bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Methods for Detection of Vaccinia Virus in Patient Specimens
Authors: Fedorko Daniel P. , Preuss Jeanne C. , Fahle Gary A. , Li Li , Fischer Steven H. , Hohman Patricia , Cohen Jeffrey I.
Published: September 2005

We analyzed a shell vial culture assay (SVA), real-time PCR, and a direct fluorescent antibody assay (DFA) for rapid detection of vaccinia virus from vaccination sites of Dryvax vaccine recipients. Of 47 samples assayed, 100% were positive by PCR, 89% were positive by SVA, and 40% were positive by DFA. DFA was limited by the need for adequate numbers of cells, with 32% of samples inadequate for interpretation. DFA performed better with specimens from patients who had not previously received the vaccine. PCR was positive for longer times postvaccination than was SVA. Infectious virus could be recovered after 45 min of acetone fixation of shell vial coverslips. Commercially available polyclonal antibodies cross-reacted with other orthopoxviruses and herpes simplex 1, but commercially available monoclonal antibodies were specific for vaccinia virus. In summary, PCR was the most sensitive test for detecting vaccinia virus in clinical specimens, while the DFA was the most rapid but the least sensitive test.
Utility of Amsel Criteria, Nugent Score, and Quantitative PCR for
Gardnerella vaginalis
,
Mycoplasma hominis
, and
Lactobacillus
spp. for Diagnosis of Bacterial Vaginosis in Human Immunodeficiency Virus-Infected Women
Authors: Sha Beverly E. , Chen Hua Y. , Wang Qiong J. , Zariffard M. Reza , Cohen Mardge H. , Spear Gregory T.
Published: September 2005

Bacterial vaginosis (BV) is a clinical syndrome presenting with a malodorous vaginal discharge and increased vaginal pH. Diagnosis has been based on clinical Amsel criteria and direct Gram stain of vaginal secretions. Human immunodeficiency virus (HIV)-infected participants in the Women's Interagency HIV Study contributed cervicovaginal lavage (CVL) samples. Lactobacilli,
Gardnerella vaginalis
, and
Mycoplasma hominis
in cervicovaginal lavage samples were quantified by PCR. Gynecologic evaluation included Nugent score and Amsel criterion assessment. We compared the gold standard Nugent score to Amsel criteria and quantitative bacterial PCR for diagnosing BV in 203 CVL samples from women with Nugent scores of 7 to 10 (BV group) and 203 samples from women with BV Nugent scores of 0 to 3 (“No-BV” group). Only 75 of the 203 CVL samples from women with Nugent scores of 7 to 10 met positive Amsel criteria. Increasing levels of
G. vaginalis
and
M. hominis
and decreasing levels of lactobacilli were significantly associated with BV by Nugent score. Of the group with Nugent scores of 7 to 10, 83% and 81% had log
10
G. vaginalis
counts and log
10
M. hominis
counts greater than 6.81 and 4.82, respectively, while only 30% and 31% of the group with Nugent scores of 0 to 3 were above these thresholds, respectively. There was significant overlap in the log
10
lactobacillus counts between the two groups. Utilizing all three log
10
bacterial counts (
G. vaginalis
,
M. hominis
, and lactobacilli) in our model improved the sensitivity and specificity to 83% and 78%, respectively, in comparison with Nugent score. In this cohort, Amsel criteria were poorly predictive of BV. PCR quantification of
G. vaginalis
and
M. hominis
from CVL is significantly more sensitive than Amsel criteria for diagnosing BV.
Reduced PCR Sensitivity Due to Impaired DNA Recovery with the MagNA Pure LC Total Nucleic Acid Isolation Kit
Authors: Schuurman Tim , van Breda Alex , de Boer Richard , Kooistra-Smid Mirjam , Beld Marcel , Savelkoul Paul , Boom René
Published: September 2005

The increasing demand for molecular diagnostics in clinical microbiology laboratories necessitates automated sample processing. In the present study, we evaluated the performance of the MagNA Pure LC total nucleic acid isolation kit (M extraction) in comparison with the manual method (Si extraction) according to Boom et al. (R. Boom, C. J. A. Sol, M. M. M. Salimans, C. L. Jansen, P. M. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990) for the detection of viral DNA by competitive quantitative PCR. Reconstruction experiments with HindIII-digested phage lambda DNA and HaeIII-digested φX174 DNA showed that the recovery of DNA from phosphate-buffered saline, cerebrospinal fluid, EDTA-anticoagulated plasma, and EDTA-anticoagulated whole blood by M extraction is, on average, 6.6-fold lower compared to Si extraction. PCR signals of spiked PCR control DNAs for Epstein-Barr virus and varicella-zoster virus were also between 1.9- and 14.2-fold lower after M extraction compared to Si extraction, also suggesting impaired DNA recovery. M extraction of spiked cytomegalovirus strain AD 169 in whole blood showed a 5- to 10-fold reduction in PCR sensitivity compared to Si extraction. This reduction of PCR sensitivity was also observed when clinical whole blood samples were processed by M extraction. Before implementing M extraction, the clinical consequences of the reduced recovery should first be considered, especially when maximal sensitivity is required.
Definitive Differentiation between Single and Mixed Mycobacterial Infections in Red Deer (Cervus elaphus) by a Combination of Duplex Amplification of p34 and f57 Sequences and Hpy188I Enzymatic Restriction of Duplex Amplicons
Authors: Godfroid Jacques , Delcorps Cathy , Irenge Leonid M. , Walravens Karl , Marché Sylvie , Gala Jean-Luc
Published: September 2005

Severe emaciation and mortalities suggestive of mycobacterial infections were recently reported for both adult and young wild red deer (Cervus elaphus) in the southeastern part of Belgium. In deer, tuberculous lesions are not pathognomonic ofMycobacterium bovisinfection due to gross and microscopic similarities with lesions caused byMycobacterium aviumsubsp.paratuberculosisorM. aviumsubsp.avium. The aim of this study was to improve molecular methods for the species-specific identification ofM. bovis,M. aviumsubsp.avium, andM. aviumsubsp.paratuberculosisin mycobacterial infections of deer. DNA banding patterns were assessed prior to and after Hpy188I restriction of f57-upstream (us)-p34 duplex amplicons. The duplex f57-us-p34 PCR differentiatedM. bovisfromM. aviumsubsp.paratuberculosisandM. aviumsubsp.aviuminfections, whereas the restriction step differentiated singleM. aviumsubsp.paratuberculosisorM. aviumsubsp.aviuminfections from mixedM. aviumsubsp.paratuberculosis/M. aviumsubsp.aviuminfections. The endonuclease Hpy188I cleaves DNA between nucleotides N and G in the unique TCNGA sequence. This restriction site was found at position 168 upstream of the us-p34 initiation codon in allM. aviumsubsp.aviumstrains tested, regardless of their origin and the results of IS901PCR. In contrast, the restriction site was abrogated in allM. aviumsubsp.paratuberculosisstrains tested, independent of their origin, Mycobactin J dependency, and IS900PCR results. Consequently, a two-step strategy, i.e., duplex us-p34-f57 PCR and Hpy188I restriction, allowed us to excludeM. bovisinfection and to identify single (M. aviumsubsp.paratuberculosisorM. aviumsubsp.avium) or mixed (M. aviumsubsp.paratuberculosis/M. aviumsubsp.avium) infections in wild red deer in Belgium. Accordingly, we propose to integrate, in a functional molecular definition ofM. aviumsubsp.paratuberculosis, the absence of the Hpy188I restriction site from the us-p34 amplicon.
Increased Genetic Diversity of
Neisseria meningitidis
Isolates after the Introduction of Meningococcal Serogroup C Polysaccharide Conjugate Vaccines
Authors: Diggle Mathew A. , Clarke Stuart C.
Published: September 2005

During the 1990s, the incidence of meningococcal disease was high in the United Kingdom. This was due primarily to an increase in serogroup C disease, particularly that within the ET-37/ST-11 genetic lineage. Serogroup C meningococcal polysaccharide conjugate vaccines were introduced in the United Kingdom in 1999, but the sequence types of meningococci causing disease since that time have not yet been reported. We have used serogrouping and multilocus sequence typing to characterize meningococci from patients with invasive disease over a 4-year period and show that there is a significant increase in genetic diversity but no genetic evidence of capsule switching.
Search for Localized Dysbiosis in Crohn's Disease Ulcerations by Temporal Temperature Gradient Gel Electrophoresis of 16S rRNA
Authors: Seksik Philippe , Lepage Patricia , de la Cochetière Marie-France , Bourreille Arnaud , Sutren Malène , Galmiche Jean-Paul , Doré Joël , Marteau Philippe
Published: September 2005

The mucosa-associated microbiota lining the gut epithelium might play a central role in the activation and/or perpetuation of mucosal inflammation in Crohn's disease (CD). We sought for localized dysbiosis by comparing the biodiversity and composition of the microbiotas in ulcerated and nonulcerated mucosal samples from patients with CD. Biopsy samples (
n
= 75) of ulcerated and adjacent nonulcerated mucosa were collected during colonoscopy from 15 patients, from the ileum, right colon, left colon, and rectum. Temporal temperature gradient gel electrophoresis (TTGE) of bacterial 16S rRNAs was used to evaluate the dominant bacterial species. TTGE profiles were compared using software that calculates similarity percentages. For a given patient, average similarity indexes between ulcerated and nonulcerated mucosal TTGE profiles ranged from 95.2% ± 4.2% to 97.9% ± 1.7% (means ± standard deviations) for the different segments. The mean values did not differ significantly. Average interindividual similarity indexes for a given segment among the different patients ranged from 33.6% ± 15.5% to 42.0% ± 25.6%. In CD, the dominant microbiotas do not differ qualitatively between ulcerated and nonulcerated mucosae. Biodiversity remains high in ulcerated mucosa. This argues against a pathogenic role of localized qualitative dysbiosis in CD-associated ulceration.
Molecular Epidemiology of Caliciviruses Detected in Sporadic and Outbreak Cases of Gastroenteritis in France from December 1998 to February 2004
Authors: Bon F. , Ambert-Balay K. , Giraudon H. , Kaplon J. , Le Guyader S. , Pommepuy M. , Gallay A. , Vaillant V. , de Valk H. , Chikhi-Brachet R. , Flahaut A. , Pothier P. , Kohli E.
Published: September 2005

We compiled sequence and epidemiological data from 172 caliciviruses detected in France from December 1998 to February 2004 in sporadic and outbreak cases. The results showed a cocirculation of strains with a majority of genogroup II (GII) noroviruses. Three groups of noroviruses, not detected before in our laboratory, emerged and spread during the period: the recombinant GGIIb and Norwalk-related strains not amplified in the polymerase gene in 2000 and a new Lordsdale variant in 2002. We observed that (i) GII-4 noroviruses were predominant in nursing home and hospital outbreaks but rare in oyster- and water-related outbreaks despite continuous circulation in the population; (ii) at the opposite, genogroup I strains were detected in the majority of environmental outbreaks; (iii) several strains were frequently found in oyster- and water-linked outbreaks (up to seven), whereas one single strain was detected when transmission was from person to person; and (iv) whereas GII noroviruses were predominant in sporadic cases where patients were under 15 years of age, GI strains were more frequent in outbreaks occurring in this age group. Finally, from a methodology point of view, this compilation shows that detection and characterization in the polymerase gene are not adequate in a significant number of cases and should be completed by amplification and sequencing in the capsid gene.
Multilocus Sequence Typing Scheme That Provides Both Species and Strain Differentiation for the
Burkholderia cepacia
Complex
Authors: Baldwin Adam , Mahenthiralingam Eshwar , Thickett Kathleen M. , Honeybourne David , Maiden Martin C. J. , Govan John R. , Speert David P. , LiPuma John J. , Vandamme Peter , Dowson Chris G.
Published: September 2005

A single multilocus sequence typing (MLST) scheme was developed for precise characterization of the opportunistic pathogens of
Burkholderia cepacia
complex (BCC), a group composed of at least nine closely related species. Seven conserved housekeeping genes were selected after a comparison of five
Burkholderia
species, and a collection of strains was subjected to nucleotide sequence analysis using a nested PCR amplification approach for each gene. MLST differentiated all nine current BCC species and identified 114 sequence types within a collection of 119 strains. No differentiation was found between strains recovered from environmental or clinical sources. The improved resolution in strain identification offered by MLST was able to identify previously characterized epidemic strain lineages and also demonstrated the presence of four novel potential species groups within the complex. There was also evidence for recombination having an important role in the recent evolution of individual BCC species. This highly transferable, validated, MLST scheme provides a new means to assist in species identification as well as unambiguous strain discrimination of the BCC by a single approach. It is also the first MLST scheme designed at the outset to incorporate multiple species and should facilitate global epidemiological investigations of the BCC.
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

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

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

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

Cryptococcus 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

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

Human 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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<0.05)
The laparoscopic nephrectomy learning curve: a single centre’s development of a de novo practice
Authors: Phillips J , Catto J W F , Lavin V , Doyle D , Smith D J , Hastie K J , Oakley N E
Published: September 2005

Objective

There has been a dramatic increase in the interest and practice of laparoscopic urology, with nephrectomy having become the commonest laparoscopic urological procedure. Compared with open nephrectomy, it results in reduced morbidity and shorter convalescence times while maintaining oncological safety. However, while these results predominately stem from institutions with well developed laparoscopic programmes, little is known about the results in centres that have newly adopted this technique. The introduction of a laparoscopic urological service at the Royal Hallamshire Hospital provided an opportunity to study these factors.

Methods

Since the appointment in October 2000 of a urological surgeon (N Oakley) to develop the laparoscopic service, there have been over 200 laparoscopic procedures including 121 nephrectomies performed at this centre. Full details were collected for each of these cases, and in addition, compared with retrospective data for 50 open nephrectomies performed during the same time period.

Results

With increased operator experience the median operative duration, complication, transfusion, and conversion rates significantly improved. While a learning curve was evident, the overall operative complication (9%) and conversion rates (6%) were low, in addition to patient morbidity (16.5%) and mortality (0%) rates, showing that this learning curve had no deleterious effects upon patient care. The median hospital stay was four days, which reduced to three with experience and was significantly shorter than for open nephrectomy at this institution (p = 0.001).

Conclusions

The development of a successful laparoscopic programme can be achieved with a comparatively short learning curve and without detriment to the patient provided the necessary steps are observed.
Ethical issues of resuscitation: an American perspective
Authors: Marco C A
Published: September 2005

Challenging issues confront emergency physicians routinely when performing cardiopulmonary resuscitation. Ethical issues surrounding resuscitation may include issues of futility, withholding or withdrawing interventions, advance directives, family presence, practising procedures on the newly dead, palliative care, and communication. Principles of bioethics can be valuable in assessing and debating ethical dilemmas. In many cases where curative care is not possible or is not desired, the goal of medical care at the end of life is to provide comfort to the patient and family, rather than initiating technological interventions that are unlikely to benefit the patient.
Potential role of interleukin 6 in reactive thrombocytosis and acute phase response in pulmonary tuberculosis
Authors: Ünsal E , Aksaray S , Köksal D , Şipit T
Published: September 2005

Objective

Reactive thrombocytosis is found in a number of clinical situations including infectious diseases such as pulmonary tuberculosis (PTB). To examine the possible role of interleukin (IL6) in reactive thrombocytosis and acute phase response in PTB this study measured serum IL6, C reactive protein (CRP), erythrocyte sedimentation rate (ESR), albumin concentrations in 62 PTB patients and 20 healthy volunteers.

Method

PTB patients were divided into two groups based on thrombocyte counts. Twenty seven PTB patients with normal thrombocyte counts constituted group 1, 35 PTB patients with thrombocytosis constituted group 2, and 20 healthy volunteers constituted group 3.

Results

The median IL6 concentration of group 1 was 12.8 pg/ml (95% CI: 12.1 to 56.9 pg/ml) and group 2 was 40.6 pg/ml (95% CI: 67.1 to 168.7 pg/ml). The comparison of IL6 concentrations in the three groups was significant (p = 0.0001). Patients in group 1 had a higher concentration of CRP (p = 0.0001) and lower concentration of albumin (p = 0.002) than group 3 whereas group 2 had higher concentration of CRP (p = 0.003) and lower concentration of albumin (p = 0.002) than group 1. Serum IL6 concentrations were significantly correlated with thrombocyte counts (p = 0.004, r = 0.36), CRP (p = 0.007, r = 0.34), and albumin concentrations (p = 0.005, r = −0.34). IL6 concentrations were significantly correlated with the number of involved zones (p = 0.005, r = 0.35) and acid fast bacilli positivity (p = 0.03, r = 0.27). Patients in group 2 had weight loss (p = 0.004), fever (p = 0.038), and night sweats (p = 0.007) more frequently than group 1. Also, group 2 had more extensive radiological findings (involved zones p = 0.001, bilateral disease p = 0.0001, presence of cavity p = 0.02) than group 1.

Conclusions

IL6 might play a contributory part in reactive thrombocytosis and acute phase response in PTB.
Diagnosis and management of gout: a rational approach
Authors: Suresh E
Published: September 2005

Gout is one of the best understood among the rheumatological disorders and one of the most satisfying to treat. Even non-specialists should be able to diagnose and treat most patients provided some important principles are appreciated. Management of a minority of patients, including those with renal impairment is difficult and often unsatisfactory, because of restricted treatment options. In this paper, the basic principles underlying the diagnosis and management of gout are discussed first, followed by practical approaches.
Assessment of the efficacy of total lymphocyte counts as predictors of AIDS defining infections in HIV-1 infected people
Authors: Stebbing J , Sawleshwarkar S , Michailidis C , Jones R , Bower M , Mandalia S , Nelson M , Gazzard B
Published: September 2005

Background

The CD4 count is a dominant prognostic and predictive factor in HIV infection. This study assessed the utility of the total lymphocyte count (TLC) in place of the CD4 count to predict the development of AIDS defining opportunistic infections (ADOI).

Methods

The Chelsea and Westminster cohort was used to identify those people with a first episode of an ADOI. Corresponding CD4 and TLCs were recorded before diagnosis or at the time of first prescribing prophylaxis; patients without an AIDS defining opportunistic infection were defined as being at “risk” and receiver operating characteristic (ROC) curves were used to display the results of sensitivity and the false positive error rate of total lymphocyte and CD4 count groups.

Results

A significant linear correlation was seen between the log10 CD4 count and log10 TLC (Pearson’s correlation coefficient = 0.70, p<0.001). The finer cut off value for TLC where false positive error rate is minimum and sensitivity maximum was 1500–2000 cells/mm3. Patients with TLC 1000–1500 cells/mm3 were estimated to be at 40% increased risk of developing an ADOI. The cut off value for CD4 counts measured 200 cells/mm3 above which the risk developing an ADOI decreased. Patients with a CD4 count of 150–200 cells/mm3 were at a 34% increased risk of developing an ADOI. The area under the ROC curve for TLC was 10% lower than that for CD4 count.

Conclusions

The TLC is minimally less reliable than the CD4 count as a predictor of ADOIs. In the absence of expensive equipment for CD4 measurement, the TLC is a useful test.
ENERGY RESOLUTION AND COUNTING PROPERTIES OF MICRO-STRIP GAS COUNTER FOR X-RAY DETECTING
Authors: SU QINGFENG , XIA YIBEN , WANG LINJUN , YANG YING , SHI WEIMIN
Published: September 2005

A two-dimensional micro-strip Gas Chamber (MSGC) with a 20 × 20 mm2 detection area had been developed. The MSGC had a thin diamond film of 10 μm deposited on a silicon wafer as substrate and lots of micro-strip anode and cathode electrodes made by multi-chip module technology. Energy resolution and pulse signal under 5.9 keV 55 Fe X-rays were measured by a multi-channel energy spectrometer with different voltage under room temperature in atmospheric pressure. Results indicated high signal-to-noise ratio, count rate ≥103 Hz and stable gas gain of the MSGC were obtained. When Ar : CH 4=90:10, drift voltage, cathode voltage and anode voltage was -1000 V, -650 V and 0 V, respectively. However, the energy resolution of 12.3% for 5.9 keV 55 Fe X-rays was achieved. The effects of cathode voltage and drift voltage on energy resolution and count rate were also obtained.
BOUND STATES OF SCALAR PARTICLES IN THE PRESENCE OF A SHORT RANGE POTENTIAL
Authors: GONZÁLEZ-DÍAZ LUIS A. , VILLALBA VICTOR M.
Published: September 2005

We analyze the behavior of the energy spectrum of the Klein–Gordon equation in the presence of a truncated hyperbolic tangent potential. From our analysis we obtain that, for some values of the potential there is embedding of the bound states into the negative energy continuum, showing that, in opposition to the general belief, relativistic scalar particles in one-dimensional short range potentials can exhibit resonant behavior and also the Schiff–Snyder effect.
THE RENORMALIZATION GROUP IMPROVED EFFECTIVE POTENTIAL IN MASSLESS MODELS
Authors: BRANDT F. T. , CHISHTIE F. A. , MCKEON D. G. C.
Published: September 2005

The effective potential V is considered in massless [Formula: see text] theory. The expansion of V in powers of the coupling λ and of the logarithm of the background field ϕ is reorganized in two ways; first as a series in λ alone, then as a series in ln ϕ alone. By applying the renormalization group (RG) equation to V, these expansions can be summed. Using the condition V′(v)=0 (where v is the vacuum expectation value of ϕ) in conjunction with the expansion of V in powers of ln ϕ fixes V provided v≠0. In this case, the dependence of V on ϕ drops out and V is not analytic in λ. Massless scalar electrodynamics is considered using the same approach.
BUCKLING ANALYSIS OF CIRCULAR FGM PLATE HAVING VARIABLE THICKNESS UNDER UNIFORM COMPRESSION BY MESH FREE METHOD
Authors: SHAMEKHI ABAZAR , NAI MOHAMMAD H.
Published: September 2005

This study presents the buckling analysis of radially-loaded circular plate with variable thickness made of functionally-graded material. The boundary conditions of the plate is either simply supported or clamped. The stability equations were obtained using energy method based on Love-Kichhoff hypothesis and Sander's nonlinear strain-displacement relation for thin plates. Mesh free method is used to determine the critical buckling load. The results obtained show good agreement with known analytical and numerical data. The effects of thickness variation and Poisson's ratio are investigated by calculating the buckling load. These effects are found not to be the same for simply supported and clamped plates.
MODIFIED DISTRIBUTION-FORMULA SCHEME FOR UNSTRUCTURED ADAPTIVE NAVIER-STOKES SOLVERS
Authors: CHAN (MAIAA) K. I. , NG (MASME) E. Y. K.
Published: September 2005

The development and validation of an improved distribution-formula method is presented in this paper. The original technique, an explicit, cell-vertex, finite volume formulation, involves calculating the change in flow variables in each finite volume cell by integration of the governing equations, and then using distribution formulas to distribute such changes to the vertices. Its application has largely been in structured meshes without mesh adaptation. The present work introduces three improvements. Firstly, the extension of the method for use on unstructured adaptive meshes. This results in the additional advantages of mesh adaptation as well as the capability to simulate flows over arbitrarily complex geometries. Secondly, for the calculation of inviscid fluxes, the central differencing portion of the original method is replaced with a suitable higher-order upwind differencing scheme. This improves the accuracy and robustness of the distribution-formula method. Three different upwind techniques are evaluated through numerical investigations. The most promising among these techniques is selected for use in the development of the improved distribution-formula scheme for unstructured adaptive viscous solutions. Thirdly, the discretization of viscous fluxes is achieved through a method which requires less computational effort. The improved scheme is tested and found to be accurate, robust and computationally efficient.