bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuing Diversification of
Neisseria meningitidis
W135 as a Primary Cause of Meningococcal Disease after Emergence of the Serogroup in 2000
Authors: Taha Muhamed-Kheir , Giorgini Dario , Ducos-Galand Magaly , Alonso Jean-Michel 
Published: September 2004

ABSTRACT
The occurrence of a clonal outbreak of serogroup W135 (of the electrophoretic type 37 [ET-37] clonal complex) meningococcal disease among Hajj pilgrims in 2000 has led to enhanced surveillance of the evolution of this particular serogroup, formerly considered rare, in invasive infections. Since the first case of meningococcal disease due to a serogroup W135 strain was detected in France in 1994, all isolates were characterized phenotypically. We further used phenotypic and genotypic approaches to type the 101 serogroup W135 strains isolated from patients with invasive meningococcal diseases in France in 2001 and 2002. Overall, 55% of these isolates had Hajj strain-related phenotypes (60 and 52% in 2001 and 2002, respectively), although only 45% belonged to the ET-37 clonal complex. Moreover, pulsed-field gel electrophoresis of the ET-37 clonal complex isolates showed that only 32% of the serogroup W135 isolates were indistinguishable from the 2000 Hajj-related strain. Our results suggest the continuous emergence of new genetic lineages of serogroup W135 independently of the 2000 global outbreak.
Complementation in Cells Cotransfected with a Mixture of Wild-Type and Mutant Human Immunodeficiency Virus (HIV) Influences the Replication Capacities and Phenotypes of Mutant Variants in a Single-Cycle HIV Resistance Assay
Authors: Mo Hongmei , Lu Liangjun , Pithawalla Ron , Kempf Dale J. , Molla Akhteruzzaman 
Published: September 2004

ABSTRACT

The impact of cotransfection of mixtures of mutant and wild type (WT) virus on the observed phenotype and replication capacity (RC) in a single-cycle human immunodeficiency virus (HIV) phenotypic assay has been investigated by cotransfecting mutant HIV clones expressing the firefly luciferase expression gene with a WT clone expressing
Renilla
luciferase. Four mutant constructs with different genotypes displayed <1% RC when transfected alone. Cotransfection of as little as 9% of the WT clone resulted in an 18- to 33-fold increase in the RC of the mutant clones. In addition, the 50% inhibitory concentration (IC
50
) of lopinavir against seven mutant clones decreased by up to 97% after incremental cotransfection of 9 to 50% of the WT clone. The enhancement of RC and decrease in IC
50
for mutant variants following cotransfection with the WT variant appear to be due to complementation rather than genetic recombination. These findings suggest that the RC and susceptibility of plasma isolates from patients who are off therapy or not adherent to treatment, in which WT virus may expand to significant levels, should be interpreted with caution.
Automated High-Throughput Mycobacterial Interspersed Repetitive Unit Typing ofMycobacterium tuberculosisStrains by a Combination of PCR and Nondenaturing High-Performance Liquid Chromatography
Authors: Evans Jason T. , Hawkey Peter M. , Smith E. Grace , Boese Kerstin A. , Warren Roderic E. , Hong George 
Published: September 2004

ABSTRACTMycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing ofMycobacterium tuberculosiscomplex isolates is portable, 100% reproducible, and highly discriminatory. Nondenaturing high-performance liquid chromatography (non-dHPLC) with use of a WAVE microbial analysis system is a promising method of PCR amplicon analysis as it is low cost and requires no preanalysis processing. The aims of this study were to validate the application of WAVE microbial analysis system technology to MIRU-VNTR typing. A collection of 70 strains were cultivated in liquid culture and extracted using the QIAamp DNA minikit. Novel primers were designed to target the 12 MIRU-VNTR loci (P. Supply et al., J. Clin. Microbiol.39:3563-3571, 2001). After amplification, each PCR product was analyzed on a WAVE microbial analysis system. The fragment size was calculated from the chromatogram, and the number of tandem repeats at each locus was determined. For the collection of 70 strains 100% concordance was achieved when comparing MIRU-VNTR profiles obtained from agarose gel electrophoresis and PCRs analyzed on a WAVE microbial analysis system. The calculated fragment sizes, obtained from the WAVE microbial analysis system, were sufficiently accurate to ensure 100% confidence when assigning the number of tandem repeats to a MIRU-VNTR locus. This study is the first to report the successful use of non-dHPLC for screening for variations in the number of MIRU-VNTRs in mycobacterial DNA. Non-dHPLC analysis was demonstrated to be a rapid, low-labor input method for the detection and analysis of MIRU-VNTR amplicons. The combination with non-dHPLC further enhances the utility of MIRU-VNTR typing.
Oligonucleotide Chip for Detection of Lamivudine-Resistant Hepatitis B Virus
Authors: Jang Hyunjung , Cho Mong , Heo Jeong , Kim Hyunghoi , Jun Hongki , Shin Woowon , Cho Byungman , Park Heekyung , Kim Cheolmin 
Published: September 2004

ABSTRACT
Hepatitis B virus (HBV) is one of the major causes of liver disease worldwide. It is important to conduct antiviral therapy against chronic hepatitis B to minimize the amount of liver damage. Lamivudine has been known to be an effective antiviral agent for the treatment of HBV infection. However, the emergence of viral mutants resistant to lamivudine is the main concern during the treatment of HBV-infected patients. Therefore, the detection of lamivudine-resistant mutants is of clinical importance. We have developed an oligonucleotide chip for the detection of lamivudine-resistant HBV which is rapid and accurate. The oligonucleotide chip consists of quality control probes, negative control probes, and specific oligonucleotide probes for the detection of lamivudine-resistant HBV. The specific probes consist of five probes for the detection of wild-type rtL180, rtM204, and rtV207 sequences and seven probes for the detection of HBV mutations. We tested 123 serum samples from patients with chronic HBV infection who had received lamivudine therapy. Eighty samples contained mutants with YMDD mutations. Among these, 17 contained rtM204V (YVDD), 24 contained rtM204I3 (YIDD3), 3 contained rtM204I2 (YIDD2), and 36 contained mixed types. We compared the results obtained with our oligonucleotide chip with those obtained by PCR-restriction fragment length polymorphism (RFLP) analysis and sequencing. The rate of concordance between the assay with the oligonucleotide chip and PCR-RFLP analysis for detection of the YMDD motif was 96.7%. The rate of concordance between the results obtained with the oligonucleotide chip for the detection of rtL180 and rtV207 and the results obtained by sequencing was 100%. Thus, the oligonucleotide chip is a reliable and useful tool for the detection of antiviral-resistant HBV.
Identification of Some Charcoal-Black-Pigmented CDC Fermentative Coryneform Group 4 Isolates asRothia dentocariosaand Some asCorynebacterium aurimucosum: Proposal ofRothia dentocariosaemend. Georg and Brown 1967,Corynebacterium aurimucosumemend. Yassin et al. 2002, andCorynebacterium nigricansShukla et al. 2003 pro synon.Corynebacterium aurimucosum
Authors: Daneshvar Maryam I. , Hollis Dannie G. , Weyant Robbin S. , Jordan Jean G. , MacGregor John P. , Morey Roger E. , Whitney Anne M. , Brenner Don J. , Steigerwalt Arnold G. , Helsel Leta O. , Raney Patti M. , Patel Jean B. , Levett Paul N. , Brown June M. 
Published: September 2004

ABSTRACTSixty-three clinical isolates of charcoal-black-pigmented, gram-positive coryneform rods were received for identification by the Centers for Disease Control and Prevention (CDC) and were provisionally designated CDC fermentative coryneform group 4 (FCG4). Forty-five of these were characterized by morphological, physiologic, antimicrobial susceptibility, cellular fatty acids, 16S rRNA gene sequencing, and DNA-DNA hybridization analyses. Nitrate reduction, cellular fatty acid analysis, 16S rRNA gene sequencing, and DNA-DNA hybridization studies segregated these strains into two groups: FCG4a (8 strains) and FCG4b (37 strains). The FCG4a strains, only one of which was from a female genitourinary source, produced cellular fatty acid and biochemical profiles similar to those observed with reference strains ofRothia dentocariosaandRothia mucilaginosa, while the FCG4b strains were similar toCorynebacteriumspecies. DNA-DNA hybridization analysis demonstrated species-level relatedness among six FCG4a tested strains and showed that they were a charcoal-black-pigmented variant ofR. dentocariosa. Sixteen isolates of the FCG4b group, mainly from female genitourinary tract specimens, as well as the type strains of two recently named species,Corynebacterium aurimucosumandCorynebacterium nigricans, were shown by DNA-DNA hybridization analysis and the sequencing of the 16S rRNA gene to be related at the species level and unrelated to the type strain ofR. dentocariosa; therefore, theCorynebacterium-like strains were classified as a charcoal-black-pigmented variant ofC. aurimucosum, because this name has nomenclatural priority overC. nigricans. These findings indicate that FCG4 represents a heterogeneous group that contains pigmented variants of bothR. dentocariosaandC. aurimucosum; hence, the descriptions of bothR. dentocariosaandC. aurimucosumhave been amended to include charcoal-black-pigmented variants, andC. nigricansis a pro synonym ofC. aurimucosum.
Correlation of Cerebrospinal Fluid (CSF) Cell Counts and Elevated CSF Protein Levels with Enterovirus Reverse Transcription-PCR Results in Pediatric and Adult Patients
Authors: Mulford William S. , Buller Richard S. , Arens Max Q. , Storch Gregory A. 
Published: September 2004

ABSTRACT
During the 2001, 2002, and 2003 enterovirus seasons, we investigated the correlations between cerebrospinal fluid (CSF) nucleated cell counts and elevated CSF protein levels and the detection of enteroviral RNA by reverse transcription (RT)-PCR. Our objective was to determine if pleocytosis and/or elevated protein levels were predictive of positive RT-PCR results for enterovirus. We were also interested in determining if the presence of West Nile virus during the 2002 enteroviral season contributed to a change in these correlations. We found that in the group of patients aged >2 months, the absence of pleocytosis was highly predictive of a negative RT-PCR result. Elevated CSF protein level was not a good predictor of RT-PCR positivity for enterovirus and did not add to the diagnostic sensitivity or specificity of pleocytosis.
Rapid Detection of Isoniazid and Rifampin Resistance Mutations in
Mycobacterium tuberculosis
Complex from Cultures or Smear-Positive Sputa by Use of Molecular Beacons
Authors: Lin S.-Y. Grace , Probert William , Lo Melanie , Desmond Edward 
Published: September 2004

ABSTRACT

The slow-growing nature of
Mycobacterium tuberculosis
complex hinders the improvement of turnaround time for phenotypic drug susceptibility testing. We designed a set of molecular beacons for the detection of isoniazid and rifampin resistance mutations in
M. tuberculosis
complex organisms from cultures or from
N
-acetyl-
l
-cysteine-NaOH-treated, smear-positive specimens. The performance of the molecular beacons was characterized by studying a total of 196 clinical isolates (127 drug-resistant isolates and 69 drug-susceptible isolates). For detection of isoniazid resistance, the sensitivity and specificity of the assay were 82.7 and 100%, and the positive predictive value (PPV) and negative predictive value (NPV) at a resistance prevalence of 10% were 100 and 98.11%, respectively. For detection of rifampin resistance, the sensitivity and specificity of the assay were 97.5 and 100%, and the PPV and NPV at a resistance prevalence of 2.0% were 100 and 99.95%, respectively.
Laboratory Reporting of Tuberculosis Test Results and Patient Treatment Initiation in California
Authors: Pascopella Lisa , Kellam Steffi , Ridderhof John , Chin Daniel P. , Reingold Arthur , Desmond Edward , Flood Jennifer , Royce Sarah 
Published: September 2004

ABSTRACT
Prompt laboratory reporting of tuberculosis (TB) test results is necessary for TB control. To understand the extent of and factors contributing to laboratory reporting delays and the impact of reporting delays on initiation of treatment of TB patients, we analyzed data from 300 consecutive culture-positive TB cases reported in four California counties in 1998. Laboratory reporting to the specimen submitter was delayed for 26.9% of smear-positive patients and 46.8% of smear-negative patients. Delays were associated with the type of laboratory that performed the testing and with delayed transport of specimens. Referral laboratories (public health and commercial) had longer median reporting time frames than hospital and health maintenance organization laboratories. Among patients whose treatment was not started until specimens were collected, those with delayed laboratory reporting were more likely to have delayed treatment than patients with no laboratory reporting delays (odds ratio [OR] of 3.9 and 95% confidence interval [CI] of 1.6 to 9.7 for smear-positive patients and OR of 13.1 and CI of 5.3 to 32.2 for smear-negative patients). This relation remained after adjustment in a multivariate model for other factors associated with treatment delays (adjusted OR of 25.64 and CI of 7.81 to 83.33 for smear-negative patients). These findings emphasize the need to reduce times of specimen transfer between institutions and to ensure rapid communication among laboratories, health care providers, and health departments serving TB patients.
Accurate Representation of the Hepatitis C Virus Quasispecies in 5.2-Kilobase Amplicons
Authors: Liu Zhi , Netski Dale M. , Mao Qing , Laeyendecker Oliver , Ticehurst John R. , Wang Xiao-Hong , Thomas David L. , Ray Stuart C. 
Published: September 2004

ABSTRACT

Hepatitis C virus (HCV) exists as a swarm of genetically distinct but related variants, or a quasispecies, whose complexity and sequence evolution are critical to studies of viral pathogenesis. Because most studies of the HCV quasispecies have focused on a relatively small genomic segment, the first hypervariable region of the E2 gene, it is possible that viral complexity is occasionally underestimated (due to primer mismatch) and that sequence evolution is misperceived due to unrecognized covariation. This report describes a sensitive and reproducible method to amplify most of the HCV genome as a single 5.2-kb amplicon by using primers directed at relatively conserved genomic segments. Using 52 specimens obtained during acute infection over a range of viral RNA concentrations, the overall rate of successful amplification was 94% and varied in a concentration-dependent manner, with successful amplification in 26 of 26 (100%) specimens at greater than 10
5
IU/ml, 15 of 16 (94%) at 10
4
to 10
5
IU/ml, 6 of 7 (86%) at 10
3
to 10
4
IU/ml, and 2 of 3 (67%) at less than 10
3
IU/ml. Quasispecies complexity, determined by using this novel long-amplicon method followed by heteroduplex mobility assay combined with single-stranded conformational polymorphism (HDA+SSCP) analysis, was very high, even during acute HCV infection, when 10 to 21 (median, 16) different HDA+SSCP patterns were detected among 33 cDNA clones examined. Replicate analyses indicate that this diversity is not dominated by random errors generated during amplification. Therefore, the HCV quasispecies is highly complex even during acute infection and is accurately represented in amplicons representing more than half of the viral genome.
Use of the Minimum Spanning Tree Model for Molecular Epidemiological Investigation of a Nosocomial Outbreak of Hepatitis C Virus Infection
Authors: Spada Enea , Sagliocca Luciano , Sourdis John , Garbuglia Anna Rosa , Poggi Vincenzo , De Fusco Carmela , Mele Alfonso 
Published: September 2004

ABSTRACT
The minimum spanning tree (MST) model was applied to identify the history of transmission of hepatitis C virus (HCV) infection in an outbreak involving five children attending a pediatric oncology-hematology outpatient ward between 1992 and 2000. We collected blood samples from all children attending since 1992, all household contacts, and one health care worker positive for antibody to HCV (anti-HCV). HCV RNA detection was performed with these samples and with smears of routinely collected bone marrow samples. For all isolates, we performed sequence analysis and phylogenetic tree analysis of hypervariable region 1 of the E2 gene. The MST model was applied to clinical-epidemiological and molecular data. No additional cases were detected. All children, but not the health care worker, showed genotype 3a. On six occasions, all but one child had shared the medication room with another patient who later seroconverted. HCV RNA detection in bone marrow smears revealed, in some cases, a delay of several months in anti-HCV responses. Sequence analysis and phylogenetic tree analysis revealed a high identity among the isolates. The MST model applied to molecular data, together with the clinical-epidemiological data, allowed us to identify the source of the outbreak and the most probable patient-to-patient chain of transmission. The management of central venous catheters was suspected to be the probable route of transmission. In conclusion, the MST model, supported by an exhaustive clinical-epidemiological investigation, appears to be a useful tool in tracing the history of transmission in outbreaks of HCV infection.
Persistent Histidine-Rich Protein 2, Parasite Lactate Dehydrogenase, and Panmalarial Antigen Reactivity after Clearance of
Plasmodium falciparum
Monoinfection
Authors: Iqbal Jamshaid , Siddique Ahmed , Jameel Mohammad , Hira Persotum R. 
Published: September 2004

ABSTRACT

We tested 240 patients with
Plasmodium falciparum
monoinfection for persistent parasite antigenemia after successful standardized antimalarial therapy by using the ICT Malaria Pf/Pv and OptiMAL-IT assays that detect the malaria antigens
Plasmodium falciparum
histidine-rich protein 2 (HRP2) and parasite lactate dehydrogenase (pLDH), respectively, as well as a panmalarial antigen (PMA). The patients were screened for antigenemia on days 0, 3, 7, and 14 of follow-up. On day 0, all 240 patients showed positive reactivity with both assays. Of the 229 cases with negative parasitemia on day 3, persistent antigenemia was observed in 207 (90.4%) of the cases: 188 (82.1%) for HRP2 antigen and 75 (32.8%) for PMA. There was a gradual decrease in antigenemia on follow-up to day 14; however, the drop in reactivity to PMA was less than that for HRP2 antigen. In contrast to HRP2 antigenemia, there was a significant decrease in pLDH antigenemia to 38.4% and to 14.8% (PMA) on day 3 (
P
< 0.03). The pLDH antigenemia level dropped further to 14.8% on day 7. There was no significant association of persistent antigenemia with gametocytemia. One case with gametocytemia was negative for both the antigens. In conclusion, the OptiMAL-IT assay is more sensitive than the ICT Malaria Pf/Pv test for monitoring therapeutic responses after antimalarial therapy since the LDH activity ceases when the malarial parasite dies.
Risk Factors for Colonization and Infection in a Hospital Outbreak Caused by a Strain of
Klebsiella pneumoniae
with Reduced Susceptibility to Expanded-Spectrum Cephalosporins
Authors: Cartelle Monica , del Mar Tomas Maria , Pertega Sonia , Beceiro Alejandro , Dominguez M. Angeles , Velasco David , Molina Francisca , Villanueva Rosa , Bou German 
Published: September 2004

ABSTRACT

Between February 2001 and January 2002, an increase in the number of
Klebsiella pneumoniae
isolates with reduced susceptibility to expanded-spectrum cephalosporins (RSKp) was detected in the neonatal unit of the Juan Canalejo Hospital, and 21 patients were either colonized or infected by the bacterial isolates. The current “gold standard” method for typing
K. pneumoniae
isolates is pulsed-field gel electrophoresis. However, this technique is expensive and time-consuming. In a search for faster and accurate alternatives to this method, we investigated PCR-based fingerprinting techniques (enterobacterial repetitive intergenic consensus sequence PCR [ERIC-PCR], repetitive extragenic palindromic sequence-based PCR [REP-PCR], and RAPD [randomly amplified polymorphic DNA]) for their ability to characterize
K. pneumoniae
isolates. The causal agent of the nosocomial outbreak was characterized by these techniques and was found to be a single epidemic strain (RSKp). A multiple regression logistic model was developed to identify potential independent factors associated with colonization and/or infection by RSKp. Logistic regression analysis was applied to all significant variables (
P
< 0.05) in the univariate analysis, and it was revealed that intubation (odds ratio [OR], 27.0; 95% confidence interval [95%CI], 5.39 to 135.14) and prematurity (OR, 4.4; 95%CI, 0.89 to 21.89) were such independent factors. Moreover, oxime cephalosporins did not appear to be statistically significant. Overall, the results showed that PCR-based techniques are expeditious and useful methods for typing
K. pneumoniae
isolates. Of the techniques studied, ERIC-PCR showed the highest discriminatory index (D = 0.828), followed by RAPD (D = 0.826) and REP-PCR (D = 0.773)
Identification and Typing of
Malassezia
Species by Amplified Fragment Length Polymorphism and Sequence Analyses of the Internal Transcribed Spacer and Large-Subunit Regions of Ribosomal DNA
Authors: Gupta Aditya K. , Boekhout Teun , Theelen Bart , Summerbell Richard , Batra Roma 
Published: September 2004

ABSTRACT

Malassezia
yeasts are associated with several dermatological disorders. The conventional identification of
Malassezia
species by phenotypic methods is complicated and time-consuming, and the results based on culture methods are difficult to interpret. A comparative molecular approach based on the use of three molecular techniques, namely, amplified fragment length polymorphism (AFLP) analysis, sequencing of the internal transcribed spacer, and sequencing of the D1 and D2 domains of the large-subunit ribosomal DNA region, was applied for the identification of
Malassezia
species. All species could be correctly identified by means of these methods. The results of AFLP analysis and sequencing were in complete agreement with each other. However, some discrepancies were noted when the molecular methods were compared with the phenotypic method of identification. Specific genotypes were distinguished within a collection of
Malassezia furfur
isolates from Canadian sources. AFLP analysis revealed significant geographical differences between the North American and European
M. furfur
strains.