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PubMed1992

Specimen flatness of thin crystalline arrays: influence of the substrate.

The extreme degree of specimen flatness (i.e. planarity) required for high-resolution electron diffraction and electron microscopy at high tilt angles cannot be realized with thin, sheet-like crystals of biological macromolecules, just on the basis of the intrinsic stiffness of the specimen itself. In an effort to improve the rate of success at which suitably flat specimens are prepared, this paper analyzes several different factors that can either limit or enhance the specimen flatness. If specimens are adsorbed (by attractive forces) to a support film, such as evaporated carbon, which itself is not flat to atomic dimensions, quantitative calculations show that it is quite likely that the specimen will be too wrinkled to be used for high-resolution studies. Adsorption to an air-water interface is more likely to result in the necessary degree of flatness. Repulsive interactions, which might be used to "sandwich" a specimen between two interfaces, are estimated to be too "soft", i.e. too long-range in character, to be effective. Finally, if only one edge of a specimen sticks firmly to a substrate, then surface tension forces can pull the specimen taut over the surface of the substrate, so that the specimen itself can be more flat than the surface of the substrate upon which it is deposited. A second, important consideration in many studies is the fact that cooling the specimen to low temperature can result in specimen wrinkling, because of the fact that the biological crystal has a much larger coefficient of thermal expansion than that of the evaporated carbon film. In this case one expects that cooling-induced wrinkling might be reduced by using a metal support grid which has a smaller thermal coefficient than that of the carbon film. The validity of this qualitative idea is supported by experiments which show that cooling-induced wrinkling of glucose-embedded purple membrane can be prevented if molybdenum grids are used rather than copper.

Artifacts↗

PubMed2001

Diagnostic quality of biopsy specimens: comparison between a conventional biopsy forceps and multibite forceps.

BACKGROUND: The endoscopic biopsy is a prerequisite for histopathologic diagnosis. Various types of forceps are used to obtain tissue specimens. The aim of this study was to assess and compare the diagnostic quality of biopsy specimens obtained with a conventional forceps and a Multibite forceps. METHODS: In a prospective, partially blinded, and randomized trial that included 250 patients referred for diagnostic upper and/or lower endoscopy, 510 biopsy specimens obtained with the Multibite forceps were compared with 520 specimens obtained with a conventional forceps. An experienced, blinded pathologist evaluated the specimens for diameter, depth of specimen, artifacts, anatomic orientation, vitality, general histologic quality, and diagnostic quality. Statistical analysis was performed by using the Fisher exact test. A p value of < 0.05 was regarded as significant. RESULTS: There were no statistically significant differences between the specimens obtained with the 2 forceps. The p values for the evaluated parameters were as follows: diameter 0.45, depth of specimen 0.56, artifacts 1.0, pathoanatomic orientation 0.40, vitality 0.45, and histologic diagnostic quality 0.53. CONCLUSION: The quality of biopsy specimens obtained with the Multibite forceps is comparable with that of specimens taken with a conventional forceps. Use of the Multibite forceps saves time in that 4 specimens can be obtained in 1 pass in situations in which a large number of specimens are needed or when the potential for transmission of infection is of concern.

Biopsy↗

PubMed1996

Identification of urinary benzodiazepines and their metabolites: comparison of automated HPLC and GC-MS after immunoassay screening of clinical specimens.

An automated high-performance liquid chromatographic method, benzodiazepines by REMEDi HS, was used to analyze benzodiazepines and their metabolites after beta-glucuronidase hydrolysis of 1-mL urine specimens from the following: 924 clinic and hospital patients whose specimens had previously been found to be presumptively positive using either EMIT or Triage immunoassay methodologies and 128 individuals whose specimens had screened negative by EMIT d.a.u.TM. REMEDi analyses did not correlate with the immunoassay results in 136 of the positive and three of the negative urine specimens. Gas chromatographic-mass spectrometric (GC-MS) confirmatory analyses were performed on these discordant specimens using 3 mL beta-glucuronidase-hydrolyzed urine followed by extraction with chloroform-isopropanol (9:1) and derivatization with N,O-bis(trimethylsilyl)trifluoroacetamide. Two benzodiazepines, flunitrazepam and clonazepam, and their 7-amino metabolites were analyzed without prior derivatization. The analyses established 87% concordance between REMEDi and GC-MS versus 13% concordance with immunoassay for the subset. GC-MS analysis of these 142 specimens demonstrated two reasons for the nonconcurrence between REMEDi and EMIT: EMIT had given either false-negative or false-positive results and EMIT had given a positive result even though the determined metabolites were below the 200-ng/mL cutoff for the immunoassay and the 80-ng/mL cutoff for REMEDi. A total of 23 specimens were found to contain only lorazepam by REMEDi and GC-MS, 15 of which had been screened by Triage. A reevaluation of these 23 specimens by EMIT d.a.u. demonstrated that 11 were positive. This finding was in contrast to previous reports that EMIT will not detect lorazepam glucuronide in urine. An unexpected finding was the REMEDi identification and subsequent GC-MS confirmation of 7-aminoflunitrazepam, a urinary metabolite of flunitrazepam that is not available in the United States and that represented illicit use by four patients. A distinct advantage of REMEDi proved to be its capability in identifying demoxepam, a major metabolite of chlordiazepoxide; GC-MS analysis could not detect this metabolite because of its thermal decomposition to nordiazepam. To further evaluate the specificity of REMEDi, we conducted GC-MS analyses in a random fashion on 55 additional nondiscordant urine specimens that were identified as either positive or negative, as well as 22 specimens identified as containing 7-aminoclonazepam by REMEDi. Concurrence was observed between the two methods for all specimens, with the exception of one apparent false positive for alpha-hydroxyalprazolam by REMEDi. The reproducibility of the REMEDi method was found to be excellent; it was assessed by comparing results of 266 specimens that were reprocessed in different batches and for known calibrators and controls also processed with each batch. Study results demonstrated that the automated REMEDi assay for urinary benzodiazepines and their metabolites was comparable with GC-MS but had distinct advantages over GC-MS because of the following reasons: simplicity of the assay, less time required for analyses, and provision of additional information concerning the parent benzodiazepine.

1-Propanol↗

PubMed2001

Visual inspection of the prostate biopsy specimen: aid to diagnosis and management.

The purpose of this article is to assess if the visual inspection of the prostate biopsy specimen can be used as a guide when deciding whether to attempt to sample another core of tissue from the same area if a less than adequate specimen was obtained during the first attempt. Five hundred thirty-seven specimens from 84 patients, referred because of an increased prostate-specific antigen (PSA) level and/or a suspicious result on digital rectal examination (DRE), were sampled and prospectively graded based on the lack of formation and amount of liquid in the specimen (grade I) compared to a highly rigid, solid core (grade V). Specimens were then fixed in formalin and retrospectively compared, and the pathologic diagnosis was compared with the subjective visual grade assigned to the specimen. Receiver-operator curve techniques were used to quantify the results and to test for statistical significance. Rigid biopsy specimens were cancer, and liquid, formless specimens were benign. Most biopsy specimens were solid, with moderate consistency, and could not be diagnosed accurately by visual inspection. Diagnosis of prostate cancer, despite the use of PSA, DRE, or diagnostic endorectal ultrasound, requires biopsy for definitive confirmation. Although the use of spring-loaded biopsy needles routinely yields good-quality cores of tissue for pathologic analysis, there are many occasions when a less than optimal specimen is obtained. The question of whether a repeat biopsy in that region is indicated always arises. These data suggest that if the initial specimen is grade I or II, repeat biopsy is probably not indicated. If the initial specimen is grade IV or V, repeat biopsy is recommended.

Journal Article↗

PubMed1987

DNA hybridization for diagnosis of enteric adenovirus infection from directly spotted human fecal specimens.

By using a genomic probe, DNA hybridization for adenovirus type 41 (Ad41) showed equivalent sensitivity with a direct spot method from clinical specimens compared with a more laborious DNA phenol extraction procedure. By using this direct spot preparation method, fecal specimens of 67 patients were examined under code for blind testing for the presence of adenovirus by DNA hybridization by using two Ad41 probes (genomic and cloned BglII-D) and an adenovirus type 2 genomic probe. Identical results were obtained with both of the Ad41 probes. Of the fecal specimens from 42 children with adenovirus gastroenteritis studied prospectively (16 of whom had enteric adenoviruses), 13 specimens (81%) were detected by DNA hybridization with a cloned Ad41 BglII-D probe. There were 14 fecal specimens that were positive by electron microscopy (EM) and culture for nonenteric adenovirus, and 2 specimens were positive by DNA hybridization (87% specificity); these 2 specimens may have been from a mixed enteric adenovirus and nonenteric adenovirus infection. None of 26 specimens from age-matched healthy control patients was positive for adenovirus by EM or DNA hybridization. Our data indicated that DNA hybridization gives highly reproducible results. The direct spot technique is the method of choice for specimen preparation in the diagnostic laboratory, since it requires only the simplest manipulations in specimen preparation. By using DNA hybridization with the BglII D fragment of a cloned enteric Ad41, both adenovirus type 40 and Ad41 were detected directly from fecal specimens, but it was less sensitive than EM following direct ultracentrifugation of specimens. The Bg1II-D Ad41 DNA probe was highly specific for enteric adenoviruses, and DNA hybridization with this probe could be a useful diagnostic test for these fastidious adenoviruses.

Adenoviridae Infections↗

PubMed1990

Enhanced radiometric detection of Mycobacterium paratuberculosis by using filter-concentrated bovine fecal specimens.

A commercial radiometric medium, BACTEC 12B, was modified by addition of mycobactin, egg yolk suspension, and antibiotics (vancomycin, amphotericin B, and nalidixic acid). Decontaminated bovine fecal specimens were filter concentrated by using 3-microns-pore-size, 13-mm-diameter polycarbonate filters, and the entire filter was placed into the radiometric broth. Comparison of the radiometric technique with conventional methods on 603 cattle from 9 Mycobacterium paratuberculosis-infected herds found that of 75 positive specimens, the radiometric technique detected 92% while conventional methods detected 60% (P less than 0.0005). Only 3.9% of radiometric cultures were contaminated. To measure the effect of filter concentration of specimens on the detection rate, 5 cattle with minimal and 5 with moderate ileum histopathology were sampled weekly for 3 weeks. M. paratuberculosis was detected in 33.3% of nonfiltered specimens and 76.7% of filtered specimens (P less than 0.005). Detection rates were directly correlated with the severity of disease, and the advantage of specimen concentration was greatest on fecal specimens from cattle with low-grade infections. Detection times were also correlated with infection severity: 13.4 +/- 5.9 days with smear-positive specimens, 27.9 +/- 8.7 days with feces from cows with typical subclinical infections, and 38.7 +/- 3.8 days with fecal specimens from cows with low-grade infections. Use of a cocktail of vancomycin, amphotericin B, and nalidixic acid for selective suppression of nonmycobacterial contaminants was better than the commercial product PANTA (Becton Dickinson Microbiologic Systems, Towson, Md.) only when specimens contained very low numbers of M. paratuberculosis. Radiometric culture of filter-concentrated specimens generally doubled the number of positive fecal specimens detected over conventional methods, making it a useful tool for diagnosis and control of bovine paratuberculosis.

Animals↗

PubMed1995

Multiplex PCR for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Genitourinary specimens.

We developed a multiplex PCR (M-PCR) assay for the simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. M-PCR employed C. trachomatis-specific primers KL1-KL2 and N. gonorrhoeae-specific primers HO1-HO3 and produced products of 241 and 390 bp, respectively. PCR products were easily detected by agarose gel electrophoresis and confirmed by Southern hybridization using labelled oligonucleotide probes. M-PCR had a sensitivity of 10 fg of C. trachomatis and N. gonorrhoeae DNA (equivalent to 1 to 2 genome copies). M-PCR detected the presence of C. trachomatis and N. gonorrhoeae DNA in 15 male urethral and 12 female endocervical specimens, 3 of which were positive for C. trachomatis, 18 of which were positive for N. gonorrhoeae and 6 of which were positive for both organisms. M-PCR was evaluated further by testing 200 male first void urine (FVU) specimens, of which 18 were positive by C. trachomatis PCR and Chlamydiazyme and 4 were positive by C. trachomatis PCR but negative by Chlamydiazyme. All 22 FVU specimens were positive by a confirmatory PCR using a second plasmid target and were positive by M-PCR. Ten of 11 men with cultures that were positive for N. gonorrhoeae had FVU specimens that were positive by both N. gonorrhoeae PCR and M-PCR. Two other men with negative N. gonorrhoeae urethral cultures had FVU specimens that were positive by N. gonorrhoeae PCR, by two confirmatory N. gonorrhoeae PCR assays using 165 rRNA and cytosine methyltransferase primers, and by M-PCR. The sensitivity of M-PCR for detecting C. trachomatis was 100% (22 of 22 specimens), compared with 81.8% (18 of 22 specimens) for enzyme immunoassay. Sensitivity of M-PCR for N. gonorrhoeae was 92.3% (12 of 13 specimens) compared with 84.6% (11 of 13 specimens) for urethral culture. The specificity of M-PCR was 100% for both C. trachomatis (178 of 13 specimens) and N. gonorrhoeae (187 of 187 specimens). M-PCR testing of FVU specimens provided a sensitive and noninvasive method for detecting C. trachomatis and N. gonorrhoeae infection in men.

Adolescent↗

PubMed1996

Patterns of detection of Strongyloides stercoralis in stool specimens: implications for diagnosis and clinical trials.

Reported efficacies of drugs used to treat Strongyloides stercoralis infection vary widely. Because diagnostic methods are insensitive, therapeutic trials generally require multiple negative posttreatment stool specimens as evidence of drug efficacy. However, only a single positive stool specimen is usually required for study enrollment. To determine the reproducibility of detection of S. stercoralis larvae in the stool, 108 asymptomatic infected men submitted 25 g of fresh stool once a week for eight consecutive weeks for examination by the Baermann technique. During the 8-week study, 239 (27.7%) of 864 stool specimens were positive for S. stercoralis. Rates of detection of larvae in the stool specimens ranged from eight of eight specimens in 3 (2.8%) men to none of eight specimens in 36 (33.3%) men. Of 43 men for whom S. stercoralis was detected in at least two of the first four stool specimens, only 1 (2.3%) man tested negative on all of the next four specimens. In comparison, of 29 men who had detectable larvae in only one of the first four specimens, 22 (75.9%) tested negative on all of the next four samples. Thus, if these 29 men had been enrolled in a therapeutic trial between the first and second sets of four specimens, the efficacy of a drug with no activity against this parasite would have been estimated to be 76%. These data suggest that patterns of S. stercoralis detection vary widely among infected persons and that intermittent larval shedding can lead to inflated estimates of drug efficacy. Before a patient is entered in a clinical trial of drug efficacy, four consecutive stool specimens should be examined for S. stercoralis; only persons with two or more positive specimens should be enrolled.

Adolescent↗

PubMed1996

Detection of PCR inhibitors in cervical specimens by using the AMPLICOR Chlamydia trachomatis assay.

To determine that susceptibility of AMPLICOR Chlamydia trachomatis PCR to inhibitory factors possibly present in cervical specimens, we obtained cervical specimens from 200 gynecology patients attending our outpatient clinic. The prevalence of C. trachomatis infection was 4.1%, as determined by cell culture. All AMPLICOR specimens were tested in one procedure as described by the manufacturer, and after the specimen was spiked with C. trachomatis, several other pretreatment protocols were used. Complete inhibition of the PCR was observed in 38 (19%) cervical specimens. Heat treatment at 95 degrees C, freeze-thawing, or 10-fold dilution of the samples reduced the initial inhibition to 9, 16, or 9%, respectively. A combination of heat treatment and 10-fold dilution reduced the inhibition to 4% of the samples. A second specimen type (swabs inoculated in 0.2 M sucrose phosphate buffer [2SP]) was also evaluated. A 10-fold dilution of the spiked 2SP specimen resulted in an inhibition rate of 6%, which was comparable to that obtained by centrifugation of the 2SP specimen prior to processing. Furthermore, it was shown that the inhibition was not correlated with blood contamination. Processing the specimens on the day of collection or the day after resulted in a higher inhibition rate than did delayed processing (27.6 versus 15.5%, respectively). An inverse correlation was found between the concentration of C. trachomatis added to the sample and the rate of inhibition observed. The inhibition was partly correlated with the pH of the cervical mucosa. Decreased inhibition was found at pH values of > or = 7.5. The effects of blood, pH, and delay in processing were all evaluated by using the AMPLICOR specimen. We conclude that the susceptibility of AMPLICOR C. trachomatis PCR to inhibiting factors in cervical specimens can be significantly reduced if the pretreatment procedure includes heat treatment or the use of 2SP transport medium. Also, a 10-fold dilution of the clinical specimen followed by heat treatment will largely prevent the inhibition of this PCR.

Cervix Uteri↗

PubMed1997

PCR detection of Pneumocystis carinii in bronchoalveolar lavage specimens: analysis of sensitivity and specificity.

Although PCR detection of Pneumocystis carinii DNA has been described, little is known about the sensitivity or specificity of the assay in routine laboratory practice. We had the unique opportunity to use a bronchoalveolar lavage (BAL) specimen bank with samples for which the direct examination results for P. carinii were known. DNA purified from 129 selected specimens was amplified by using the primers described previously (A. E. Wakefield, F. J. Pixley, S. Banerji, K. Sinclair, R. F. Miller, E. R. Moton, and J. M. Hopkin, Mol. Biochem. Parasitol. 43:69-76, 1990). Of the 129 specimens, 37 were positive for P. carinii by direct examination. All 37 specimens were positive for P. carinii by PCR, yielding a 100% sensitivity and 100% negative predictive value for the assay. An additional 23 specimens were repeatedly positive for P. carinii by PCR but were not positive by direct examination. Review of the patient charts for these specimens with discordant results demonstrated that five of the patients were actually positive for P. carinii, as determined by either biopsy or examination of repeat or prior BAL specimens. A response to empiric therapy for P. carinii pneumonia was seen in an additional two patients. Of the remaining specimens, 8 produced no significant isolates other than P. carinii, while 12 contained culture-confirmed significant respiratory pathogens in addition to P. carinii (two fungal, nine bacterial, and one viral pathogen). Cytomegalovirus, which was of unknown significance, was isolated from 16 additional specimens. Overall, the specificity of the PCR assay was 79.3% compared to the results of direct examination. We hypothesized that the apparently poor specificity of the PCR assay was due to the increased sensitivity of the assay compared to that of direct examination. The sensitivity of the PCR assay was therefore assessed with BAL specimens containing P. carinii cysts. Serial dilutions of this preparation were evaluated by direct examination and PCR. PCR was found to be 100-fold more sensitive than direct examination, which detected one to two cysts per amplification. No false-positive results were detected in controls containing no DNA or by using target DNA from various fungal, viral, or bacterial respiratory pathogens. We conclude that PCR detection of P. carinii in BAL specimens is very sensitive and should be considered for patients whose specimens do not yield a diagnosis. The increased sensitivity of the PCR assay may help to identify those patients with low-titer infections who might benefit from directed antibiotic therapy for P. carinii and would otherwise be missed by direct examination alone.

Bronchoalveolar Lavage↗

PubMed1997

Vulval swabs as alternative specimens for ligase chain reaction detection of genital chlamydial infection in women.

A ligase chain reaction (LCR)-based assay was recently shown to be highly sensitive and specific for the detection of Chlamydia trachomatis not only in cervical specimens but also in first-void urine (FVU) specimens form women. The suitability of using vulval swabs as an alternative specimen that can be obtained by noninvasive means for the diagnosis of genital chlamydial infection by LCR was investigated. In a first study of 169 women, vulval, endocervical, and urethral swabs were tested by LCR, culture, and a combination of enzyme immunoassay (EIA) followed by confirmation by direct fluorescent-antibody assay (DFA), and the results were compared with those obtained by testing FVU specimens by LCR and EIA-DFA by using a specimen from an infected patient as a reference standard. Of the 169 women tested, 27 (16%) were shown to be infected. Whereas LCR showed high sensitivities with all specimen types (85.2% for vulval, urine, and endocervical specimens; 92.6% for urethral swabs), the sensitivities of culture and EIA-DFA were high only with endocervical swabs (74.1 and 70.4%, respectively), being 22.2 and 40.7%, respectively, with vulval swabs. In addition, urine testing by EIA-DFA also showed a poor sensitivity (48.1%). In order to further compare LCR performance with vulval specimens to that with FVU specimens, a second study was carried out with specimens from 312 women, of whom 26 were infected. Comparable sensitivity was obtained by LCR with vulval swabs (88.5%; 23 of 26) and FVU specimens (92.3%; 24 of 26). The results indicate that vulval swabs may serve as suitable alternative to specimens that can be obtained by noninvasive means for the detection of C. trachomatis by LCR.

Bacterial Typing Techniques↗

PubMed1998

Value of examining multiple sputum specimens in the diagnosis of pulmonary tuberculosis.

To objectively assess the value of examining multiple sputum specimens in maximizing the sensitivity of detection of Mycobacterium tuberculosis, we retrospectively reviewed the acid-fast bacillus smear and culture results of patients diagnosed with culture-proven pulmonary tuberculosis (TB) at Hennepin County Medical Center between 1986 and 1996. Two hundred and forty six persons were diagnosed with pulmonary TB in the time period analyzed. In 93% of these cases (229 of 246) the laboratory diagnosis was made by detection of M. tuberculosis in sputum specimens; however, only 52% (120 of 229) of these patients had at least three sputum specimens submitted to the laboratory at the time of diagnosis. Of the patients from whom at least three specimens were collected, 47% (56 of 120) had at least one smear-positive specimen; the third or later specimen submitted was the first smear-positive specimen for 13% (7 of 56) of these persons but was the first culture-positive specimen for only 7% (4 of 56). Of the 64 patients with smear-negative specimens, for only 5% (3 of 64) was the third or subsequent specimen submitted the first from which M. tuberculosis was recovered. This data indicates that, in our institution, the overwhelming majority of culture-proven pulmonary TB cases are diagnosed from the first or second sputum specimen submitted to the laboratory and that only rarely is a third specimen of diagnostic value.

Culture Media↗

PubMed1998

Detection of cytomegalovirus in plasma and cerebrospinal fluid specimens from human immunodeficiency virus-infected patients by the AMPLICOR CMV test.

We have developed the AMPLICOR CMV Test, which is rapid and sensitive for the detection of cytomegalovirus (CMV) in plasma and cerebrospinal fluid (CSF) specimens. The test incorporated an internal control in the reaction mixture to monitor the amplification efficiency and the presence of inhibitors. The AMPLICOR CMV Test was very specific in detecting 12 clinical CMV isolates and four laboratory CMV strains tested. Cross-reactivity with 26 non-CMV pathogens was not observed. The AMPLICOR CMV Test requires only 50 microl of specimen (plasma or CSF) for processing. The performance of the AMPLICOR CMV Test was compared to those of the CMV antigenemia assay and the conventional tube culture method. Among 112 plasma specimens from 43 human immunodeficiency virus-infected patients, CMV was detected in 20 (18%) of the specimens by the AMPLICOR CMV Test, 21 (19%) of the specimens by the CMV antigenemia assay, and 10 (9%) of the specimens by culture. In CSF specimens from AIDS patients, CMV was detected in 10 of 58 (17%) specimens tested by the AMPLICOR CMV Test, 5 of 28 (18%) specimens tested by the antigen assay, and none of the 25 specimens tested by culture. While the performance of the AMPLICOR CMV Test in this study was comparable to that of the CMV antigen assay, processing of specimens by the AMPLICOR CMV Test was much simpler than that by the antigen assay; in addition, the antigen assay requires greater than 10(5) leukocytes from blood or 1 ml of CSF to perform the assay. Our study suggested that the AMPLICOR CMV Test could provide a rapid and sensitive assay for the detection of CMV in plasma and CSF specimens.

AIDS-Related Opportunistic Infections↗

PubMed2003

Evaluation of culture methods and a DNA probe-based PCR assay for detection of Campylobacter species in clinical specimens of feces.

Campylobacter species are the leading agents of bacterial gastroenteritis in developed countries. In this study 320 specimens of feces from patients with symptoms of acute gastroenteritis were cultured for Campylobacter species by direct plating on modified charcoal cefoperazone deoxycholate agar and by enrichment in modified Preston broth, with or without blood added, for 48 h at 37 degrees C prior to plating. A 16S/23S PCR/DNA probe membrane-based colorimetric detection assay was evaluated on a subset of the feces (n = 127), including 18 culture-positive and 109 culture-negative specimens. DNA was extracted directly from the fecal specimens by using the QIAamp DNA stool Minikit for the DNA probe-based PCR assay (PCR/DNA probe assay). A second PCR/DNA probe assay based on the 16S rRNA gene in Campylobacter spp. was applied to all specimens that were culture negative, PCR/DNA positive on initial analysis. Campylobacter species were cultured in 20 of the 320 specimens. The 16S/23S PCR/DNA probe assay detected campylobacter DNA in 17 of 18 (94% sensitivity) culture-positive specimens and in 41 (38%) culture-negative specimens. The presence of campylobacter DNA in 35 of 41 culture-negative specimens was confirmed by the 16S PCR/DNA probe assay. DNA sequence analysis of seven 16S/23S PCR products and five 16S PCR products amplified from a selection of these specimens confirmed the presence of campylobacter DNA and more specifically Campylobacter jejuni, C. concisus, C. curvus, and C. gracilis DNA in these specimens. The molecular assays described in this study are rapid methods for the detection and identification of Campylobacter species in fecal specimens. The finding of Campylobacter spp. DNA in a large number of specimens of feces from patients with no other identified cause of diarrhea may suggest that Campylobacter spp. other than C. jejuni and C. coli may account for a proportion of cases of acute gastroenteritis in which no etiological agent is currently identified.

Campylobacter↗

PubMed1995

Detecting residual tumor after excisional biopsy of impalpable breast carcinoma: efficacy of comparing preoperative mammograms with radiographs of the biopsy specimen.

OBJECTIVE: The purpose of this study was to ascertain whether a comparison of preoperative mammograms with radiographs of biopsy specimens is useful for determining the presence of residual breast tumor after an initial excision of impalpable breast cancer. MATERIALS AND METHODS: Radiographs of tissue specimens obtained at the initial biopsy of 125 impalpable breast cancers were compared with the preoperative mammograms to determine if the lesion seen on the mammogram was completely excised. All tumors were impalpable, necessitating preoperative wire localization. The biopsies were usually excisional, and no special efforts were made to remove additional surrounding tissue. Specimen radiographs were rated as showing no residual tumor if the lesion appeared to be completely excised, showing residual tumor if the lesion did not appear to be completely removed, or indeterminate for residual tumor if adequacy of excision was uncertain. The presence or absence of tumor at the margins of the surgical specimen was determined by histologic examination. These results were correlated with the presence or absence of residual breast cancer at subsequent mastectomy (n = 71) or reexcision (n = 54). RESULTS: The specimen radiograph showed complete excision of the mammographic lesion in 79 (63%) of the 125 cases. Tumor was found at mastectomy or reexcision in 35 of these cases, giving a false-negative rate for residual tumor of 44%. Incomplete excision was shown on 39 specimen radiographs. Eight of these 39 had no residual tumor, giving a false-positive rate of 21%. The sensitivity of the specimen radiograph for predicting the presence of residual tumor was 49%, specificity was 77%, and overall accuracy was 62%. The accuracy of pathologic examination of the margins of the biopsy specimen for predicting residual breast cancer was 58%. The specimen radiograph alone correctly identified 18 cases of residual tumor in which biopsy margins were indeterminate or negative for the presence of tumor. CONCLUSION: The specimen radiograph is not reliable enough to be used alone for determining the presence or absence of residual breast cancer after the initial excision of impalpable breast cancer. However, it can be of value in predicting the presence of residual tumor in those cases in which results of pathologic examination of biopsy specimen margins are either indeterminate or negative for the presence of tumor but the specimen radiograph shows incomplete excision of the mammographic lesion.

Biopsy↗

PubMed2005

Application of nested polymerase chain reaction (nPCR) using MPB 64 gene primers to detect Mycobacterium tuberculosis DNA in clinical specimens from extrapulmonary tuberculosis patients.

BACKGROUND & OBJECTIVE: The conventional culture technique for diagnosis of extrapulmonary tuberculosis is time consuming. In order to find a sensitive and rapid technique nested polymerase chain reaction (nPCR) targeting the conserved MPB 64 gene of Mycobacterium tuberculosis was evaluated for detection of M. tuberculosis DNA directly from clinical specimens of extrapulmonary origin. METHODS: A total of 400 clinical specimens from clinically suspected cases of extrapulmonary tuberculosis and 30 control specimens of nontuberculous aetiology were processed by smear and culture and by nPCR technique for detection of M. tuberculosis. The specimens were divided into 3 groups, (group I--280 specimens [104 peritoneal fluid (PF), 120 cerebrospinal fluid (CSF), 44 lymph node biopsies 3 pericardial fluid and 9 other biopsy specimens], group II--120 aqueous humour (AH) from idiopathic granulomatous uveitis cases, and group III--30 control specimens (10 CSF and 20AH). RESULTS: The conventional culture was positive only in 16 of 400 specimens. The overall positivity of nPCR was 35.2 per cent (141/400). Among the 280 specimens from extrapulmonary lesions (group I), 15 were bacteriologically positive, while 115 of 265 bacteriologically negative specimens (43.4%) were positive by nPCR. All the 30 control specimens were negative by nPCR. INTERPRETATION & CONCLUSION: The nPCR using MPB64 gene primers might be a rapid and reliable diagnostic technique for detection of M. tuberculosis genome in clinically suspected extrapulmonary tuberculosis specimens, as compared to the conventional techniques.

Aqueous Humor↗

PubMed1993

Lack of effect of prophylactic aerosolized pentamidine on the detection of Pneumocystis carinii in induced sputum or bronchoalveolar lavage specimens.

Two independent studies were undertaken to determine the effect of prophylactic treatment with aerosolized pentamidine on the laboratory diagnosis of Pneumocystis carinii pneumonia in individuals at risk for or with the acquired immunodeficiency syndrome. The first study was a retrospective analysis to determine the effect of prophylactic treatment with aerosolized pentamidine on the diagnostic yield and sensitivity of detection of P carinii in induced sputum specimens. The results of examinations of 110 induced sputum specimens from patients who had not received aerosolized pentamidine were compared with the findings in 57 specimens from patients who had. There was no statistically significant difference between the two groups for the diagnostic yield in induced sputum specimens (48% vs 47%) or in bronchoalveolar lavage fluid specimens subsequently obtained from patients with nondiagnostic induced sputum examinations (33% vs 37%). The sensitivity of induced sputum specimens for identifying P carinii was 76% to 78% for patients who had not received aerosolized pentamidine and 71% to 75% for patients who had received the drug. The second study was a prospective comparison of 118 bronchoalveolar lavage fluid specimens to determine the effect of prophylactic treatment with aerosolized pentamidine on the number of organisms present. One hundred eighteen bronchoalveolar lavage fluid specimens were quantitatively examined and scored according to the number of clumps of P carinii present. No statistically significant difference was seen in the number of clumps of P carinii found in specimens from patients who had received aerosolized pentamidine vs the number of clumps found in specimens from patients who had not. In conclusion, prophylactic treatment with aerosolized pentamidine had no effect on (1) the diagnostic yield and sensitivity of detection of P carinii in induced sputum specimens or (2) the number of organisms detected in bronchoalveolar lavage fluid specimens obtained from individuals at risk for or with the acquired immunodeficiency syndrome.

AIDS-Related Opportunistic Infections↗

PubMed2005

Reflex high-risk human papillomavirus DNA testing (Hybrid Capture 2) of bloody ThinPrep specimens with atypical squamous cells of undetermined significance interpretation: does pretreatment with acetic acid affect test performance?

BACKGROUND: The current study was conducted to evaluate the efficacy of human papillomavirus (HPV) DNA testing of residual ThinPrep specimens, which were pretreated with acetic acid to optimize cellularity with a special focus on atypical squamous cells of undetermined significance (ASCUS) specimens. METHODS: A total of 120 ThinPrep gynecologic samples were chosen for a pilot study including cases with a normal or abnormal interpretation and those with or without blood. Each residual specimen was divided into two portions. One portion was treated with glacial acetic acid (GAA) and the other half remained untreated. Both aliquots were tested for high-risk HPV DNA using the Hybrid Capture 2 test. After internal validation, reflex HPV DNA testing was performed on all consecutive 1776 ASCUS specimens including 98 acid-washed bloody specimens in routine practice. RESULTS: Of the 120 specimens with paired aliquots, 117 specimens had concordant HPV DNA test results in the treated and untreated groups with a squared correlation coefficient value of 0.97 and a kappa value of 0.95. Subsequently, in the clinical setting, 43 of 98 (43.9%) acid-washed specimens and 845 of 1676 (50.4%) routine specimens with an ASCUS interpretation tested positive for high-risk HPV DNA. There was no statistically significant difference noted between these two groups with regard to age, percentage HPV DNA positivity, or viral load. CONCLUSIONS: The pretreatment of bloody specimens with GAA did not appear to significantly affect high-risk HPV DNA testing in specimens with an ASCUS interpretation.

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