bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Roche
Neisseria gonorrhoeae
16S rRNA PCR for Confirmation of AMPLICOR PCR-Positive Samples and Comparison of Its Diagnostic Performance According to Storage Conditions and Preparation of Endocervical Specimens
Authors: Van Dyck E. , Smet H. , Van Damme L. , Laga M. 
Published: July 2002

ABSTRACT

The AMPLICOR PCR was used to detect
Neisseria gonorrhoeae
in endocervical specimens. A 16S rRNA PCR performed on
N. gonorrhoeae-
positive samples showed sensitivities of 73.2, 64.3, and 94.4% for samples treated directly with AMPLICOR lysis buffer, samples suspended in 2-sucrose phosphate, and samples suspended in diluted phosphate-buffered saline, respectively.
Biofilm Formation by Gram-Negative Bacteria on Central Venous Catheter Connectors: Effect of Conditioning Films in a Laboratory Model
Authors: Murga R. , Miller J. M. , Donlan R. M. 
Published: July 2002

ABSTRACT

Human blood components have been shown to enhance biofilm formation by gram-positive bacteria. We investigated the effect of human blood on biofilm formation on the inner lumen of needleless central venous catheter connectors by several gram-negative bacteria, specifically
Enterobacter cloacae, Pseudomonas aeruginosa
, and
Pantoea agglomerans
. Results suggest that a conditioning film of blood components promotes biofilm formation by these organisms in an in vitro system.
Basidiobolus ranarum
as an Etiologic Agent of Gastrointestinal Zygomycosis
Authors: Khan Z. U. , Khoursheed M. , Makar R. , Al-Waheeb S. , Al-Bader I. , Al-Muzaini A. , Chandy R. , Mustafa A. S. 
Published: July 2002

ABSTRACT

Basidiobolus ranarum
is a known cause of subcutaneous zygomycosis. Recently, its etiologic role in gastrointestinal infections has been increasingly recognized. While the clinical presentation of the subcutaneous disease is quite characteristic and the disease is easy to diagnose, gastrointestinal basidiobolomycosis poses diagnostic difficulties; its clinical presentation is nonspecific, there are no identifiable risk factors, and all age groups are susceptible. The case of gastrointestinal basidiobolomycosis described in the present report occurred in a 41-year-old Indian male who had a history of repair of a left inguinal hernia 2 years earlier and who is native to the southern part of India, where the subcutaneous form of the disease is indigenous. Diagnosis is based on the isolation of
B. ranarum
from cultures of urine and demonstration of broad, sparsely septate hyphal elements in histopathologic sections of the colon, with characteristic eosinophilic infiltration and the Splendore-Hoeppli phenomenon. The titers of both immunoglobulin G (IgG) and IgM antibodies to locally produced antigen of the fungus were elevated. The patient failed to respond to 8 weeks of amphotericin B therapy, and the isolate was later found to be resistant to amphotericin B, itraconazole, fluconazole, and flucytosine but susceptible to ketoconazole and miconazole. One other noteworthy feature of the fungus was that the patient's serum showed raised levels of Th2-type cytokines (interleukins 4 and 10) and tumor necrosis factor alpha. The present report underscores the need to consider gastrointestinal basidiobolomycosis in the differential diagnosis of inflammatory bowel diseases and suggests that, perhaps, more time should be invested in developing standardized serologic reagents that can be used as part of a less invasive means of diagnosis of the disease.
Evaluation of BACTEC MYCO/F Lytic Medium for Recovery of Mycobacteria, Fungi, and Bacteria from Blood
Authors: Fuller DeAnna D. , Davis Thomas E. , Denys Gerald A. , York Mary K. 
Published: July 2002

ABSTRACT

MYCO/F Lytic medium (MFL), a liquid medium developed for use with the BACTEC 9240 blood culture system, was compared to the Isolator system (IS) for the recovery of fungi and to the BACTEC 13A medium for the recovery of mycobacteria. Recovery of bacteria was compared to routine BACTEC Plus Aerobic/F (AF) blood cultures. Microbial growth was detected in 203 (17%) of 1,166 blood cultures. Fifty-seven specimens were positive for fungi: 35 were positive with both IS and MFL; six were positive with IS only (three
Candida albicans
, one
Histoplasma capsulatum
, one
Candida glabrata
, and one
Fusarium
species isolate); three were positive with AF only (two
C. albicans
and one
Candida parapsilosis
isolate); and 13 were positive with MFL only (five
C. glabrata
, three
C. albicans
, two
Candida krusei
, two
Candida tropicalis
, and one
C. parapsilosis
isolate;
P
> 0.05 versus IS). Eighteen of 19 blood cultures positive for
H. capsulatum
grew in both IS and MFL, although the time to detection for MFL was greater. The mean time to detection for all fungi was 8.15 days for IS and 12.07 days for MFL. Seven hundred forty specimens were also cultured for mycobacteria with MFL and 13A. Forty-four grew mycobacteria; 38 were positive with both 13A and MFL; and 16 were positive with MFL only.
Mycobacterium avium
was recovered from 41 specimens; 36 were positive for both systems and 5 were positive for MFL alone. MFL was also compared to the AF bottle for the same 740 specimens. MFL and AF both detected 34 of the 40 clinically significant bacteria, while IS detected only 15 of 40. In summary, MFL is an excellent medium for the recovery of fungi, mycobacteria, and bacteria; however, the time to detection of
H. capsulatum
is increased.
Seven Human Immunodeficiency Virus (HIV) Antigen-Antibody Combination Assays: Evaluation of HIV Seroconversion Sensitivity and Subtype Detection
Authors: Ly Thoai Duong , Martin Lynn , Daghfal David , Sandridge Arnold , West Daniel , Bristow Richard , Chalouas Laurence , Qiu Xiaoxing , Lou Sheng C. , Hunt Jeffrey C. , Schochetman Gerald , Devare Sushil G. 
Published: July 2002

ABSTRACT
In this study, we evaluated the performance of two prototype human immunodeficiency virus (HIV) antigen-antibody (Ag-Ab) combination assays, one from Abbott Laboratories (AxSYM HIV Ag-Ab) and the other from bioMerieux (VIDAS HIV Duo Ultra), versus five combination assays commercially available in Europe. The assays were Enzygnost HIV Integral, Genscreen Plus HIV Ag-Ab, Murex HIV Ag-Ab Combination, VIDAS HIV Duo, and Vironostika HIV Uniform II Ag-Ab. All assays were evaluated for the ability to detect p24 antigen from HIV-1 groups M and O, antibody-positive plasma samples from HIV-1 groups M and O, HIV-2, and 19 HIV seroconversion panels. Results indicate that although all combination assays can detect antibodies to HIV-1, group M, subtypes A to G, circulating recombinant form (CRF) A/E, and HIV-1 group O, their sensitivity varied considerably when tested using diluted HIV-1 group O and HIV-2 antibody-positive samples. Among combination assays, the AxSYM, Murex, and VIDAS HIV Duo Ultra assays exhibited the best antigen sensitivity (at ∼25 pg of HIV Ag/ml) for detection of HIV-1 group M, subtypes A to G and CRF A/E, and HIV-1 group O isolates. However, the VIDAS HIV Duo Ultra assay had a lower sensitivity for HIV-1 group M and subtype C, and was unable to detect subtype C antigen even at 125 pg of HIV Ag/ml. The HIV antigen sensitivity of the VIDAS HIV Duo and Genscreen Plus combination assays was ∼125 pg of HIV Ag/ml for detection of all HIV-1 group M isolates except HIV-1 group O while the sensitivity of Vironostika HIV Uniform II Ag-Ab and Enzygnost HIV Integral Ag-Ab assays for all the group M subtypes was >125 pg of HIV Ag/ml. Among the combination assays, the AxSYM assay had the best performance for detection of early seroconversion samples, followed by the Murex and VIDAS HIV Duo Ultra assays.
Antibiotic-Resistant Cell-Detaching
Escherichia coli
Strains from Nigerian Children
Authors: Okeke Iruka N. , Steinrück Hartmut , Kanack Kristen J. , Elliott Simon J. , Sundström Lars , Kaper James B. , Lamikanra Adebayo 
Published: July 2002

ABSTRACT

The properties of 23 cell-detaching
Escherichia coli
strains that were isolated from stool specimens in Nigeria are described. Common properties of the strains included the presence of genes encoding α-hemolysin (100%), pyelonephritis-associated pili (100%), and cytotoxic necrotizing factor 1 (70%) as well as lactose negativity (70%) and multiple antibiotic resistance (74%). Antibiotic resistance was shown in most cases to be transferable and associated with the presence of class 1 integrons. Phenotypic properties and pulsed-field gel electrophoresis analysis demonstrated that the majority of the strains, particularly multiply resistant, lactose-negative O4:H40 strains, were closely related. Multiply-resistant cell-detaching
E. coli
strains may represent an important reservoir for antibiotic resistance genes.
Frequency of Isolation of
Staphylococcus lugdunensis
in Consecutive Urine Cultures and Relationship to Urinary Tract Infection
Authors: Haile D. T. , Hughes J. , Vetter E. , Kohner P. , Snyder R. , Patel R. , Cockerill F. R. 
Published: July 2002

ABSTRACT

Recent reports associate
Staphylococcus lugdunensis
with severe infection in humans. The frequency of this microorganism in urine cultures is unknown. Five hundred isolates of coagulase-negative staphylococci (CoNS) were recovered from 4,652 consecutive urine specimens submitted for culture to the Mayo Clinic Microbiology Laboratory. Thirty-one (6%) of 500 isolates of CoNS were identified as
S. lugdunensis
. In no case was
S. lugdunensis
isolated in pure culture; 29 (94%) of 31
S. lugdunensis
isolates were part of mixed nonpathogenic flora. Medical records were reviewed for 30 of the 31 patients from whom these 31 isolates were isolated. Twenty-one (70%) of the 30 evaluable patients were not treated with antibiotics; the remaining 9 (30%) of 30 patients were treated with antibiotics that may be effective against
S. lugdunensis. S. lugdunensis
may be an unrecognized yet infrequent cause of urinary tract infection.
Genomic Variation of
Bartonella henselae
Strains Detected in Lymph Nodes of Patients with Cat Scratch Disease
Authors: Zeaiter Zaher , Fournier Pierre-Edouard , Raoult Didier 
Published: July 2002

ABSTRACT

Bartonella henselae
is the primary agent of cat scratch disease (CSD). In order to study the genetic variation of
B. henselae
and the correlation of the various genotypes with epidemiological and clinical findings, two seminested,
groEL
- and
pap31
-based PCR assays were carried out with specimens from 273 patients. Amplicons were sequenced to determine the genotype of the causative
Bartonella
species. Compared to our reference intergenic spacer region-based PCR, the
groEL
- and
pap31
-based assays were 1.7 and 1.9 times more sensitive, respectively. All 107 positive patients were infected with
B. henselae
; neither
Bartonella clarridgeiae
nor other species were detected. Based on the
groEL
and
pap31
sequences,
B. henselae
amplicons were classified into two genogroups, Marseille and Houston-1, and into four variants, Marseille, CAL-1, Houston-1, and a new variant, ZF-1. Patients infected with either one or the other genogroup did not exhibit different epidemiological or clinical characteristics. Our study highlights the genotypic heterogeneity of
B. henselae
in patients with CSD.
Food-Borne Outbreak of Gastroenteritis Associated with Genogroup I Calicivirus
Authors: Johansson P. J. Hugo , Torvén Maria , Hammarlund Ann-Christin , Björne Ulla , Hedlund Kjell-Olof , Svensson Lennart 
Published: July 2002

ABSTRACT
An outbreak of gastroenteritis affecting 158 of 219 (72%) guests and employees at a hotel is described. Food served at the hotel restaurant is believed to have been the source of the outbreak and to have been contaminated by sick employees working in the restaurant. A secondary attack rate of 22% was seen involving 43 persons in all. In stool specimens from seven of eight patients, Norwalk-like viruses (NLVs) were detected by electron microscopy. While NLV-specific PCR using primers JV12 and JV13 were negative, all specimens examined with primers NVp69 and NVp110 were positive. The failure of primers JV12 and JV13 was attributed to several mismatches in the JV12 primer. Genotyping and sequence analysis revealed that all samples had identical sequences and clustered with genogroup I, and the most closely related well-characterized genotype is Desert Shield. This is the first described food-borne outbreak associated with genogroup I virus in Sweden.
Evaluation of INNO-LIA Syphilis Assay as a Confirmatory Test for Syphilis
Authors: Hagedorn Hans-Jochen , Kraminer-Hagedorn Anna , De Bosschere Katrien , Hulstaert Frank , Pottel Hans , Zrein Maan 
Published: July 2002

ABSTRACT

We evaluated the sensitivity and specificity of a new confirmatory test for treponemal antibodies, INNO-LIA Syphilis (Innogenetics NV, Ghent, Belgium), on a large number of sera from a clinical laboratory. This multiparameter line immunoassay (LIA) uses recombinant and synthetic polypeptide antigens derived from
Treponema pallidum
proteins. In a single-blinded cross-sectional retrospective study, 289 seronegative sera, 219 seropositive sera, and 23 sera with an indeterminate serological status for syphilis were analyzed. All sera were tested by the
T. pallidum
hemagglutination assay (TPHA), the immunoglobulin (IgG)-fluorescent
T. pallidum
absorption assay (IgG-FTA-ABS), and the Venereal Disease Research Laboratory (VDRL) test. In addition, some seropositive samples were analyzed by the 19S-IgM-FTA-ABS test, an enzyme immunoassay (IgM-EIA), and the MarDx immunoblotting assay. Based on a consensus diagnosis derived from conventional serology, all of the sera were classified as positive, negative, or indeterminate, and the results were compared with the findings of the INNO-LIA Syphilis assay. The sensitivity and specificity of the LIA were 100% (219 of 219) and 99.3% (286 of 288), respectively. Compared to TPHA and IgG-FTA-ABS, the new test gave a significantly higher number (
P
= 0.021 and
P
< 0.0001, respectively) of correct results than either of the other two tests. The multiparameter INNO-LIA Syphilis assay is a useful confirmatory test for syphilis because it increases the reliability of syphilis diagnosis with respect to current conventional techniques.
Automated Extraction of Genomic DNA from Medically Important Yeast Species and Filamentous Fungi by Using the MagNA Pure LC System
Authors: Loeffler Juergen , Schmidt Kathrin , Hebart Holger , Schumacher Ulrike , Einsele Hermann 
Published: July 2002

ABSTRACT

A fully automated assay was established for the extraction of DNA from clinically important fungi by using the MagNA Pure LC instrument. The test was evaluated by DNA isolation from 23 species of yeast and filamentous fungi and by extractions (
n
= 28) of serially diluted
Aspergillus fumigatus
conidia (10
5
to 0 CFU/ml). Additionally, DNA from 67 clinical specimens was extracted and compared to the manual protocol. The detection limit of the MagNA Pure LC assay of 10 CFU corresponded to the sensitivity when DNA was extracted manually; in 9 of 28 runs, we could achieve a higher sensitivity of 1 CFU/ml blood, which was found to be significant (p ≤ 0.004). DNA from all fungal species analyzed could be extracted and amplified by real-time PCR. Negative controls from all MagNA Pure isolations remained negative. Sixty-three clinical samples showed identical results by both methods, whereas in 4 of 67 samples, discordant results were obtained. Thus, the MagNA Pure LC technique offers a fast protocol for automated DNA isolation from numerous fungi, revealing high sensitivity and purity.
Botulism Due to
Clostridium baratii
Type F Toxin
Authors: Harvey Sydney M. , Sturgeon Joan , Dassey David E. 
Published: July 2002

ABSTRACT

Botulism results from consumption of preformed toxin or in vivo toxin elaboration in wounds or intestine. Of U.S. food-borne botulism cases since 1950, the majority were due to toxin A, but a significant number of suspect cases were never confirmed by culture or toxin detection. We report here a possible case of food-borne botulism attributed to toxin F production by a
Clostridium baratii
organism isolated from food consumed by the patient. The isolation of a toxin-producing
Clostridium
species other than
Clostridium botulinum
from food and stool requires deviation from the usual laboratory protocols, which may account for the lack of complete laboratory confirmation of clinically diagnosed cases.
Asynchronous Accumulation of
Lettuce Infectious Yellows Virus
RNAs 1 and 2 and Identification of an RNA 1
trans
Enhancer of RNA 2 Accumulation
Authors: Yeh Hsin-Hung , Tian Tongyan , Rubio Luis , Crawford Brett , Falk Bryce W. 
Published: July 2002

ABSTRACT

Time course and mutational analyses were used to examine the accumulation in protoplasts of progeny RNAs of the bipartite
Crinivirus
,
Lettuce infectious yellow virus
(LIYV; family
Closteroviridae
). Hybridization analyses showed that simultaneous inoculation of LIYV RNAs 1 and 2 resulted in asynchronous accumulation of progeny LIYV RNAs. LIYV RNA 1 progeny genomic and subgenomic RNAs could be detected in protoplasts as early as 12 h postinoculation (p.i.) and accumulated to high levels by 24 h p.i. The LIYV RNA 1 open reading frame 2 (ORF 2) subgenomic RNA was the most abundant of all LIYV RNAs detected. In contrast, RNA 2 progeny were not readily detected until ca. 36 h p.i. Mutational analyses showed that in-frame stop codons introduced into five of seven RNA 2 ORFs did not affect accumulation of progeny LIYV RNA 1 or RNA 2, confirming that RNA 2 does not encode proteins necessary for LIYV RNA replication. Mutational analyses also supported that LIYV RNA 1 encodes proteins necessary for replication of LIYV RNAs 1 and 2. A mutation introduced into the LIYV RNA 1 region encoding the overlapping ORF 1B and ORF 2 was lethal. However, mutations introduced into only LIYV RNA 1 ORF 2 resulted in accumulation of progeny RNA 1 near or equal to wild-type RNA 1. In contrast, the RNA 1 ORF 2 mutants did not efficiently support the
trans
accumulation of LIYV RNA 2. Three distinct RNA 1 ORF 2 mutants were analyzed and all exhibited a similar phenotype for progeny LIYV RNA accumulation. These data suggest that the LIYV RNA 1 ORF 2 encodes a
trans
enhancer for RNA 2 accumulation.
Isolation of Human Immunodeficiency Virus Type 1 Cores: Retention of Vpr in the Absence of p6

gag
Authors: Accola Molly A. , Öhagen Åsa , Göttlinger Heinrich G. 
Published: July 2002

ABSTRACT

Mature human immunodeficiency virus type 1 (HIV-1) virions contain a typically cone-shaped core that encases the viral genome. In this study, we established conditions which allowed the efficient isolation of morphologically intact HIV-1 cores from virions. The isolated cores consisted mostly of cones which appeared uniformly capped at both ends but were heterogeneous with respect to the shape of the broad cap as well as the dimensions and angle of the cone. Vpr, a nonstructural virion component implicated in the nuclear import of the viral genome, was recovered in core preparations of HIV-1 and simian immunodeficiency viruses from African green monkeys. Unexpectedly, p6

gag

, a structural protein required for the incorporation of Vpr, was absent from HIV-1 core preparations. Taken together, our results indicate that the incorporation of Vpr into the virion core is a conserved feature of primate lentiviruses and that the interactions required for the uptake of Vpr into assembling particles differ from those which confine Vpr within the core.
Immune Response to Recombinant Adenovirus in Humans: Capsid Components from Viral Input Are Targets for Vector-Specific Cytotoxic T Lymphocytes
Authors: Molinier-Frenkel Valérie , Gahery-Segard Hanne , Mehtali Majid , Le Boulaire Christophe , Ribault Sébastien , Boulanger Pierre , Tursz Thomas , Guillet Jean-Gérard , Farace Françoise 
Published: July 2002

ABSTRACTWe previously demonstrated that a single injection of 109PFU of recombinant adenovirus into patients induces strong vector-specific immune responses (H. Gahéry-Ségard, V. Molinier-Frenkel, C. Le Boulaire, P. Saulnier, P. Opolon, R. Lengagne, E. Gautier, A. Le Cesne, L. Zitvogel, A. Venet, C. Schatz, M. Courtney, T. Le Chevalier, T. Tursz, J.-G. Guillet, and F. Farace, J. Clin. Investig. 100:2218–2226, 1997). In the present study we analyzed the mechanism of vector recognition by cytotoxic T lymphocytes (CTL). CD8+CTL lines were derived from two patients and maintained in long-term cultures. Target cell infections with E1-deleted and E1-plus E2-deleted adenoviruses, as well as transcription-blocking experiments with actinomycin D, revealed that host T-cell recognition did not require viral gene transcription. Target cells treated with brefeldin A were not lysed, indicating that viral input protein-derived peptides are associated with HLA class I molecules. Using recombinant capsid component-loaded targets, we observed that the three major proteins could be recognized. These results raise the question of the use of multideleted adenoviruses for gene therapy in the quest to diminish antivector CTL responses.
Identification of a Minimal Size Requirement for Termination of Vesicular Stomatitis Virus mRNA: Implications for the Mechanism of Transcription
Authors: Whelan Sean P. J. , Barr John N. , Wertz Gail W. 
Published: July 2002

ABSTRACT

The nonsegmented negative-strand RNA (NNS) viruses have a single-stranded RNA genome tightly encapsidated by the viral nucleocapsid protein. The viral polymerase transcribes the genome responding to specific gene-start and gene-end sequences to yield a series of discrete monocistronic mRNAs. These mRNAs are not produced in equimolar amounts; rather, their abundance reflects the position of the gene with respect to the single 3′-proximal polymerase entry site. Promoter-proximal genes are transcribed in greater abundance than more distal genes due to a localized transcriptional attenuation at each gene junction. In recent years, the application of reverse genetics to the NNS viruses has allowed an examination of the role of the gene-start and gene-end sequences in regulating mRNA synthesis. These studies have defined specific sequences required for initiation, 5′ modification, termination, and polyadenylation of the viral mRNAs. In the present report, working with
Vesicular stomatitis virus
, the prototypic
Rhabdovirus
, we demonstrate that a gene-end sequence must be positioned a minimal distance from a gene-start sequence for the polymerase to efficiently terminate transcription. Gene-end sequences were almost completely ignored in transcriptional units less than 51 nucleotides. Transcriptional units of 51 to 64 nucleotides allowed termination at the gene-end sequence, although the frequency with which polymerase failed to terminate and instead read through the gene-end sequence to generate a bicistronic transcript was enhanced compared to the observed 1 to 3% for wild-type viral mRNAs. In all instances, failure to terminate at the gene end prevented initiation at the downstream gene start site. In contrast to this size requirement, we show that the sequence between the gene-start and gene-end signals, or its potential to adopt an RNA secondary structure, had only a minor effect on the efficiency with which polymerase terminated transcription. We suggest three possible explanations for the failure of polymerase to terminate transcription in response to a gene-end sequence positioned close to a gene-start sequence which contribute to our emerging picture of the mechanism of transcriptional regulation in this group of viruses.