Advances in nucleic acid-based detection methods

Organic Electrochemical Transistors for Biomarker Detections

The improvement of living standards and the advancement of medical technology have led to an increased focus on health among individuals. Detections of biomarkers are feasible approaches to obtaining information about health status, disease progression, and response to treatment of an individual. In recent years, organic electrochemical transistors (OECTs) have demonstrated high electrical performances and effectiveness in detecting various types of biomarkers. This review provides an overview of the working principles of OECTs and their performance in detecting multiple types of biomarkers, with a focus on the recent advances and representative applications of OECTs in wearable and implantable biomarker detections, and provides a perspective for the future development of OECT-based biomarker sensors.

CRISPR/Cas-powered nanobiosensors for diagnostics

CRISPR diagnostics (CRISPR-Dx) offer a wide range of enhancements compared to traditional nanobiosensors by taking advantage of the excellent trans-cleavage activity of the CRISPR/Cas systems. However, the single-stranded DNA/RNA reporters of the current CRISPR-Dx suffer from poor stability and limited sensitivity, which make their application in complex biological environments difficult. In comparison, nanomaterials, especially metal nanoparticles, exhibits robust stability and desirable optical and electrocatalytical properties, which make them ideal as reporter molecules. Therefore, biosensing research is moving towards the use of the trans-cleavage activity of CRISPR/Cas effectors on metal nanoparticles and apply the new phenomenon to develop novel nanobiosensors to target various targets such as viral infections, genetic mutations and tumor biomarkers, by using different sensing methods, including, but not limited to fluorescence, luminescence resonance, colorimetric and electrochemical signal readout. In this review, we explore some of the most recent advances in the field of CRISPR-powered nanotechnological biosensors. Demonstrating high accuracy, sensitivity, selectivity and versatility, nanobiosensors along with CRISPR/Cas technology offer tremendous potential for next-generation diagnostics of multiple targets, especially at the point of care and without any target amplification.

COVID-19: An insight into the developments in diagnostics and therapeutics in India

The unexpected pandemic set off by the novel coronavirus (SARS-CoV2) has spread to more than 210 countries across the globe, including India. In the current pandemic situation, various steps have been taken by the Indian government to prevent and control the spread of the SARS-CoV2 infection. To date, there are no proven vaccines or effective therapeutic interventions against the virus. Current clinical management includes infection prevention and control, symptom-specific relief and supportive care. Physicians and scientists across the country have been tirelessly working on developing effective diagnostic and therapeutic strategies and to combat and control this infection. As the demand for diagnostics and therapeutics continues to rise in India and around the globe, it is essential to rapidly develop various algorithms to successfully identify and contain the virus. This review discusses the updates on the recent developments in COVID-19 diagnostics and therapeutics in India.

A lateral flow strip combined with Cas9 nickase-triggered amplification reaction for dual food-borne pathogen detection

Nucleic acid-based detection methods are accurate and rapid, which are widely-used in food-borne pathogen detection. However, traditional nucleic acid-based detection methods usually rely on special instruments, weakening their practicality for on-site tests in resource-limited locations. In this work, we developed a convenient and affordable method for food-borne pathogen detection based on a lateral flow strip combined with Cas9 nickase-triggered isothermal DNA amplification, which allows instrument-free and dual target detection. The genomic DNAs of two most common foodborne pathogens, Salmonella typhimurium and Escherichia coli, were simultaneously amplified in a one-pot reaction using specific sgRNAs and primers. The amplicons of genomic DNAs were double-labelled by digoxin/biotin and FITC/biotin tags, respectively, and directly visualized on a simple lateral flow strip. Our method exhibited a high specificity and sensitivity with a detection limit of 100 copies for genomic DNAs and 100 CFU/mL for bacteria. We believe that this method has potential to provide a convenient and low-cost point-of-care test for pathogen detection in the food quality surveillance.

Multiplex optical detection and quantification of DNA fragments by metallo-peptide assemblies

Rapid detection of infectious agents such as bacteria and viruses are important for proper health management, agriculture and homeland security. This paper presents a multiplex DNA detection system self-assembled by a metallo-peptide complex. Within five minutes, the system can simultaneously detect multiple DNA fragments, without any need for their separation. The presence of proteins in the sample does not harm the detection capabilities of the system, which can discriminate even between one base-pair mismatch and can perform at concentrations as low as 200 pM.

Amplification chemistries in clinical virology

Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.

Direct buffer composition of blood pre-process for nucleic acid based diagnostics

Recently, a variety of methods, so called “direct buffer”, have been developed to utilize nucleic acid in the blood for the measurement of infectious bacteria and virus without any equipment in the field. In here, we first investigated the individual and combinatory effects of candidate chemicals which might be composed of the direct buffer on the PCR inhibition reduction of main compositions in whole blood. The long and short PEGs, Na₂SO₄ and GuSCN were selected as representative kosmotropic and chaotropic salts, respectively. MgCl₂ were chosen as divalent cation source and NaOH was used to control blood pH. The effect of common non-ionic biological detergent was tested with Triton X-100 and SDS (Sodium Dodecyl sulfate) was chosen as anionic detergent. These results could provide a foundation for the development of sample preparation solution in nucleic acid based diagnostic field. As a result, the direct buffer developed in this study was able to detect viruses with a concentration of 10² pfu/100 μL of whole blood by a very simple method.

Simultaneous detection of multiple pathogens by multiplex PCR coupled with DNA biochip hybridization

Traditional serological enzyme-linked immunosorbent assay (ELISA) is routinely used to monitor pathogens during quarantine in most animal facilities to prevent possible infection. However, the ELISA platform is a single-target assay, and screening all targeted pathogens is time-consuming and laborious. In this study, to increase sensitivity and to reduce diagnosis time for high-throughput processes, multiplex PCR and DNA biochip techniques were combined to develop a multi-pathogen diagnostic method for use instead of routine ELISA. Eight primer sets were designed for multiplex PCR to detect genes from seven targeted bacterial and viral pathogens. DNA-DNA hybridization was conducted on a biochip following the multiple PCR analysis. Using this method, a total of 24 clinical samples were tested, and the result showed that not only single infection but also co-infection by multi-pathogens can be detected. In conclusion, multiplex PCR coupled with a DNA biochip is an efficient method for detecting multi-pathogens in a reaction. This platform is a useful tool for quarantine services and disease prevention in animal facilities.

Integrated dielectrophoretic and surface plasmonic platform for million-fold improvement in the detection of fluorescent events

We present an integrated dielectrophoretic (DEP) and surface plasmonic technique to quantify ∼1 pM of fluorescent molecules in low conductivity buffers. We have established a DEP force on target molecules to bring those molecules and place them on the nanometallic structures (hotspots) for quantification through surface plasmonic effects. Our results show that the DEP is capable of placing the fluorescent molecules on the hotspots, which are depicted as a significant reduction in the fluorescence lifetime of those molecules. To efficiently integrate the DEP and plasmonic effects, we have designed and utilized pearl-shaped interdigitated electrodes (PIDEs) in experiments. These electrodes generate 2-3 times higher DEP force than traditional interdigitated electrodes. Therefore, high-throughput assays can be developed. The nanometallic structures were strategically fabricated in the periphery of PIDEs for smooth integration of DEP and plasmonic detection. With the introduction of DEP, about 10⁶-fold improvement was achieved over existing plasmonic-based detection. Therefore, this simple addition to the existing surface plasmonic-based detection will enable the disease related protein detection.

Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics

Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.

Fluorometric detection of mutant DNA oligonucleotide based on toehold strand displacement-driving target recycling strategy and exonuclease III-assisted suppression

We describe here a fluorometric assay for sensitive detection of oligonucleotides, based on a target recycling amplification strategy driven by toehold-mediated strand displacement reaction and on exonuclease III (Exo Ш)-assisted fluorescence background suppression strategy. The network consists of a pair of partially complementary DNA hairpins (HP1 and HP2) with 3' overhang ends, between which the spontaneous hybridization is kinetically hindered by the stems. The target DNA is repeatedly used to trigger a recycling progress between the hairpins, generating numerous HP1-HP2 duplex complexes. Exo III was then employed to digest the double strand parts of the residual hairpins and the intermediate products. The fluorescent dye, SYBR Green I, binds to the double-strand DNA products and emits strong fluorescence to achieve sensitive detection of the target DNA with the detection limit of 5.34 pM. Moreover, this proposed strategy showed high discrimination efficiency towards target DNA against mismatched DNA and was successfully applied in the analysis of human serum sample.

Establishment of immunoassay for detecting HPV16 E6 and E7 RNA

Cervical carcinoma is the most prevalent malignancy second only to breast cancer among women worldwide. Since more than 99% of cervical cancers are caused by human papilloma virus (HPV), measurement of HPV (HPV test) was commonly used in screening risk and/or early stage of cervical cancer as well as assessing the efficacies of the treatments that can decrease the incidence of cervical cancer. Many approaches that diagnose HPV infections have been developed, while most of them have distinct shortcomings. We here established a novel immunoassay method in which the pairs of unlabeled DNA probes firstly bind to HPV16 E6 and E7 RNAs to form the DNA-RNA hybrids, and the hybrids will subsequently be identified by S9.6 antibody. The sensitivity of this highly specific method can reach ~0.923 pg/mL and ~0.424 pg/mL of in vitro transcribed HPV16 E6 and E7 RNA, respectively, and reverse transcription and polymerase chain reaction (PCR) amplification were no longer needed. Thus, our immunoassay approaches can precisely reflect the actually viral load that is related to the course of HPV infection. In addition, it has also fast and low cost characteristic feature.

Inter-Laboratory Variability in Array-Based RNA Quantification Methods

Ribonucleic acids (RNA) are hypothesized to have preceded their derivatives, deoxyribonucleic acids (DNA), as the molecular media of genetic information when life emerged on earth. Molecular biologists are accustomed to the dramatic effects a subtle variation in the ribose moiety composition between RNA and DNA can have on the stability of these molecules. While DNA is very stable after extraction from biological samples and subsequent treatment, RNA is notoriously labile. The short half-life property, inherent to RNA, benefits cells that do not need to express their entire repertoire of proteins. The cellular machinery turns off the production of a given protein by shutting down the transcription of its cognate coding gene and by either actively degrading the remaining mRNA or allowing it to decay on its own. The steady-state level of each mRNA in a given cell varies continuously and is specified by changing kinetics of synthesis and degradation. Because it is technically possible to simultaneously measure thousands of nucleic acid molecules, these quantities have been studied by the life sciences community to investigate a range of biological problems. Since the RNA abundance can change according to a wide range of perturbations, this makes it the molecule of choice for exploring biological systems; its instability, on the other hand, could be an underestimated source of technical variability. We found that a large fraction of the RNA abundance originally present in the biological system prior to extraction was masked by the RNA labeling and measurement procedure. The method used to extract RNA molecules from cells and to label them prior to hybridization operations on DNA arrays affects the original distribution of RNA. Only if RNA measurements are performed according to the same procedure can biological information be inferred from the assay read out.

Hibridização in situ fluorescente: princípios básicos e perspectivas para o diagnóstico de doenças infecciosas em medicina veterinária

Nesse manuscrito são discutidos aspectos relevantes sobre desenvolvimento da técnica de hibridização fluorescente in situ, seus princípios básicos, aplicações e perspectivas em medicina veterinária. Além disso, compara as vantagens e desvantagens em relação às outras técnicas de diagnóstico in situ. A FISH demonstra ser uma técnica com grande potencialidade de uso rotineiro, pois associa agilidade de execução, alta sensibilidade e especificidade e visualização do agente infeccioso viável no tecido.

Rapid microarray detection of DNA and proteins in microliter volumes with surface plasmon resonance imaging measurements

A four-chamber microfluidic biochip is fabricated for the rapid detection of multiple proteins and nucleic acids from microliter volume samples with the technique of surface plasmon resonance imaging (SPRI). The 18 mm × 18 mm biochip consists of four 3 μL microfluidic chambers attached to an SF10 glass substrate, each of which contains three individually addressable SPRI gold thin film microarray elements. The 12-element (4 × 3) SPRI microarray consists of gold thin film spots (1 mm(2) area; 45 nm thickness), each in individually addressable 0.5 μL volume microchannels. Microarrays of single-stranded DNA and RNA (ssDNA and ssRNA, respectively) are fabricated by either chemical and/or enzymatic attachment reactions in these microchannels; the SPRI microarrays are then used to detect femtomole amounts (nanomolar concentrations) of DNA and proteins (ssDNA binding protein and thrombin via aptamer-protein bioaffinity interactions). Microarrays of ssRNA microarray elements are also used for the ultrasensitive detection of zeptomole amounts (femtomolar concentrations) of DNA via the technique of RNase H-amplified SPRI. Enzymatic removal of ssRNA from the surface due to the hybridization adsorption of target ssDNA is detected as a reflectivity decrease in the SPR imaging measurements. The observed reflectivity loss is proportional to the log of the target ssDNA concentration with a detection limit of 10 fM or 30 zeptomoles (18 000 molecules). This enzymatic amplified ssDNA detection method is not limited by diffusion of ssDNA to the interface, and thus is extremely fast, requiring only 200 s in the microliter volume format.

Affinity and selectivity of C2- and C5-substituted "chiral-box" PNA in solution and on microarrays

Two peptide nucleic acids (PNAs) containing three adjacent modified chiral monomers (chiral box) were synthesized. The chiral monomers contained either a C2- or a C5-modified backbone, synthesized starting from D- and L-arginine, respectively (2D- and 5L-PNA). The C2-modified chiral PNA was synthesized using a submonomeric strategy to avoid epimerization during solid-phase synthesis, whereas for the C5-derivative, the monomers were first obtained and then used in solid-phase synthesis. The melting temperature of these PNA duplexes formed with the full-match or with single-mismatch DNA were measured both by UV and by CD spectroscopy and compared with the unmodified PNA. The 5L-chiral-box-PNA showed the highest T(m) with full-match DNA, whereas the 2D-chiral-box-PNA showed the highest sequence selectivity. The PNA were spotted on microarray slides and then hybridized with Cy5-labeled full match and mismatched oligonucleotides. The results obtained showed a signal intensity in the order achiral >2D-chiral box >5L-chiral box, whereas the full-match/mismatch selectivity was higher for the 2D chiral box PNA.

Feasibility of methods based on nucleic acid amplification techniques to fulfil the requirements for microbiological analysis of water quality

Molecular methods based on nucleic acid recognition and amplification are valuable tools to complement and support water management decisions. At present, these decisions are mostly supported by the principle of end-point monitoring for indicators and a small number of selected measured by traditional methods. Nucleic acid methods show enormous potential for identifying isolates from conventional culture methods, providing data on cultivable and noncultivable micro-organisms, informing on the presence of pathogens in waters, determining the causes of waterborne outbreaks, and, in some cases, detecting emerging pathogens. However, some features of water microbiology affect the performance of nucleic acid-based molecular techniques and thus challenge their suitability for routine water quality control. These features include the variable composition of target water samples, the generally low numbers of target micro-organisms, the variable water quality required for different uses and the physiological status or condition of such micro-organisms. The standardization of these molecular techniques is also an important challenge for its routine use in terms of accuracy (trueness and precision) and robustness (reproducibility and reliability during normal usage). Most of national and international water regulations recommend the application of standard methods, and any new technique must be validated respect to established methods and procedures. Moreover, molecular methods show a high cost-effectiveness value that limits its practicability on some microbial water analyses. However, new molecular techniques could contribute with new information or at least to supplement the limitation of traditional culture-based methods. Undoubtedly, challenges for these nucleic acid-based methods need to be identified and solved to improve their feasibility for routine microbial water monitoring.

Sensitivity enhancement in DNA hybridization assay using gold nanoparticle-labeled two reporting probes

A simple and sensitive method for DNA detection using gold nanoparticle (AuNP) two-probe detection system (AuNP-TP) was developed. Preliminary experiment was carried out by optimizing slide types, blocking agents and hybridization times. Fluorescent-labeled probes were used along with AuNP-labeled probes to confirm specific binding event between target DNA and probes. The sensitivities between AuNP single-probe (AuNP-SP) and AuNP-TP systems using sandwich-typed assay were compared. The AuNP-TP on epoxide-coated (EP) slides increased sensitivity 1000-fold at the detection limit of 100fM when compared to the AuNP-SP. This result indicates that the assay sensitivity was simply enhanced by simultaneous adding two AuNP labeled probes which selectively recognize different regions of the target DNA. The concept of AuNP-TP could potentially be applied to a macroarray format to detect multiple DNA targets simultaneously; thereby making the assay becomes more affordable and more sensitive.

Highly selective single nucleotide polymorphism recognition by a chiral (5S) PNA beacon

A chiral peptide nucleic acid (PNA) beacon containing a C-5 modified monomer based on L-lysine was synthesized. The terminal amino group of the lysine side chain was linked to a spacer for future applications on surfaces. The PNA beacon bears a carboxyfluorescein fluorophore and a dabcyl quencher at opposite ends. The DNA binding properties were compared with those of a homologous PNA beacon containing only achiral monomers. Both beacons underwent a fluorescence increase in the presence of complementary DNA, with higher efficiency and higher selectivity (evaluated using single mismatched DNA sequences) observed for the chiral monomer containing PNA. Ion exchange (IE) HPLC with fluorimetric detection was used in combination with the beacon for the selective detection of complementary DNA. A fluorescent peak corresponding to the PNA beacon:DNA duplex was observed at a very low detection limit (1 nM). The discriminating capacity of the chiral PNA beacon for a single mismatch was found to be superior to those observed with the unmodified one, thus confirming the potency of chirality for increasing the affinity and specificity of DNA recognition.

All-in-one tube method for quantitative gene expression analysis in oligo-dT(30) immobilized PCR tube coated with MPC polymer

In this report, we have developed a novel quantitative RT-PCR protocol in which the procedure including mRNA purification can be performed in an all-in-one tube. To simplify gene expression analysis, oligo-dT(30) immobilized PCR tubes were used serially to capture mRNA, synthesize solid-phase cDNA, and amplify specific genes. The immobilized oligo-dT(30) can efficiently capture mRNA directly from crude human cell lysates. The captured mRNA is then amplified by one-step reverse transcription PCR (RT-PCR) with initial cDNA synthesis followed by PCR. In RT-PCR, this new reusable PCR tube device can be employed for multiple PCR amplifications with different primer sets from a solid-phase oligo-dT(30) primed cDNA library. This paper introduces a novel and highly reliable all-in-one tube method for rapid cell lysis, followed by quantitative preparation and expression analysis of target mRNA molecules with small amounts of sample. This procedure allows all steps to be carried out by sequential dilution in a single tube, without chemical extraction. We demonstrate the utility of this novel method by quantification of two housekeeping genes, beta-actin and GAPDH, in HeLa cells. We believe this new PCR device can be useful as a platform for various mRNA expression analyses, including basic research, drug screening, and molecular toxicology, as well as for molecular pathological diagnostics.

Scanning electrochemical microscopy imaging of DNA microarrays using methylene blue as a redox-active intercalator

Scanning electrochemical microscopy (SECM) has been employed in the imaging of DNA microarrays fabricated on gold substrates using methylene blue (MB) as a redox-active intercalator and ferrocyanide as the SECM mediator in solution. MB intercalated between base pairs of immobilized ds-DNA is electrochemically reduced via electron transfer from the underlying gold substrate, and the product is reoxidized in solution by SECM tip-generated ferricyanide. The resulting feedback current allows a heterogeneous electron-transfer rate constant for the MB-intercalated DNA to be deduced. Moreover, DNA microarray spots can be imaged at a detection level of 14 fmol/spot for ds-DNA consisting of 15 base pairs. Microarrays prepared using 20 microM DNA solutions are easily visualized, and the feasibility of detecting base pair mismatches is also demonstrated.

Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction

Microarray-hybridization specificity is one of the main effectors of microarray result quality. In the present review, we suggest a definition for specificity that spans four hybridization levels, from the single probe to the microarray platform. For increased hybridization specificity, it is important to quantify the extent of the specificity at each of these levels, and correct the data accordingly. We outline possible effects of low hybridization specificity on the obtained results and list possible effectors of hybridization specificity. In addition, we discuss several studies in which theoretical approaches, empirical means or data filtration were used to identify specificity effectors, and increase the specificity of the hybridization results. However, these various approaches may not yet provide an ultimate solution; rather, further tool development is needed to enhance microarray-hybridization specificity.

Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays

A strand-specific DNA sensory method is described based on surface-bound peptide nucleic acids and water-soluble cationic conjugated polymers. The main transduction mechanism operates by taking advantage of the net increase in negative charge at the peptide nucleic acid surface that occurs upon single-stranded DNA hybridization. Electrostatic forces cause the oppositely charged cationic conjugated polymer to bind selectively to the "complementary" surfaces. This approach circumvents the current need to label the probe or target strands. The polymer used in these assays is poly[9,9'-bis(6''-N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide], which was specifically designed and synthesized to be compatible with excitation sources used in commonly used DNA microarray readers. Furthermore, the utility of poly[9,9'-bis(6''-N,N,N-trimethylammonium)-hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] has been demonstrated in homogenous and solid-state assays that involve fluorescence resonance energy transfer to a reporter dye (Cy5) and that can benefit from the light harvesting properties observed in water-soluble conjugated polymers.

Real-time nucleic acid-based detection methods for pathogenic bacteria in food

Quality assurance in the food industry in recent years has involved the acceptance and implementation of a variety of nucleic acid-based methods for rapid and sensitive detection of food-associated pathogenic bacteria. Techniques such as polymerase chain reaction have greatly expedited the process of pathogen detection and have in some cases replaced traditional methods for bacterial enumeration in food. Conventional PCR, albeit sensitive and specific under optimized conditions, obligates the user to employ agarose gel electrophoresis as the means for endpoint analysis following sample processing. For the last few years, a variety of real-time PCR chemistries and detection instruments have appeared on the market, and many of these lend themselves to applications in food microbiology. These approaches afford a user the ability to amplify DNA or RNA, as well as detect and confirm target sequence identity in a closed-tube format with the use of a variety of fluorophores, labeled probes, or both, without the need to run gels. Such real-time chemistries also offer greater sensitivity than traditional gel visualization and can be semiquantitative and multiplexed depending on the specific experimental objectives. This review emphasizes the current systems available for real-time PCR-based pathogen detection, the basic mechanisms and requirements for each, and the prospects for development over the next few years in the food industry.

Recent advances in laboratory procedures for pathogenic mycobacteria

Just as tuberculosis has persisted for many centuries as one of most serious and deadly infectious diseases in many parts of the world, so has the motivation to develop improved laboratory methods for characterizing M. tuberculosis isolates. Modern technology has lead to great improvements in mycobacteriology laboratory procedures, particularly in detection, identification, epidemiologic strain typing, and drug susceptibility testing. Although the usefulness of some of these newer methods is under evaluation, many already are showing potential as adjuncts to clinical diagnostic procedures.

Moving to nucleic acid-based detection of genital Chlamydia trachomatis

Laboratory diagnosis of the bacterium Chlamydia trachomatis has gone through a complete phase of evolution since it was first identified as a significant cause of sexually transmitted infection. As a fragile, obligatory intracellular organism, it was initially only grown in eggs. Subsequently, diagnosis relied on culture in continuous cell lines. To address the limitations of culture, immunological methods were developed and direct antigen detection using enzyme immunoassay and immunofluorescence flourished. With the advent of molecular technologies, nucleic acid-based amplification techniques became the methods of choice, offering improved standard of care for diagnosis and opening up the possibility of screening using noninvasive, patient-acceptable specimens. In this article, the various currently available molecular methods are examined, some of the existing problems discussed and a view on what we think might happen in the next 5 years to the technology and requirement in diagnosis and screening is given.

PreservCyt transport medium used for the ThinPrep Pap test is a suitable medium for detection of Chlamydia trachomatis by the COBAS Amplicor CT/NG test: results of a preliminary study and future implications

The commercial COBAS Amplicor CT/NG test (Roche Diagnostic Systems, Meylan, France) is a sensitive and specific method for detection of Chlamydia trachomatis infections. This test currently consists of using a nucleic acid amplification method to detect C. trachomatis in first-void urine specimens and in endocervical swabs collected in 2-sucrose-phosphate (2SP) transport medium. We conducted a prospective study to determine whether the automated COBAS Amplicor CT/NG test can detect C. trachomatis in cervical specimens collected in PreservCyt transport medium (ThinPrep Pap Test; Cytyc Corporation, Boxborough, Mass.). PreservCyt medium is used to preserve cervical samples before the preparation of ThinPrep slides. We collected 1,000 cervical specimens from young women (age range, 15 to 25 years) during routine Pap smear tests. Only specimens with normal cytology and in which the gynecologist found no clinical evidence of urogenital infections were selected. The samples were stored in PreservCyt transport medium at 15 to 20 degrees C. C. trachomatis was detected in 22 of the 1,000 cervical specimens that had been stored in PreservCyt. To confirm the positive samples, the test was repeated on new endocervical swab specimens collected in 2SP transport medium. Only 9 of the 22 positive patients agreed to undergo this control, but all 9 retested positive. To evaluate the influence of storage conditions on the sensitivity of the C. trachomatis PCR test, all of the positive samples were stored at 15 to 20 degrees C in PreservCyt transport medium and were retested every 2 weeks for 6 weeks. C. trachomatis was successfully amplified from all 22 specimens for the whole 6-week period. The prevalence of C. trachomatis infection was 2.2% in our study population. These results demonstrate that PreservCyt transport medium is a suitable transport medium for detection of C. trachomatis by the COBAS Amplicor CT/NG test. The ThinPrep Pap Test may enable gynecologists to monitor for both cervical lesions and C. trachomatis infections with a single endocervical specimen.

Multiplex PCR: optimization and application in diagnostic virology

PCR has revolutionized the field of infectious disease diagnosis. To overcome the inherent disadvantage of cost and to improve the diagnostic capacity of the test, multiplex PCR, a variant of the test in which more than one target sequence is amplified using more than one pair of primers, has been developed. Multiplex PCRs to detect viral, bacterial, and/or other infectious agents in one reaction tube have been described. Early studies highlighted the obstacles that can jeopardize the production of sensitive and specific multiplex assays, but more recent studies have provided systematic protocols and technical improvements for simple test design. The most useful of these are the empirical choice of oligonucleotide primers and the use of hot start-based PCR methodology. These advances along with others to enhance sensitivity and specificity and to facilitate automation have resulted in the appearance of numerous publications regarding the application of multiplex PCR in the diagnosis of infectious agents, especially those which target viral nucleic acids. This article reviews the principles, optimization, and application of multiplex PCR for the detection of viruses of clinical and epidemiological importance.

Multiplex PCR: optimization and application in diagnostic virology

PCR has revolutionized the field of infectious disease diagnosis. To overcome the inherent disadvantage of cost and to improve the diagnostic capacity of the test, multiplex PCR, a variant of the test in which more than one target sequence is amplified using more than one pair of primers, has been developed. Multiplex PCRs to detect viral, bacterial, and/or other infectious agents in one reaction tube have been described. Early studies highlighted the obstacles that can jeopardize the production of sensitive and specific multiplex assays, but more recent studies have provided systematic protocols and technical improvements for simple test design. The most useful of these are the empirical choice of oligonucleotide primers and the use of hot start-based PCR methodology. These advances along with others to enhance sensitivity and specificity and to facilitate automation have resulted in the appearance of numerous publications regarding the application of multiplex PCR in the diagnosis of infectious agents, especially those which target viral nucleic acids. This article reviews the principles, optimization, and application of multiplex PCR for the detection of viruses of clinical and epidemiological importance.

Filtration capture immunoassay for bacteria: optimization and potential for urinalysis

A novel assay utilizing immuno-labeling, filtration, and electrochemistry for the rapid detection of bacteria has been optimized for the detection of Escherichia coli O157:H7. Bacteria were specifically labeled with alkaline phosphatase conjugated polyclonal antibodies and captured on a polycarbonate track-etched membrane filter (0.2 microm pore size). The filter was then placed directly against a glassy carbon electrode, incubated with enzyme substrate, and the product detected by square wave voltammetry. The high speed and capture efficiency of membrane filtration and inherent sensitivity of electrochemical detection produced a 25-min assay with a detection limit of 5 x 10(3) E. coli O157:H7 per ml using a filtration volume of 100 microl (i.e. 500 cells filtered). The labeling, filtration, and electrochemical steps were optimized, and the assay performance using electrochemical and colorimetric detection methods was compared. The assay was used to detect E. coli O157:H7 that was spiked into filter-sterilized urine at clinically relevant concentrations.

Vibrio cholerae O1 strain TSI-4 produces the exopolysaccharide materials that determine colony morphology, stress resistance, and biofilm formation

Vibrio cholerae O1 strain TSI-4 (El Tor, Ogawa) can shift to a rugose colony morphology from its normal translucent colony morphology in response to nutrient starvation. We have investigated differences between the rugose and translucent forms of V. cholerae O1 strain TSI-4. Electron microscopic examination of the rugose form of TSI-4 (TSI-4/R) revealed thick, electron-dense exopolysaccharide materials surrounding polycationic ferritin-stained cells, while the ferritin-stained material was absent around the translucent form of TSI-4 (TSI-4/T). The exopolysaccharide produced by V. cholerae TSI-4/R was found to have a composition of N-acetyl-D-glucosamine, D-mannose, 6-deoxy-D-galactose, and D-galactose (7.4:10.2:2.4:3.0). The expression of an amorphous exopolysaccharide promotes biofilm development under static culture conditions. Biofilm formation by the rugose strain was determined by scanning electron microscopy, and most of the surface of the film was colonized by actively dividing rod cells. The corresponding rugose and translucent strains were compared for stress resistance. By having exopolysaccharide materials, the rugose strains acquired resistance to osmotic and oxidative stress. Our data indicated that an exopolysaccharide material on the surface of the rugose strain promoted biofilm formation and resistance to the effects of two stressing agents.

Comparison of sample preparation methods for detection of Legionella pneumophila in culture-positive bronchoalveolar lavage fluids by PCR

A prospective study was conducted on 25 Legionella pneumophila culture-positive and 98 culture-negative bronchoalveolar lavage fluid samples to compare two DNA preparation methods: a rapid modified Chelex-based protocol and a proteinase K method. PCR was found to be more sensitive with the Chelex-based method (P = 0.03). N difference was found concerning the inhibition rate.

Comparison between microwell and bead supports for the detection of human cytomegalovirus amplicons by sandwich hybridization

In this study, we compared the efficiency of capture DNA probes covalently bound onto magnetic beads or microplates for their hybridization with target human cytomegalovirus (HCMV) DNA amplicons. Polystyrene supports were first aminated by wet chemistry to allow covalent grafting of the capture probes. The level of amines grafted was three times higher on beads than on microwells. Increasingly higher sizes of capture probes were fixed on both supports and the best reaction yield ranged from 300 to 500 fmol. The sizes of the capture and detection probes were optimized in order to obtain high target DNA hybridization yield. Long capture probes were more accessible than short ones to the target, with faster kinetics of hybridization obtained on beads than on microplates. Sensitivity of the hybridization assay was then determined with a nonisotopic method and the detection limit found was 30 amol of HCMV amplicons on both supports. HCMV DNA extracted from clinical samples were amplified by PCR. The resulting amplicons were then analyzed using the optimized sandwich hybridization assay discussed here. The results perfectly fitted with the qualitative conclusions obtained after a nested PCR analyzed on agarose gel.

The future of HPV testing in clinical laboratories and applied virology research

BACKGROUND

Human papillomaviruses (HPV) are now considered etiologic agents of cancer of the uterine cervix. Adjunctive diagnostic procedures for the detection of HPV infection could increase the sensitivity of primary and secondary screening of cervical cancer. HPV testing could also improve the specificity of screening programs resulting in avoidance of overtreatment and saving of costs for confirmatory procedures.

OBJECTIVES

To review the rationale of HPV testing in genital diseases and the potential applications of HPV DNA detection methods for clinical and epidemiological purposes.

RESULTS

Progression of HPV infection is associated with the persistence of HPV infection, involvement of high-risk HPV types, high HPV viral load in specimens, integration of viral DNA and possibly the presence of cofactors. The design of HPV diagnostic tests will need to take into account these parameters of disease progression. HPV DNA detection techniques based on signal-amplification are standardized, commercially available and detect several high-risk HPV types. They increase the sensitivity of screening for high-grade and low-grade lesions. Although they may yield false-negative results in the presence of significant HPV-related disease, new test formats could resolve this weakness. Amplification techniques are ideal instruments for epidemiologic purposes since they minimize misclassification of HPV infection status and allow for the detection of low viral burden infections. They are currently not readily applicable to diagnostic laboratories.

CONCLUSIONS

Before recommending HPV testing, prospective trials of untreated LSIL with HPV testing as well as the determination of the efficacy and cost-effectiveness of novel HPV tests, need to be completed.