Rapid detection of urinary tract pathogens using microcalorimetry: principle, technique and first results

Again and Again-Survival of Candida albicans in Urine Containing Antifungals

BACKGROUND

Relapse of Candida albicans urinary tract infection (UTI) is frequent despite appropriate treatment, as commonly used antifungals such fluconazole and flucytosine are only fungistatics. To improve treatment of Candida UTI and decrease relapses, understanding the long-term metabolic activity and survival of C. albicans in urine containing antifungals at minimal inhibitory concentration (MIC) is needed.

METHODS

we monitored the survival, metabolic activity and consumption of glucose and proteins by C. albicans using conventional methods and isothermal microcalorimetry (IMC). We also investigated the influence of dead Candida cells on the growth of their living counterparts.

RESULTS

For 33 days, weak activity was observed in samples containing antifungals in which C. albicans growth rate was reduced by 48%, 60% and 88%, and the lag increased to 172 h, 168 h and 6 h for amphotericin, flucytosine and fluconazole, respectively. The metabolic activity peaks corresponded to the plate counts but were delayed compared to the exhaustion of resources. The presence of dead cells promoted growth in artificial urine, increasing growth rate and reducing lag in similar proportions.

CONCLUSIONS

Even with antifungal treatment, C. albicans relapses are possible. The low metabolic activity of surviving cells leading to regrowth and chlamydospore formation possibly supported by autophagy are likely important factors in relapses.

The potential for isothermal microcalorimetry to detect venous catheter infection isolates and establish antibiograms

OBJECTIVES

Because bloodstream infection and venous catheter (or cannula) bloodstream infection are associated with high morbidity and cost, early identification and treatment are important. Isothermal microcalorimetry can detect microbial growth using thermal power (heat flow), essentially in real time. The aim of this study was to examine the potential of this technique in clinical practice.

METHODS

Thermal power of wild-type bacteria (Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae, and Enterococcus faecium) isolated from blood cultures of adult inpatients receiving parenteral nutrition in routine clinical practice was measured at 37°C every 10s using a Thermometric 2277 instrument. Temporal patterns of heat flow were used to detect the presence of bacteria, differentiate between them, and test their antibiotic sensitivity. Within and between batch reproducibility (% coefficient of variation [%CV]) was also established.

RESULTS

Isothermal microcalorimetry always correctly detected the absence or presence of wild-type bacteria. Thermograms differed distinctly between species. Key thermographic features, such as peak heights, timing of peak heights, and interval between peak heights, were highly reproducible within each species (within-batch %CV usually about ≤1%, although between-batch %CV was usually higher). The antibiotic sensitivities (tested only for S. epidermidis and K. pneumoniae) confirmed the results obtained from the hospital laboratory.

CONCLUSIONS

Isothermal microcalorimetry is a promising and highly reproducible real-time measurement technique with potential application to the investigation, species identification, and targeted antibiotic treatment of bloodstream infection and venous catheter (or cannula) bloodstream infection.

Real time detection of pathogenic bacteria in veterinary microbiology using isothermal microcalorimetry - A different approach

With today's challenges regarding antibiotic resistance and the importance of the implementation of prudent use of antibiotics, fast and reliable diagnostic tools for bacterial infections and subsequent antimicrobial susceptibility testing are of utmost relevance. Isothermal microcalorimetry (IMC) is a broadly applicable method, with which metabolic heat flow in reproducing bacteria can be measured in real time. To the best of the authors' knowledge, this is the first report on examination of 124 urine samples from feline and canine urinary tract infection with an IMC-based prototype instrument. A concentration-dependent time of peak heat flow by dilution series with Escherichia coli and Enterococcus faecalis reference strains demonstrated the general good performance of the prototype for detection of these bacteria. With diagnostic culture being set as a gold standard, the diagnostic sensitivity of IMC compared to bacteriological culture was 80 %, the diagnostic specificity was 97 %. With a Cohens' kappa value (κ) of 0.80, the two methods show good concordance. The results from our study demonstrate that the IMC technology is suitable to allow reliable, but much faster detection of bacteria than conventional culture, especially for Escherichia coli. Thus, implementing IMC technology could markedly speed up the bacteriological diagnostic process in veterinary medicine.

Isothermal microcalorimetry improves accuracy and time to bacterial detection of periprosthetic joint infection after total joint arthroplasty

Isothermal microcalorimetry (IMC) was evaluated compared to conventional cultures to determine the clinical performance for diagnosing periprosthetic joint infection (PJI) of hip/knee replacements. We prospectively collected three to five deep tissue samples per patient from 152 patients undergoing conversion or revision hip/knee arthroplasty from July 2020 to November 2022. Cultures and IMC for each sample were compared for concordance, median time to detection (TTD), and diagnostic performance based on 2013 Musculoskeletal Infection Society criteria. Secondary analyses involved patients on antibiotics at sampling. The 152 total patients had 592 tissue samples (mean 3.9 ± 0.3) with sample concordance between cultures and IMC of 90%. IMC demonstrated a sensitivity of 83%, specificity of 100%, negative predictive value (NPV) of 89%, and positive predictive value (PPV) of 100% for PJI. Cultures resulted in 69% sensitivity, 100% specificity, 81% NPV, and 100% PPV. The accuracy of IMC was 93% compared to 87% for cultures (P < 0.001). The median TTD of PJI by cultures was 51 (21-410) hours compared to 10 (0.5-148) hours for IMC (P < 0.001). For 39 patients on chronic antibiotics, sensitivity in PJI detection was 93%, specificity 100%, NPV 85%, and PPV 100% by IMC compared to 79% sensitivity, 100% specificity, 65% NPV, and 100% PPV for cultures. The accuracy was 95% for IMC compared to 85% for cultures (P < 0.001) with median TTD of 12 (0.5-127) hours compared to 52 (21-174) hours (P < 0.001). Utilizing IMC for PJI detection improves TTD by nearly 2 days while improving diagnostic accuracy compared to cultures, particularly in patients on chronic antibiotics.

Analytical methods for assessing antimicrobial activity of nanomaterials in complex media: advances, challenges, and perspectives

Assessing the antimicrobial activity of engineered nanomaterials (ENMs), especially in realistic scenarios, is of great significance for both basic research and applications. Multiple analytical methods are available for analysis via off-line or on-line measurements. Real-world samples are often complex with inorganic and organic components, which complicates the measurements of microbial viability and/or metabolic activity. This article highlights the recent advances achieved in analytical methods including typical applications and specifics regarding their accuracy, cost, efficiency, and user-friendliness. Methodological drawbacks, technique gaps, and future perspectives are also discussed. This review aims to help researchers select suitable methods for gaining insight into antimicrobial activities of targeted ENMs in artificial and natural complex matrices.

Microcalorimetric growth behavior of E. coli ATCC 25922 in an MCDSC

Isothermal microcalorimetry can provide a general analytical tool for the characterization of bacterial growth. Methodologies and equipment have been studied to expand the application and disseminate the use of the technique. The MCDSC is a microcalorimeter capable of measuring in the range of 0.2 μW that can operate at a temperature range of -20 to 140 °C or under isothermal conditions. Here, we present the first investigation of MCDSC for E. coli growth with the Baranyi and Roberts modeling application. This study presented the calorimetric E. coli fingerprint at MCDSC and compares it with the plate count technique, giving the data more biological meaning. The calorimeter was able to accurately detect growth metabolism and discriminate E. coli at different inoculum densities. Additionally, the MCDSC can offer a new point of view for evaluating microbial growth, such as the significant reduction in error due to dispersed data by the viable counting method.

Isothermal Microcalorimetry Improves the Time to Diagnosis of Fracture-related Infection Compared With Conventional Tissue Cultures

BACKGROUND

A consensus definition recently was formulated for fracture-related infection, which centered on confirmatory criteria including conventional cultures that take time to finalize and have a 10% to 20% false-negative rate. During this time, patients are often on broad-spectrum antibiotics and may remain hospitalized until cultures are finalized to adjust antibiotic regimens.

QUESTIONS/PURPOSES

(1) What is the diagnostic accuracy of isothermal microcalorimetry, and how does its accuracy compare with that of conventional cultures? (2) Does isothermal microcalorimetry decrease time to detection (or diagnosis) of fracture-related infection compared with conventional cultures? (3) Does isothermal microcalorimetry have a diagnostic accuracy or time advantage over conventional cultures in patients on chronic suppressive antibiotics?

METHODS

Between July 2020 and August 2021, we treated 310 patients with concerns for infection after prior fracture repair surgery. Of those, we considered all patients older than 18 years of age with fixation hardware in place at the time of presentation as potentially eligible. All included patients returned to the operating room with cultures obtained and assessed by both isothermal microcalorimetry and conventional cultures, and all were diagnosed using the consensus criteria for fracture-related infection. Based on that, 81% (250 of 310) of patients were eligible; a further 51% (157 of 310) were excluded because of the following reasons: the capacity of the isothermal microcalorimetry instrument limited the throughput on that day (34% [106 of 310]), they had only swab cultures obtained in surgery (15% [46 of 310]), or they had less than 3 months follow-up after surgery for infectious concerns (2% [5 of 310]), leaving 30% (93 of 310) of the originally identified patients for analysis. We obtained two to five cultures from each patient during surgery, which were sent to our clinical microbiology laboratory for standard processing (conventional cultures). This included homogenization of each tissue sample individually and culturing for aerobic, anaerobic, acid-fast bacilli, and fungal culturing. The remaining homogenate from each sample was then taken to our orthopaedic research laboratory, resuspended in growth media, and analyzed by isothermal microcalorimetry for a minimum of 24 hours. Aerobic and anaerobic cultures were maintained for 5 days and 14 days, respectively. Overall, there were 93 patients (59 males), with a mean age of 43 ± 14 years and a mean BMI of 28 ± 8 kg/m 2 , and 305 tissue samples (mean 3 ± 1 samples per patient) were obtained and assessed by conventional culturing and isothermal microcalorimetry. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of isothermal microcalorimetry to diagnose fracture-related infection were compared with conventional cultures using a McNemar test based on the consensus definition of fracture-related infection. This consensus criteria is comprised of two levels of certainty for the diagnostic variables. The first is confirmatory criteria, where infection is considered definitely present and includes the presence of fistula/sinus tract/wound breakdown, purulent drainage or the presence of pus, presence of microorganisms in deep tissue specimens on histopathologic examination, presence of more than five neutrophils/high-powered field by histopathologic examination (only for chronic/late onset cases), and identification of phenotypically indistinguishable pathogens by conventional culture from at least two separate deep tissue/implant specimens. The second is suggestive criteria in which further investigation is required to achieve confirmatory status. Fracture-related infection was diagnosed for this study to minimize subjectivity based on the presence of at least one of the confirmatory criteria as documented by the managing surgeon. When suggestive criteria were present without confirmatory criteria, patients were considered negative for fracture-related infection and followed further in clinic after surgical exploration (n = 25 patients). All 25 patients deemed not to have fracture-related infection were considered infection-free at latest follow-up (range 3 to 12 months). The time to detection or diagnosis was recorded and compared via the Mann-Whitney U test.

RESULTS

Using the consensus criteria for fracture-related infection, there were no differences with the numbers available between isothermal microcalorimetry and conventional cultures in terms of sensitivity (87% [95% confidence interval 77% to 94%] versus 81% [95% CI 69% to 89%]), specificity (100% [95% CI 87% to 100%] versus 96% [95% CI 79% to 99%]), PPV (100% [95% CI 90% to 100%] versus 98% [95% CI 89% to 99%]), NPV (74% [95% CI 60% to 84%] versus 65% [95% CI 52% to 75%]), or accuracy (90% [95% CI 83% to 96%] versus 85% [95% CI 76% to 91%]; p = 0.13). The concordance by sample between conventional cultures and isothermal microcalorimetry was 85%. Isothermal microcalorimetry had a shorter median (range) time to detection or diagnosis compared with conventional cultures (2 hours [0.5 to 66] versus 51 hours [18 to 147], difference of medians 49 hours; p < 0.001). Additionally, 32 patients used antibiotics for a median (range) duration of 28 days (7 to 1095) before presentation. In these unique patients, there were no differences with the numbers available between isothermal microcalorimetry and conventional cultures in terms of sensitivity (89% [95% CI 71% to 98%] versus 74% [95% CI 53% to 88%]), specificity (100% [95% CI 48% to 100%] versus 83% [95% CI 36% to 99%]), PPV (100% [95% CI 85% to 100%] versus 95% [95% CI 77% to 99%]), NPV (63% [95% CI 37% to 83%] versus 42% [95% CI 26% to 60%]), or accuracy (91% [95% CI 75% to 98%] versus 78% [95% CI 57% to 89%]; p = 0.17). Isothermal microcalorimetry again had a shorter median (range) time to detection or diagnosis compared with conventional cultures (1.5 hours [0.5 to 48] versus 51.5 hours [18 to 125], difference of medians 50 hours; p < 0.001).

CONCLUSION

Given that isothermal microcalorimetry considerably decreases the time to the diagnosis of a fracture-related infection without compromising the accuracy of the diagnosis, managing teams may eventually use isothermal microcalorimetry-pending developmental improvements and regulatory approval-to rapidly detect infection and begin antibiotic management while awaiting speciation and susceptibility testing to modify the antibiotic regimen. Given the unique thermograms generated, further studies are already underway focusing on speciation based on heat curves alone. Additionally, increased study sizes are necessary for both overall fracture-related infection diagnostic accuracy and test performance on patients using long-term antibiotics given the promising results with regard to time to detection for this groups as well.

LEVEL OF EVIDENCE

Level II, diagnostic study.

A Method to Determine the Efficacy of a Commercial Phage Preparation against Uropathogens in Urine and Artificial Urine Determined by Isothermal Microcalorimetry

Background: Urinary tract infections are commonly encountered and often treated with antibiotics. However, the inappropriate use of the latter has led to the appearance of resistant strains. In this context we investigate the use of calorimetry to rapidly determine if a phage cocktail can be used as alternative to antibiotics. Methods: We used a commercially available phage cocktail from an online pharmacy and tested it against a strain of Escherichia coli and a strain of Proteus mirabilis. We used isothermal microcalorimetry to follow the metabolic activity of the bacterial culture treated with the phage cocktail. Results: Isothermal microcalorimetry was able to follow the dynamic of the bacterial metabolic activity reduction by the phage cocktail. Both pathogens were strongly inhibited; however, some regrowth was observed for E. coli in urine. Conclusions: Isothermal microcalorimetry proved to be a valuable technique when investigating the efficacy of phage cocktails against uropathogens. We foresee that isothermal microcalorimetry could be used to obtain rapid phagograms.

Aerial warfare: An inducible production of volatile bioactive metabolites in a novel species of Scytinostroma sp

Antimicrobial volatile organic compounds (VOCs) may provide fungi an advantage over other competing microorganisms. As these defensive metabolites are often produced in response to microbial competitors, they are easily overlooked in axenic cultures. We used media supplemented with spent medium from Candida albicans to induce the expression of a broad-spectrum antimicrobial response in a previously uncharacterised white-rot fungus, Scytinostroma sp. Crude extractions of Scytinostroma sp. metabolites were found to be cytotoxic to fibroblast cells and antimicrobial to filamentous fungi, yeasts and Gram-positive bacteria. Volatile antimicrobial activity was observed for Scytinostroma sp. cultures and metabolite extracts using antimicrobial assays in bi-compartmentalised plates. Culture headspace analysis using solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) revealed a pronounced shift in Scytinostroma sp. VOCs when cultured on media supplemented with C. albicans spent medium. We observed a significant increase in the levels of 45 identified VOCs, including 7 metabolites with reported antimicrobial activity. Using preparative HPLC combined with GC-MS, we determined that isovelleral is likely to be the main broad-spectrum antimicrobial metabolite produced by Scytinostroma sp. Isovelleral is a sesquiterpene dialdehyde with both antibiotic and antifeedant properties, previously detected in fruit bodies of other Basidiomycetes.

Detection and Drug Susceptibility Testing of Neisseria gonorrhoeae Using Isothermal Microcalorimetry

Background: Gonorrhea is a frequently encountered sexually transmitted disease that results in urethritis and can further lead to pelvic inflammatory disease, infertility, and possibly disseminated gonococcal infections. Thus, it must be diagnosed promptly and accurately. In addition, drug susceptibility testing should be performed rapidly as well. Unfortunately, Neisseria gonorrhoea is a fastidious microorganism that is difficult to grow and requires culturing in an opaque medium. Methods: Here, we used isothermal microcalorimetry (IMC) to monitor the growth and the antimicrobial susceptibility of N. gonorrhoea. Results: Using IMC, concentrations of N. gonorrhoea between 2000 and 1 CFU·mL⁻¹ were detected within 12 to 33 h. In addition, drug susceptibility could be monitored easily. Conclusions: The use of isothermal microcalorimetry provides an interesting and useful tool to detect and characterize fastidious microbes such as N. gonorrhoea that require media incompatible with optical detection conventionally used in many commercial systems.

Kinetic analysis of microcalorimetric data derived from microbial growth: Basic theoretical, practical and industrial considerations

We report here a mathematical framework for the quantitative interpretation of exponential bacterial growth measured with isothermal microcalorimetry. The method allows determination of many parameters that define the exponential growth phase. To automate the analysis, we also wrote a coding program, so that the approach could be embedded in a commercial setting. As an exemplar, we apply the method to a commercial probiotic product. The outcome was that we could identify characteristic parameters of growth (including rate constant and doubling time), and hence authenticate product quality, within 15 h. This compares favourably with the current 7-10 days required for conventional microbiological assessment (to allow release of product for bottling and marketing) via plating methods. The method would lend itself to growth analysis of single and mixed bacterial cultures.

How to Evaluate Non-Growing Cells-Current Strategies for Determining Antimicrobial Resistance of VBNC Bacteria

Thanks to the achievements in sanitation, hygiene practices, and antibiotics, we have considerably improved in our ongoing battle against pathogenic bacteria. However, with our increasing knowledge about the complex bacterial lifestyles and cycles and their plethora of defense mechanisms, it is clear that the fight is far from over. One of these resistance mechanisms that has received increasing attention is the ability to enter a dormancy state termed viable but non-culturable (VBNC). Bacteria that enter the VBNC state, either through unfavorable environmental conditions or through potentially lethal stress, lose their ability to grow on standard enrichment media, but show a drastically increased tolerance against antimicrobials including antibiotics. The inability to utilize traditional culture-based methods represents a considerable experimental hurdle to investigate their increased antimicrobial resistance and impedes the development and evaluation of effective treatments or interventions against bacteria in the VBNC state. Although experimental approaches were developed to detect and quantify VBNCs, only a few have been utilized for antimicrobial resistance screening and this review aims to provide an overview of possible methodological approaches.

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance

Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.

Comparison of isothermal microcalorimetry and BACTEC MGIT960 for the detection of the metabolic activity of Mycobacterium tuberculosis in sputum samples

INTRODUCTION

This study explores the uses of microcalorimetry to detect Mycobacterium tuberculosis (TB) in sputum. Microcalorimetry measures metabolic heat evolution during cellular proliferation of tuberculosis (TB) and is considered as a possible alternative to conventional diagnostic tools.

OBJECTIVES

To compare the time to detection (TTD) from the BACTEC™ MGIT™ 960 and the calScreener™ calorimetric system.

METHODS

Sixty-four sputa samples were selected from patients with confirmed pulmonary tuberculosis. Those sample were then decontaminated and analysed using calorimetry and BACTEC MGIT 960 system.

RESULTS

The incubation period until detection of M. tuberculosis in the sample was 8·5 ± 3·7 days for the MGIT system and 10·1 ± 4·1 days (mean ± SD) for calorimetry.

CONCLUSIONS

The microincubations in the 48-well format calScreener offers potential for rapid and accurate diagnostic of TB in different samples. Although TTD from calorimetry is still longer than with the MGIT, our findings suggest that several improvements are possible. Still, the instrument is ideal for continuous, real-time analysis of net metabolic heat release of limited sample numbers.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our result emphasizes that with further optimization, calorimetry can become an alternative detection method for tuberculosis.

Personalized Treatment Response Assessment for Rare Childhood Tumors Using Microcalorimetry-Exemplified by Use of Carbonic Anhydrase IX and Aquaporin 1 Inhibitors

We present a novel approach to a personalized therapeutic concept for solid tumors. We illustrate this on a rare childhood tumor for which only a generalized treatment concept exists using carbonic anhydrase IX and aquaporin 1 inhibitors. The use of microcalorimetry as a refined in vitro method for evaluation of drug susceptibility in organotypic slice culture has not previously been established. Rapid microcalorimetric drug response assessment can refine a general treatment concept when it is applied in cases in which tumors do not respond to conventional chemo-radiation treatment. For solid tumors, which do not respond to classical treatment, and especially for rare tumors without an established protocol rapid microcalorimetric drug response testing presents an elegant novel approach to test alternative therapeutic approaches. While improved treatment concepts have led to improved outcome over the past decades, the prognosis of high risk disease is still poor and rethinking of clinical trial design is necessary. A small patient population combined with the necessity to assess experimental therapies for rare solid tumors rather at the time of diagnosis than in relapsed or refractory patients provides great challenges. The possibility to rapidly compare established protocols with innovative therapeutics presents an elegant novel approach to refine and personalize treatment.

Direct determination of anaerobe contributions to the energy metabolism of Trypanosoma cruzi by chip calorimetry

We describe a chip calorimetric technique that allows the investigation of biological material under anoxic conditions in a micro-scale and in real time. Due to the fast oxygen exchange through the sample flow channel wall, the oxygen concentration inside the samples could be switched between atmospheric oxygen partial pressure to an oxygen concentration of 0.5% within less than 2 h. Using this technique, anaerobic processes in the energy metabolism of Trypanosoma cruzi could be studied directly. The comparison of the calorimetric and respirometric response of T. cruzi cells to the treatment with the mitochondrial inhibitors oligomycin and antimycin A and the uncoupler FCCP revealed that the respiration-related heat rate is superimposed by strong anaerobic contributions. Calorimetric measurements under anoxic conditions and with glycolytic inhibitors showed that anaerobic metabolic processes contribute from 30 to 40% to the overall heat production rate. Similar basal and antimycin A heat rates with cells under anoxic conditions indicated that the glycolytic rates are independent of the oxygen concentration which confirms the absence of the "Pasteur effect" in Trypanosomes. Graphical abstract.

Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations

BACKGROUND

Quantification of viable microorganisms is an important step in microbiological research as well as in microbial product formulation to develop biological control products or probiotics. Often, the efficiency of the resulting product is dependent on the microbial cell density and their viability, which may decrease over time. Commonly, the number of viable cells is determined by serial dilution and plating techniques or flow cytometry. In 2017, we developed a mathematical model for isothermal microcalorimetry (IMC) data analysis and showed that the new method allows for a more rapid quantification of viable fresh and freeze-dried anaerobic Lactobacillus reuteri cells than traditional viable count methods.

RESULTS

This study developed the new method further by applying it to well-known aerophilic plant-beneficial microbial species (Pseudomonas brassicacearum, Bacillus amyloliquefaciens subsp. plantarum and Clonostachys rosea) used in biological control products. We utilized IMC to quantify viable cells in microbial pure cultures as well as when coated onto wheat seeds. The results from this study confirmed that thermal viable count methods are more rapid and sensitive than traditional viable count techniques. Most interestingly, a thermal viable count method was able to quantify microbes coated on seeds despite the presence of the natural microbiota of the seeds. Our results also showed that, in contrast to plating techniques for which clustered cells skew the results, IMC does not require single cells for accurate viable counts.

CONCLUSIONS

Thermal viable count methods are novel methods for the rapid quantification of divergent bacterial and fungal species and enhance the speed, sensitivity, and accuracy of routine viable counts of pure cultures and controlled microbiomes such as plant seed coatings.

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.

Advances in online methods for monitoring microbial growth

Understanding the characteristics of microbial growth is of great significance to many fields including in scientific research, the food industry, health care, and agriculture. Many methods have been established to characterize the process of microbial growth. Online and automated methods, in which sample transfer is avoided, are popular because they can facilitate the development of simple, safe, and effective growth monitoring. This review focuses on advances in online monitoring methods over the last decade (2008-2018). We specifically focus on optic- and electrochemistry-based techniques, either through contact measurements or contactless measurement. Strengths and weaknesses of each set of methods are described and we also speculate on forthcoming trends in the field.

Online Monitoring of Bacterial Growth with an Electrical Sensor

Herein, we developed an automatic electrical bacterial growth sensor (EBGS) based on a multichannel capacitively coupled contactless conductivity detector (C⁴D). With the use of the EBGS, up to eight culture samples of E. coli in disposable tubes were online monitored simultaneously in a noninvasive manner. Growth curves with high resolution (on the order of a time scale of seconds) were generated by plotting normalized apparent conductivity value against incubation time. The characteristic data of E. coli growth (e.g., growth rate) obtained here were more accurate than those obtained with optical density and contact conductivity methods. And the correlation coefficient of the regression line ( r) for quantitative determination of viable bacteria was 0.9977. Moreover, it also could be used for other tasks, such as the investigation of toxic/stress effects from chemicals and antimicrobial susceptibility testing. All of these performances required neither auxiliary devices nor additional chemicals and biomaterials. Taken together, this strategy has the advantages of simplicity, accuracy, reproducibility, affordability, versatility, and miniaturization, liberating the users greatly from financial and labor costs.

[New microbiological techniques]

Microbiological diagnostic procedures have changed rapidly in recent years. This is especially true in the field of molecular diagnostics. Classical culture-based techniques are still the gold standard in many areas; however, they are already complemented by automated and also molecular techniques to guarantee faster and better quality results. The most commonly used techniques include real-time polymerase chain reaction (RT-PCR) based systems and nucleic acid hybridization. These procedures are used most powerfully from direct patient samples or in assays to detect the presence of nonculturable or fastidious organisms. Further techniques such as DNA sequencing are not yet used routinely for urological samples and can be considered experimental. However, in conjunction with dropping prices and further technical developments, these techniques promise to be used much more in the near future. Regarding bacterial identification from culture, mass spectrometry (MALDI-TOF MS) has become the technique of choice in recent years especially in Europe. It has tremendously shortened the time to result. This is now going to be extended to antibiotic susceptibility testing. This is of paramount importance in view of ever rising antimicrobial resistance rates. Techniques described in this review offer a faster and better microbiological diagnosis. Such continuous improvements are critical especially in times of cost pressure and rising antimicrobial resistance rates. It is in our interest to provide the best possible care for patients and in this regard a good and effective communication between the laboratory and the clinician is of vital importance.

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

AIMS

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens.

METHODS AND RESULTS

The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection.

CONCLUSIONS

The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.

Rapid Antibiotic Susceptibility Testing of Uropathogenic E. coli by Tracking Submicron Scale Motion of Single Bacterial Cells

To combat antibiotic resistance, a rapid antibiotic susceptibility testing (AST) technology that can identify resistant infections at disease onset is required. Current clinical AST technologies take 1-3 days, which is often too slow for accurate treatment. Here we demonstrate a rapid AST method by tracking sub-μm scale bacterial motion with an optical imaging and tracking technique. We apply the method to clinically relevant bacterial pathogens, Escherichia coli O157: H7 and uropathogenic E. coli (UPEC) loosely tethered to a glass surface. By analyzing dose-dependent sub-μm motion changes in a population of bacterial cells, we obtain the minimum bactericidal concentration within 2 h using human urine samples spiked with UPEC. We validate the AST method using the standard culture-based AST methods. In addition to population studies, the method allows single cell analysis, which can identify subpopulations of resistance strains within a sample.

Current and emerging techniques for antibiotic susceptibility tests

Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.

Integrated Biosensor Assay for Rapid Uropathogen Identification and Phenotypic Antimicrobial Susceptibility Testing

BACKGROUND

Standard diagnosis of urinary tract infection (UTI) via urine culture for pathogen identification (ID) and antimicrobial susceptibility testing (AST) takes 2-3 d. This delay results in empiric treatment and contributes to the misuse of antibiotics and the rise of resistant pathogens. A rapid diagnostic test for UTI may improve patient care and antibiotic stewardship.

OBJECTIVE

To develop and validate an integrated biosensor assay for UTI diagnosis, including pathogen ID and AST, with determination of the minimum inhibitory concentration (MIC) for ciprofloxacin.

DESIGN, SETTING, AND PARTICIPANTS

Urine samples positive for Enterobacteriaceae (n=84) or culture-negative (n=23) were obtained from the Stanford Clinical Microbiology Laboratory between November 2013 and September 2014. Each sample was diluted and cultured for 5h with and without ciprofloxacin, followed by quantitative detection of bacterial 16S rRNA using a single electrochemical biosensor array functionalized with a panel of complementary DNA probes. Pathogen ID was determined using universal bacterial, Enterobacteriaceae (EB), and pathogen-specific probes. Phenotypic AST with ciprofloxacin MIC was determined using an EB probe to measure 16S rRNA levels as a function of bacterial growth.

MEASUREMENTS

Electrochemical signals for pathogen ID at 6 SD over background were considered positive. An MIC signal of 0.4 log units lower than the no-antibiotic control indicated sensitivity. Results were compared to clinical microbiology reports.

RESULTS AND LIMITATIONS

For pathogen ID, the assay had 98.5% sensitivity, 96.6% specificity, 93.0% positive predictive value, and 99.3% negative predictive value. For ciprofloxacin MIC the categorical and essential agreement was 97.6%. Further automation, testing of additional pathogens and antibiotics, and a full prospective study will be necessary for translation to clinical use.

CONCLUSIONS

The integrated biosensor platform achieved microbiological results including MIC comparable to standard culture in a significantly shorter assay time. Further assay automation will allow clinical translation for rapid molecular diagnosis of UTI.

PATIENT SUMMARY

We have developed and validated a biosensor test for rapid diagnosis of urinary tract infections. Clinical translation of this device has the potential to significantly expedite and improve treatment of urinary tract infections.

Susceptibility testing of Mycobacterium abscessus by isothermal microcalorimetry

We evaluated a new method for susceptibility testing of a rapidly growing mycobacterium using real-time measurement of heat (microcalorimetry). MICs of 2 clinical Mycobacterium abscessus isolates were determined by microbroth dilution and E-test. For microcalorimetry, Middlebrook-7H10 agar+10% oleic acid-albumin-dextrose-catalase, containing amikacin, clarithromycin, linezolid, and ciprofloxacin was inoculated with ~10(5)CFU/mL. Heat production was measured at 37°C for 72h. Minimal heat inhibition concentration (MHIC) was defined as the lowest antibiotic concentration inhibiting growth-related heat production. Growth of M. abscessus was detected after a median of 16.5h (range, 8.5-26.9h). Heat detection was proportionally delayed with increasing concentration of antibiotics. MHICs for the tested strains were 16 to >16mg/L for amikacin, >8mg/L for clarithromycin, 4 to >16mg/L for ciprofloxacin, 24 to >32mg/L for linezolid. MHICs were in agreement within two 2-fold dilutions with conventional MICs. Microcalorimetry may accelerate antimicrobial susceptibility testing in mycobacteria and provide additional real-time information on the drug effect.

Isothermal microcalorimetry accurately detects bacteria, tumorous microtissues, and parasitic worms in a label-free well-plate assay

Isothermal microcalorimetry is a label-free assay that allows monitoring of enzymatic and metabolic activities. The technique has strengths, but most instruments have a low throughput, which has limited their use for bioassays. Here, an isothermal microcalorimeter, equipped with a vessel holder similar to a 48-well plate, was used. The increased throughput of this microcalorimeter makes it valuable for biomedical and pharmaceutical applications. Our results show that the sensitivity of the instrument allows the detection of 3 × 10⁴ bacteria per vial. Growth of P. mirabilis in Luria Broth medium was detected between 2 and 9 h with decreasing inoculum. The culture released 2.1J with a maximum thermal power of 76 μW. The growth rate calculated using calorimetric and spectrophotometric data were 0.60 and 0.57 h^–1, respectively. Additional insight on protease activities of P. mirabilis matching the last peak in heat production could be gathered as well. Growth of tumor microtissues releasing a maximum thermal power of 2.1 μW was also monitored and corresponds to a diameter increase of the microtissues from ca. 100 to 428 μm. This opens new research avenues in cancer research, diagnostics, and development of new antitumor drugs. For parasitic worms, the technique allows assessment of parasite survival using motor and metabolic activities even with a single worm.

[Areas of application of isothermal microcalorimetry in urology: an overview]

Isothermal microcalorimetry (IMC) is a nonspecific analytical tool for measurement of heat. With sensitivity in the order of 0.2 μW, IMC can detect very small amounts of heat produced by only a small number of microorganisms or eukaryotic cells. This report is intended to introduce IMC to the urological audience and to give an overview about the past, present and future of this cutting edge technology in the urological context.

Seven hours to adequate antimicrobial therapy in urosepsis using isothermal microcalorimetry

Urosepsis can progress toward severe sepsis, septic shock, and, ultimately, death. Rapid antimicrobial susceptibility testing is crucial to decrease mortality and morbidity. This report shows that isothermal microcalorimetry can provide an antibiogram within 7 h with a sensitivity of 95% and specificity of 91% using Vitek-2 system as a reference.

Next-generation antimicrobial susceptibility testing

Antimicrobial resistance has emerged as one of the most-significant health care problems of the new millennium, and the clinical microbiology laboratory plays a central role in optimizing the therapeutic management of patients with infection. This minireview explores the potential value of innovative methods for antimicrobial susceptibility testing of microorganisms that could provide valuable alternatives to existing methodologies in the very near future.

Rapid clinical bacteriology and its future impact

Clinical microbiology has always been a slowly evolving and conservative science. The sub-field of bacteriology has been and still is dominated for over a century by culture-based technologies. The integration of serological and molecular methodologies during the seventies and eighties of the previous century took place relatively slowly and in a cumbersome fashion. When nucleic acid amplification technologies became available in the early nineties, the predicted "revolution" was again slow but in the end a real paradigm shift did take place. Several of the culture-based technologies were successfully replaced by tests aimed at nucleic acid detection. More recently a second revolution occurred. Mass spectrometry was introduced and broadly accepted as a new diagnostic gold standard for microbial species identification. Apparently, the diagnostic landscape is changing, albeit slowly, and the combination of newly identified infectious etiologies and the availability of innovative technologies has now opened new avenues for modernizing clinical microbiology. However, the improvement of microbial antibiotic susceptibility testing is still lagging behind. In this review we aim to sketch the most recent developments in laboratory-based clinical bacteriology and to provide an overview of emerging novel diagnostic approaches.

Comparison of the roll-plate and sonication techniques in the diagnosis of microbial ureteral stent colonisation: results of the first prospective randomised study

BACKGROUND

Microbial ureteral stent colonisation (MUSC) is one leading risk factor for complications associated with ureteral stent placement. As MUSC remains frequently undetected by standard urine cultures, its definitive diagnosis depends on microbiological investigation of the stent. However, a standard reference laboratory technique for studying MUSC is still lacking.

MATERIALS AND METHODS

A total of 271 ureteral stents removed from 199 consecutive patients were investigated. Urine samples were obtained prior to device removal. Stents were divided into four parts. Each part was separately processed by the microbiology laboratory within 6 h. Ureteral stents were randomly allocated to roll-plate or sonication, respectively, and analysed using standard microbiological techniques. Demographic and clinical data were prospectively collected using a standard case-report form.

RESULTS

Overall, roll-plate showed a higher detection rate of MUSC compared with sonication (35 vs. 28 %, p < 0.05) and urine culture (35 vs. 8 %, p < 0.05). No inferiority of Maki's technique was observed even when stents were stratified according to indwelling time below or above 30 days. Compared with roll-plate, sonication commonly failed to detect Enterococcus spp., coagulase-negative staphylococci (CoNS) and Enterobacteriaceae. In addition, sonication required more hands-on time, more equipment and higher training than roll-plate in the laboratory.

CONCLUSIONS

This prospective randomised study demonstrates the superiority of Maki's roll-plate technique over sonication in the diagnosis of MUSC and that urine culture is less sensitive than both methods. The higher detection rate, simplicity and cost-effectiveness render roll-plate the methodology of choice for routine clinical investigation as well as basic laboratory research.

Growth of mycobacteria in urine determined by isothermal microcalorimetry: implications for urogenital tuberculosis and other mycobacterial infections

OBJECTIVE

To overcome the limitations of current urine-based diagnostic assays of urogenital tuberculosis, we used isothermal microcalorimetry to detect the metabolic activity of Mycobacterium tuberculosis and other commonly neglected pathogenic mycobacteria in urine and accurately determine their growth parameters.

METHODS

A microcalorimeter equipped with 48 channels was used. Detection was accomplished, and growth was monitored for 4 different Mycobacterium species in sterilized and modified urine at 37 °C by measuring metabolic heat flow (μW = μJ/s) as a function of time. These strains were M. smegmatis, M. phlei, M. kansasii, and M. tuberculosis. The data were integrated to perform curve fitting and extract the growth parameter from the raw data.

RESULTS

In sterilized urine, M. smegmatis showed the fastest growth rate (0.089 ± 0.017 [h(-1)]), followed by M. phlei (0.072 ± 0.016 [h(-1)]) and M. kansasii (0.007 ± 0.001 [h(-1)]). No growth of M. tuberculosis was detected in sterilized urine. However, in serum-supplemented urine, growth of M. tuberculosis was observed within 3 weeks at a growth rate of 0.008 ± 0.001 [h(-1)]. Biofilm formation was enhanced in the serum supplemented urine.

CONCLUSION

Isothermal microcalorimetry allows rapid and accurate detection of mycobacterial growth in urine. Given the absence of data on the mycobacterial growth in urine, isothermal microcalorimetry could be used to unravel key aspects of Mycobacterium physiology in the urinary tract and potentially contribute to improvement in the diagnosis and treatment of urogenital tuberculosis.