bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiology of
Mycobacterium tuberculosis
in Norwa
y
Authors: Dahle Ulf R. , Sandven Per , Heldal Einar , Caugant Dominique A. 
Published: July 2002

ABSTRACT

The incidence of tuberculosis in Norway is one of the lowest in the world, and approximately half of the cases occur in first- and second-generation immigrants. In the present study, the genetic diversity of 92% of all strains of
Mycobacterium tuberculosis
isolated in Norway in 1994 to 1998 was assessed using restriction fragment length polymorphism (RFLP) analysis, with the insertion sequence IS
6110
and the repetitive element DR as probes, to determine the degree of active transmission between patients. The DR probe was used as a secondary molecular marker to support or rule out clustering of strains with fewer than five copies of IS
6110
. After exclusion of 20 cultures representing laboratory contamination, 573 different IS
6110
patterns were found among the 698 strains analyzed. Of these 573 patterns, 542 were observed only once and 31 were shared by 2 to 14 isolates. Among 81 strains (11.5%) carrying fewer than five copies of IS
6110,
56 RFLP patterns were found when the results of both the IS
6110
and DR methods were combined. Among the 698 strains, 570 were considered to be independent cases. A total of 14.5% of the native Norwegians and 19.7% of the foreign patients were part of a cluster. Thus, the degree of recent transmission of tuberculosis in Norway is low and the great majority of the cases are due to reactivation of previous disease. Transmission between immigrants and native Norwegians is uncommon. Two outbreaks, one among native Norwegians and one mainly among immigrants, have been ongoing for several years, indicating that, even in a low-incidence country such as Norway, with a good national program for tuberculosis surveillance, certain transmission chains are difficult to break.
Quantitation of Human Immunodeficiency Virus Type 1 (HIV-1) RNA in Cell-Free Cervicovaginal Secretions: Comparison of Reverse Transcription-PCR Amplification (AMPLICOR HIV-1 MONITOR 1.5) with Enhanced-Sensitivity Branched-DNA Assay (Quantiplex 3.0)
Authors: Si-Mohamed Ali , Andreoletti Laurent , Colombet Isabelle , Carreno Marie-Paule , Lopez Gladys , Chatelier Gilles , Kazatchkine Michel D. , Belec Laurent 
Published: July 2002

ABSTRACT
Two commercially available hypersensitive assays for human immunodeficiency virus type 1 (HIV-1) RNA quantitation, AMPLICOR HIV-1 Monitor Test 1.5 and Quantiplex HIV RNA 3.0, were compared to detect and quantify HIV-1 RNA in the cell-free fraction of cervicovaginal secretions collected by vaginal washing. Three panel specimens were used: pooled cervicovaginal secretions spiked with HIV-1 subtype A or HIV-1 subtype B and cervicovaginal lavages from HIV-positive and HIV-negative women. Compared to the AMPLICOR HIV-1 Monitor Test 1.5 assay, the Quantiplex HIV-1 3.0 assay yielded higher estimates of HIV-1 RNA concentrations in several tested samples spiked with HIV-1 RNA subtype A, as well as subtype B, particularly samples containing low amounts of HIV-1 RNA. The sensitivity and specificity of the AMPLICOR HIV-1 Monitor Test 1.5 assay were 93 and 100%, respectively; the sensitivity and specificity of the Quantiplex HIV RNA 3.0 assay were 97 and 50%, respectively. In conclusion, in quantifying HIV-1 RNA in cervicovaginal secretions, the Quantiplex HIV RNA 3.0 may lack specificity, and the AMPLICOR HIV-1 Monitor Test 1.5 assay, although highly specific, may lack sensitivity.
Reemergence of Gentamicin-Susceptible Strains of Methicillin-Resistant
Staphylococcus aureus
in France: a Phylogenetic Approach
Authors: Blanc D. S. , Francioli P. , Le Coustumier A. , Gazagne L. , Lecaillon E. , Gueudet P. , Vandenesch F. , Etienne J. 
Published: July 2002

ABSTRACT

The reemergence of gentamicin-susceptible (Gen
s
) methicillin-resistant
Staphylococcus aureus
(MRSA) isolates in France between 1992 and 1996 was investigated using a phylogenetic approach (multiprimer randomly amplified polymorphic DNA typing). Eighty-six percent (65 of 85) of the French strains were grouped into one phylogenetic cluster within which all but one Gen
s
strain were grouped into a subcluster. Thus, the reemergence of Gen
s
MRSA strains in France was likely due to the spread of one specific clone which belonged to a cluster comprising most French gentamicin-resistant (Gen
r
) strains. This suggests that the Gen
s
clone has emerged from a Gen
r
strain of this cluster.
Rapid Diagnosis of
Histoplasma capsulatum
Endocarditis Using the AccuProbe on an Excised Valve
Authors: Chemaly Roy F. , Tomford J. Walton , Hall Gerri S. , Sholtis Mary , Chua Jimmy D. , Procop Gary W. 
Published: July 2002

ABSTRACT

Histoplasma capsulatum
is an infrequent but serious cause of endocarditis. The definitive diagnosis requires culture, which may require a long incubation. We demonstrated the ability of the
Histoplasma capsulatum
AccuProbe to accurately identify this organism when applied directly on an excised valve that contained abundant yeast forms consistent with
H. capsulatum
.
Use of a Reverse Dot Blot Procedure To Identify the Presence of Multiple Serovars inChlamydia trachomatisUrogenital Infection
Authors: Stothard Diane R. 
Published: July 2002

ABSTRACTEpidemiologic research requires identification ofChlamydia trachomatisserovars and detection of mixed infection. Antibody-based serotyping is unworkable when specimens are urine or vaginal swabs. We developed a reverse dot blot (RDB) to screen for multiple serotypes in these specimens. RDB yielded the predicted results on all artificially mixed samples and on seven of eight clinically mixed samples.
Multicenter Evaluation of a Pathogenic
Mycobacterium
Screening Probe
Authors: Emler Stefan , Feldmann Knut , Giacuzzo Véronique , Hewitt Peter L. , Klapper Paul E. , Lagrange Philippe H. , Wilkins Ed W. , Young Karen K. Y. , Herrmann Jean-Louis 
Published: July 2002

ABSTRACT

The introduction of nucleic acid amplification assays into the clinical laboratory has reduced the time needed to diagnose diseases caused by members of the
Mycobacterium tuberculosis
complex (MTBC). However, several mycobacterial species other than those of the MTBC are known to cause disease, especially in immunocompromised individuals. A screening assay has been developed for the detection of the major pathogenic mycobacterial species. The assay utilizes pan-genus primers to amplify mycobacterial DNA and a screening probe (KY493) that detects all major pathogenic mycobacteria. A multicenter European study was conducted to assess the performance of the screening probe in the clinical laboratory. The screening probe was evaluated against individual probes specific for
M. tuberculosis
,
M. avium
, and
M. intracellulare
, a genus-specific probe with broader species coverage, and culture. The screening probe had a sensitivity equivalent to that of the species-specific probes; all specimens positive with any of the species-specific probes were also positive with the screening probes. Compared to culture, the sensitivity of the screening probe was 89% (154 of 173) for all culture-positive specimens tested. This value was 89.6% for the genus-specific probe. The screening probe was more specific than the genus-specific probe. Specificity was 93.9% (661 of 704) compared to culture results alone. The comparable specificity value for the genus-specific probe was 84.8%. When clinical data were taken into consideration, the sensitivity of the screening assay was similar to that of culture (81% versus 76.2%) but the positive predictive value of the test was lower (76.2% versus 100% for culture). However, the screening probe was more sensitive than smear and may be a useful tool in the rapid diagnosis of mycobacterial disease.
Characterization of
Borrelia burgdorferi
Isolated from Erythema Migrans Lesions: Interrelationship of Three Molecular Typing Methods
Authors: Iyer Radha , Liveris Dionysios , Adams Atoya , Nowakowski John , McKenna Donna , Bittker Susan , Cooper Denise , Wormser Gary P. , Schwartz Ira 
Published: July 2002

ABSTRACT

Genetic diversity among
Borrelia burgdorferi
isolates recovered from the skin of Lyme disease patients was assessed by ribosomal DNA (rDNA) spacer restriction fragment length polymorphism analysis, genomic restriction site polymorphism analysis, and plasmid content analysis. There was a significant association between the three rDNA spacer types, the six pulsed-field gel types, and plasmid content (
P
< 0.001). The association between distinct chromosomal and plasmid markers implies a clonal origin for each genotype.
Concomitant Infection of Enterotoxigenic
Escherichia coli
in an Outbreak of Cholera Caused by
Vibrio cholerae
O1 and O139 in Ahmedabad, India
Authors: Chakraborty Subhra , Deokule J. S. , Garg Pallavi , Bhattacharya S. K. , Nandy R. K. , Nair G. Balakrish , Yamasaki S. , Takeda Y. , Ramamurthy T. 
Published: July 2002

ABSTRACT

In Ahmedabad, a major city in the state of Gujarat, India, an outbreak of acute secretory diarrhea caused by
Vibrio cholerae
O1 Ogawa El Tor,
V. cholerae
O139, and multiple serotypes of enterotoxigenic
Escherichia coli
(ETEC) occurred in January 2000. All of the representative
V. cholerae
O1 and O139 isolates examined harbored the
ctxA
gene (encoding the A subunit of cholera toxin) and the El Tor variant of the
tcpA
gene (encoding toxin-coregulated pilus). ETEC isolates of different serotypes were positive for the
elt
gene, encoding heat-labile enterotoxin. To further understand the molecular characteristics of the pathogens, representative isolates were examined by ribotyping and pulsed-field gel electrophoresis (PFGE). Ribotyping showed that the isolates of
V. cholerae
O1 Ogawa exhibited a pattern identical to that of the prevailing clone of O1 in areas where cholera is endemic in India, and all of the O139 isolates were identical to the BII clone of
V. cholerae
O139. PFGE of the representative O1 Ogawa isolates exhibited an identical pattern, comparable to the H pattern of the new clone of O1 reported in Calcutta, India. PFGE analysis of the
V. cholerae
O139 isolates showed identical patterns, but these differed from the PFGE patterns of O139 isolates reported during 1992 to 1997 in Calcutta. ETEC isolates showed genetic heterogeneity among isolates belonging to the same serotype, although the identical PFGE pattern was also observed among ETEC isolates of different serotypes. Antibiograms of the isolates were unusual, because all of the O139 isolates were resistant to nalidixic acid. Likewise, all of the
E. coli
isolates showed resistance to ciprofloxacin, norfloxacin, and nalidixic acid. This is a unique outbreak, and we believe that it is the first in which
V. cholerae
and ETEC were concomitantly involved.
Comparison of Two Culture Methods for Detection of Tobramycin-Resistant Gram-Negative Organisms in the Sputum of Patients with Cystic Fibrosis
Authors: Van Dalfsen Jill M. , Stapp Jenny R. , Phelps Charles , Stewart Patricia , Burns Jane L. 
Published: July 2002

ABSTRACT

A culture method utilizing quantitative plating on antibiotic-containing media has been proposed as a technique for the detection of tobramycin-resistant organisms that is more sensitive than standard methods. Typical sputum culture methods quantitate the relative amounts of each distinct morphotype, followed by antibiotic susceptibility testing of a single colony of each morphotype. Sputum specimens from 240 cystic fibrosis patients were homogenized, serially diluted, and processed in parallel by the standard method (MacConkey agar and OF basal medium with agar, polymyxin, bacitracin, and lactose) and by plating on antibiotic-containing media (MacConkey agar with tobramycin added at 25 μg/ml [MAC-25] and 100 μg/ml [MAC-100]). MICs of tobramycin were determined for all
Pseudomonas aeruginosa
isolates by broth microdilution. Growth of
P. aeruginosa
on MAC-25 was considered to be equivalent to a tobramycin MIC of ≥16 μg/ml, and growth on MAC-100 was considered to be equivalent to a tobramycin MIC of ≥128 μg/ml. Analysis of method-specific detection rates showed that tobramycin-containing medium was more sensitive than the standard method for the detection of tobramycin-resistant
P. aeruginosa, Stenotrophomonas maltophilia
, and
Achromobacter xylosoxidans
but was less sensitive for the detection of
Burkholderia cepacia
than the standard method. When MICs for
P. aeruginosa
that grew on tobramycin-containing medium were tested by broth microdilution, the MICs for 28 of 121 strains (23%) growing on MAC-25 and 22 of 56 strains (39%) growing on MAC-100 were MICs <16 and <128 μg/ml, respectively. Addition of a tobramycin-containing MacConkey plate to the routine media for sputum culture may provide additional, clinically relevant microbiologic data.
Ratio of Two Successive Optical Densities from the Roche HIV-1 Monitor Test as a Measure of Accuracy of Estimates of Human Immunodeficiency Virus RNA Concentration
Authors: Jennings Cheryl , Brambilla Donald J. , Bremer James W. 
Published: July 2002

ABSTRACT
In the Roche Amplicor HIV-1 Monitor Test, the ratio of the optical density used to estimate the RNA concentration and the optical density of the preceding or the following dilution can be used to identify specimens with inaccurate results which should be retested. We present an algorithm for the identification of such results.
Four Strains of
Escherichia coli
O157:H7 Isolated from Patients during an Outbreak of Disease Associated with Ground Beef: Importance of Evaluating Multiple Colonies from an Outbreak-Associated Product
Authors: Proctor Mary E. , Kurzynski Terry , Koschmann Cindy , Archer John R. , Davis Jeffrey P. 
Published: July 2002

ABSTRACT

This report describes the investigation of a ground-beef-associated outbreak that involved five genetically distinct patient strains of
Escherichia coli
O157:H7. Human and product isolates were evaluated by pulsed-field gel electrophoresis (PFGE) with two endonucleases. The multiple-strain etiology of this outbreak underscores the importance of isolating and evaluating multiple colonies from outbreak-related products and comparing two endonuclease PFGE patterns of all product and human isolates identified during outbreak periods. This investigation emphasizes the importance of interviewing all confirmed and suspected case patients during the outbreak period, regardless of the PFGE pattern of their isolate, to confirm or rule out an epidemiologic link to the outbreak.
Invasive Meningococcal Disease in Scotland, 1994 to 1999, with Emphasis on Group B Meningococcal Disease
Authors: Kyaw Moe H. , Clarke Stuart C. , Christie Peter , Jones Ian G. , Campbell Harry 
Published: July 2002

ABSTRACT
A review was carried out on 774 invasive meningococcal isolates reported to the active meningococcal surveillance system in Scotland from 1994 to 1999. This showed that serogroups B (51.7%) and C (39.2%) caused the majority of disease. The six common PorB proteins (4, 1, 15, 2B, 12, and 21) and PorA proteins (serosubtypes) (P1.4, P1.15, P1.9, P1.14, P1.7, and P1.16) accounted for 50 and 51% of all group B isolates, respectively, during the study period.
Determining the Genomic Locations of Repetitive DNA Sequences with a Whole-Genome Microarray: IS
6110
in
Mycobacterium tuberculosis
Authors: Kivi Mårten , Liu Xuemin , Raychaudhuri Soumya , Altman Russ B. , Small Peter M. 
Published: July 2002

ABSTRACT

The mycobacterial insertion sequence IS
6110
has been exploited extensively as a clonal marker in molecular epidemiologic studies of tuberculosis. In addition, it has been hypothesized that this element is an important driving force behind genotypic variability that may have phenotypic consequences. We present here a novel, DNA microarray-based methodology, designated SiteMapping, that simultaneously maps the locations and orientations of multiple copies of IS
6110
within the genome. To investigate the sensitivity, accuracy, and limitations of the technique, it was applied to eight
Mycobacterium tuberculosis
strains for which complete or partial IS
6110
insertion site information had been determined previously. SiteMapping correctly located 64% (38 of 59) of the IS
6110
copies predicted by restriction fragment length polymorphism analysis. The technique is highly specific; 97% of the predicted insertion sites were true insertions. Eight previously unknown insertions were identified and confirmed by PCR or sequencing. The performance could be improved by modifications in the experimental protocol and in the approach to data analysis. SiteMapping has general applicability and demonstrates an expansion in the applications of microarrays that complements conventional approaches in the study of genome architecture.
Interactions between Hepatitis Delta Virus Proteins
Authors: Moraleda Gloria , Dingle Kate , Biswas Preetha , Chang Jinhong , Zuccola Harmon , Hogle James , Taylor John 
Published: July 2002

ABSTRACT

The 195- and 214-amino-acid (aa) forms of the delta protein (δAg-S and δAg-L, respectively) of hepatitis delta virus (HDV) differ only in the 19-aa C-terminal extension unique to δAg-L. δAg-S is needed for genome replication, while δAg-L is needed for particle assembly. These proteins share a region at aa 12 to 60, which mediates protein-protein interactions essential for HDV replication. H. Zuccola et al. (Structure 6:821–830, 1998) reported a crystal structure for a peptide spanning this region which demonstrates an antiparallel coiled-coil dimer interaction with the potential to form tetramers of dimers. Our studies tested whether predictions based on this structure could be extrapolated to conditions where the peptide was replaced by full-length δAg-S or δAg-L, and when the assays were not in vitro but in vivo. Nine amino acids that are conserved between several isolates of HDV and predicted to be important in multimerization were mutated to alanine on both δAg-S and δAg-L. We found that the predicted hierarchy of importance of these nine mutations correlated to a significant extent with the observed in vivo effects on the ability of these proteins to (i) support in
trans
the replication of the HDV genome when expressed on δAg-S and (ii) act as dominant-negative inhibitors of replication when expressed on δAg-L. We thus infer that these biological activities of δAg depend on ordered protein-protein interactions.
Simian and Human Immunodeficiency Virus Nef Proteins Use Different Surfaces To Downregulate Class I Major Histocompatibility Complex Antigen Expression
Authors: Swigut Tomek , Iafrate A. John , Muench Jan , Kirchhoff Frank , Skowronski Jacek 
Published: July 2002

ABSTRACT
Simian immunodeficiency virus (SIV) and human immunodeficiency virus type 1 (HIV-1) Nef proteins are related regulatory proteins that share several functions, including the ability to downregulate class I major histocompatibility complex (MHC) and CD4 expression on the cell surface and to alter T-cell-receptor-initiated signal transduction in T cells. We compared the mechanisms used by SIV mac239 Nef and HIV-1 Nef to downregulate class I MHC and found that the ability of SIV Nef to downregulate class I MHC requires a unique C-terminal region of the SIV mac239 Nef molecule which is not found in HIV-1 Nef. Interestingly, mutation of the PxxP motif in SIV Nef, unlike in HIV-1 Nef, does not affect class I MHC downregulation. We also found that downregulation of class I MHC by SIV Nef requires a conserved tyrosine in the cytoplasmic domain of the class I MHC heavy chain and involves accelerated endocytosis of class I complexes, as previously found with HIV-1 Nef. Thus, while SIV and HIV-1 Nef proteins use a similar mechanism to downregulate class I MHC expression, they have evolved different surfaces for molecular interactions with cell factors that regulate class I MHC traffic. Mutations in the C-terminal domain of SIV mac239 Nef selectively disrupt class I MHC downregulation, having no detectable effect on other functions of Nef, such as the downregulation of CD4 and CD3 surface expression, the stimulation of SIV virion infectivity, and the induction of SIV replication from T cells infected in the absence of stimulation. The resulting mutants will be useful reagents for studying the importance of class I MHC downregulation for SIV replication and AIDS pathogenesis in infected rhesus macaques.
Evidence for the Packaging of Multiple Copies of Tf1 mRNA into Particles and the
trans
Priming of Reverse Transcription
Authors: Haag Amanda Leigh , Lin Jia-Hwei , Levin Henry L. 
Published: July 2002

ABSTRACT

Long terminal repeat (LTR)-containing retrotransposons and retroviruses are close relatives that possess similar mechanisms of reverse transcription. The particles of retroviruses package two copies of viral mRNA that both function as templates for the reverse transcription of the element. We studied the LTR-retrotransposon Tf1 of
Schizosaccharomyces pombe
to test whether multiple copies of transposon mRNA participate in the production of cDNA. Using the unique self-priming property of Tf1, we obtained evidence that multiple copies of Tf1 mRNA were packaged into virus-like particles. By coexpressing two distinct versions of Tf1, we found that the bulk of reverse transcription that was initiated on one mRNA template was subsequently transferred to others. In addition, the first 11 nucleotides of one mRNA were able to prime, in
trans
, the reverse transcription of another mRNA.
Essential and Dispensable Virus-Encoded Replication Elements Revealed by Efforts To Develop Hypoviruses as Gene Expression Vectors
Authors: Suzuki Nobuhiro , Geletka Lynn M. , Nuss Donald L. 
Published: July 2002

ABSTRACT

We have investigated whether hypoviruses, viral agents responsible for virulence attenuation (hypovirulence) of the chestnut blight fungus
Cryphonectria parasitica
, could serve as gene expression vectors. The infectious cDNA clone of the prototypic hypovirus CHV1-EP713 was modified to generate 20 different vector candidates. Although transient expression was achieved for a subset of vectors that contained the green fluorescent protein gene from
Aequorea victoria
, long-term expression (past day 8) was not observed for any vector construct. Analysis of viral RNAs recovered from transfected fungal colonies revealed that the foreign genes were readily deleted from the replicating virus, although small portions of foreign sequences were retained by some vectors after months of replication. However, the results of vector viability and progeny characterization provided unexpected new insights into essential and dispensable elements of hypovirus replication. The N-terminal portion (codons 1 to 24) of the 5′-proximal open reading frame (ORF), ORF A, was found to be required for virus replication, while the remaining 598 codons of this ORF were completely dispensable. Substantial alterations were tolerated in the pentanucleotide UAAUG that contains the ORF A termination codon and the overlapping putative initiation codon of the second of the two hypovirus ORFs, ORF B. Replication competence was maintained following either a frameshift mutation that caused a two-codon extension of ORF A or a modification that produced a single-ORF genomic organization. These results are discussed in terms of determinants of hypovirus replication, the potential utility of hypoviruses as gene expression vectors, and possible mechanisms by which hypoviruses recognize and delete foreign sequences.