Evaluation of a combination of SIFT-MS and multivariate data analysis for the diagnosis of Mycobacterium bovis in wild badgers

Detection of Mycobacterium tuberculosis complex field infections in cattle using fecal volatile organic compound analysis through gas chromatography-ion mobility spectrometry combined with chemometrics

Bovine tuberculosis is considered a re-emerging disease caused by different species from the Mycobacterium tuberculosis complex (MTC), important not only for the livestock sector but also for public health due to its zoonotic character. Despite the numerous efforts that have been carried out to improve the performance of the current antemortem diagnostic procedures, nowadays, they still pose several drawbacks, such as moderate to low sensitivity, highlighting the necessity to develop alternative and innovative tools to complement control and surveillance frameworks. Volatilome analysis is considered an innovative approach which has been widely employed in animal science, including animal health field and diagnosis, due to the useful and interesting information provided by volatile metabolites. Therefore, this study assesses the potential of gas chromatography coupled to ion mobility spectrometry (GC-IMS) to discriminate cattle naturally infected (field infections) by MTC from non-infected animals. Volatile organic compounds (VOCs) produced from feces were analyzed, employing the subsequent information through chemometrics. After the evaluation of variable importance for the projection of compounds, the final discriminant models achieved a robust performance in cross-validation, as well as high percentages of correct classification (>90%) and optimal data of sensitivity (91.66%) and specificity (99.99%) in external validation. The tentative identification of some VOCs revealed some coincidences with previous studies, although potential new compounds associated with the discrimination of infected and non-infected subjects were also addressed. These results provide strong evidence that a volatilome analysis of feces through GC-IMS coupled to chemometrics could become a valuable methodology to discriminate the infection by MTC in cattle. IMPORTANCE Bovine tuberculosis is endemic in many countries worldwide and poses important concerns for public health because of their zoonotic condition. However, current diagnostic techniques present several hurdles, such as low sensitivity and complexity, among others. In this regard, the development of new approaches to improve the diagnosis and control of this disease is considered crucial. Volatile organic compounds are small molecular mass metabolites which compose volatilome, whose analysis has been widely employed with success in different areas of animal science including animal health. The present study seeks to evaluate the combination of fecal volatilome analysis with chemometrics to detect field infections by bovine tuberculosis (Mycobacterium tuberculosis complex) in cattle. The good robust performance of discriminant models as well as the optimal data of sensitivity and specificity achieved highlight volatilome analysis as an innovative approach with huge potential.

Application of Volatilome Analysis to the Diagnosis of Mycobacteria Infection in Livestock

Volatile organic compounds (VOCs) are small molecular mass metabolites which compose the volatilome, whose analysis has been widely employed in different areas. This innovative approach has emerged in research as a diagnostic alternative to different diseases in human and veterinary medicine, which still present constraints regarding analytical and diagnostic sensitivity. Such is the case of the infection by mycobacteria responsible for tuberculosis and paratuberculosis in livestock. Although eradication and control programs have been partly managed with success in many countries worldwide, the often low sensitivity of the current diagnostic techniques against Mycobacterium bovis (as well as other mycobacteria from Mycobacterium tuberculosis complex) and Mycobacterium avium subsp. paratuberculosis together with other hurdles such as low mycobacteria loads in samples, a tedious process of microbiological culture, inhibition by many variables, or intermittent shedding of the mycobacteria highlight the importance of evaluating new techniques that open different options and complement the diagnostic paradigm. In this sense, volatilome analysis stands as a potential option because it fulfills part of the mycobacterial diagnosis requirements. The aim of the present review is to compile the information related to the diagnosis of tuberculosis and paratuberculosis in livestock through the analysis of VOCs by using different biological matrices. The analytical techniques used for the evaluation of VOCs are discussed focusing on the advantages and drawbacks offered compared with the routine diagnostic tools. In addition, the differences described in the literature among in vivo and in vitro assays, natural and experimental infections, and the use of specific VOCs (targeted analysis) and complete VOC pattern (non-targeted analysis) are highlighted. This review emphasizes how this methodology could be useful in the problematic diagnosis of tuberculosis and paratuberculosis in livestock and poses challenges to be addressed in future research.

Review on Volatolomic Studies as a Frontier Approach in Animal Research

This paper presents a comprehensive review of the research studies in volatolomics performed on animals so far. At first, the procedures proposed for the collection, preconcentration, and storing of the volatile organic compounds emitted by various biological samples of different animals are presented and discussed. Next, the results obtained in the analysis of the collected volatile samples with analytical equipment are shown. The possible volatile biomarkers identified for various diseases are highlighted for different types of diseases, animal species, and biological samples analyzed. The chemical classes of these compounds, as well as the biomarkers found in a higher number of animal diseases, are indicated, and their possible origin is analyzed. The studies that dealt with the diagnosis of various diseases from sample measurement with electronic nose systems are also presented and discussed. The paper ends with a final remark regarding the necessity of optimization and standardization of sample collection and analysis procedures for obtaining meaningful results.

Multimodal combination of GC × GC-HRTOFMS and SIFT-MS for asthma phenotyping using exhaled breath

Chronic inflammatory lung diseases impact more than 300 million of people worldwide. Because they are not curable, these diseases have a high impact on both the quality of life of patients and the healthcare budget. The stability of patient condition relies mostly on constant treatment adaptation and lung function monitoring. However, due to the variety of inflammation phenotypes, almost one third of the patients receive an ineffective treatment. To improve phenotyping, we evaluated the complementarity of two techniques for exhaled breath analysis: full resolving comprehensive two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC × GC-HRTOFMS) and rapid screening selected ion flow tube MS (SIFT-MS). GC × GC-HRTOFMS has a high resolving power and offers a full overview of sample composition, providing deep insights on the ongoing biology. SIFT-MS is usually used for targeted analyses, allowing rapid classification of samples in defined groups. In this study, we used SIFT-MS in a possible untargeted full-scan mode, where it provides pattern-based classification capacity. We analyzed the exhaled breath of 50 asthmatic patients. Both techniques provided good classification accuracy (around 75%), similar to the efficiency of other clinical tools routinely used for asthma phenotyping. Moreover, our study provides useful information regarding the complementarity of the two techniques.

Evaluation of Volatile Organic Compounds Obtained from Breath and Feces to Detect Mycobacterium tuberculosis Complex in Wild Boar (Sus scrofa) in Doñana National Park, Spain

The presence of Mycobacterium tuberculosis complex (MTBC) in wild swine, such as in wild boar (Sus scrofa) in Eurasia, is cause for serious concern. Development of accurate, efficient, and noninvasive methods to detect MTBC in wild swine would be highly beneficial to surveillance and disease management efforts in affected populations. Here, we describe the first report of identification of volatile organic compounds (VOC) obtained from the breath and feces of wild boar to distinguish between MTBC-positive and MTBC-negative boar. We analyzed breath and fecal VOC collected from 15 MTBC-positive and 18 MTBC-negative wild boar in Donaña National Park in Southeast Spain. Analyses were divided into three age classes, namely, adults (>2 years), sub-adults (12–24 months), and juveniles (<12 months). We identified significant compounds by applying the two-tailed statistical t-test for two samples assuming unequal variance, with an α value of 0.05. One statistically significant VOC was identified in breath samples from adult wild boar and 14 were identified in breath samples from juvenile wild boar. One statistically significant VOC was identified in fecal samples collected from sub-adult wild boar and three were identified in fecal samples from juvenile wild boar. In addition, discriminant function analysis (DFA) was used to build classification models for MTBC prediction in juvenile animals. Using DFA, we were able to distinguish between MTBC-positive juvenile wild boar and MTBC-negative juvenile wild boar using breath VOC or fecal VOC. Based on our results, further research is warranted and should be performed using larger sample sizes, as well as wild boar from various geographic locations, to verify these compounds as biomarkers for MTBC infection in this species. This new approach to detect MTBC infection in free-ranging wild boar potentially comprises a reliable and efficient screening tool for surveillance in animal populations.

An in vitro collagen perfusion wound biofilm model; with applications for antimicrobial studies and microbial metabolomics

Background

The majority of in vitro studies of medically relevant biofilms involve the development of biofilm on an inanimate solid surface. However, infection in vivo consists of biofilm growth on, or suspended within, the semi-solid matrix of the tissue, whereby current models do not effectively simulate the nature of the in vivo environment. This paper describes development of an in vitro method for culturing wound associated microorganisms in a system that combines a semi-solid collagen gel matrix with continuous flow of simulated wound fluid. This enables culture of wound associated reproducible steady state biofilms under conditions that more closely simulate the dynamic wound environment. To demonstrate the use of this model the antimicrobial kinetics of ceftazidime, against both mature and developing Pseudomonas aeruginosa biofilms, was assessed. In addition, we have shown the potential application of this model system for investigating microbial metabolomics by employing selected ion flow tube mass spectrometry (SIFT-MS) to monitor ammonia and hydrogen cyanide production by Pseudomonas aeruginosa biofilms in real-time.

Results

The collagen wound biofilm model facilitates growth of steady-state reproducible Pseudomonas aeruginosa biofilms under wound like conditions. A maximum biofilm density of 10¹⁰ cfu slide^− 1 was achieved by 30 h of continuous culture and maintained throughout the remainder of the experiment. Treatment with ceftazidime at a clinically relevant dose resulted in a 1.2–1.6 log reduction in biofilm density at 72 h compared to untreated controls. Treatment resulted in loss of complex biofilm architecture and morphological changes to bacterial cells, visualised using confocal microscopy. When monitoring the biofilms using SIFT-MS, ammonia and hydrogen cyanide levels peaked at 12 h at 2273 ppb (±826.4) and 138 ppb (±49.1) respectively and were detectable throughout experimentation.

Conclusions

The collagen wound biofilm model has been developed to facilitate growth of reproducible biofilms under wound-like conditions. We have successfully used this method to: (1) evaluate antimicrobial efficacy and kinetics, clearly demonstrating the development of antimicrobial tolerance in biofilm cultures; (2) characterise volatile metabolite production by P. aeruginosa biofilms, demonstrating the potential use of this method in metabolomics studies.

In vitro discrimination of wound-associated bacteria by volatile compound profiling using selected ion flow tube-mass spectrometry

AIMS

To determine if bacterial species responsible for clinically relevant wound infection produce specific volatile profiles that would allow their speciation.

METHODS AND RESULTS

Selected ion flow tube-mass spectrometry (SIFT-MS) in full mass scan mode was used to analyse headspace gases produced by wound-associated bacteria grown in vitro, so as to enable identification of bacterial volatile product ion profiles in the resulting mass spectra. Applying multivariate statistical analysis (hierarchical clustering and principal component analysis) to the resultant mass spectra enabled clear speciation. Moreover, bacterial volatile product ions could be detected from artificially contaminated wound dressing material, although the pattern of product ions detected was influenced by culture conditions.

CONCLUSIONS

Using selected product ions from the SIFT-MS mass spectra it is possible to discriminate wound-associated bacterial species grown under specific in vitro culture conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study have shown that wound-associated bacteria can be discriminated using volatile analysis in vitro and that bacterial volatiles can be detected from wound dressing material. This indicates that volatile analysis of wounds or dressing material to identify infecting microbes has potential and warrants further study.

SIFT-MS and FA-MS methods for ambient gas phase analysis: developments and applications in the UK

The origins of SIFT created to study interstellar chemistry and SIFT-MS developed for ambient gas and exhaled breath analysis and the UK centres in which these techniques are being exploited.

Rapid diagnosis of TB using GC-MS and chemometrics

The search continues for a rapid diagnostic test for TB that has high sensitivity and specificity and is useable in sophisticated environments and in deprived regions with poor infrastructure. We discuss here the modern bioanalytical techniques that can be used to discover biomarkers of infection with Mycobacterium tuberculosis, focusing on techniques using GC. We will also discuss the use of GC-MS to identify volatile organic compounds in the headspace of bacterial culture or in samples of breath, serum or urine. Biomarkers discovered in the 'clean' environment of culture may differ from those in patients. A number of biomarkers have been found in patients, with little consistency in the various studies to date. Reproducibility is difficult; the impressive results found initially with a few patients are rarely repeatable when a larger sample series is tested. Mycobacterial lipids offer promise for distinguishing M. tuberculosis from nontuberculous mycobacteria directly in sputum.

A pilot study exploring the use of breath analysis to differentiate healthy cattle from cattle experimentally infected with Mycobacterium bovis

Bovine tuberculosis, caused by Mycobacterium bovis, is a zoonotic disease of international public health importance. Ante-mortem surveillance is essential for control; however, current surveillance tests are hampered by limitations affecting ease of use or quality of results. There is an emerging interest in human and veterinary medicine in diagnosing disease via identification of volatile organic compounds produced by pathogens and host-pathogen interactions. The objective of this pilot study was to explore application of existing human breath collection and analysis methodologies to cattle as a means to identify M. bovis infection through detection of unique volatile organic compounds or changes in the volatile organic compound profiles present in breath. Breath samples from 23 male Holstein calves (7 non-infected and 16 M. bovis-infected) were collected onto commercially available sorbent cartridges using a mask system at 90 days post-inoculation with M. bovis. Samples were analyzed using gas chromatography-mass spectrometry, and chromatographic data were analyzed using standard analytical chemical and metabolomic analyses, principle components analysis, and a linear discriminant algorithm. The findings provide proof of concept that breath-derived volatile organic compound analysis can be used to differentiate between healthy and M. bovis-infected cattle.

Diagnostic potential of the pulsed discharged helium ionization detector (PDHID) for pathogenic Mycobacterial volatile biomarkers

Pathogenic Mycobacteria cause diseases in animals and humans with significant economic and societal consequences. Current methods for Mycobacterial detection relies upon time- and labor-intensive techniques such as culturing or DNA analysis. Using gas chromatography and mass spectrometry, four volatile compounds (methyl phenylacetate, methyl p-anisate, methyl nicotinate and o-phenyl anisole) were recently proposed as potential biomarkers for Mycobacteria. We demonstrate for the first time the capabilities of a field-deployable, pulsed discharge helium ionization detector (PDHID) for sensing these volatiles. We determined the analytical performance of the PDHID toward these Mycobacterial volatiles. Detector performance was moderately affected over the temperature range of 150 to 350 °C. The linear dynamic range for all four analytes exceeded three orders of magnitude. The limits of detection (LOD) and quantitation (LOQ) were calculated as 150 and 450 pg respectively, for all compounds, except methyl phenylacetate (LOD and LOQ, 90 and 270 pg, respectively). Control charts revealed that the PDHID detection system was generally stable, and deviations could be traced to common causes and excluded special causes. Grob tests and ionization potential data suggest that the PDHID is capable of detecting Mycobacterial volatiles in a complex milieu such as culture headspace or breath samples from tuberculosis patients. The diagnostic potential of the PDHID is critical to our goal of a handheld, field-deployable 'sniffer' system for biological pathogens and chemical warfare agents.

Facts and dilemmas in diagnosis of tuberculosis in wildlife

Mycobacterium bovis, causing bovine tuberculosis (BTB), has been recognized as a global threat at the wildlife-livestock-human interface, a clear "One Health" issue. Several wildlife species have been identified as maintenance hosts. Spillover of infection from these species to livestock or other wildlife species may have economic and conservation implications and infection of humans causes public health concerns, especially in developing countries. Most BTB management strategies rely on BTB testing, which can be performed for a range of purposes, from disease surveillance to diagnosing individual infected animals. New diagnostic assays are being developed for selected wildlife species. This review investigates the most frequent objectives and associated requirements for testing wildlife for tuberculosis at the level of individual animals as well as small and large populations. By aligning those with the available (immunological) ante mortem diagnostic assays, the practical challenges and limitations wildlife managers and researchers are currently faced with are highlighted.

Ambient analysis of trace compounds in gaseous media by SIFT-MS

The topic of ambient gas analysis has been rapidly developed in the last few years with the evolution of the exciting new techniques such as DESI, DART and EESI. The essential feature of all is that analysis of trace gases can be accomplished either in the gas phase or those released from surfaces, crucially avoiding sample collection or modification. In this regard, selected ion flow tube mass spectrometry, SIFT-MS, also performs ambient analyses both accurately and rapidly. In this focused review we describe the underlying ion chemistry underpinning SIFT-MS through a discourse on the reactions of different classes of organic and inorganic molecules with H(3)O(+), NO(+) and O(2)(+)˙ studied using the SIFT technique. Rate coefficients and ion products of these reactions facilitate absolute SIFT-MS analyses and can also be useful for the interpretation of data obtained by the other ambient analysis methods mentioned above. The essential physics and flow dynamics of SIFT-MS are described that, together with the reaction kinetics, allow SIFT-MS to perform absolute ambient analyses of trace compounds in humid atmospheric air, exhaled breath and the headspace of aqueous liquids. Several areas of research that, through pilot experiments, are seen to benefit from ambient gas analysis using SIFT-MS are briefly reviewed. Special attention is given to exhaled breath and urine headspace analysis directed towards clinical diagnosis and therapeutic monitoring, and some other areas researched using SIFT-MS are summarised. Finally, extensions to current areas of application and indications of other directions in which SIFT-MS can be exploited for ambient analysis are alluded to.

Progress in SIFT-MS: breath analysis and other applications

The development of selected ion flow tube mass spectrometry, SIFT-MS, is described from its inception as the modified very large SIFT instruments used to demonstrate the feasibility of SIFT-MS as an analytical technique, towards the smaller but bulky transportable instruments and finally to the current smallest Profile 3 instruments that have been located in various places, including hospitals and schools to obtain on-line breath analyses. The essential physics and engineering principles are discussed, which must be appreciated to design and construct a SIFT-MS instrument. The versatility and sensitivity of the Profile 3 instrument is illustrated by typical mass spectra obtained using the three precursor ions H(3)O(+), NO(+) and O(2)(+)·, and the need to account for differential ionic diffusion and mass discrimination in the analytical algorithms is emphasized to obtain accurate trace gas analyses. The performance of the Profile 3 instrument is illustrated by the results of several pilot studies, including (i) on-line real time quantification of several breath metabolites for cohorts of healthy adults and children, which have provided representative concentration/population distributions, and the comparative analyses of breath exhaled via the mouth and nose that identify systemic and orally-generated compounds, (ii) the enhancement of breath metabolites by drug ingestion, (iii) the identification of HCN as a marker of Pseudomonas colonization of the airways and (iv) emission of volatile compounds from urine, especially ketone bodies, and from skin. Some very recent developments are discussed, including the quantification of carbon dioxide in breath and the combination of SIFT-MS with GC and ATD, and their significance. Finally, prospects for future SIFT-MS developments are alluded to.