bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Degree of Interlaboratory Reproducibility of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Sequencing of Plasma Samples from Heavily Treated Patients
Authors: Shafer Robert W. , Hertogs Kurt , Zolopa Andrew R. , Warford Ann , Bloor Stuart , Betts Bradley J. , Merigan Thomas C. , Harrigan Richard , Larder Brendon A. 
Published: July 2002

ABSTRACTWe assessed the reproducibility of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and protease sequencing using cryopreserved plasma aliquots obtained from 46 heavily treated HIV-1-infected individuals in two laboratories using dideoxynucleotide sequencing. The rates of complete sequence concordance between the two laboratories were 99.1% for the protease sequence and 99.0% for the RT sequence. Approximately 90% of the discordances were partial, defined as one laboratory detecting a mixture and the second laboratory detecting only one of the mixture's components. Only 0.1% of the nucleotides were completely discordant between the two laboratories, and these were significantly more likely to occur in plasma samples with lower plasma HIV-1 RNA levels. Nucleotide mixtures were detected at approximately 1% of the nucleotide positions, and in every case in which one laboratory detected a mixture, the second laboratory either detected the same mixture or detected one of the mixture's components. The high rate of concordance in detecting mixtures and the fact that most discordances between the two laboratories were partial suggest that most discordances were caused by variation in sampling of the HIV-1 quasispecies by PCR rather than by technical errors in the sequencing process itself.
Secondary Typing of
Mycobacterium tuberculosis
Isolates with Matching IS
6110
Fingerprints from Different Geographic Regions of the United States
Authors: Yang Z. H. , Bates J. H. , Eisenach K. D. , Cave M. D. 
Published: July 2002

ABSTRACT

Fifty-nine isolates of
Mycobacterium tuberculosis
obtained from different states in the United States and representing 25 interstate clusters were investigated. These clusters were identified by computer-assisted analysis of DNA fingerprints submitted during 1996 and 1997 by different laboratories participating in the CDC National Genotyping and Surveillance Network. Isolates were fingerprinted with the IS
6110
right-hand probe (IS
6110
-3′), the IS
6110
left-hand probe (IS
6110
-5′), and the probe pTBN12, containing the polymorphic GC-rich sequence (PGRS). Spoligotyping based on the polymorphism in the 36-bp direct-repeat locus was also performed. As a control, 43
M. tuberculosis
isolates in 17 clusters obtained from patients in Arkansas during the study period were analyzed. Of the 25 interstate clusters, 19 were confirmed as correctly clustered when all the isolates were analyzed on the same gel using the IS
6110
-3′ probe. Of the 19 true IS
6110
-3′ clusters, 10 (53%) were subdivided by one or more secondary typing methods. Clustering of the control group was virtually identical by all methods. Of the three different secondary typing methods, spoligotyping was the least discriminating. IS
6110
-5′ fingerprinting was as discriminating as PGRS fingerprinting. The data indicate that the IS
6110
-5′ probe not only is a useful secondary typing method but also probably would prove to be a more useful primary typing method for a genotyping network which involves isolates from different geographic regions.
Mycolic Acid Index Susceptibility Method for
Mycobacterium tuberculosis
Authors: Viader-Salvadó José M. , Garza-González Elvira , Valdez-Leal Ramón , de los Angeles del Bosque-Moncayo M. , Tijerina-Menchaca Rolando , Guerrero-Olazarán Martha 
Published: July 2002

ABSTRACT

A rapid drug susceptibility test to measure the susceptibility of
Mycobacterium tuberculosis
to isoniazid (INH) and rifampin (RIF) using clinical isolates and a newly defined mycolic acid index (MAI) was evaluated. A total of 200 clinical isolates of
M. tuberculosis
were tested for susceptibility or resistance to INH and RIF by the MAI susceptibility and indirect-proportion methods. Overall, there was agreement between the two methods for 398 (99.5%) of the 400 total tests. Specifically, the sensitivity of the MAI susceptibility method for INH and RIF was 97.6 and 100%, respectively. The specificity and positive predictive value were 100% for both drugs, and the negative predictive value for INH and RIF was 98.3 and 100%, respectively. In conclusion, the MAI susceptibility method described here can be used for rapid drug susceptibility testing of
M. tuberculosis
clinical isolates within 5 days after clinical isolates are incubated in the presence or absence of an antituberculosis drug.
Variation in Restriction Fragment Length Polymorphisms among Serial Isolates from Patients with
Trichophyton rubrum
Infection
Authors: Gupta Aditya K. , Kohli Yatika , Summerbell Richard C. 
Published: July 2002

ABSTRACT

Molecular genotyping of strains of
Trichophyton rubrum
and
T. mentagrophytes
from patients with onychomycosis of the toes was performed to ascertain whether the fungal genotype changes over the course of time as sequential samples were obtained from patients receiving antifungal therapy and during follow-up. Sixty-six serial strains of
T. rubrum
and 11 strains of
T. mentagrophytes
were obtained from 20 patients (16 patients with
T. rubrum
, 4 with
T. mentagrophytes
) who were treated with oral antifungal therapy and observed over periods of up to 36 months. These strains were screened for genetic variation by hybridization of
Eco
RI-digested genomic DNAs with a probe amplified from the small-subunit (18S) ribosomal DNA and adjacent internal transcribed spacer regions. A total of five restriction fragment length polymorphism (RFLP) types were observed among 66 strains of
T. rubrum
. Two major RFLP types, differentiated by one band shift, represented 68% of the samples. None of the patients had a unique genotype. More than one RFLP type was often observed from a single patient (same nail) over a period of 1, 2, or 3 years, even in cases that did not appear cured at any time. Samples taken from different nails of the same patient had either the same or a different genotype. The genotypic variation did not correspond to any detectable phenotypic variation. Furthermore, no correlation was observed between the efficacy of the treatment administered and the genotype observed. While the DNA region studied distinguished among
T. rubrum, T. mentagrophytes
, and
T. tonsurans
, intraspecific RFLP variation was observed for
T. rubrum
and
T. mentagrophytes
strains. While independent multiple infection and coinhabitation of multiple strains may explain the presence of different genotypes in a nail, microevolutionary events such as rapid substrain shuffling, as seen in studies of repetitive regions in
Candida
species, may also produce the same result. The recovery of multiple strains during the course of sequential sampling of uncured patients further suggests that the typing system is not able to distinguish between relapse or reinfection, ongoing infection, and de novo infection.
Clinical and Virological Aspects of Blood Donors Infected with Hepatitis B Virus Genotypes B and C
Authors: Kao Jia-Horng , Chen Pei-Jer , Lai Ming-Yang , Chen Ding-Shinn 
Published: July 2002

ABSTRACT
Pathogenic and therapeutic differences among hepatitis B virus (HBV) genotypes have been documented. However, the association of virological characteristics with clinical differences among HBV genotypes remains unclear. We therefore studied the clinical and virological characteristics of Taiwanese volunteer blood donors infected with HBV genotypes B and C. HBV genotypes were determined in 300 candidate blood donors positive for HBV surface antigen (HBsAg), and sequences of the precore gene of the HBV genome were determined in 50 HBV e antigen (HBeAg)-positive and 50 HBeAg-negative blood donors. Of 300 HBsAg-positive blood donors, 10% had elevated serum aminotransferase levels and 27% were positive for HBeAg. HBV genotype distribution in 264 viremic carriers was as follows: B, 221 (83.7%); C, 39 (14.8%); F, 1 (0.4%); and mixed infection, 3 (1.1%). Blood donors with genotype C infection tended to have a higher frequency of HBeAg positivity and a higher serum HBV DNA level than those with genotype B infection. The frequency of precore stop codon mutation was significantly higher in HBeAg-negative blood donors than HBeAg-positive ones, irrespective of HBV genotypes. Meanwhile, only 5% of blood donors with genotype C infection had C-1858 strains. In conclusion, mixed infection of HBV genotypes indeed occurs, and genotype C has a higher serum HBV DNA level than genotype B. Precore stop codon mutation is common in HBeAg-negative HBV carriers, irrespective of HBV genotypes. In contrast, precore C-1858 strains are rarely identified in Taiwanese HBV genotype C.
Human Immunodeficiency Virus Type 1 Group M Protease in Cameroon: Genetic Diversity and Protease Inhibitor Mutational Features
Authors: Fonjungo Peter N. , Mpoudi Eitel N. , Torimiro Judith N. , Alemnji George A. , Eno Laura T. , Lyonga Esther J. , Nkengasong John N. , Lal Renu B. , Rayfield Mark , Kalish Marcia L. , Folks Thomas M. , Pieniazek Danuta 
Published: July 2002

ABSTRACT

To establish a baseline for monitoring resistance to protease inhibitors (PIs) and examining the efficacy of their use among persons in Cameroon infected with human immunodeficiency virus type 1 (HIV-1), we analyzed genetic variability and PI resistance-associated substitutions in PCR-amplified protease (PR) sequences in strains isolated from 110 HIV-1-infected, drug-naïve Cameroonians. Of the 110 strains, 85 were classified into six HIV-1 PR subtypes, A (
n
= 1), B (
n
= 1), F (
n
= 4), G (
n
= 7), H (
n
= 1), and J (
n
= 7), and a circulating recombinant form, CRF02-AG (
n
= 64). PR genes from the remaining 25 (23%) specimens were unclassifiable, whereas 2% (7 of 301) unclassifiable PR sequences were reported for a global collection. Two major PI resistance-associated mutations, 20M and 24I, were detected in strains from only two specimens, whereas secondary mutations were found in strains from all samples except one strain of subtype B and two strains of CRF02-AG. The secondary mutations showed the typical PI resistance-associated pattern for non-subtype B viruses in both classifiable and unclassifiable PR genes, with 36I being the predominant (99%) mutation, followed by 63P (18%), 20R (15%), 77I (13%), and 10I or 10V (11%). Of these mutations, dual and triple PI resistance-associated substitutions were found in 38% of all the Cameroonian strains. Compared with classifiable PR sequences, unclassifiable sequences had significantly more dual and triple substitutions (64% versus 30%;
P
= 0.004). Phenotypic and clinical evaluations are needed to estimate whether PI resistance during antiretroviral drug treatment occurs more rapidly in individuals infected with HIV-1 strains harboring multiple PI resistance-associated substitutions. This information may be important for determination of appropriate drug therapies for HIV-1-infected persons in Cameroon, where more than one-third of HIV-1 strains were found to carry dual and triple minor PI resistance-associated mutations.
Burkholderia cepacia
Complex Bacteria from Clinical and Environmental Sources in Italy: Genomovar Status and Distribution of Traits Related to Virulence and Transmissibility
Authors: Bevivino Annamaria , Dalmastri Claudia , Tabacchioni Silvia , Chiarini Luigi , Belli Maria L. , Piana Sandra , Materazzo Alberto , Vandamme Peter , Manno Graziana 
Published: July 2002

ABSTRACT

Sixty-eight
Burkholderia cepacia
complex isolates recovered from the sputum of 53 cystic fibrosis patients and 75 isolates collected from the maize rhizosphere were compared to each other to assess their genomovar status as well as some traits related to virulence such as antibiotic susceptibility, proteolytic and hemolytic activities, and transmissibility, in which transmissibility is determined by detection of the
esmR
and
cblA
genes. Among the clinical isolates,
B. cepacia
genomovar III comprised the majority of isolates examined and only a very few isolates were assigned to
B. cepacia
genomovar I,
B. stabilis
, and
B. pyrrocinia
; among the environmental isolates a prevalence of
B. cepacia
genomovar III and
B. ambifaria
was observed, whereas few environmental isolates belonging to
B. cepacia
genomovar I and
B. pyrrocinia
were found. Antibiotic resistance analysis revealed a certain degree of differentiation between clinical and environmental isolates. Proteolytic activity and onion tissue maceration ability were found to be spread equally among both clinical and environmental isolates, whereas larger percentages of environmental isolates than clinical isolates had hemolytic activity. The
esmR
gene was found exclusively among isolates belonging to
B. cepacia
genomovar III, with a marked prevalence in clinical isolates, whereas only one clinical isolate belonging to
B. cepacia
genomovar III was found to bear the
cblA
gene. In conclusion, the results of the present study show that the species compositions of the clinical and environmental
B. cepacia
complex populations examined are quite different and that some of the candidate determinants related to virulence and transmissibility are not confined solely to clinical isolates but are also spread among environmental isolates belonging to different species of the
B. cepacia
complex.
Comparison of Four Antiseptic Preparations for Skin in the Prevention of Contamination of Percutaneously Drawn Blood Cultures: a Randomized Trial
Authors: Calfee David P. , Farr Barry M. 
Published: July 2002

ABSTRACT

A number of skin antiseptics have been used to prevent the contamination of blood cultures, but the comparative efficacies of these agents have not been extensively evaluated. We therefore sought to compare the efficacy of four skin antiseptics in preventing blood culture contamination in a randomized, crossover, investigator-blinded study conducted in an emergency department and the inpatient wards of a university hospital. The patient group included all patients from whom blood samples were obtained percutaneously for culture. Skin antisepsis was performed with 10% povidone-iodine, 70% isopropyl alcohol, tincture of iodine, or povidone-iodine with 70% ethyl alcohol (i.e., Persist). The blood culture contamination rate associated with each antiseptic was then determined. A total of 333 (2.62%) of 12,692 blood cultures were contaminated during the study period compared to 413 (3.21%) of 12,859 blood cultures obtained during the previous 12-month period (relative risk = 0.82; 95% confidence interval, 0.71 to 0.94;
P
= 0.006). During the study, the contamination rates were determined to be 2.93% with povidone-iodine, 2.58% with tincture of iodine, 2.50% with isopropyl alcohol, and 2.46% with Persist (
P
= 0.62). We detected no significant differences in the blood culture contamination rates among these four antiseptics, although there was some evidence suggesting greater efficacy among the alcohol-containing antiseptics. Among the evaluated antiseptics, isopropyl alcohol may be the optimal antiseptic for use prior to obtaining blood for culture, given its convenience, low cost, and tolerability.
Molecular Subtyping Methods for Detection of
Salmonella enterica
Serovar Oranienburg Outbreaks
Authors: Kumao Toshio , Ba-Thein William , Hayashi Hideo 
Published: July 2002

ABSTRACT

This study involved 82
Salmonella enterica
serovar Oranienburg isolates from patients with gastroenteritis and/or focal infections, healthy carriers, and cuttlefish chips which were epidemiologically linked to a major outbreak that had affected 1,505 people in Japan between 1998 and 1999. We concurrently investigated four different molecular subtyping methods using human salmonellosis-associated
Salmonella
serovars and their applicability in detection of serovar Oranienburg in an outbreak. Pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic sequence PCR (ERIC2-PCR), or 16S/23S rRNA ribotyping provided a high degree of interserovar discrimination for most of the serovars, with PFGE being the most discriminatory. For intraserovar typing of serovar Oranienburg, ERIC2-PCR was found to be the most sensitive. Native plasmid profiling, however, revealed nine different subgroups among epidemiologically and genetically related outbreak strains. Using these methods, a link was confirmed between food (cuttlefish chips) and patients in the serovar Oranienburg outbreak. This study underscores the limitations of chromosome-based and plasmid-based typing methods.
Genetic Structure ofCandida glabrataPopulations in AIDS and Non-AIDS Patients
Authors: de Meeûs T. , Renaud F. , Mouveroux E. , Reynes J. , Galeazzi G. , Mallié M. , Bastide J. M. 
Published: July 2002

ABSTRACTThe genotypes of 63 strains (11 reference strains and 52 strains from hospitalized patients) of the haploid yeastCandida glabratawere determined from 33 putative gene enzymatic loci. This enabled the characterization of 26 different multilocus genotypes. Genetic differentiation was found between distant hospitals (located in Montpellier and Paris, France) but not for other parameters (anatomic origins or human immunodeficiency virus-positive [HIV+] and HIV−patients). Strong nonrandom association between loci could be seen. Such statistical linkages were confirmed upon comparing the patterns of 14 RAPD [random(ly) amplified polymorphic DNA] primers from 20 of these strains to results obtained from multilocus enzyme electrophoresis analysis. This finding suggests a mainly clonal mode of reproduction ofC. glabrata. The consequences of the clonality displayed byC. glabratapopulations on the epidemiology of this yeast are also discussed.
Expression of Hepatitis C Virus Proteins Interferes with the Antiviral Action of Interferon Independently of PKR-Mediated Control of Protein Synthesis
Authors: François C. , Duverlie G. , Rebouillat D. , Khorsi H. , Castelain S. , Blum H. E. , Gatignol A. , Wychowski C. , Moradpour D. , Meurs E. F. 
Published: July 2002

ABSTRACT
Hepatitis C virus (HCV) of genotype 1 is the most resistant to interferon (IFN) therapy. Here, we have analyzed the response to IFN of the human cell line UHCV-11 engineered to inducibly express the entire HCV genotype 1a polyprotein. IFN-treated, induced UHCV cells were found to better support the growth of encephalomyocarditis virus (EMCV) than IFN-treated, uninduced cells. This showed that expression of the HCV proteins allowed the development of a partial resistance to the antiviral action of IFN. The nonstructural 5A (NS5A) protein of HCV has been reported to inhibit PKR, an IFN-induced kinase involved in the antiviral action of IFN, at the level of control of protein synthesis through the phosphorylation of the initiation factor eIF2α (M. Gale, Jr., C. M. Blakely, B. Kwieciszewski, S. L. Tan, M. Dossett, N. M. Tang, M. J. Korth, S. J. Polyak, D. R. Gretch, and M. G. Katze, Mol. Cell. Biol. 18:5208–5218, 1998). Accordingly, cell lines inducibly expressing NS5A were found to rescue EMCV growth (S. J. Polyak, D. M. Paschal, S. McArdle, M. J. Gale, Jr., D. Moradpour, and D. R. Gretch, Hepatology 29:1262–1271, 1999). In the present study we analyzed whether the resistance of UHCV-11 cells to IFN could also be attributed to inhibition of PKR. Confocal laser scanning microscopy showed no colocalization of PKR, which is diffuse throughout the cytoplasm, and the induced HCV proteins, which localize around the nucleus within the endoplasmic reticulum. The effect of expression of HCV proteins on PKR activity was assayed in a reporter assay and by direct analysis of the in vivo phosphorylation of eIF2α after treatment of cells with poly(I)-poly(C). We found that neither PKR activity nor eIF2α phosphorylation was affected by coexpression of the HCV proteins. In conclusion, expression of HCV proteins in their biological context interferes with the development of the antiviral action of IFN. Although the possibility that some inhibition of PKR (by either NS5A or another viral protein) occurs at a very localized level cannot be excluded, the resistance to IFN, resulting from the expression of the HCV proteins, cannot be explained solely by inhibition of the negative control of translation by PKR.
Interaction of Human Immunodeficiency Virus Type 2 Vpx and Invariant Chain
Authors: Pancio Heather A. , Vander Heyden Nancy , Kosuri Kavitha , Cresswell Peter , Ratner Lee 
Published: July 2002

ABSTRACTVpx is a virion-associated protein of human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency viruses. The yeast two-hybrid system was used to identify invariant chain (Ii) as a cellular protein that interacts with HIV-2 Vpx. Vpx-Ii interaction was confirmed in cell-free reactions using bacterially expressed glutathioneS-transferase fusion proteins and by coimmunoprecipitation in transfected and infected cells. In chronically infected cells expressing Vpx, Ii levels were markedly decreased, presumably due to enhanced degradation. These findings suggest that Vpx may disrupt major histocompatibility complex class II antigen presentation.
The Rous Sarcoma Virus Long Terminal Repeat Promoter Is Regulated by TFII-I
Authors: Mobley Constance M. , Sealy Linda 
Published: July 2002

ABSTRACT

Many viral genes contain core promoters with two basal control elements, the TATA box and the pyrimidine-rich initiator (Inr). However, the molecular mechanisms involved in transcription initiation from composite core promoters (TATA
+
Inr
+
) containing Inr elements are unclear. The Rous sarcoma virus (RSV) long terminal repeat (LTR) contains a transcriptionally potent enhancer and core promoter composed of a TATA box and an Inr-like sequence, termed the transcription start site core (TSSC). Previously we demonstrated that the TSSC binds the multifunctional Inr-binding protein YY1. Here we present evidence that the TSSC also binds the multifunctional transcription factor TFII-I and that both TFII-I and YY1 are required for RSV LTR transcriptional activity. Gel shift assays using anti-TFII-I antibody show that TFII-I is present in a protein complex that specifically binds to the TSSC. Mutations in the TSSC that reduce TFII-I binding also reduce RSV LTR enhancer and promoter activity. Transient-transfection assays demonstrate that TFII-I transactivates the RSV LTR from ca. fourfold (basal) to ca. sevenfold (enhanced) in both human and natural host cell lines. Importantly, the activity of the TSSC element can be attributed to the binding activity of TFII-I and the YY1 protein, since mutation of each of these binding sites within the TSSC element abolishes all viral expression as demonstrated by transient-transfection assays. Taken together, these data demonstrate that expression of RSV viral mRNA is dependent on both TFII-I and YY1.