bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multisite Comparison of Reproducibility and Recovery from the Standard and Ultrasensitive Roche AMPLICOR HIV-1 MONITOR Assays
Authors: Brambilla Donald J. , Granger Suzanne , Jennings Cheryl , Bremer James W. 
Published: July 2002

ABSTRACT
Reproducibility and recovery from the standard and ultrasensitive Roche AMPLICOR HIV-1 MONITOR kits were compared in 19 laboratories. The results were generally similar, but the consistently low level of recovery from the ultrasensitive assay in one laboratory points to the need to include external controls in order to track assay performance.
Comparison between the LCx Probe System and the COBAS AMPLICOR System for Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
Infections in Patients Attending a Clinic for Treatment of Sexually Transmitted Diseases in Amsterdam, The Netherlands
Authors: van Doornum G. J. J. , Schouls L. M. , Pijl A. , Cairo I. , Buimer M. , Bruisten S. 
Published: July 2002

ABSTRACT

Two assays for the detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
were compared: the LCx Probe system (the LCx system; Abbott Diagnostic Laboratories, North Chicago, Ill.) and the COBAS AMPLICOR
C. trachomatis/N. gonorrhoeae
system (the COBAS AMPLICOR system; Roche Diagnostic Systems, Branchburg, N.J.). Endocervical swab specimens, male urethral swab specimens, and female and male urine specimens were collected from 503 female and 498 male visitors attending a sexually transmitted diseases clinic in Amsterdam, The Netherlands. Prevalences for
C. trachomatis
were 12.5% (63 of 503) and 10.0% (50 of 498) in females and males, respectively. The prevalences for
N. gonorrhoeae
were 1.2% (6 of 503) and 4.2% (21 of 498) in females and males, respectively. Both assays showed high values for sensitivity and specificity with regard to the detection of
C. trachomatis
in endocervical swab specimens, male urethral swab specimens, and female and male urine specimens. The sensitivities for the LCx system were 92.1, 90.0, 88.9, and 94.0% for each type of specimen, respectively; and the sensitivies for the COBAS AMPLICOR system were 96.8, 98.0, 82.5, and 92.0% for each type of specimen, respectively. Specificities ranged between 98.4 and 100%. The sensitivity of the LCx system for the detection of
N. gonorrhoeae
was 100% for female cervical swab and urine specimens and male urethral swab specimens, while for male urine specimens the sensitivity was 95.2%; the specificity was 100% for all types of specimens. For the detection of
N. gonorrhoeae
by the COBAS AMPLICOR assay, the sensitivity for female cervical swab and male urethral swab specimens was 100%, that for female urine specimens was 66.7%, and that for male urine specimens was 95.2%. However, the predictive values of a positive test for female cervical swab specimens and urine specimens were 31.6 and 36.4%, respectively. Sequence analysis of the amplimers obtained by an in-house 16S rRNA PCR of the solely COBAS AMPLICOR system-positive swab specimens revealed neither
N. gonorrhoeae
nor other
Neisseria
spp. The COBAS AMPLICOR assay was considered not suitable for screening for infections with
N. gonorrhoeae
. If this assay is used for detection of
N. gonorrhoeae
, confirmation of positive results by a reliable test is mandatory.
Comparative Performance of Three Viral Load Assays on Human Immunodeficiency Virus Type 1 (HIV-1) Isolates Representing Group M (Subtypes A to G) and Group O: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR Version 1.5, and Quantiplex HIV-1 RNA Version 3.0
Authors: Swanson Priscilla , Soriano Vincent , Devare Sushil G. , Hackett John 
Published: July 2002

ABSTRACT

The performance of the LCx HIV RNA Quantitative (LCx HIV), AMPLICOR HIV-1 MONITOR version 1.5 (MONITOR v1.5), and Quantiplex HIV-1 RNA version 3.0 (bDNA v3.0) viral load assays was evaluated with 39 viral isolates (3 A, 7 B, 6 C, 4 D, 8 E, 4 F, 1 G, 4 mosaic, and 2 group O). Quantitation across the assay dynamic ranges was assessed using serial fivefold dilutions of the viruses. In addition, sequences of
gag
-encoded p24 (
gag
p24),
pol
-encoded integrase, and
env
-encoded gp41 were analyzed to assign group and subtype and to assess nucleotide mismatches at primer and probe binding sites. For group M isolates, quantification was highly correlated among all three assays. In contrast, only the LCx HIV assay reliably quantified group O isolates. The bDNA v3.0 assay detected but consistently underquantified group O viruses, whereas the MONITOR v1.5 test failed to detect group O viruses. Analysis of target regions revealed fewer primer or probe mismatches in the LCx HIV assay than in the MONITOR v1.5 test. Consistent with the high level of nucleotide conservation is the ability of the LCx HIV assay to quantify efficiently human immunodeficiency virus type 1 group M and the genetically diverse group O.
Detection of
Mycobacterium bovis
in Bovine Clinical Specimens Using Real-Time Fluorescence and Fluorescence Resonance Energy Transfer Probe Rapid-Cycle PCR
Authors: Taylor Malcolm James , Hughes Mary Siobhan , Skuce Robin Alfred , Neill Sydney Donnelly 
Published: July 2002

ABSTRACT

Nucleic acid sequence capture extraction was coupled with LightCycler PCR amplification and product detection using real-time fluorescence for rapid, definitive detection of
Mycobacterium bovis
in lymph node specimens from 38 cattle with bovine tuberculosis lesions. PCR amplification of sequence-captured DNA using both a conventional heating block thermocycler and a LightCycler thermocycler was compared with culture and histopathological analyses. Conventional PCR enabled detection of 26 of 28 culture-positive specimens (93%) in approximately 9 h, and the LightCycler PCR detected 20 of 28 culture-positive specimens (71%) in only 30 min. Specific confirmation of
Mycobacterium tuberculosis
complex DNA was achieved by LightCycler PCR amplification using Syb Green 1 and an
M. tuberculosis
complex-specific Cy5-labeled fluorescence resonance energy transfer probe. The system described here enabled rapid and specific laboratory confirmation of bovine tuberculosis, and this is the first report of the detection of
M. bovis
in tissues using LightCycler PCR. The fluorescence technology used in the study has potential to allow development of a high-throughput molecular diagnostic test for bovine tuberculosis.
Fluconazole and Voriconazole Multidisk Testing of
Candida
Species for Disk Test Calibration and MIC Estimation
Authors: Kronvall Göran , Karlsson Inga 
Published: July 2002

ABSTRACT

Fluconazole and voriconazole MICs were determined for 114 clinical
Candida
isolates, including isolates of
Candida albicans, Candida glabrata, Candida krusei, Candida lusitaniae, Candida parapsilosis
, and
Candida tropicalis
. All strains were susceptible to voriconazole, and most strains were also susceptible to fluconazole, with the exception of
C. glabrata
and
C. krusei
, the latter being fully fluconazole resistant. Single-strain regression analysis (SRA) was applied to 54 strains, including American Type Culture Collection reference strains. The regression lines obtained were markedly different for the different
Candida
species. Using an MIC limit of susceptibility to fluconazole of ≤8 μg/ml, according to NCCLS standards, the zone breakpoint for susceptibility for the 25-μg fluconazole disk was calculated to be ≥18 mm for
C. albicans
and ≥22 mm for
C. glabrata
and
C. krusei
. SRA results for voriconazole were used to estimate an optimal disk content according to rational criteria. A 5-μg disk content of voriconazole gave measurable zones for a tentative resistance limit of 4 μg/ml, whereas a 2.5-μg disk gave zones at the same MIC level for only three of the species. A novel SRA modification, multidisk testing, was also applied to the two major species,
C. albicans
and
C. glabrata
, and the MIC estimates were compared with the true MICs for the isolates. There was a significant correlation between the two measurements. Our results show that disk diffusion methods might be useful for azole testing of
Candida
isolates. The method can be calibrated using SRA. Multidisk testing gives direct estimations of the MICs for the isolates.
Application and Evaluation of the Interlaboratory Reproducibility of tRNA Intergenic Length Polymorphism Analysis (tDNA-PCR) for Identification of
Streptococcus
Species
Authors: Baele Margo , Storms Virginie , Haesebrouck Freddy , Devriese Luc A. , Gillis Monique , Verschraegen Gerda , de Baere Thierry , Vaneechoutte Mario 
Published: July 2002

ABSTRACT

The discriminatory power, speed, and interlaboratory reproducibility of tRNA intergenic length polymorphism analysis (tDNA-PCR) combined with capillary electrophoresis was evaluated for the identification of streptococci. This method was carried out in three different laboratories under highly standardized conditions for 54 strains belonging to 18 different species. It was concluded that interlaboratory reproducibility of tDNA fingerprints produced by means of capillary electrophoresis was sufficiently high to permit the exchange between different laboratories and the construction of common libraries which can be consulted for comparison with fingerprints obtained independently in separate laboratories. In a second step, 17 other species were included in the study and examined in one of the participating laboratories. All
Streptococcus
species studied, except
S. mitis, S. oralis, S. parasanguinis, S. pneumoniae, S. thermophilus
, and
S. vestibularis
, showed distinguishable tDNA fingerprints. A database of well-characterized strains was constructed to enable computer-aided identification of unknown streptococcal isolates.
Serum Is the Preferred Clinical Specimen for Diagnosis of Human Brucellosis by PCR
Authors: Zerva L. , Bourantas K. , Mitka S. , Kansouzidou A. , Legakis N. J. 
Published: July 2002

ABSTRACT

Human brucellosis poses a significant public health problem in many developing countries and requires fast and accurate diagnosis. A PCR assay amplifying part of the 31-kDa
Brucella abortus
antigenic protein gene sequence was developed and applied to whole-blood and serum samples from 31 brucellosis patients and 45 healthy individuals. All patients except one had detectable
Brucella
DNA in either whole blood or serum (combined sensitivity, 97%), but the assay sensitivity was higher with serum samples (94%) than with whole-blood samples (61%). The assay specificity was excellent (100%). A confirmatory PCR assay targeting another
Brucella
gene region (
omp-2
) was also developed but lacked sensitivity. Serum is the optimal specimen for the diagnosis of brucellosis by PCR, a choice that leads to assay simplification and shortens turnaround time.
Three Days of Incubation May Be Sufficient for Routine Blood Cultures with BacT/Alert FAN Blood Culture Bottles
Authors: Bourbeau Paul P. , Pohlman Janice K. 
Published: July 2002

ABSTRACT
BacT/Alert FAN blood culture bottles have been shown to enhance the recovery of bacteria and yeast from blood compared with standard BacT/Alert bottles. It is well established that standard BacT/Alert blood culture bottles require no more than 5 days of incubation for the detection of routine bacteria and yeast. It is less clear, however, whether FAN bottles also routinely require 5 days of incubation. To address this question, we recently reviewed the results of 17,887 blood culture sets collected in FAN blood culture bottles at Geisinger Medical Center. Of these cultures, 1,780 were positive for bacteria or yeast, yielding a total of 1,242 clinically significant isolates. The numbers of isolates recovered on days 1, 2, 3, 4, and 5 were as follows: (values in parentheses are percentages of total significant isolates): 877 (71%), 269 (22%), 65 (5%), 18 (1%) and, 13 (1%), respectively. In total, 97.5% of all clinically significant isolates were detected in the first 3 days of incubation. Of the 31 significant isolates detected on day 4 or 5 of incubation, 17 were detected in concurrent blood cultures within the first 3 days of incubation. Chart reviews were conducted for the 13 patients with the remaining 14 isolates detected on day 4 or 5 to determine whether therapy was changed due to this blood culture result. Therapy was changed for only 1 patient. These results suggest that it may not be necessary to routinely incubate FAN blood culture bottles for more than 3 days.
Evaluation of a Modified Sanitary Napkin as a Sample Self-Collection Device for the Detection of Genital Chlamydial Infection in Women
Authors: Alary Michel , Poulin Céline , Bouchard Céline , Fortier Michel , Murray Gilles , Gingras Suzanne , Aubé Michel , Morin Carol 
Published: July 2002

ABSTRACTA modified sanitary napkin was compared with endocervical swab and urine specimens for the detection of urogenitalChlamydia trachomatisinfection. Endocervical swabs and/or first-catch urine were collected from 510 women at medical or community settings in Quebec City. Participants were also asked to wear a modified sanitary napkin (Ezy-Detek) during 4 consecutive hours and to bring it back to the clinic or mail it to the laboratory. Endocervical and urine specimens were tested using the Cobas Amplicor CT/NG assay (Roche Diagnostic Systems) according to the manufacturer's instructions, as were specimens collected with the napkin after adequate preparation. If the PCR test result was positive on the endocervical sample or on any two samples, a woman was considered to be infected. PCR testing results on paired samples were identical for 493 (96.6%) of 510 women. According to the definition given above, 58 (11.3%; 95% confidence interval [CI], 8.7 to 14.5%) women were infected withC. trachomatis. The sensitivity and specificity of PCR testing on modified sanitary napkin specimens were, respectively, 93.1% (54 of 58; 95% CI, 83.3 to 98.1%) and 98.9% (447 of 452; 95% CI, 97.4 to 99.6%) compared to 81.0% (47 of 58; 95% CI, 68.6 to 90.1%) and 100% (451 of 451; 95% CI, 99.2 to 100%) for urine specimens. The positive and negative predictive values were, respectively, 91.5% (54 of 59) and 99.1% (447 of 451) for the sanitary napkin specimens compared to 100% (47 of 47) and 97.6% (451 of 462) for urine samples. These results suggest that a modified sanitary napkin represents an effective noninvasive device for self-collection of specimens to detect urogenitalC. trachomatisinfection.
Identification of Rifampin-Resistant
Mycobacterium tuberculosis
Strains by Hybridization, PCR, and Ligase Detection Reaction on Oligonucleotide Microchips
Authors: Mikhailovich Vladimir , Lapa Sergey , Gryadunov Dimitry , Sobolev Alexander , Strizhkov Boris , Chernyh Nikolai , Skotnikova Olga , Irtuganova Olga , Moroz Arkadii , Litvinov Vitalii , Vladimirskii Mikhail , Perelman Mikhail , Chernousova Larisa , Erokhin Vladislav , Zasedatelev Alexander , Mirzabekov Andrei 
Published: July 2002

ABSTRACT

Three new molecular approaches were developed to identify drug-resistant strains of
Mycobacterium tuberculosis
using biochips with oligonucleotides immobilized in polyacrylamide gel pads. These approaches are significantly faster than traditional bacteriological methods. All three approaches—hybridization, PCR, and ligase detection reaction—were designed to analyze an 81-bp fragment of the gene
rpoB
encoding the β-subunit of RNA polymerase, where most known mutations of rifampin resistance are located. The call set for hybridization analysis consisted of 42 immobilized oligonucleotides and enabled us to identify 30 mutant variants of the
rpoB
gene within 24 h. These variants are found in 95% of all mutants whose rifampin resistance is caused by mutations in the 81-bp fragment. Using the second approach, allele-specific on-chip PCR, it was possible to directly identify mutations in clinical samples within 1.5 h. The third approach, on-chip ligase detection reaction, was sensitive enough to reveal rifampin-resistant strains in a model mixture containing 1% of resistant and 99% of susceptible bacteria. This level of sensitivity is comparable to that from the determination of
M. tuberculosis
drug resistance by using standard bacteriological tests.
Endophthalmitis Caused by
Listeria monocytogenes
Authors: Betriu Carmen , Fuentemilla Santos , Méndez Rosalı́a , Picazo Juan J. , Garcı́a-Sánchez Julián 
Published: July 2002

ABSTRACT

Listeria monocytogenes
was isolated from the aqueous chamber of an immunodepressed patient with acute hypertensive uveitis, who developed a dark hypopyon and pigment dispersion. No extraocular septic focus was found. Treatment was successful with intravitreal vancomycin, anterior chamber irrigation with vancomycin, orally administered ciprofloxacin, and topical fortified vancomycin.
Identification of 54 Mycobacterial Species by PCR-Restriction Fragment Length Polymorphism Analysis of the
hsp65
Gene
Authors: Brunello Francesca , Ligozzi Marco , Cristelli Emanuela , Bonora Stefano , Tortoli Enrico , Fontana Roberta 
Published: July 2002

ABSTRACT
A total of 121 reference and clinical strains of both slowly and rapidly growing mycobacteria belonging to 54 species were studied for restriction fragment length polymorphism of a PCR-amplified 439-bp segment of the gene encoding the 65-kDa heat shock protein. Restriction digests were separated by 10% polyacrylamide gel electrophoresis (PAGE). By including a size standard in each sample, the restriction fragment profile was calculated using a computer-aided comparison program. An algorithm describing these 54 species (including 22 species not previously described) is proposed. We found that this assay based on 10% PAGE provided a more precise estimate than that based on agarose gel electrophoresis of the real size of restriction fragments as deduced from the sequence analysis and allowed identification of mycobacteria whose PCR-restriction fragment length polymorphism analysis patterns were unequivocally identified by fragments shorter than 60 bp.
Detection and Quantification of Infectious Hypodermal and Hematopoietic Necrosis Virus and White Spot Virus in Shrimp Using Real-Time Quantitative PCR and SYBR Green Chemistry
Authors: Dhar Arun K. , Roux Michelle M. , Klimpel Kurt R. 
Published: July 2002

ABSTRACT

A rapid and highly sensitive real-time PCR detection and quantification method for infectious hypodermal and hematopoietic necrosis virus (IHHNV), a single-stranded DNA virus, and white spot virus (WSV), a double-stranded DNA (dsDNA) virus infecting penaeid shrimp (
Penaeus
sp.), was developed using the GeneAmp 5700 sequence detection system coupled with SYBR Green chemistry. The PCR mixture contains a fluorescence dye, SYBR Green, which upon binding to dsDNA exhibits fluorescence enhancement. The enhancement of fluorescence was proportional to the initial concentration of the template DNA. A linear relationship was observed between the amount of input plasmid DNA and cycle threshold (

C
T

) values over a range of 1 to 10
5
copies of the viral genome. To control the variation in sampling and processing among samples, the shrimp β-actin gene was amplified in parallel with the viral DNA. The

C
T

values of IHHNV- and WSV-infected samples were used to determine absolute viral copy numbers from the standard

C
T

curves of these viruses. For each virus and its β-actin control, the specificity of amplification was monitored by using the dissociation curve of the amplified product. Using genomic DNA as a template, SYBR Green PCR was found to be 100- to 2000-fold more sensitive than conventional PCR, depending on the virus, for the samples tested. The results demonstrate that SYBR Green PCR can be used as a rapid and highly sensitive detection and quantification method for shrimp viruses and that it is amenable to high-throughout assay.
Transmission of Hepatitis C Virus in a Gynecological Surgery Setting
Authors: Massari Marco , Petrosillo Nicola , Ippolito Giuseppe , Solforosi Laura , Bonazzi Lucio , Clementi Massimo , Manzin Aldo 
Published: July 2002

ABSTRACT

A cluster of hepatitis C virus (HCV) infections among gynecological patients who underwent surgical intervention in the same setting is described. An epidemiological investigation was conducted to identify the cases, the likely source of infection, and the route of transmission. Four recent HCV infections were identified. Based on molecular fingerprinting analysis and epidemiological investigation, transmission between the putative source patient (an HCV-positive woman who was the first patient of the surgical session) and outbreak patients was highly suggestive. All patients, including the source patient, were infected with HCV type 1b. Molecular characterization of HCV clones by sequence analysis of both structural envelope regions (20 clones from the source patient and 58 from the outbreak patients) and the nonstructural NS5 region of the viral genome (12 clones from the source patient and 32 from the outbreak patients) showed close homology between the viral isolates from the source and those from the outbreak patients that was higher than that observed between the viral isolates from the source and those from four unrelated, HCV type 1b-infected patients from the same geographical area (in the latter case, 33 clones were sequenced for the envelope regions and 30 were sequenced for the NS5 region). The mean percent divergence between clones was 4.69 for the envelope and 3.71 for the NS5 region in the source patient and the outbreak patients compared with 6.76 (
P
= 0.001) and 5.22 (
P
= 0.01) in the source patient and control patients, respectively. Among the risk factors investigated, only that of having undergone surgery in the morning session of the same day reached statistical significance (
P
= 0.003). The investigation showed that the source patient and outbreak patients shared only the administration of propofol in multidose vials. The study documents the risk of nosocomial transmission of HCV and the importance of infection control procedures in the operating room and highlights the crucial role of molecular strategies, especially sequence-based phylogenetic analysis of cloned viral isolates, in the investigation of HCV outbreaks.
Detection of Antibodies to U.S. Isolates of Avian Pneumovirus by a Recombinant Nucleocapsid Protein-Based Sandwich Enzyme-Linked Immunosorbent Assay
Authors: Gulati Baldev R. , Munir Shirin , Patnayak Devi P. , Goyal Sagar M. , Kapur Vivek 
Published: July 2002

ABSTRACT

The nucleocapsid (N) protein of subgroup C (United States-specific) avian pneumovirus (APV/US) was expressed in
Escherichia coli
, and antibodies to the recombinant N protein were shown to specifically recognize the ≈47-kDa N protein of APV/US by Western immunoblot analysis. The recombinant APV/US N protein was used in a sandwich-capture enzyme-linked immunosorbent assay (ELISA), and the resulting assay was found to be more sensitive and specific than the routine indirect ELISA for the detection of APV/US antibodies in turkey sera.