Infectious Disease Diagnostics Research Articles

The GenePOC Platform, a Rational Solution for Extreme Point-of-Care Testing.

Extreme point-of-care (POC) testing for infections, as performed (endured) in low-resource settings, developing countries, tropical areas, or in conditions following emergency crises or natural disasters, must be undertaken under environmental, logistic, and societal conditions which impose a significant deal of stress on local human populations and healthcare providers. For disease diagnostics or management, simple and robust biomedical equipment and reagents are required and needed. This chapter aims to overview some of these stresses (requirements) and intends to describe some of the solutions already engineered at the heart of centripetal (centrifugal) microfluidic platforms such as that of GenePOC Inc. to enable rapid, robust, and reproducible nucleic acid-based diagnostics of infectious diseases, to better control the morbidity and mortality of infections and the expanding threat posed by antimicrobial resistance.

Palm-Sized Device for Point-of-Care Ebola Detection.

We show the utilization of a recently developed cellphone-sized real-time polymerase chain reaction (PCR) device to detect Ebola virus RNA using single-step reverse transcription PCR (RT-PCR). The device was shown to concurrently perform four PCRs, each with a sample volume of 100 nL: one positive control with both Ebola and GAPDH RNA and one negative control. The last two positions were used to measure the GAPDH and the Ebola content of a sample. A comparison of threshold cycles (CT) from the two samples provided relative quantification. The entire process, which consisted of reverse transcription, PCR amplification, and melting curve analysis (MCA), was conducted in less than 37 min. The next step will be integration with a sample preparation unit to form an integrated sample-to-answer system for point-of-care infectious disease diagnostics.

Your Viral Past: A Comprehensive Method for Serological Profiling to Explore the Human Virome.

This is an exciting time of rapid advancement in the field of infectious diseases diagnostics. Traditional methods to diagnose infections have typically been slow and relied on culture for detection of infectious agents. In recent years, however, there has been an explosion in new methodologies and instrumentation to diagnose infections, with a focus on optimization of therapy and antimicrobial stewardship. Newer assays have improved diagnostic testing in several ways, including reductions in turnaround time and improvements in analytical sensitivity and specificity. A major theme in testing for infectious diseases has been multiplexing of diagnostic tests, to allow simultaneous testing for several different pathogens within a single assay. The use of multiplex molecular assays, such as multiplex PCR, is now well established, and tests have been approved by the US Food and Drug Administration for 20 or more pathogens and genetic markers of antibiotic resistance from a single specimen. Although multiplex tests are increasingly common for detecting pathogens, they are much less common for detecting antibodies specific for pathogens. Although antibody responses against pathogens take a week or more to develop after initial infection, they are often long lived, so detecting these responses has the potential to indicate present, recent, or long-past infections. Most immunoassays detect antibodies against a single pathogen. These may be clinically useful, but clinical judgment must be used in the selection of assays, and the cause of an infection may not be detected if the appropriate antibody is not sought. Moreover, it would be cumbersome to use conventional immunoassays to try to determine the cumulative viral infections that a person has encountered over a lifetime. Our improved understanding of the many microorganisms that infect and colonize our bodies has led to a specific interest in the cumulative history of viral infections in humans. This has grown out …

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology.

Clinicogenomics is the exploitation of genome sequence data for diagnostic, therapeutic, and public health purposes. Central to this field is the high-throughput DNA sequencing of genomes and metagenomes. The role of clinicogenomics in infectious disease diagnostics and public health microbiology was the topic of discussion during a recent symposium (session 161) presented at the 115th general meeting of the American Society for Microbiology that was held in New Orleans, LA. What follows is a collection of the most salient and promising aspects from each presentation at the symposium.

A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics.

The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC’s ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC’s performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings.

Recent trends on hydrogel based drug delivery systems for infectious diseases.

Since centuries, the rapid spread and cure of infectious diseases have been a major concern to the progress and survival of humans. These diseases are a global burden and the prominent cause for worldwide deaths and disabilities. Nanomedicine has emerged as the most excellent tool to eradicate and halt their spread. Various nanoformulations (NFs) using advanced nanotechnology are in demand. Recently, hydrogel and nanogel based drug delivery devices have posed new prospects to simulate the natural intelligence of various biological systems. Owing to their unique porous interpenetrating network design, hydrophobic drug incorporation and stimulus sensitivity hydrogels owe excellent potential as targeted drug delivery systems. The present review is an attempt to highlight the recent trends of hydrogel based drug delivery systems for the delivery of therapeutic agents and diagnostics for major infectious diseases including acquired immune deficiency syndrome (AIDS), malaria, tuberculosis, influenza and ebola. Future prospects and challenges are also described.

Diagnostics and Resistance Profiling of Bacterial Pathogens.

Worldwide infectious disease is one of the leading causes of death. Despite improvements in technology and healthcare services, morbidity and mortality due to infections have remained unchanged over the past few decades. The high and increasing rate of antibiotic resistance is further aggravating the situation. Growing resistance hampers the use of conventional antibiotics, and substantial higher mortality rates are reported in patients given ineffective empiric therapy mainly due to resistance to the agents used. These infections cause suffering, incapacity, and death and impose an enormous financial burden on both healthcare systems and on society in general. The accelerating development of multidrug resistance is one of the greatest diagnostic and therapeutic challenges to modern medicine. The lack of new antibiotic options underscores the need for optimization of current diagnostics, therapies, and prevention of the spread of multidrug-resistant organisms. The so-called -omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have yielded large-scale datasets that advanced the search for biomarkers of infectious diseases in the last decade. One can imagine that in the future the implementation of biomarker-driven molecular test systems will transform diagnostics of infectious diseases and will significantly accelerate the identification of the bacterial pathogens at the infected host site. Furthermore, molecular tests based on the identification of markers of antibiotic resistance will dramatically change resistance profiling. The replacement of culturing methods by molecular test systems for early diagnosis will provide the basis not only for a prompt and targeted therapy, but also for a much more effective stewardship of antibiotic agents and a reduction of the spread of multidrug resistance as well as the appearance of new antibiotic resistances.

Chair/bedside diagnosis of oral and respiratory tract infections, and identification of antibiotic resistances for personalised monitoring and treatment.

Global healthcare systems are struggling with the enormous burden associated with infectious diseases, as well as the incessant rise of antimicrobial resistance. In order to adequately address these issues, there is an urgent need for rapid and accurate infectious disease diagnostics. The H2020 project DIAGORAS aims at diagnosing oral and respiratory tract infections using a fully integrated, automated and user-friendly platform for physicians' offices, schools, elderly care units, community settings, etc. Oral diseases (periodontitis, dental caries) will be detected via multiplexed, quantitative analysis of salivary markers (bacterial DNA and host response proteins) for early prevention and personalised monitoring. Respiratory Tract Infections will be diagnosed by means of DNA/RNA differentiation so as to identify their bacterial or viral nature. Together with antibiotic resistance screening on the same platform, a more efficient treatment management is expected at the point-of-care. At the heart of DIAGORAS lies a centrifugal microfluidic platform (LabDisk and associated processing device) integrating all components and assays for a fully automated analysis. The project involves an interface with a clinical algorithm for the comprehensive presentation of results to end-users, thereby increasing the platform's clinical utility. DIAGORAS' performance will be validated at clinical settings and compared with gold standards.

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics.

ABSTRACTNext-generation DNA sequencing (NGS) has progressed enormously over the past decade, transforming genomic analysis and opening up many new opportunities for applications in clinical microbiology laboratories. The impact of NGS on microbiology has been revolutionary, with new microbial genomic sequences being generated daily, leading to the development of large databases of genomes and gene sequences. The ability to analyze microbial communities without culturing organisms has created the ever-growing field of metagenomics and microbiome analysis and has generated significant new insights into the relation between host and microbe. The medical literature contains many examples of how this new technology can be used for infectious disease diagnostics and pathogen analysis. The implementation of NGS in medical practice has been a slow process due to various challenges such as clinical trials, lack of applicable regulatory guidelines, and the adaptation of the technology to the clinical environment. In April 2015, the American Academy of Microbiology (AAM) convened a colloquium to begin to define these issues, and in this document, we present some of the concepts that were generated from these discussions.

Commentary On: Performance of the Cobas(®) Influenza A/B Assay for Rapid Pcr-Based Detection of Influenza Compared to Prodesse ProFlu+ and Viral Culture: Molecular Technology Poised to Change Testing for Influenza at the Point-of-Care.

Commentary On: Performance of the Cobas(®) Influenza A/B Assay for Rapid Pcr-Based Detection of Influenza Compared to Prodesse ProFlu+ and Viral Culture: Molecular Technology Poised to Change Testing for Influenza at the Point-of-Care.

Recent patents in infectious disease diagnostics and treatment

Recent patents in infectious disease diagnostics and treatment

Effective and Efficient Management of Proficiency Testing in a Large Integrated Health System Core Laboratory

NSLIJ Laboratories offer comprehensive laboratory services to the NYC metropolitan community. The Core Laboratory is comprised of 17 different technical departments ranging from routine chemistry and hematology to more esoteric disciplines of infectious disease and molecular diagnostics. As required by regulatory and accrediting agencies such as CLIA, JCAHO, NYS, CAP, and ISO, we currently subscribe to over 200 different proficiency …

T2MR and T2Candida: novel technology for the rapid diagnosis of candidemia and invasive candidiasis.

Candidemia and other forms of invasive candidiasis pose a significant diagnostic challenge. In order to provide the best treatment, it is important to accurately detect the fungal infection and identify the species. Historically, diagnosis of Candida infections depended upon three classical laboratory approaches: microbiologic, immunologic, histopathologic; and now includes new methods such as radiographic techniques, molecular, proteomic and biochemical methods. The T2Candida Panel has introduced a new class of infectious disease diagnostics that can rapidly detect and identify the causative pathogen of sepsis directly from a patient blood sample in a culture-independent manner. This test enables detection of Candida directly from the patient sample, a significant advance for the rapid and accurate diagnosis of invasive candidiasis.

Management of Work and Procedure for the Laboratory Diagnostics of Infectious Diseases during the Winter XXII Olympics and XI Paralympics, 2014

Analyzed is the management system for laboratory diagnostics of infectious diseases during the XXII Olympics and XI Paralympics, 2014 in Sochi. Reviewed is piece of work, executed in the pre-Olympic period as regards provision of laboratory facilities deployed for clinical material investigation, development of normative and regulatory documentation which considers peculiarities of the situation, identification of diagnostic capacities of the laboratories, and forecasting of the probable volume of laboratory studies by reference to various groups of infections. Put forward is the procedure for arrangement of work at the different stages of laboratory diagnostics, cooperation and response in case of emergency situation in the sphere of sanitary-epidemiological welfare of the population. Discussed is the role of geo-information system and current means of monitoring over epidemiological situation in the participating states and in the region of the Olympics in laboratory support organization.

Printed Flexible Plastic Microchip for Viral Load Measurement through Quantitative Detection of Viruses in Plasma and Saliva.

We report a biosensing platform for viral load measurement through electrical sensing of viruses on a flexible plastic microchip with printed electrodes. Point-of-care (POC) viral load measurement is of paramount importance with significant impact on a broad range of applications, including infectious disease diagnostics and treatment monitoring specifically in resource-constrained settings. Here, we present a broadly applicable and inexpensive biosensing technology for accurate quantification of bioagents, including viruses in biological samples, such as plasma and artificial saliva, at clinically relevant concentrations. Our microchip fabrication is simple and mass-producible as we print microelectrodes on flexible plastic substrates using conductive inks. We evaluated the microchip technology by detecting and quantifying multiple Human Immunodeficiency Virus (HIV) subtypes (A, B, C, D, E, G, and panel), Epstein-Barr Virus (EBV), and Kaposi’s Sarcoma-associated Herpes Virus (KSHV) in a fingerprick volume (50 µL) of PBS, plasma, and artificial saliva samples for a broad range of virus concentrations between 102 copies/mL and 107 copies/mL. We have also evaluated the microchip platform with discarded, de-identified HIV-infected patient samples by comparing our microchip viral load measurement results with reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) as the gold standard method using Bland-Altman Analysis.

Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics.

Despite the great promise of nucleic acid aptamers in the areas of diagnostics and therapeutics for their facile in vitro development, lack of immunogenicity and other desirable properties, few truly successful aptamer-based products exist in the clinical or other markets. Core reasons for these commercial deficiencies probably stem from industrial commitment to antibodies including a huge financial investment in humanized monoclonal antibodies and a general ignorance about aptamers and their performance among the research and development community. Given the early failures of some strong commercial efforts to gain government approval and bring aptamer-based products to market, it may seem that aptamers are doomed to take a backseat to antibodies forever. However, the key advantages of aptamers over antibodies coupled with niche market needs that only aptamers can fill and more recent published data still point to a bright commercial future for aptamers in areas such as infectious disease and cancer diagnostics and therapeutics. As more researchers and entrepreneurs become familiar with aptamers, it seems inevitable that aptamers will at least be considered for expanded roles in diagnostics and therapeutics. This review also examines new aptamer modifications and attempts to predict new aptamer applications that could revolutionize biomedical technology in the future and lead to marketed products.

A Book Review on: Sherris Medical Microbiology – International Edition, 6th Edition

A Book Review on: Sherris Medical Microbiology – International Edition, 6th Edition

Human Urine Is Not Sterile - Shift of Paradigm

Objective: Until recently the generally accepted paradigm implied that urine of healthy people is sterile. In the present study, urine of healthy subjects was investigated by extended bacteriological methods. Material and Methods: Three midstream urine samples from 52 healthy subjects each (24 females, 28 males; 18-25 years of age) were investigated by an extended set of culture media for identification of facultative aerobic (FAB) and nonclostridial anaerobic bacteria (NCAB). Ward's method (Euclidean distance) was used for similarity analysis. Results: The bacterial count of FAB in urine was usually low (≤10² colony-forming units/ml) in both groups. In contrast, the bacterial count of NCAB was higher (≥10³ colony-forming units/ml), at least in some species, with significant differences between genders. The average number of bacterial species found was 5.8 in female and 7.1 in male urine. Half of the females were assigned to a specific ‘female' microbial spectrum, different from that of males. In the mixed-gender clusters, the males showed a greater similarity among themselves. Conclusions: As also shown by other investigators, urine of healthy people is normally not sterile. The role of the routinely not cultivated bacteria in healthy and diseased subjects needs to be established. It may alter the diagnostics of infectious and inflammatory diseases of the urogenital tract.

Molecular Diagnostics of Infectious Diseases, 3rd ed.

Edited by Harald H. Kessler, 237 pages. Berlin/Boston: Walter de Gruyter GmbH. $126.00. ISBN: 978-3-11-032788-5. This book is a useful resource for quickly reading about a certain topic or relevant pathogen in infectious disease molecular diagnostics. It is not encyclopedic in covering all details; rather, it gives an overview of important issues in the field, which makes it very readable and able to serve well as a starting point or a refresher. The book is organized into 13 chapters and follows a logical order, with the first several chapters covering issues of specimen collection (in outline format, listed by pathogen), specimen integrity and stability, quality assurance and quality control, and nucleic-acid extraction techniques. Regulatory issues are mostly discussed in the context of European and international guidelines (because most of the contributing authors are from Europe); still, regulations set by the United States Food and Drug Administration are also mentioned. Different amplification and detection methods are discussed in one chapter, which are covered thoroughly enough for …

Rapid ultrasonic isothermal amplification of DNA with multiplexed melting analysis – applications in the clinical diagnosis of sexually transmitted diseases.

We describe a nucleic acid testing (NAT) platform for infectious disease diagnostics at the point-of-care, using surface acoustic waves (SAW) to perform a multiplexed loop-mediated isothermal amplification (LAMP) test for sexually transmitted diseases. The ultrasonic actuation not only enables faster NAT reactions but also provides a route towards integrating low-cost, low-power molecular diagnostics into disposable sensors.