Detection of Candida spp. in blood cultures using nucleic acid sequence-based amplification (NASBA)

Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review

BACKGROUND

Fungal infections have increased during the last years due to the AIDS epidemic and immunosuppressive therapies. The available diagnostic methods, such as culture, histopathology and serology, have several drawbacks regarding sensitivity, specificity and time-consuming, while molecular methods are still expensive and dependent on many devices. In order to overcome these challenges, isothermal nucleic acid amplification techniques (INAT) arose as promising diagnostic methods for infectious diseases.

OBJECTIVE

This review aimed to present and discuss the main contributions of the isothermal nucleic acid amplification techniques applied in medical mycology.

METHODS

Papers containing terms for each INAT (NASBA, RCA, LAMP, CPA, SDA, HAD or PSR) and the terms 'mycoses' or 'disease, fungal' were obtained from National Center for Biotechnology Information database until August 2019.

RESULTS

NASBA, RCA, LAMP and PSR are the INAT reported in the literature for detection and identification of pathogenic fungi. Despite the need of a previous conventional PCR, the RCA technique might also be used for genotyping or cryptic species differentiation, which may be important for the treatment of certain mycoses; nevertheless, LAMP is the most used INAT for pathogen detection.

CONCLUSION

Among all INATs herein reviewed, LAMP seems to be the most appropriate method for fungal detection, since it is affordable, sensitive, specific, user-friendly, rapid, robust, equipment-free and deliverable to end-users, fulfilling all ASSURED criteria of the World Health Organization for an ideal diagnostic method.

A Real Time PCR strategy for the detection and quantification of Candida albicans in human blood

Candidemia is a significant cause of bloodstream infections (BSI) in nosocomial settings. The identification of species can potentially improve the quality of care and decrease human mortality. Quantitative PCR (qPCR) was evaluated for Candida albicans detection using culture suspensions containing C. albicans , spiked human blood, the cloned qPCR target fragment (ITS2 region) and the results of these assays were compared. The assays showed a good detection limit: C. albicans DNA extracted from yeast (sensitivity 0.2 CFU/µL), spiked human blood (sensitivity 10 CFU/mL), and cloned fragment of ITS2 region (sensitivity 20 target copies/μL). The efficiency of ITS2 fragment-qPCR ranged from 89.67 to 97.07, and the linearity (R²) of the standard curve ranged from 0.992 to 0.999. The results showed that this ITS2-qPCR has a great potential as a molecular prototype model for the development of a test to be applied in clinical practice, greatly reducing the time of candidemia diagnosis, which is extremely important in this clinical setting.

Microfluidic Chip for Detection of Fungal Infections

Fungal infections can lead to severe clinical outcomes such as multiple organ failure and septic shock. Rapid detection of fungal infections allows clinicians to treat patients in a timely manner and improves clinical outcomes. Conventional detection methods include blood culture followed by plate culture and polymerase chain reaction. These methods are time-consuming and require expensive equipment, hence, they are not suitable for point-of-care and clinical settings. There is an unmet need to develop a rapid and inexpensive detection method for fungal infections such as candidemia. We developed an innovative immuno-based microfluidic device that can rapidly detect and capture Candida albicans from phosphate-buffered saline (PBS) and human whole blood. Our microchip technology showed an efficient capture of C. albicans in PBS with an efficiency of 61-78% at various concentrations ranging from 10 to 10⁵ colony-forming units per milliliter (cfu/mL). The presented microfluidic technology will be useful to screen for various pathogens at the point-of-care and clinical settings.

Visual analysis of DNA microarray data for accurate molecular identification of non-albicans Candida isolates from patients with candidemia episodes

The performance of a visual slide-based DNA microarray for the identification of non-albicans Candida spp. was evaluated. Among 167 isolates that had previously been identified by Vitek 2, the agreement between DNA microarray and sequencing results was 97.6%. This DNA microarray platform showed excellent performance.

Fungal diagnosis: how do we do it and can we do better?

BACKGROUND

Morbidity and mortality remain high for patients with invasive fungal infections (IFIs) despite an increasing number of antifungals and other treatments. Many studies indicate that delayed or inaccurate diagnosis and treatment are major causes of poor outcomes in patients with IFIs.

OBJECTIVE

The aim of the current paper is to provide a review of traditional and newer approaches to the diagnosis of IFIs, with a particular focus on invasive candidiasis (IC) and aspergillosis (IA). Recent studies from the author's institution are highlighted, along with an advancement in cryptococcal meningitis diagnosis that should improve the care of AIDS and its opportunistic infection in many developing countries.

FINDINGS

Currently available tools for the diagnosis of IFIs include traditional methods like histopathology, culture, and radiology, and newer antigen- and PCR-based diagnostic assays. Attempts have also been made to predict IFIs based on colonization or other factors, including genetic polymorphisms impacting IFI susceptibility in high-risk patients. Biopsy with histopathologic analysis is often not possible in patients suspected of pulmonary aspergillosis due to increased bleeding risk, and blood cultures for IC, IA, or other IFIs are hindered by poor sensitivity and slow turnaround time which delays diagnosis. Radiology is often used to predict IFI but suffers from inability to differentiate certain pathogens and does not generally provide certainty of IFI diagnosis. Newer antigen-based diagnostics for early diagnosis include the β-glucan assay for IFIs, galactomannan assay for IA, and a recent variation on the traditional cryptococcal antigen (CRAG) test with a Lateral Flow Assay for invasive cryptococcosis. PCR-based diagnostics represent additional tools with high sensitivity for the rapid diagnosis of IFIs, although better standardization of these methods is still required for their routine clinical use.

CONCLUSION

Better understanding of the strengths and weaknesses of currently available diagnostic tools, and further devising linked strategies to best implement them either alone or in combination, would greatly improve early and accurate diagnosis of IFIs and improve their successful management.

Conventional and molecular techniques for the early diagnosis of bacteraemia

Bloodstream infections account for 30-40% of all cases of severe sepsis and septic shock, and are major causes of morbidity and mortality. Diagnosis of bloodstream infections must be performed promptly so that adequate antimicrobial therapy can be started and patient outcome improved. An ideal diagnostic technology would identify the infecting organism(s) and their determinants of antibiotic resistance, in a timely manner, so that appropriate pathogen-driven therapy could begin promptly. Unfortunately, despite the essential information it provides, blood culture, the gold standard, largely fails in this purpose because time is lost waiting for bacterial or fungal growth. Several efforts have been made to optimise the performance of blood culture, such as the development of technologies to obtain rapid detection of microorganism(s) directly in blood samples or in a positive blood culture. The ideal molecular method would analyse a patient's blood sample and provide all the information needed to immediately direct optimal antimicrobial therapy for bacterial or fungal infections. Furthermore, it would provide data to assess the effectiveness of the therapy by measuring the clearance of microbial nucleic acids from the blood over time. None of the currently available molecular methods is sufficiently rapid, accurate or informative to achieve this. This review examines the principal advantages and limitations of some traditional and molecular methods commercially available to help the microbiologist and the clinician in the management of bloodstream infections.

Recent Advances in the Detection of Neonatal Candidiasis

Neonatal candidiasis is serious and often fatal. Blood culture, the standard for diagnosis, has a sensitivity of 50% or less, and isolate speciation and susceptibility takes several days. This review explores recent advances in Candida detection using various diagnostic strategies.

Current status and future perspectives on molecular and serological methods in diagnostic mycology

Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.

Rapid real-time nucleic Acid sequence-based amplification-molecular beacon platform to detect fungal and bacterial bloodstream infections

Bloodstream infections (BSIs) are a significant cause of morbidity and mortality. Successful patient outcomes are diminished by a failure to rapidly diagnose these infections and initiate appropriate therapy. A rapid and reliable diagnostic platform of high sensitivity is needed for the management of patients with BSIs. The combination of an RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) detection system in multiplex format was developed to rapidly detect medically important BSI organisms. Probes and primers representing pan-gram-negative, pan-gram-positive, pan-fungal, pan-Candida, and pan-Aspergillus organisms were established utilizing 16S and 28S rRNA targets for bacteria and fungi, respectively. Two multiplex panels were developed to rapidly discriminate bacterial or fungal infections at the subkingdom/genus level with a sensitivity of 1 to 50 genomes. A clinical study was performed to evaluate the accuracy of this platform by evaluating 570 clinical samples from a tertiary-care hospital group using blood bottle samples. The sensitivity, specificity, and Youden's index values for pan-gram-positive detection and pan-gram-negative detection were 99.7%, 100%, 0.997 and 98.6%, 95.9%, 0.945, respectively. The positive predictive values (PPV) and the negative predictive values (NPV) for these two probes were 100, 90.7, and 99.4, 99.4, respectively. Pan-fungal and pan-Candida probes showed 100% sensitivity, specificity, PPV, and NPV, and the pan-Aspergillus probe showed 100% NPV. Robust signals were observed for all probes in the multiplex panels, with signal detection in <15 min. The multiplex real-time NASBA-MB assay provides a valuable platform for the rapid and specific diagnosis of bloodstream pathogens, and reliable pathogen identification and characterization can be obtained in under 3 h.

Multiplex tandem PCR: a novel platform for rapid detection and identification of fungal pathogens from blood culture specimens

We describe the first development and evaluation of a rapid multiplex tandem PCR (MT-PCR) assay for the detection and identification of fungi directly from blood culture specimens that have been flagged as positive. The assay uses a short-cycle multiplex amplification, followed by 12 simultaneous PCRs which target the fungal internal transcribed spacer 1 (ITS1) and ITS2 region, elongation factor 1-alpha (EF1-alpha), and beta-tubulin genes to identify 11 fungal pathogens: Candida albicans, Candida dubliniensis, Candida glabrata, Candida guilliermondii, Candida krusei, Candida parapsilosis complex, Candida tropicalis, Cryptococcus neoformans complex, Fusarium solani, Fusarium species, and Scedosporium prolificans. The presence or absence of a fungal target was confirmed by melting curve analysis. Identification by MT-PCR correlated with culture-based identification for 44 (100%) patients. No cross-reactivity was detected in 200 blood culture specimens that contained bacteria or in 30 blood cultures without microorganisms. Fungi were correctly identified in five specimens with bacterial coinfection and in blood culture samples that were seeded with a mixture of yeast cells. The MT-PCR assay was able to provide rapid (<2 h), sensitive, and specific simultaneous detection and identification of fungal pathogens directly from blood culture specimens.

Preparation of combined extract of cell wall and cytosol antigens of Candida albicans for immunoblot analysis

Immunoblot analysis is not in wide use for diagnosis of invasive candidiasis, mostly because the procedure is not standardized and hence not reliable. This work describes a standardized method for C. albicans antigen extract preparation and immunochemical detection. The major improvement of the method is the preparation of combined antigen extract -- consisting of the cell wall and cytosol antigens. The fungal cells and lysis buffer were mixed at a 1:3 ratio and disintegrated by ultrasound for six cycles of one minute each. After centrifugation, cytosol antigens were obtained in the supernatant and cell wall antigens were in the precipitate. Precipitate was dissolved in lysis buffer with 2% sodium dodecyl sulfate (SDS) and boiled at 100 degrees C for 2 min. After centrifugation, the supernatant was combined with the previous one, so the extract of the combined antigens was obtained in the mixture. With those combined antigen extracts and with sera of three different groups of patients, immunoblot analysis showed sensitivity of 90.2%, specificity of 84.4%, and accuracy of 88.0%.

Efficient identification of clinically relevant Candida yeast species by use of an assay combining panfungal loop-mediated isothermal DNA amplification with hybridization to species-specific oligonucleotide probes

The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus Candida remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of nonspecific primers to amplify a region of the 26S rRNA gene, followed by reverse hybridization of the digoxigenin-labeled products to a panel of species-specific oligonucleotide probes arranged on a nylon membrane macroarray format. DNA amplification was achieved by the recently developed loop-mediated isothermal DNA amplification technology, a promising option for the development of improved laboratory diagnostic kits. The newly developed method was successful in distinguishing among the major clinically relevant yeasts associated with bloodstream infections by using simple, rapid, and cost-effective procedures and equipment.

Yeast identification--past, present, and future methods

The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.

Rapid identification of fungal pathogens in BacT/ALERT, BACTEC, and BBL MGIT media using polymerase chain reaction and DNA sequencing of the internal transcribed spacer regions

We report a direct polymerase chain reaction/sequence (d-PCRS)-based method for the rapid identification of clinically significant fungi from 5 different types of commercial broth enrichment media inoculated with clinical specimens. Media including BacT/ALERT FA (BioMérieux, Marcy l'Etoile, France) (n = 87), BACTEC Plus Aerobic/F (Becton Dickinson, Microbiology Systems, Sparks, MD) (n = 16), BACTEC Peds Plus/F (Becton Dickinson) (n = 15), BACTEC Lytic/10 Anaerobic/F (Becton Dickinson) (n = 11) bottles, and BBL MGIT (Becton Dickinson) (n = 11) were inoculated with specimens from 138 patients. A universal DNA extraction method was used combining a novel pretreatment step to remove PCR inhibitors with a column-based DNA extraction kit. Target sequences in the noncoding internal transcribed spacer regions of the rRNA gene were amplified by PCR and sequenced using a rapid (24 h) automated capillary electrophoresis system. Using sequence alignment software, fungi were identified by sequence similarity with sequences derived from isolates identified by upper-level reference laboratories or isolates defined as ex-type strains. We identified Candida albicans (n = 14), Candida parapsilosis (n = 8), Candida glabrata (n = 7), Candida krusei (n = 2), Scedosporium prolificans (n = 4), and 1 each of Candida orthopsilosis, Candida dubliniensis, Candida kefyr, Candida tropicalis, Candida guilliermondii, Saccharomyces cerevisiae, Cryptococcus neoformans, Aspergillus fumigatus, Histoplasma capsulatum, and Malassezia pachydermatis by d-PCRS analysis. All d-PCRS identifications from positive broths were in agreement with the final species identification of the isolates grown from subculture. Earlier identification of fungi using d-PCRS may facilitate prompt and more appropriate antifungal therapy.

Comparison of the effect of delayed entry into 2 different blood culture systems (BACTEC 9240 and BacT/ALERT 3D) on culture positivity

The effect of delayed entry (2-48 h) into BacTAlert 3D and BACTEC 9240 and the effect of 2 storage temperatures (22 degrees C vs 35 degrees C) on bacterial growth was evaluated. The delay in transportation of blood culture bottles stored at room temperature had no effect on the recovery rate for the first 12 h. Culture positivity was between 74.4% and 100% for different microorganisms at less than 24 h preincubation time. The positivity rate decreased significantly for Acinetobacter baumannii, Bacteroides fragilis, Escherichia coli, Enterococcus faecalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Streptococcus pneumoniae for more than 24 h of delay. Culture positivity was higher at 22 degrees C for all microorganisms especially for Enterococcus faecalis and P. aeruginosa. Effects of instrument, preincubation time, and temperature showed that the risk of culture negativity increased 1.5 times for BACTEC compared with BacTAlert 3D and increased 2.5 times for 35 degrees C compared with 22 degrees C. The negativity increased 5.5 times and 8.5 times at 24 and 48 h of delay respectively, compared with no delay.

Diagnosis of candidemia by polymerase chain reaction and blood culture: prospective study in a high-risk population and identification of variables associated with development of candidemia

The diagnosis of candidemia is important for prompt initiation of antifungal therapy. Two hundred twenty-five patients at high risk for candidemia who had blood cultures drawn and were hospitalized for more than 15 days were followed-up prospectively over a 2-year period. Polymerase chain reaction (PCR) and whole-blood cultures monitored by the automated BactAlert system (Organon Teknika, Durham, NC, USA) were used to detect candidemia in all patients hospitalized in high-risk areas for more than 15 days. DNA was extracted and amplified using ITS5 and ITS4 base pair primers, and the PCR products were sequenced for identification of Candida spp. A blood culture positive for Candida was considered the gold standard for diagnosis of candidemia. Variables associated with the development of candidemia diagnosed by positive blood culture were also evaluated in the patients. The overall mortality rate was 26.1%. Mortality in candidemic patients was 41.9% and in noncandidemic patients 22.5% (p = 0.009). PCR sensitivity and specificity were 72.1 and 91.2%, respectively. Positive and negative predictive values were 65.9 and 93.2%, respectively. The logistic regression of the multivariate analysis showed that parenteral nutrition (p < 0.0001), fever (p = 0.01), neutropenia (p = 0.04), and an indwelling urinary catheter (p = 0.02) were significant variables associated with the development of candidemia. The PCR technique in conjunction with DNA sequencing was a helpful tool in the diagnosis of candidemia.

Detection and identification of Candida species associated with Candida vaginitis by real-time PCR and pyrosequencing

Real-time polymerase chain reaction (PCR) is currently considered the most sensitive method to detect low abundance DNA of pathogens in clinical samples. Furthermore, obtaining DNA sequence is the 'gold standard' of precise molecular detection. Here we combine species-specific real-time PCR and pyrosequencing to rapidly amplify and sequence ribosomal DNA from Candida albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis, which are commonly associated with candida vaginitis (CV). A standard curve was developed from plasmids containing the target DNA for each of the Candida species. A minimum real-time PCR and pyrosequencing detection limit of 100 copies per reaction was achieved. The combined technique was applied to the identification of the four Candida species in DNA extracts from vaginal samples. The results from 231 samples were compared with conventional PCR methods of identification. The results of both methods agreed on all but two samples, which were determined by both methods to contain C. albicans, but real-time PCR and pyrosequencing identified a second species that went undetected by conventional PCR. This is the first application of real-time PCR and pyrosequencing to DNA from vaginal samples for identification of four Candida species associated with CV, without the need for time-consuming culture methods.

New developments in the diagnosis of bloodstream infections

New techniques have emerged for the detection of bacteria in blood, because the blood culture as gold standard is slow and insufficiently sensitive when the patient has previously received antibiotics or in the presence of fastidious organisms. DNA-based techniques, hybridisation probes, and PCR-based detection or protein-based detection by mass spectroscopy are aimed at rapid identification of bacteria and provide results within 2 h after the first signal of growth in conventional blood cultures. Also, detection of microorganisms directly in blood by pathogen-specific or broad-range PCR assays (eubacterial or panfungal) shows promising results. Interpretation is complex, however, because of detection of DNA rather than living pathogens, the risk of interfering contamination, the presence of background DNA in blood, and the lack of a gold standard. As these techniques are emerging, clinical value and cost-effectiveness have to be assessed. Nevertheless, molecular assays are expected eventually to replace the current conventional microbiological techniques for detection of bloodstream infections.

False-positive results and contamination in nucleic acid amplification assays: suggestions for a prevent and destroy strategy

Contamination of samples with DNA is still a major problem in microbiology laboratories, despite the wide acceptance of PCR and other amplification techniques for the detection of frequently low amounts of target DNA. This review focuses on the implications of contamination in the diagnosis and research of infectious diseases, possible sources of contaminants, strategies for prevention and destruction, and quality control. Contamination of samples in diagnostic PCR can have far-reaching consequences for patients, as illustrated by several examples in this review. Furthermore, it appears that the (sometimes very unexpected) sources of contaminants are diverse (including water, reagents, disposables, sample carry over, and amplicon), and contaminants can also be introduced by unrelated activities in neighboring laboratories. Therefore, lack of communication between researchers using the same laboratory space can be considered a risk factor. Only a very limited number of multicenter quality control studies have been published so far, but these showed false-positive rates of 9-57%. The overall conclusion is that although nucleic acid amplification assays are basically useful both in research and in the clinic, their accuracy depends on awareness of risk factors and the proper use of procedures for the prevention of nucleic acid contamination. The discussion of prevention and destruction strategies included in this review may serve as a guide to help improve laboratory practices and reduce the number of false-positive amplification results.

Rapid identification of commonly encountered Candida species directly from blood culture bottles

We report a rapid-cycle, real-time PCR method for identifying six Candida spp. directly from BACTEC blood culture bottles. Target sequences in the noncoding internal transcribed spacer regions of the rRNA operon were simultaneously amplified and interrogated with fluorescent probes to identify Candida albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. lusitaniae; these account for 88% of the yeast species isolated from positive blood cultures in our laboratory. Any of the first four species can be identified in a single reaction using two fluorescent hybridization probe sets. The antifungal-resistant species C. krusei and C. lusitaniae are detected in a second reaction, also with two probe sets. The assay was validated with DNA extracted from BACTEC blood culture bottles positive for yeasts (n = 62) and was 100% concordant with culture identification based on biochemical and morphological features of C. albicans (n = 22), C. parapsilosis (n = 10), C. tropicalis (n = 1) C. glabrata (n = 22), C. krusei (n = 2), and C. lusitaniae (n = 1). No cross-reactivity was observed in blood culture samples growing yeasts other than the above-mentioned species (n = 4), in those growing bacteria (n = 12), or in the absence of microbial growth. Our assay allows rapid (</=2 h) and specific detection of the most common Candida spp. directly from positive blood cultures and may facilitate delivery of optimal antifungal therapy.

Rapid detection of Candida albicans in clinical blood samples by using a TaqMan-based PCR assay

We describe a rapid and reproducible PCR assay for quantitation of the Candida albicans ribosomal DNA (rDNA) in clinical blood samples based on the TaqMan principle (Applied Biosystems), in which a signal is generated by cleavage of a template-specific probe during amplification. We used two fluorogenic probes based on universal, fungus-specific primers, one for the detection of C. albicans species DNA and one for the detection of all Candida genus DNA. C. albicans blastoconidia mixed with whole blood in a titration experiment yielded a linear PCR signal over a range of 3 orders of magnitude. The TaqMan-based PCR assay for C. albicans exhibited a low limit of detection (5 CFU/ml of blood) and an excellent reproducibility (96 to 99%). While the C. albicans species-specific probe had 100% specificity for C. albicans, all Candida genus-specific probes cross-reacted with other organisms likely to coinfect patients with C. albicans infections. On the basis of these data, we determined the C. albicans loads with a species-specific probe from 122 blood samples from 61 hematology or oncology patients with clinically proven or suspected systemic Candida infections. Eleven positive samples exhibited a wide range of C. albicans loads, extending from 5 to 100,475 CFU/ml of blood. The sensitivity and specificity of the present assay were 100 and 97%, respectively, compared with the results of blood culture. These data indicate that the TaqMan-based PCR assay for quantitation of C. albicans with a species-specific probe provides an attractive alternative for the identification and quantitation of C. albicans rDNA in pure cultures and blood samples.

Laboratory diagnosis of invasive mycoses

Rising numbers of immunocompromised patients have led to an ever-increasing population at risk of invasive fungal disease. Much has been achieved in the laboratory diagnosis of these infections, such as advances in blood culture systems, and the development of new biochemical, antigen detection assays, and molecular methodologies. More standardized susceptibility testing guidelines provide for better therapeutic interventions. In an era of economic cutbacks in health care, future challenges include the development of cost-effective and technically simplified systems, which provide early detection and identification of common and emerging fungal pathogens. It will, however, take some time to establish the clinical relevance of these new methodologies in different patient populations.

Rapid and sensitive detection of avian influenza virus subtype H7 using NASBA

Nucleic acid sequence-based amplification with electrochemiluminescent detection (NASBA/ECL) is an isothermal technique allowing rapid amplification and detection of specific regions of nucleic acid from a diverse range of sources. It is especially suitable for amplifying RNA. A NASBA/ECL technique has been developed allowing the detection of RNA from avian influenza virus subtype H7 derived from allantoic fluid harvested from inoculated chick embryos and from cell cultures. Degenerate amplification primers and amplicon capture probes were designed enabling the detection of low and highly pathogenic avian influenza of the H7 subtype from the Eurasian and North American lineages and the Australian sub-lineage. The NASBA/ECL technique is specific for subtype H7 and does not cross-react with other influenza subtypes or with viruses containing haemagglutinin-like genes. The assay is 10- to 100-fold more sensitive than a commercially available antigen capture immunoassay system. The NASBA/ECL assay could be used in high throughput poultry screening programmes.

A method to detect major serotypes of foot-and-mouth disease virus

Nucleic acid sequence-based amplification (NASBA) is an isothermal technique that allows the rapid amplification of specific regions of nucleic acid obtained from a diverse range of sources. It is especially suitable for amplifying RNA sequences. A rapid and specific NASBA technique was developed, allowing the detection of foot-and-mouth disease virus genetic material in a range of sample material, including preserved skin biopsy material from infected animals, vaccines prepared from denatured cell-free material, and cell-free antigen-based detection kits. A single pair of DNA oligonucleotide primers was able to amplify examples of all major FMD virus subtypes. The amplified viral RNA was detected by electrochemiluminescence. The method was at least as sensitive as existing cell-free antigen detection methods.

Detection of highly pathogenic and low pathogenic avian influenza subtype H5 (Eurasian lineage) using NASBA

Nucleic acid sequence-based amplification (NASBA) is a technique that allows the rapid amplification of specific regions of nucleic acid obtained from a diverse range of sources. It is especially suitable for amplifying RNA sequences. A NASBA technique has been developed that allows the detection of avian influenza A subtype H5 from allantoic fluid harvested from inoculated chick embryos. The amplified viral RNA is detected by electrochemiluminescence. The NASBA technique described below is rapid and specific for the identification of influenza A subtype H5 viruses of the Eurasian lineage. More importantly, it can be used to distinguish highly pathogenic and low pathogenic strains of the H5 subtype.