Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “clinical samples”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6Linked to original sources
PubMed1993

Use of PCR-mediated amplification of Mycobacterium leprae DNA in different types of clinical samples for the diagnosis of leprosy.

DNA of Mycobacterium leprae, obtained by a highly efficient nucleic acid extraction procedure, was used for standardisation of the amplification of an M. leprae-specific repetitive sequence by use of the polymerase chain reaction (PCR). With pure DNA, M. leprae-specific amplification was obtained with as low as 100 ag (1 ag = 10(-18) g) of target DNA, a quantity equal to about one-tenth of the bacterial genome. Optimal processing of different types of clinical samples such as biopsy material, blood and lymph fluid, from multibacillary leprosy patients, was studied. Simple freezing-boiling cycles in the presence of Triton X100, with some additional sample-specific modifications such as pre-treatment with NaOH to eliminate PCR inhibitors, was found to be sufficient to yield amplification of bacterial DNA in samples from paucibacillary patients. Clinical samples from 27 untreated leprosy patients, covering the various clinical forms of the disease, and with a bacterial index ranging from 5+ to 0, were collected and processed for PCR analysis. After hybridisation of the amplified material with a specific sequence, 25 of 27 patients analysed gave positive results for M. leprae in at least one of the samples. The potential of PCR for the diagnosis of leprosy is discussed.

Base Sequence↗
PubMed2006

Habitual physical activity and sedentary behaviour in a clinical sample of obese children.

OBJECTIVE: To objectively measure habitual physical activity and sedentary behaviour in a clinical sample of obese children and to compare with age- and sex-matched non-obese controls. DESIGN: Pairwise comparison of obese children matched for age and gender with non-obese controls. SUBJECTS: A total of 116 obese children (body mass index (BMI)> or =98th centile) and 53 non-obese control children (BMI<85th centile). Controls were matched with 53 of the obese children (mean age 8.6, s.d. 2.0 years; 25 M and 28 F). MEASUREMENT: Habitual physical activity and sedentary behaviour were measured over a 7-day period using CSA accelerometers. Total physical activity (mean accelerometry count per minute (c.p.m.)), percentage of monitored time in sedentary behaviour, light and moderate to vigorous intensity physical activity (MVPA) were compared. RESULTS: Obese children (n=116) spent on average 80.4% of their monitored time in sedentary behaviour and 2.5% of their monitored time in MVPA. Total activity (mean c.p.m.) was significantly higher in the non-obese group (n=53) than the obese group (n=53), 729 vs 648 c.p.m.; 95% confidence interval (CI) 7, 155. Time spent in sedentary behaviour averaged 80.9% (s.d. 6.6) in the obese group and 79.3% (s.d. 6.2) in the non-obese group, with no significant between-group difference (95% CI -3.9, 0.6). Light intensity activity was similar in the obese and non-obese groups (15.9 vs 17.3%; 95% CI -0.3, 3.0). Participation in MVPA was significantly higher in the non-obese vs obese group (3.9 vs 2.4%; 95% CI 0.6, 2.0). CONCLUSION: This study supports the hypothesis that a clinical sample of obese children is less physically active than non-obese children, although the difference in total activity and MVPA between the groups was small.

Acceleration↗
PubMed1995

Comparison of Amplicor, in-house PCR, and conventional culture for detection of Mycobacterium tuberculosis in clinical samples.

Five hundred four clinical specimens (337 sputum and 167 bronchial samples) from 340 patients were tested for the presence of M. tuberculosis complex by the Amplicor M. tuberculosis test and by an in-house PCR. The results were compared with those obtained by conventional culture and by direct microscopy. Thirty specimens (from 14 patients) were positive by in-house PCR, 25 (from 13 patients) were positive by the Amplicor M. tuberculosis test, and 24 (from 10 patients) were positive by culture. Cultures from 16 specimens were contaminated with other bacteria. Strong inhibition of in-house PCR was found with three samples. After discordancy analyses, with clinical data as supportive evidence for tuberculosis, 27 true-positive and 458 true-negative samples were defined. On the basis of these figures, the sensitivities of the Amplicor M. tuberculosis test, in-house PCR, culture, and microscopy were 70.4, 92.6, 88.9, and 52.4%, respectively. The specificities of all four tests were higher than 98%. The good performance of the in-house PCR for detection of M. tuberculosis makes it a very useful additional tool in M. tuberculosis diagnostics. In contrast, the Amplicor test needs to be improved. Twenty-three of the Amplicor-negative samples were further tested for inhibition of the Amplicor system by retesting the DNA extracts after the addition of M. tuberculosis DNA. In 15 of these samples, 5 true positives and 10 true negatives, inhibition of the Amplicor test was demonstrated. This might explain the lack of sensitivity of the Amplicor test. If the inhibition problem can be solved, the Amplicor M. tuberculosis test, which is already rapid, very user-friendly, and reasonably priced, may certainly become very useful in microbiological laboratories.

Bacteriological Techniques↗
PubMed2003

The contribution of perceived control of stressful life events and thought suppression to the symptoms of obsessive-compulsive disorder in both non-clinical and clinical samples.

The two studies presented in this paper investigated the impact of controllable versus uncontrollable stressful life events (SLE) and low versus high thought suppression upon symptoms of obsessive-compulsive disorder (OCD) in both a non-clinical sample (Study 1) and a clinical sample (Study 2). The sample for Study 1 consisted of 269 undergraduate university students and the sample for Study 2 consisted of 91 participants obtained from the Obsessive Compulsive and Anxiety Disorders Foundation of Victoria, Australia. Participants in both studies were given identical questionnaires measuring anxiety, depression, thought suppression, OCD, and, the control, magnitude and number of SLEs suffered during the previous 18 months. In both studies, analysis of covariance (ANCOVA) followed by post hoc tests indicated that high OCD scores were associated with high thought suppression and low perceived control over high magnitude stressful life events relative to controls. The results suggest that high thought suppression coupled with low control over stressful life events may interact with other predisposing factors, such as genetic vulnerability to produce OCD symptoms.

Adolescent↗
PubMed1999

Multiplex polymerase chain reaction for subgenus-specific detection of human adenoviruses in clinical samples.

The polymerase chain reaction (PCR) has been used previously for the detection and typing of adenoviruses directly in clinical samples. Since under clinical conditions subgenus-specific identification is often sufficient, we extended the genus- and type-specific PCR by a subgenus-specific PCR. By sequencing several loop I4 gene regions of the hexon (major adenovirus coat protein) and comparing them to published sequences, subgenus-specific sequences were identified in this region. By using primers targeted to this region and to a conserved hexon gene region, a multiplex, nonnested PCR for the detection and subgenus-specific identification of adenoviruses could be established. The six subgenus-specific amplimers are distinguishable by agarose gel electrophoresis, and subsequent restriction analysis is not necessary. The specificity of the subgenus-specific primer pairs was tested on 23 adenovirus prototypes, representing all six subgenera, on 9 subgenus B and D intermediate strains, and on 16 subgenus C genome types. Furthermore, multiplex, subgenus-specific PCR was performed directly with 100 clinical specimens, including stool samples, ocular swabs, and throat swabs. Adenoviruses of all subgenera could be detected. Especially for clinical application, the rapid, one-step differentiation between subgenus D adenoviruses, causing the severe and highly contagious epidemic keratoconjunctivitis, and subgenus B and E adenoviruses, causing relative harmless ocular infections, is of great importance. The subgenus-specific PCR could also facilitate the primary classification of unknown virus isolates.

Adenovirus Infections, Human↗
PubMed2005

Direct detection of Nocardia spp. in clinical samples by a rapid molecular method.

We developed a 16S PCR-based assay for the rapid detection of Nocardia spp. directly from human clinical samples. The applicability of the assay was confirmed by using 18 samples from patients with nocardiosis as diagnosed by conventional cultures and 20 clinical samples from patients with confirmed tuberculosis used as negative controls.

Biopsy↗
PubMed2001

Comparison of the adaptive functioning of children prenatally exposed to alcohol to a nonexposed clinical sample.

BACKGROUND: Several studies show impairments in the social and adaptive behaviors of children prenatally exposed to alcohol. However, there remains limited consensus on whether the alcohol exposure directly affects social functioning or whether its effect is mediated by deficits in IQ. In addition, no studies have investigated whether deficits in social functioning are significantly more pronounced in children prenatally exposed to alcohol than in children referred to psychiatric treatment who were not prenatally exposed. We explored the effect of alcohol exposure on social and adaptive functioning and explored whether or not social and adaptive functioning are significantly more impaired in children prenatally exposed to alcohol than in a clinical sample of children. METHODS: A sample of 33 alcohol-exposed children was compared with a sample of 33 clinic-referred nonexposed children. The groups were compared on measures of communication, daily living skills, and socialization. The groups were matched on sex, age, IQ, and outpatient or inpatient status. RESULTS: Analyses revealed that the prenatally alcohol-exposed children did not differ significantly from the nonexposed children in any of the domains of adaptive functioning. However, with age, exposed children showed a more rapid decline in socialization standard scores compared with the nonexposed clinical sample. CONCLUSIONS: Young children who were exposed to alcohol prenatally show deficits in all domains of adaptive functioning. Although these deficits do not seem to differ from those exhibited by young children with psychiatric problems but no prenatal exposure, deficits in socialization behavior of prenatally exposed children may become more significant with age.

Adaptation, Psychological↗
PubMed1993

Detection of bluetongue virus in clinical samples by polymerase chain reaction.

A previously described bluetongue virus (BTV) serogroup polymerase chain reaction (PCR) assay was applied to clinical samples. The sensitivity of the BTV serogroup PCR was increased by the use of non-radioactive chemiluminescent hybridization. Unfractionated whole blood samples from rams experimentally inoculated with cell culture-adapted BTV-11 UC-8 were analyzed by virus isolation (VI) on Vero cells and PCR. VI and PCR were in agreement, with the exception of 3 blood samples that were VI negative and PCR positive. In semen spiked with BTV-11 UC-8, PCR detected as little as 1.6 x 10(2) plaque-forming units of BTV/ml of semen. BTV in the spleen of a sheep submitted for necropsy for suspect BTV infection was detected by both PCR and VI in embryonated chicken eggs. BTV PCR with nonradioactive chemiluminescent hybridization resulted in a level of sensitivity comparable to that of VI and likely more sensitive than VI on Vero cells for blood. This BTV PCR has great promise for rapid, sensitive, and specific detection of active BTV infection in a variety of clinical samples.

Animals↗
PubMed1989

Detection of Mycoplasma pneumoniae in simulated clinical samples by polymerase chain reaction. Brief report.

Polymerase chain reaction (PCR) was used to detect Mycoplasma (M) pneumoniae DNA in simulated clinical samples. Throat swabs were mixed with known amounts of broth-grown M. pneumoniae cells. An estimated detection limit of less than 40 colony forming units (cfu) was obtained without the need for time-consuming hybridization. The PCR is completed in one day and may be useful for the early detection of M. pneumoniae in clinical samples.

DNA, Bacterial↗
PubMed1994

Rapid detection of mycobacterial DNA in clinical samples by multiplex PCR.

Triplex-polymerase chain reaction technique (PCR) was developed for the detection and identification of mycobacterial DNA sequences in uncultured clinical samples. A 123 bp fragment corresponding to a specific Mycobacterium tuberculosis sequence complex, a 383 bp DNA fragment encoding for part of the 65 kD mycobacterial surface antigen, and a 268 bp fragment of the human beta-globin gene to demonstrate the presence of suitable DNA were amplified by triplex PCR. To demonstrate the applicability of this method, 206 alcohol-fixed, paraffin-embedded sputum samples from 47 patients with culture-proven tuberculosis were investigated. Of 206 samples, 157 were PCR positive, resulting in correct diagnosis of tuberculosis in 46 of 47 (97.8%) patients. Furthermore, 165 alcohol-fixed, auramin-stained sputum smears were examined in a blind trial. Triplex PCR revealed tuberculosis in 20 of 21 samples from patients with tuberculosis. In comparison, cultures were positive in 20 of 21 samples, and acid-fast organisms were found by microscopy in 18 of 21 samples. We conclude that triplex PCR is a rapid and sensitive technique for the detection of mycobacterial DNA in uncultured clinical samples and offers equivalent sensitivity (95.2%) and specificity (98.6%) as do culture methods.

Base Sequence↗
PubMed1994

Detection of measles virus from clinical samples using the polymerase chain reaction.

OBJECTIVE: To evaluate the usefulness of the polymerase chain reaction to detect the measles virus sequence using clinical samples. DESIGN: Centers for Disease Control and Prevention case definition of measles with or without IgM serology as a standard. SETTING: A laboratory in the Department of Pediatrics of the Hokkaido University Hospital, Sapporo, Japan. PATIENTS: Thirty-two serum samples, 16 throat swab samples, and nine cerebrospinal fluid samples from 32 patients with measles, including four patients with central nervous system involvement, and one serum sample and two throat swab samples from two patients with modified courses of measles were obtained. Ten serum samples, 10 throat swab samples, and 10 cerebrospinal fluid samples were obtained from patients without apparent measles infection as negative controls. MEASUREMENTS AND MAIN RESULTS: Sensitivity and specificity were comparable with those as obtained by culture or other methods reported in the literature. The polymerase chain reaction was positive in 24 (75.0%) of 32 by serum samples and in 13 (81.3%) of 16 by throat swab samples from the patients with measles, in contrast to none within the negative control group. In three of the four patients with central nervous system involvement, the measles virus sequence was detected in cerebrospinal fluid samples obtained within 1 day following the onset of the manifestations. All three samples from the patients with modified measles yielded positive results. CONCLUSIONS: The polymerase chain reaction can be used with sufficient sensitivity and specificity to detect the measles virus sequence using clinical samples. Transient and direct invasion of the central nervous system by this virus at the initial stage of the central nervous system involvement was strongly suggested.

Adolescent↗
PubMed1997

Characterization of monoclonal antibodies for rapid identification of Actinomyces naeslundii in clinical samples.

The purpose of this study was to generate highly specific serological reagents for the quantitative identification of Actinomyces naeslundii in clinical samples, in particular dental plaque. Balb/c mice were immunized with pasteurized human A. naeslundii strains representing different genospecies and serotypes. Ten hybrid cell lines secreting monoclonal antibodies reactive with A. naeslundii were isolated and characterized. Antibody specificity was determined by indirect immunofluo-rescence and enzyme-linked immunosorbent assay using strains from 59 species and by immunofluorescence analyses of supragingival plaque from 10 gingivitis patients. Nine monoclonal antibodies reacted selectively with A. naeslundii, whereas one additionally bound to Actinomyces israelii. They recognized at least nine different epitopes with characteristic expression patterns among the test strains. Six clusters of antigenically unique or closely related strains could be distinguished. Clusters 1, 4, and 5 represented by 12, 18, and 5 strains, respectively, comprised over 80% of the A. naeslundii strains tested. All reference strains for genospecies 1 grouped with cluster 1. Strains associated with genospecies 2 fell into clusters 4 and 5. Tests with mutant strains indicated that three monoclonal antibodies recognize type 2 and one type 1 fimbriae of genospecies 2. Only four isolates grouped with clusters 2 and 3 characterized by the expression of cluster-specific antigens. Interestingly, cluster 2 and 3 bacteria were markedly more abundant in vivo than indicated by their sparse representation in our strain collection. Overall, all but one of the new monoclonal antibodies should prove of value for the serological classification and rapid quantitative determination of A. naeslundii in clinical samples.

Actinomyces↗
PubMed2002

Polymerase chain reaction as a sensitive and rapid method for specific detection of Mycoplasma pneumoniae in clinical samples.

The fast diagnosis of Mycoplasma primary atypical pneumonia is impaired by the lack of routinely available culture methods for isolation of Mycoplasma pneumoniae from clinical specimens. Likewise, serological methods commonly used for diagnosis are insensitive and non-specific. In this study, we have established and applied the polymerase chain reaction (PCR) technique to detect M. pneumoniae DNA in clinical samples originating from the respiratory tract. The PCR results were compared with those from culture and serology tests. To standardize the detection of M. pneumoniae by PCR, we first used DNA from culture grown organisms and clinical samples seeded with M. pneumoniae. PCR amplification was performed with M. pneumoniae-specific primers to amplify 144, 153 and 631 bp DNA fragments by using primer pairs MP5-1/MP5-2, P1-178/P1-331 and P1-178/P1-809, respectively. The amplification of the 631 bp DNA fragment was found to be most sensitive for the detection of M. pneumoniae. Using the most sensitive PCR, a total of 47 respiratory specimens from patients suspected of community acquired pneumonia were tested. While none of the specimens were positive for M. pneumoniae in culture, 6 specimens gave positive results by PCR. In 4 out of the 5 PCR positive samples tested serologically, the results were supported by elevated levels of anti-mycoplasma IgG/IgM/IgA. Thus, these results suggest that PCR is the most sensitive method to detect M. pneumoniae in clinical specimens.

Adult↗
PubMed1992

[Comparison of the Bacter system and Löwenstein-Jensen medium for cultivation of Mycobacterium tuberculosis in clinical samples].

Over a period of two years, 1364 clinical samples from pulmonary sources, were studied in order to compare the Bactec-TB system with the Löwenstein-Jensen medium, for isolation of mycobacteria. Within this period of time, 93 strains of Mycobacterium tuberculosis were isolated, 71 (76%) were isolated by the Bactec system, and 69 (74%) were isolated by the Löwenstein-Jensen. The number of contaminations was lower for the Bactec system (3.2%) than for the Löwenstein-Jensen medium (5.3%). The mean time of isolation with the Bactec was 16.4 days. The mean time of isolation with Löwenstein-Jensen medium was 21.9 days. Identification of the strains with the Bactec system by the p-nitro-a-acetilamin-beta-hidroxipropiphenone inhibition test gave a 100% correlation with the conventional biochemical methods used for the identification of the same strains growth of Löwenstein-Jensen.

Bacteriological Techniques↗
PubMed1992

Detection of CMV DNA in clinical samples of AIDS patients by chemiluminescence hybridization.

A sensitive chemiluminescence dot-blot hybridization assay for the detection of CMV DNA in clinical samples of AIDS patients is described. In the chemiluminescence hybridization assay, digoxigenin-labelled CMV DNA probes were used and when hybridized they were detected by anti-digoxigenin Fab fragments conjugated with alkaline phosphatase. Adamantyl 1,2-dioxetane phenyl phosphate was used as the chemiluminescent substrate. The results were recorded by instant photographic films. The results obtained with the chemiluminescence hybridization assay were compared with the results obtained by hybridization with colourimetric detection. The chemiluminescent assay proved specific, sensitive and reliable and thus can be used as a valuable routine diagnostic test for the detection of CMV DNA in clinical samples.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Detection of epizootic hemorrhagic disease virus serotypes 1 and 2 in cell culture and clinical samples using polymerase chain reaction.

The potential for the use of the polymerase chain reaction (PCR) in detecting epizootic hemorrhagic disease virus (EHDV) ribonucleic acid in cell cultures and clinical samples was studied. Using oligoribonucleotide primers selected from genome segment 6 of EHDV-2 (Alberta strain), the PCR-based assay resulted in a 387-base pair (bp) PCR product. EHDV RNA from US prototype serotypes 1 and 2 and a number of EHDV field isolates, propagated in cell cultures, were detected by this EHDV PCR-based assay. Amplification products were visualized on ethidium bromide-stained agarose gels or detected by chemiluminescent hybridization. The sensitivity of the PCR assay was 100 fg of virus RNA (equivalent to 6 x 10(3) virus particles) with ethidium bromide-stained agarose gels. Chemiluminescent hybridization increased the sensitivity of the PCR assay 1,000 times, and specific signals were detected from 0.1 fg of virus RNA (equivalent to 6 virus particles). Amplification product was not detected when the PCR-based assay was applied to RNA from the US bluetongue (BT) virus prototype serotypes 2, 10, 11, 13, and 17 or total nucleic acid extracts from uninfected baby hamster kidney-21 cells, Vero cells, and blood cells from deer that were EHDV seronegative and virus isolation negative. Application of this EHDV PCR-based assay to clinical samples resulted in detection of EHDV RNA from blood and spleen samples from a deer in California with clinical hemorrhagic disease. This EHDV PCR-based assay could provide a rapid, sensitive, and specific assay for detection of EHDV infection in susceptible ruminants.

Animals↗
PubMed1997

Evaluation of a nonradiometric system (BACTEC 9000 MB) for detection of mycobacteria in human clinical samples.

This study was carried out to evaluate the rate of recovery and time required for detection of mycobacteria from pulmonary and extrapulmonary human clinical samples, by using a fluorescence-quenching-based oxygen sensor (BACTEC 9000 MB; Becton Dickinson Microbiology Systems, Sparks, Md.). The results were compared with those obtained by microscopy, conventional culture in Lowenstein-Jensen (LJ) medium, and a BACTEC radiometric system (BACTEC 460 TB; Becton Dickinson). Of the 779 clinical samples processed, 364 from pulmonary sites and 415 from extrapulmonary sites, 62 (7.9%) were positive for mycobacterial isolates; of the positive samples, 59 (95.1%) were detected with the fluorescent BACTEC 9000 MB system, 57 (91.9%) were detected with the radiometric system (BACTEC 460 TB), and 43 (69.3%) were detected with LJ conventional culture. The mean times to detection of all mycobacteria with BACTEC 9000 MB and BACTEC 460 TB were similar (10.3 and 10.0 days, respectively). The results obtained indicate that the nonradiometric BACTEC (BACTEC 9000 MB) system is as efficient as Bactec 460 TB and significantly more efficient than LJ for the rapid recovery of mycobacteria from both pulmonary and extrapulmonary clinical specimens. Though the BACTEC 9000 MB system is recommended for respiratory specimens, we demonstrated that it can be successfully used also for recovery of mycobacteria from clinical specimens from various extrapulmonary sites.

Bacteriological Techniques↗
PubMed1997

Prenatal diagnosis of rubella virus infection by direct detection and semiquantitation of viral RNA in clinical samples by reverse transcription-PCR.

A reverse transcription-nested PCR (RT-nPCR) method for prenatal diagnosis of rubella virus (RV) infection was developed. In the first step of RT-nPCR a synthetic RNA molecule (pRRV) differing from the RV target sequence by having a 21-nucleotide insertion was used as the internal control of amplification for the detection of PCR inhibitors. In addition, comparison of pRRV and RV-specific PCR signals allowed for the semiquantitation of RV input target sequences (range, 10 to > and = 1,000 RV genomes). In parallel, a complete RT-nPCR assay was performed with the same samples in the absence of the internal control to confirm the results of the first step and to detect RV RNA-positive samples containing < 10 RV genomes. Subsequently, the RT-nPCR method was used to examine retrospectively clinical samples (direct RT-nPCR) from eight congenitally infected and eight uninfected fetuses for RV RNA. RT-nPCR was also used to detect RV RNA in cell cultures (culture-RT-nPCR) 96 h after inoculation with the same specimens. With amniotic fluid (AF) samples, direct RT-nPCR identified eight of eight cases of RV transmission (sensitivity, 100%), whereas culture-RT-nPCR and virus isolation detected only six of eight cases (sensitivity, 75%). However, when the culture-RT-nPCR results were positive, culture-RT-nPCR confirmed the direct RT-nPCR results 3 days to 3 weeks earlier than virus isolation. The specificity of direct RT-nPCR was 100%, with eight of eight uninfected fetuses being negative. Semiquantitation showed only small amounts (< and = 100 copies) of viral RNA in clinical samples. In conclusion, direct RT-nPCR with AF samples (i) shows 100% sensitivity and specificity for prenatal diagnosis of RV infection and (ii) is a rapid technique, giving results in 24 to 48 h after sampling.

Base Sequence↗