Real-time, sequence-specific detection of nucleic acids during strand displacement amplification

Strand displacement amplification (SDA) is an isothermal nucleic acid amplification method based on the primer-directed nicking activity of a restriction enzyme and the strand displacement activity of an exonuclease-deficient polymerase. Here we describe fluorogenic reporter probes that permit real-time, sequence-specific detection of targets amplified during SDA. The new probes possess the single-strand half of a BsoBI recognition sequence flanked on opposite sides by a fluorophore and a quencher. The probes also contain target-binding sequences located 3' to the BsoBI site. Fluorophore and quencher are maintained in sufficiently close proximity that fluorescence is quenched in the intact single-stranded probe. If target is present during SDA, the probe is converted into a fully double-stranded form and is cleaved by the restriction enzyme BsoBI, which also serves as the nicking agent for SDA. Fluorophore and quencher diffuse apart upon probe cleavage, causing increased fluorescence. Target replication may thus be followed in real time during the SDA reaction. Probe performance may be enhanced by embedding the fluorogenic BsoBI site within the loop of a folded hairpin structure. The new probe designs permit detection of as few as 10 target copies within 30 min in a closed-tube, real-time format, eliminating the possibility of carry-over contamination. The probes may be used to detect RNA targets in SDA mixtures containing reverse transcriptase. Furthermore, a two-color competitive SDA format permits accurate quantification of target levels from the real-time fluorescence data.

Multiplex strand displacement amplification (SDA) and detection of DNA sequences from Mycobacterium tuberculosis and other mycobacteria

Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying a DNA target sequence prior to detection [Walker et al (1992) Nucleic Acids Res., 20, 1691-1693]. Here we describe a multiplex form of SDA that allows two target sequences and an internal amplification control to be co-amplified by a single pair of primers after common priming sequences are spontaneously appended to the ends of target fragments. Multiplex SDA operates at a single temperature, under the same simple protocol previously developed for single-target SDA. We applied multiplex SDA to co-amplification of a target sequence (IS6110) that is specific to members of the Mycobacterium tuberculosis-complex and a target (16S ribosomal gene) that is common to most clinically relevant species of mycobacteria. Both targets are amplified 10(8)-fold during a 2 hour, single temperature incubation. The relative sensitivity of the system was evaluated across a number of clinically relevant mycobacteria and checked for crossreactivity against organisms that are closely related to mycobacteria.

Strand displacement amplification--an isothermal, in vitro DNA amplification technique

Strand Displacement Amplification (SDA) is an isothermal, in vitro nucleic acid amplification technique based upon the ability of HincII to nick the unmodified strand of a hemiphosphorothioate form of its recognition site, and the ability of exonuclease deficient klenow (exo- klenow) to extend the 3'-end at the nick and displace the downstream DNA strand. Exponential amplification results from coupling sense and antisense reactions in which strands displaced from a sense reaction serve as target for an antisense reaction and vice versa. In the original design (G. T. Walker, M. C. Little, J. G. Nadeau and D. D. Shank (1992) Proc. Natl. Acad. Sci 89, 392-396), the target DNA sample is first cleaved with a restriction enzyme(s) in order to generate a double-stranded target fragment with defined 5'- and 3'-ends that can then undergo SDA. Although effective, target generation by restriction enzyme cleavage presents a number of practical limitations. We report a new target generation scheme that eliminates the requirement for restriction enzyme cleavage of the target sample prior to amplification. The method exploits the strand displacement activity of exo- klenow to generate target DNA copies with defined 5'- and 3'-ends. The new target generation process occurs at a single temperature (after initial heat denaturation of the double-stranded DNA). The target copies generated by this process are then amplified directly by SDA. The new protocol improves overall amplification efficiency. Amplification efficiency is also enhanced by improved reaction conditions that reduce nonspecific binding of SDA primers. Greater than 10(7)-fold amplification of a genomic sequence from Mycobacterium tuberculosis is achieved in 2 hours at 37 degrees C even in the presence of as much as 10 micrograms of human DNA per 50 microL reaction. The new target generation scheme can also be applied to techniques separate from SDA as a means of conveniently producing double-stranded fragments with 5'- and 3'-sequences modified as desired.

Dual-enzyme cascade-magnetic separation immunoassay for respiratory syncytial virus

A new immunoassay developed for the detection of respiratory syncytial virus (RSV) makes use of magnetic separation and amplification by a dual-enzyme cascade for signal generation. Magnetic particles are conjugated to monoclonal anti-RSV antibodies through the heterobifunctional crosslinker sulfosuccinimidyl 4-(maleimidomethyl)cyclohexane-1-carboxylate, yielding particles of high specific activity and low background. The dual-enzyme cascade is initiated by activation of a masked inhibitor for the enzyme rabbit liver esterase (RLE) by an alkaline phosphatase-antibody conjugate. The esterase activity is then measured to determine the degree of inhibition and, hence, the amount of specifically labeled antigen. These methods yield an immunoassay which is rapid and sensitive. Formation of the immunometric complex requires only 7 min and the total assay time is 40 min. The limit of detection for RSV fusion protein was found to be 1 ng or 10(-14) mol per test. Pre-clinical evaluation of the assay with 52 clinical specimens (nasal washes or aspirates) gave 96% sensitivity (25/26) and 96% specificity (25/26) with respect to a microtiter ELISA procedure and blocking antibody assay.

Fluorescent staining of intracellular and extracellular bacteria in blood

The fluorescent dye ethidium bromide stains Escherichia coli and Staphylococcus aureus in whole blood. The staining is rapid, relatively specific, and does not require fixation of the sample. Furthermore, stained bacteria can be seen microscopically without the need for a final wash to remove unbound dye. By using lysostaphin, an S. aureus-specific lytic enzyme, we have demonstrated that S. aureus can be stained with ethidium bromide even after phagocytosis. After short periods of incubation with the dye (less than 5 min), bacteria, both intracellular and extracellular, were the predominant fluorescent particles. With increasing time of incubation, blood cell components, notably leukocyte nuclei, began to fluoresce.

Experimental otitis media in chinchillas

Otitis media was induced in chinchillas by intrabullar injection of type 3 Streptococcus pneumoniae. It was found that the severity of a primary infection was related to the dose of bacteria injected, and animals that had recovered from a primary infection were resistant to reinfection with type 3 S pneumoniae. Middle ear effusions from infected animals contained antibodies to type 3 pneumococcal polysaccharide, whereas the sera of these animals lacked this antibody, suggesting that resistance to reinfectin was due to local immune mechanisms. This idea was tested by immunizing chinchillas by various routes. Animals immunized with formalin-killed type 3 S pneumoniae by intramuscular injection (to stimulate the systemic immune system) or by intranasal inoculation (to stimulate the secretory immune system) were found to be susceptible to infection with type 3 pneumonococcus, while animals immunized by inoculation of bacterial suspension directly into the middle ear were resistant to infection. In addition, we found that ampicillin treatment of a primary infection blocks the development of resistance since antibiotic-treated animals were susceptible to reinfection with the type 3 pneumococcus. These results indicate that chinchillas develop an immunity to pneumococcal otitis media following recovery from primary infection and that this immunity is mediated primarily by local immune mechanisms rather than systemic immune responses.

Antibiotic-resistant bacteria in otitis media with effusion

Eighty-two bacterial isolates recovered from the middle ear effusions (192) of children with otitis media with effusion (OME) were tested for antibiotic sensitivity. Nearly 50% of all bacteria isolated were found to be resistant to penicillin, and in particular, 61% of the Haemophilus isolates were penicillin-resistant; 48% of the Haemophilus isolates were ampicillin-resistant. In addition, we we compared the bacterial recovery rate from effusions of patients who were receiving antibiotics with those who were not. Among patients who were receiving antibiotics, 33% of the effusions were culture positive, while 82% of the effusions were culture positive in the patients who were not given antibiotics. These results are discussed with respect to the possible role of bacteria in the pathogenesis of OME.

Otitis media with effusion. Cytological and microbiological correlates

A quantitative cytologic study of 83 middle ear effusions from children with otitis media with effusion (OME) was made with the use of cytocentrifuge-prepared smears and was correlated with bacteriological findings. The identification of the types of cell present in an effusion was confirmed by electron microscopic findings. The most common cell types were neutrophilic leukocytes, lymphocytes, and macrophages, but a few eosinophils were found in only one case. The cytologic profile of an effusion correlated well with the bacterial culture results. Neutrophil counts were significantly higher in effusions that contained pathogenic bacteria (P less than .01) than in culture-negative effusions. Lymphocytes were the dominant cell type in culture-negative effusions. The results support the idea that bacteria are involved in the pathogenesis of many cases of OME.

Antibody activity in otitis media with effusion

Bacteria were isolated from a high percentage of the effusions from patients with otitis media with effusion (OME, serous otitis media). In an attempt to determine if the isolated bacteria were involved in the disease process, we analyzed the serum and effusion of 25 OME patients for the presence of antibacterial antibodies by the indirect immunofluorescence antibody method. Specific antibody activity was detected in 20 of 25 effusions (80%) and 19 of 22 sera (86%). IgG antibodies were the most frequently found class of antibodies in both sera and effusions, but IgA antibodies were detected more frequently in the effusions than in the sera. Hemophilus influenzae, Streptococcus pneumoniae, and diphtheroids were the most frequently isolated organisms, and antibody activity to all bacterial species isolated was detected. The results support the concept that the isolated bacteria are not contaminants but are actively involved in the disease process.

Immunoglobulin E in chronic middle ear effusions: conmparison of RIST, PRIST, and RIA techniques

To investigate the possible role of allergy in otitis media with effusion (OME), the immunoglobulin E (IgE) content of 138 middle ear effusions (MEE) and paired serum samples from patients with chronic otitis media with effusion was determined. The initial 62 paired specimens were assayed for IgE by the radioimmunosorbent test (RIST), while the later 76 paired specimens were assayed for IgE by the paper radioimmunosorbent test (PRIST). When the results obtained by these two techniques were compared, it was noted that the PRIST procedure gave significantly lower IgE values for effusions than the RIST method. When the effusion-to-serum ratios (E/S ratios) were computed from the PRIST data, the E/S ratio was less than one, while RIST data gave an E/S ratio greater than one. The results obtained with the PRIST procedure were confirmed by double antibody radioimmunoassay for IgE. Thus, the PRIST procedure appears to measure the IgE content of MEE more accurately, and the results obtained by this procedure fail to support the concept of allergy as a major causative factor in OME.