subset of these metabolites generated in the human body are volatile, known as volatile organic compounds (VOCs), which can be detected in exhaled breath. These can diffuse from their point of origin throughout the body into the bloodstream and exchange into the air in the lungs. For this reason, breath VOC analysis has become a focus of biomedical research hoping to translate new useful biomarkers by taking advantage of the non-invasive nature of breath sampling, as well as the rapid rate of collection over short periods of time that can occur. Despite the promise of breath analysis as an additional platform for metabolomic analysis, no VOC breath biomarkers have successfully been implemented into a clinical setting as of the time of this review. AIM OF REVIEW This review aims to summarize the progress made to address the major methodological challenges, including standardization, that have historically limited the translation of breath VOC biomarkers into the clinic. We highlight what steps can be taken to improve these issues within new and ongoing breath research to promote the successful development of the VOCs in breath as a robust source of candidate biomarkers. We also highlight key recent papers across select fields, critically reviewing the progress made in the past few years to advance breath research. KEY SCIENTIFIC CONCEPTS OF REVIEW VOCs are a set of metabolites that can be sampled in exhaled breath to act as advantageous biomarkers in a variety of clinical contexts.
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Sasiene ZJ, LeBrun ES, Schaller E, Mach PM, Taylor R, Candelaria L, Glaros TG, Baca J, McBride EM. Real-time breath analysis towards a healthy human breath profile. J Breath Res 2024; 18:026003. [PMID: 38198707 DOI: 10.1088/1752-7163/ad1cf1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/10/2024] [Indexed: 01/12/2024]
Abstract
The direct analysis of molecules contained within human breath has had significant implications for clinical and diagnostic applications in recent decades. However, attempts to compare one study to another or to reproduce previous work are hampered by: variability between sampling methodologies, human phenotypic variability, complex interactions between compounds within breath, and confounding signals from comorbidities. Towards this end, we have endeavored to create an averaged healthy human 'profile' against which follow-on studies might be compared. Through the use of direct secondary electrospray ionization combined with a high-resolution mass spectrometry and in-house bioinformatics pipeline, we seek to curate an average healthy human profile for breath and use this model to distinguish differences inter- and intra-day for human volunteers. Breath samples were significantly different in PERMANOVA analysis and ANOSIM analysis based on Time of Day, Participant ID, Date of Sample, Sex of Participant, and Age of Participant (p< 0.001). Optimal binning analysis identify strong associations between specific features and variables. These include 227 breath features identified as unique identifiers for 28 of the 31 participants. Four signals were identified to be strongly associated with female participants and one with male participants. A total of 37 signals were identified to be strongly associated with the time-of-day samples were taken. Threshold indicator taxa analysis indicated a shift in significant breath features across the age gradient of participants with peak disruption of breath metabolites occurring at around age 32. Forty-eight features were identified after filtering from which a healthy human breath profile for all participants was created.
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Affiliation(s)
- Zachary Joseph Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Erick Scott LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Eric Schaller
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131, United States of America
| | - Phillip Michael Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Robert Taylor
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131, United States of America
| | - Lionel Candelaria
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131, United States of America
| | - Trevor Griffiths Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Justin Baca
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131, United States of America
| | - Ethan Matthew McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
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3
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Gaida M, Stefanuto PH, Focant JF. Theoretical modeling and machine learning-based data processing workflows in comprehensive two-dimensional gas chromatography-A review. J Chromatogr A 2023; 1711:464467. [PMID: 37871505 DOI: 10.1016/j.chroma.2023.464467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
In recent years, comprehensive two-dimensional gas chromatography (GC × GC) has been gradually gaining prominence as a preferred method for the analysis of complex samples due to its higher peak capacity and resolution power compared to conventional gas chromatography (GC). Nonetheless, to fully benefit from the capabilities of GC × GC, a holistic approach to method development and data processing is essential for a successful and informative analysis. Method development enables the fine-tuning of the chromatographic separation, resulting in high-quality data. While generating such data is pivotal, it does not necessarily guarantee that meaningful information will be extracted from it. To this end, the first part of this manuscript reviews the importance of theoretical modeling in achieving good optimization of the separation conditions, ultimately improving the quality of the chromatographic separation. Multiple theoretical modeling approaches are discussed, with a special focus on thermodynamic-based modeling. The second part of this review highlights the importance of establishing robust data processing workflows, with a special emphasis on the use of advanced data processing tools such as, Machine Learning (ML) algorithms. Three widely used ML algorithms are discussed: Random Forest (RF), Support Vector Machine (SVM), and Partial Least Square-Discriminate Analysis (PLS-DA), highlighting their role in discovery-based analysis.
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Affiliation(s)
- Meriem Gaida
- Organic and Biological Analytical Chemistry Group (OBiAChem), MolSys Research Unit, Liège University, Belgium
| | - Pierre-Hugues Stefanuto
- Organic and Biological Analytical Chemistry Group (OBiAChem), MolSys Research Unit, Liège University, Belgium
| | - Jean-François Focant
- Organic and Biological Analytical Chemistry Group (OBiAChem), MolSys Research Unit, Liège University, Belgium
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4
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Gaida M, Cain CN, Synovec RE, Focant JF, Stefanuto PH. Tile-Based Random Forest Analysis for Analyte Discovery in Balanced and Unbalanced GC × GC-TOFMS Data Sets. Anal Chem 2023; 95:13519-13527. [PMID: 37647642 DOI: 10.1021/acs.analchem.3c01872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In this study, we introduce a new nontargeted tile-based supervised analysis method that combines the four-grid tiling scheme previously established for the Fisher ratio (F-ratio) analysis (FRA) with the estimation of tile hit importance using the machine learning (ML) algorithm Random Forest (RF). This approach is termed tile-based RF analysis. As opposed to the standard tile-based F-ratio analysis, the RF approach can be extended to the analysis of unbalanced data sets, i.e., different numbers of samples per class. Tile-based RF computes out-of-bag (oob) tile hit importance estimates for every summed chromatographic signal within each tile on a per-mass channel basis (m/z). These estimates are then used to rank tile hits in a descending order of importance. In the present investigation, the RF approach was applied for a two-class comparison of stool samples collected from omnivore (O) subjects and stored using two different storage conditions: liquid (Liq) and lyophilized (Lyo). Two final hit lists were generated using balanced (8 vs Eight comparison) and unbalanced (8 vs Nine comparison) data sets and compared to the hit list generated by the standard F-ratio analysis. Similar class-distinguishing analytes (p < 0.01) were discovered by both methods. However, while the FRA discovered a more comprehensive hit list (65 hits), the RF approach strictly discovered hits (31 hits for the balanced data set comparison and 29 hits for the unbalanced data set comparison) with concentration ratios, [OLiq]/[OLyo], greater than 2 (or less than 0.5). This difference is attributed to the more stringent feature selection process used by the RF algorithm. Moreover, our findings suggest that the RF approach is a promising method for identifying class-distinguishing analytes in settings characterized by both high between-class variance and high within-class variance, making it an advantageous method in the study of complex biological matrices.
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Affiliation(s)
- Meriem Gaida
- Organic and Biological Analytical Chemistry Group, Molecular Systems Research Unit, University of Liège, 4000 Liège, Belgium
| | - Caitlin N Cain
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Robert E Synovec
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Jean-François Focant
- Organic and Biological Analytical Chemistry Group, Molecular Systems Research Unit, University of Liège, 4000 Liège, Belgium
| | - Pierre-Hugues Stefanuto
- Organic and Biological Analytical Chemistry Group, Molecular Systems Research Unit, University of Liège, 4000 Liège, Belgium
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5
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Ketchanji Mougang YC, Endale Mangamba LM, Capuano R, Ciccacci F, Catini A, Paolesse R, Mbatchou Ngahane HB, Palombi L, Di Natale C. On-Field Test of Tuberculosis Diagnosis through Exhaled Breath Analysis with a Gas Sensor Array. BIOSENSORS 2023; 13:bios13050570. [PMID: 37232931 DOI: 10.3390/bios13050570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/21/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
Tuberculosis (TB) is among the more frequent causes of death in many countries. For pulmonary TB, early diagnosis greatly increases the efficiency of therapies. Although highly sensitive tests based on nucleic acid amplification tests (NAATs) and loop-mediated isothermal amplification (TB-LAMP) are available, smear microscopy is still the most widespread diagnostics method in most low-middle-income countries, and the true positive rate of smear microscopy is lower than 65%. Thus, there is a need to increase the performance of low-cost diagnosis. For many years, the use of sensors to analyze the exhaled volatile organic compounds (VOCs) has been proposed as a promising alternative for the diagnosis of several diseases, including tuberculosis. In this paper, the diagnostic properties of an electronic nose (EN) based on sensor technology previously used to identify tuberculosis have been tested on-field in a Cameroon hospital. The EN analyzed the breath of a cohort of subjects including pulmonary TB patients (46), healthy controls (38), and TB suspects (16). Machine learning analysis of the sensor array data allows for the identification of the pulmonary TB group with respect to healthy controls with 88% accuracy, 90.8% sensitivity, 85.7% specificity, and 0.88 AUC. The model trained with TB and healthy controls maintains its performance when it is applied to symptomatic TB suspects with a negative TB-LAMP. These results encourage the investigation of electronic noses as an effective diagnostic method for future inclusion in clinical practice.
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Affiliation(s)
| | - Laurent-Mireille Endale Mangamba
- Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Carrefour Ange Raphael, Douala P.O. Box 4035, Cameroon
- Center for Respiratory Diseases, Douala Laquintinie Hospital, Avenue du Jamot, Douala P.O. Box 4035, Cameroon
| | - Rosamaria Capuano
- Department of Electronic Engineering, University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
- Interdepartmental Centre for Volatilomics "A D'Amico", University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
| | - Fausto Ciccacci
- UniCamillus, Saint Camillus International University of Health and Medical Sciences, 00131 Rome, Italy
| | - Alexandro Catini
- Department of Electronic Engineering, University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
- Interdepartmental Centre for Volatilomics "A D'Amico", University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
| | - Roberto Paolesse
- Interdepartmental Centre for Volatilomics "A D'Amico", University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
- Department of Chemical Science and Technology, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133 Rome, Italy
| | - Hugo Bertrand Mbatchou Ngahane
- Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Carrefour Ange Raphael, Douala P.O. Box 4035, Cameroon
- Internal Medicine Service, Douala General Hospital, Douala P.O. Box 4856, Cameroon
| | - Leonardo Palombi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Viale Montpellier 1, 00133 Roma, Italy
| | - Corrado Di Natale
- Department of Electronic Engineering, University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
- Interdepartmental Centre for Volatilomics "A D'Amico", University of Rome Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
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Fu L, Wang L, Wang H, Yang M, Yang Q, Lin Y, Guan S, Deng Y, Liu L, Li Q, He M, Zhang P, Chen H, Deng G. A cross-sectional study: a breathomics based pulmonary tuberculosis detection method. BMC Infect Dis 2023; 23:148. [PMID: 36899314 PMCID: PMC9999612 DOI: 10.1186/s12879-023-08112-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Diagnostics for pulmonary tuberculosis (PTB) are usually inaccurate, expensive, or complicated. The breathomics-based method may be an attractive option for fast and noninvasive PTB detection. METHOD Exhaled breath samples were collected from 518 PTB patients and 887 controls and tested on the real-time high-pressure photon ionization time-of-flight mass spectrometer. Machine learning algorithms were employed for breathomics analysis and PTB detection mode, whose performance was evaluated in 430 blinded clinical patients. RESULTS The breathomics-based PTB detection model achieved an accuracy of 92.6%, a sensitivity of 91.7%, a specificity of 93.0%, and an AUC of 0.975 in the blinded test set (n = 430). Age, sex, and anti-tuberculosis treatment does not significantly impact PTB detection performance. In distinguishing PTB from other pulmonary diseases (n = 182), the VOC modes also achieve good performance with an accuracy of 91.2%, a sensitivity of 91.7%, a specificity of 88.0%, and an AUC of 0.961. CONCLUSIONS The simple and noninvasive breathomics-based PTB detection method was demonstrated with high sensitivity and specificity, potentially valuable for clinical PTB screening and diagnosis.
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Affiliation(s)
- Liang Fu
- Division Two of the Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Lei Wang
- Breax Laboratory, PCAB Research Center of Breath and Metabolism, Beijing, 100074, China
| | - Haibo Wang
- Peking University Clinical Research Institute, Peking University First Hospital, Beijing, 100000, China
| | - Min Yang
- Division Two of the Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Qianting Yang
- Institute for Hepatology, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yi Lin
- Division Two of the Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Shanyi Guan
- Medical Examination Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yongcong Deng
- Pulmonary Diseases Out-Patient Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Lei Liu
- Division Two of the Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Qingyun Li
- Breax Laboratory, PCAB Research Center of Breath and Metabolism, Beijing, 100074, China
| | - Mengqi He
- Breax Laboratory, PCAB Research Center of Breath and Metabolism, Beijing, 100074, China
| | - Peize Zhang
- Division Two of the Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China.
| | - Haibin Chen
- Breax Laboratory, PCAB Research Center of Breath and Metabolism, Beijing, 100074, China.
| | - Guofang Deng
- Division Two of the Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, 518112, China.
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7
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Nick JA, Malcolm KC, Hisert KB, Wheeler EA, Rysavy NM, Poch K, Caceres S, Lovell VK, Armantrout E, Saavedra MT, Calhoun K, Chatterjee D, Aboellail I, De P, Martiniano SL, Jia F, Davidson RM. Culture independent markers of nontuberculous mycobacterial (NTM) lung infection and disease in the cystic fibrosis airway. Tuberculosis (Edinb) 2023; 138:102276. [PMID: 36417800 PMCID: PMC10965158 DOI: 10.1016/j.tube.2022.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic pathogens that affect a relatively small but significant portion of the people with cystic fibrosis (CF), and may cause increased morbidity and mortality in this population. Cultures from the airway are the only test currently in clinical use for detecting NTM. Culture techniques used in clinical laboratories are insensitive and poorly suited for population screening or to follow progression of disease or treatment response. The lack of sensitive and quantitative markers of NTM in the airway impedes patient care and clinical trial design, and has limited our understanding of patterns of acquisition, latency and pathogenesis of disease. Culture-independent markers of NTM infection have the potential to overcome many of the limitations of standard NTM cultures, especially the very slow growth, inability to quantitate bacterial burden, and low sensitivity due to required decontamination procedures. A range of markers have been identified in sputum, saliva, breath, blood, urine, as well as radiographic studies. Proposed markers to detect presence of NTM or transition to NTM disease include bacterial cell wall products and DNA, as well as markers of host immune response such as immunoglobulins and the gene expression of circulating leukocytes. In all cases the sensitivity of culture-independent markers is greater than standard cultures; however, most do not discriminate between various NTM species. Thus, each marker may be best suited for a specific clinical application, or combined with other markers and traditional cultures to improve diagnosis and monitoring of treatment response.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katherine B Hisert
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Emily A Wheeler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Emily Armantrout
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Milene T Saavedra
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kara Calhoun
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ibrahim Aboellail
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Fan Jia
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
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Exhaled breath condensate as bioanalyte: from collection considerations to biomarker sensing. Anal Bioanal Chem 2023; 415:27-34. [PMID: 36396732 PMCID: PMC9672542 DOI: 10.1007/s00216-022-04433-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Since the SARS-CoV-2 pandemic, the potential of exhaled breath (EB) to provide valuable information and insight into the health status of a person has been revisited. Mass spectrometry (MS) has gained increasing attention as a powerful analytical tool for clinical diagnostics of exhaled breath aerosols (EBA) and exhaled breath condensates (EBC) due to its high sensitivity and specificity. Although MS will continue to play an important role in biomarker discovery in EB, its use in clinical setting is rather limited. EB analysis is moving toward online sampling with portable, room temperature operable, and inexpensive point-of-care devices capable of real-time measurements. This transition is happening due to the availability of highly performing biosensors and the use of wearable EB collection tools, mostly in the form of face masks. This feature article will outline the last developments in the field, notably the novel ways of EBA and EBC collection and the analytical aspects of the collected samples. The inherit non-invasive character of the sample collection approach might open new doors for efficient ways for a fast, non-invasive, and better diagnosis.
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9
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Mani-Varnosfaderani A, Gao A, Poch KR, Caceres SM, Nick JA, Hill JE. Breath biomarkers associated with nontuberculosis mycobacteriadisease status in persons with cystic fibrosis: a pilot study. J Breath Res 2022; 16:031001. [PMID: 35487186 DOI: 10.1088/1752-7163/ac6bb6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/29/2022] [Indexed: 11/11/2022]
Abstract
Pulmonary infections caused by mycobacteria cause significant mortality and morbidity in the human population. Diagnosing mycobacterial infections is challenging. An infection can lead to active disease or remain indolent with little clinical consequence. In patients with pulmonarynontuberculosis mycobacteria(PNTM) identification of infection and diagnosis of disease can take months to years. Our previous studies showed the potential diagnostic power of volatile molecules in the exhaled breath samples to detect active pulmonaryM. tuberculosisinfection. Herein, we demonstrate the ability to detect the disease status of PNTM in the breath of persons with cystic fibrosis (PwCF). We putatively identified 17 volatile molecules that could discriminate between active-NTM disease (n= 6), indolent patients (n= 3), and those patients who have never cultured an NTM (n= 2). The results suggest that further confirmation of the breath biomarkers as a non-invasive and culture-independent tool for diagnosis of NTM disease in a larger cohort of PwCF is warranted.
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Affiliation(s)
- Ahmad Mani-Varnosfaderani
- Department of Chemical and Biological Engineering, School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
| | - Antao Gao
- Department of Chemical and Biological Engineering, School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
| | - Katie R Poch
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Silvia M Caceres
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Jane E Hill
- Department of Chemical and Biological Engineering, School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
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10
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Chew B, Pimentel Contreras R, McCartney MM, Borras E, Kenyon NJ, Davis CE. A low cost, easy-to-assemble, open-source modular mobile sampler design for thermal desorption analysis of breath and environmental VOCs. J Breath Res 2022; 16. [PMID: 35508102 DOI: 10.1088/1752-7163/ac6c9f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/04/2022] [Indexed: 11/12/2022]
Abstract
Exhaled breath vapor contains hundreds of volatile organic compounds (VOCs), which are the byproducts of health and disease metabolism, and they have clinical and diagnostic potential. Simultaneous collection of breath VOCs and background environmental VOCs is important to ensure analyses eliminate exogenous compounds from clinical studies. We present a mobile sampling system to extract gaseous VOCs onto commercially available sorbent-packed thermal desorption tubes. The sampler can be connected to a number of commonly available disposable and reusable sampling bags, in the case of this study, a Tedlar bag containing a breath sample. Alternatively, the inlet can be left open to directly sample room or environmental air when obtaining a background VOC sample. The system contains a screen for the operator to input a desired sample volume. A needle valve allows the operator to control the sample flow rate, which operates with an accuracy of -1.52 ± 0.63% of the desired rate, and consistently generated that rate with 0.12 ± 0.06% error across repeated measures. A flow pump, flow sensor and microcontroller allow volumetric sampling, as opposed to timed sampling, with 0.06 ± 0.06% accuracy in the volume extracted. Four samplers were compared by sampling a standard chemical mixture, which resulted in 6.4 ± 4.7% error across all four replicate modular samplers to extract a given VOC. The samplers were deployed in a clinical setting to collect breath and background/environmental samples, including patients with active SARS-CoV-2 infections, and the device could easily move between rooms and can undergo required disinfection protocols to prevent transmission of pathogens on the case exterior. All components required for assembly are detailed and are made publicly available for non-commercial use, including the microcontroller software. We demonstrate the device collects volatile compounds, including use of chemical standards, and background and breath samples in real use conditions.
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Affiliation(s)
- Bradley Chew
- Department of Mechanical and Aerospace Engineering, University of California - Davis, Davis, USA, Davis, California, 95616, UNITED STATES
| | - Raquel Pimentel Contreras
- Department of Mechanical and Aerospace Engineering, University of California - Davis, Davis, USA, Davis, California, 95616, UNITED STATES
| | - Mitchell M McCartney
- Mechanical and Aerospace Engineering, University of California - Davis, One Shields Avenue, Davis, California, 95616, UNITED STATES
| | - Eva Borras
- Department of Mechanical and Aerospace Engineering, University of California, Davis, One Shields Avenue, Davis, California, 95616, UNITED STATES
| | - Nicholas J Kenyon
- Sacramento Medical Center, UC Davis Health System, Sacramento, CA 795187, USA, Sacramento, California, 95616, UNITED STATES
| | - Cristina E Davis
- Department of Mechanical and Aerospace Engineering, University of California - Davis, Davis, USA, Davis, California, 95616, UNITED STATES
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11
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Stefanuto PH, Romano R, Rees CA, Nasir M, Thakuria L, Simon A, Reed AK, Marczin N, Hill JE. Volatile organic compound profiling to explore primary graft dysfunction after lung transplantation. Sci Rep 2022; 12:2053. [PMID: 35136125 PMCID: PMC8827074 DOI: 10.1038/s41598-022-05994-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/29/2021] [Indexed: 01/07/2023] Open
Abstract
Primary graft dysfunction (PGD) is a major determinant of morbidity and mortality following lung transplantation. Delineating basic mechanisms and molecular signatures of PGD remain a fundamental challenge. This pilot study examines if the pulmonary volatile organic compound (VOC) spectrum relate to PGD and postoperative outcomes. The VOC profiles of 58 bronchoalveolar lavage fluid (BALF) and blind bronchial aspirate samples from 35 transplant patients were extracted using solid-phase-microextraction and analyzed with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry. The support vector machine algorithm was used to identify VOCs that could differentiate patients with severe from lower grade PGD. Using 20 statistically significant VOCs from the sample headspace collected immediately after transplantation (< 6 h), severe PGD was differentiable from low PGD with an AUROC of 0.90 and an accuracy of 0.83 on test set samples. The model was somewhat effective for later time points with an AUROC of 0.80. Three major chemical classes in the model were dominated by alkylated hydrocarbons, linear hydrocarbons, and aldehydes in severe PGD samples. These VOCs may have important clinical and mechanistic implications, therefore large-scale study and potential translation to breath analysis is recommended.
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Affiliation(s)
- Pierre-Hugues Stefanuto
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA.,Organic and Biological Analytical Chemistry Group, Liège University, Liège, Belgium
| | - Rosalba Romano
- Department of Surgery and Cancer, Section of Anaesthetics, Imperial College of London, London, UK.,Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, Harefield, UK
| | | | - Mavra Nasir
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Louit Thakuria
- Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, Harefield, UK
| | - Andre Simon
- Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, Harefield, UK
| | - Anna K Reed
- Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, Harefield, UK
| | - Nandor Marczin
- Department of Surgery and Cancer, Section of Anaesthetics, Imperial College of London, London, UK.,Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, Harefield, UK.,Department of Anesthesia and Intensive Care, Semmelweis University, Budapest, Hungary
| | - Jane E Hill
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA. .,Geisel School of Medicine, Dartmouth College, Hanover, NH, USA. .,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada.
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12
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Issitt T, Wiggins L, Veysey M, Sweeney S, Brackenbury W, Redeker K. Volatile compounds in human breath: critical review and meta-analysis. J Breath Res 2022; 16. [PMID: 35120340 DOI: 10.1088/1752-7163/ac5230] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/04/2022] [Indexed: 11/12/2022]
Abstract
Volatile compounds contained in human breath reflect the inner workings of the body. A large number of studies have been published that link individual components of breath to disease, but diagnostic applications remain limited, in part due to inconsistent and conflicting identification of breath biomarkers. New approaches are therefore required to identify effective biomarker targets. Here, volatile organic compounds have been identified in the literature from four metabolically and physiologically distinct diseases and grouped into chemical functional groups (e.g. - methylated hydrocarbons or aldehydes; based on known metabolic and enzymatic pathways) to support biomarker discovery and provide new insight on existing data. Using this functional grouping approach, principal component analysis doubled explanatory capacity from 19.1% to 38% relative to single individual compound approaches. Random forest and linear discriminant analysis reveal 93% classification accuracy for cancer. This review and meta-analysis provides insight for future research design by identifying volatile functional groups associated with disease. By incorporating our understanding of the complexities of the human body, along with accounting for variability in methodological and analytical approaches, this work demonstrates that a suite of targeted, functional volatile biomarkers, rather than individual biomarker compounds, will improve accuracy and success in diagnostic research and application.
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Affiliation(s)
- Theo Issitt
- Biology, University of York, University of York, York, York, YO10 5DD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Laura Wiggins
- Biology, University of York, University of York, York, York, YO10 5DD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Martin Veysey
- The University of Newcastle, School of Medicine & Public Health, Callaghan, New South Wales, 2308, AUSTRALIA
| | - Sean Sweeney
- Biology, University of York, University of York, York, York, YO10 5DD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - William Brackenbury
- Biology, University of York, University of York, York, York, YO10 5DD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Kelly Redeker
- Biology, University of York, Biology Dept. University of York, York, York, North Yorkshire, YO10 5DD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
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13
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Khan MS, Cuda S, Karere GM, Cox LA, Bishop AC. Breath biomarkers of insulin resistance in pre-diabetic Hispanic adolescents with obesity. Sci Rep 2022; 12:339. [PMID: 35013420 PMCID: PMC8748903 DOI: 10.1038/s41598-021-04072-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
Insulin resistance (IR) affects a quarter of the world's adult population and is a major factor in the pathogenesis of cardio-metabolic disease. In this pilot study, we implemented a non-invasive breathomics approach, combined with random forest machine learning, to investigate metabolic markers from obese pre-diabetic Hispanic adolescents as indicators of abnormal metabolic regulation. Using the ReCIVA breathalyzer device for breath collection, we have identified a signature of 10 breath metabolites (breath-IR model), which correlates with Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) (R = 0.95, p < 0.001). A strong correlation was also observed between the breath-IR model and the blood glycemic profile (fasting insulin R = 0.91, p < 0.001 and fasting glucose R = 0.80, p < 0.001). Among tentatively identified metabolites, limonene, undecane, and 2,7-dimethyl-undecane, significantly cluster individuals based on HOMA-IR (p = 0.003, p = 0.002, and p < 0.001, respectively). Our breath-IR model differentiates between adolescents with and without IR with an AUC-ROC curve of 0.87, after cross-validation. Identification of a breath signature indicative of IR shows utility of exhaled breath metabolomics for assessing systemic metabolic dysregulation. A simple and non-invasive breath-based test has potential as a diagnostic tool for monitoring IR progression, allowing for earlier detection of IR and implementation of early interventions to prevent onset of type 2 diabetes mellitus.
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Affiliation(s)
- Mohammad S Khan
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Suzanne Cuda
- Health and Weight Management Clinic, Children's Hospital of San Antonio, San Antonio, TX, 78207, USA
- Baylor College of Medicine, Houston, TX, 77030, USA
| | - Genesio M Karere
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Laura A Cox
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Andrew C Bishop
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
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14
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Zaid A, Khan MS, Yan D, Marriott PJ, Wong YF. Comprehensive two-dimensional gas chromatography with mass spectrometry: an advanced bioanalytical technique for clinical metabolomics studies. Analyst 2022; 147:3974-3992. [DOI: 10.1039/d2an00584k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review highlights the current state of knowledge in the development of GC × GC-MS for the analysis of clinical metabolites. Selected applications are described as well as our perspectives on current challenges and potential future directions.
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Affiliation(s)
- Atiqah Zaid
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Mohammad Sharif Khan
- Cargill Research and Development Center, Cargill, 14800 28th Ave N, Plymouth, MN 55447, USA
| | - Dandan Yan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Yong Foo Wong
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
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15
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Abstract
BACKGROUND Starkly highlighted by the current COVID-19 pandemic, infectious diseases continue to have an outsized impact on human health worldwide. Diagnostic testing for infection can be challenging due to resource limitations, time constraints, or shortcomings in the accuracy of existing diagnostics. Rapid, simple diagnostics are highly desirable. There is increasing interest in the development of diagnostics that use exhaled breath analysis as a convenient and safe diagnostic method, as breath sampling is noninvasive, secure, and easy to perform. Volatile organic compounds (VOCs) present in exhaled breath reflect the fingerprint of the underlying metabolic and biophysical processes during disease. CONTENT In this review, we overview the major biomarkers present in exhaled breath in infectious diseases. We outline the promising recent advances in breath-based diagnosis of respiratory infections, including those caused by influenza virus, SARS-CoV-2, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Aspergillus fumigatus. In addition, we review the current landscape of diagnosis of 2 other globally important infections: Helicobacter pylori gastrointestinal infection and malaria. SUMMARY Characteristic and reproducible breath VOCs are associated with several infectious diseases, suggesting breath analysis as a promising strategy for diagnostic development. Ongoing challenges include poor standardization of breath collection and analysis and lack of validation studies. Further research is required to expand the applicability of breath analysis to clinical settings.
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Affiliation(s)
- Amalia Z Berna
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Audrey R Odom John
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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16
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Oeschger TM, McCloskey DS, Buchmann RM, Choubal AM, Boza JM, Mehta S, Erickson D. Early Warning Diagnostics for Emerging Infectious Diseases in Developing into Late-Stage Pandemics. Acc Chem Res 2021; 54:3656-3666. [PMID: 34524795 DOI: 10.1021/acs.accounts.1c00383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of infectious diseases due to travel and trade can be seen throughout history, whether from early settlers or traveling businessmen. Increased globalization has allowed infectious diseases to quickly spread to different parts of the world and cause widespread infection. Posthoc analysis of more recent outbreaks-SARS, MERS, swine flu, and COVID-19-has demonstrated that the causative viruses were circulating through populations for days or weeks before they were first detected, allowing disease to spread before quarantines, contact tracing, and travel restrictions could be implemented. Earlier detection of future novel pathogens could decrease the time before countermeasures are enacted. In this Account, we examined a variety of novel technologies from the past 10 years that may allow for earlier detection of infectious diseases. We have arranged these technologies chronologically from pre-human predictive technologies to population-level screening tools. The earliest detection methods utilize artificial intelligence to analyze factors such as climate variation and zoonotic spillover as well as specific species and geographies to identify where the infection risk is high. Artificial intelligence can also be used to monitor health records, social media, and various publicly available data to identify disease outbreaks faster than traditional epidemiology. Secondary to predictive measures is monitoring infection in specific sentinel animal species, where domestic animals or wildlife are indicators of potential disease hotspots. These hotspots inform public health officials about geographic areas where infection risk in humans is high. Further along the timeline, once the disease has begun to infect humans, wastewater epidemiology can be used for unbiased sampling of large populations. This method has already been shown to precede spikes in COVID-19 diagnoses by 1 to 2 weeks. As total infections increase in humans, bioaerosol sampling in high-traffic areas can be used for disease monitoring, such as within an airport. Finally, as disease spreads more quickly between humans, rapid diagnostic technologies such as lateral flow assays and nucleic acid amplification become very important. Minimally invasive point-of-care methods can allow for quick adoption and use within a population. These individual diagnostic methods then transfer to higher-throughput methods for more intensive population screening as an infection spreads. There are many promising early warning technologies being developed. However, no single technology listed herein will prevent every future outbreak. A combination of technologies from across our infection timeline would offer the most benefit in preventing future widespread disease outbreaks and pandemics.
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Affiliation(s)
| | | | | | | | | | - Saurabh Mehta
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York 10065, United States
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17
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Investigating Bacterial Volatilome for the Classification and Identification of Mycobacterial Species by HS-SPME-GC-MS and Machine Learning. Molecules 2021; 26:molecules26154600. [PMID: 34361751 PMCID: PMC8348828 DOI: 10.3390/molecules26154600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 11/23/2022] Open
Abstract
Species of Mycobacteriaceae cause disease in animals and humans, including tuberculosis and leprosy. Individuals infected with organisms in the Mycobacterium tuberculosis complex (MTBC) or non-tuberculous mycobacteria (NTM) may present identical symptoms, however the treatment for each can be different. Although the NTM infection is considered less vital due to the chronicity of the disease and the infrequency of occurrence in healthy populations, diagnosis and differentiation among Mycobacterium species currently require culture isolation, which can take several weeks. The use of volatile organic compounds (VOCs) is a promising approach for species identification and in recent years has shown promise for use in the rapid analysis of both in vitro cultures as well as ex vivo diagnosis using breath or sputum. The aim of this contribution is to analyze VOCs in the culture headspace of seven different species of mycobacteria and to define the volatilome profiles that are discriminant for each species. For the pre-concentration of VOCs, solid-phase micro-extraction (SPME) was employed and samples were subsequently analyzed using gas chromatography–quadrupole mass spectrometry (GC-qMS). A machine learning approach was applied for the selection of the 13 discriminatory features, which might represent clinically translatable bacterial biomarkers.
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18
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Sola Martínez RA, Pastor Hernández JM, Yanes Torrado Ó, Cánovas Díaz M, de Diego Puente T, Vinaixa Crevillent M. Exhaled volatile organic compounds analysis in clinical pediatrics: a systematic review. Pediatr Res 2021; 89:1352-1363. [PMID: 32919397 DOI: 10.1038/s41390-020-01116-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/09/2020] [Accepted: 08/04/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Measured exhaled volatile organic compounds (VOCs) in breath also referred to as exhaled volatilome have been long claimed as a potential source of non-invasive and clinically applicable biomarkers. However, the feasibility of using exhaled volatilome in clinical practice remains to be demonstrated, particularly in pediatrics where the need for improved non-invasive diagnostic and monitoring methods is most urgent. This work presents the first formal evidence-based judgment of the clinical potential of breath volatilome in the pediatric population. METHODS A rigorous systematic review across Web of Science, SCOPUS, and PubMed databases following the PRISMA statement guidelines. A narrative synthesis of the evidence was conducted and QUADAS-2 was used to assess the quality of selected studies. RESULTS Two independent reviewers deemed 22 out of the 229 records initially found to satisfy inclusion criteria. A summary of breath VOCs found to be relevant for several respiratory, infectious, and metabolic pathologies was conducted. In addition, we assessed their associated metabolism coverage through a functional characterization analysis. CONCLUSION Our results indicate that current research remains stagnant in a preclinical exploratory setting. Designing exploratory experiments in compliance with metabolomics practice should drive forward the clinical translation of VOCs breath analysis. IMPACT What is the key message of your article? Metabolomics practice could help to achieve the clinical utility of exhaled volatilome analysis. What does it add to the existing literature? This work is the first systematic review focused on disease status discrimination using analysis of exhaled breath in the pediatric population. A summary of the reported exhaled volatile organic compounds is conducted together with a functional characterization analysis. What is the impact? Having noted challenges preventing the clinical translation, we summary metabolomics practices and the experimental designs that are closer to clinical practice to create a framework to guide future trials.
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Affiliation(s)
- Rosa A Sola Martínez
- Department of Biochemistry and Molecular Biology (B) and Immunology, University of Murcia and Murcian Institute of Biosanitary Research Virgen de la Arrixaca (IMIB), Murcia, Spain
| | - José M Pastor Hernández
- Department of Biochemistry and Molecular Biology (B) and Immunology, University of Murcia and Murcian Institute of Biosanitary Research Virgen de la Arrixaca (IMIB), Murcia, Spain
| | - Óscar Yanes Torrado
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Metabolomics Platform, Reus, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology (B) and Immunology, University of Murcia and Murcian Institute of Biosanitary Research Virgen de la Arrixaca (IMIB), Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology (B) and Immunology, University of Murcia and Murcian Institute of Biosanitary Research Virgen de la Arrixaca (IMIB), Murcia, Spain.
| | - María Vinaixa Crevillent
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain.,Institut d'Investigació Sanitària Pere Virgili (IISPV), Metabolomics Platform, Reus, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
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19
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Wu X, Zhang J, Yan X, Zhu Y, Li W, Li P, Chen H, Zhang W, Cheng N, Xiang T. Characterization of Liver Failure by the Analysis of Exhaled Breath by Extractive Electrospray Ionization Mass Spectrometry (EESI-MS): A Pilot Study. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1793993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Xiaoping Wu
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianguo Zhang
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xingyan Yan
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ying Zhu
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Li
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Penghui Li
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, China
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, China
| | - Wei Zhang
- Department of Respiratory, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Na Cheng
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tianxin Xiang
- Department of Infectious Disease, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Liver Regeneration Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
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20
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Pierre-Louis MH, Rouzier V, Rivera V, Systrom HK, Julma P, Jean E, Francois LC, Pape JW, Ocheretina O, Wright PF. Diagnosis of Tuberculosis Using Gastric Aspirates in Pediatric Patients in Haiti. J Pediatric Infect Dis Soc 2021; 10:22-26. [PMID: 32092136 DOI: 10.1093/jpids/piaa012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 01/28/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND We aimed to determine whether the Xpert MTB/RIF (Xpert) assay is a useful adjunct to culture for the rapid diagnosis of tuberculosis (TB) using gastric lavage aspirates (GLAs) in children aged < 5 years. METHODS We reviewed the yield from diagnostic modalities in children suspected of having TB followed at an infectious disease research and treatment center in Port-au-Prince, Haiti, from 2011 to 2016. RESULTS In 187 children clinically diagnosed with TB, a microbiologic diagnosis could be established in 40 (21%). Cultures, Xpert, and smears were positive in 30 (19%), 28 (17%), and 3 (1.6%) children, respectively. Ten cases that would not have been diagnosed by culture alone were found by the use of the Xpert assay. Collecting 2 GLA samples optimized microbiologic yield. CONCLUSIONS In GLAs, Xpert increased the yield of microbiologically documented cases by 33%. Additionally, the rapidity of diagnosis potentially makes Xpert a valuable adjunct in initiating treatment for TB in children. Smear microscopy has low sensitivity in GLA and did not add to the documented cases. Our findings also highlight the low rate of microbiologic confirmation of clinically diagnosed TB.
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Affiliation(s)
| | - Vanessa Rouzier
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Vanessa Rivera
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Hannah K Systrom
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Pierrot Julma
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Elsie Jean
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Lovely Cassandra Francois
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Jean W Pape
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Oksana Ocheretina
- Haitian Group for the Study of Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Peter F Wright
- Division of Infectious Disease and International Health, Dartmouth Hitchcock Medical Center, Lebanon New Hampshire, USA
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21
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Bobak CA, Kang L, Workman L, Bateman L, Khan MS, Prins M, May L, Franchina FA, Baard C, Nicol MP, Zar HJ, Hill JE. Breath can discriminate tuberculosis from other lower respiratory illness in children. Sci Rep 2021; 11:2704. [PMID: 33526828 PMCID: PMC7851130 DOI: 10.1038/s41598-021-80970-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/28/2020] [Indexed: 01/30/2023] Open
Abstract
Pediatric tuberculosis (TB) remains a global health crisis. Despite progress, pediatric patients remain difficult to diagnose, with approximately half of all childhood TB patients lacking bacterial confirmation. In this pilot study (n = 31), we identify a 4-compound breathprint and subsequent machine learning model that accurately classifies children with confirmed TB (n = 10) from children with another lower respiratory tract infection (LRTI) (n = 10) with a sensitivity of 80% and specificity of 100% observed across cross validation folds. Importantly, we demonstrate that the breathprint identified an additional nine of eleven patients who had unconfirmed clinical TB and whose symptoms improved while treated for TB. While more work is necessary to validate the utility of using patient breath to diagnose pediatric TB, it shows promise as a triage instrument or paired as part of an aggregate diagnostic scheme.
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Affiliation(s)
- Carly A. Bobak
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Geisel School of Medicine, Dartmouth College, Hanover, NH USA
| | - Lili Kang
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Lesley Workman
- grid.415742.10000 0001 2296 3850Department of Pediatrics and Child Health, MRC Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Lindy Bateman
- grid.415742.10000 0001 2296 3850Department of Pediatrics and Child Health, MRC Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Mohammad S. Khan
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Margaretha Prins
- grid.415742.10000 0001 2296 3850Department of Pediatrics and Child Health, MRC Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Lloyd May
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Flavio A. Franchina
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA ,grid.4861.b0000 0001 0805 7253Molecular Systems, Organic and Biological Analytical Chemistry Group, University of Liège, Liège, Belgium
| | - Cynthia Baard
- grid.415742.10000 0001 2296 3850Department of Pediatrics and Child Health, MRC Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Mark P. Nicol
- grid.7836.a0000 0004 1937 1151Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa ,grid.1012.20000 0004 1936 7910School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Heather J. Zar
- grid.415742.10000 0001 2296 3850Department of Pediatrics and Child Health, MRC Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Jane E. Hill
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA
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22
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Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:57-67. [PMID: 33791974 DOI: 10.1007/978-3-030-51652-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Compared to one-dimensional gas chromatography with mass spectrometry (GC-MS), GC × GC-MS provides significantly increased peak capacity, resolution, and sensitivity for analysis of complex biological samples. In the last decade, GC × GC-MS has been increasingly applied to the discovery of metabolite biomarkers and elucidation of metabolic mechanisms in human diseases. The recent development of coupling GC × GC with a high-resolution mass spectrometer further accelerates these metabolomic applications. In this chapter, we will briefly review the instrumentation, sample preparation, data analysis, and applications of GC × GC-MS-based metabolomic analysis.
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Park CW, Seo SW, Kang N, Ko B, Choi BW, Park CM, Chang DK, Kim H, Kim H, Lee H, Jang J, Ye JC, Jeon JH, Seo JB, Kim KJ, Jung KH, Kim N, Paek S, Shin SY, Yoo S, Choi YS, Kim Y, Yoon HJ. Artificial Intelligence in Health Care: Current Applications and Issues. J Korean Med Sci 2020; 35:e379. [PMID: 33140591 PMCID: PMC7606883 DOI: 10.3346/jkms.2020.35.e379] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, artificial intelligence (AI) technologies have greatly advanced and become a reality in many areas of our daily lives. In the health care field, numerous efforts are being made to implement the AI technology for practical medical treatments. With the rapid developments in machine learning algorithms and improvements in hardware performances, the AI technology is expected to play an important role in effectively analyzing and utilizing extensive amounts of health and medical data. However, the AI technology has various unique characteristics that are different from the existing health care technologies. Subsequently, there are a number of areas that need to be supplemented within the current health care system for the AI to be utilized more effectively and frequently in health care. In addition, the number of medical practitioners and public that accept AI in the health care is still low; moreover, there are various concerns regarding the safety and reliability of AI technology implementations. Therefore, this paper aims to introduce the current research and application status of AI technology in health care and discuss the issues that need to be resolved.
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Affiliation(s)
- Chan Woo Park
- Department of Orthopedic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - Sung Wook Seo
- Department of Orthopedic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - Noeul Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - BeomSeok Ko
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Byung Wook Choi
- Department of Radiology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Min Park
- Department of Radiology, Seoul National University College of Medicine, Seoul, Korea
| | - Dong Kyung Chang
- Division of Gastroenterology, Department of Medicine, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - Hwiyoung Kim
- Department of Radiology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyunchul Kim
- Department of R&D Planning, Korea Health Industry Development Institute (KHIDI), Cheongju, Korea
| | - Hyunna Lee
- Health Innovation Big Data Center, Asan Institute for Life Science, Asan Medical Center, Seoul, Korea
| | - Jinhee Jang
- Department of Radiology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jong Chul Ye
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jong Hong Jeon
- Protocol Engineering Center, Electronics and Telecommunications Research Institute (ETRI), Daejeon, Korea
| | - Joon Beom Seo
- Department of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kwang Joon Kim
- Division of Geriatrics, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | | | - Namkug Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Soo Yong Shin
- Big Data Research Center, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - Soyoung Yoo
- Health Innovation Big Data Center, Asan Institute for Life Science, Asan Medical Center, Seoul, Korea
| | | | - Youngjun Kim
- Center for Bionics, Korea Institute of Science and Technology (KIST), Seoul, Korea
| | - Hyung Jin Yoon
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Korea.
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Wilde MJ, Zhao B, Cordell RL, Ibrahim W, Singapuri A, Greening NJ, Brightling CE, Siddiqui S, Monks PS, Free RC. Automating and Extending Comprehensive Two-Dimensional Gas Chromatography Data Processing by Interfacing Open-Source and Commercial Software. Anal Chem 2020; 92:13953-13960. [PMID: 32985172 PMCID: PMC7644112 DOI: 10.1021/acs.analchem.0c02844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Comprehensive
two-dimensional gas chromatography (GC×GC) is
a powerful analytical tool for both nontargeted and targeted analyses.
However, there is a need for more integrated workflows for processing
and managing the resultant high-complexity datasets. End-to-end workflows
for processing GC×GC data are challenging and often require multiple
tools or software to process a single dataset. We describe a new approach,
which uses an existing underutilized interface within commercial software
to integrate free and open-source/external scripts and tools, tailoring
the workflow to the needs of the individual researcher within a single
software environment. To demonstrate the concept, the interface was
successfully used to complete a first-pass alignment on a large-scale
GC×GC metabolomics dataset. The analysis was performed by interfacing
bespoke and published external algorithms within a commercial software
environment to automatically correct the variation in retention times
captured by a routine reference standard. Variation in 1tR and 2tR was reduced on average
from 8 and 16% CV prealignment to less than 1 and 2% post alignment,
respectively. The interface enables automation and creation of new
functions and increases the interconnectivity between chemometric
tools, providing a window for integrating data-processing software
with larger informatics-based data management platforms.
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Affiliation(s)
- Michael J Wilde
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K.,Department of Respiratory Sciences, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Bo Zhao
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
| | - Rebecca L Cordell
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Wadah Ibrahim
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester LE1 7RH, U.K.,Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
| | - Amisha Singapuri
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester LE1 7RH, U.K.,Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
| | - Neil J Greening
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester LE1 7RH, U.K.,Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
| | - Chris E Brightling
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester LE1 7RH, U.K.,Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
| | - Salman Siddiqui
- Department of Respiratory Sciences, University of Leicester, University Road, Leicester LE1 7RH, U.K.,Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
| | - Paul S Monks
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Robert C Free
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester LE3 9QP, U.K
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Lawson J, Boyle B, Beauchamp J. Driving progress in exhaled breath biomarkers: Breath Biopsy Conference 2019. J Breath Res 2020; 14:030202. [PMID: 32662449 DOI: 10.1088/1752-7163/ab9424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
November 2019 saw Cambridge, UK play host to the second Breath Biopsy Conference, a community-focused event aimed at sharing and supporting advancements in the collection and analysis of volatile organic compounds in exhaled breath. The event expanded upon the previous year's format, spanning two days and concluding with an expert panel discussion. Presentations covered detection, monitoring and precision medicine studies examining diseases including asthma, cirrhosis, cancer and tuberculosis. The meeting attracted representatives from diverse backgrounds, such as metabolomics, artificial intelligence, clinical research and chemical analysis. This meeting report offers an overview of what was presented and discussed during the conference.
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Affiliation(s)
- Jonathan Lawson
- Owlstone Medical Ltd., 183 Cambridge Science Park, Milton Road, Cambridge CB4 0GJ, United Kingdom
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26
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Perspectives of Biological Analysis in Latin America Using Multi and Comprehensive Two-Dimensional Gas Chromatography: A Mini-review. Chromatographia 2020. [DOI: 10.1007/s10337-020-03910-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
One of the most logical applications of modern breath analysis techniques is to provide information on respiratory infections. Ongoing work in various types of pulmonary infections has begun to denote candidate breath biomarkers of bacterial, viral, and fungal lung infections. Groundbreaking studies have been performed in naturally occurring cases with humans and with animal models of the disease. This has been coupled with cell culture work to understand the nature of the origins of breath biomarkers generated from the pathogen itself as it proliferates. Much work remains to be done, and the published studies described in this chapter are helping to set a foundation for this research area.
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Amaral MSS, Nolvachai Y, Marriott PJ. Comprehensive Two-Dimensional Gas Chromatography Advances in Technology and Applications: Biennial Update. Anal Chem 2019; 92:85-104. [DOI: 10.1021/acs.analchem.9b05412] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michelle S. S. Amaral
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Yada Nolvachai
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
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Pleil JD, Wallace MAG, McCord J, Madden MC, Sobus J, Ferguson G. How do cancer-sniffing dogs sort biological samples? Exploring case-control samples with non-targeted LC-Orbitrap, GC-MS, and immunochemistry methods. J Breath Res 2019; 14:016006. [PMID: 31505485 PMCID: PMC8649743 DOI: 10.1088/1752-7163/ab433a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Early identification of disease onset is regarded as an important factor for successful medical intervention. However, cancer and other long-term latency diseases are rare and may take years to manifest clinically. As such, there are no gold standards with which to immediately validate proposed preclinical screening methodologies. There is evidence that dogs can sort samples reproducibly into yes/no categories based on case-control training, but the basis of their decisions is unknown. Because dogs are sniffing air, the distinguishing chemicals must be either in the gas-phase or attached to aerosols and/or airborne particles. Recent biomonitoring research has shown how to extract and analyze semi- and non-volatile compounds from human breath in exhaled condensates and aerosols. Further research has shown that exhaled aerosols can be directly collected on standard hospital-style olefin polypropylene masks and that these masks can be used as a simple sampling scheme for canine screening. In this article, detailed liquid chromatography-high resolution mass spectrometry (LC-HR-MS) with Orbitrap instrumentation and gas chromatography-mass spectrometry (GC-MS) analyses were performed on two sets of masks sorted by consensus of a four-dog cohort as either cancer or control. Specifically, after sorting by the dogs, sample masks were cut into multiple sections and extracted for LC-MS and GC-MS non-targeted analyses. Extracts were also analyzed for human cytokines, confirming the presence of human aerosol content above levels in blank masks. In preliminary evaluations, 345 and 44 high quality chemical features were detected by LC-MS and GC-MS analyses, respectively. These features were used to develop provisional orthogonal projection to latent structures-discriminant analysis (OPLS-DA) models to determine if the samples classified as cancer (case) or non-cancer (control) by the dogs could be separated into the same groups using analytical instrumentation. While the OPLS-DA model for the LC-HR-MS data was able to separate the two groups with statistical significance, although weak explanatory power, the GC-MS model was not found to be significant. These results suggest that the dogs may rely on the less volatile compounds from breath aerosol that were analyzed by LC-HR-MS than the more volatile compounds observed by GC-MS to sort mask samples into groups. These results provide justification for more expansive studies in the future that aim to characterize specific chemical features, and the role(s) of these features in maintaining homeostatic biological processes.
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Affiliation(s)
- Joachim D Pleil
- US Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109T. W. Alexander Drive, Research Triangle Park, NC, 27709, United States of America
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Aspromonte J, Wolfs K, Adams E. Current application and potential use of GC × GC in the pharmaceutical and biomedical field. J Pharm Biomed Anal 2019; 176:112817. [DOI: 10.1016/j.jpba.2019.112817] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 01/25/2023]
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31
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Saktiawati AMI, Putera DD, Setyawan A, Mahendradhata Y, van der Werf TS. Diagnosis of tuberculosis through breath test: A systematic review. EBioMedicine 2019; 46:202-214. [PMID: 31401197 PMCID: PMC6712009 DOI: 10.1016/j.ebiom.2019.07.056] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 12/28/2022] Open
Abstract
Background Breath tests may diagnose tuberculosis (TB) through detecting specific volatile organic compounds produced by Mycobacterium tuberculosis or the infected host. Methods To estimate the diagnostic accuracy of breath test with electronic-nose and other devices against culture or other tests for TB, we screened multiple databases until January 6, 2019. Findings We included fourteen studies, with 1715 subjects in the analysis. The pooled sensitivity and specificity of electronic-nose were 0.93 (95% CI 0.82–0.97) and 0.93 (95% CI 0.82–0.97), respectively, and no heterogeneity was found. The sensitivity and specificity of other breath test devices ranged from 0.62 to 1.00, and 0.11 to 0.84, respectively. Interpretation The low to moderate evidence of these studies shows that breath tests can diagnose TB accurately, however, to give a real-time test result, additional development is needed. Research should also focus on sputum smear negative TB, children, and the positioning of breath testing in the diagnostic work flow. Funding The authors received no specific funding for this work.
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Affiliation(s)
- Antonia M I Saktiawati
- Department of Internal Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; University of Groningen, University Medical Centre Groningen, Department of Pulmonary Diseases and Tuberculosis, Groningen, the Netherlands; Center for Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Althaf Setyawan
- Department of Biostatistics, Epidemiology, and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yodi Mahendradhata
- Center for Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Health Policy and Management, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tjip S van der Werf
- University of Groningen, University Medical Centre Groningen, Department of Pulmonary Diseases and Tuberculosis, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Internal Medicine-Infectious Diseases, Groningen, the Netherlands.
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Kapoor R, Walters SP, Al-Aswad LA. The current state of artificial intelligence in ophthalmology. Surv Ophthalmol 2019; 64:233-240. [DOI: 10.1016/j.survophthal.2018.09.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
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Breath analysis by two-dimensional gas chromatography with dual flame ionisation and mass spectrometric detection - Method optimisation and integration within a large-scale clinical study. J Chromatogr A 2019; 1594:160-172. [PMID: 30755317 PMCID: PMC6491496 DOI: 10.1016/j.chroma.2019.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/24/2018] [Accepted: 02/01/2019] [Indexed: 12/15/2022]
Abstract
New method for the analysis of exhaled breath VOCs by TD-GC × GC-FID/qMS. Optimisation of flow modulation and dual detection alongside clinical requirements. Addresses key challenges of using GC × GC for large-scale breath metabolomics.
Precision medicine has spurred new innovations in molecular pathology leading to recent advances in the analysis of exhaled breath as a non-invasive diagnostic tool. Volatile organic compounds (VOCs) detected in exhaled breath have the potential to reveal a wealth of chemical and metabolomic information. This study describes the development of a method for the analysis of breath, based on automated thermal desorption (TD) combined with flow modulated comprehensive two-dimensional gas chromatography (GC×GC) with dual flame ionisation and quadrupole mass spectrometric detection (FID and qMS). The constrained optimisation and analytical protocol was designed to meet the practical demands of a large-scale multi-site clinical study, while maintaining analytical rigour to produce high fidelity data. The results demonstrate a comprehensive method optimisation for the collection and analysis of breath VOCs by GC×GC, integral to the standardisation and integration of breath analysis within large clinical studies.
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Pesesse R, Stefanuto PH, Schleich F, Louis R, Focant JF. Multimodal chemometric approach for the analysis of human exhaled breath in lung cancer patients by TD-GC × GC-TOFMS. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1114-1115:146-153. [PMID: 30745111 DOI: 10.1016/j.jchromb.2019.01.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022]
Abstract
Lung cancer is the deadliest cancer in developed countries. To reduce its mortality rate, it is important to enhance our capability to detect it at earlier stages by developing early diagnostic methods. In that context, the analysis of exhaled breath is an interesting approach because of the simplicity of the medical act and its non-invasiveness. Thermal desorption comprehensive two-dimensional gas chromatography time of flight mass spectrometry (TD-GC × GC-TOFMS) has been used to characterize and compare the volatile content of human breath of lung cancer patients and healthy volunteers. On the sampling side, the contaminations induced by the bags membrane and further environmental migration of VOCs during and after the sampling have also been investigated. Over a realistic period of 6 h, the concentration of contaminants inside the bag can increase from 2 to 3 folds based on simulated breath samples. On the data processing side, Fisher ratio (FR) and random forest (RF) approaches were applied and compared in regards to their ability to reduce the data dimensionality and to extract the significant information. Both approaches allow to efficiently smooth the background signal and extract significant features (27 for FR and 17 for RF). Principal component analysis (PCA) was used to evaluate the clustering capacity of the different models. For both approaches, a separation along PC-1 was obtained with a variance score around 35%. The combined model provides a partial separation with a PC-1 score of 52%. This proof-of-concept study further confirms the potential of breath analysis for cancer detection but also underlines the importance of quality control over the full analytical procedure, including the processing of the data.
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Affiliation(s)
- R Pesesse
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, B6c, Agora District, 4000 Liège, Belgium
| | - P-H Stefanuto
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, B6c, Agora District, 4000 Liège, Belgium
| | - F Schleich
- Pneumology and Allergology, GIGA Research Group, CHU of Liège, University of Liege, B35, Hospital District, Liege, Belgium
| | - R Louis
- Pneumology and Allergology, GIGA Research Group, CHU of Liège, University of Liege, B35, Hospital District, Liege, Belgium
| | - J-F Focant
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, B6c, Agora District, 4000 Liège, Belgium.
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35
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Keppler EAH, Jenkins CL, Davis TJ, Bean HD. Advances in the application of comprehensive two-dimensional gas chromatography in metabolomics. Trends Analyt Chem 2018; 109:275-286. [PMID: 30662103 PMCID: PMC6333419 DOI: 10.1016/j.trac.2018.10.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Due to excellent separation capacity for complex mixtures of chemicals, comprehensive two-dimensional gas chromatography (GC × GC) is being utilized with increasing frequency for metabolomics analyses. This review describes recent advances in GC × GC method development for metabolomics, organismal sampling techniques compatible with GC × GC, metabolomic discoveries made using GC × GC, and recommendations and best practices for collecting and reporting GC × GC metabolomics data.
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Affiliation(s)
| | - Carrie L Jenkins
- School of Life Sciences, Arizona State University, Tempe, AZ, 85283, USA
| | - Trenton J Davis
- School of Life Sciences, Arizona State University, Tempe, AZ, 85283, USA
| | - Heather D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, 85283, USA
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Beccaria M, Bobak C, Maitshotlo B, Mellors TR, Purcaro G, Franchina FA, Rees CA, Nasir M, Black A, Hill JE. Exhaled human breath analysis in active pulmonary tuberculosis diagnostics by comprehensive gas chromatography-mass spectrometry and chemometric techniques. J Breath Res 2018; 13:016005. [PMID: 30394364 DOI: 10.1088/1752-7163/aae80e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tuberculosis (TB) is the deadliest infectious disease, and yet accurate diagnostics for the disease are unavailable for many subpopulations. In this study, we investigate the possibility of using human breath for the diagnosis of active TB among TB suspect patients, considering also several risk factors for TB for smokers and those with human immunodeficiency virus (HIV). The analysis of exhaled breath, as an alternative to sputum-dependent tests, has the potential to provide a simple, fast, non-invasive, and readily available diagnostic service that could positively change TB detection. A total of 50 individuals from a clinic in South Africa were included in this pilot study. Human breath has been investigated in the setting of active TB using the thermal desorption-comprehensive two-dimensional gas chromatography-time of flight mass spectrometry methodology and chemometric techniques. From the entire spectrum of volatile metabolites in breath, three machine learning algorithms (support vector machines, partial least squares discriminant analysis, and random forest) to select discriminatory volatile molecules that could potentially be useful for active TB diagnosis were employed. Random forest showed the best overall performance, with sensitivities of 0.82 and 1.00 and specificities of 0.92 and 0.60 in the training and test data respectively. Unsupervised analysis of the compounds implicated by these algorithms suggests that they provide important information to cluster active TB from other patients. These results suggest that developing a non-invasive diagnostic for active TB using patient breath is a potentially rich avenue of research, including among patients with HIV comorbidities.
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Affiliation(s)
- Marco Beccaria
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, United States of America. KU Leuven-University of Leuven, Department for Pharmaceutical and Pharmacological Sciences, Leuven, B-3000, Belgium
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37
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Mellors TR, Nasir M, Franchina FA, Smolinska A, Blanchet L, Flynn JL, Tomko J, O’Malley M, Scanga CA, Lin PL, Wagner J, Hill JE. Identification of Mycobacterium tuberculosis using volatile biomarkers in culture and exhaled breath. J Breath Res 2018; 13:016004. [DOI: 10.1088/1752-7163/aacd18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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