(1)H NMR spectroscopy in the diagnosis of Pseudomonas aeruginosa-induced urinary tract infection

The Role of Metabolomics and Microbiology in Urinary Tract Infection

One of the common illnesses that affect women's physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient's urine in relation to their role in supporting host health.

Hyperpolarization-Enhanced NMR Spectroscopy of Unaltered Biofluids Using Photo-CIDNP

The direct and unambiguous detection and identification of individual metabolite molecules present in complex biological mixtures constitute a major challenge in (bio)analytical research. In this context, nuclear magnetic resonance (NMR) spectroscopy has proven to be particularly powerful owing to its ability to provide both qualitative and quantitative atomic-level information on multiple analytes simultaneously in a noninvasive manner. Nevertheless, NMR suffers from a low inherent sensitivity and, moreover, lacks selectivity regarding the number of individual analytes to be studied in a mixture of a myriad of structurally and chemically very different molecules, e.g., metabolites in a biofluid. Here, we describe a method that circumvents these shortcomings via performing selective, photochemically induced dynamic nuclear polarization (photo-CIDNP) enhanced NMR spectroscopy on unmodified complex biological mixtures, i.e., human urine and serum, which yields a single, background-free one-dimensional NMR spectrum. In doing this, we demonstrate that photo-CIDNP experiments on unmodified complex mixtures of biological origin are feasible, can be performed straightforwardly in the native aqueous medium at physiological metabolite concentrations, and act as a spectral filter, facilitating the analysis of NMR spectra of complex biofluids. Due to its noninvasive nature, the method is fully compatible with state-of-the-art metabolomic protocols providing direct spectroscopic information on a small, carefully selected subset of clinically relevant metabolites. We anticipate that this approach, which, in addition, can be combined with existing high-throughput/high-sensitivity NMR methodology, holds great promise for further in-depth studies and development for use in metabolomics and many other areas of analytical research.

Untargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus

While bacterial metabolism is known to impact antibiotic efficacy and virulence, the metabolic capacities of individual microbes in cystic fibrosis lung infections are difficult to disentangle from sputum samples. Here, we show that untargeted metabolomic profiling of supernatants of multiple strains of Pseudomonas aeruginosa and Staphylococcus aureus grown in monoculture in synthetic cystic fibrosis media (SCFM) reveals distinct species-specific metabolic signatures despite intraspecies metabolic variability. We identify a set of 15 metabolites that were significantly consumed by both P. aeruginosa and S. aureus, suggesting that nutrient competition has the potential to impact community dynamics even in the absence of other pathogen-pathogen interactions. Finally, metabolites that were uniquely produced by one species or the other were identified. Specifically, the virulence factor precursor anthranilic acid, as well as the quinoline 2,4-quinolinediol (DHQ), were robustly produced across all tested strains of P. aeruginosa. Through the direct comparison of the extracellular metabolism of P. aeruginosa and S. aureus in a physiologically relevant environment, this work provides insight toward the potential for metabolic interactions in vivo and supports the development of species-specific diagnostic markers of infection. IMPORTANCE Interactions between P. aeruginosa and S. aureus can impact pathogenicity and antimicrobial efficacy. In this study, we aim to better understand the potential for metabolic interactions between P. aeruginosa and S. aureus in an environment resembling the cystic fibrosis lung. We find that S. aureus and P. aeruginosa consume many of the same nutrients, suggesting that metabolic competition may play an important role in community dynamics during coinfection. We further identify metabolites uniquely produced by either organism with the potential to be developed into species-specific biomarkers of infection in the cystic fibrosis lung.

Biomarkers in urinary tract infections - which ones are suitable for diagnostics and follow-up?

Introduction: Urinary tract infections (UTIs) are one of the most common infections worldwide. Under special circumstances, clinicians must rely on laboratory findings, which might have a weak predicting value, misguiding the practitioners and leading to incorrect diagnosis and overuse of antibiotics. Therefore, there is an urgent need for reliable biomarkers in UTIs. Methods: We performed a literature search for biomarkers used in UTIs from January 1999 until May 2020. We used "urinary tract infection" and "biomarker" as the main key words in the PubMed, Medline and Cochrane databases. After peer review, we excluded the duplicates and identified the suitable articles, from which we collected the data and divided the available biomarkers into 5 groups: i) conventional markers; ii) promising, thoroughly studied biomarkers; iii) promising biomarkers that need further studies; iv) biomarkers of unknown significance; v) controversial, not useful markers. Results: We found 131 articles, mostly from the paediatric population. Neutrophil gelatinase-associated lipocalin (NGAL) and interleukins (IL) have a leading role in diagnosing and differentiating UTIs based on a lot of observational, comparative trials. Heparin Binding Protein (HBP), Lactoferrin (LF), Heat-Shock Protein-70 (HSP-70), Human Defensin-5 (HD-5), Lipopolysaccharide Binding Protein (LBP) and mass spectrometry studies are promising, but confirming data are lacking. The measurable components of the innate immune system and local host cell response could be appropriate biomarkers, but their significance is currently unknown. Conclusions: Conventional biomarkers for UTIs have low specificity. The use of urinary NGAL and interleukins could improve the sensitivity and specificity of laboratory diagnosis of UTIs.

Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends

Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.

1H NMR spectroscopy-based metabolomics analysis for the diagnosis of symptomatic E. coli-associated urinary tract infection (UTI)

BACKGROUND

Urinary tract infection (UTI) is one of the most common diagnoses in girls and women, and to a lesser extent in boys and men younger than 50 years. Escherichia coli, followed by Klebsiella spp. and Proteus spp., cause 75-90% of all infections. Infection of the urinary tract is identified by growth of a significant number of a single species in the urine, in the presence of symptoms. Urinary culture is an accurate diagnostic method but takes several hours or days to be carried out. Metabolomics analysis aims to identify biomarkers that are capable of speeding up diagnosis.

METHODS

Urine samples from 51 patients with a prior diagnosis of Escherichia coli-associated UTI, from 21 patients with UTI caused by other pathogens (bacteria and fungi), and from 61 healthy controls were analyzed. The ¹H-NMR spectra were acquired and processed. Multivariate statistical models were applied and their performance was validated using permutation test and ROC curve.

RESULTS

Orthogonal Partial Least Squares-discriminant Analysis (OPLS-DA) showed good separation (R²Y = 0.76, Q2=0.45, p < 0.001) between UTI caused by Escherichia coli and healthy controls. Acetate and trimethylamine were identified as discriminant metabolites. The concentrations of both metabolites were calculated and used to build the ROC curves. The discriminant metabolites identified were also evaluated in urine samples from patients with other pathogens infections to test their specificity.

CONCLUSIONS

Acetate and trimethylamine were identified as optimal candidates for biomarkers for UTI diagnosis. The conclusions support the possibility of a fast diagnostic test for Escherichia coli-associated UTI using acetate and trimethylamine concentrations.

Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome

Identification of bacterial species is a crucial bottleneck for clinical diagnosis of infectious diseases. Quick and reliable identification is a key factor to provide suitable antibiotherapies and avoid the development of multiple-drug resistance. We propose a novel nuclear magnetic resonance (NMR)-based metabolomics strategy for rapid discrimination and identification of several bacterial species that relies on untargeted metabolic profiling of supernatants from bacterial culture media. We show that six bacterial species (Gram negative: Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis; Gram positive: Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus saprophyticus) can be well discriminated from multivariate statistical analysis, opening new prospects for NMR applications to microbial clinical diagnosis.

Serum procalcitonin levels in combination with (1)H NMR spectroscopy: A rapid indicator for differentiation of urosepsis

BACKGROUND

Urosepsis, a severe form of sepsis requires immediate medical attention for prognosis. It is clinically diagnosed by estimating serum procalcitonin (PCT) levels along with time taking urine and blood cultures. We explored NMR based profiling, deriving metabolites that could potentially aid diagnosis.

METHODS

The proton NMR of serum and urine samples of healthy control subjects (n=32) and urosepsis cases (n=35) based on PCT levels, were analyzed. Four clinically identified non-urosepsis cases with high PCT levels were also differentiated through principal component analysis (PCA) of the serum samples.

RESULTS

Quantification of serum and urine through Discriminant Function Analysis (DFA) afforded 93.7% and 91.7% correct classification respectively, along with identification of malonate and urea as potential biomarkers for the disease in both urine and serum samples. The partial least square discriminant analysis (PLS-DA) showed an R(2) value of 0.97 in both biofluids with Q(2)=0.87 and 0.85 for serum and urine respectively. The training set of serum samples provided precise prediction of the test set in a small cohort through random re-sampling method, while in urine samples, the predictions were inconclusive.

CONCLUSIONS

Our pilot study reveals that (1)H NMR of serum metabolic profiling in combination with PCT levels may provide a rapid method for differentiation of urosepsis.

Nuclear Magnetic Resonance (NMR) as a tool for the study of the metabolism of Rickettsia slovaca

Rickettsial infections are caused by intracellular bacteria. They do not grow in standard culture media so there are limitations in routine practice to study their metabolism. Nuclear Magnetic Resonance (NMR) spectroscopy is used for identification of metabolites in biological samples. Vero cells infected with Rickettsia slovaca as well as uninfected cells were monitored by (1)H NMR showing the presence of ethanol and lactic acid. As no differences were observed, labeled compounds were added into cultures. When D-[1-13C]glucose was monitored by (13)C NMR no differences among infected and uninfected cells were observed in metabolic profiles. Glucose was transformed into ethanol in all cultures. Monitored experiments carried out with [2-13C]glycine showed differences between infected and uninfected cell cultures spectra. Glycine was partially transformed into serine, but the amount of the serine formed was larger in those infected. Moreover, L-[2-13C]leucine, L-[1-13C]isoleucine and L-[15N]tyrosine were evaluated. No differences among infected and uninfected cells were observed in the metabolic profiles when tyrosine and leucine were monitored. The amino acid L-[1-13C]isoleucine exhibited different metabolism in presence of the R. slovaca, showing a promising behavior as biomarker. In this work we focused on finding one or more compounds that could be metabolized specifically by R. slovaca and could be used as an indicator of its activity.

Proton Nuclear Magnetic Resonance Spectroscopy as a Technique for Gentamicin Drug Susceptibility Studies with Escherichia coli ATCC 25922

Antimicrobial drug susceptibility tests involving multiple time-consuming steps are still used as reference methods. Today, there is a need for the development of new automated instruments that can provide faster results and reduce operating time, reagent costs, and labor requirements. Nuclear magnetic resonance (NMR) spectroscopy meets those requirements. The metabolism and antimicrobial susceptibility of Escherichia coli ATCC 25922 in the presence of gentamicin have been analyzed using NMR and compared with a reference method. Direct incubation of the bacteria (with and without gentamicin) into the NMR tube has also been performed, and differences in the NMR spectra were obtained. The MIC, determined by the reference method found in this study, would correspond with the termination of the bacterial metabolism observed with NMR. Experiments carried out directly into the NMR tube enabled the development of antimicrobial drug susceptibility tests to assess the effectiveness of the antibiotic. NMR is an objective and reproducible method for showing the effects of a drug on the subject bacterium and can emerge as an excellent tool for studying bacterial activity in the presence of different antibiotic concentrations.

Quantitative metabolomics of urine for rapid etiological diagnosis of urinary tract infection: evaluation of a microbial-mammalian co-metabolite as a diagnostic biomarker

BACKGROUND

We have previously reported a NMR-based urinalysis for the screening of urinary tract infection (UTI) with high accuracy and reproducibility. Urinary acetic acid per creatinine was found to be a diagnostic marker of bacterial UTI with an area-under-receiver operating characteristic (ROC) curve of 0.97. In addition, we identified trimethylamine (TMA) as a human-microbial marker of Escherichia coli (EC)-associated UTI. Here, we evaluate the clinical application of NMR-based urinalysis in aiding the etiological diagnosis of bacterial UTI.

METHODS

Proton NMR spectroscopy was acquired using a Bruker 600MHz spectroscopy for 88 urine samples from patients with bacterial UTI, confirmed by urine culture. The spectra were analyzed using orthogonal partial least squares-discriminant analysis (OPLS-DA). ROC curve analysis was performed after the quantitation of the urine metabolites.

RESULTS

The TMA/creatinine (mmol/mmol) level was determined to be a specific marker for EC-associated UTI. It has an area-under-ROC=0.85 (95% confidence interval: 0.75-0.91). For the etiological diagnosis, the cutoff for 97.0% specificity was at 0.0117mmol/mmol creatinine for EC-associated UTI with a sensitivity of 66.7%. The mean of TMA/creatinine of EC is 21-fold that of non-EC.

CONCLUSIONS

The co-metabolism of TMA by EC and human cells makes TMA an ideal urine biomarker for UTI. The presence of TMA in a freshly collected sample eliminates the possibility of contamination of urine by bacteria during the collection process resulting in a positive bacterial culture result. We envisage the NMR-based urinalysis of urinary TMA that can be a useful method for the etiological diagnosis of EC-associated UTI.

Nuclear magnetic resonance applied to antimicrobial drug susceptibility

There are many conventional microbiological methods in routine clinical practice to determine the sensitivity of common bacteria. The problem with these methods arises with bacteria that do not grow on habitual media (Rickettsia spp., Coxiella spp. and Anaplasma spp., among others) and for which there are no standardized techniques to determine their antimicrobial susceptibility. In addition, the techniques that are used for the culture of these fastidious bacteria show problems in both accuracy and reproducibility and, in some cases, the in vitro antimicrobial susceptibility of bacteria shows poor correlation with therapeutic outcome. Therefore, it becomes difficult to determine the antimicrobial drug susceptibility of some bacteria and, thus, to assess the therapeutic effect of drugs. The scientific breakthroughs that have taken place in recent years have allowed the use of new techniques that facilitate and improve microbiological study. This paper reviews the use of nuclear magnetic resonance spectroscopy as an alternative tool for determining antimicrobial drug susceptibility.

(1)H NMR-based metabolic profiling of urinary tract infection: combining multiple statistical models and clinical data

Urinary tract infection (UTI) encompasses a variety of clinical syndromes ranging from mild to life-threatening conditions. As such, it represents an interesting model for the development of an analytically based scoring system of disease severity and/or host response. Here we test the feasibility of this concept using (1)H NMR based metabolomics as the analytical platform. Using an exhaustively clinically characterized cohort and taking advantage of the multi-level study design, which opens possibilities for case-control and longitudinal modeling, we were able to identify molecular discriminators that characterize UTI patients. Among those discriminators a number (e.g. acetate, trimethylamine and others) showed association with the degree of bacterial contamination of urine, whereas others, such as, for instance, scyllo-inositol and para-aminohippuric acid, are more likely to be the markers of morbidity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0411-y) contains supplementary material, which is available to authorized users.

Metabolomics of urinary tract infection: a new uroscope in town

Urinary tract infection (UTI) is a potentially life-threatening infectious disease. For rapid directed therapy of UTIs, it is essential to determine the causative microorganism. To date, there is no single test that has been proven to reliably, rapidly and accurately identify the etiologic organism in UTI. The molecular methods for diagnosing the cause of UTI and prognostic development of clinically important metabolomic evaluations and their limitations for use in the diagnosis and monitoring of infections are discussed in this review article. The application of the emerging investigative device NMR spectroscopy as a surrogate method for the diagnosis of UTI is also addressed.

Broad identification of bacterial type in urinary tract infection using (1)h NMR spectroscopy

To address the shortcomings of urine culture for the rapid identification of urinary tract infection (UTI), we applied (1)H-nuclear magnetic resonance (NMR) spectroscopy as a surrogate method for fast screening of microorganisms. Study includes 682 urine samples from suspected UTI patients, 50 healthy volunteers, and commercially available standard strains of gram negative bacilli (GNB) (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Enterobacter, Acinetobacter, Proteus mirabilis, Citrobacter frundii) and gram positive cocci (GPC) (Enterococcus faecalis, Streptococcus group B, Staphylococcus saprophyticus). Acetate, lactate, ethanol, succinate, creatinine, trimethylamine (TMA), citrate, trimethylamin-N-oxide, glycine, urea, and hippurate were measured by (1)H NMR spectroscopy. All urine specimens were evaluated with culture method. Multivariate discriminant function analysis (DFA) reveals that acetate, lactate, succinate, and formate were able to differentiate, with high accuracy (99.5%), healthy controls from UTI patients. This statistical analysis was also able to classify GNB to GPC infected urine samples with high accuracy (96%). This technique appears to be a promising, rapid, and noninvasive approach to probing GNB and GPC infected urine specimens with its distinguishing metabolic profile. The determination of infection will be very important for rapidly and efficiently measuring the efficacy of a tailored treatment, leading to prompt and appropriate care of UTI patients.

Time-resolved metabolic footprinting for nonlinear modeling of bacterial substrate utilization

Untargeted profiling of small-molecule metabolites from microbial culture supernatants (metabolic footprinting) has great potential as a phenotyping tool. We used time-resolved metabolic footprinting to compare one Escherichia coli and three Pseudomonas aeruginosa strains growing on complex media and show that considering metabolite changes over the whole course of growth provides much more information than analyses based on data from a single time point. Most strikingly, there was pronounced selectivity in metabolite uptake, even when the bacteria were growing apparently exponentially, with certain groups of metabolites not taken up until others had been entirely depleted from the medium. In addition, metabolite excretion showed some complex patterns. Fitting nonlinear equations (four-parameter sigmoids) to individual metabolite data allowed us to model these changes for metabolite uptake and visualize them by back-projecting the curve-fit parameters onto the original growth curves. These "uptake window" plots clearly demonstrated strain differences, with the uptake of some compounds being reversed in order between different strains. Comparison of an undefined rich medium with a defined complex medium designed to mimic cystic fibrosis sputum showed many differences, both qualitative and quantitative, with a greater proportion of excreted to utilized metabolites in the defined medium. Extending the strain comparison to a more closely related set of isolates showed that it was possible to discriminate two species of the Burkholderia cepacia complex based on uptake dynamics alone. We believe time-resolved metabolic footprinting could be a valuable tool for many questions in bacteriology, including isolate comparisons, phenotyping deletion mutants, and as a functional complement to taxonomic classifications.

Severe pseudomonal infections

PURPOSE OF REVIEW

To review the most recent data on severe Pseudomonas aeruginosa infections. The focus will be on clinical studies with an emphasis on the critically ill.

RECENT FINDINGS

The frequency of P. aeruginosa as the etiologic agent of infections associated with high morbidity and mortality in hospitalized patients continues to increase. Unfortunately, pan-resistant isolates are now emerging as a significant clinical problem. Highly or pan-resistant isolates are associated with more frequent inappropriate initial therapy and increased mortality. Prevention relies on limitation of antibiotic pressure. Unfortunately, antibiotic class rotation has not resulted in persistent decreases in resistant isolates and the increased use of treatment protocols may actually increase selection.

SUMMARY

Because of the frequency of antibiotic resistance in clinical isolates of P. aeruginosa and the high associated mortality, combination, broad-spectrum antibiotic therapy should be used for empiric coverage of suspected P. aeruginosa infections. Accurate diagnostic testing can help to discontinue unnecessary antibiotics and decrease the overall selective pressure. Increasing resistance without new antibiotic classes on the horizon suggests the need for better use of available antibiotics and an emphasis on innovative treatment strategies in the future.

1H NMR spectroscopy in the diagnosis of Klebsiella pneumoniae-induced urinary tract infection

The (1)H NMR spectroscopic method is suggested and its utility is demonstrated for the diagnosis of Klebsiella pneumoniae (K. pneumoniae) in urinary tract infection (UTI). K. pneumoniae have the specific property of metabolizing glycerol to 1,3-propanediol (1,3-PD), acetate, ethanol and succinate. The quantity of 1,3-PD produced correlates well with the viable bacterial count. Other common bacteria causing UTI (except for Citrobacter frundii), such as Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Enterobacter aerogenes, Acinetobacter baumanii, Proteus mirabilis, Enterococcus faecalis, Streptococcus gp B and Staphylococcus aureus do not metabolize glycerol under similar conditions. Citrobacter frundii (C. frundii) also gives the same NMR results but is easily differentiated as being motile on direct microscopic examination of urine and it is not common nosocomial infectious agent in urinary tract infection. The method provides a single-step documentation of K. pneumoniae (and C. frundii) qualitatively as well as quantitatively. Out of the total 614 subjects considered, clinical diagnosis of UTI was obtained in 516 cases (84%). The NMR-based screening had a sensitivity of 90%, a specificity of 100% and a false negativity of 10% relative to the conventional quantitative culture method. In the present authors' experience, the results of NMR spectroscopy based screening show a very good correlation with the diagnosis of urinary tract infected patients.