Principles of molecular microbiology testing methods

The Development of a Specific Nanofiber Bioreceptor for Detection of Escherichia coli and Staphylococcus aureus from Air

Polluted air and the presence of numerous airborne pathogens affect our daily lives. The sensitive and fast detection of pollutants and pathogens is crucial for environmental monitoring and effective medical diagnostics. Compared to conventional detection methods (PCR, ELISA, metabolic tests, etc.), biosensors bring a very attractive possibility to detect chemicals and organic particles with the mentioned reliability and sensitivity in real time. Moreover, by integrating nanomaterials into the biosensor structure, it is possible to increase the sensitivity and specificity of the device significantly. However, air quality monitoring could be more problematic even with such devices. The greatest challenge with conservative and sensing methods for detecting organic matter such as bacteria is the need to use liquid samples, which slows down the detection procedure and makes it more difficult. In this work, we present the development of a polyacrylonitrile nanofiber bioreceptor functionalized with antibodies against bacterial antigens for the specific interception of bacterial cells directly from the air. We tested the presented novel nanofiber bioreceptor using a unique air filtration system we had previously created. The prepared antibody-functionalized nanofiber membranes for air filtration and pathogen detection (with model organisms E. coli and S. aureus) show a statistically significant increase in bacterial interception compared to unmodified nanofibers. Creating such a bioreceptor could lead to the development of an inexpensive, fast, sensitive, and incredibly selective bionanosensor for detecting bacterial polluted air in commercial premises or medical facilities.

Portable Pathogen Diagnostics Using Microfluidic Cartridges Made from Continuous Liquid Interface Production Additive Manufacturing

Biomedical diagnostics based on microfluidic devices have the potential to significantly benefit human health; however, the manufacturing of microfluidic devices is a key limitation to their widespread adoption. Outbreaks of infectious disease continue to demonstrate the need for simple, sensitive, and translatable tests for point-of-care use. Additive manufacturing (AM) is an attractive alternative to conventional approaches for microfluidic device manufacturing based on injection molding; however, there is a need for development and validation of new AM process capabilities and materials that are compatible with microfluidic diagnostics. In this paper, we demonstrate the development and characterization of AM cartridges using continuous liquid interface production (CLIP) and investigate process characteristics and capabilities of the AM microfluidic device manufacturing. We find that CLIP accurately produces microfluidic channels as small as 400 μm and that it is possible to routinely produce fluid channels as small as 100 μm with high repeatability. We also developed a loop-mediated isothermal amplification (LAMP) assay for detection of E. coli from whole blood directly on the CLIP-based AM microfluidic cartridges, with a 50 cfu/μL limit of detection, validating the use of CLIP processes and materials for pathogen detection. The portable diagnostic platform presented in this paper could be used to investigate and validate other AM processes for microfluidic diagnostics and could be an important component of scaling up the diagnostics for current and future infectious diseases and pandemics.

Culturomic and quantitative real-time-polymerase chain reaction analyses for early contamination of abutments with different surfaces: A randomized clinical trial

BACKGROUND

Rough and/or plasma-activated abutments seem to be able to increase soft tissue adhesion and stability; however, limited evidence is available about bacterial contamination differences.

PURPOSE

The aim was to investigate the oral microbiota on four dental abutments with different surfaces by quantitative real-time polymerase chain reaction (qRT-PCR) and culturomic approach.

METHODS

Forty patients needing a single implant rehabilitation were involved in the study. Forty healing abutments, especially designed for the study, were divided into four groups according to the surface topography (1. machined [MAC], 2. machined plasma of argon treated [plasmaMAC], 3. ultrathin threaded microsurface [UTM], 4. UTM plasma of argon treated [Plasma UTM]). Random assignment was performed according to predefined randomization tables. All patients underwent surgical intervention for implant and contextual healing abutment positioning. After 2 months of healing, a sterile cotton swab was used for microbiological sampling for culturomics, while sterile paper points inserted into the sulcus were used for qRT-PCR.

RESULTS

At the end of the study, 36 patients completed all procedures and a total of 36 abutments (9 per group) were analyzed. qRT-PCR retrieved data for 23 bacterial species whereas culturomics revealed the presence of 74 different bacteria, most of them not routinely included into oral cavity microbiological kits of analysis or never found before in the oral microenvironment. No statistically significant differences emerged analyzing the four different surfaces (p = 0.053). On the contrary, higher total and specific bacterial counts were detected in the plasma-treated surfaces compared to the untreated ones (p = 0.021).

CONCLUSIONS

Abutments with different topographies and surface treatments resulted contaminated by similar oral bacterial flora. Abutments with moderately rough surface were not associated with a greater bacterial adhesion compared to machined ones. Conversely, more bacteria were found around plasma-treated abutments. Furthermore, data reported suggested to include new species not previously sought in the routine analyses of the oral bacterial microflora.

Pathologic Features of Infectious Gastritis

This manuscript presents a review of infectious causes of gastritis aimed at the practicing anatomic pathologist. We shall highlight unique histologic findings and clinical attributes that will assist those analyzing endoscopically obtained mucosal biopsies of the stomach or resection specimens.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

Lung Infections

A review of pulmonary infections of all types with diagnostic and morphological features.

Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium

Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

Emperor's new clothes: Is particle disease really infected particle disease?

Aseptic loosening remains the most significant long-term complication of total hip replacement. The current paradigm points to an inflammatory response to wear particles as its main trigger. Recently, there have been increasing numbers of positive bacterial isolates reported among patients with clinically absent infection. This paper reviews existing evidence on possible involvement of bacteria and microbial-associated molecular patterns in the pathology of so-called "aseptic loosening." © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1497-1504, 2016.

Diagnosis of Neisseria gonorrhoeae using molecular beacon

Neisseria gonorrhoeae is an important sexually transmitted diseases (STD) causing pathogen worldwide. Due to absence of an affordable diagnostic assay, routine screening of gonococcal infection becomes impossible in developing countries where infection rates are maximum. Treatment is given on the basis of symptoms alone which leads to spread of infection. Thus, development of a rapid, sensitive, specific, and PCR based visual diagnostic assay suitable for developing countries, required for better disease management, is aimed at in present study. Endocervical swabs were collected from patients visiting gynecology department of various hospitals in Delhi. In-house PCR based assay was developed and modified to visual assay using molecular beacon for end-point detection. It was evaluated against Roche AMPLICOR NG kit and rmp gene. Specificity of beacon was confirmed by competition experiments. Diagnostic test was 98.21% specific and 99.59% sensitive whereas negative and positive predicted value were 99.40% and 98.78%, respectively. We also observed that twice the concentration (2X) of premix was stable at 4°C for 4 months and dry swab samples gave concordant results with that of wet swabs. These features make the test best suitable for routine diagnosis of genital infections in developing countries.

Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR

An alternative to qPCR was developed for nucleic acid assays, involving signal rather than target amplification. The new technology, Restriction Cascade Exponential Amplification (RCEA), relies on specific cleavage of probe-target hybrids by restriction endonucleases (REase). Two mutant REases for amplification (Ramp), S17C BamHI and K249C EcoRI, were conjugated to oligonucleotides, and immobilized on a solid surface. The signal generation was based on: (i) hybridization of a target DNA to a Ramp-oligonucleotide probe conjugate, followed by (ii) specific cleavage of the probe-target hybrid using a non-immobilized recognition REase. The amount of Ramp released into solution upon cleavage was proportionate to the DNA target amount. Signal amplification was achieved through catalysis, by the free Ramp, of a restriction cascade containing additional oligonucleotide-conjugated Ramp and horseradish peroxidase (HRP). Colorimetric quantification of free HRP indicated that the RCEA achieved a detection limit of 10 aM (10⁻¹⁷ M) target concentration, or approximately 200 molecules, comparable to the sensitivity of qPCR-based assays. The RCEA assay had high specificity, it was insensitive to non-specific binding, and detected target sequences in the presence of foreign DNA. RCEA is an inexpensive isothermal assay that allows coupling of the restriction cascade signal amplification with any DNA target of interest.

Acid-fast Smear and Histopathology Results Provide Guidance for the Appropriate Use of Broad-Range Polymerase Chain Reaction and Sequencing for Mycobacteria

Context

New molecular diagnostic tests are attractive because of the potential they hold for improving diagnostics in microbiology. The value of these tests, which is often assumed, should be investigated to determine the best use of these potentially powerful tools.

Objective

To investigate the usefulness of broad-range polymerase chain reaction (PCR), followed by sequencing, in mycobacterial infections.

Design

We reviewed the test performance of acid-fast bacilli (AFB) PCR and traditional diagnostic methods (histopathology, AFB smear, and culture). We assessed the diagnostic effect and cost of the unrestricted ordering of broad-range PCR for the detection and identification of mycobacteria in clinical specimens.

Results

The AFB PCR was less sensitive than culture and histopathology and was less specific than culture, AFB smear, and histopathology. During 18 months, $93 063 was spent on 183 patient specimens for broad-range PCR and DNA sequencing for mycobacteria to confirm one culture-proven Mycobacterium tuberculosis infection that was also known to be positive by AFB smear and histopathology. In this cohort, there was a false-negative AFB PCR for M tuberculosis and a false-positive AFB PCR for Mycobacterium lentiflavum.

Conclusion

Testing of AFB smear–negative specimens from patients without an inflammatory response supportive of a mycobacterial infection is costly and has not been proven to improve patient care. Traditional diagnostics (histopathology, AFB smear, and culture) should remain the primary methods for the detection of mycobacteria in clinical specimens.

Prevalence of suspected tuberculosis in the Kingdom of Saudi Arabia according to conventional and molecular methods

Background:

Although the prevalence of suspected tuberculosis (TB) in the Kingdom of Saudi Arabia remains high, there has been a modest decrease in recent years. In this multi-center cross-sectional study, the prevalence of TB was determined by various techniques with the aim of identifying differences and indicating where there is uniformity in findings.

Materials and Methods:

A total of 3404 samples were collected from Saudi TB patients from different regions in Saudi Arabia: Riyadh, Dammam, Jeddah, Madinah, Hail, Qassim, Jazan, and Taif. Different techniques including Ziehl–Neelsen (ZN), Mycobacteria growth indicator tube (MGiT), Lowenstein–Jensen (LJ), and polymerase chain reaction (PCR) were used to screen for the presence of Mycobacterium tuberculosis (MTB).

Results:

ZN stain showed that Riyadh and Dammam had the highest prevalence of MTB with 22% and 21%, respectively, while prevalence was lowest in Jazan and Hail with an incidence of 2% and 3%, respectively. MGiT culture showed that Riyadh, Dammam, and Jeddah had the highest prevalence with a rate of 26%, 22%, and 22%, respectively. LJ culture showed the highest prevalence in Riyadh and Dammam with 22% and 21%, respectively. Of all the techniques, the highest detection rate was by PCR which was 10.46% while ZN stain technique was 6.64%, for MGiT culture it was 8.34%, and for LJ culture it was 7.7%.

Conclusion:

This study is the first in which different methods have been used for detection in the various regions of Saudi Arabia. Collected data are important not only for patients and physicians but for future epidemiological studies to monitor the spread of MTB infection in Saudi Arabia.

A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus

PCR multiplexing has proven to be challenging, and thus has provided limited means for pathogen genotyping. We developed a new approach for analysis of PCR amplicons based on restriction endonuclease digestion. The first stage of the restriction enzyme assay is hybridization of a target DNA to immobilized complementary oligonucleotide probes that carry a molecular marker, horseradish peroxidase (HRP). At the second stage, a target-specific restriction enzyme is added, cleaving the target-probe duplex at the corresponding restriction site and releasing the HRP marker into solution, where it is quantified colorimetrically. The assay was tested for detection of the methicillin-resistant Staphylococcus aureus (MRSA) pathogen, using the mecA gene as a target. Calibration curves indicated that the limit of detection for both target oligonucleotide and PCR amplicon was approximately 1 nM. Sequences of target oligonucleotides were altered to demonstrate that (i) any mutation of the restriction site reduced the signal to zero; (ii) double and triple point mutations of sequences flanking the restriction site reduced restriction to 50–80% of the positive control; and (iii) a minimum of a 16-bp target-probe dsDNA hybrid was required for significant cleavage. Further experiments showed that the assay could detect the mecA amplicon from an unpurified PCR mixture with detection limits similar to those with standard fluorescence-based qPCR. Furthermore, addition of a large excess of heterologous genomic DNA did not affect amplicon detection. Specificity of the assay is very high because it involves two biorecognition steps. The proposed assay is low-cost and can be completed in less than 1 hour. Thus, we have demonstrated an efficient new approach for pathogen detection and amplicon genotyping in conjunction with various end-point and qPCR applications. The restriction enzyme assay may also be used for parallel analysis of multiple different amplicons from the same unpurified mixture in broad-range PCR applications.

Evolving gene targets and technology in influenza detection

Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past two decades due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, have benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods has lagged somewhat behind. The purpose of this chapter is to review and discuss the interpretation and relevance of results produced by these advanced molecular techniques. Moreover, this chapter will address the “myths” of NAATs, as these myths can markedly influence the interpretation and relevance of these results.

Assessment of Aspergillus fumigatus in guinea pig bronchoalveolar lavages and pulmonary tissue by culture and realtime polymerase chain reaction studies

In this study we pursued a diagnostic target in Aspergillus fumigatus (AF) by using qualitative Realtime PCR combined with proprietary DNA primers and a hydrolysis probe specific for this fungal target. Qualitative Realtime PCR is a diagnostic tool that utilizes Realtime PCR technology and detects the presence or absence target specific DNA within a predetermined detection range. Respiratory tissue and fluids from experimentally infected guinea pigs were tested by extracting DNA from the samples which were amplified and detected using AF specific DNA primers and probe. This study included qualitative evaluations of all specimens for the presence of the DNA of AF. The findings in the tissues after AF infection were compared to the numbers of spores in aerosolized samples used to inoculate the animals. Results demonstrated that the specific probe and primer set could detect the presence or absence of AF DNA in the sample. The qualitative detection limit of the assay ranged from 6 × 10⁴ copies to 6 copies. Since blood cultures are rarely positive for Aspergillosis, our data indicate that qualitative Realtime PCR, in combination with the appropriate DNA primers and probe can serve as an effective diagnostic tool in the early detection of fungal infections.

A fatal case of neonatal adenovirus infection

Adenovirus can produce severe disease and even death in the immunocompromised neonate. Symptoms of adenovirus infection are similar to those seen with bacterial infections in neonates, making early recognition and diagnosis difficult. Consideration of adenovirus as a causative agent is important to early diagnosis. Currently available culture techniques, particularly the shell vial culture technique, make more rapid identification of adenovirus infection possible. Early identification and treatment are necessary to improve patient outcomes and prevent the spread of infection to other neonates. Available agents for the treatment of adenovirus have had mixed results, yet their use is preferable to nontreatment of critical patients. This article presents the case of a preterm infant who became fatally ill from disseminated adenoviral infection.

Diagnosing emerging and reemerging infectious diseases: the pivotal role of the pathologist

CONTEXT

Molecular diagnostics continues to evolve very rapidly, and its impact in the diagnosis of infectious diseases is undeniable. Molecular tools have played a pivotal role in discovering and characterizing several emerging infectious agents and have now become the gold standard for the diagnosis of infectious diseases caused by fastidious or uncultivable agents. Multiple challenges still remain for the widespread use of cost-effective, validated, and commercially available molecular tools. Automated instruments capable of sample processing and multiplex nucleic acid amplification and postamplification analysis have already been approved by the US Food and Drug Administration (FDA) for use in the clinical setting. Nanobiotechnology is beginning to impact laboratory diagnostics in the clinical setting.

OBJECTIVE

To address current nucleic acid techniques used in the clinical laboratory for diagnosis of infectious diseases. FDA-approved tests are listed, as well as molecular techniques (amplification and postamplification analysis). A comprehensive list of emerging pathogens during the last 4 decades is also presented. Biosurveillance systems are discussed in the context of molecular tools. The rapidly evolving field of nanobiotechnology is briefly addressed.

DATA SOURCES

Original publications, major reviews, and book chapters were used to present a comprehensive, yet short, review of molecular diagnostics in infectious diseases.

CONCLUSIONS

We will continue to witness an exponential growth of molecular techniques used for the initial diagnosis of infectious diseases. Molecular tools will also continue to have an impact on disease prognosis and response to therapeutic interventions. Automation, multiplexing, and miniaturization will continue to be driving forces in the development of new instruments.

Panniculitis attributable to Mycobacterium goodii in an immunocompetent dog in Georgia

CASE DESCRIPTION

A 5-year-old 38.3-kg (84.5-lb) mixed-breed dog was examined because of acute onset of lethargy and anorexia. Four days later, a raised, firm, warm 15 × 10-cm lesion was detected in the right caudal paralumbar area.

CLINICAL FINDINGS

Cephalexin treatment yielded a poor response. Formalin-fixed tissue and fluid samples from the cystic areas of the lesion were submitted for cytologic and histologic examinations, routine bacterial and mycobacterial culture, and genus identification and 16S partial sequencing via PCR assays. Cytologic examination revealed chronic pyogranulomatous inflammation. Histologic examination by use of routine, Giemsa, silver, acid-fast, and modified acid-fast stains revealed multifocal nodular granulomatous panniculitis without identifiable organisms. Mycobacteria were initially identified via PCR assay and mycobacterial culture within 3 days. Mycobaterium goodii was speciated by use of partial 16S RNA sequence analysis.

TREATMENT AND OUTCOME

The lesion resolved after long-term treatment with a combination of rifampin and clarithromycin and insertion of a Penrose drain. There has been no recurrence of the condition.

CLINICAL RELEVANCE

M goodii is an environmental rapidly growing mycobacterium and is a zoonotic pathogen. Infections have not been previously reported in domestic animals in North America, although there are rare reports of infection in humans associated with surgery, especially surgical implants. Domestic animals are a potential sentinel for this non-tuberculous mycobacterial infection in humans, although lack of speciation in infections of domestic animals likely underestimates the potential public health importance of this pathogenic organism. Current microbiological molecular methods allow for a rapid and inexpensive diagnosis.

Molecular Diagnostics and Comparative Genomics in Clinical Microbiology

Initially, the availability of molecular diagnostics was considered a panacea, but replacement of conventional tests for detection and identification of microorganisms by molecular procedures eventually gathered momentum. This chapter describes current state-of-the-art molecular diagnostics and comparative genomics in medical microbiology to provide an understanding of infectious disease over the coming years. Nucleic acid-based tests are being introduced with increasing speed into routine clinical microbiology laboratories. Some of the problems remaining to be solved prior to general acceptance of nucleic acid-mediated detection and identification of microbial pathogens are reviewed. Historic objections are slowly being taken apart, and an accelerated introduction of molecular diagnostics is being pursued in many cases. Clear improvement in clinical testing is achieved by introducing molecular tests. Therefore, swift introduction of such tests into clinical practice is important to be pursued. Several PCR tests show increased sensitivity, excellent specificity, and cost effectiveness highlighting the success of the novel applications in the field of bacterial infections. Finally, some of the problems remaining to be solved prior to general acceptation of nucleic acid-mediated detection and identification of microbial pathogens are also reviewed.

Mycotoxin detection in human samples from patients exposed to environmental molds

The goal of this study was to determine if selected mycotoxins (trichothecenes, aflatoxins, and ochratoxins) could be extracted and identified in human tissue and body fluids from patients exposed to toxin producing molds in their environment. Human urine and methanol extracted tissues and sputum were examined. Trichothecenes were tested using competitive ELISA techniques. Aflatoxins B1, B2, G1, and G2, and ochratoxin A were tested by using immunoaffinity columns and fluorometry. Test sensitivity and specificity were determined. Levels of detection for the various mycotoxins varied from 0.2 ppb for trichothecenes, 1.0 ppb for aflatoxins, and 2.0 ppb for ochratoxins. Trichothecene levels varied in urine, sputum, and tissue biopsies (lung, liver, brain) from undetectable (<0.2 ppb) to levels up to 18 ppb. Aflatoxin levels from the same types of tissues varied from 1.0 to 5.0 ppb. Ochratoxins isolated in the same type of tissues varied from 2.0 ppb to > 10.0 ppb. Negative control patients had no detectable mycotoxins in their tissues or fluids. These data show that mycotoxins can be detected in body fluids and human tissue from patients exposed to mycotoxin producing molds in the environment, and demonstrate which human tissues or fluids are the most likely to yield positive results.

Principles and applications of polymerase chain reaction in medical diagnostic fields: a review

Recent developments in molecular methods have revolutionized the detection and characterization of microorganisms in a broad range of medical diagnostic fields, including virology, mycology, parasitology, microbiology and dentistry. Among these methods, Polymerase Chain Reaction (PCR) has generated great benefits and allowed scientific advancements. PCR is an excellent technique for the rapid detection of pathogens, including those difficult to culture. Along with conventional PCR techniques, Real-Time PCR has emerged as a technological innovation and is playing an ever-increasing role in clinical diagnostics and research laboratories. Due to its capacity to generate both qualitative and quantitative results, Real-Time PCR is considered a fast and accurate platform. The aim of the present literature review is to explore the clinical usefulness and potential of both conventional PCR and Real-Time PCR assays in diverse medical fields, addressing its main uses and advances.

Quantitative real-time polymerase chain reaction for evaluating DNAemia due to cytomegalovirus, Epstein-Barr virus, and BK virus in solid-organ transplant recipients

Testing for cytomegalovirus-, Epstein-Barr virus-, and BK virus-specific gene targets in specimens from solid-organ transplant recipients for DNA by quantitative real-time polymerase chain reaction has been implemented in many diagnostic facilities. This technology provides rapid, accurate, and reproducible results for early detection, monitoring, and medical management of patients with these infections. Because these assays are becoming commonly used in clinical practice, the technical variables associated with specimen processing (e.g., nucleic acid extraction, gene target, and result reporting), amplification, and unique patient characteristics (e.g., age, sex, underlying diseases, immune status, and immunosuppressive regimens received) are factors that may influence the understanding and interpretation of test results. We emphasize the need for standardization of existing variables through parallel comparative and proficiency testing, uniform units for expressing results, to provide for clinical correlation with the results of these molecular assays.

Clinical Applications of the Polymerase Chain Reaction: An Update

The development, in the past decade, of nucleic acid amplification and detection methods is useful in the study of the etiopathogenesis, diagnosis, and management of a variety of clinical (including rheumatologic) disorders. An association between infectious agents and rheumatic disorders has been established through such methods as polymerase chain reaction. This article describes the principles behind polymerase chain reaction-based diagnosis and updates its clinical applications. It is beyond the scope of this article, however, to describe other nucleic acid amplification methods or to include a complete list of all polymerase chain reaction assays that have been developed. Other recent reviews offer additional details.

Pathogen Detection in the Genomic Era

In the 21st century, one of the greatest challenges to public health and clinical microbiologists is the rapid detection and identification of emerging and reemerging pathogens. Complex factors such as genetic variation in the host and pathogen, environmental changes, population pressures, and global travel can all influence the emergence of infectious diseases. The SARS epidemic of 2003 highlighted the potential of an emerging pathogen to spread globally in a very short time frame (Peruski and Peruski, 2003). The diagnostics of such infectious diseases has been greatly affected in the past 20 years. No longer is cultivation and microscopy the only means of detecting infectious agents. With the introduction of molecular diagnostics, the ability to detect minute amounts of microbial nucleic acids in clinical specimens has revolutionized clinical microbiology. In particular, the utility of PCR allows the detection and quantitation of specific agents in a matter of hours. PCR sequencing of specific segments of nucleic acid allows for the determination of specific drug resistance that now aids in guiding viral therapies.

Survey of the large-animal diplomates of the American College of Veterinary Internal Medicine regarding knowledge and clinical use of polymerase chain reaction: implications for veterinary education

A questionnaire was developed to document the knowledge base of large-animal diplomates of the American College of Veterinary Internal Medicine (ACVIM) regarding polymerase chain reaction (PCR) technology and to identify the common use of this technology in equine practice. Ninety-three of the 278 mailed questionnaires were returned, for an overall response rate of 33.4%. Ninety respondents (99%) reported being familiar with the general principles of nucleic acid probe technology; however, only 52 (57%) knew the difference between conventional (traditional) and real-time (second-generation) PCR. The majority of the respondents (88%) emphasized the need for continuing education on molecular diagnostics. Eighty-four (92%) of the respondents regularly use PCR (conventional and/or real-time) for the detection of equine pathogens, and 80 (88%) commonly submit their samples to university/state veterinary laboratories. Blood, nasal swabs, and feces are the three equine specimens most commonly submitted for PCR analysis of Streptococcus equi, Lawsonia intracellularis, Neorickettsia risticii, equine herpesvirus 1/4, Rhodococcus equi, Sarcocystis neurona, and equine influenza virus. Diplomates reported costs associated with molecular diagnostics and unreliability of PCR as the most common limitations of PCR. Didactic training in veterinary curricula and during continuing-education opportunities continues to be necessary to produce veterinarians who have an understanding of the clinical applications of molecular diagnostics.

Sporadic amyotrophic lateral sclerosis: a hypothesis of persistent (non-lytic) enteroviral infection

Because of recently reported reverse transcriptase polymerase chain reaction evidence of enterovirus in sporadic amyotrophic lateral sclerosis (SALS) and because of newly available anti-enteroviral drugs binding enteroviral capsids, it is reasonable to re-formulate an enteroviral hypothesis of SALS using recent advances in molecular virology. Viral persistence is non-lytic and non-cytopathic infection that evades host's immune surveillance. Enteroviruses are known to cause persistent as well as lytic infection both in vitro and in vivo. Both virion as well as host factors modulate between persistent and lytic infection. Apoptosis, or programmed cell death, is a process of active non-necrotic cell death. It has complex interplay with viruses and may be either promoted or opposed by them. Apoptosis is a major factor in motor neuron death in SALS. Viral tropism is the process by which viruses select and propagate to target cells. It is controlled by capsid conformation and surface receptors on host cells. Enteroviruses have a region on their capsids known as the canyon which docks on such receptors. Docking induces conformational changes of the capsid and genome release. Poliovirus, tropic for motor neurons, docks on the poliovirus receptor, about which much is known. The virus penetrates the motor system focally after crossing either the blood-muscle or the blood-brain barriers. It propagates bidirectionally along axons and synapses to contiguous motor neurons, upper as well as lower, which sequester infection and create avenues for spread over long distances. If chronic and persistent rather than acute and lytic, such viruses trafficking in a finite system of non-dividing cells and inducing apoptosis would cause cell death that summates linearly rather than exponentially. Taken together, these explain signature clinical features of SALS - focal onset weakness, contiguous or regional spread of weakness, confinement to upper and lower motor neurons, and linear rates of progression. The hypothesis predicts the following testable investigations: 1) viral detection may be possible by applying amplification technology to optimally acquired nervous tissue processed by laser microdissection; 2) genetic susceptibility factors such as cell surface receptor polymorphisms may combine with sporadic exposure and chance penetration of the motor system in SALS; 3) a transgenic animal model might be created by inserting such genetic factors into an animal host and inoculating intramuscularly rather than intracerebrally biochemical fractions of SALS motor neurons at vulnerable periods in the developmental life cycle of the transgenic host; and 4) continual long-term administration of anti-enteroviral agents called capsid-binding compounds which stabilize capsids and prevent genome release might be efficacious.

Outbreak of extended spectrum beta-lactamase-producing Klebsiella pneumoniae infection in a neonatal intensive care unit related to onychomycosis in a health care worker

Four cases of infection by extended spectrum beta-lactamase-producing Klebsiella pneumoniae occurred in the neonatal intensive care unit. Isolation, empiric therapy change and education produced no effect. Newborn weekly colonization rates were 0-18.7%. One health care worker with onychomycosis was positive for extended spectrum beta-lactamase-producing K. pneumoniae. Isolates were identical by molecular typing. Outbreak was controlled when the health care worker was excluded from the neonatal intensive care unit.

Confidence in polymerase chain reaction diagnosis can be improved by Bayesian estimation of post-test disease probability

OBJECTIVE

Polymerase chain reaction (PCR) techniques allow highly sensitive detection of specific DNA for diagnosis of infectious and genetic disease, but uncertainty relating to sensitivity and contamination has frequently resulted in controversy over results. We propose a new design in which the PCR contamination rate is estimated experimentally. The sensitivity of duplicate test results, and hence the post-test disease probabilities, can be derived algebraically, but wide confidence limits around these point estimates reduce their usefulness.

STUDY DESIGN AND SETTING

We have developed a Bayesian method which gives better estimates of post-test disease probability and can substantially reduce uncertainty by using the prior belief that sensitivity is not lower than 90%.

RESULTS

With 100 duplicate test samples and 100 control samples, we find that the post-test disease probability for concordant results (both positive or both negative) is generally unequivocal. The post-test disease probability for discordant results (one test positive and one negative) is often sufficiently clear to allow useful interpretation of individual test results, depending on the context.

CONCLUSION

Using this approach, the performance of a PCR can be evaluated experimentally allowing post-test disease probability to be estimated, giving improved confidence in test results.

Molecular genetic methods for the diagnosis of fastidious microorganisms

Technological innovations in the detection and identification of microorganisms using molecular techniques such as polymerase chain reaction (PCR) have ushered in a new era with respect to diagnostic microbiology. PCR using universal or specific primers followed by identification of amplified product, mainly by sequencing, has enabled the rapid identification of cultured or uncultured bacteria. Thus, PCR may allow quick diagnosis of infections caused by fastidious pathogens for which culture could be extremely difficult. However, several pitfalls, such as false positives, have been observed with PCR, underlining the necessity to interpret the results obtained with caution. At present, certain improvements in the molecular genetic methods may be helpful for the diagnosis of infectious diseases. Indeed, the recent development of bacterial genome sequencing has provided an important source of potential targets for PCR, allowing rational choice of primers for diagnosis and genotyping. In addition, the development of new techniques such as real-time PCR offers several advantages in comparison to conventional PCR, including speed, simplicity, reproducibility, quantitative capability and low risk of contamination. Herein, we review the general principles of PCR-based diagnosis and molecular genetic methods for the diagnosis of several hard-to-culture bacteria, such as Rickettsia spp., Ehrlichia spp., Coxiella burnetii, Bartonella spp., Tropheryma whipplei and Yersinia pestis.

Major factors affecting the emergence and re-emergence of infectious diseases

The diversity of infectious disease threats currently facing humanity is unprecedented because of the remarkable emergence and reemergence of pathogens worldwide. Because of population mobility, globalization of commerce and the food supply, and the effects of the HIV/AIDS pandemic, infections in the developing world must be addressed to prevent infections in industrialized countries. Because pathogens do not recognize national boundaries, the rapidity with which individuals can circumnavigate the globe incubating infections makes the control of communicable diseases an enormous challenge for governments as well as for the public and primary health care systems. A global strategy for dealing with infectious disease threats must be developed and implemented as soon as possible.

Molecular Methods in the Diagnosis of Endocarditis

Advances in molecular microbiologic diagnostics have yielded new tools to diagnose infective endocarditis. These tools can detect microorganisms that are difficult to grow or are uncultivable, because of prior antimicrobial therapy or because of innate characteristics of the microorganisms. This paper reviews molecular microbiologic diagnostic techniques and their role in the diagnosis of infective endocarditis.

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

Detection and differentiation of Plasmodium species by polymerase chain reaction and colorimetric detection in blood samples of patients with suspected malaria

Polymerase chain reaction (PCR) is now recognized as a sensitive and specific method for detecting Plasmodium species in blood. In this study, we tested 279 blood samples, from patients with suspected malaria, by a PCR assay utilizing species-specific colorimetric detection, and compared the results to light microscopy. Overall, both assays were in agreement for 270 of the 279 specimens. P. vivax was detected in 131 (47.0%) specimens, P. falciparum in 64 (22.9%) specimens, P. ovale in 6 (2.1%) specimens, and P. malariae in 5 (1.8%) specimens. Both P. falciparum and P. vivax were detected in a further 10 (3.6%) specimens, and 54 (19.3%) specimens were negative by both assays. In the remaining nine specimens, microscopy either failed to detect the parasite or incorrectly identified the species present. In summary, the sensitivity, specificity and simplicity of the PCR assay makes it particularly suitable for use in a diagnostic laboratory.

Molecular diagnosis of viral infections of the central nervous system

The development of techniques for the amplification of DNA and RNA opened the way for the creation of extremely specific, sensitive, and rapid diagnostic tests for the detection of viral infections of the central nervous system. Polymerase chain reaction (PCR) and reverse transcription PCR diagnostic assays have revolutionized the approach to the diagnosis of important viral pathogens--in particular, enteroviruses (EVs), herpes viruses, and JC virus (JCV). These molecular approaches to diagnosis have led to improvements in clinical outcome and patient care. Additionally, their use has permitted a better understanding of the natural history and clinical spectrum of the syndromes caused by these important human pathogens. This article summarizes the current understanding with regard to the available, molecularly based, diagnostic assays for the detection of EVs, herpes viruses, and JCV.

Molecular and antibiofilm approaches to prosthetic joint infection

The majority of patients with prosthetic joint replacement (arthroplasty) experience dramatic relief of pain and restoration of satisfactory joint function. In the United States, more than.5 million people have a primary arthroplasty each year. Less than 10% of prosthesis recipients have complications develop during their lifetime, commonly as a result of aseptic biomechanical failure, followed by prosthetic joint infection. The pathogenesis of prosthetic joint infection is related to bacteria in biofilms, in which they are protected from antimicrobial killing and host responses rendering these infections difficult to eradicate. Current microbiology laboratory methods for diagnosis of prosthetic joint infection depend on isolation of a pathogen by culture. However, these methods have neither ideal sensitivity nor ideal specificity. Therefore, culture-independent molecular methods have been used to improve the diagnosis of prosthetic joint infection. In the research setting, detection of 16S ribosomal deoxyribonucleic acid by polymerase chain reaction has been used in the molecular diagnosis of prosthetic joint infection. Various antibiofilm strategies directed at disruption of adherent bacteria are the focus of intense research to improve the detection of biofilm organisms and their eradication. In this article, molecular and antibiofilm approaches to prosthetic joint infection are reviewed.

Introducing a molecular test into the clinical microbiology laboratory: development, evaluation, and validation

CONTEXT

In the mid-1980s, the polymerase chain reaction methodology for the amplification of minute amounts of target DNA was successfully developed and then introduced into clinical use; such technology has led to a revolution in diagnostic testing. Despite enormous advances in the detection of infectious agents by amplification methods, there are also limitations that must be addressed.

OBJECTIVE

To highlight the pertinent steps and issues associated with the introduction of an amplification assay into a clinical microbiology laboratory as well as the subsequent ongoing activities following its introduction into routine laboratory use.

DATA SOURCES

Data were obtained from literature searches from 1990 through September 2002 using the subject headings "polymerase chain reaction," "molecular assays," and "amplification" as well as publications of the National Committee for Clinical Laboratory Standards.

DATA EXTRACTION AND SYNTHESIS

Using the findings obtained from these studies and publications, the process of introducing a molecular assay into the clinical microbiology laboratory was broken down into 4 major components: (1) initial phase of assay development, (2) polymerase chain reaction assay verification in which analytic sensitivity and specificity is determined, (3) assay validation to determine clinical sensitivity and specificity, and (4) interpretation of results and ongoing, required activities. The approach, as well as the advantages and limitations involved in each step of the process, was highlighted and discussed within the context of the published literature.

CONCLUSIONS

The application of molecular testing methods in the clinical laboratory has dramatically improved our ability to diagnose infectious diseases. However, the clinical usefulness of molecular testing will only be maximized to its fullest benefit by appropriate and careful studies correlating clinical findings with assay results.