Breath metabolome of mice infected with Pseudomonas aeruginosa

Fulfilling the Promise of Breathomics: Considerations for the Discovery and Validation of Exhaled Volatile Biomarkers

The exhaled breath represents an ideal matrix for noninvasive biomarker discovery, and exhaled metabolomics have the potential to be clinically useful in the era of precision medicine. In this concise translational review, we specifically address volatile organic compounds in the breath, with a view toward fulfilling the promise of these as actionable biomarkers, in particular, for lung diseases. We review the literature paying attention to seminal work linked to key milestones in breath research; discuss potential applications for breath biomarkers across disease areas and healthcare systems, including the perspectives of industry; and outline critical aspects of study design that will need to be considered for any pivotal research going forward if breath analysis is to provide robust validated biomarkers that meet the requirements for future clinical implementation.

Modern approaches for detection of volatile organic compounds in metabolic studies focusing on pathogenic bacteria: Current state of the art

Pathogenic microorganisms produce numerous metabolites, including volatile organic compounds (VOCs). Monitoring these metabolites in biological matrices (e.g., urine, blood, or breath) can reveal the presence of specific microorganisms, enabling the early diagnosis of infections and the timely implementation of targeted therapy. However, complex matrices only contain trace levels of VOCs, and their constituent components can hinder determination of these compounds. Therefore, modern analytical techniques enabling the non-invasive identification and precise quantification of microbial VOCs are needed. In this paper, we discuss bacterial VOC analysis under in vitro conditions, in animal models and disease diagnosis in humans, including techniques for offline and online analysis in clinical settings. We also consider the advantages and limitations of novel microextraction techniques used to prepare biological samples for VOC analysis, in addition to reviewing current clinical studies on bacterial volatilomes that address inter-species interactions, the kinetics of VOC metabolism, and species- and drug-resistance specificity.

Exhaled Breath Analysis Detects the Clearance of Staphylococcus aureus from the Airways of Children with Cystic Fibrosis

BACKGROUND

Electronic nose (eNose) technology can be used to characterize volatile organic compound (VOC) mixes in breath. While previous reports have shown that eNose can detect lung infections with pathogens such as Staphylococcus aureus (SA) in people with cystic fibrosis (CF), the clinical utility of eNose for longitudinally monitoring SA infection status is unknown.

METHODS

In this longitudinal study, a cloud-connected eNose, the SpiroNose, was used for the breath profile analysis of children with CF at two stable visits and compared based on changes in SA infection status between visits. Data analysis involved advanced sensor signal processing, ambient correction, and statistics based on the comparison of breath profiles between baseline and follow-up visits.

RESULTS

Seventy-two children with CF, with a mean (IQR) age of 13.8 (9.8-16.4) years, were studied. In those with SA-positive airway cultures at baseline but SA-negative cultures at follow-up (n = 19), significant signal differences were detected between Baseline and Follow-up at three distinct eNose sensors, i.e., S4 (p = 0.047), S6 (p = 0.014), and S7 (p = 0.014). Sensor signal changes with the clearance of SA from airways were unrelated to antibiotic treatment. No changes in sensor signals were seen in patients with unchanged infection status between visits.

CONCLUSIONS

Our results demonstrate the potential applicability of the eNose as a non-invasive clinical tool to longitudinally monitor pulmonary SA infection status in children with CF.

A systematic review on the detection of volatile organic compounds in exhaled breath in experimental animals in the context of gastrointestinal and hepatic diseases

BACKGROUND

Analysis of volatile organic compounds (VOCs) in exhaled breath has the potential to serve as an accurate diagnostic tool for gastro-intestinal diseases. Animal studies could be instrumental as a preclinical base and subsequent clinical translation to humans, as they are easier to standardize and better equipped to relate specific VOCs to metabolic and pathological processes. This review provides an overview of the study design, characteristics and methodological quality of previously published animal studies on analysis of exhaled breath in gastrointestinal and hepatic diseases. Guidelines are provided for standardization in study design and breath collection methods to improve comparability, avoid duplication of research and reduce discomfort of animals in future studies.

METHODS

PubMed and Embase database were searched for animal studies using exhaled breath analysis to detect gastro-intestinal diseases. Risk of bias was assessed using the SYRCLE's risk of bias tool for animal studies. Information on study design, standardization methods, animal models, breath collection methods and identified VOCs were extracted from the included studies.

RESULTS

10 studies were included (acute liver failure n = 1, non-alcoholic steatohepatitis n = 1, hepatic ischemia n = 2, mesenteric ischemia n = 2, sepsis and peritonitis n = 3, colitis n = 1). Rats were used in most of the studies. Exhaled breath was mostly collected using invasive procedures as tracheal cannulation or tracheostomy. Poor reporting on standardization, breath collection methods, analytical techniques, as well as heterogeneity of the studies, complicate comparison of the different studies.

CONCLUSION

Poor reporting of essential methodological details impaired comprehensive summarizing the various studies on exhaled breath in gastrointestinal and hepatic diseases. Potential pitfalls in study design, and suggestions for improvement of study design are discussed which, when applied, lead to consistent and generalizable results and a reduction in the use of laboratory animals. Refining the methodological quality of animal studies has the potential to improve subsequent clinical trial design.

Volatile Metabolites in Lavage Fluid Are Correlated with Cytokine Production in a Valley Fever Murine Model

Coccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this proof-of-concept study, we explored the feasibility of developing breath-based diagnostics for Valley fever using a murine lung infection model. To investigate potential volatile biomarkers of Valley fever that arise from host−pathogen interactions, we infected C57BL/6J mice with C. immitis RS (n = 6), C. posadasii Silveira (n = 6), or phosphate-buffered saline (n = 4) via intranasal inoculation. We measured fungal dissemination and collected bronchoalveolar lavage fluid (BALF) for cytokine profiling and for untargeted volatile metabolomics via solid-phase microextraction (SPME) and two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS). We identified 36 volatile organic compounds (VOCs) that were significantly correlated (p < 0.05) with cytokine abundance. These 36 VOCs clustered mice by their cytokine production and were also able to separate mice with moderate-to-high cytokine production by infection strain. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect coccidioidal infection and provide clinically relevant information on primary pulmonary disease severity.

Pseudomonas aeruginosa reference strains PAO1 and PA14: A genomic, phenotypic, and therapeutic review

Pseudomonas aeruginosa is a ubiquitous, motile, gram-negative bacterium that has been recently identified as a multi-drug resistant pathogen in critical need of novel therapeutics. Of the approximately 5,000 strains, PAO1 and PA14 are common laboratory reference strains, modeling moderately and hyper-virulent phenotypes, respectively. PAO1 and PA14 have been instrumental in facilitating the discovery of novel drug targets, testing novel therapeutics, and supplying critical genomic information on the bacterium. While the two strains have contributed to a wide breadth of knowledge on the natural behaviors and therapeutic susceptibilities of P. aeruginosa, they have demonstrated significant deviations from observations in human infections. Many of these deviations are related to experimental inconsistencies in laboratory strain environment that complicate and, at times, terminate translation from laboratory results to clinical applications. This review aims to provide a comparative analysis of the two strains and potential methods to improve their clinical relevance.

Comprehensive two-dimensional gas chromatographic platforms comparison for exhaled breath metabolites analysis

The high potential of exhaled breath for disease diagnosis has been highlighted in numerous studies. However, exhaled breath analysis is suffering from a lack of standardized sampling and analysis procedures, impacting the robustness of inter-laboratory results, and thus hampering proper external validation. The aim of this work was to verify compliance and validate the performance of two different comprehensive two-dimensional gas chromatography coupled to mass spectrometry platforms in different laboratories by monitoring probe metabolites in exhaled breath following the Peppermint Initiative guidelines. An initial assessment of the exhaled breath sampling conditions was performed, selecting the most suitable sampling bag material and volume. Then, a single sampling was performed using Tedlar bags, followed by the trapping of the volatile organic compounds into thermal desorption tubes for the subsequent analysis using two different analytical platforms. The thermal desorption tubes were first analyzed by a (cryogenically modulated) comprehensive two-dimensional gas chromatography system coupled to high-resolution time-of-flight mass spectrometry. The desorption was performed in split mode and the split part was recollected in the same tube and further analyzed by a different (flow modulated) comprehensive two-dimensional gas chromatography system with a parallel detection, specifically using a quadrupole mass spectrometer and a vacuum ultraviolet detector. Both the comprehensive two-dimensional gas chromatography platforms enabled the longitudinal tracking of the peppermint oil metabolites in exhaled breath. The increased sensitivity of comprehensive two-dimensional gas chromatography enabled to successfully monitor over a 6.5 h period a total of 10 target compounds, namely α-pinene, camphene, β-pinene, limonene, cymene, eucalyptol, menthofuran, menthone, isomenthone, and neomenthol.

Non-invasive breath collection in murine models using a newly developed sampling device

Volatile organic compounds (VOCs) in exhaled breath have the potential to be used as biomarkers for screening and diagnosis of diseases. Clinical studies are often complicated by both modifiable and non-modifiable factors influencing the composition of VOCs in exhaled breath. Small laboratory animal studies contribute in obtaining fundamental insight in alterations in VOC composition in exhaled breath and thereby facilitate the design and analysis of clinical research. However, long term animal experiments are often limited by invasive breath collection methods and terminal experiments. To overcome this problem, a novel device was developed for non-invasive breath collection in mice using glass nose-only restrainers thereby omitting the need of anesthetics. C57Bl/6J mice were used to test reproducibility and different air sampling settings for air-flow (ml/min) and time (minutes). Exhaled air was collected on desorption tubes and analysed for VOCs by gas chromatography time-of-flight mass spectrometry (GC-tof-MS). In total 27 compounds were putatively identified and used to assess the variability of the VOC measurements in the breath collections. Best reproducibility is obtained when using an air flow of 185 ml/min and a collection time of 20 minutes. Due to the non-invasive nature of breath collections in murine models, this device has the potential to facilitate VOC research in relation to disturbed metabolism and or disease pathways.

An Investigation of Stability and Species and Strain-Level Specificity in Bacterial Volatilomes

Microbial volatilomics is a rapidly growing field of study and has shown great potential for applications in food, farming, and clinical sectors in the future. Due to the varying experimental methods and growth conditions employed in microbial volatilomic studies as well as strain-dependent volatilomic differences, there is limited knowledge regarding the stability of microbial volatilomes. Consequently, cross-study comparisons and validation of results and data can be challenging. In this study, we investigated the stability of the volatilomes of multiple strains of Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli across three frequently used nutrient-rich growth media. Volatilomic stability was assessed based on media-, time- and strain-dependent variation across the examined bacterial volatilomes. Strain-level specificity of the observed volatilomes of E. coli and P. aeruginosa strains was further investigated by comparing the emission of selected compounds at varying stages of cell growth. Headspace solid phase microextraction (HS-SPME) sampling coupled with gas chromatography mass spectrometry (GC-MS) was used to analyze the volatilome of each strain. The whole volatilomes of the examined strains demonstrate a high degree of stability across the three examined growth media. At the compound-level, media dependent differences were observed particularly when comparing the volatilomes obtained in glucose-containing brain heart infusion (BHI) and tryptone soy broth (TSB) growth media with the volatilomes obtained in glucose-free Lysogeny broth (LB) media. These glucose-dependent volatilomic differences were primarily seen in the emission of primary metabolites such as alcohols, ketones, and acids. Strain-level differences in the emission of specific compounds in E. coli and P. aeruginosa samples were also observed across the media. These strain-level volatilomic differences were also observed across varying phases of growth of each strain, therefore confirming that these strains had varying core and accessory volatilomes. Our results demonstrate that, at the species-level, the examined bacteria have a core volatilome that exhibits a high-degree of stability across frequently-used growth media. Media-dependent differences in microbial volatilomes offer valuable insights into identifying the cellular origin of individual metabolites. The observed differences in the core and accessory volatilomes of the examined strains illustrate the complexity of microbial volatilomics as a study while also highlighting the need for more strain-level investigations to ultimately elucidate the whole volatilomic capabilities of microbial species in the future.

Chromatographic Fingerprinting Enables Effective Discrimination and Identitation of High-Quality Italian Extra-Virgin Olive Oils

The challenging process of high-quality food authentication takes advantage of highly informative chromatographic fingerprinting and its identitation potential. In this study, the unique chemical traits of the complex volatile fraction of extra-virgin olive oils from Italian production are captured by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry and explored by pattern recognition algorithms. The consistent realignment of untargeted and targeted features of over 73 samples, including oils obtained by different olive cultivars (n = 24), harvest years (n = 3), and processing technologies, provides a solid foundation for sample identification and discrimination based on production region (n = 6). Through a dedicated multivariate statistics workflow, identitation is achieved by two-level partial least-square (PLS) regression, which highlights region diagnostic patterns accounting between 58 and 82 of untargeted and targeted compounds, while sample classification is performed by sequential application of soft independent modeling for class analogy (SIMCA) models, one for each production region. Samples are correctly classified in five of the six single-class models, and quality parameters [i.e., sensitivity, specificity, precision, efficiency, and area under the receiver operating characteristic curve (AUC)] are equal to 1.00.

Breath-Based Diagnosis of Infectious Diseases: A Review of the Current Landscape

Various analytical methods can be applied to concentrate, separate, and examine trace volatile organic metabolites in the breath, with the potential for noninvasive, rapid, real-time identification of various disease processes, including an array of microbial infections. Although biomarker discovery and validation in microbial infections can be technically challenging, it is an approach that has shown great promise, especially for infections that are particularly difficult to identify with standard culture and molecular amplification-based approaches. This article discusses the current state of breath analysis for the diagnosis of infectious diseases.

Breath analysis for respiratory infections

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.