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PubMed1997

The alcohol use disorder and associated disabilities interview schedule (AUDADIS): reliability of alcohol and drug modules in a clinical sample.

The alcohol use disorder and associated disabilities interview schedule (AUDADIS), was designed for use in the general population, and was previously shown to have good reliability in a sample of household residents. However, measurement problems are different in clinical samples. Thus, a test-retest study was conducted of the AUDADIS in a clinical sample of 296 substance-using patients from substance- and psychiatrically-identified treatment settings. Reliability for current drug-specific AUDADIS dependence diagnoses was good to excellent for high-prevalence as well as low-prevalence drug categories. Reliability for abuse diagnoses was not as good, although this was due to the hierarchical nature of the abuse diagnosis itself, rather than its defining criteria. Demographic and other factors were investigated for their potential effects on the reliability of alcohol and cocaine diagnoses; low severity was the only consistent predictor of unreliability for both of these categories. Reliability of consumption variables was generally good, with a few notable exceptions. Results suggest that the AUDADIS can be used in research comparing treated to community samples of individuals with alcohol and drug diagnoses.

Adolescent↗
PubMed2003

Readiness to adopt a self-management approach to pain: evaluation of the pain stages of change model in a non-pain-clinic sample.

The Transtheoretical model of stages of behaviour change has stimulated research interest in relation to chronic pain, yet studies using the Pain Stages of Change Questionnaire (PSOCQ; Pain (72) 1997 227) have reported inconsistent findings and have generally utilized pain-clinic samples. The aims of the current study were to assess the general validity of the PSOCQ with a non-pain-clinic sample of patients with chronic pain, and to examine the utility of the stages of change model as applied to this population. The study employed multi-stage, cluster-sampling methodology, with 90 participants recruited from 19 medical and allied health clinics and practices. The findings demonstrated a number of limitations of the PSOCQ in terms of its ability to classify individuals into specific stages of change. The stages of change model requires adaptation in order to be useful for treatment planning in a non-pain-clinic sample of patients with chronic pain.

Adult↗
PubMed2003

Exploratory factor analysis of the Wechsler Abbreviated Scale of Intelligence (WASI) in adult standardization and clinical samples.

Exploratory factor analyses were conducted separately on the Wechsler Abbreviated Scale of Intelligence (WASI; The Psychological Corporation, 1999) adult standardization sample (n = 1,145) and a diagnostically heterogeneous adult clinical sample (n = 201). In the latter group, means for age, education, and WASI Full Scale IQ were 59.25 years (SD = 17.52), 12.39 years (SD = 2.88), and 89.91 (SD = 16.00). For each sample, the four WASI subtests were subjected to a principal-axis factor analysis followed by varimax and promax rotations. Two factors were specified to be retained. Verbal Comprehension and Perceptual Organization factors were identified in both analyses. Coefficients of congruence were 0.98 for Factor I and 0.99 for Factor II, suggesting factorial equivalence across the standardization and clinical samples.

Adolescent↗
PubMed2005

Surveillance of extended-spectrum beta-lactamases from clinical samples and faecal carriers in Barcelona, Spain.

OBJECTIVES: The aim of the present study was to characterize and compare the extended-spectrum beta-lactamase (ESBL)-producing organisms isolated from clinical samples and faecal carriers in 2001 and 2002. METHODS: A total of 5251 Enterobacteriaceae isolated from clinical samples and 1321 stool samples were evaluated for the presence of ESBLs. The stool samples were spread onto plates of MacConkey agar containing 2 mg/L cefotaxime for selection of ESBL-producing strains. These strains were defined as those showing synergism between amoxicillin/clavulanic acid and third-generation cephalosporins. The beta-lactamases involved were characterized by isoelectric focusing, PCR assays and DNA sequencing. RESULTS: The prevalence of ESBL-producing strains among clinical Enterobacteriaceae was 1.7%. Of these, 87.6% produced CTX-M, 25.8% produced SHV and 2.2% were TEM-type-producing strains. All clinical ESBL-producing strains were Escherichia coli, with the exception of four Klebsiella pneumoniae and one Citrobacter freundii. The prevalence of faecal carriage of ESBL-producing organisms was 3.3%. Of these, 75% produced CTX-M-type enzymes followed by 22.7% SHV-producing strains. All faecal ESBL-producing strains were E. coli except for one Enterobacter cloacae and one Proteus mirabilis. This latter strain produced the PER-1 enzyme reported for the first time in Spain. CONCLUSIONS: The prevalence of ESBL-producing strains in stool samples was higher than that observed in clinical samples from the same period. The different types of ESBLs found were similar in both contexts. The most prevalent ESBLs were the CTX-M-related enzymes, with nine different types, followed by SHV-12.

Carrier State↗
PubMed2004

Development of a real-time reverse-transcription PCR for detection of newcastle disease virus RNA in clinical samples.

A real-time reverse-transcription PCR (RRT-PCR) was developed to detect avian paramyxovirus 1 (APMV-1) RNA, also referred to as Newcastle disease virus (NDV), in clinical samples from birds. The assay uses a single-tube protocol with fluorogenic hydrolysis probes. Oligonucleotide primers and probes were designed to detect sequences from a conserved region of the matrix protein (M) gene that recognized a diverse set (n = 44) of APMV-1 isolates. A second primer-probe set was targeted to sequences in the fusion protein (F) gene that code for the cleavage site and detect potentially virulent NDV isolates. A third set, also directed against the M gene, was specific for the North American (N.A.) pre-1960 genotype that includes the common vaccine strains used in commercial poultry in the United States. The APMV-1 M gene, N.A. pre-1960 M gene, and F gene probe sets were capable of detecting approximately 10(3), 10(2), and 10(4) genome copies, respectively, with in vitro-transcribed RNA. Both M gene assays could detect approximately 10(1) 50% egg infective doses (EID(50)), and the F gene assay could detect approximately 10(3) EID(50). The RRT-PCR test was used to examine clinical samples from chickens experimentally infected with the NDV strain responsible for a recent epizootic in the southwestern United States. Overall, a positive correlation was obtained between the RRT-PCR results and virus isolation for NDV from clinical samples.

Animals↗
PubMed1998

Working models of attachment and representations of the object in a clinical sample of sexually abused women.

This study examined internal working models of attachment as assessed by the Adult Attachment Interview (AAI; George, Kaplan, & Main, 1984) and self-other differentiation as assessed by the Description of Significant Other (Marziali & Oleniuk, 1990) in a clinical sample of 40 women reporting a history of childhood sexual abuse. Although there was some relationship between the two measures, the association was not strong. The Cannot Classify category of the AAI, which is increasingly being assigned in clinical samples, needs refinement to increase the usefulness of the AAI for clinical purposes. Integration of concepts from objects relations theory may also enhance the value of the AAI in studies of clinical samples.

Adult↗
PubMed2001

Development of an ICP-HRIDMS method for accurate determination of traces of silicon in biological and clinical samples.

An inductively coupled plasma-high resolution isotope dilution mass spectrometric (ICP-HRIDMS) method in combination with a microwave-assisted decomposition technique has been developed for the determination of traces of silicon in biological and clinical samples. A 30Si-enriched spike solution was used for the isotope dilution step. Decomposition of the samples was achieved by use either of HNO3 or a mixture of HNO3 and HF. By application of both methods of digestion to the same sample it was possible to differentiate between a poorly soluble silicate fraction and an HNO3-soluble silicon species. Traces of silicon were determined in different reference materials, which are not certified for this element, and in other biological and clinical samples. A concentration range of 1-600 microgram g(-1) was covered by the different samples. For homogeneous samples relative standard deviations of 2-4% were obtained. The detection limit was strongly affected by the blank. In this connection purification of water, used in the analytical procedure, was especially critical. The blank contribution of the ICP-MS instrument could be minimized by applying a nebulizer and a spray chamber made of PFA, a sapphire injection tube, and a silicon nitride torch. Under these conditions detection limits of 0.15 microgram g(-1) and 0.2 microgram g(-1) were obtained for the HNO3 and HNO3-HF digestion methods, respectively, when a sample weight of 0.5 g was used. With regard to expected silicon content this enables determination in almost all biological and clinical samples. The ICP-HRIDMS results were compared with those recently obtained in an interlaboratory study. This isotope-dilution method is an potential option for certification of silicon in reference materials, a method for which is still required.

Animals↗
PubMed2002

Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain.

AIMS: To study the phenotypic characteristics of Aeromonas spp. from environmental and clinical samples in Spain and to cluster these strains by numerical taxonomy. METHODS AND RESULTS: A collection of 202 Aeromonas strains isolated from bivalve molluscs, water and clinical samples was tested for 64 phenotypic properties; 91% of these isolates were identified at species level. Aeromonas caviae was predominant in bivalve molluscs and Aerom. bestiarum in freshwater samples. Cluster analyses revealed eight different phena: three containing more than one DNA-DNA hybridization group but including strains that belong to the same phenospecies complex (Aerom. hydrophila, Aerom. sobria and Aerom. caviae), Aerom. encheleia, Aerom. trota and three containing unidentified Aeromonas strains isolated from bivalve molluscs. CONCLUSIONS: Aeromonas spp. are widely distributed in environmental and clinical sources. A selection of 16 of the phenotypical tests chosen allowed the identification of most isolates (91%), although some strains remain unidentified, mainly isolates from bivalve molluscs, suggesting the presence of new Aeromonas species. Numerical taxonomy was not in total concordance with the identification of the studied strains. SIGNIFICANCE AND IMPACT OF THE STUDY: Numerical taxonomy of Aeromonas strains isolated from different sources revealed the presence of potentially pathogenic Aeromonas spp., especially in bivalve molluscs, and phena with unidentified strains that suggest new Aeromonas species.

Aeromonas↗
PubMed1998

Comparison of culture and acid-fast bacilli stain to PCR for detection of Mycobacterium tuberculosis in clinical samples.

The major drawback in effective use of polymerase chain reaction (PCR) for detecting Mycobacterium tuberculosis (MTB) in clinical samples is the presence of PCR inhibitors and unique cell components of the organism that complicate DNA extraction and subsequent PCR amplification. A PCR assay with a unique multistep DNA extraction method that minimizes these problems was compared in a prospective study to acid-fast bacilli stain (AFBS) and culture for detecting MTB in clinical samples. A total of 254 clinical specimens in two separate studies were processed for MTB by these techniques. While PCR and culture were 100% sensitive and specific, culture required up to 8 weeks of incubation and additional time to perform biochemical testing to identify the isolated micro-organism. Acid-fast bacilli stain had a specificity of about 87% and did not differentiate among Mycobacterial species. In contrast, the results from PCR were available within 48 h and did not require additional testing to attain a final result. Polymerase chain reaction was highly reliable for detection and confirmation and interpretation of positive AFBS results. The assay was easy to perform with a turn around time of about 2 days.

Bacteriological Techniques↗
PubMed2000

Single-tube multiplex PCR for rapid and sensitive diagnosis of subgenus B and other subgenera adenoviruses in clinical samples.

We developed a new diagnostic method of subgenus (Sub) B adenovirus (Ad) in clinical samples using non-nested polymerase chain reaction (PCR). Sequences of the conserved hexon-coding region of representative strains of eight serotypes (3, 7, 11, 14, 16, 21, 34 and 35) of Sub B Ad were heterogeneous. In order to distinguish Ad serotype 3 (Ad 3) and Ad 7 from the other serotypes of Sub B Ad, and to differentiate Ad 3 and 7 from each other, 3 different downstream primers were designed based on the sequence heterogeneity. By a single-tube PCR method using a combination of 6 primers including the 3 new primers, Ads demonstrated to amplify 188, 206, 284, and 301 bp DNA fragments for Ad 3, Ad 7, other Sub B Ads, and non-Sub B Ads, respectively. A total of 114 clinical samples were selected to evaluate the direct applicability of our PCR. The results were compared with previous culture results. Sixty-seven out of 71 (94%) Sub B Ad culture-positive samples, and 15 out of 19 (79%) Sub C or E-positive samples amplified products of the expected size. Two of 20 (10%) culture-negative samples from pharyngoconjunctival fever patients were identified as Ad 3 by the PCR. Four samples, from which non-Ad viruses were isolated, were negative by the PCR. The present study might provide a rapid and sensitive diagnosis method for infections caused by Sub B Ads.

Adenovirus Infections, Human↗
PubMed2005

Direct detection in clinical samples of multiple gene mutations causing resistance of Mycobacterium tuberculosis to isoniazid and rifampicin using fluorogenic probes.

BACKGROUND: This study evaluates a method based on real-time PCR for direct detection in clinical samples of the common mutations responsible for isoniazid and rifampicin resistance of Mycobacterium tuberculosis. METHODS: Six pairs of fluorogenic 5' exonuclease probes (Taqman), mutated and wild-type, were designed for six targets: codon 315 of katG, substitution C209T in the regulatory region of inhA, and codons 513, 516, 526 and 531 of rpoB. RESULTS: A total of 98 clinical samples harbouring resistant bacilli from 55 patients and 126 samples harbouring susceptible bacilli from 126 patients were processed. The isolates from samples were tested for drug susceptibility with the radiometric method and sequenced for the same genetic targets. Among the samples, 93 harboured isoniazid-resistant bacilli. According to the sequencing results, 30 had mutations in katG, 30 in inhA and 33 (35.4%) had no mutations in these targets. All 27 clinical specimens harbouring rifampicin-resistant bacilli showed mutations in rpoB. The detection threshold of this method in detecting target genes in serial dilutions of artificial samples was 1.5 x 10(3) cfu/mL. In clinical samples, the sensitivity ranged from 30.4 to 35.3% for smear-negative samples and from 95.1 to 99.2% for smear-positive samples, with a specificity of 100%. In this study, the overall sensitivity in detecting patients having the target mutations was 74.3%. CONCLUSIONS: The main advantage of the described method is the possibility of detecting rifampicin and isoniazid resistance within 48-72 h after sample collection, with a sensitivity of nearly 100% in smear-positive samples if the chosen target is responsible for the resistance.

Antitubercular Agents↗
PubMed1988

[A study of 6-day subrenal capsule assay with cyclophosphamide pretreatment--histological evaluation of clinical samples].

In order to suppress the host immune reaction in subrenal capsule assay (SRCA), effect of cyclophosphamide (CPM) was evaluated histologically in 25 fresh clinical samples. In 21 out of 25 clinical samples, the extent of lymphocyte infiltration was minimal, and in all samples the host reaction was suppressed significantly by CPM pretreatment. However, tumor cells were well preserved in only 10 out of 20 samples obtained from esophageal cancer patients. With the samples obtained from gastric and colorectal cancer patients, there were no tumor cells in the subrenal space on day 6. Persistence of tumor cells was well recognized in the samples having rich tumor and less stromal cells. The xenografts with moderately to well-preserved cancer cells showed an increase of the tumor size as expressed by delta TS. Though many xenografts showed a positive delta TS, preservation of tumor cells was poor. In each of the drug treated groups, a decrease of the tumor size and the histological effects were well correlated. It is suggested that 6-day SRCA with CPM pretreatment is useful as a chemosensitivity test, especially for the esophageal cancer whose tumor cells were well preserved.

Colonic Neoplasms↗
PubMed2005

Relative sensitivity of polymerase chain reaction assays used for detection of feline herpesvirus type 1 DNA in clinical samples and commercial vaccines.

OBJECTIVE: To determine relative detection rates and detection limits for 6 published polymerase chain reaction (PCR) assays used for detection of feline herpesvirus type 1 (FHV-1) DNA. SAMPLE POPULATION: 5 vaccines licensed for use in preventing FHV-1-associated disease; 15 conjunctival biopsy specimens collected from cats with keratitis, conjunctivitis, or both; and a plaque-purified field isolate of FHV-1 cultured in vitro. PROCEDURE: Vaccines and clinical samples were assessed for FHV-1 DNA by use of all 6 assays. Detection rates were calculated by assuming that any sample in which FHV-1 DNA was detected was a true-positive result. Detection limits were estimated by use of serial dilutions of DNA extracted from cultured FHV-1 and 1 clinical sample. RESULTS: Testing by use of all 6 assays resulted in detection of FHV-1 DNA in all 5 vaccines. Testing by use of all 6 assays yielded concordant results for 9 of 15 conjunctival biopsy specimens (8 with negative results and 1 with a positive result). Calculated detection rates for clinical samples ranged from 29% to 86%. Assay sensitivity was ranked similarly by use of detection rate or detection limit. CONCLUSIONS AND CLINICAL RELEVANCE: Testing by use of all assays was equally likely to detect vaccine virus. Therefore, a positive PCR result in a cat may reflect vaccine virus rather than wild-type virus. Test sensitivity as assessed by detection limits and detection rates varied greatly. Because FHV-1 can be shed in clinically normal animals, high detection rate will not necessarily correlate with high diagnostic sensitivity.

Animals↗
PubMed2006

Prevalence of dermatophytes and other fungal agents isolated from clinical samples.

The common cause of skin infections are dermatophytes and opportunistic fungi. Aim of this study was to isolate and identify the fungal agents from clinical samples from patients with different mycoses. Clinical samples from 165 patients were subjected to potassium hydroxide (KOH) examination and culture isolation; causative agents were identified macroscopically and microscopically. All the 165 specimens were KOH positive and 110/165 (66.7%) samples were culture positive. Of these, highest isolation rate was obtained in opportunistic mycoses such as candidiasis (29/29, 100%). Dermatophytes were isolated in 53/80 (66.3%) specimens and Trichophyton rubrum was the commonest isolate in skin samples (17/24) among the patients suffering from dermatophytosis. Phaeoannellomyces wernecki was isolated in a patient suffering from tinea nigra. The study signifies the importance of mycological examination in the diagnosis of various mycoses for their effective management.

Arthrodermataceae↗
PubMed2003

Incidence of Listeria monocytogenes in food and environmental samples in Italy between 1990 and 1999: serotype distribution in food, environmental and clinical samples.

We report the findings of the study of 4185 food samples and 958 environmental samples collected in Italy in the period 1990-1999 and tested for the presence of Listeria monocytogenes. The strains isolated were biochemically and serologically characterised. We found a fairly high percentage of L. monocytogenes contamination in food (12.8%), whereas the level of contamination was lower in the environment (environment and work surfaces in food processing plants) (6.1%). Serotyping showed a prevalence of a few serotypes (i.e., 1/2a, 1/2b, 1/2c and 4b), which were the same as those found in clinical samples collected during outbreaks and from sporadic cases of listeriosis reported in Italy in the period considered. The geographical distribution of the strains of L. monocytogenes isolated from food samples is very similar to that of the clinical strains.

Disease Outbreaks↗
PubMed2006

A comparison of five methods for extracting DNA from paucicellular clinical samples.

Translational protocols in cancer and carcinogenesis often require isolation of genomic DNA from paucicellular clinical samples. DNA extraction methods for PCR-based applications should optimize the recovery of amplifiable DNA. We compared five methods for DNA extraction in paucicellular epithelial and lymphocyte samples using proportion of extractions producing amplifiable DNA and mean real-time PCR Ct values for GAPDH as the endpoint measures. The methods included solid-phase DNA adsorption (QIAamp), sequential protein and DNA precipitation (Puregene), magnetic bead adsorption (Dynabeads), phenol-chloroform extraction, and single-step proteinase K digestion. In general, the performance of the three commercial kits was superior to either phenol-chloroform extraction or single-step proteinase K digestion. However, QIAamp and Puregene produced amplifiable DNA more frequently than Dynabeads for starting cell numbers <50,000. GAPDH Ct values for QIAamp extractions showed the greatest dynamic range and the best linearity across the range of starting cell numbers, but QIAamp was not statistically significantly superior to Puregene. Of the three commercial kits, Puregene is the least expensive. QIAamp and Puregene DNA extraction methods are well-suited for the preparation of paucicellular clinical samples for PCR-based assays.

Cell Line, Tumor↗
PubMed2006

A new MSPQC system for rapid detection of pathogens in clinical samples.

A new multi-channel series piezoelectric quartz crystal (MSPQC) system for detection of pathogens in clinical sample was proposed. Some factors, which affect the detection of pathogens by using MSPQC, were all investigated. A total of 650 clinical samples were detected by MSPQC and compared with licensed BACTEC 9120 system (Becton Dickinson Diagnostic Instrument Systems, Sparks, MD, USA) simultaneously in the Third Xiangya Hospital of Central South University, China. When the incubation period was 5 days, two systems had similar detected results: the MSPQC system detected 123 growth of 650 (18.92%) bottles while the BACTEC 9120 detected 125 growth of 650 (19.23%) bottles. The MSPQC had 2 false-positive signals and 2 false-negative signals. However, BACTEC 9120 had 3 false-positive signals and 0 false-negative signals. Further identifications of bacteria were run by VITEK-2 (bioMérieux China Ltd.), 5% sheep blood trypticase soy agar (SBA) and chocolate agar (CA). Comparing with BACTEC 9120, MSPQC system possesses following advantages: shorter average detection time, less blood volume needed, less false-positive results and low cost. It can also provide information in real time. So MSPQC has a wonderful perspective in clinical application.

Bacteremia↗
PubMedDate not supplied

Genetic heterogeneity of ribosomal internal transcribed spacer in clinical samples of Leishmania donovani spotted on filter paper as revealed by single-strand conformation polymorphisms and sequencing.

A polymerase chain reaction and single-strand conformation polymorphism determination (PCR-SSCP) was used to detect deoxyribonucleic acid sequence polymorphisms in the transcribed non-coding regions between the small and large sub-unit ribosomal ribonucleic acid (rRNA) genes in Leishmania donovani from 63 clinical samples collected in eastern Sudan, between April 1997 and October 1998. Specific Leishmania primers were used to amplify the internal transcribed spacer (ITS) regions of L. donovani isolates directly from clinical samples spotted on filter papers. Amplification products were subsequently analysed by SSCP. Eleven polymorphic patterns were detected in the first part of the spacer, the ITS1 region, and were sequenced. Most of the changes were due to deletions of adenine bases and AT pairs within the first 192 nucleotides of the ITS region. This is the first application of PCR-linked SSCP analysis for the detection of population variation with direct display of sequence variation in parasitologically positive clinical samples spotted on filter paper. Culturing the parasite is thus not required, which is beneficial particularly in epidemiological studies based on field work where obtaining cultures can be extremely difficult.

Animals↗