Expanding the Klebsiella pneumoniae volatile metabolome using advanced analytical instrumentation for the detection of novel metabolites

GC-IMS facilitates identification of carbapenem-resistant Klebsiella pneumoniae in simulated blood cultures

This study aimed to identify carbapenem-resistant Klebsiella pneumoniae (CRKP) based on changes in levels of its volatile organic compounds (VOCs) in simulated blood cultures (BCs) using the gas chromatography-ion mobility spectrometry (GC-IMS) technique. A comprehensive analysis of volatile metabolites produced by Klebsiella pneumoniae (K. pneumoniae) in BC bottles was conducted using GC-IMS. Subsequently, the released VOCs were analyzed to examine differences in VOC release between CRKP and carbapenem-susceptible Klebsiella pneumoniae (CSKP). A total of 54 VOCs were detected, of which 18 (6 VOCs found in both monomer and dimer forms) were successfully identified. The VOCs produced by K. pneumoniae in BC bottles (BacT/ALERT® SA) were primarily composed of organic acids, alcohols, esters, and ketones. The content of certain VOCs was significantly different between CRKP and CSKP after the addition of imipenem (IPM). Moreover, the inclusion of carbapenemase inhibitors facilitated the identification of carbapenemase-producing K. pneumoniae based on the variations in VOCs. This study demonstrates the utility of GC-IMS technology in identifying CRKP, and reveals that changes in VOCs are closely related to the growth and metabolism of K. pneumoniae, indicating that they can be leveraged to promote early identification of CRKP bacteremia. However, further in-depth studies and experiments are needed to validate our findings.

Rapid Identification of Carbapenemase-Producing Klebsiella pneumoniae Using Headspace Solid-Phase Microextraction Combined with Gas Chromatography-Mass Spectrometry

Background

Carbapenemase-producing Klebsiella pneumoniae is an unprecedented threat to public health, and its detection remains challenging. Analysis of microbial volatile organic compounds (VOCs) may offer a rapid way to determine bacterial antibiotic susceptibility.

Purpose

The aim of this study was to explore the VOCs released by carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) using headspace solid-phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS).

Methods

Test bacteria were incubated in trypticase soy broth to the end of exponential growth phase, and imipenem was added in the middle time. Headspace VOCs were concentrated and analyzed using HS-SPME/GC-MS.

Results

The compound 3-methyl-1-butanol was found to be a biomarker among the 26 bacterial isolates (10 KPC-positive, 10 NDM-positive, 2 IMP-positive, 2 carbapenemase-negative CRKP, and 2 carbapenem-susceptible K. pneumonoiae).

Conclusion

This study explored a promising new strategy for the screening of carbapenemase-producing CRKP strains. Further research with larger sample sizes will potentially accelerate the application of biomarkers in routine microbiology.

Occurrence of volatile contaminants in recycled poly(ethylene terephthalate) by HS-SPME-GC×GC-QTOF-MS combined with chemometrics for authenticity assessment of geographical recycling regions

A comparison was performed on various methods detecting the volatile contaminants (VCs) in recycled poly(ethylene terephthalate) (rPET) flakes, the results demonstrated that head-space solid phase micro-extraction combined with comprehensive two-dimensional gas chromatograph-tandem quadrupole-time-of-flight mass spectrometry (HS-SPME-GC×GC-QTOF-MS) was a sensitive, effective, accurate method, and successfully applied to analyze 57 rPET flakes collected from different recycling plants in China. A total of 212 VCs were tentatively identified, and the possible source were associated with plastic, food, and cosmetics. 45 VCs are classified as high-priority compounds with toxicity level IV or V and may pose a risk to human health. Combined chemometrics for further analysis revealed that significant differences among these three geographical recycling regions. 6, 7, and 6 volatile markers were chosen based on VIP values and S-plot among plant1 plant 2 and plant 3, respectively. The markers differed significantly between recycled rPET samples in three geographical recycling regions based on chemometrics analysis. The initial classification rate and cross-validation accuracy were 100% on the identified VCs. These significant differences demonstrate that a systematic study is needed to obtain a comprehensive data on the contamination of rPET for food contact applications in China.

GC-MS profiling of volatile metabolites produced by Klebsiella pneumoniae

Currently used methods for diagnosing ventilator-associated pneumonia (VAP) are complex, time-consuming and require invasive procedures while empirical antibacterial therapy applies broad spectrum antibiotics that may promote antimicrobial resistance. Hence, novel and fast methods based on alternative markers are needed for VAP detection and differentiation of causative pathogens. Pathogenic bacteria produce a broad range of volatile organic compounds (VOCs), some of which may potentially serve as biomarkers for microorganism identification. Additionally, monitoring of dynamically changing VOCs concentration profiles may indicate emerging pneumonia and allow timely implementation of appropriate antimicrobial treatment. This study substantially extends the knowledge on bacterial metabolites providing the unambiguous identification of volatile metabolites produced by carbapenem-resistant and susceptible strains of Klebsiella pneumoniae (confirmed with pure standards in addition to mass spectra match) but also revealing their temporary concentration profiles (along the course of pathogen proliferation) and dependence on the addition of antibiotic (imipenem) to bacteria. Furthermore, the clinical strains of K. pneumoniae isolated from bronchoalveolar lavage specimens collected from mechanically ventilated patients were investigated to reveal, whether bacterial metabolites observed in model experiments with reference strains could be relevant for wild pathogens as well. In all experiments, the headspace samples from bacteria cultures were collected on multibed sorption tubes and analyzed by GC-MS. Sampling was done under strictly controlled conditions at seven time points (up to 24 h after bacteria inoculation) to follow the dynamic changes in VOC concentrations, revealing three profiles: release proportional to bacteria load, temporary maximum and uptake. Altogether 32 VOCs were released by susceptible and 25 VOCs by resistant strain, amongst which 2-pentanone, 2-heptanone, and 2-nonanone were significantly higher for carbapenem-resistant KPN. Considerably more metabolites (n = 64) were produced by clinical isolates and in higher diversity compared to reference KPN strains.

Identification of metabolite extraction method for targeted exploration of antimicrobial resistance associated metabolites of Klebsiella pneumoniae

Antimicrobial resistant Klebsiella pneumoniae (K. pneumoniae), as being a pathogen of critical clinical concern, urgently demands effective therapeutic options. However, the discovery of novel antibiotics over the last three decades has declined drastically and necessitates exploring novel strategies. Metabolomic modulation has been the promising approach for the development of effective therapeutics to deal with AMR; however, only limited efforts have been made to-date, possibly due to the unavailability of suitable metabolites extraction protocols. Therefore, in order to establish a detailed metabolome of K. pneumoniae and identify a method for targeted exploration of metabolites that are involved in the regulation of AMR associated processes, metabolites were extracted using multiple methods of metabolites extraction (freeze-thaw cycle (FTC) and sonication cycle (SC) method alone or in combination (FTC followed by SC; FTC + SC)) from K. pneumoniae cells and then identified using an orbitrap mass analyzer (ESI-LC-MS/MS). A total of 151 metabolites were identified by using FTC, 132 metabolites by using FTC+SC, 103 metabolites by using SC and 69 metabolites common among all the methods used which altogether enabled the identification of 199 unique metabolites. Of these 199, 70 metabolites were known to have an association with AMR phenotype and among these, the FTC + SC method yielded better (identified 55 metabolites), quantitatively and qualitatively compared to FTC and SC alone (identified 51 and 41 metabolites respectively). Each method of metabolite extraction showed a definite degree of biasness and specificity towards chemical classes of metabolites and jointly contributed to the development of a detailed metabolome of the pathogen. FTC method was observed to give higher metabolomic coverage as compared to SC alone and FTC + SC. However, FTC + SC resulted in the identification of a higher number of AMR associated metabolites of K. pneumoniae compared to FTC and SC alone.

Mapping Aspergillus niger Metabolite Biomarkers for In Situ and Early Evaluation of Table Grapes Contamination

The Aspergillus niger exometabolome was recently investigated using advanced gas chromatography in tandem with multivariate analysis, which allowed a metabolite biomarker pattern to be proposed. Microbial metabolomics patterns have gained enormous relevance, mainly due to the amount of information made available, which may be useful in countless processes. One of the great challenges in microbial metabolomics is related to applications in more complex systems of metabolomics information obtained from studies carried out in culture media, as complications may occur due to the dynamic nature of biological systems. Thus, the main objective of this research was to evaluate the applicability of the A. niger metabololite biomarkers pattern for in situ and early evaluation of table grapes contamination, used as study model. A. niger is a ubiquitous fungus responsible for food contamination, being reported as one of the main agents of the black mold disease, a serious post-harvest pathology of table grapes. This work included analysis from 1 day of growth time of pure A. niger cultures, A. niger cultures obtained from previously contaminated grapes, and finally, an in situ solid-phase microextraction (SPME) approach directly on previously contaminated table grapes. Supervised multivariate analysis was performed which revealed that after 1 day of inoculation it was possible to detect A. niger biomarkers, which can be extremely useful in making this type of method possible for the rapid detection of food contamination. The results obtained confirm the potential applicability of the pattern of A. niger biomarkers for early detection of the fungi (after 1 day of contamination), and may be further explored for access food susceptibility to fungi contamination, based on direct analysis of the food item.

Recognition of pathogens in food matrixes based on the untargeted in vivo microbial metabolite profiling via a novel SPME/GC × GC-QTOFMS approach

Foodborne diseases incurred by pathogenic bacteria are one of the major threats in food safety, and thus it is important to develop facile and effective recognition methodology of pathogens in food. Herein, a new automatic approach for detection of in vivo volatile metabolites emitted from foodborne pathogens was proposed by coupling solid phase microextraction (SPME) technique with a comprehensive two-dimensional gas chromatography quadrupole time-of-flight mass spectrometry (GC × GC-QTOFMS). A novel polymer composite based SPME probe which possessed high-coverage of microbial metabolites was utilized in this contribution to realize the sensitive extraction of untargeted metabolites. As a result, a total of 126 in vivo metabolites generated by the investigated pathogens were detected and identified, with 33, 29, 25, 21 and 18 volatile metabolites belonging to Shigella sonnei, Escherichia coli, Salmonella typhimurium, Vibrio parahaemolyticus and Staphylococcus aureus, respectively. Multivariate statistical analyses were applied for further analysis of metabolic data and separation of responsive metabolic features among different microbial systems were found, which were also successfully verified in foodstuffs contaminated by microorganisms. The growth trend of the potential volatile markers of each pathogen in food samples kept consistent with that of the pure strain incubated in medium during the whole incubation time. This study promotes the application of SPME technology in microbial volatile metabolomics and contributes to the development of new approaches for foodborne pathogens recognition.

Dependence of the Staphylococcal Volatilome Composition on Microbial Nutrition

In vitro cultivation of staphylococci is fundamental to both clinical and research microbiology, but few studies, to-date, have investigated how the differences in rich media can influence the volatilome of cultivated bacteria. The objective of this study was to determine the influence of rich media composition on the chemical characteristics of the volatilomes of Staphylococcus aureus and Staphylococcus epidermidis. S. aureus (ATCC 12600) and S. epidermidis (ATCC 12228) were cultured in triplicate in four rich complex media (brain heart infusion (BHI), lysogeny broth (LB), Mueller Hinton broth (MHB), and tryptic soy broth (TSB)), and the volatile metabolites produced by each culture were analyzed using headspace solid-phase microextraction combined with comprehensive two-dimensional gas chromatography—time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS). When comparing the chemical compositions of the staph volatilomes by the presence versus absence of volatiles produced in each medium, we observed few differences. However, when the relative abundances of volatiles were included in the analyses, we observed that culturing staph in media containing free glucose (BHI and TSB) resulted in volatilomes dominated by acids and esters (67%). The low-glucose media (LB and MHB) produced ketones in greatest relative abundances, but the volatilome compositions in these two media were highly dissimilar. We conclude that the staphylococcal volatilome is strongly influenced by the nutritional composition of the growth medium, especially the availability of free glucose, which is much more evident when the relative abundances of the volatiles are analyzed, compared to the presence versus absence.

Recent advances in the application of metabolomics for food safety control and food quality analyses

As one of the omics fields, metabolomics has unique advantages in facilitating the understanding of physiological and pathological activities in biology, physiology, pathology, and food science. In this review, based on developments in analytical chemistry tools, cheminformatics, and bioinformatics methods, we highlight the current applications of metabolomics in food safety, food authenticity and quality, and food traceability. Additionally, the combined use of metabolomics with other omics techniques for "foodomics" is comprehensively described. Finally, the latest developments and advances, practical challenges and limitations, and requirements related to the application of metabolomics are critically discussed, providing new insight into the application of metabolomics in food analysis.

Influence of media on the differentiation of Staphylococcus spp. by volatile compounds

Staphylococcus aureus asymptomatically colonizes a third of the world's population, and it is an opportunistic pathogen that can cause life threatening diseases. To diagnose S. aureus infections, it is necessary to differentiate S. aureus from the ubiquitous human commensal Staphylococcus epidermidis, which beneficially colonizes the skin of all humans. Efforts are underway to identify volatile biomarkers for diagnosing S. aureus infections, but to date no studies have investigated whether S. aureus and S. epidermidis can be reliably differentiated under a variety of growth conditions. The overall goal of this study was to evaluate the influence of growth medium on the ability to differentiate S. aureus and S. epidermidis based on their volatile profiles. We used headspace solid-phase microextraction (HS-SPME) and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC×GC-TOFMS) to examine the headspace volatiles of S. aureus and S. epidermidis when aerobically grown in four different complex media. We detected 337 volatile features when culturing S. aureus and S. epidermidis in four complex media, termed the staph volatiles, and found only 20%-40% concurrence in the volatiles produced by these two species in any single medium. Using principal components analysis and hierarchical clustering analysis on the staph volatiles, we observed that S. aureus and S. epidermidis clustered independently from each other, and distinctly clustered by growth medium within species. Removing volatiles that are species and/or media-specific from the analysis reduced the resolution between species clusters, but in all models clustering by species overrode clustering by media type. These analyses suggest that, while volatile profiles are media-specific, species differences dominate the staph volatilome. These data enable future investigations into the identification of volatile biomarkers to discriminate staphylococcal pathogens versus commensals, which will improve staph diagnoses and provide insights into the biochemistry of staph infections and immunity.

Sniffing out resistance - Rapid identification of urinary tract infection-causing bacteria and their antibiotic susceptibility using volatile metabolite profiles

Antibiotic resistance is set to be an unprecedented threat to modern medicine. 'Sniffing' bacteria potentially offers a rapid way to determine susceptibility. A successful proof-of-principle study is described, using thermal desorption-gas chromatography-mass spectrometry (TDGCMS) to 'smell' cephalexin and ciprofloxacin resistant and sensitive Urinary Tract Infection (UTI)-causing bacteria. 578 peaks at unique retention times were detected from 86 chromatograms of 18 bacterial isolates (E. coli, K. pneumoniae and P. aeruginosa). The isolates were grown with and without the presence of antibiotic. Chi-square analysis found 9 compounds that differed significantly between cephalexin sensitive and resistant isolates, and 22 compounds that differed significantly between ciprofloxacin sensitive and resistant isolates, at p ≤ 0.05. When antibiotic was added to the media, more differences were found in the cephalexin group, attributed to lysis, but not in the ciprofloxacin group. Further work with large sample sizes will potentially enable the development of diagnostic algorithms using presence/absence of particular compounds of interest.

Advances in the application of comprehensive two-dimensional gas chromatography in metabolomics

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.

Impact of meropenem on Klebsiella pneumoniae metabolism

The aim of this study was to analyze the metabolome of several Klebsiella pneumoniae strains characterized by different resistance patterns. A total of 59 bacterial strains (27 carbapenemase-negative and 32 carbapenemase-positive) were included and their metabolic features were assessed in basal conditions. Moreover, 8 isolates (4 wild-type and 4 KPC-producers) were randomly selected to evaluate the impact of sub-lethal concentrations of meropenem on bacterial metabolism. The metabolomic analysis was performed by ¹H-NMR spectroscopy both on filtered supernatants and cell lysates. A total of 40 and 20 molecules were quantified in the intracellular and the extracellular metabolome, respectively. While in basal conditions only five metabolites showed significant differences between carbapenemase-positive and negative strains, the use of meropenem had a profound impact on the whole bacterial metabolism. In the intracellular compartment, a reduction of different overflow metabolites and organic acids (e.g. formate, acetate, isobutyrate) was noticed, whereas, in the extracellular metabolome, the levels of several organic acids (e.g. succinate, acetate, formate, lactate) and amino acids (aspartate, threonine, lysine, alanine) were modified by meropenem stimulation. Interestingly, carbapenemase-positive and negative strains reacted differently to meropenem in terms of number and type of perturbed metabolites. In wild-type strains, meropenem had great impact on the metabolic pathways related to methane metabolism and alanine, aspartate and glutamate metabolism, whereas in KPC-producers the effect was predominant on pyruvate metabolism. The knowledge about the bacterial metabolic profiles could help to set up innovative diagnostic methods and new antimicrobial strategies to fight the global crisis against carbapenemase-positive K. pneumoniae.

Detection of high-risk carbapenem-resistant Klebsiella pneumoniae and Enterobacter cloacae isolates using volatile molecular profiles

Infections caused by carbapenem-resistant Enterobacteriaceae (CRE) are alarming in the clinical setting, as CRE isolates often exhibit resistance to most clinically-available antibiotics. Klebsiella pneumoniae carbapenemase (KPC) is the most common carbapenemase carried by CRE in North America and Europe, frequently detected in isolates of K. pneumoniae, Escherichia coli, and Enterobacter cloacae. Notably, KPC-expressing strains often arise from clonal lineages, with sequence type 258 (ST258) representing the dominant lineage in K. pneumoniae, ST131 in E. coli, and ST78 and ST171 in E. cloacae. Prior studies have demonstrated that carbapenem-resistant K. pneumoniae differs from carbapenem-susceptible K. pneumoniae at both the transcriptomic and soluble metabolomic levels. In the present study, we sought to determine whether carbapenem-resistant and carbapenem-susceptible isolates of K. pneumoniae, E. coli, and E. cloacae produce distinct volatile metabolic profiles. We were able to identify a volatile metabolic fingerprint that could discriminate between CRE and non-CRE with an area under the receiver operating characteristic curve (AUROC) as high as 0.912. Species-specific AUROCs were as high as 0.988 for K. pneumoniae and 1.000 for E. cloacae. Paradoxically, curing of KPC-expressing plasmids from a subset of K. pneumoniae isolates further accentuated the metabolic differences observed between ST258 and non-ST258.

Opportunities for green microextractions in comprehensive two-dimensional gas chromatography / mass spectrometry-based metabolomics - A review

Microextractions have become an attractive class of techniques for metabolomics. The most popular technique is solid-phase microextraction that revolutionized the field of modern sample preparation in the early nineties. Ever since this milestone, microextractions have taken on many principles and formats comprising droplets, fibers, membranes, needles, and blades. Sampling devices may be customized to impart exhaustive or equilibrium-based characteristics to the extraction method. Equilibrium-based approaches may rely on additional methods for calibration, such as diffusion-based or on-fiber kinetic calibration to improve bioanalysis. In addition, microextraction-based methods may enable minimally invasive sampling protocols and measure the average free concentration of analytes in heterogeneous multiphasic biological systems. On-fiber derivatization has evidenced new opportunities for targeted and untargeted analysis in metabolomics. All these advantages have highlighted the potential of microextraction techniques for in vivo and on-site sampling and sample preparation, while many opportunities are still available for laboratory protocols. In this review, we outline and discuss some of the most recent applications using microextractions techniques for comprehensive two-dimensional gas chromatography-based metabolomics, including potential research opportunities.

SPME-GC×GC-TOF MS fingerprint of virally-infected cell culture: Sample preparation optimization and data processing evaluation

Untargeted metabolomics study of volatile organic compounds produced by different cell cultures is a field that has gained increasing attention over the years. Solid-phase microextraction has been the sampling technique of choice for most of the applications mainly due to its simplicity to implement. However, a careful optimization of the analytical conditions is necessary to obtain the best performances, which are highly matrix-dependent. In this work, five different solid-phase microextraction fibers were compared for the analysis of the volatiles produced by cell culture infected with the human respiratory syncytial virus. A central composite design was applied to determine the best time-temperature combination to maximize the extraction efficiency and the salting-out effect was evaluated as well. The linearity of the optimized method, along with limits of detection and quantification and repeatability was assessed. Finally, the effect of i) different normalization techniques (i.e. z-score and probabilistic quotient normalization), ii) data transformation (i.e. in logarithmic scale), and iii) different feature selection algorithms (i.e. Fisher ratio and random forest) on the capability of discriminating between infected and not-infected cell culture was evaluated.

Headspace volatile organic compounds from bacteria implicated in ventilator-associated pneumonia analysed by TD-GC/MS

Ventilator-associated pneumonia (VAP) is a healthcare-acquired infection arising from the invasion of the lower respiratory tract by opportunistic pathogens in ventilated patients. The current method of diagnosis requires the culture of an airway sample such as bronchoalveolar lavage, which is invasive to obtain and may take up to seven days to identify a causal pathogen, or indeed rule out infection. While awaiting results, patients are administered empirical antibiotics; risks of this approach include lack of effect on the causal pathogen, contribution to the development of antibiotic resistance and downstream effects such as increased length of intensive care stay, cost, morbidity and mortality. Specific biomarkers which could identify causal pathogens in a timely manner are needed as they would allow judicious use of the most appropriate antimicrobial therapy. Volatile organic compound (VOC) analysis in exhaled breath is proposed as an alternative due to its non-invasive nature and its potential to provide rapid diagnosis at the patient's bedside. VOCs in exhaled breath originate from exogenous, endogenous, as well as microbial sources. To identify potential markers, VAP-associated pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus were cultured in both artificial sputum medium and nutrient broth, and their headspaces were sampled and analysed for VOCs. Previously reported volatile markers were identified in this study, including indole and 1-undecene, alongside compounds that are novel to this investigation, cyclopentanone and 1-hexanol. We further investigated media components (substrates) to identify those that are essential for indole and cyclopentanone production, with potential implications for understanding microbial metabolism in the lung.

Comprehensive volatile metabolic fingerprinting of bacterial and fungal pathogen groups

The identification of pathogen-specific volatile metabolic 'fingerprints' could lead to the rapid identification of disease-causing organisms either directly from ex vivo patient bio-specimens or from in vitro cultures. In the present study, we have evaluated the volatile metabolites produced by 100 clinical isolates belonging to ten distinct pathogen groups that, in aggregate, account for 90% of bloodstream infections, 90% of urinary tract infections, and 80% of infections encountered in the intensive care unit setting. Headspace volatile metabolites produced in vitro were concentrated using headspace solid-phase microextraction and analyzed via two-dimensional gas chromatography time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS). A total of 811 volatile metabolites were detected across all samples, of which 203 were: (1) detected in 9 or 10 (of 10) isolates belonging to one or more pathogen groups, and (2) significantly more abundant in cultures relative to sterile media. Network analysis revealed a distinct metabolic fingerprint associated with each pathogen group, and analysis via Random Forest using leave-one-out cross-validation resulted in a 95% accuracy for the differentiation between groups. The present findings support the results of prior studies that have reported on the differential production of volatile metabolites across pathogenic bacteria and fungi, and provide additional insight through the inclusion of pathogen groups that have seldom been studied previously, including Acinetobacter spp., coagulase-negative Staphylococcus, and Proteus mirabilis, as well as the utilization of HS-SPME-GC×GC-TOFMS for improved sensitivity and resolution relative to traditional gas chromatography-based techniques.

Sniffing out the hypoxia volatile metabolic signature of Aspergillus fumigatus

Invasive aspergillosis (IA) is a life-threatening infectious disease caused by fungi from the genus Aspergillus, with an associated mortality as high as 90% in certain populations. IA-associated pulmonary lesions are characteristically depleted in oxygen relative to normal lung tissue, and it has been shown that the most common causal agent of IA, Aspergillus fumigatus, must respond to low-oxygen environments for pathogenesis and disease progression. Previous studies have demonstrated marked alterations to the Aspergillus fumigatus transcriptome in response to low-oxygen environments that induce a 'hypoxia response'. Consequently, we hypothesized that these transcriptomic changes would alter the volatile metabolome and generate a volatile hypoxia signature. In the present study, we analyzed the volatile molecules produced by A. fumigatus in both oxygen replete (normoxia) and depleted (hypoxia) environments via headspace solid-phase micro-extraction coupled to two-dimensional gas chromatography-time-of-flight mass spectrometry. Using the machine learning algorithm random forest, we identified 19 volatile molecules that were discriminatory between the four growth conditions assessed in this study (i.e., early hypoxia (1 h), late hypoxia (8 h), early normoxia (1 h), and late normoxia (8 h)), as well as a set of 19 that were discriminatory between late hypoxia cultures and all other growth conditions in aggregate. Nine molecules were common to both comparisons, while the remaining 20 were specific to only one of two. We assigned putative identifications to 13 molecules, of which six were most highly abundant in late hypoxia cultures. Previously acquired transcriptomic data identified putative biochemical pathways induced in hypoxia conditions that plausibly account for the production of a subset of these molecules, including 2,3-butanedione and 3-hydroxy-2-butanone. These two molecules may represent a novel hypoxia fitness pathway in A. fumigatus, and could be useful in the detection of hypoxia-associated A. fumigatus lesions that develop in established IA infections.

Volatile metabolic diversity of Klebsiella pneumoniae in nutrient-replete conditions

INTRODUCTION

Microorganisms catabolize carbon-containing compounds in their environment during growth, releasing a subset of metabolic byproducts as volatile compounds. However, the relationship between growth media and the production of volatile compounds has been largely unexplored to-date.

OBJECTIVES

To assess the core and media-specific components of the Klebsiella pneumoniae volatile metabolome via growth in four in vitro culture media.

METHODS

Headspace volatiles produced by cultures of K. pneumoniae after growth to stationary phase in four rich media (brain heart infusion broth, lysogeny broth, Mueller-Hinton broth, and tryptic soy broth) were analyzed using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS). Differences in the composition of headspace volatiles as a function of growth media was assessed using hierarchical clustering analysis (HCA) and principal component analysis (PCA).

RESULTS

A total of 365 volatile compounds were associated with the growth of K. pneumoniae across all media, of which 36 (10 %) were common to all growth media, and 148 (41 %) were specific to a single medium. In addition, utilizing all K. pneumoniae-associated volatile compounds, strains clustered as a function of growth media, demonstrating the importance of media in determining the metabolic profile of this organism.

CONCLUSION

K. pneumoniae produces a core suite of volatile compounds across all growth media studied, although the volatile metabolic signature of this organism is fundamentally media-dependent.