Comparison of Gen-Probe DNA probe test and culture for the detection of Neisseria gonorrhoeae in endocervical specimens.

A 2-h nonisotopic DNA probe assay for the direct detection of Neisseria gonorrhoeae in urogenital specimens has recently been modified (PACE 2; Gen-Probe, San Diego, Calif.). The new assay format was developed to increase the sensitivity of the assay and simplify procedural steps. In this study, the new DNA probe test was compared with a culture reference method for the detection of N. gonorrhoeae in endocervical specimens. The results of the DNA probe test were expressed as a ratio of relative light units (RLU) of the specimen/RLU of the cutoff recommended by the manufacturer. All patient samples with sample RLU/cutoff RLU ratios less than 0.7 were interpreted as negative, and ratios greater than 2.0 were interpreted as positive for gonorrhea. Samples with sample RLU/cutoff RLU ratios between 0.7 and 2.0 were repeated until two or more consistent negative or positive ratios were obtained. A total of 469 specimens were tested with an overall disease prevalence of 6.1%. Of the 469 patients tested, 5 specimens (1.0%) fell in this borderline region and were retested. If the manufacturer's recommended cutoff value had been used, the original DNA probe results would have resulted in two false-positives. Our data were analyzed for both symptomatic (prevalence, 11.7%) and asymptomatic (prevalence, 2%) women. The study indicated that with our modification of the manufacturer's endpoint interpretation, the DNA probe test was essentially equivalent to the culture method in terms of sensitivity, specificity, and positive and negative predictive values in both symptomatic and asymptomatic patient populations. The new DNA probe test can serve as a suitable screening and diagnostic test for the diagnosis of gonorrheal genital infections in women. Additionally, it offers the advantages of rapid turnaround time and ease of use and allows simultaneous testing for Chlamydia trachomatis on the same specimen.     

Retrospective study of Gen-Probe rapid diagnostic system for detection of legionellae in frozen clinical respiratory tract samples.

The Gen-Probe Rapid Diagnostic System for legionellae, which uses 125I-labeled cDNA directed against the rRNAs of legionellae, was evaluated for its ability to detect members of the genus by using clinical specimens which had been frozen at -70 degrees C for 2 to 8 years. Culture and direct immunofluorescence (DFA) results obtained at the time of specimen collection were used to categorize samples. The specimens tested were 112 samples culture positive for legionellae and 230 samples negative on culture and DFA tests. They were tested in a blinded and randomized fashion. Results were expressed in terms of the ratio of counts per minute of the sample to the counts per minute of the provided negative control. A ratio of greater than or equal to 4.0 was picked for optimal specificity. Of the 112 previously positive specimens, 63 (57%) were positive by the probe assay, and of the 230 previously negative samples, 228 (99.1%) were negative. The 51 discrepant specimens were reexamined by culture and DFA testing if adequate amounts remained; this was possible for 34 specimens. On repeat culture, 22 of 33 previously culture-positive samples yielded legionellae and 11 were negative. Ten of the positive repeat cultures yielded two or fewer colonies per plate. One probe-positive but previously culture-negative sample was overgrown by contaminants on repeat culture. Reanalysis of data after exclusion of the 17 unavailable, 11 repeat culture-negative, and 1 unevaluable specimen gave a probe sensitivity of 74% and specificity of 100%. The Gen-Probe test is therefore specific and is of useful sensitivity.     

Value of a DNA probe assay (Gen-Probe) compared with that of culture for diagnosis of gonococcal infection.

The Gen-Probe PACE 2 system for Neisseria gonorrhoeae (GP), which uses a chemiluminescently labeled DNA probe, was compared with conventional culture as the method of reference. A total of 1,750 specimens were collected from 496 females and 623 males visiting the outpatient clinic of the Sexually Transmitted Diseases Department of the Westeinde Hospital, The Hague, The Netherlands, during the year 1991. The prevalences of gonorrhea culture-positive men and women were 14.9 and 7.7%, respectively. The overall positive rate was 8.7%. Sensitivity, specificity, and positive and negative predictive values of GP were 97.1, 99.1, 90.6, and 99.8%, respectively. A total of 12 of 13 patients with positive GP results and negative cultures may have had a gonococcal infection, a conclusion based on clinical symptoms, positive methylene blue smears, and high relative light unit ratios. The DNA probe test can be useful as a suitable screening and diagnostic test for gonorrheal infection in men and women. An advantage of using this DNA probe technique is that simultaneous testing for Chlamydia trachomatis of the same specimen is possible. We also examined whether (all) rRNA had disappeared after adequate treatment for gonococcal and/or chlamydial infection in 30 patients. None of those positive patients showed a positive result in the DNA probe assay after treatment.     

Enzyme-linked immunoassay for detection of PCR-amplified DNA of legionellae in bronchoalveolar fluid.

A nonradioactive method is described that detects 10 to 100 legionellae in 1 ml of bronchoalveolar lavage fluid. DNA is purified by a proteinase K-phenol protocol or with a commercial DNA preparation kit and amplified by PCR with amplimers specific for the 16S rRNA gene of Legionella pneumophila. The upstream primer is 5' biotinylated. The amplification product is immobilized on streptavidin-coated microtiter plates. Because of the high binding capacity, no removal of nonincorporated biotin from the PCR product is required. After alkaline denaturation, the single-stranded PCR product is hybridized with a 5' digoxigenin-labeled probing oligomer. The amplification product is then detected by using peroxidase-labeled anti-digoxigenin antibodies in a luminescence or colorimetric reaction. The assay detects as few as 10 legionellae in 1-ml bronchoalveolar lavage fluid specimens. It is specific for medically relevant Legionella species, including Legionella pneumophila, L. bozemanii, and L. longbeachae. Of over 250 clinical specimens examined, 8 were positive for legionellae by both culture and the PCR assay. Six further specimens were culture negative but PCR positive for legionellae; of these, five specimens were from patients receiving high-dose erythromycin therapy for suspected or previously diagnosed legionella pneumonia. None of the remaining 240 specimens that were culture negative for legionellae yielded a positive PCR test, although a total of over 30 different bacterial species were cultured from these specimens. The PCR assay therefore appears to exhibit high sensitivity and specificity and thus could prove suitable for use in the routine microbiological diagnostic laboratory.     

Evaluation of a DNA probe test for the detection of Legionella SPP

Seventeen suspension of Legionella pneumophila and ten of Legionella bozemanii in saline or bronchoalveolar lavage (BAL) fluid were tested using the Gen Probe technique. The detection threshold was found to be 10(3)-10(4) CFU/ml. Specificity and sensitivity were evaluated by using the probe on 8 suspensions of bacteria other than Legionella and by performing a comparative study of the probe test, direct immunofluorescence and culture with 103 specimens (BAL fluid in most instances) from 92 patients with possible legionellosis. Sensitivity was found to be acceptable (3 of the 4 culture-positive specimens were positive by the probe test) and specificity was 100% despite the fact that most (80/99) BAL specimens were not sterile and regardless of the cutoff level used to define positivity. The advantages of the DNA probe test, including rapidity, simplicity and objectivity, should be weighed against its disadvantage, i.e., only acceptable sensitivity and use of radioactivity.     

Comparison of a DNA probe assay with culture for the detection of Chlamydia trachomatis

A new DNA probe assay (PACE 2, Gen-probe) was compared with cell culture for the detection of Chlamydia trachomatis in 909 women attending the Royal Women's Hospital, Melbourne, Victoria. The DNA probe assay had a sensitivity of 86.2%, a specificity of 99.9% and a positive predictive value of 96.2% in a population with 3.2% prevalence, indicating that it may be a suitable alternative to culture for the detection of C. trachomatis in specimens from the genital tract.     

Evaluation of reformulated chemiluminescent DNA probe (AccuProbe) for culture identification of Mycobacterium kansasii.

A panel of 104 isolates belonging to the species Mycobacterium kansasii and 78 mycobacterial isolates belonging to other species was tested in parallel with the present commercially available DNA probe (AccuProbe; Gen-Probe) and with a new probe just developed by the same manufacturer. While the old version of the probe confirmed the previously reported low sensitivity (only 59% of the M. kansasii isolates reacted), the new one was 100% sensitive. Only two non-M. kansasii strains, both M. gastri isolates, gave false-positive hybridization results.     

A species-specific DNA probe for the detection of Mycoplasma gallisepticum.

An 800-base-pair DNA fragment from a partial genomic library of Mycoplasma gallisepticum was selected and used as a probe for the selective detection of this avian pathogen. The specificity and sensitivity of this probe were demonstrated by using dot blot and Southern hybridizations.     

Evaluation of culture and the Gen-Probe PACE 2 assay for detection of Neisseria gonorrhoeae and Chlamydia trachomatis in endocervical specimens transported to a state health laboratory.

The Gen-Probe PACE 2 assay (Gen-Probe Inc., San Diego, Calif.) was compared with culture for the detection of Neisseria gonorrhoeae in endocervical specimens that were mailed to the laboratory. During mail transport, the specimens were exposed to extremes of hot and cold weather for several days before arriving in the laboratory. Specimens on culture plates deteriorated during transport, as evidenced by many dead gonococcus-like colonies. The manufacturer's recommendation for reporting PACE 2 assay-positive results was modified to create a suspicious category for samples with relative light units near the positive cutoff value. Of a total of 4,869 specimens tested, 30 were positive by both methods and 102 were positive only by the PACE 2 assay. These additional 102 positive specimens were likely to be true positives, as indicated by several lines of indirect evidence, including detailed probe competition analysis, patient history, and the lack of false-positive results in hand-delivered specimens. Although Gen-Probe Inc. indicates that specimens are stable for up to 7 days, N. gonorrhoeae was easily detectable by the PACE 2 assay after 1 month of incubation at room temperature in the PACE 2 transport buffer. We also compared the Gen-Probe PACE 2 assay for Chlamydia trachomatis with culture on endocervical specimens delivered by same-day courier. Of 398 endocervical specimens tested, the PACE 2 assay detected 19 of 20 culture-positive samples. Although the assay failed to detect one culture-positive sample, it was able to detect two very weak culture-suspicious samples. Finally, PACE 2 assays for N. gonorrhoeae and C. trachomatis performed on the same samples indicated that the coinfection rate was 40% for women attending five family planning clinics. We concluded that the Gen-Probe PACE 2 assay system should be considered for use in testing those specimens that are transported to the laboratory through the mail.     

Comparison of DNA probe, monoclonal antibody enzyme immunoassay, and cell culture for the detection of Chlamydia trachomatis.

A total of 201 endocervical specimens were obtained from patients with a clinical or epidemiological history suggestive of chlamydial infection. These specimens were tested by DNA probe (Gen-Probe, San Diego, Calif.) and the IDEIA III (Boots-Celltech, Berkshire, United Kingdom) monoclonal antibody enzyme immunoassay and compared with cell culture for detection of Chlamydia trachomatis. Discrepancies between cell culture and antigen detection methods were resolved by direct fluorescent-antibody testing. In a population with a 17.4% prevalence, the sensitivities and specificities of these assays were 82.8 and 99.4%, respectively, for the DNA probe assay and 97.1 and 98.1%, respectively, for the IDEIA III.     

DNA probe culture confirmation assay for identification of thermophilic Campylobacter species.

We studied the ability of a new DNA probe-based assay system to correctly identify isolates of the thermophilic campylobacters Campylobacter jejuni, C. coli, and C. laridis grown in vitro. We examined 424 organisms, including 214 Campylobacter isolates and 210 other aerobic and anaerobic isolates. The probe assay, which uses a new homogeneous system in which all reactions take place within a single tube, demonstrated 100% accuracy, producing neither false-positive nor false-negative results. The assay does not, however, distinguish among C. jejuni, C. coli, and C. laridis.     

DNA probe for detection of the Leptospira interrogans serovar hardjo genotype hardjo-bovis.

A DNA probe is described for the diagnostic and taxonomic identification of the North American cattle pathogen Leptospira interrogans genotype hardjo-bovis. The probe is specific for this genotype and does not hybridize to genomic DNA of any other leptospire pathogen commonly found in North America.     

DNA probe technology for rapid detection of Haemophilus influenzae in clinical specimens.

In a previous study, we reported that a 5-kilobase Haemophilus influenzae DNA fragment involved in penicillin-binding protein expression could be used as a probe for specific detection of H. influenzae strains (F. Malouin and L. E. Bryan, Mol. Cell. Probes 1:221-232, 1987). Here, we report the ability of this probe to detect H. influenzae in clinical specimens. In a bacterial dot experiment, there was strong hybridization of the 32P-labeled probe to nonencapsulated and serotype a through f H. influenzae strains. The detection of H. influenzae in body fluids was then evaluated by using pooled human serum, urine, cerebrospinal fluid, and sputum as dilution media for H. influenzae, Haemophilus aegyptius, Haemophilus parainfluenzae, and Escherichia coli cells. At 65 degrees C, the probe hybridized to H. influenzae and H. aegyptius (greater than or equal to 10(5) cells) in all fluids. There was no hybridization with the E. coli negative control, and H. parainfluenzae hybridized when greater than or equal to 10(7) cells were used. Experiments performed at 73 and 80 degrees C permitted elimination of H. parainfluenzae hybridization. The detection of H. influenzae in 232 sputa from patients with respiratory tract infections was very specific (96 to 97%) and sensitive (74 to 100%) when the total time of the procedure was sufficient (6 to 24 h) and when the experiments were performed at 80 degrees C. In addition, the probe detected three of three and four of four H. influenzae-infected cerebrospinal fluids and blood cultures, respectively, and did not react with pneumococcus- or streptococcus-infected cerebrospinal fluids. Finally, by using a small-scale procedure, the probe rapidly detected H. influenzae in cerebrospinal fluid and sputum specimens (4 and 8 h, respectively). These results imply prompt diagnosis of H. influenzae infections caused by nonencapsulated and serotype a through f strains.     

Evaluation of Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test and PCR for direct detection of Mycobacterium tuberculosis in clinical specimens.

The Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (AMTD) is a direct specimen assay for the identification of Mycobacterium tuberculosis from respiratory samples. rRNA is amplified, and the product is detected with a specific chemiluminescent probe. We performed a retrospective evaluation of three separate respiratory specimens from each of 250 patients by using the AMTD and compared the results with those of microscopy, culturing, and a patient chart review. From the latter results, 198 patients (594 specimens) were found negative for M. tuberculosis by culturing and clinical criteria. The overall specificity of the AMTD after discrepancy resolution was 98.5% (585 of 594). There were 52 patients with culture-proven and/or clinically diagnosed tuberculosis. Of these 156 specimens, the organism was cultured from 142 (91%), and acid-fast microscopy was positive for 105 (67.3%). The AMTD was positive for 142 (91%) specimens from these patients. Tuberculosis patient samples were tested by a PCR assay which uses primers for amplification of the IS6110 insertion sequence of the M. tuberculosis complex. The PCR assay detected 144 of the 156 (92.3%) specimens. Overall, when three specimens per patient were examined, the AMTD found all 52 patients positive for tuberculosis, while the PCR assay found 51 patients positive by agarose gel analysis and all 52 patients positive by Southern blot hybridization.     

Highly sensitive digoxigenin-labelled DNA probe for the detection of potato spindle tuber viroid.

A molecular probe pSPAv6.2(+), with concatameric insert representing 6.2-times repeated copy of potato spindle tuber viroid (PSTV) RNA, was labelled with digoxigenin and used to detect PSTV by dot-blot hybridization assay. The probe was highly sensitive and specific, detecting as little as 2.5 pg of PSTV RNA. Both severe and mild PSTV strains were detectable in 64-512-times diluted crude extracts from infected tomato leaves, and potato leaves, sprouts, and seeds. For extraction of plant tissue three buffers were compared to determine the lowest non-specific background and the highest sensitivity. The results showed that the digoxigenin-labelled probe is as sensitive as the 32P-labelled probe and can replace radioactive techniques in PSTV detection. With such high sensitivity, the probe is also potentially useful for detecting the viroid in composite samples of mass-indexing programs.     

Evaluation of an rRNA-derived oligonucleotide probe for culture confirmation of Neisseria gonorrhoeae.

The reliability of an rRNA-derived oligonucleotide probe for Neisseria gonorrhoeae was tested with 187 N. gonorrhoeae isolates, 81 Neisseria meningitidis isolates, and several strains of other bacterial species. The probe proved to be 100% specific and 100% sensitive. N. gonorrhoeae cells could also be reliably identified in contaminated cultures with the oligonucleotide probe. The 2.6-megadalton cryptic plasmid used as a probe for N. gonorrhoeae was shown to be less sensitive, detecting 179 of 181 N. gonorrhoeae isolates.     

Use of a Chlamydia trachomatis DNA probe for detection of ocular chlamydiae.

We examined the efficacy of a Chlamydia trachomatis DNA probe in detecting ocular chlamydiae by comparing it with tissue culture isolation, direct fluorescent-antibody cytology, and clinical eye exams. In a trachoma-endemic area of Nepal, 430 Nepalese villagers were examined according to the World Health Organization trachoma grading scale. Upper tarsal conjunctival specimens from each subject were obtained for DNA probing, tissue culture, and fluorescent-antibody screening. Moderate to severe intensity of inflammation was found in 85 (21%) of 430 people studied. An additional 25 (7.2%) of 345 people with low or no intensity of inflammation also had microbiologically proven infection, which may reflect asymptomatic carriage. Compared with culture, the DNA probe had a sensitivity of 86.9% and a specificity of 91%. For direct fluorescent antibody versus culture, the values were 47.8 and 96.9%, respectively. Results from this study indicate that the DNA probe for C. trachomatis might be considered a valuable epidemiologic tool in screening trachoma-endemic populations for ocular chlamydiae.     

Evaluation of a prototype DNA probe test for the noncultural diagnosis of gonorrhea.

A prototype, nonisotopic, chemiluminescent DNA probe test called the Gen-Probe PACE (Probe Assay-Chemiluminescence Enhanced) system for Neisseria gonorrhoeae (Gen-Probe, San Diego, Calif.) was compared with conventional Martin-Lewis culture medium in JEMBEC plates for the laboratory diagnosis of gonorrhea. This 2-h noncultural assay is based upon the use of an acridinium ester-labeled DNA probe. The rRNA-directed DNA probe hybridizes with the target rRNA, and the hybridized probe is separated from the unhybridized probe through the use of magnetic microparticles. The esterified acridinium is hydrolyzed from the hybridized probe by the addition of an alkaline hydrogen peroxide solution, resulting in the production of visible light which is measured in a luminometer. The amount of light generated is directly proportional to the amount of gonococcal target rRNA present in the sample. A total of 407 clinical specimens (203 urethral and 204 endocervical) were collected from high-risk walk-in patients attending a sexually transmitted disease clinic. Separate patient specimens were collected for culture on Martin-Lewis medium in JEMBEC plates and for DNA probe assay. Statistical analysis of the overall comparative results showed that the DNA probe assay had a sensitivity, specificity, and positive and negative predictive values of 93, 99, 97, and 99%, respectively, in a patient population with a gonococcal disease prevalence of 21%. The results of this comparative study showed that the prototype chemiluminescent DNA probe assay is a rapid and reliable noncultural alternative for the laboratory diagnosis of gonorrhea.     

Comparison of Gen-Probe commercial kit and culture technique for the diagnosis of Mycoplasma pneumoniae infection.

The Gen-Probe rapid diagnostic system was compared with a culture method for the detection of Mycoplasma pneumoniae in clinical specimens. Of 116 clinical specimens, 103 (88.8%) yielded identical results. The relative sensitivity and specificity of the probe were both 89%. Rapid turnaround time and its sensitivity and specificity indicate that the probe test is a practical method for the rapid diagnosis of M. pneumoniae infections.