bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Evaluation of the Digene Hybrid Capture II Test and the COBAS AMPLICOR Monitor Test for Determination of Hepatitis B Virus DNA Levels
Authors: Yuan He-Jun , Yuen Man-Fung , Wong Danny Ka-Ho , Sum Simon Siu-Man , Lai Ching-Lung 
Published: August 2004

ABSTRACT

The measurement of hepatitis B virus (HBV) DNA is important for the assessment of liver disease and treatment efficacy. Most commercially available assays for the determination of HBV DNA levels have limited linear ranges. This study was performed to evaluate the clinical performance of the Digene Hybrid Capture II (Digene HC II assay) and the COBAS AMPLICOR Monitor test (COBAS-AM assay), with special emphasis on anti-HBV e antigen (HBeAg)-positive patients with low HBV DNA levels. A total of 425 Chinese patients with chronic hepatitis B were recruited. A total of 107 patients were HBeAg positive, and 318 patients were HBeAg negative. The Digene HC II assay and the COBAS-AM assay had similar intra-assay and interassay variabilities. A total of 264 patients (62.1%) had HBV DNA levels undetectable by the Digene HC II assay, and 47 patients (11.1%) had HBV DNA levels undetectable by the COBAS-AM assay (
P
< 0.001). For the 161 patients with HBV DNA levels detectable by the Digene HC II assay, the HBV DNA levels obtained by the Digene HC II assay and by the COBAS-AM assay showed an excellent correlation (
r
= 0.95;
P
< 0.001). The linear ranges of the Digene HC II assay and the COBAS-AM assay marginally overlapped. Before HBV DNA levels could be determined by the COBAS-AM assay, predilution had to be performed for 158 of 161 patients (98.1%) with HBV DNA levels detectable by the Digene HC II assay and for 10 of 264 patients (3.8%) with HBV DNA levels undetectable by the Digene HC II assay. The cost for assaying each serum sample by using different strategies was calculated. The COBAS-AM assay was more sensitive than the Digene HC II assay and more suitable for monitoring low levels of HBV viremia.
Comparison of the BBL CHROMagar Staph aureus Agar Medium to Conventional Media for Detection of
Staphylococcus aureus
in Respiratory Samples
Authors: Flayhart Diane , Lema Clara , Borek Anita , Carroll Karen C. 
Published: August 2004

ABSTRACT

Screening for
Staphylococcus aureus
has become routine in certain patient populations. This study is the first clinical evaluation of the BBL CHROMagar Staph aureus agar (CSA) medium (BD Diagnostics, Sparks, Md.) for detection of
S. aureus
in nasal surveillance cultures and in respiratory samples from cystic fibrosis (CF) patients.
S. aureus
colonies appear mauve on CSA. Other organisms are inhibited or produce a distinctly different colony color.
S. aureus
was identified from all media by slide coagulase, exogenous DNase, and mannitol fermentation assays. Susceptibility testing was performed using the agar dilution method. A total of 679 samples were evaluated. All samples were inoculated onto CSA. Nasal surveillance cultures were inoculated onto sheep blood agar (SBA) (BD Diagnostics), and samples from CF patients were inoculated onto mannitol salt agar (MSA) (BD Diagnostics). Of the 679 samples cultured, 200 organisms produced a mauve color on CSA (suspicious for
S. aureus
) and 180 were positive for
S. aureus
on SBA or MSA. Of 200 CSA-positive samples 191 were identified as
S. aureus
. Nine mauve colonies were slide coagulase negative and were subsequently identified as
Staphylococcus lugdunensis
(one),
Staphylococcus epidermidis
(three),
Staphylococcus haemolyticus
(one), and
Corynebacterium
species (four). CSA improved the ability to detect
S. aureus
by recovering 12
S. aureus
isolates missed by conventional media. Of the 192
S. aureus
isolates recovered, 122 were methicillin susceptible and 70 were methicillin resistant. Overall, the sensitivity and specificity of CSA in this study were 99.5 and 98%, respectively. There was no difference in the performance of the slide coagulase test or in susceptibility testing performed on
S. aureus
recovered from CSA compared to SBA or MSA. Our data support the use of CSA in place of standard culture media for detection of
S. aureus
in heavily contaminated respiratory samples.
Use of Fluorescent Amplified Fragment Length Polymorphism for Molecular Epidemiology of Leptospirosis in India
Authors: Vijayachari P. , Ahmed Niyaz , Sugunan A. P. , Ghousunnissa Sheikh , Rao K. Rajender , Hasnain Seyed E. , Sehgal Subhash C. 
Published: August 2004

ABSTRACT
Nineteen isolates of leptospires recovered from patients during three epidemics that occurred at different places and different times in the Andaman Islands and eight isolates from sporadic cases were characterized using serological and molecular genetic techniques. Group sera and monoclonal antibodies were used for antigenic characterization, whereas fluorescent amplified fragment length polymorphism (FAFLP) was used for genotyping. Of the 27 isolates, 19 were identified as belonging to serogroup Grippotyphosa, 3 belonged to serogroup Australis, 2 belonged to serogroup Icterohaemorrhagiae, and 1 each belonged to serogroups Hebdomadis, Canicola, and Sejroe. Analysis of FAFLP data grouped these 27 isolates into two main clusters of genotypes. One of the clusters, populated by 19 isolates, included 16 outbreak isolates. Seven of these 19 isolates belonged to serovar Ratnapura, 10 belonged to serovar Valbuzzi, and 1 each belonged to serovar Grippotyphosa and serovar Saxkoebing. Of the 27 patients from whom isolates were obtained, 9 had severe illness, and 6 of these 9 patients had pulmonary involvement, 1 had pulmonary and hepatorenal involvement, and the remaining 2 had hepatorenal involvement alone. Two patients out of the nine severe cases died subsequently. The isolates from sporadic cases showed great genetic diversity and were also diverse antigenically. Perhaps the strains belonging to a dominant genotype (the outbreak-associated cluster) possessed epidemic potential and higher virulence with a greater predilection to cause pulmonary complications than strains belonging to other genetic backgrounds.
Molecular Epidemiology of Hospital-Associated and Community-Acquired
Clostridium difficile
Infection in a Swedish County
Authors: Norén T. , Åkerlund T. , Bäck E. , Sjöberg L. , Persson I. , Alriksson I. , Burman L. G. 
Published: August 2004

ABSTRACT

All episodes of
Clostridium difficile
associated diarrhea (CDAD) diagnosed in a defined population of 274,000 including one tertiary and two primary hospitals and their catchment areas were studied during 12 months. The annual CDAD incidence in the county was 97 primary episodes per 100,000, and 78% of all episodes were classified as hospital associated with a mean incidence of 5.3 (range, 1.4 to 6.5) primary episodes per 1,000 admissions. The incidence among hospitalized individuals was 1,300-fold higher than that in the community (33,700 versus 25 primary episodes per 100,000 persons per year), reflecting a 37-fold difference in antibiotic consumption (477 versus 13 defined daily doses [DDD]/1,000 persons/day) and other risk factors. Three tertiary hospital wards with the highest incidence (13 to 36 per 1,000) had CDAD patients of high age (median age of 80 years versus 70 years for other wards,
P
< 0.001), long hospital stay (up to 25 days versus 4 days), or a high antibiotic consumption rate (up to 2,427 versus 421 DDD/1,000 bed days). PCR ribotyping of
C. difficile
isolates available from 330 of 372 CDAD episodes indicated nosocomial acquisition of the strain in 17 to 27% of hospital-associated cases, depending on the time interval between index and secondary cases allowed (2 months or up to 12 months), and only 10% of recurrences were due to a new strain of
C. difficile
(apparent reinfection). In other words, most primary and recurring episodes were apparently caused by the patient's endogenous strain rather than by one of hospital origin. Typing also indicated that a majority of
C. difficile
strains belonged to international serotypes, and the distribution of types was similar within and outside hospitals and in primary and relapsing CDAD. However, type SE17 was an exception, comprising 22% of hospital isolates compared to 6% of community isolates (
P
= 0.008) and causing many minor clusters and a silent nosocomial outbreak including 36 to 44% of the CDAD episodes in the three high-incidence wards.
New Genome Type of Adenovirus Serotype 4 Caused Nosocomial Infections Associated with Epidemic Conjunctivitis in Japan
Authors: Ariga Toshihide , Shimada Yasushi , Ohgami Kazuhiro , Tagawa Yoshitsugu , Ishiko Hiroaki , Aoki Koki , Ohno Shigeaki 
Published: August 2004

ABSTRACT
Human adenovirus type 4 is one of the major serotypes isolated from patients with adenoviral conjunctivitis. In 2001 we encountered nosocomial infections with epidemic conjunctivitis in the ophthalmology ward of one hospital in Sapporo, which is in the northern part of Japan. Adenoviruses were isolated from the patients with this nosocomial infection and identified as adenovirus type 4 (AdV-4) by a neutralization test with serotype-specific antiserum. When the cleavage patterns of the isolates were compared with the full viral genome with BamHI and SmaI, the cleavage patterns of the isolates were shown to be different from those of AdV-4p and other previously known AdV-4 variants. The nucleotide sequences of the fiber gene of the isolates showed the highest homologies (94.3%) with AdV-4 among the nucleotide sequences available from GenBank and formed a monophyletic cluster along with the prototype strain of AdV-4. The isolates, however, were located in a different lineage from those of AdV-4p and the AdV-4 variant from the sporadic infections. We conclude that the nosocomial infection that appeared in 2001 was caused by a new genome type of AdV-4, which was designated AdV-4c.
Comparison of a New Lateral-Flow Chromatographic Membrane Immunoassay to Viral Culture for Rapid Detection and Differentiation of Influenza A and B Viruses in Respiratory Specimens
Authors: Cazacu Andreea C. , Demmler Gail J. , Neuman Mark A. , Forbes Betty A. , Chung Sooyoung , Greer Jewel , Alvarez Ana E. , Williams Robin , Bartholoma Nadine Y. 
Published: August 2004

ABSTRACT
The performance of a new rapid lateral-flow chromatographic membrane immunoassay test kit for detection of influenza virus was evaluated and compared to that of viral culture in respiratory secretions collected from 400 adults and children seen at three large university hospitals during the recent 2003 influenza season. The rapid test provided results in 15 min, with excellent overall performance statistics (sensitivity, 94.4%; specificity, 100%; positive predictive value, 100%; negative predictive value, 97.5%). Both influenza A and B type viruses were reliably detected, with no significant difference in performance statistics noted by influenza virus type or by the center performing the test.
Recommended Test Panel for Differentiation of
Klebsiella
Species on the Basis of a Trilateral Interlaboratory Evaluation of 18 Biochemical Tests
Authors: Hansen Dennis S. , Aucken Hazel M. , Abiola Titi , Podschun Rainer 
Published: August 2004

ABSTRACT

Klebsiella pneumoniae
and
Klebsiella oxytoca
are the two most frequently encountered
Klebsiella
species giving rise to infections in humans, but other
Klebsiella
species can also be found in clinical specimens:
Klebsiella ozaenae
,
Klebsiella rhinoscleromatis
,
Klebsiella terrigena
,
Klebsiella planticola
,
Klebsiella ornithinolytica
, and
Enterobacter aerogenes
(
Klebsiella mobilis
). However, many of these species are indistinguishable by the conventional methods employed routinely in the clinical microbiological laboratory. Several investigators have suggested various additional tests, but as yet there is no standardized test panel for identifying all
Klebsiella
species and subspecies. In the present study, performed in three national
Klebsiella
reference laboratories, we have evaluated a test panel consisting of 18 biochemical tests on 242 strains comprising all
Klebsiella
species and subspecies. The test panel was designed to identify organisms preliminarily identified as belonging to the genus
Klebsiella
on the basis of conventional methods or automated identification systems. With the described test panel it is possible to find one or more positive test results differentiating any
Klebsiella
species, except
Klebsiella rhinoscleromatis
, from its closest relative.
Comparison of Oligonucleotide Ligation Assay and Consensus Sequencing for Detection of Drug-Resistant Mutants of Human Immunodeficiency Virus Type 1 in Peripheral Blood Mononuclear Cells and Plasma
Authors: Ellis Giovanina M. , Mahalanabis Madhumita , Beck Ingrid A. , Pepper Gregory , Wright Amy , Hamilton Shannon , Holte Sarah , Naugler Willscott E. , Pawluk Diane M. , Li Chung-Chen , Frenkel Lisa M. 
Published: August 2004

ABSTRACTDrug-resistant mutants of human immunodeficiency virus type 1 (HIV-1) recede below the limit of detection of most assays applied to plasma when selective pressure is altered due to changes in antiretroviral treatment (ART). Viral variants with different mutations are selected by the new ART when replication is not suppressed or wild-type variants with greater replication fitness outgrow mutants following the cessation of ART. Mutants selected by past ART appear to persist in reservoirs even when not detected in the plasma, and when conferring cross-resistance they can compromise the efficacy of novel ART. Oligonucleotide ligation assay (OLA) of virus in plasma and peripheral blood mononuclear cells (PBMC) was compared to consensus sequence dideoxynucleotide chain terminator sequencing for detection of 91 drug resistance mutations that had receded below the limit of detection by sequencing of plasma. OLA of plasma virus detected 27.5% (95% confidence interval [CI], 19 to 39%) of mutant genotypes; consensus sequencing of the PBMC amplicon from the same specimen detected 23.1% (95% CI, 14 to 34%); and OLA of PBMC detected 53.8% (95% CI, 44 to 64%). These data suggest that concentrations of drug-resistant mutants were greater in PBMC than in plasma after changes in ART and indicate that the OLA was more sensitive than consensus sequencing in detecting low levels of select drug-resistant mutants.
Use of 16S rRNA, 23S rRNA, and
gyrB
Gene Sequence Analysis To Determine Phylogenetic Relationships of
Bacillus cereus
Group Microorganisms
Authors: Bavykin Sergei G. , Lysov Yuri P. , Zakhariev Vladimir , Kelly John J. , Jackman Joany , Stahl David A. , Cherni Alexey 
Published: August 2004

ABSTRACT

In order to determine if variations in rRNA sequence could be used for discrimination of the members of the
Bacillus cereus
group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species in the
B. cereus
group. We also analyzed 30
gyrB
sequences for
B. cereus
group strains with published 16S rRNA sequences. Our findings indicated that the three most common species of the
B. cereus
group,
B. cereus, Bacillus thuringiensis
, and
Bacillus mycoides
, were each heterogeneous in all three gene sequences, while all analyzed strains of
Bacillus anthracis
were found to be homogeneous. Based on analysis of 16S and 23S rRNA sequence variations, the microorganisms within the
B. cereus
group were divided into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, and these seven subgroups were further organized into two distinct clusters. This classification of the
B. cereus
group conflicts with current taxonomic groupings, which are based on phenotypic traits. The presence of
B. cereus
strains in six of the seven subgroups and the presence of
B. thuringiensis
strains in three of the subgroups do not support the proposed unification of
B. cereus
and
B. thuringiensis
into one species. Analysis of the available phenotypic data for the strains included in this study revealed phenotypic traits that may be characteristic of several of the subgroups. Finally, our results demonstrated that rRNA and
gyrB
sequences may be used for discriminating
B. anthracis
from other microorganisms in the
B. cereus
group.
Performance Characteristics of a Quantitative TaqMan Hepatitis C Virus RNA Analyte-Specific Reagent
Authors: Barbeau James M. , Goforth Jennifer , Caliendo Angela M. , Nolte Frederick S. 
Published: August 2004

ABSTRACT

We determined the dynamic range, reproducibility, accuracy, genotype bias, and sensitivity of the TaqMan hepatitis C virus (HCV) analyte-specific reagent (ASR). Serum samples were processed using the MagNA Pure LC instrument and run on the COBAS TaqMan 48 analyzer. The performance characteristics of the ASR were also compared with those of the qualitative AMPLICOR and quantitative AMPLICOR MONITOR HCV tests. The ASR exhibited a ≥6-log
10
linear dynamic range and excellent reproducibility, with a mean coefficient of variation of 14%. HCV RNA concentration measured with the ASR agreed within an average of 0.42 log
10
(2.6-fold) of the labeled concentration with members of a standard reference panel. HCV genotypes 1 to 4 were amplified with similar efficiencies with the ASR. The ASR and AMPLICOR MONITOR viral load results were significantly correlated (
r
= 0.8898;
P
< 0.01), but the agreement was poor (mean difference, 0.45 ± 0.35 log
10
) for 72 HCV RNA-positive clinical samples. However, 98.9% agreement between the ASR and qualitative AMPLICOR test results was found with 60 positive and 29 negative samples. Limiting-dilution experiments demonstrated that the limits of detection for ASR and AMPLICOR tests were 84 and 26 IU/ml, respectively. The performance characteristics of the TaqMan HCV ASR are appropriate for all clinical applications of HCV RNA testing.
Multicenter Evaluation of Use of Penicillin and Ampicillin as Surrogates for In Vitro Testing of Susceptibility of Enterococci to Imipenem
Authors: Weinstein Melvin P. , Mirrett Stanley , Kannangara Saman , Monahan Jan , Harrell Lizzie J. , Wilson Alan C. , Reller L. Barth 
Published: August 2004

ABSTRACT

Imipenem is approved by the U.S. Food and Drug Administration (FDA) for treatment of infections caused by
Enterococcus faecalis
. However, there are no NCCLS guidelines for testing susceptibility of enterococci against imipenem. To assess whether or not ampicillin or penicillin could be used as a surrogate for broth microdilution (BMD) testing of imipenem versus
Enterococcus
species, 633 strains of
E. faecalis
,
E. faecium
, and other enterococci isolated from blood cultures of patients at three geographically distinct university hospitals were tested by the NCCLS BMD and disk diffusion (DD) methods. Using FDA susceptibility breakpoints for imipenem and NCCLS breakpoints for penicillin and ampicillin, categorical agreement (CA) for penicillin-imipenem and ampicillin-imipenem tested with
E. faecalis
and
E. faecium
by BMD was ≥94% but was ≤90% for other enterococci. Using the DD method, CA for ampicillin-imipenem tested with
E. faecalis
and
E. faecium
was ≥98% and was 92% for other enterococci; CA for penicillin-imipenem was 91% for
E. faecalis
, 98% for
E. faecium
, and 87% for other enterococci. Further analysis showed that testing
E. faecalis
with ampicillin resulted in no false-susceptible (FS) or false-resistant (FR) results by BMD, no FS results by DD, and a single FR result by DD (0.2%), whereas testing with penicillin resulted in no FS results by BMD or DD and two FR results by BMD (0.4%). For
E. faecium
and other enterococci, the combination of FS and FR results was such that surrogate testing with penicillin or ampicillin appears not to be sufficiently reliable to be used clinically. We conclude that ampicillin is an accurate predictor of the in vitro activity of imipenem against
E. faecalis
.
Molecular Characteristics of Nosocomial and Native American Community-Associated Methicillin-ResistantStaphylococcus aureusClones from Rural Wisconsin
Authors: Shukla Sanjay K. , Stemper Mary E. , Ramaswamy Srinivas V. , Conradt Jennifer M. , Reich Robert , Graviss Edward A. , Reed Kurt D. 
Published: August 2004

ABSTRACTIn central and northern Wisconsin methicillin-resistantStaphylococcus aureus(MRSA) was first detected in 1989. Over the next 10-year period, 581 MRSA isolates were collected, 17.2% of which came from patients who were treated at five Native American clinics. These isolates were typed by SmaI-macrorestricted pulsed-field gel electrophoresis (PFGE). The PFGE patterns clustered the isolates into six major clonal groups (MCGs), i.e., MCGs 1 to 6, and 19 minor clonal groups (mCGs). The 25 clonal groups were represented by 109 unique PFGE types. Sixty-five percent of the MCG-2 isolates were recovered from patients who were treated at Native American clinics. Ninety-four percent of the MCG-2 isolates harbored the staphylococcal cassette chromosomemec(SCCmec) IVa. These isolates also had PFGE profiles that were clonally related to the midwestern community-associated MRSA (CA-MRSA) strain, MW2. The representative isolates from MCG-2 had the multilocus sequence type allelic profile 1-1-1-1-1-1-1 and containedpvlgenes. They were also susceptible to various antibiotics, a finding consistent with the CA-MRSA phenotype. SCCmecIV was also present in othermCGs. Unlike MCG-2, isolates from the remaining five MCGs harbored SCCmecII and were resistant to multiple antibiotics, suggesting their nosocomial origin. The 19mCGs were represented by diverse SCCmectypes and three putative new variants referred to as SCCmecIb, IIa, and IIb.
Detection of
Haemophilus influenzae
Type b by Real-Time PCR
Authors: Marty Adrian , Greiner Oliver , Day Philip J. R. , Gunziger Sibylle , Mühlemann Kathrin , Nadal David 
Published: August 2004

ABSTRACT

A real-time PCR assay targeting the capsulation locus of
Haemophilus influenzae
type b (Hib) was developed. The linear detection range was from 1 to 10
6
microorganisms per reaction mixture. No
H. influenzae
other than Hib or any other control bacteria typically found in the upper respiratory tract was detected.
Isolation of
Bartonella rattimassiliensis
sp. nov. and
Bartonella phoceensis
sp. nov. from European
Rattus norvegicus
Authors: Gundi Vijay A. K. B. , Davoust Bernard , Khamis Atieh , Boni Mickaël , Raoult Didier , La Scola Bernard 
Published: August 2004

ABSTRACT

Thirty-three isolates of
Bartonella
spp., including 11 isolates not belonging to previously known species, were isolated from 66
Rattus norvegicus
subjects trapped in the city of Marseille, France. Based on seven different gene sequences, the 11 isolates were assigned to
Bartonella rattimassiliensis
sp. nov. and
Bartonella phoceensis
sp. nov.
Analysis of
p51
,
groESL
, and the Major Antigen P51 in Various Species of
Neorickettsia
, an Obligatory Intracellular Bacterium That Infects Trematodes and Mammals
Authors: Rikihisa Yasuko , Zhang Chunbin , Kanter Manuel , Cheng Zhihui , Ohashi Norio , Fukuda Takeo 
Published: August 2004

ABSTRACT

The
p51
gene that encodes the major antigenic 51-kDa protein in
Neorickettsia risticii
was identified in strains of
Neorickettsia sennetsu
and the
Stellantchasmus falcatus
agent but not in
Neorickettsia helminthoeca
, suggesting that
p51
-based diagnosis would be useful to distinguish among them.
groESL
sequencing results delineated the phylogenic relationships among
Neorickettsia
spp.
Real-Time TaqMan PCR for Quantifying Oral Bacteria during Biofilm Formation
Authors: Suzuki Nao , Nakano Yoshio , Yoshida Akihiro , Yamashita Yoshihisa , Kiyoura Yusuke 
Published: August 2004

ABSTRACT
A TaqMan PCR was developed for quantifying early colonizer microorganisms in dental biofilms. To design species-specific primers and TaqMan probes, genomic subtractive hybridization was used. This quantitative assay in combination with subtractive hybridization may be of value in the study of microbial ecosystems consisting of related species that are involved in the formation and etiology of biofilms.