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HLA-DQ tetramers identify epitope-specific T cells in peripheral blood of herpes simplex virus type 2-infected individuals: direct detection of immunodominant antigen-responsive cells.

Ag-specific CD4+ T cells are present in peripheral blood in low frequency, where they undergo recruitment and expansion during immune responses and in the pathogenesis of numerous autoimmune diseases. MHC tetramers, which constitute a labeled MHC-peptide ligand suitable for binding to the Ag-specific receptor on T cells, provide a novel approach for the detection and characterization of such rare cells. In this study, we utilized this technology to identify HLA DQ-restricted Ag-specific T cells in the peripheral blood of human subjects and to identify immunodominant epitopes associated with viral infection. Peptides representing potential epitope regions of the VP16 protein from HSV-2 were loaded onto recombinant DQ0602 molecules to generate a panel of Ag-specific DQ0602 tetramers. VP16 Ag-specific DQ-restricted T cells were identified and expanded from the peripheral blood of HSV-2-infected individuals, representing two predominant epitope specificities. Although the VP16 369-380 peptide has a lower binding affinity for DQ0602 molecules than the VP16 33-52 peptide, T cells that recognized the VP16 369-380 peptide occurred at a much higher frequency than those that were specific for the VP16 33-52 peptide.

Amino Acid Sequence↗

Use of the polymerase chain reaction to directly detect malaria parasites in blood samples from the Venezuelan Amazon.

We have examined the reproducibility, sensitivity, and specificity of detecting Plasmodium falciparum using the polymerase chain reaction (PCR) and the species-specific probe pPF14 under field conditions in the Venezuelan Amazon. Up to eight samples were field collected from each of 48 consenting Amerindians presenting with symptoms of malaria. Sample processing and analysis was performed at the Centro Amazonico para la Investigacion y Control de Enfermedades Tropicales Simon Bolivar. A total of 229 samples from 48 patients were analyzed by PCR methods using four different P. falciparum-specific probes. One P. vivax-specific probe and by conventional microscopy. Samples in which results from PCR and microscopy differed were reanalyzed at a higher sensitivity by microscopy. Results suggest that microscopy-negative, PCR-positive samples are true positives, and that microscopy-positive and PCR-negative samples are true negatives. The sensitivity of the DNA probe/PCR method was 78% and its specificity was 97%. The positive predictive value of the PCR method was 88%, and the negative predictive value was 95%. Through the analysis of multiple blood samples from each individual, the DNA probe/PCR methodology was found to have an inherent reproducibility that was highly statistically significant.

Animals↗

Direct detection and identification of lactic acid bacteria in a food processing plant and in meat products using denaturing gradient gel electrophoresis.

We established a novel system using denaturing gradient gel electrophoresis (DGGE) to quickly identify bacteria known to be responsible for spoilage in meat processing plants and meat products. We extracted bacterial DNA from swabbed samples at various locations in the plant and from meat products and performed PCR amplification, targeting 16S rDNA from the dominant organisms. The amplification products were subjected to DGGE, and the contaminating bacteria in the meat products and the plant were analyzed. This analysis indicated that lactic acid bacteria and spoilage-causing bacteria are widely distributed within the meat processing plant. We developed molecular size markers to identify the dominant organisms obtained from the plant and meat products. The establishment of the present method allows quick and simple identification of bacteria causing the possible deterioration of products and contamination and thus permits constant monitoring of any harmful bacteria within meat processing plants.

Animals↗

Performance characteristics of the Becton Dickinson ProbeTec System for direct detection of Chlamydia trachomatis and Neisseria gonorrhoeae in male and female urine specimens in comparison with the Roche Cobas System.

OBJECTIVE: The Becton Dickinson BDProbeTec ET System is a new semiautomated system using strand displacement amplification technology that simultaneously amplifies and detects Chlamydia trachomatis and Neisseria gonorrhoeae DNA. The strand displacement amplification products are hybridized with a fluorescent detector probe and are captured by a chemiluminescent assay in a microwell format. An amplification control is also included to monitor assay inhibition. This study evaluated the performance of the BDProbTec ET system in detecting C trachomatis and N gonorrhoeae in male and female urine specimens, calculated its ability to process large volumes of specimens, and determined the inhibition rate. MATERIALS AND METHODS: Eight hundred twenty-five male and 399 female urine specimens were tested for both C trachomatis and N gonorrhoeae with the BDProbeTec ET system, and results were compared with those of the Roche Amplicor Cobas system. All urine specimens were processed on both assays on the same day they were received, according to the manufacturers' instructions. Discrepant results were resolved by in-house polymerase chain reaction assays. Internal or amplification controls were also used in each specimen assay to monitor inhibition. The throughput of the BDProbTec ET system was further tested with 150 urine specimens on an 8-hour shift for 2 days. RESULTS: The overall sensitivity, specificity, positive predicative value, and negative predicative value for for detection of chlamydia were 95.3%, 99.3%, 95.9%, and 99.2% for strand displacement amplification and 95.9%, 98.3%, 90.6%, and 99.3% for the Roche Amplicor system. For detection of gonorrhea, these values were 100%, 99.7%, 88.2%, and 100% and 96.7%, 98.9%, 69%, and 99.9%, respectively. The overall inhibition rates for both strand displacement amplification and Roche Amplicor were less than 3.5%. The BDProbTec ET system was able to produce 150 results each for chlamydia and gonorrhea and the internal control within the 8-hour shift. CONCLUSIONS: The performance characteristics of the BDProbeTec ET assay are similar to those of the Roche Amplicor polymerase chain reaction for detection of chlamydia and gonorrhea in male and female urine specimens. The system was able to produce 300 results in an 8-hour shift.

Chlamydia trachomatis↗

Relation between directly detected patent foramen ovale and ischemic brain lesions in sport divers.

BACKGROUND: In divers, the significance of a patent foramen ovale and its potential relation to paradoxical gas emboli remain uncertain. OBJECTIVE: To assess the prevalence of symptoms of decompression illness and ischemic brain lesions in divers with regard to the presence of a patent foramen ovale. DESIGN: Retrospective cohort study. SETTING: University hospital and three diving clubs in Switzerland. PARTICIPANTS: 52 sport divers and 52 nondiving controls. MEASUREMENTS: Prevalence of self-reported decompression events, patent foramen ovale on contrast transesophageal echocardiography, and ischemic brain lesions on magnetic resonance imaging. RESULTS: The risk for decompression illness events was 4.5-fold greater in divers with patent foramen ovale than in divers without patent foramen ovale (risk ratio, 4.5 [95% CI, 1.2 to 18.0]; P = 0.03). Among divers, 1.23 +/- 2.0 and 0.64 +/- 1.22 ischemic brain lesions per person (mean +/- SD) were detected in those with and those without patent foramen ovale, respectively. Among controls, 0.22 +/- 0.44 and 0.12 +/- 0.63 lesion per person were detected (P < 0.001 for all groups). CONCLUSIONS: Regardless of whether a diver has a patent foramen ovale, diving is associated with ischemic brain lesions.

Adult↗

Direct detection of nitric oxide in rat urinary bladder during ischemia-reperfusion.

PURPOSE: We attempted to investigate the role of nitric oxide (NO) in ischemia-reperfusion injury in the rat bladder. MATERIALS AND METHODS: Rat abdominal aorta were clamped with a small clip to induce ischemia-reperfusion injury in the rat bladder dome. To investigate the role of NO in ischemia-reperfusion injury, N(G)-nitro-L-arginine methylester (L-NAME, 30 mg./kg.) was injected intraperitoneally to measure carbachol-induced contractions of 60 minutes ischemia-30 minutes reperfusion in the rat bladder dome. In vivo real-time blood flow and NO release were measured in the rat bladder with a laser Doppler flowmeter and an NO-selective electrode, respectively. Moreover, participation of NO synthase subtypes was investigated by immunohistochemical staining of bladder sections with anti-endothelial I and anti-inducible NO synthase subtype antibodies. RESULT: Treatment with L-NAME (30 mg./kg., i.p.) partially prevented the reduction of bladder strips in contraction induced by the ischemia-reperfusion. Clamping of the aorta decreased blood flow to 10% of the basal level measured before the clamping. Administration of L-NAME reduced the blood flow to the bladder by 65% compared to the control level during ischemia-reperfusion. Real-time monitoring of NO in the bladder revealed that ischemia increased NO release, which, in turn, reached a plateau 30-40 minutes after the induction of ischemia. Immediately after the reperfusion, NO release returned to the basal level. In the control rat bladder, the endothelial subtype (eNOS) was observed in the mucosa. After the ischemia-reperfusion, iNOS was detected in the infiltrated neutrophils in the muscular and submucosal regions. CONCLUSION: Our data indicate that NO from leukocytes may participate in cell/tissue injury during ischemia-reperfusion of the rat bladder and that the damage may be preventable by treatment with L-NAME.

Animals↗

Comparative performance of PCR-based assay versus microscopy and culture for the direct detection of Mycobacterium tuberculosis in clinical respiratory specimens in Lebanon.

SETTING: American University of Beirut Medical Center, Lebanon. OBJECTIVE: To assess the performance of a polymerase chain reaction (PCR) using primers that flank 542 bp within IS6110 in Mycobacterium tuberculosis (TB) vs. microscopy and BACTEC culture, in the diagnosis of tuberculosis. DESIGN: A total of 82 clinical respiratory pulmonary specimens and 73 samples from BACTEC vials were tested by the three methods. RESULTS: Of 24 smear-positive culture-positive (SP-CP) and 11 smear-negative culture-positive (SN-CP) TB specimens, PCR detected 83% and 64%, respectively. Among 17 specimens yielding mycobacteria other than tuberculosis (MOTT), the PCR was positive in 33% SP-CP and 14% SN-CP specimens. Among the 73 BACTEC vials, PCR was positive in 36 of 38 (95%) yielding culture-positive TB, and in one of 20 (5%) yielding culture positive MOTT. None of the 30 smear-negative culture-negative (SN-CN) clinical specimens and 15 of the CN vials were positive by PCR. The overall sensitivity of PCR was 77% and 95% for TB detection in respiratory specimens and BACTEC vials, respectively, and the specificity was 94% in both. CONCLUSIONS: Because a substantial number of TB cases are missed, especially in SN-CP specimens, a PCR-based assay utilizing these primers cannot be used reliably, alone, in clinical laboratory diagnosis of mycobacterial respiratory infections.

Bacteriological Techniques↗

[Routine direct detection of Mycobacterium tuberculosis with a rapid test of polymerase chain reaction applied to a Hungarian patient population].

The results of the present study, based on 1869 examined clinical specimens of 543 patients, represent the Hungarian parameters of a PCR test. By using the final and resolved results, the clinical sensitivity, specificity, positive and negative predictive values were 83.8%, 99.2%, 95.4% and 97%, respectively for PCR, 63.5%, 100%, 100% and 93.5%, respectively for culture, and 16.2%, 100%, 100% and 86.3%, respectively for Ziehl-Neelsen (ZN) staining. These results are essential to allow Hungarian clinicians to interpret PCR results in accordance with local conditions. The present study has demonstrated a high sensitivity (PCR vs. culture and smear, p < 0.01) and an excellent specificity of PCR. Our results indicate that the majority of M. tuberculosis-positive specimens can be identified rapidly with the test and, because of the high negative predictive value, the PCR test can help to exclude tuberculosis from the differential diagnosis in 24 hours. Moreover, the PCR can detect the presence of M. tuberculosis in 66.6% of ZN-negative and subsequently culture-positive specimens at the time of admission. The results of PCR must be interpreted with extreme caution, and the procedure is recommended only for laboratories, which simultaneously perform culture and microscopy for control of the performance of PCR tests.

Humans↗

Evaluation of the FASTPlaqueTB assay for direct detection of Mycobacterium tuberculosis in sputum specimens.

SETTING: Sputum samples were collected from suspected tuberculosis patients attending out-patient clinics at the Ojha Institute of Chest Diseases, Karachi, Pakistan. OBJECTIVE: To evaluate the performance of the FASTPlaqueTB assay for rapid diagnosis of pulmonary tuberculosis. DESIGN: A comparative study of 584 sputum samples using acid-fast smear microscopy, Lowenstein-Jensen culture and FASTPlaqueTB. RESULTS: A total of 514 samples yielded complete results. Seventy specimens were lost to analysis due to the overgrowth of contaminants. The addition of antimicrobials inhibited growth of gram-positive contaminants, and reduced the overall contamination rate from 18.2% to 7.2%. Mycobacterium tuberculosis was isolated from 175 smear-positive and 70 smear-negative specimens. FASTPlaqueTB detected M. tuberculosis in 81.6% of specimens, with a specificity of 97.7%. The sensitivity and specificity of the assay for smear-positive specimens were respectively 87.4% and 88.2%. For smear-negative specimens, the sensitivity of the assay was 67.1% and the specificity was 98.4%. The combined sensitivity of smear and FASTPlaqueTB for M. tuberculosis was 90%. Test results were available in 48 hours. CONCLUSION: FASTPlaqueTB is a sensitive and specific test for rapid diagnosis of pulmonary tuberculosis in high prevalence areas. The test is sensitive enough to confirm a large number of clinically suspected smear-negative cases and improve case finding.

Bacteriophage Typing↗

Direct detection and quantitation of a distinct T-cell epitope derived from tumor-specific epithelial cell-associated mucin using human recombinant antibodies endowed with the antigen-specific, major histocompatibility complex-restricted specificity of T cells.

The recent characterization of MHC-displayed tumor-associated antigens that recognize effector cells of the immune system has created new perspectives for cancer therapy. Antibodies that recognize these tumor-associated MHC-peptide complexes with the same specificity as the T-cell antigen receptor will therefore be valuable tools for immunotherapy, as well as for studying antigen presentation in human cancers. Most tumor-associated antigens are expressed in only one or a few tumor types; however, specific T-cell epitopes derived from the Mucin-1 tumor-associated antigen (MUC1) that are widely expressed in many cancers were identified and shown to be recognized by CTLs. We selected a large nonimmune repertoire of phage Fab antibodies on recombinant human class I HLA-A2 complexes displaying an antigenic T-cell epitope derived from MUC1. High frequency of anti-MHC-peptide binders was observed (84%), and surprisingly, a high percentage (80%) of antibodies was fully specific for the MUC1 epitope. We isolated a surprisingly large panel of 16 different high-affinity human recombinant Fab antibodies that exhibited peptide-specific, MHC-restricted binding characteristics of T cells. The analyzed Fabs not only recognize the cognate MHC-peptide complex in a recombinant soluble form but also the native complex as displayed on the surface of antigen-presenting cells and breast tumor cells. Therefore, these findings demonstrate the ability to transform the unique fine specificity but low intrinsic affinity of T-cell receptors on T cells into high-affinity soluble antibody molecules endowed with a T-cell antigen receptor-like specificity. These molecules may prove to be very important and widely applicable for monitoring the expression of specific MHC-peptide complexes on the surface of tumor and immune cells for structure-function studies of T-cell receptor-peptide-MHC interactions, as well as for developing new targeting agents for immunotherapy.

Antibodies, Neoplasm↗

[Diarlex LA and Diarlex MB: study for direct detection of rotaviruses and adenoviruses in stools].

Gastro-enteritis have an important frequency in clinician consultation especially in pediatric department. Viral responsible for these diseases are, in most cases rotaviruses and adenoviruses. From the use of electronic microscopy, the identification of these viruses has advanced : Elisa methods are now usually used in that area. More recently, easier methods using sensitized latex particles (Diarlex LA Orion Diagnostica) and immunochromatography (Diarlex MB , Orion Diagnostica) appeared and,in that study, their accuracy is compared to the electronic microscopy (for Adenoviruses) and Elisa method IDEIA Rotavirus trade mark (Dako) (for rotaviruses). Reliability, easy use, immediate results and moderate cost may assure to these new tests a leader place in all kinds of clinical laboratories.

Adenoviridae↗

Evaluation of in-house optimized semi-nested PCR and EIA for direct detection of mycobacterial DNA in CSF.

A rapid and correct diagnosis of mycobacterial infections is important for effective patient treatment. Semi-nested-PCR with Fl-16 SOL, 16SOR and 16SNSR primers based on the 16S rRNA gene, under optimized conditions, can detect 499 bp amplified products from all tested mycobacteria. The assay could detect as little as 100 fg of mycobacterial DNA except for rapid growing mycobacteria, whose detection limits ranged from 1 ng to 10 pg. The specificities of the capture probes were assessed with 96 mycobacterial strains (22 species) and 33 nonmycobacterial strains (30 species). The specificities of pAll1, pTbc1 and pMar1 were 94%, 93% and 82%, respectively, and that of pAvi1, pInt1, pChe1 and pFor1 were 100%. The pTbc1 and pAvi1 were tested with DNA from 108 CSF samples, and the sensitivity and specificity of the detection method were 56% and 84% compared to culture and patient histories. The assay should be used for rapid detection and concurrent identification of slow growing mycobacteria without parallel conventional culture verification.

Animals↗

DNA diagnosis of cystic fibrosis by direct detection of the delta F508 mutation.

Cystic fibrosis (CF) is one of the most frequent recessive disorders among Caucasians. DNA analysis is performed by linkage analysis with DNA markers tightly linked to the CF gene. Cloning and sequencing of the cystic fibrosis gene, however, revealed that the major disease mutation is a phenylalanine deletion at amino acid position 508 of the mature protein (delta F508). These recent discoveries open great perspectives for the diagnosis of cystic fibrosis and for the detection of carriers in the normal population. In the present study we have used the polymerase chain reaction to detect the delta F508 mutation. This mutation was present on 80.3% of the CF chromosomes in the Belgian population. Twenty-three of 740 normal individuals (3.1%) were heterozygous carriers. Therefore, the frequency of heterozygous carriers in the Belgian population is estimated to be about 3.9% or 1 in every 26 individuals.

Cystic Fibrosis↗

Comparison of the automated Cobas Amplicor Mycobacterium tuberculosis assay with the conventional methods for direct detection of Mycobacterium tuberculosis complex in respiratory and extrapulmonary specimens.

OBJECTIVE: To evaluate the recently available Cobas Amplicor polymerase chain reaction (PCR) system for the detection of Mycobacterium tuberculosis complex (MTBC) in well-characterized clinical specimens and to compare the results with clinical classification, conventional culture and staining techniques. METHODS: Three hundred and forty-four clinical specimens consecutively received for culture of acid-fast bacilli by the laboratory of Zayed Military Hospital, Abu Dhabi, United Arab Emirates, from 2004 to 2005, were used in this study. Acid-fast bacilli and culture for tuberculosis were compared with Cobas Amplicor PCR. RESULTS: The final diagnostic evaluation of the Cobas Amplicor MTB showed the followings: sensitivity 73.3%, specificity 99.4%, positive predictive value 84.6%, negative predictive value 98.8% and with accuracy of 98.2% for the Cobas Amplicor MTB assay. CONCLUSION: The automated Cobas Amplicor MTB assay is suitable for routine use in clinical laboratories.

Bronchi↗