Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine

Rapid detection of carbapenem resistance among gram-negative organisms directly from positive blood culture bottles

Background

Carbapenemase producing gram-negative bacteria (GNB) has become a huge problem in majority of tertiary care centers worldwide. They are associated with very high morbidity and mortality rates, especially when they cause invasive infections. Therefore, rapid detection of these organisms is very important for prompt and adequate antibiotic therapy as well as infection control. The aim of this study was rapid detection of carbapenemase genes and thereby likely carbapenem resistance, 24-48 hours in advance, directly from the positive-flagged blood culture bottles using CHROMagar and Xpert® Carba-R.

Methods

Aspirate from positively flagged blood culture bottles was subjected to differential centrifuge. All gram-negative bacilli on gram stain from the deposit were processed in Xpert® Carba-R and inoculated on CHROMagar. The presence of genes and growth on CHROMagar was compared with carbapenem resistance on VITEK-2 Compact.

Results

A total of 119 GNB isolates were processed. One or more of the carbapenemase genes were detected in 80 isolates. On comparison with VITEK-2 result, 92 samples showed concordance for carbapenem resistance 48 hours in advance. There was discordance in 21 isolates with 12 major errors and 09 minor errors. The sensitivity of direct Xpert® Carba-R test for rapid detection of carbapenem resistance, 48 hours in advance, was 81.42%. The sensitivity of direct CHROMagar test for accurate detection of carbapenem resistance, 24 hours in advance, was 92.06%.

Conclusion

The ability to detect carbapenem resistance with very high accuracy, 48 hours in advance, helps in appropriate antibiotic therapy and implementation of effective infection control practices.

Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics

Bacterial CRISPR systems provide acquired immunity against invading nucleic acids by activating RNA-programmable RNases and DNases. Cas13a and Cas12a enzymes bound to CRISPR RNA (crRNA) recognize specific nucleic acid targets, initiating cleavage of the targets as well as non-target (trans) nucleic acids. Here, we examine the kinetics of single-turnover target and multi-turnover trans-nuclease activities of both enzymes. High-turnover, non-specific Cas13a trans-RNase activity is coupled to rapid binding of target RNA. By contrast, low-turnover Cas12a trans-nuclease activity is coupled to relatively slow cleavage of target DNA, selective for DNA over RNA, indifferent to base identity, and preferential for single-stranded substrates. Combining multiple crRNA increases detection sensitivity of targets, an approach we use to quantify pathogen DNA in samples from patients suspected of Buruli ulcer disease. Results reveal that these enzymes are kinetically adapted to play distinct roles in bacterial adaptive immunity and show how kinetic analysis can be applied to CRISPR-based diagnostics.

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Cas13a HEPN trans-RNase activation is directly coupled to rapid target RNA binding

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Cas12a RuvC trans-nuclease activity is coupled to slow target DNA cleavage

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Individual crRNA generate widely varying levels of targeted trans-cleavage

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Pooling multiple crRNA allows pathogen quantification without target amplification

Hybrid Complexes of Photosensitizers with Luminescent Nanoparticles: Design of the Structure

Increasing the efficiency of the photodynamic action of the dyes used in photodynamic therapy is crucial in the field of modern biomedicine. There are two main approaches used to increase the efficiency of photosensitizers. The first one is targeted delivery to the object of photodynamic action, while the second one is increasing the absorption capacity of the molecule. Both approaches can be implemented by producing dye-nanoparticle conjugates. In this review, we focus on the features of the latter approach, when nanoparticles act as a light-harvesting agent and nonradiatively transfer the electronic excitation energy to a photosensitizer molecule. We will consider the hybrid photosensitizer-quantum dot complexes with energy transfer occurring according to the inductive-resonance mechanism as an example. The principle consisting in optimizing the design of hybrid complexes is proposed after an analysis of the published data; the parameters affecting the efficiency of energy transfer and the generation of reactive oxygen species in such systems are described.

Theranostics: is it really a revolution? Evaluating a new term in medicine

Theranostics or theragnostics are new terms which start to appear occasionally in publications from 2001 onwards, with a marked increase in references from 2011. In the last few years more than 1100 articles using this term were published each year. In 2011 the journal Theranostics was founded. This paper addresses the question of whether this new term is appropriate. The etymology of the term is analysed. A literature search for definitions of "theranostics" is carried out and the definitions examined as to whether they give grounds for justifying the use of a new term. The differences between diagnostics and therapy are explored. A broad and a narrow definition are found. According to the broad definition theranostics provides a closer relationship between diagnostics and therapy. According to the narrow definition diagnostics and therapy become a single intervention. On closer examination it turns out that in the narrow definition the diagnostics capacities are limited to monitoring. Neither the broad nor the narrow definition actually demonstrate a new concept in medicine. Rather, they describe the well-known practice of medical decision making. In this respect, the new term cannot be justified. The level of diagnostics is new (molecular/nano) but not the relationship between diagnostics and therapy. The term theranostics is misleading as it obscures the existing differences between diagnostics and therapy and wrongly insinuates that steps between diagnostics and therapy could be omitted.

Brain-eating Amoebae Infection: Challenges and Opportunities in Chemotherapy

Pathogenic free-living amoeba are known to cause a devastating infection of the central nervous system and are often referred to as "brain-eating amoebae". The mortality rate of more than 90% and free-living nature of these amoebae is a cause for concern. It is distressing that the mortality rate has remained the same over the past few decades, highlighting the lack of interest by the pharmaceutical industry. With the threat of global warming and increased outdoor activities of public, there is a need for renewed interest in identifying potential anti-amoebic compounds for successful prognosis. Here, we discuss the available chemotherapeutic options and opportunities for potential strategies in the treatment and diagnosis of these life-threatening infections.

Portable devices and mobile instruments for infectious diseases point-of-care testing

INTRODUCTION

Rapidity, simplicity, and portability are highly desirable characteristics of tests and devices designed for performing diagnostics at the point of care (POC), either near patients managed in healthcare facilities or to offer bioanalytical alternatives in external settings. By reducing the turnaround time of the diagnostic cycle, POC diagnostics can reduce the dissemination, morbidity, and mortality of infectious diseases and provide tools to control the global threat of antimicrobial resistance. Areas covered: A literature search of PubMed and Google Scholar, and extensive mining of specialized publications, Internet resources, and manufacturers' websites have been used to organize and write this overview of the challenges and requirements associated with the development of portable sample-to-answer diagnostics, and showcase relevant examples of handheld devices, portable instruments, and less mobile systems which may or could be operated at POC. Expert commentary: Rapid (<1 h) diagnostics can contribute to control infectious diseases and antimicrobial resistant pathogens. Portable devices or instruments enabling sample-to-answer bioanalysis can provide rapid, robust, and reproducible testing at the POC or close from it. Beyond testing, to realize some promises of personalized/precision medicine, it will be critical to connect instruments to healthcare data management systems, to efficiently link decentralized testing results to the electronic medical record of patients.

Infectomics and autoinfectomics: a tool to study infectious-induced autoimmunity

The exposome represents all exogenous and endogenous environmental exposures that begin at preconception and carry on throughout life, while the microbiome reflects the microbial component of the exposome. We recently introduced the concept of infectome and autoinfectome as a means of studying the totality of infections throughout life that participate in the induction as well as the progression of autoimmune diseases in an affected individual. The investigation of the autoinfectome could help us understand why some patients develop more than one autoimmune disease, a phenomenon also known as mosaic of autoimmunity. It could also explain the infectious and autoantibody burden of various autoimmune rheumatic diseases. The close interplay between infections and the immune system should be studied over time, long before the onset of autoaggression and autoimmunity. Tracking down each individual's exposure to infectious agents (as defined by the autoinfectome) would be important for the establishment of a causative link between infection and autoimmunity.

Efficacy of the FilmArray blood culture identification panel for direct molecular diagnosis of infectious diseases from samples other than blood

Molecular-based techniques reduce the delay in diagnosing infectious diseases and therefore contribute to better patient outcomes. We assessed the FilmArray blood culture identification (BCID) panel (Biofire Diagnostics/bioMérieux) directly on clinical specimens other than blood: cerebrospinal, joint, pleural and ascitic fluids, bronchoscopy samples and abscesses. We compared the results from 88 samples obtained by culture-based techniques. The percentage of agreement between the two methods was 75 % with a Cohen κ value of 0.51. Global sensitivity and specificity using the FilmArray BCID panel were 71 and 97 %, respectively. Sensitivity was poorer in samples with a low bacterial load, such as ascitic and pleural fluids (25 %), whereas the sensitivity for abscess samples was high (89 %). These findings suggest that the FilmArray BCID panel could be useful to perform microbiological diagnosis directly from samples other than positive blood cultures, as it offers acceptable sensitivity and moderate agreement with conventional microbiological methods. Nevertheless, cost-benefit studies should be performed before introducing this method into algorithms for microbiological diagnostics.

Tracing environmental markers of autoimmunity: introducing the infectome

We recently introduced the concept of the infectome as a means of studying all infectious factors which contribute to the development of autoimmune disease. It forms the infectious part of the exposome, which collates all environmental factors contributing to the development of disease and studies the sum total of burden which leads to the loss of adaptive mechanisms in the body. These studies complement genome-wide association studies, which establish the genetic predisposition to disease. The infectome is a component which spans the whole life and may begin at the earliest stages right up to the time when the first symptoms manifest, and may thus contribute to the understanding of the pathogenesis of autoimmunity at the prodromal/asymptomatic stages. We provide practical examples and research tools as to how we can investigate disease-specific infectomes, using laboratory approaches employed from projects studying the “immunome” and “microbiome”. It is envisioned that an understanding of the infectome and the environmental factors that affect it will allow for earlier patient-specific intervention by clinicians, through the possible treatment of infectious agents as well as other compounding factors, and hence slowing or preventing disease development.

Emerging technologies for point-of-care genetic testing

In the coming years, genetic test results will be increasingly used as indicators that influence medical decision making. Novel instrumentation that is able to detect relevant mutations in a point-of-care setting is being developed to facilitate this increase, frequently as a spin-off from recent research in the area of biothreat monitoring. This market review will describe the current generation of instrumentation that is most suitable for use in a point-of-care setting; it will also try to identify some of the technologies that will make-up the next generation of instrumentation currently being prepared for the market.

Microfluidics and Raman microscopy: current applications and future challenges

Raman microscopy systems are becoming increasingly widespread and accessible for characterising chemical species. Microfluidic systems are also progressively finding their way into real world applications. Therefore, it is anticipated that the integration of Raman systems with microfluidics will become increasingly attractive and practical. This review aims to provide an overview of Raman microscopy-microfluidics integrated systems for researchers who are actively interested in utilising these tools. The fundamental principles and application strengths of Raman microscopy are discussed in the context of microfluidics. Various configurations of microfluidics that incorporate Raman microscopy methods are presented, with applications highlighted. Data analysis methods are discussed, with a focus on assisting the interpretation of Raman-microfluidics data from complex samples. Finally, possible future directions of Raman-microfluidic systems are presented.

Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery

Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed.

Microbead-based technologies in diagnostic autoantibody detection

BACKGROUND

There is a rapid proliferation of new technologies to identify a spectrum of autoantibodies in medical conditions that range from organ-specific autoimmune diseases to systemic rheumatic diseases. Although many laboratories have adopted high-throughput diagnostic platforms such as enzyme linked immunoassays (ELISA), other technologies such as microbead-based assays are emerging as an alternative diagnostic platform.

OBJECTIVE

To understand the performance and importance of bead based immunoassays in clinical diagnostics and therapeutics.

METHOD

Current literature was reviewed using the PubMed search engine combining keywords of immunoassay and Luminex, as well as a personal literature database. Included in the evaluation and commentary are bead-based assays such as addressable laser bead immunoassays and related magnetic bead assays.

CONCLUSIONS

Comparison with other conventional technologies has indicated that laser microbead immunoassays are reliable, accurate, cost-effective, highly sensitive and have rapid turn around time for results. While there are advantages to this diagnostic platform, there are challenges that must be addressed before wider acceptance or long-term use of this technology platform in the routine clinical diagnostic laboratory.

European quality clearance of new microbiological diagnostics

Laboratory-based diagnosis of infectious diseases is evolving quickly. New technologies and new tests are frequently commercialized, and although guidelines for their proper clinical validation do exist, these are often at the national or regional level. Therefore, the guidelines remain open to interpretation, and are not always applied properly. One of the main questions is how a high level of test quality can be maintained by European legislation. How can product quality be reliably and independently assessed and how can the penetration of sub-standard assays in the European market be managed and hopefully prevented? We here propose that local initiatives, including external quality assessment, public health initiatives, and close multidisciplinary collaborations between manufacturers and academic research institutes, may accelerate decision-making. Vigilance in test quality assessment and legal simplification are important key concepts warranting selective use of those diagnostic tests that comply with the highest quality standards.

Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies

Infectious disease management essentially consists in identifying the microbial cause(s) of an infection, initiating if necessary antimicrobial therapy against microbes, and controlling host reactions to infection. In clinical microbiology, the turnaround time of the diagnostic cycle (>24 hours) often leads to unnecessary suffering and deaths; approaches to relieve this burden include rapid diagnostic procedures and more efficient transmission or interpretation of molecular microbiology results. Although rapid nucleic acid-based diagnostic testing has demonstrated that it can impact on the transmission of hospital-acquired infections, we believe that such life-saving procedures should be performed closer to the patient, in dedicated 24/7 laboratories of healthcare institutions, or ideally at point of care. While personalized medicine generally aims at interrogating the genomic information of a patient, drug metabolism polymorphisms, for example, to guide drug choice and dosage, personalized medicine concepts are applicable in infectious diseases for the (rapid) identification of a disease-causing microbe and determination of its antimicrobial resistance profile, to guide an appropriate antimicrobial treatment for the proper management of the patient. The implementation of point-of-care testing for infectious diseases will require acceptance by medical authorities, new technological and communication platforms, as well as reimbursement practices such that time- and life-saving procedures become available to the largest number of patients.

Angiopoietin-2 levels are associated with retinopathy and predict mortality in Malawian children with cerebral malaria: a retrospective case-control study*

OBJECTIVE

To investigate the relationship among the angiopoietin-Tie-2 system, retinopathy, and mortality in children with cerebral malaria.

DESIGN

A case-control study of retinopathy-positive vs. retinopathy-negative children with clinically defined cerebral malaria.

SETTING

Queen Elizabeth Central Hospital in Blantyre, Malawi.

SUBJECTS

One hundred fifty-five children presenting with severe malaria and meeting a strict definition of clinical cerebral malaria (Blantyre Coma Score ≤ 2, Plasmodium falciparum parasitemia, no other identifiable cause for coma) were included in the study.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Clinical and laboratory parameters were recorded at admission and funduscopic examinations were performed. Admission levels of angiopoietin-1, angiopoietin-2, and a soluble version of their cognate receptor were measured by enzyme-linked immunosorbent assay. We show that angiopoietin-1 levels are decreased and angiopoietin-2 and soluble Tie-2 levels are increased in children with cerebral malaria who had retinopathy compared with those who did not. Angiopoietin-2 and soluble Tie-2 were independent predictors of retinopathy (adjusted odds ratio [95% CI], angiopoietin-2, 4.3 [1.3-14.6], p = .019; soluble Tie-2, 9.7 [2.1-45.8], p = .004). Angiopoietin-2 and soluble Tie-2 were positively correlated with the number of hemorrhages, the severity or retinal whitening, and the extent of capillary whitening observed on funduscopic examination (p < .05 after adjustment for multiple comparisons). Angiopoietin-2 and soluble Tie-2 levels were elevated in children with cerebral malaria who subsequently died and angiopoetin-2 was an independent predictor of death (adjusted odds ratio: 3.9 [1.2-12.7], p = .024). When combined with clinical parameters, angiopoetin-2 improved prediction of mortality using logistic regression models and classification trees.

CONCLUSIONS

These results provide insights into mechanisms of endothelial activation in cerebral malaria and indicate that the angiopoietin-Tie-2 axis is associated with retinopathy and mortality in pediatric cerebral malaria.

Multiphoton microscopy of transdermal quantum dot delivery using two photon polymerization-fabricated polymer microneedles

Due to their ability to serve as fluorophores and drug delivery vehicles, quantum dots are a powerful tool for theranostics-based clinical applications. In this study, microneedle devices for transdermal drug delivery were fabricated by means of two-photon polymerization of an acrylate-based polymer. We examined proliferation of cells on this polymer using neonatal human epidermal keratinocytes and human dermal fibroblasts. The microneedle device was used to inject quantum dots into porcine skin; imaging of the quantum dots was performed using multiphoton microscopy.

Diagnosing infections--current and anticipated technologies for point-of-care diagnostics and home-based testing

In recent years, we have witnessed many transitions in healthcare systems around the globe. For example, population expansion and ageing, and the human immunodeficiency virus (HIV)-AIDS epidemics, have exerted pressure to decentralize the practice of healthcare outside of traditional settings to bring care to those in need. Upstream of patient management, diagnosis is aimed at adequately orienting medical decisions, and considerable efforts have been made to make this process faster and more efficient. However, there are several diseases and medical conditions that may/will benefit from technologies and tests that can be performed closer to the patient, at the point of care or even in the home. In this review, and in light of the paradox that technology and assay developers and healthcare officials must take into consideration for advancing human health in developed and developing countries, we present an overview of rapid diagnosis of infectious diseases at the point of care and of technologies that may contribute to enhancement of the worldwide point-of-care testing market.

Validation of a centrifugal microfluidic sample lysis and homogenization platform for nucleic acid extraction with clinical samples

The applications of microfluidic technologies in medical diagnostics continue to increase, particularly in the field of nucleic acid diagnostics. While much attention has been focused on the development of nucleic acid amplification and detection platforms, sample preparation is often taken for granted or ignored all together. Specifically, little or no consideration is paid to the development of microfluidic systems that efficiently extract nucleic acids from biological samples. Here, a centrifugal microfluidic platform for mechanical sample lysis and homogenization is presented. The system performs sample lysis through a magnetically actuated bead-beating system followed by a centrifugal clarification step. The supernatant is then transferred for extraction using a unique siphon. Several other new microfluidic functions are implemented on this centrifugal platform as well, including sample distribution, a unique hydraulic capillary valve, and self-venting. Additionally, the improved system has features with a small footprint designed specifically for integration with further downstream processing steps. Biological validation of the platform is performed using Bacillus subtilis spores and clinical samples (nasopharyngeal aspirates) for respiratory virus detection. The platform was found to be as efficient as in-tube bead-beating lysis and homogenization for nucleic acid extraction, and capable of processing 4 samples in batch to near PCR-ready products in under 6 min.

Innovations in optical microfluidic technologies for point-of-care diagnostics

Despite a growing focus from the academic community, the field of microfluidics has yet to produce many commercial devices for point-of-care (POC) diagnostics. One of the main reasons for this is the difficulty in producing low-cost, sensitive, and portable optical detection systems. Although electrochemical methods work well for certain applications, optical detection is generally regarded as superior and is the method most widely employed in laboratory clinical chemistry. Conventional optical systems, however, are costly, require careful alignment, and do not translate well to POC devices. Furthermore, many optical detection paradigms such as absorbance and fluorescence suffer at smaller geometries because the optical path length through the sample is shortened. This review examines the innovative techniques which have recently been developed to address these issues. We highlight microfluidic diagnostic systems which demonstrate practical integration of sample preparation, analyte enrichment, and optical detection. We also examine several emerging detection paradigms involving nanoengineered materials which do not suffer from the same miniaturization disadvantages as conventional measurements.

PathogenMip assay: a multiplex pathogen detection assay

The Molecular Inversion Probe (MIP) assay has been previously applied to a large-scale human SNP detection. Here we describe the PathogenMip Assay, a complete protocol for probe production and applied approaches to pathogen detection. We have demonstrated the utility of this assay with an initial set of 24 probes targeting the most clinically relevant HPV genotypes associated with cervical cancer progression. Probe construction was based on a novel, cost-effective, ligase-based protocol. The assay was validated by performing pyrosequencing and Microarray chip detection in parallel experiments. HPV plasmids were used to validate sensitivity and selectivity of the assay. In addition, 20 genomic DNA extracts from primary tumors were genotyped with the PathogenMip Assay results and were in 100% agreement with conventional sequencing using an L1-based HPV genotyping protocol. The PathogenMip Assay is a widely accessible protocol for producing and using highly discriminating probes, with experimentally validated results in pathogen genotyping, which could potentially be applied to the detection and characterization of any microbe.

Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics

Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving the use of custom zinc finger proteins, offers the potential for direct detection of dsDNA in cells, with implications for cell-based diagnostics and therapeutics.