bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of DNA Polymerases and Their Buffer Systems on Quantitative Real-Time PCR
Authors: Wolffs Petra , Grage Halfdan , Hagberg Oskar , Rådström Peter 
Published: January 2004

ABSTRACT
An investigation of the influence of five DNA polymerase-buffer systems on real-time PCR showed that the choice of both DNA polymerase and the buffer system affected the amplification efficiency as well as the detection window. The analytical repeatability of the data for different systems changed clearly, leading us to conclude that basing quantitative measurements on single-data-set standard curves can lead to significant errors.
Survival of
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
Frozen in Skim Milk- Tryptone-Glucose-Glycerol Medium
Authors: Kaijalainen Tarja , Ruokokoski Esa , Ukkonen Pentti , Herva Elja 
Published: January 2004

ABSTRACT

In STGG (skim milk, tryptone, glucose, glycerol) medium at −80°C,
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
isolates survived for at least 3 years, and the same species have survived in nasopharyngeal swabs for at least 1.5 years. At −20°C,
S. pneumoniae
and
M. catarrhalis
survived for 1.5 years, but
H. influenzae
survived for only 2 months.
Prevalence and Antimicrobial Susceptibility of Serogroup D Nontyphoidal
Salmonella
in a University Hospital in Taiwan
Authors: Chiu Cheng-Hsun , Su Lin-Hui , Hung Ching-Chi , Chen Kuo-Lung , Chu Chishih 
Published: January 2004

ABSTRACT

The incidence of serogroup D
Salmonella
has been increasing in Taiwan. Most of these isolates belonged to
Salmonella enterica
serovar Enteritidis and showed a relatively higher rate of resistance to sulfamethoxazole-trimethoprim than to other antimicrobial agents. The results of molecular experiments indicated that genes responsible for the resistance were located on plasmids. The resistance may occur via horizontal gene transfer. Furthermore, the first identification of ciprofloxacin and ceftriaxone resistance in serogroup D
Salmonella
in our hospital is also than they did to other antimicrobial agents cause for concern.
Evaluation of Four Commercial Test Systems for Identification of
Actinomyces
and Some Closely Related Species
Authors: Santala Anne-Marie , Sarkonen Nanna , Hall Val , Carlson Petteri , Jousimies-Somer Hannele , Könönen Eija 
Published: January 2004

ABSTRACT

We evaluated four commercially available kits for rapid identification of
Actinomyces
and related species. The kits identified correctly 26 to 65% of “classical”
Actinomyces
strains to the species level and 13 to 49% of newly described
Actinomyces
strains to the genus level, thus indicating relatively poor applicability and a need to update these kits.
Strengths and Limitations of Commercial Tests for Hepatitis C Virus RNA Quantification
Authors: Morishima Chihiro , Chung Minjun , Ng Ka Wing , Brambilla Donald J. , Gretch David R. 
Published: January 2004

ABSTRACT
The sensitivity of the Roche COBAS Monitor v.2.0 test was slightly better than that of the Bayer bDNA 3.0 test, but the Monitor test underquantified specimens by 2.5- to 10.6-fold even at relatively low hepatitis C virus RNA concentrations. Dilution prior to assay minimally decreased the reproducibility of the Monitor assay, leading to the recommendation for all specimens to be diluted 1:100 prior to testing by this assay.
Prevalence of Human Immunodeficiency Virus Drug Resistance Mutations and Subtypes in Drug-Naive, Infected Individuals in the Army Health Service of Rio de Janeiro, Brazil
Authors: Pires Ivone L. , Soares Marcelo A. , Speranza Francisco A. B. , Ishii Solange K. , Vieira Maria C. G. , Gouvêa Maria I. F. S. , Guimarães Maria A. A. M. , de Oliveira Fátima E. , Magnanini Monica M. F. , Brindeiro Rodrigo M. , Tanuri Amilcar 
Published: January 2004

ABSTRACT
The prevalence of mutations that confer resistance to antiretroviral drugs was examined in 56 drug-naive, human immunodeficiency virus type 1 (HIV-1)-infected individuals from the Army Health Service in Rio de Janeiro, Brazil. No primary protease inhibitor mutations were found, but secondary mutations were observed in 51.2% of the samples. Fourteen percent of the viruses had reverse transcriptase inhibitor-associated mutations. Comparative analysis of protease secondary mutations from four different time periods in drug-naive patients in the city of Rio de Janeiro has indicated constant rates for particular mutations. Changes in CD4 cell counts and HIV viral load over time in subtype B- and non-B-infected drug-naive patients were not significantly different.
Molecular Epidemiology of Disease Due to
Mycobacterium bovis
in Humans in the United Kingdom
Authors: Gibson Andrea L. , Hewinson Glyn , Goodchild Tony , Watt Brian , Story Alistair , Inwald Jacqueline , Drobniewski Francis A. 
Published: January 2004

ABSTRACT

Mycobacterium bovis
is the causative agent of bovine tuberculosis, with a wide host range. Fifty human
M. bovis
isolates were typed using spoligotyping and variable number tandem repeats (VNTR). Fifteen of these spoligotypes have not yet been recorded in cattle. The predominant spoligotype in humans and cattle was subdivided by VNTR.
Efficacy of Galactomannan Antigen in the Platelia
Aspergillus
Enzyme Immunoassay for Diagnosis of Invasive Aspergillosis in Liver Transplant Recipients
Authors: Kwak Eun Jeong , Husain Shahid , Obman Asia , Meinke Lisa , Stout Janet , Kusne Shimon , Wagener Marilyn M. , Singh Nina 
Published: January 2004

ABSTRACT
The utility of galactomannan antigen for diagnosing invasive aspergillosis was evaluated in 154 liver transplant recipients. Sample agreement was 98.5%, and patient specificity was 87%. Galactomannan positivity correlated with mortality, even when controlled for the number of tests performed. Whether galactomannan positivity identifies a subgroup at risk for poor outcome warrants further evaluation.
Automated Procedure for Improving the RNA Isolation Step in Viral Load Testing for Human Immunodeficiency Virus
Authors: Xu Min , Chan Yung , Fischer Steven H. , Remaley Alan T. 
Published: January 2004

ABSTRACT
An automated RNA isolation procedure on the Qiagen BioRobot is described for performing viral load tests for human immunodeficiency virus (HIV) with the Amplicor HIV type 1 test. The new procedure improves the precision of the assay and requires significantly less labor than the presently used manual RNA isolation procedure.
Detection of an Unusual Human Rotavirus Strain with G5P[8] Specificity in a Cameroonian Child with Diarrhea
Authors: Esona Mathew D , Armah George E. , Geyer Annelise , Steele A. Duncan 
Published: January 2004

ABSTRACT
Rotavirus strains detected as part of ongoing strain surveillance in Cameroon, and whose first-round reverse transcription-PCR product could not be genotyped by using conventional genotyping primers, were subjected to sequence analysis for strain characterization. We detected for the first time in Africa a human rotavirus with G5 specificity. The Cameroonian G5 strain had a short electrophoretic pattern and was of VP6 subgroup I specificity and a VP4 P[8] type. The VP7 gene shared a higher nucleic acid and amino acid homology with the porcine G5 strain CC117 (90 and 96%, respectively) than with human G5 strain IAL-28 (86 and 92%, respectively). Phylogenetic analysis showed Cameroonian strain MRC3105 clustered together in the same lineage as two other reported porcine G5 strains. The Cameroonian G5 strain, the first to be reported in humans outside of Latin America, may be a natural reassortant between animal and human rotavirus strains.
Antimicrobial Susceptibility and Epidemiology of a Worldwide Collection of
Chryseobacterium
spp.: Report from the SENTRY Antimicrobial Surveillance Program (1997-2001)
Authors: Kirby Jeffrey T. , Sader Helio S. , Walsh Timothy R. , Jones Ronald N. 
Published: January 2004

ABSTRACT

Limited data are available on
Chryseobacterium
spp. leading to an evaluation of the patient demographics and susceptibility patterns for
Chryseobacterium
spp. collected in the first 5 years of the SENTRY Antimicrobial Surveillance Program (1997 to 2001). Fifty isolates (24
Chryseobacterium meningosepticum
, 20
Chryseobacterium indologenes
, two
Chryseobacterium gleum
, and 4
Chryseobacterium
spp. isolates) were collected. The highest
Chryseobacterium
prevalence was detected among the elderly. The most active antimicrobials were the newer quinolones (garenoxacin, gatifloxacin, and levofloxacin, each with a MIC at which 90 percent of the isolates are inhibited [MIC
90
] of 1 μg/ml and 98.0% susceptibility) followed by rifampin (MIC
90
, 2 μg/ml and 85.7% susceptibility). Trimethoprim-sulfamethoxazole, ciprofloxacin, and piperacillin-tazobactam also showed reasonable activity; vancomycin showed poor potency.
Serodiagnosis of Chronic and Acute Chagas' Disease with
Trypanosoma cruzi
Recombinant Proteins: Results of a Collaborative Study in Six Latin American Countries
Authors: Umezawa Eufrosina S. , Luquetti Alejandro O. , Levitus Gabriela , Ponce Carlos , Ponce Elisa , Henriquez Diana , Revollo Susana , Espinoza Bertha , Sousa Octavio , Khan Baldip , da Silveira José Franco 
Published: January 2004

ABSTRACT

An enzyme-linked immunosorbent assay to diagnose Chagas' disease by a serological test was performed with
Trypanosoma cruzi
recombinant antigens (JL8, MAP, and TcPo). High sensitivity (99.4%) and specificity (99.3%) were obtained when JL8 was combined with MAP (JM) and tested with 150 serum samples from chagasic and 142 nonchagasic individuals. Moreover, JM also diagnosed 84.2% of patients in the acute phase of
T. cruzi
infection.
Multiplex Real-Time PCR Assay for Detection of Influenza and Human Respiratory Syncytial Viruses
Authors: Boivin Guy , Côté Stéphanie , Déry Pierre , De Serres Gaston , Bergeron Michel G. 
Published: January 2004

ABSTRACT
A multiplex real-time PCR assay was developed with a LightCycler instrument for detection of influenza viruses A and B and the human respiratory syncytial virus (HRSV). Detection of each viral product and of an internal control was based on determination of specific melting temperatures by the LightCycler software. The lower limit of detection in the multiplex PCR assay was found to be 50 copies for each viral target. In an evaluation of nasopharyngeal samples collected from hospitalized children (ages, 0 to 3 years) with acute respiratory tract infections during the winter of 2001 to 2002, a viral pathogen was detected by the multiplex PCR test in 139 (66.8%) of 208 cases, including 45 (21.6%) influenza A virus infections, no (0%) influenza B virus infections, 106 (51%) HRSV infections, and 12 (5.8%) coinfections. The multiplex PCR test was compared to rapid antigen detection assays for influenza viruses A and B (Directigen; Becton Dickinson, Sparks, Md.) and HRSV (RSV TestPack; Abbott Laboratories, Abbott Park, Ill.) in 172 and 204 samples, respectively. After resolution of discrepant test results by use of additional PCR assays targeting other viral genes, the sensitivity (Se) and specificity (Sp) of the multiplex PCR assay for influenza A virus were 100 and 97.7% compared to 43.6 and 98.5% for the antigenic test. Similarly, the Se and Sp of the multiplex PCR assay for HRSV were 94.5 and 98.9% compared to 81.6 and 94.7% for the antigenic test. In conclusion, our multiplex real-time PCR assay combines both rapidity and sensitivity for detecting the most important respiratory viral pathogens in children.
Development of a Single-Tube, Cell Lysis-Based, Genus-Specific PCR Method for Rapid Identification of Mycobacteria: Optimization of Cell Lysis, PCR Primers and Conditions, and Restriction Pattern Analysis
Authors: Khan Izhar U. H. , Yadav Jagjit S. 
Published: January 2004

ABSTRACT

A single-tube PCR method was developed for efficient identification of nontuberculous mycobacteria (NTM) and their environmental isolates in about 3 h without conventional DNA isolation. The following three steps were optimized or developed: (i) a simple, 6-min direct cell lysis protocol as a PCR prestep for generation of DNA-template, (ii) an improved
Mycobacterium
-specific PCR amplification protocol with a broader species specificity using newly designed primers targeting a 228-bp region of the 65-kDa heat shock protein (
hsp
) gene and optimal PCR amplification conditions, and (iii) a genus-specific restriction analysis of the PCR product for conclusive identification of the unknown NTM isolates.
Clinical and Environmental Distributions of
Legionella
Strains in France Are Different
Authors: Doleans Anne , Aurell Helena , Reyrolle Monique , Lina Gerard , Freney Jean , Vandenesch Francois , Etienne Jerome , Jarraud Sophie 
Published: January 2004

ABSTRACT

In France, the clinical distribution of
Legionella
species and serogroups does not correspond to their environmental distribution.
Legionella pneumophila
serogroup 1 is more prevalent among clinical isolates (95.4%) than in the environment (28.2%), whereas
L. anisa
is more frequent in the environment (13.8%) than in the clinical setting (0.8%).
Genetic Diversity and Population Structure ofMycobacterium tuberculosisin Casablanca, a Moroccan City with High Incidence of Tuberculosis
Authors: Tazi Loubna , El Baghdadi Jamila , Lesjean Sarah , Locht Camille , Supply Philip , Tibayrenc Michel , Bañuls Anne-Laure 
Published: January 2004

ABSTRACTAlthough lower-resource countries have by far the highest burden of tuberculosis, knowledge ofMycobacterium tuberculosispopulation structure and genetic diversity in these regions remains almost nonexistent. In this paper, 150 MoroccanM. tuberculosisisolates circulating in Casablanca were genotyped by random amplified polymorphic DNA analysis using 10 different primers and by mycobacterial interspersed repetitive units-variable number of tandem repeats typing at 12 loci. The population genetic tests revealed a basically clonal structure for this population, without excluding rare genetic exchanges. Genetic analysis also showed a notable genetic polymorphism for the speciesM. tuberculosis, a weak cluster individualization, and an unexpected genetic diversity for a population in such a high-incidence community. Phylogenetic analyses of this Moroccan sample also supported that these isolates are genetically heterogeneous.
Comparison of Diagnostic Sensitivities of Three Assays (Bartels Enzyme Immunoassay [EIA], Biotest EIA, and Binax NOW Immunochromatographic Test) for Detection of
Legionella pneumophila
Serogroup 1 Antigen in Urine
Authors: Guerrero Carmen , Toldos Carmen M. , Yagüe Genoveva , Ramírez Cristobal , Rodríguez Tomás , Segovia Manuel 
Published: January 2004

ABSTRACT

The Bartels enzyme immunoassay (EIA), Biotest EIA, and Binax NOW immunochromatographic test (ICT) urinary antigen kits for the detection of
Legionella pneumophila
serogroup 1 were compared using 178 frozen urine samples. When nonconcentrated urine samples were used, the sensitivity levels of both enzyme EIAs were significantly higher than the sensitivity level of the ICT (Bartels EIA, 71.3%; Biotest EIA, 65.1%; Binax NOW ICT, 37% [
P
< 0.001]). After concentration of the urine samples, no significant differences in sensitivity were found among the three tests.
Identification and Molecular Characterization of Beta-Hemolytic Streptococci Isolated from Harbor Seals (
Phoca vitulina
) and Grey Seals (
Halichoerus grypus
) of the German North and Baltic Seas
Authors: Vossen A. , Abdulmawjood A. , Lämmler C. , Weiß R. , Siebert U. 
Published: January 2004

ABSTRACT

Bacteriological investigations of seals of the German North and Baltic seas resulted in the isolation of bacteria of the genus
Streptococcus
belonging to Lancefield's serological groups C, F, and L. According to biochemical, serological, and 16S ribosomal DNA analysis, the group C and group F streptococci were identified as
Streptococcus phocae
. The group L streptococci could be classified as
Streptococcus dysgalactiae
subsp.
dysgalactiae
.
Transfer of a
Mycobacterium tuberculosis
Genotyping Method, Spoligotyping, from a Reverse Line-Blot Hybridization, Membrane-Based Assay to the Luminex Multianalyte Profiling System
Authors: Cowan Lauren S. , Diem Lois , Brake Mary Catherine , Crawford Jack T. 
Published: January 2004

ABSTRACT
Spoligotyping using Luminex technology was shown to be a highly reproducible method suitable for high-throughput analysis. Spoligotyping of 48 isolates using the traditional membrane-based assay and the Luminex assay yielded concordant results for all isolates. The Luminex platform provides greater flexibility and cost effectiveness than the membrane-based assay.
Disseminated Infection with
Nattrassia mangiferae
in an Immunosuppressed Patient
Authors: Willinger Birgit , Kopetzky Gerhard , Harm Ferdinand , Apfalter Petra , Makristathis Athanasios , Berer Andrea , Bankier Alexander , Winkler Stefan 
Published: January 2004

ABSTRACT

Disseminated infection with the coelomycetous fungus
Nattrassia mangiferae
is a very rare disease affecting only the immunocompromised host. We report the first case of a disseminated infection with spondylodiscitis and granular skin lesions due to
N. mangiferae
in a renal transplant patient.
First Report of a Case of Meningitis Caused by
Cryptococcus adeliensis
in a Patient with Acute Myeloid Leukemia
Authors: Rimek Dagmar , Haase Gerhard , Lück Andreas , Casper Jochen , Podbielski Andreas 
Published: January 2004

ABSTRACT

Cryptococcus adeliensis
is a recently described new fungal species which has been isolated from decaying algae in Terre Adelie, Antarctica. We report the first known case of meningitis caused by
C. adeliensis
in a patient with acute myeloid leukemia undergoing allogeneic peripheral blood stem cell transplantation.
Osteosynthesis-Associated Bone Infection Caused by a Nonproteolytic, Nontoxigenic
Clostridium botulinum
-Like Strain
Authors: Carlier Jean-Philippe , K'ouas Guylène , Lozniewski Alain , Sirveaux François , Cailloux Philippe , Mory Francine 
Published: January 2004

ABSTRACT

A nonproteolytic, nontoxigenic
Clostridium botulinum
strain identified by conventional and molecular techniques as type B-, E-, or F-like (BEF-like) was isolated from a human postsurgical wound. All previous reports of such strains have been from environmental sources. Since toxin production is the main taxonomic denominator for
C. botulinum
, a new name is needed for nonproteolytic, nontoxigenic BEF-like clinical isolates.
Disseminated Mucormycosis in a Patient with Acute Myeloblastic Leukemia Misdiagnosed as Infection by
Enterococcus faecium
Authors: Sammassimo S. , Mazzotta S. , Tozzi M. , Gentili S. , Lenoci M. , Santopietro R. , Bucalossi A. , Bocchia M. , Lauria F. 
Published: January 2004

ABSTRACT

Mucormycosis is a rare complication in cancer patients. This report presents the case of a acute myeloblastic leukemia patient who developed an ascending paralysis due to disseminated mucormycosis. The presentation was unusual because the early symptoms were fever and pain, and the disease was misdiagnosed because of a concomitant infection by
Enterococcus faecium
.
Characterization of a Novel Group of Mycobacteria and Proposal of
Mycobacterium sherrisii
sp. nov
Authors: Selvarangan Rangaraj , Wu Whei-Kuo , Nguyen Trang T. , Carlson La Donna C. , Wallis Carolyn K. , Stiglich Susan K. , Chen Yi-Ching , Jost Kenneth C. , Prentice Jennifer L. , Wallace Richard J. , Barrett Sara L. Rassoulian , Cookson Brad T. , Coyle Marie B. 
Published: January 2004

ABSTRACT

We describe here the characterization of five isolates of
Mycobacterium simiae
-like organisms representing a novel group based on whole-cell fatty acid analysis and genotypic evaluation. Two of the five isolates in this study, W55 and W58, were previously considered to belong to
M. simiae
serotype 2. Analysis of cellular fatty acids by gas-liquid chromatography indicated a close clustering of this group, which was well differentiated from the other
M. simiae
-like species. Molecular characterization was performed by nucleic acid sequencing of the small subunit rRNA gene and the gene encoding the 65-kDa heat shock protein and genomic DNA hybridization. Sequence analysis of the entire 16S rRNA gene showed a unique sequence most closely related to those of
M. triplex
and
M. simiae
. The
hsp65
partial gene sequence was identical for the five isolates, with 97% identity to the
M. simiae
type strain. However, qualitative whole genomic DNA hybridization analysis confirmed that this group is genetically distinct from
M. simiae
and
M. triplex
. Antimicrobial susceptibilities for this group resemble those of
M. simiae
and
M. lentiflavum
. We conclude that this group represents a unique
Mycobacterium
species for which we propose the name
Mycobacterium sherrisii
sp. nov.
Practical Bench Comparison of BBL CHROMagar Orientation and Standard Two-Plate Media for Urine Cultures
Authors: D'Souza Holly A. , Campbell Mary , Baron Ellen Jo 
Published: January 2004

ABSTRACT

A total of 1,023 urine samples sent for routine culture were plated onto sheep blood and MacConkey agars and a BBL CHROMagar Orientation (CO; Becton Dickinson, Cockeysville, Md.) plate, and the results were compared. Of these, 250 urine samples (24%) grew >10,000 CFU of one or two putative pathogens/ml and 773 showed no growth (NG), mixed growth of <10,000 CFU/ml, or three or more strains (mixed). The CO and conventional medium results agreed completely for 595 cultures with NG or <10,000 CFU/ml. An additional 178 urine samples yielded clinically insignificant differences. Both medium sets essentially agreed on quantities and identification for 400 single-pathogen cultures and 9 mixed cultures. With the caveat that CO cannot differentiate
Klebsiella
,
Enterobacter
, and
Serratia
spp., enteric pathogens were identified only by morphology and color on CO. Direct visual differentiation of group B streptococci from lactobacilli is not possible, but lactobacillus cells always exhibited easily recognizable morphology on Gram stain. Of 108 paired organism susceptibility results encompassing 2,268 drug-pathogen combinations, there were 3% errors and only 1% very major errors. Use of CO allowed a >50% reduction in inoculation time and a >20% reduction in work-up time. For our laboratory, with 50% “no growth” and ca. 25% significant results (50%
Escherichia coli
), CO allowed time and workup cost savings for a majority of cultures. A cost analysis (time and supplies for our laboratory) showed that if CO is used alone, the break-even level for CO pricing is $1.78; if CO and blood agar are both used, the break-even pricing for CO is $1.53.