Faecal volatile biomarkers of Clostridium difficile infection

Synthetic β-d-Glucuronides: Substrates for Exploring Glucuronide Degradation by Human Gut Bacteria

The human gut microbiota (HGM) is a complex ecosystem subtly dependent on the interplay between hundreds of bacterial species and numerous metabolites. Dietary phenols, whether ingested (e.g., plant-derived guaiacol, mequinol, or resveratrol) or products of bacterial fermentation (e.g., p-cresol), have been attributed with influencing bacterial growth and host health. They are cleared by phase II metabolism, one form utilizing β-d-glucuronidation, but encounter bacterially derived glucuronidases capable of hydrolyzing them to release their phenolic and glucuronic acid moieties with potential effects on host cells or the surrounding bacterial population. Tools to enable the detailed study of their activity are currently lacking. Syntheses of β-d-glucuronides from methyl 1,2,3,4 tetra-acetyl β-d-glucopyranosyluronate by direct glycosylation with 2-, 3-, or 4-methoxy- and 4-fluorophenol acceptors employing trimethylsilyl triflate catalysis are reported. Yields (methoxy series) were modest. An improved route from methyl 1,2,3,4-tetra-acetyl β-d-glucopyranosyluronate via selective anomeric deprotection (N-methyl piperazine) and conversion to an α-trichloroacetimidate glycosyl donor was employed. Coupling with 2- and 3-methoxyphenol acceptors and deprotection provided 2- and 3-methoxyphenyl β-d-glucuronides in 2-fold improved overall yield. These naturally occurring methoxyphenyl glucuronides augment available model substrates of dietary glucuronides, which include 3- and 4'-linked resveratrol. The use of model glucuronides as substrates was illustrated in studies of β-d-glucuronidase activity employing cell lysates of 9 species of HGM (Bacteroidetes), revealing distinct outcomes. Contrasting effects on bacterial growth were also observed between the free phenolic components, their respective glucuronides, and glucuronic acid. The glucuronide of 4-fluorophenol provided sensitive and background-free detection of β-glucuronidase activity using 19F NMR.

Characterization of the hepatic flora and metabolome in nonalcoholic fatty liver disease

Background/aim

The purpose of this study was to examine the hepatic bacterial composition and metabolome characteristics of patients with NAFLD using 16S rDNA sequencing and metabolomics. The results of the study revealed substantial differences in hepatic bacterial composition and metabolites between the NAFLD group and the control group. These differences were used to identify potential biomarkers that could be employed to diagnose NAFLD.

Subjects/methods

Liver tissues from 13 patients in the NAFLD group and 12 patients in the control group were collected for microbiota examination.

Results

The bacterial DNA profiles of the liver were significantly different between NAFLD patients and controls. NAFLD patients exhibited an enrichment of Enterobacterales, Mycobacteriales, Pseudomonadales, Flavobacteriales and Xanthomonadales, Sphingomonadales, Lysobact, which was characterised by a lack of erales. At the genus level, the abundance values of Escherichia-Shigella, Rhodococcus, and Chryseobacterium in the NAFLD group were significantly elevated, while the abundance values of Stenotrophomonas, Lawsonella and Sphingobium were significantly reduced. A total of 402 distinct metabolites were identified between the two groups, with 78 metabolites that were up-regulated and 14 metabolites that were down-regulated. The enrichment of metabolic pathways indicated that linoleic acid metabolism was the most significant contributor to the metabolic differences, and lipid metabolism was substantially differentiated. The hepatic metabolite levels were substantially correlated with the changes in hepatic microflora, as demonstrated by the correlation analysis.

Conclusion

Differences in pathogenesis and host physiological function of NAFLD may be attributed to the hepatic flora and metabolomic characteristics. In the future, this presents new opportunities for the investigation of prospective diagnostic and therapeutic targets for NAFLD.

Metataxonomics and Metabolomics Profiles in Metabolic Dysfunction-Associated Fatty Liver Disease Patients on a "Navelina" Orange-Enriched Diet

BACKGROUND/OBJECTIVES

Metabolic dysfunction-associated fatty liver disease (MAFLD) is currently the most common cause of chronic liver disease. Systemic inflammatory status and peripheral metabolic symptoms in the clinical picture have an impact on gut commensal bacteria.

METHODS

Our designed clinical trial was based on a cohort of patients with MAFLD whose diet included the daily consumption of 400 g of "Navelina" oranges for 28 days, compared with a control group of patients with the same pathologic conditions whose diet did not include the consumption of oranges and other foods containing similar nutrients/micronutrients. We used 16S metataxonomics and GC/MS analyses to identify taxa and urine/fecal VOCs, respectively.

RESULTS

A set of micronutrients from the diet were inspected, and some specific fatty acids were identified as the main contributors in terms of cluster sample separation. Metataxonomics and metabolomics profiles were obtained, and a stringent statistical approach allowed for the identification of significant taxa/VOCs, which emerged from pairwise group comparisons in both fecal and urine samples.

CONCLUSIONS

In conclusion, a set of taxa/VOCs can be directly referred to as a marker of dysbiosis status and other comorbidities that, together, make up the pathologic burden associated with MAFLD. The investigated variables can be a target of therapeutic strategies.

Progress and challenges of developing volatile metabolites from exhaled breath as a biomarker platform

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.

Faecal volatile organic compounds differ according to inflammatory bowel disease sub-type, severity, and response to treatment in paediatric patients

BACKGROUND

Faecal volatile organic compounds (VOCs) differ with disease sub-type and activity in adults with established inflammatory bowel disease (IBD) taking therapy.

OBJECTIVE

To describe patterns of faecal VOCs in children newly presented with IBD according to disease sub-type, severity, and response to treatment.

METHODS

Children presenting with suspected IBD were recruited from three UK hospitals. Children in whom IBD was diagnosed were matched with a non-IBD child for age, sex, and recruitment site. Faecal VOCs were characterised by gas chromatography-mass spectrometry at presentation and 3 months later in children with IBD.

RESULTS

In 132 case/control pairs, median (inter-quartile range) age in IBD was 13.3 years (10.2-14.7) and 38.6% were female. Compared with controls, the mean abundance of 27/62 (43.6%) faecal VOCs was statistically significantly decreased in Crohn's disease (CD), ulcerative colitis (UC) or both especially amongst ketones/diketones, fatty acids, and alcohols (p < 0.05). Short-chain, medium chain, and branched chain fatty acids were markedly reduced in severe colitis (p < 0.05). Despite clinical improvement in many children with IBD, the number and abundance of almost all VOCs did not increase following treatment, suggesting persistent dysbiosis. Oct-1-en-3-ol was increased in CD (p = 0.001) and UC (p = 0.012) compared with controls and decreased following treatment in UC (p = 0.01). In CD, propan-1-ol was significantly greater than controls (p < 0.001) and extensive colitis (p = 0.001) and fell with treatment (p = 0.05). Phenol was significantly greater in CD (p < 0.001) and fell with treatment in both CD (p = 0.02) and UC (p = 0.01).

CONCLUSION

Characterisation of faecal VOCs in an inception cohort of children with IBD reveals patterns associated with diagnosis, disease activity, and extent. Further work should investigate the relationship between VOCs and the microbiome in IBD and their role in diagnosis and disease monitoring.

C. difficile biomarkers, pathogenicity and detection

BACKGROUND

Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy.

APPROACH

A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods.

RESULTS

The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected.

CONCLUSION

To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.

Long-wave infrared pulsed external-cavity QCL spectrometer using a hollow waveguide gas cell

A spectrometer built using an external cavity pulsed quantum cascade laser is described. The spectrometer has a tuning range from 10 - 13 µm (1,000 - 769 cm-1) and is designed to target volatile organic compounds (VOCs) which often exhibit water-free molecular absorption within the region. The spectrometer utilizes a hollow silica waveguide gas cell which has an internal volume of a few millilitres, a fast response time (∼1 s), and is advantageous when only low sample volumes, similar to the cell volume, are available. Propane is used as a test gas because it is easy to handle, and its spectral profile is comparable to VOCs of interest. Its absorption in the region is primarily within the ν21 band which spans from 10.55 - 11.16 µm (948 - 896 cm-1). Spectral measurements at a range of concentrations show good linearity and an Allan deviation of absorbance values recorded over a 100-minute period indicates a minimum detectable absorbance of 3.5×10-5 at an integration time of 75 s.

Detection ofClostridioides difficileinfection by assessment of exhaled breath volatile organic compounds

Clostridioides difficileinfection (CDI) is the leading cause of hospital-acquired infective diarrhea. Current methods for diagnosing CDI have limitations; enzyme immunoassays for toxin have low sensitivity andClostridioides difficilepolymerase chain reaction cannot differentiate infection from colonization. An ideal diagnostic test that incorporates microbial factors, host factors, and host-microbe interaction might characterize true infection. Assessing volatile organic compounds (VOCs) in exhaled breath may be a useful test for identifying CDI. To identify a wide selection of VOCs in exhaled breath, we used thermal desorption-gas chromatography-mass spectrometry to study breath samples from 17 patients with CDI. Age- and sex-matched patients with diarrhea and negativeC.difficiletesting (no CDI) were used as controls. Of the 65 VOCs tested, 9 were used to build a quadratic discriminant model that showed a final cross-validated accuracy of 74%, a sensitivity of 71%, a specificity of 76%, and a receiver operating characteristic area under the curve of 0.72. If these findings are proven by larger studies, breath VOC analysis may be a helpful adjunctive diagnostic test for CDI.

Volatilome: Smells like microbial spirit

In recent years, the study of volatile compounds has sparked interest due to their implications in signaling and the enormous variety of bioactive properties attributed to them. Despite the absence of analysis methods standardization, there are a multitude of tools and databases that allow the identification and quantification of volatile compounds. These compounds are chemically heterogeneous and their diverse properties are exploited by various fields such as cosmetics, the food industry, agriculture and medicine, some of which will be discussed here. In virtue of volatile compounds being ubiquitous and fast chemical messengers, these molecules mediate a large number of interspecific and intraspecific interactions, which are key at an ecological level to maintaining the balance and correct functioning of ecosystems. This review briefly summarized the role of volatile compounds in inter- and intra-specific relationships as well as industrial applications associated with the use of these compounds that is emerging as a promising field of study.

Volatilomes of human infection

The human volatilome comprises a vast mixture of volatile emissions produced by the human body and its microbiomes. Following infection, the human volatilome undergoes significant shifts, and presents a unique medium for non-invasive biomarker discovery. In this review, we examine how the onset of infection impacts the production of volatile metabolites that reflects dysbiosis by pathogenic microbes. We describe key analytical workflows applied across both microbial and clinical volatilomics and emphasize the value in linking microbial studies to clinical investigations to robustly elucidate the metabolic species and pathways leading to the observed volatile signatures. We review the current state of the art across microbial and clinical volatilomics, outlining common objectives and successes of microbial-clinical volatilomic workflows. Finally, we propose key challenges, as well as our perspectives on emerging opportunities for developing clinically useful and targeted workflows that could significantly enhance and expedite current practices in infection diagnosis and monitoring.

Comprehensive evaluation of the prebiotic properties of Dendrobium officinale polysaccharides, β-glucan, and inulin during in vitro fermentation via multi-omics analysis

Dietary fiber is crucial for human health mainly due to its impact on gut microbiota structure and metabolites. This study aimed to investigate the impact of Dendrobium officinale polysaccharides (DOP) and two common fibers (β-glucan and inulin) on the gut microbiome structure and metabolic profile in vitro. Fecal samples were obtained from 30 healthy volunteers, which were then individually subjected to fermentation with each type of fiber. The results revealed that all fibers were efficiently degraded by gut microbiota, with DOP exhibiting a slower fermentation rate compared to β-glucan and inulin. The fermentation of all fibers led to a significant increase in the production of short-chain fatty acids (SCFAs) and a reduction in branched-chain fatty acids (BCFAs), sulfides, phenols, and indole. Moreover, the abundance of unclassified Enterobacteriaceae, which was positively correlated with sulfide, phenols, and indole levels, was significantly reduced by all fibers. Additionally, DOP specifically promoted the growth of Parabacteroides, while β-glucan and inulin promoted the growth of Bifidobacterium and Faecalibacterium. Taken together, these findings enhance our understanding of the role of DOP, β-glucan, and inulin in modulating gut microbiota and metabolites, where the fermentation with fecal bacteria from different volunteers could provide valuable insights for personalized therapeutic approaches.

p-Cresol Sulfate Is a Sensitive Urinary Marker of Fecal Microbiota Transplantation and Antibiotics Treatments in Human Patients and Mouse Models

Fecal microbiota transplantation (FMT) has emerged as a highly effective therapy for recurrent Clostridioides difficile infection (rCDI) and also a potential therapy for other diseases associated with dysbiotic gut microbiota. Monitoring metabolic changes in biofluids and excreta is a noninvasive approach to identify the biomarkers of microbial recolonization and to understand the metabolic influences of FMT on the host. In this study, the pre-FMT and post FMT urine samples from 11 rCDI patients were compared through metabolomic analyses for FMT-induced metabolic changes. The results showed that p-cresol sulfate in urine, a microbial metabolite of tyrosine, was rapidly elevated by FMT and much more responsive than other microbial metabolites of aromatic amino acids (AAAs). Because patients were treated with vancomycin prior to FMT, the influence of vancomycin on the microbial metabolism of AAAs was examined in a mouse feeding trial, in which the decreases in p-cresol sulfate, phenylacetylglycine, and indoxyl sulfate in urine were accompanied with significant increases in their AAA precursors in feces. The inhibitory effects of antibiotics and the recovering effects of FMT on the microbial metabolism of AAAs were further validated in a mouse model of FMT. Overall, urinary p-cresol sulfate may function as a sensitive and convenient therapeutic indicator on the effectiveness of antibiotics and FMT for the desired manipulation of gut microbiota in human patients.

Clostridioides difficile Infection in Children: Recent Updates on Epidemiology, Diagnosis, Therapy

Clostridioides (formerly Clostridium) difficile is the most important infectious cause of antibiotic-associated diarrhea worldwide and a leading cause of healthcare-associated infection in the United States. The incidence of C. difficile infection (CDI) in children has increased, with 20 000 cases now reported annually, also posing indirect educational and economic consequences. In contrast to infection in adults, CDI in children is more commonly community-associated, accounting for three-quarters of all cases. A wide spectrum of disease severity ranging from asymptomatic carriage to severe diarrhea can occur, varying by age. Fulminant disease, although rare in children, is associated with high morbidity and even fatality. Diagnosis of CDI can be challenging as currently available tests detect either the presence of organism or disease-causing toxin but cannot distinguish colonization from infection. Since colonization can be high in specific pediatric groups, such as infants and young children, biomarkers to aid in accurate diagnosis are urgently needed. Similar to disease in adults, recurrence of CDI in children is common, affecting 20% to 30% of incident cases. Metronidazole has long been considered the mainstay therapy for CDI in children. However, new evidence supports the safety and efficacy of oral vancomycin and fidaxomicin as additional treatment options, whereas fecal microbiota transplantation is gaining popularity for recurrent infection. Recent advancements in our understanding of emerging epidemiologic trends and management of CDI unique to children are highlighted in this review. Despite encouraging therapeutic advancements, there remains a pressing need to optimize CDI therapy in children, particularly as it pertains to severe and recurrent disease.

Volatile Markers for Cancer in Exhaled Breath-Could They Be the Signature of the Gut Microbiota?

It has been shown that the gut microbiota plays a central role in human health and disease. A wide range of volatile metabolites present in exhaled breath have been linked with gut microbiota and proposed as a non-invasive marker for monitoring pathological conditions. The aim of this study was to examine the possible correlation between volatile organic compounds (VOCs) in exhaled breath and the fecal microbiome by multivariate statistical analysis in gastric cancer patients (n = 16) and healthy controls (n = 33). Shotgun metagenomic sequencing was used to characterize the fecal microbiota. Breath-VOC profiles in the same participants were identified by an untargeted gas chromatography-mass spectrometry (GC-MS) technique. A multivariate statistical approach involving a canonical correlation analysis (CCA) and sparse principal component analysis identified the significant relationship between the breath VOCs and fecal microbiota. This relation was found to differ between gastric cancer patients and healthy controls. In 16 cancer cases, 14 distinct metabolites identified from the breath belonging to hydrocarbons, alcohols, aromatics, ketones, ethers, and organosulfur compounds were highly correlated with 33 fecal bacterial taxa (correlation of 0.891, p-value 0.045), whereas in 33 healthy controls, 7 volatile metabolites belonging to alcohols, aldehydes, esters, phenols, and benzamide derivatives correlated with 17 bacterial taxa (correlation of 0.871, p-value 0.0007). This study suggested that the correlation between fecal microbiota and breath VOCs was effective in identifying exhaled volatile metabolites and the functional effects of microbiome, thus helping to understand cancer-related changes and improving the survival and life expectancy in gastric cancer patients.

Roles of gut microbiota and metabolites in overweight and obesity of children

The prevalence of overweight and obesity in children and adolescents is an increasing public health problem. Pediatric overweight and obesity result from multiple factors, including genetic background, diet, and lifestyle. In addition, the gut microbiota and their metabolites play crucial roles in the progression of overweight and obesity of children. Therefore, we reviewed the roles of gut microbiota in overweight/obese children. The relationship between pediatric overweight/obesity and gut metabolites, such as short-chain fatty acids, medium-chain fatty acids, amino acids, amines, and bile acids, are also summarized. Targeting gut microbiota and metabolites might be a promising strategy for interventions aimed at reducing pediatric overweight/obesity.

Regulation of para-cresol production in Clostridioides difficile

The human pathogen Clostridioides difficile colonises the gastrointestinal tract following antibiotic exposure, which causes perturbations in the beneficial microbiome. An unusual feature of C. difficile among the gut microbiota is its ability to produce high concentrations of the antimicrobial compound para-cresol, which selectively targets Gram-negative bacteria. Production of p-cresol occurs either by: (a) tyrosine fermentation via the intermediate para-hydroxyphenylacetate (p-HPA), or (b) direct turnover of exogenous p-HPA in the human gut. p-HPA is decarboxylated to produce p-cresol, by the action of HpdBCA decarboxylase encoded by the hpdBCA operon. HpdBCA decarboxylase production is induced at the transcriptional level by elevated p-HPA, which causes elevated p-cresol production, that significantly reduces microbiome diversity and richness. This deleterious effect of p-cresol on the beneficial gut microbiome is advantageous for C. difficile pathogenesis and infection relapse. Inhibiting this pathway would provide a highly specific therapeutic.

Pediatric Clostridioides difficile Infection: Diagnosis and Diagnostic Stewardship

Although the pathogenesis of Clostridioides difficile infection (CDI) is complex and incompletely understood, it is believed that the elaboration of C. difficile toxins is necessary for disease. There are a variety of tests available for the detection of both the C. difficile organism and its toxins; however, each has limitations and the best application of these tests to the diagnosis of CDI in children remains uncertain. Nucleic acid amplification tests are unable to reliably discriminate between CDI and C. difficile colonization, while commercially available enzyme immunoassays for toxin detection lack sensitivity. An understanding of preanalytic factors, relevant patient features, and test performance characteristics is essential to the accurate diagnosis of CDI in children. Specific diagnostic stewardship strategies can also increase the likelihood that positive tests reflect disease rather than colonization. Ultimately, CDI remains a clinical diagnosis and clinical judgment is essential when interpreting test results, regardless of the methods used.

The future of Clostridioides difficile diagnostics

PURPOSE OF REVIEW

Although the epidemiology of Clostridioides difficile has changed, this organism continues to cause significant morbidity and mortality. This review addresses current and future approaches to the diagnosis of C. difficile disease.

RECENT FINDINGS

Over the last several years, large prospective studies have confirmed that there is no single optimal test for the diagnosis of C. difficile disease. The pendulum has swung from a focus on rapid molecular diagnosis during the years of the ribotype 027 epidemic, to a call for use of algorithmic approaches that include a test for toxin detection. In addition, diagnostic stewardship has been shown to improve test utilization, especially with molecular methods. Advances in testing include development of ultrasensitive toxin tests and an expansion of biomarkers that may be more C. difficile specific. Microbiome research may be leveraged to inform novel diagnostic approaches based on measurements of volatile and nonvolatile organic compounds in stool.

SUMMARY

As rates of C. difficile infection decline, emphasis is now on improving test utilization and a quest for improved diagnostic approaches. These approaches may involve implementation of technologies that improve toxin testing, predict patients likely to have disease and/or a severe outcome, and harnessing research on changes in the microbiome to advance metabolomics.

Effects of the L-tyrosine-derived bacterial metabolite p-cresol on colonic and peripheral cells

Specific families of bacteria present within the intestinal luminal content produce p-cresol from L-tyrosine. Although the hosts do not synthesize p-cresol, they can metabolize this compound within their colonic mucosa and liver leading to the production of co-metabolites including p-cresyl sulfate (p-CS) and p-cresyl glucuronide (p-CG). p-Cresol and its co-metabolites are recovered in the circulation mainly conjugated to albumin, but also in their free forms that are excreted in the urine. An increased dietary protein intake raises the amount of p-cresol recovered in the feces and urine, while fecal excretion of p-cresol is diminished by a diet containing undigestible polysaccharides. p-Cresol in excess is genotoxic for colonocytes. In addition, in these cells, this bacterial metabolite decreases mitochondrial oxygen consumption, while increasing the anion superoxide production. In chronic kidney disease (CKD), marked accumulation of p-cresol and p-CS in plasma is measured, and in renal tubular cells, p-cresol and p-CS increase oxidative stress, affect mitochondrial function, and lead to cell death, strongly suggesting that these 2 compounds act as uremic toxins that aggravate CKD progression. p-Cresol and p-CS are also suspected to play a role in the CKD-associated adverse cardiovascular events, since they affect endothelial cell proliferation and migration, decrease the capacity of endothelial wound repair, and increase the senescence of endothelial cells. Finally, the fact that concentration of p-cresol is transiently increased in young autistic children biological fluids, and that intraperitoneal injection of p-cresol in animal models induces some behavioral characteristics observed in the autism spectrum disorders (ASD), raise the view that p-cresol may possibly represent one of the components involved in ASD etiology. Further pre-clinical and clinical studies are obviously needed to determine if the lowering of p-cresol and/or p-CS circulating concentrations, by dietary and/or pharmacological means, would allow, by itself or in combination with other interventions, to improve CKD progression and associated cardiovascular outcomes, as well as some neurological outcomes in children with an early diagnosis of autism.

Identification of volatile compounds from bacteria by spectrometric methods in medicine diagnostic and other areas: current state and perspectives

Diagnosis of bacterial infections until today mostly relies on conventional microbiological methods. The resulting long turnaround times can lead to delayed initiation of adequate antibiotic therapy and prolonged periods of empiric antibiotic therapy (e.g., in intensive care medicine). Therewith, they contribute to the mortality of bacterial infections and the induction of multidrug resistances. The detection of species specific volatile organic compounds (VOCs) emitted by bacteria has been proposed as a possible diagnostic approach with the potential to serve as an innovative point-of-care diagnostic tool with very short turnaround times. A range of spectrometric methods are available which allow the detection and quantification of bacterial VOCs down to a range of part per trillion. This narrative review introduces the application of spectrometric analytical methods for the purpose of detecting VOCs of bacterial origin and their clinical use for diagnosing different infectious conditions over the last decade. KEY POINTS: • Detection of VOCs enables bacterial differentiation in various medical conditions. • Spectrometric methods may function as point-of-care diagnostics in near future.

Diagnosis of Clostridioides difficile infection by analysis of volatile organic compounds in breath, plasma, and stool: A cross-sectional proof-of-concept study

Clostridioides difficile infection (CDI) is an important infectious cause of antibiotic-associated diarrhea, with significant morbidity and mortality. Current diagnostic algorithms are based on identifying toxin by enzyme immunoassay (EIA) and toxin gene by real-time polymerase chain reaction (PCR) in patients with diarrhea. EIA’s sensitivity is poor, and PCR, although highly sensitive and specific, cannot differentiate infection from colonization. An ideal test that incorporates microbial factors, host factors, and host-microbe interaction might characterize true infection, and assess prognosis and recurrence. The study of volatile organic compounds (VOCs) has the potential to be an ideal diagnostic test. The presence of VOCs accounts for the characteristic odor of stool in CDI but their presence in breath and plasma has not been studied yet. A cross-sectional proof-of-concept study analyzing VOCs using selected ion flow tube mass spectrometry (SIFT-MS) was done on breath, stool, and plasma of patients with clinical features and positive PCR for CDI (cases) and compared with patients with clinical features but a negative PCR (control). Our results showed that VOC patterns in breath, stool, and plasma, had good accuracy [area under the receiver operating characteristic curve (ROC) 93%, 86%, and 91%, respectively] for identifying patients with CDI.

Production, Storage Stability, and Susceptibility Testing of Reuterin and Its Impact on the Murine Fecal Microbiome and Volatile Organic Compound Profile

Background: Probiotics are generally considered as safe, but infections may rarely occur in vulnerable patients. Alternatives to live microorganisms to manage dysbiosis may be of interest in these patients. Reuterin is a complex component system exhibiting broad spectrum antimicrobial activity and a possible candidate substance in these cases.

Methods: Reuterin supernatant was cultured from Lentilactobacillus diolivorans in a bioreactor in a two-step process. Storage stability at −20°C and effect of repeated freeze-thaw cycles were assessed by high performance liquid chromatography (HPLC). Antimicrobial activity was tested against Clostridium difficile, Listeria monocytogenes, Escherichia coli, Enterococcus faecium, Staphylococcus (S.) aureus, Staphylococcus epidermidis, Streptococcus (S.) agalactiae, Propionibacterium acnes, and Pseudomonas aeruginosae. Male BALBc mice were gavage fed with reuterin supernatant (n = 10) or culture medium (n = 10). Fecal volatile organic compounds (VOC) were assessed by gas chromatography mass spectroscopy; the microbiome was examined by 16S rRNA gene sequencing.

Results: The supernatant contained 13.4 g/L reuterin (3-hydroxypropionaldehyde; 3-HPA). 3-HPA content remained stable at −20°C for 35 days followed by a slow decrease of its concentration. Repeated freezing/thawing caused a slow 3-HPA decrease. Antimicrobial activity was encountered against S. aureus, S. epidermidis, and S. agalactiae. Microbiome analysis showed no differences in alpha and beta diversity markers. Linear discriminant effect size (LEfSe) analysis identified Lachnospiraceae_bacterium_COE1 and Ruminoclostridium_5_uncultured_Clostridiales_ bacterium (in the reuterin medium group) and Desulfovibrio_uncultured_ bacterium, Candidatus Arthromitus, Ruminococcae_NK4A214_group, and Eubacterium_xylanophilum_group (in the reuterin group) as markers for group differentiation. VOC analysis showed a significant decrease of heptane and increase of 3-methylbutanal in the reuterin group.

Conclusion: The supernatant produced in this study contained acceptable amounts of 3-HPA remaining stable for 35 days at −20°C and exhibiting an antimicrobial effect against S. aureus, S. agalactiae, and S. epidermidis. Under in vivo conditions, the reuterin supernatant caused alterations of the fecal microbiome. In the fecal, VOC analysis decreased heptane and increased 3-methylbutanal were encountered. These findings suggest the high potential of the reuterin system to influence the intestinal microbiome in health and disease, which needs to be examined in detail in future projects.

Learning about microbial language: possible interactions mediated by microbial volatile organic compounds (VOCs) and relevance to understanding Malassezia spp. metabolism

BACKGROUND

Microorganisms synthesize and release a large diversity of small molecules like volatile compounds, which allow them to relate and interact with their environment. Volatile organic compounds (VOCs) are carbon-based compounds with low molecular weight and generally, high vapor pressure; because of their nature, they spread easily in the environment. Little is known about the role of VOCs in the interaction processes, and less is known about VOCs produced by Malassezia, a genus of yeasts that belongs to the human skin mycobiota. These yeasts have been associated with several dermatological diseases and currently, they are considered as emerging opportunistic yeasts. Research about secondary metabolites of these yeasts is limited. The pathogenic role and the molecular mechanisms involved in the infection processes of this genus are yet to be clarified. VOCs produced by Malassezia yeasts could play an important function in their metabolism; in addition, they might be involved in either beneficial or pathogenic host-interaction processes. Since these yeasts present differences in their nutritional requirements, like lipids to grow, it is possible that these variations of growth requirements also define differences in the volatile organic compounds produced in Malassezia species.

AIM OF REVIEW

We present a mini review about VOCs produced by microorganisms and Malassezia species, and hypothesize about their role in its metabolism, which would reveal clues about host-pathogen interaction.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Since living organisms inhabit a similar environment, the interaction processes occur naturally; as a result, a signal and a response from participants of these processes become important in understanding several biological behaviors. The efforts to elucidate how living organisms interact has been studied from several perspectives. An important issue is that VOCs released by the microbiota plays a key role in the setup of relationships between living micro and macro organisms. The challenge is to determine what is the role of these VOCs produced by human microbiota in commensal/pathogenic scenarios, and how these allow understanding the species metabolism. Malassezia is part of the human mycobiota, and it is implicated in commensal and pathogenic processes. It is possible that their VOCs are involved in these behavioral changes, but the knowledge about this remains overlocked. For this reason, VOCs produced by microorganisms and Malassezia spp. and their role in several biological processes are the main topic in this review.

Advances and required improvements in methods to diagnosing Clostridioides difficile infections in the healthcare setting

INTRODUCTION

Clostrididioides difficile is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs.Areas Covered: We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review addresses the evolving epidemiology of Clostridioides difficile infection (CDI) and discusses novel methods/approaches for improving the diagnosis of this important disease.

EXPERT OPINION

No single diagnostic test to date has demonstrated optimum sensitivity and specificity for detection of CDI. Many institutions have developed multi-step algorithms consistent with guidelines established by various professional societies. Some institutions have successfully tried to improve the pretest probability of molecular assays by implementing appropriate sample rejection criteria and establishing best practice alerts at the time of electronic order entry. Others have established PCR cycle threshold cutoffs to attempt to differentiate symptomatic patients from asymptomatic carriers or to make predictions about severity of disease with variable success. As research advances our understanding of C. difficile pathogenesis and pathophysiology, more information on CDI specific biomarkers is emerging. Finally, assessments of the microbiome and metabolome may expand the diagnostic armamentarium with advances in mass spectrometry and sequencing technologies.

Associations between and risks of trace elements related to skin and liver damage induced by arsenic from coal burning

Long-term exposure to high levels of arsenic has been documented to induce skin and liver damage, affecting hundreds of millions of people. While arsenic-induced skin and liver damage and trace element alterations have been studied, their correlations and risks have not been explained. Based on the above premise, this study included a total of 172 subjects from a coal-burning arsenic poisoning area. The levels of 18 trace elements in hair and six liver function indices in serum were detected, and the associations between and risks of trace elements related to skin and liver damage were analyzed. Finally, the receiver operating characteristic (ROC) curve and areas under the curve (AUC) were used to analyze the diagnostic values of certain trace elements for arsenic-induced skin and liver damage. The results found that a decrease in Se was a risk factor for arsenic-induced skin and liver damage (OR = 8.33 and 1.92, respectively). Furthermore, increases in Al and V were risk factors for arsenic-induced skin damage (OR = 1.05) and liver damage (OR = 13.16), respectively. In addition, the results found that Se and Al possessed certain diagnostic values for arsenic-induced skin damage (AUC = 0.93, 0.80), that Se possessed a diagnostic value for liver damage (AUC = 0.93), and that the combination of Se and Al increased the diagnostic value for skin damage (AUC = 0.96). This study provides an important research basis for further understanding the reasons for arsenic-induced skin and liver damage, for screening and identifying candidate diagnostic biomarkers, and for improving prevention and control strategies for arsenism.

Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis

Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.

Volatilomes of Bacterial Infections in Humans

Sense of smell in humans has the capacity to detect certain volatiles from bacterial infections. Our olfactory senses were used in ancient medicine to diagnose diseases in patients. As humans are considered holobionts, each person's unique odor consists of volatile organic compounds (VOCs, volatilome) produced not only by the humans themselves but also by their beneficial and pathogenic micro-habitants. In the past decade it has been well documented that microorganisms (fungi and bacteria) are able to emit a broad range of olfactory active VOCs [summarized in the mVOC database (http://bioinformatics.charite.de/mvoc/)]. During microbial infection, the equilibrium between the human and its microbiome is altered, followed by a change in the volatilome. For several decades, physicians have been trying to utilize these changes in smell composition to develop fast and efficient diagnostic tools, particularly because volatiles detection is non-invasive and non-destructive, which would be a breakthrough in many therapies. Within this review, we discuss bacterial infections including gastrointestinal, respiratory or lung, and blood infections, focusing on the pathogens and their known corresponding volatile biomarkers. Furthermore, we cover the potential role of the human microbiota and their volatilome in certain diseases such as neurodegenerative diseases. We also report on discrete mVOCs that affect humans.

Characterization of the Immune Response during Infection Caused by Clostridioides difficile

The high risk of complications and death following Clostridioides difficile infection (CDI) requires identifying patients with severe disease and treating them accordingly. We characterized the immune response of CDI patients in relation to infection severity. Concentrations of 28 cytokines and chemokines were measured in serum samples, obtained from 54 CDI patients within a median timeframe of 24–48 h after laboratory confirmation of C. difficile infection. Demographic and clinical data were retrospectively collected from medical records. Disease severity score was determined by “Score indices for Clostridioides difficile infection severity”. Of 54 patients (mean age, 76.6 years, 61.1% female), 38 (70.4%) had mild disease and 16 (29.6%) had moderate disease. Seven cytokines were associated with a more severe CDI: granulocyte-macrophage colony-stimulating factor (p = 0.0106), interleukin (IL)-1β (p = 0.004), IL-8 (p = 0.0098), IL-12p70 (p = 0.0118), interferon-α (p = 0.0282), IL-15 (p = 0.0015), and IL-2 (p = 0.0031). Additionally, there was an increased T-helper 1 response in more severe cases of CDI. Cytokines may serve as biomarkers for early prediction of CDI severity. Better and earlier assessment of illness severity will contribute to the adjustment of medical treatment, including monitoring and follow-up.

Assessment of gut microbiota fecal metabolites by chromatographic targeted approaches

Gut microbiota, the specific microbial community of the gastrointestinal tract, by means of the production of microbial metabolites provides the host with several functions affecting metabolic and immunological homeostasis. Insights into the intricate relationships between gut microbiota and the host require not only the understanding of its structure and function but also the measurement of effector molecules acting along the gut microbiota axis. This article reviews the literature on targeted chromatographic approaches in analysis of gut microbiota specific metabolites in feces as the most accessible biological matrix which can directly probe the connection between intestinal bacteria and the (patho)physiology of the holobiont. Together with a discussion on sample collection and preparation, the chromatographic methods targeted to determination of some classes of microbiota-derived metabolites (e.g., short-chain fatty acids, bile acids, low molecular masses amines and polyamines, vitamins, neurotransmitters and related compounds) are discussed and their main characteristics, summarized in Tables.

The path toward using microbial metabolites as therapies

Metabolites have emerged as the quintessential effectors mediating the impact of the commensal microbiome on human physiology, both locally at the sites of microbial colonization and systemically. The endocrine activity of the microbiome and its involvement in a multitude of complex diseases has made microbiome-modulated metabolites an attractive target for the development of new therapies. Several properties make metabolites uniquely suited for interventional strategies: natural occurrence in a broad range of concentrations, functional pleiotropy, ease of administration, and tissue bioavailability. Here, we provide an overview of recently discovered physiological effects of microbiome-associated small molecules that may serve as the first examples of metabolite-based therapies. We also highlight challenges and obstacles that the field needs to overcome on the path toward successful clinical trials of microbial metabolites for human disease.