bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Pooled Urine Samples and Automated DNA Isolation To Achieve Improved Sensitivity and Cost-Effectiveness of Large-Scale Testing for
Chlamydia trachomatis
in Pregnant Women
Authors: Rours G. I. J. G. , Verkooyen R. P. , Willemse H. F. M. , van der Zwaan E. A. E. , van Belkum A. , de Groot R. , Verbrugh H. A. , Ossewaarde J. M. 
Published: September 2005

ABSTRACT

The success of large-scale screening for
Chlamydia trachomatis
depends on the availability of noninvasive samples, low costs, and high-quality testing. To evaluate
C. trachomatis
testing with pregnant women, first-void urine specimens from 750 consecutive asymptomatic pregnant women from the Rotterdam area (The Netherlands) were collected. Initially, we investigated the performance of three different DNA isolation methods with 350 of these urines and 70 pools of 5 of the same subset of urine samples. The routinely used COBAS AMPLICOR test was compared to the COBAS AMPLICOR test with prior DNA isolation by use of the MagNA Pure large-volume kit and the MagNA Pure bacterial DNA isolation kit. The latter combination provided the best DNA test for pooled urines, with a sensitivity twice that of the other methods. Next, using all 750 urines, the COBAS AMPLICOR performance for individual testing was compared to pooled testing with the standard COBAS AMPLICOR procedure and subsequently to pooled testing with COBAS AMPLICOR in combination with the MagNA Pure bacterial DNA isolation kit. The sensitivity of COBAS AMPLICOR was 65% on individual and 42% on pooled urines but improved to 92% on pooled urines with the MagNA Pure bacterial DNA isolation kit, making this combination the best screening method. The
C. trachomatis
prevalence in this population appeared to be 6.4%. Additionally, the cost of the combined MagNA Pure bacterial DNA isolation kit and COBAS AMPLICOR method on pooled urines was only 56% of the cost of the standard COBAS AMPLICOR test applied to individual urines. Costs per positive case detected in the combined method were 39% of standard costs.
Successful Multiresistant Community-Associated Methicillin-Resistant
Staphylococcus aureus
Lineage from Taipei, Taiwan, That Carries Either the Novel Staphylococcal Chromosome Cassette
mec
(SCC
mec
) Type V
T
or SCC
mec
Type IV
Authors: Boyle-Vavra Susan , Ereshefsky Ben , Wang Chih-Chien , Daum Robert S. 
Published: September 2005

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) isolates carry the methicillin resistance gene (
mecA
) on a horizontally transferred genetic element called the staphylococcal chromosome cassette
mec
(SCC
mec
). Community-acquired MRSA (CAMRSA) isolates usually carry SCC
mec
type IV. We previously reported that 76% of 17 CAMRSA isolates (multilocus sequence type 59) obtained from pediatric patients with skin and soft tissue infections (SSTI) from Taipei did not carry SCC
mec
types I to IV. We used DNA sequence analysis to determine that the element harbored by these nontypeable isolates is a novel subtype of SCC
mec
V called SCC
mec
V
T.
It contains a
ccrC
recombinase gene variant (
ccrC2
) and
mec
complex C2. One SSTI isolate contained molecular features of SCC
mec
IV but also contained
ccrC2
(a feature of SCC
mec
V
T
), suggesting that it may harbor a composite SCC
mec
element. The genes
lukS-PV
and
lukF-PV
encoding the Panton-Valentine leukocidin (PVL) were present in all CAMRSA SSTI isolates whether they contained SCC
mec
type IV or V
T
. SCC
mec
V
T
was also present in 5 of 34 (14.7%) CAMRSA colonization isolates collected from healthy children from Taipei who lacked MRSA risk factors. Four (80%) of the these isolates contained
lukS-PV
and
lukF-PV
, as did 1 of 27 (3.7%) SCC
mec
IV-containing colonization isolates. A total of 63% (10 of 16) of the SSTI isolates and 61.7% (21 of 34) of the colonization isolates tested were resistant to at least four classes of non-β-lactam antimicrobials. SCC
mec
V
T
is a novel SCC
mec
variant that is found in multiply resistant CAMRSA strains with sequence type 59 in Taipei in association with the PVL leukotoxin genes.
Validation of a pXO2-A PCR Assay To Explore Diversity among Italian Isolates of
Bacillus anthracis
Strains Closely Related to the Live, Attenuated Carbosap Vaccine
Authors: Muscillo M. , La Rosa G. , Sali M. , De Carolis E. , Adone R. , Ciuchini F. , Fasanella A. 
Published: September 2005

ABSTRACT

Several circulating
Bacillus anthracis
strains isolated in Italy and belonging to the A1.a cluster, genotype 3 (A1.a-3) are genotypically indistinguishable from Carbosap, a live attenuated vaccine strain, containing both pXO1 and pXO2 plasmids. The genotype was assessed by using eight-locus multilocus variable-number tandem repeat analysis. We describe here the use of a ninth locus able to explore variability among strains that have the same genotype. It is important to be able to genotype the wild isolate of
B. anthracis
strains from outbreaks of anthrax in areas where Carbosap vaccination of cattle and sheep is common practice. A total of 27 representative field strains isolated in Italy and four vaccinal strains, namely, Carbosap, Sterne, Pasteur I, and Pasteur II, were characterized by a ninth marker, called pXO2-A. Twenty-three field strains were genotype 3 and therefore identical to Carbosap. The marker was in the pXO2 plasmid and is based on the polymorphism of the already-known VX2-3 locus. Detection was obtained by PCR with fluorescence-labeled forward primers in order to produce appropriate fragments for capillary electrophoresis with an ABI 310 genetic analyzer. Genetic relationships showed heterogeneity in all of the examined samples. Interestingly, with respect to genotype 3, samples grouped into eight different subtypes, A to H, and the subtype G, had only two samples indistinguishable from Carbosap. The results of the present study confirm the validity of a hierarchical progressive protocol for discrimination among closely related isolates.
Dual Infections with Pigmented and Albino Strains ofCryptococcus neoformansin Patients with or without Human Immunodeficiency Virus Infection in India
Authors: Mandal Piyali , Banerjee Uma , Casadevall Arturo , Nosanchuk Joshua D. 
Published: September 2005

ABSTRACTCryptococcus neoformansis an encapsulated yeast-like fungus of worldwide distribution. Melanin production is an important virulence factor ofC. neoformans. We report the identification of distinct cryptococcal isolates with either pigmented or white colony phenotypes onl-dihydroxyphenylalanine agar plates in three patients who presented with meningitis to the All India Institute of Medical Sciences in India. Two of the patients were also infected with human immunodeficiency virus. Biochemical studies, India ink analysis, immunofluorescence with antibodies specific to capsular antigen, and serotyping confirmed that the melanotic and albino strains wereC. neoformansserotypes A and D, respectively. Genotyping with M13 and [GACA]4 primers revealed that all theC. neoformansisolates were genetically different. The CNLAC1 gene associated with melanin production was identified in all the strains by PCR. Standard MIC testing revealed that the strains had similar susceptibilities to amphotericin B, but time-kill assays with the antifungal showed reduced susceptibility in melanin-producing strains. Infection studies with A/Jcr mice showed that the melanin-lacking yeast were less virulent than melanin-producing isolates. These findings indicate that these patients had dual infections with pigmented and albino strains ofC. neoformansthat were phenotypically and biologically different. Continued surveillance of primary isolates from patients with cryptococcosis by analyzing phenotypic differences and by molecular methods may reveal that mixed infections occur more commonly than is currently realized.
Use of Molecular Beacons for Rapid, Real-Time, Quantitative Monitoring of Cytotoxic T-Lymphocyte Epitope Mutations in Simian Immunodeficiency Virus
Authors: Peyerl Fred W. , Barouch Dan H. , Bazick Heidi S. , Manuel Edwin , Letvin Norman L. 
Published: September 2005

ABSTRACT
Immune pressure on lentiviruses exerted by cytotoxic T lymphocytes (CTL) selects for virus CTL epitope mutations. Currently employed methods for monitoring emerging CTL epitope mutations rely on the labor-intensive and time-consuming techniques of virus population or clonal sequencing. Here we describe the development of a high-throughput quantitative reverse transcription-PCR assay that facilitates large-scale CTL epitope monitoring. This approach utilizes both sequence-specific molecular beacons and the sequence-independent double-stranded DNA binding dye Sybr Green. We show that this assay detects single-nucleotide mutations in an immunodominant CTL epitope in viral RNA isolated from both viral culture supernatants and plasma samples from simian immunodeficiency virus (SIV)-infected rhesus monkeys. Furthermore, mutant viruses can be detected even when they represent as few as 500 mutant copies in a sample containing 10,000 total copies. This real-time PCR technique for evaluating CTL epitope mutations may prove to be a useful tool for monitoring the genetic drift of human immunodeficiency virus and SIV in infected individuals.
Dot Enzyme-Linked Immunosorbent Assay for More Reliable Staging of Patients with Human African Trypanosomiasis
Authors: Courtioux Bertrand , Bisser Sylvie , M'Belesso Pascal , Ngoungou Edgard , Girard Murielle , Nangouma Auguste , Josenando Théophile , Jauberteau-Marchan Marie-Odile , Bouteille Bernard 
Published: September 2005

ABSTRACTHuman African trypanosomiasis (HAT) or sleeping sickness is a disease characterized by a hemolymphatic stage 1 followed by a meningoencephalitic stage 2 which is fatal without specific treatment. Furthermore, due to the toxicity of drugs used to treat stage 2 (mainly melarsoprol) accurate staging is required. Actual criteria employed during field surveys are not sensitive enough for precise staging. Antineurofilament (anti-NF) and antigalactocerebrosides (anti-GalC) antibodies have been identified in cerebrospinal fluid (CSF) as potential markers of central nervous system (CNS) involvement. We describe a dot enzyme-linked immunosorbent assay (dot-ELISA) to detect anti-GalC and anti-NF antibodies and its value in staging. NF- and GalC-dotted nitrocellulose strips were first developed in our laboratory. They were then evaluated in Angola and Central African Republic on 140 CSF samples. Compared to our staging criteria (i.e., CSF cell count ≥ 20 cells/μl, CSF immunoglobulin M concentration ≥ 100 mg/liter, and/or the presence of trypanosomes in the CSF), combined detection of both CSF anti-NF and CSF anti-GalC by dot-ELISA showed 83.2% sensitivity and 100.0% specificity. Dot-ELISA could be a useful test to diagnose CNS involvement in HAT in the less-equipped laboratories or in the field situation and to improve patient treatment.
Use of Rapid Dipstick and Latex Agglutination Tests and Enzyme-Linked Immunosorbent Assay for Serodiagnosis of Amebic Liver Abscess, Amebic Colitis, and
Entamoeba histolytica
Cyst Passage
Authors: van Doorn H. Rogier , Hofwegen Henk , Koelewijn Rob , Gilis Henk , Peek Ron , Wetsteyn Jose C. F. M. , van Genderen Perry J. J. , Vervoort Tony , van Gool Tom 
Published: September 2005

ABSTRACT

A homemade enzyme-linked immunosorbent assay (ELISA) and a dipstick assay (Dipstick) for the detection of anti-
Entamoeba histolytica
antibodies in serum were developed and evaluated together with a commercially available latex agglutination test (LAT; Laboratoires Fumouze) for their use in serodiagnosis of amebiasis. The sensitivity of these assays was evaluated with sera from 27 patients with radiologically proven, cellulose acetate precipitation (CAP) test-positive amebic liver abscess, 7 patients with parasitologically and PCR-proven amebic colitis, and 11 patients with parasitologically and PCR-proven
E. histolytica
cyst passage. The sensitivities of the ELISA, Dipstick, and LAT were all 93.3% (42/45). With a combination of Dipstick and LAT, all abscess and colitis patients had at least one positive result. The specificity was assessed with 238 sera from patients with various parasitic, bacterial, viral, and fungal infectious diseases, sera containing autoimmune antibodies, and sera from healthy blood donors. The specificities of the ELISA, Dipstick, and LAT were 97.1%, 98.1%, and 99.5%, respectively. Of 61 sera from patients with PCR-proven
E. dispar
infection, 60 (98.4%) were negative in both Dipstick and LAT and 59 (96.7%) were negative in ELISA. Our data suggest that all three assays are sensitive serological tests. The rapid LAT and Dipstick provide fast results and can easily be applied in routine laboratories in order to facilitate the diagnosis of amebiasis.
PCR-Based Diagnosis of Neonatal Staphylococcal Bacteremias
Authors: Makhoul Imad R. , Smolkin Tatiana , Sujov Polo , Kassis Imad , Tamir Ada , Shalginov Raia , Sprecher Hannah 
Published: September 2005

ABSTRACT
We compared PCR with blood cultures in the diagnosis of neonatal staphylococcal sepsis. Significant association was observed between PCR-based and culture-based diagnosis of staphylococcal bacteremia. Positive and negative predictive values for PCR were 100% and 98%, respectively. These data indicate that PCR may serve as a useful adjunct for the rapid diagnosis of staphylococcal sepsis.
Comparative Evaluation of Three Commercial Systems for Nucleic Acid Extraction from Urine Specimens
Authors: Tang Yi-Wei , Sefers Susan E. , Li Haijing , Kohn Debra J. , Procop Gary W. 
Published: September 2005

ABSTRACT
A nucleic acid extraction system that can handle small numbers of specimens with a short test turnaround time and short hands-on time is desirable for emergent testing. We performed a comparative validation on three systems: the MagNA Pure compact system (Compact), the NucliSens miniMAG extraction instrument (miniMAG), and the BioRobot EZ1 system (EZ1). A total of 75 urine specimens submitted for polyomavirus BK virus detection were used. The human β-actin gene was detected on 75 (100%), 75 (100%), and 72 (96%) nucleic acid extracts prepared by the miniMAG, EZ1, and Compact, respectively. The miniMAG produced the highest quantity of nucleic acids and the best precision among the three systems. The agreement rate was 100% for BKV detection on nucleic acid extracts prepared by the three extraction systems. When a full panel of specimens was run, the hands-on time and test turnaround time were 105.7 and 121.1 min for miniMAG, 6.1 and 22.6 min for EZ1, and 7.4 and 33.7 min for Compact, respectively. The EZ1 and Compact systems processed automatic nucleic acid extraction properly, providing a good solution to the need for sporadic but emergent specimen detection. The miniMAG yielded the highest quantity of nucleic acids, suggesting that this system would be the best for specimens containing a low number of microorganisms of interest.
Outbreaks of Gastroenteritis That Occurred during School Excursions in Korea Were Associated with Several Waterborne Strains of Norovirus
Authors: Kim Sung-Han , Cheon Doo-Sung , Kim Jin-Hyeun , Lee Dong-Han , Jheong Won-hwa , Heo Young-Joo , Chung Hyen-Mi , Jee Youngmee , Lee Joo-Shil 
Published: September 2005

ABSTRACT
In May 2004, 97 of 309 (31%) and 97 of 207 (47%) school students from geographically distant areas were affected by acute gastroenteritis during excursions to neighboring hotels. The two hotels were 300 m apart, on Jeju Island, South Korea. Several strains of norovirus, including both genogroup I and genogroup II viruses, were identified in stool samples from the students and food handlers and in groundwater from the hotels. Of these several strains of norovirus, the nucleotide sequences for one strain were identical for samples from the students, food handlers, and groundwater.
Characterization of Ureaplasmas Isolated from Preterm Infants with and without Bronchopulmonary Dysplasia
Authors: Katz Brenda , Patel Padma , Duffy Lynn , Schelonka Robert L. , Dimmitt Reed A. , Waites Ken B. 
Published: September 2005

ABSTRACT

A PCR assay was used to analyze endotracheal aspirates from preterm infants for
Ureaplasma parvum
versus
U. urealyticum. U. parvum
was detected more often than
U. urealyticum
. There was no significant difference or trend in the prevalence of either species between infants with or without bronchopulmonary dysplasia when isolated alone.
Rapid Identification of
Staphylococcus aureus
in Blood Cultures by a Combination of Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes and Flow Cytometry
Authors: Hartmann Hanna , Stender Henrik , Schäfer Andrea , Autenrieth Ingo B. , Kempf Volkhard A. J. 
Published: September 2005

ABSTRACT

Fluorescence in situ hybridization (FISH) using peptide nucleic acid probes (PNAs) allows the identification of
Staphylococcus aureus
from human blood culture samples. We present data revealing that the combination of PNA FISH and flow cytometry is a possible approach for the noncultural identification of staphylococci in blood cultures.
Variable-Number Tandem Repeat Analysis of Meningococcal Isolates Belonging to the Sequence Type 162 Complex
Authors: Yazdankhah Siamak P. , Kesanopoulos Konstantinos , Tzanakaki Georgina , Kremastinou Jenny , Caugant Dominique A. 
Published: September 2005

ABSTRACT
Thirty-one meningococcal isolates from carriers and disease cases belonging to the sequence type (ST) 162 complex, isolated in Greece in 1999 and 2000, were studied by the use of variable-number tandem repeat analysis. Our study demonstrated that the isolates belonging to the ST-162 clonal complex were a heterogeneous group. Based on this heterogeneity, it is unlikely that the disease-associated isolates represent an outbreak.
Direct Application of the INNO-LiPA Rif.TB Line-Probe Assay for Rapid Identification of
Mycobacterium tuberculosis
Complex Strains and Detection of Rifampin Resistance in 360 Smear-Positive Respiratory Specimens from an Area of High Incidence of Multidrug-Resistant Tuberculosis
Authors: Viveiros Miguel , Leandro Clara , Rodrigues Liliana , Almeida Josefina , Bettencourt Rosário , Couto Isabel , Carrilho Lurdes , Diogo José , Fonseca Ana , Lito Luís , Lopes João , Pacheco Teresa , Pessanha Mariana , Quirim Judite , Sancho Luísa , Salfinger Max , Amaral Leonard 
Published: September 2005

ABSTRACT

The INNO-LiPA Rif.TB assay for the identification of
Mycobacterium tuberculosis
complex strains and the detection of rifampin (RIF) resistance has been evaluated with 360 smear-positive respiratory specimens from an area of high incidence of multidrug-resistant tuberculosis (MDR-TB). The sensitivity when compared to conventional identification/culture methods was 82.2%, and the specificity was 66.7%; the sensitivity and specificity were 100.0% and 96.9%, respectively, for the detection of RIF resistance. This assay has the potential to provide rapid information that is essential for the effective management of MDR-TB.
Brain Abscess Caused by
Nocardia cyriacigeorgica
in a Patient with Human Immunodeficiency Virus Infection
Authors: Barnaud G. , Deschamps C. , Manceron V. , Mortier E. , Laurent F. , Bert F. , Boiron P. , Vinceneux P. , Branger C. 
Published: September 2005

ABSTRACT

Nocardia cyriacigeorgica
is a recently characterized species within the genus of
Nocardia
. We report a brain abscess, following a primary pulmonary colonization, due to this species in a human immunodeficiency virus-infected patient. This case confirms that isolation of
Nocardia
in sputum is associated with a high risk of disseminated infection in immunocompromised patients.
Human Infective Endocarditis Caused by
Streptococcus suis
Serotype 2
Authors: Heidt Martin C. , Mohamed Walid , Hain Torsten , Vogt Paul Robert , Chakraborty Trinad , Domann Eugen 
Published: September 2005

ABSTRACT

Human infective endocarditis due to
Streptococcus suis
occurs infrequently. The case of a 43-year-old male who sustained life-threatening infective endocarditis is reported. Since growth of
S. suis
on commonly used sheep blood agar plates resembles viridans streptococci, diagnosis of
S. suis
constitutes a diagnostic pitfall. Identification was accomplished by using molecular methods.
Imported Crimean-Congo Hemorrhagic Fever
Authors: Jauréguiberry Stéphane , Tattevin Pierre , Tarantola Arnaud , Legay François , Tall Adama , Nabeth Pierre , Zeller Hervé , Michelet Christian 
Published: September 2005

ABSTRACT
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease that may also be transmitted through person-to-person transmission by exposure to infected body fluids. Despite its wide geographic distribution in animals, CCHF virus is rarely associated with recognized human diseases. We report the first case of imported CCHF in France.
Molecular Evidence of Recurrent Histoplasmosis with 9-Year Latency in a Patient with Addison's Disease
Authors: Tseng Tai-Chung , Liaw Shwu-Jen , Hsiao Cheng-Hsiang , Wang Cheng-Yi , Lee Li-Na , Huang Tien-Shang , Hsueh Po-Ren 
Published: September 2005

ABSTRACT

We present a case of fatal histoplasmosis in a patient with Addison's disease and long-term use of corticosteroid. The patient acquired
Histoplasma capsulatum
in China and initially presented with a laryngeal mass. He developed fulminant pneumonia and respiratory failure 9 years later. Nucleotide sequences of internal transcribed spacer regions of rRNA genes of the
H. capsulatum
isolate recovered from biopsied lung tissue and of the extracted fungal DNA from the laryngeal lesion were identical, indicating the recurrent nature of infection.
Cocaine and the heart
Authors: Egred M , Davis G K 
Published: September 2005

Abstract
Cocaine is the second commonest illicit drug used and the most frequent cause of drug related deaths. Its use is associated with both acute and chronic complications that may involve any system, the most common being the cardiovascular system. Cocaine misuse has a major effect in young adult drug users with resulting loss of productivity and undue morbidity with cocaine related cardiac and cerebrovascular effects. Many cocaine users have little or no idea of the risks associated with its use. Patients, health care professionals, and the public should be educated about the dangers and the considerable risks of cocaine use. This review concentrates on the cardiovascular effects of cocaine and their management.
Utilisation of redundant time on trauma list for carpal tunnel decompression
Authors: Theruvil B , Choudhary R K , Kapoor V , Hargreaves D G , Warwick D J 
Published: September 2005

Abstract
This audit reviewed the trauma theatre time utilisation during April 2000 to March 2001. Instead of a scheduled 8 30 am start, first patient was on the table by only 9 40 am because of various reasons. To use this redundant time carpal tunnel release was started under local anaesthesia, as first case. On re-auditing, it was found that the patient for carpal tunnel release was on the table at 8 44 am. The first trauma case was on the table at 9 46 am. This simple idea has helped in the performing of an additional case every day with a delay to the trauma list of only six minutes (p&lt;0.05)