bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Rapid PCR Method Using the Insertion Sequence IS
1203
for Genotyping Shiga Toxin-Producing
Escherichia coli
O157
Authors: Suzuki Masahiro , Matsumoto Masakado , Hata Mami , Takahashi Masao , Sakae Kenji 
Published: December 2004

ABSTRACT

We developed a rapid PCR method utilizing the diversity of the insertion site IS
1203
for genotyping Shiga toxin-producing
Escherichia coli
(STEC) O157 (IS
1203
PCR typing). DNA fragments digested by PvuII, which cut IS
1203
at one site, were ligated with themselves and detected by PCR with outward-facing primer pairs for IS
1203
. To minimize nonspecific bands, nested PCR was also performed. Two fingerprinting patterns produced from the upstream or downstream regions of IS
1203
were obtained within 1 or 2 days. By combining the two patterns, 79 STEC O157 isolates were classified into 39 types, which were then classified into 36 subtypes by pulsed-field gel electrophoresis (PFGE). The discriminatory power of IS
1203
PCR typing (
D
= 0.974) is similar to that of PFGE (
D
= 0.981). This method can be used for rapid and simplified genotyping.
Sequencing Needs for Viral Diagnostics
Authors: Gardner Shea N. , Lam Marisa W. , Mulakken Nisha J. , Torres Clinton L. , Smith Jason R. , Slezak Tom R. 
Published: December 2004

ABSTRACT
We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (near neighbors) that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near-neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near-neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. Severe acute respiratory syndrome and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near-neighbor sequences are urgently needed. Our results also indicate that double-stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.
Exploration of Biases That Affect the Interpretation of Restriction Fragment Patterns Produced by Pulsed-Field Gel Electrophoresis
Authors: Singer Randall S. , Sischo William M. , Carpenter Tim E. 
Published: December 2004

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) has been used extensively in epidemiological investigations of bacteria, especially during food-borne outbreaks or nosocomial infections. The relationship between similarities in PFGE patterns and true genetic relatedness is poorly understood. In this study, computer-simulated populations of
Escherichia coli
isolates were created by mutating the sequence of
E. coli
K-12 strain MG1655. The simulated populations of isolates were then digested, again through simulation, with different restriction enzymes and were analyzed for their relatedness by different techniques. Errors associated with band determination and band matching were incorporated into the analyses, as both of these error types have been shown to affect PFGE interpretations. These errors increased the apparent similarities of the isolates. The use of multiple enzymes improved the fidelity between the results of PFGE analyses and the true sequence similarities. These findings, when they are combined with results from laboratory studies, emphasize the need for the inclusion of multiple enzymes and additional epidemiological data in order to make more accurate interpretations.
Shedding of Ovine Herpesvirus 2 in Sheep Nasal Secretions: the Predominant Mode for Transmission
Authors: Li Hong , Taus Naomi S. , Lewis Gregory S. , Kim Okjin , Traul Donald L. , Crawford Timothy B. 
Published: December 2004

ABSTRACT

Ovine herpesvirus 2 (OvHV-2), the major causative agent of malignant catarrhal fever in ruminant species worldwide, has never been propagated in vitro. Using real-time PCR, a striking, short-lived, peak of viral DNA, ranging from 10
5
to over 10
8
copies/2 μg of DNA, was detected in nasal secretions from over 60.7% of adolescent sheep (
n
= 56) at some point during the period from 6 to 9 months of age. In contrast, only about 18% of adult sheep (
n
= 33) experienced a shedding episode during the study period. The general pattern of the appearance of viral DNA in nasal secretions was a dramatic rise and subsequent fall within 24 to 36 h, implying a single cycle of viral replication. These episodes occurred sporadically and infrequently, but over the 3-month period most of the 56 lambs (33, or 60.7%) experienced at least one episode. No corresponding fluctuations in DNA levels were found in either peripheral blood leukocytes or plasma. In a DNase protection assay, complete, enveloped OvHV-2 virions were demonstrated in the nasal secretions of all sheep examined during the time when they were experiencing an intense shedding episode. OvHV-2 infectivity in nasal secretions was also demonstrated by aerosolization of the secretions into OvHV-2-negative sheep. The data herein show that nasal shedding is the major mode of OvHV-2 transmission among domestic sheep and that adolescents represent the highest risk group for transmission.
Direct Identification of Gram-Positive Cocci from Routine Blood Cultures by Using AccuProbe Tests
Authors: Lindholm Laura , Sarkkinen Hannu 
Published: December 2004

ABSTRACT

Rapid and reliable identification of bacteria directly from blood cultures is important in clinical practice to guide appropriate antibiotic therapy. In this study, the performance of the AccuProbe (Gen-Probe, Inc., San Diego, Calif.) in direct identification of
Staphylococcus aureus
,
Streptococcus pneumoniae
, enterococci, and group A and B streptococci from positive blood culture bottles was evaluated by using 6-year routine clinical laboratory blood culture material from Päijät-Häme Central Hospital, Lahti, Finland. With the enterococcal and group A and B streptococcal probes, the diagnostic performance of the test was excellent at a cutoff value of 50,000 relative light units (RLU) as recommended by the manufacturer. However, with the
S. aureus
probe, although the specificity was very high (99.8%), the sensitivity was low (72.4%). To improve the clinical usability of the direct AccuProbe identification, optimal cutoff values for the individual AccuProbe tests were defined by using receiver-operating characteristic analysis. Consequently, cutoff values for
S. aureus
and
S. pneumoniae
tests were adjusted to 30,000 RLU and for enterococci and to 55,000 RLU for group A and B streptococci. With these adjustments, the performance of the AccuProbe tests, especially that for
S. aureus
, was significantly improved.
Epidemiology and Typing of
Staphylococcus aureus
Strains Isolated from Bloodstream Infections
Authors: van der Mee-Marquet Nathalie , Domelier Anne-Sophie , Girard Nicole , Quentin Roland ,   the Bloodstream Infection Study Group of the Relais d'Hygiène du Centre
Published: December 2004

ABSTRACT

We carried out an epidemiological study covering 2,365,067 patient days of hospitalization between 2000 and 2003. During this time, 413
Staphylococcus aureus
bloodstream infections occurred. This corresponds to 15% of the 2,676 bloodstream infections observed during this period in the 31 hospitals in our region of France, which has 2.5 million inhabitants. The incidence of nosocomial
S. aureus
bloodstream infections was 0.11 per 1,000 days of hospitalization. The prevalence of methicillin-resistant
S. aureus
(MRSA) strains, of which 13% were nonmultiresistant MRSA (NORSA), was 33%, and this percentage was stable over the 4 years. In contrast, the prevalence of
S. aureus
strains susceptible to methicillin but resistant to quinolones or susceptible to methicillin but multiresistant to antibiotics (EMSSA strains) increased from 4% in 2000 to 23% in 2003. As previously reported, MRSA strains were mostly recovered from nosocomial bloodstream infections, whereas NORSA strains—generally considered to be responsible for community-acquired infections—were always isolated from nosocomial bloodstream infections. Pulsed-field gel electrophoresis (PFGE) analysis of 109 MRSA strains and 15 EMSSA strains demonstrated clonal diffusion of the three major French MRSA clones and revealed considerable genetic heterogeneity among EMSSA strains. Although no epidemiologically related NORSA strains clustered in particular PFGE groups, the distribution of MRSA strains isolated from bloodstream infections according to the portal of entry (vascular devices, pulmonary, and urinary) was not random for the major PFGE clones, suggesting that each MRSA lineage displays particular virulence features.
Multiplex PCR Targetingtpi(Triose Phosphate Isomerase),tcdA(Toxin A), andtcdB(Toxin B) Genes for Toxigenic Culture ofClostridium difficile
Authors: Lemee Ludovic , Dhalluin Anne , Testelin Sabrina , Mattrat Marie-Andre , Maillard Karine , Lemeland Jean-François , Pons Jean-Louis 
Published: December 2004

ABSTRACTA multiplex PCR toxigenic culture approach was designed for simultaneous identification and toxigenic type characterization ofClostridium difficileisolates. Three pairs of primers were designed for the amplification of (i) a species-specific internal fragment of thetpi(triose phosphate isomerase) gene, (ii) an internal fragment of thetcdB(toxin B) gene, and (iii) an internal fragment of thetcdA(toxin A) gene allowing distinction between toxin A-positive, toxin B-positive (A+B+) strains and toxin A-negative, toxin B-positive (A−B+) variant strains. The reliability of the multiplex PCR was established by using a panel of 72C. difficilestrains including A+B+, A−B−, and A−B+ toxigenic types and 11 otherClostridiumspecies type strains. The multiplex PCR assay was then included in a toxigenic culture approach for the detection, identification, and toxigenic type characterization ofC. difficilein 1,343 consecutive human and animal stool samples. Overall, 111 (15.4%) of 721 human samples were positive forC. difficile; 67 (60.4%) of these samples contained A+B+ toxigenic isolates, and none of them contained A−B+ variant strains. Fifty (8%) of 622 animal samples containedC. difficilestrains, which were toxigenic in 27 (54%) cases, including 1 A−B+ variant isolate. Eighty of the 721 human stool samples (37 positive and 43 negative forC. difficileculture) were comparatively tested by Premier Toxins A&B (Meridian Bioscience) and TriageC. difficilePanel (Biosite) immunoassays, the results of which were found concordant with toxigenic culture for 82.5 and 92.5% of the samples, respectively. The multiplex PCR toxigenic culture scheme described here allows combined diagnosis and toxigenic type characterization for human and animalC. difficileintestinal infections.
Use of Highly Variable Intergenic Spacer Sequences for Multispacer Typing ofRickettsia conoriiStrains
Authors: Fournier Pierre-Edouard , Zhu Yong , Ogata Hiroyuki , Raoult Didier 
Published: December 2004

ABSTRACTBy use of the nearly perfectly colinear genomes ofRickettsia conoriiandRickettsia prowazekii, we compared the usefulness of three types of sequences for typing ofR. conoriiisolates: (i) 5 variable coding genes comprising the 16S ribosomal DNA,gltA,ompB, andsca4(gene D) genes, which are present in both genomes, and theompAgene, which is degraded inR. prowazekii; (ii) 28 genes degraded inR. conoriibut intact inR. prowazekii, including 23 split and 5 remnant genes; and (iii) 27 conserved and 25 variable intergenic spacers. The 4 conserved and 23 split genes as well as the 27 conserved intergenic spacers each had identical sequences in 34 human and 5 tick isolates ofR. conorii. Analysis of theompAsequences identified three genotypes ofR. conorii. The variable intergenic spacers were significantly more variable than conserved genes, split genes, remnant genes, and conserved spacers (P< 10−2in all cases). Four of the variable intergenic spacers (dksA-xerC,mppA-purC,rpmE-tRNAfMet, and tRNAGly-tRNATyr) had highly variable sequences; when they were combined for typing, multispacer typing (MST) identified 27 different genotypes in the 39R. conoriiisolates. Two batches from the sameR. conoriistrain, Malish (Seven), with different culture passage histories were found to exhibit the same MST type. MST was more discriminatory for strain genotyping than multiple gene sequencing (P< 10−2). Phylogenetic analysis based on MST sequences was concordant with the geographic origins ofR. conoriiisolates. Our study supports the usefulness of MST for strain genotyping. This tool may be useful for tracing a strain and identifying its source during outbreaks, including those resulting from bioterrorism.
Surface Immunoglobulin-Deficient Epstein-Barr Virus-Infected B Cells in the Peripheral Blood of Pediatric Solid-Organ Transplant Recipients
Authors: Schauer Elizabeth , Webber Steven , Green Michael , Rowe David 
Published: December 2004

ABSTRACTEpstein-Barr virus (EBV), a ubiquitous human herpesvirus, normally causes an asymptomatic latent infection with very low levels of circulating virus in the peripheral blood of infected individuals. However, EBV does have pathogenic potential and has been linked to several diseases, including posttransplant lymphoproliferative disease (PTLD), which involves very high circulating viral loads. As a consequence of immunosuppression associated with transplantation, children in particular are at risk for PTLD. Even in the absence of symptoms of PTLD, very high viral loads are often observed in these patients. EBV-infected B cells in the circulations of 16 asymptomatic pediatric solid-organ transplant recipients from Children's Hospital of Pittsburgh were simultaneously characterized for their surface immunoglobulin (sIg) isotypes and EBV genome copy numbers. Patients were characterized as having high and low viral loads on the basis of their stable levels of circulating virus. Patients with high viral loads had both high- and low-copy-number cells. Cells with a high numbers of viral episomes (>20/cell) were predominantly Ig null, and cells with low numbers of episomes were predominantly sIgM positive. Patients with low viral loads carried the vast majority of their viral load in low-copy-number cells, which were predominantly IgM positive. The very rare high-copy-number cells detected in carriers with low viral loads were also predominantly Ig-null cells. This suggests that two distinct types of B-lineage cells contribute to the viral load in transplant recipients, with cells bearing high genome copy numbers having an aberrant Ig-null cellular phenotype.
Diverse CTX Phages among Toxigenic
Vibrio cholerae
O1 and O139 Strains Isolated between 1994 and 2002 in an Area Where Cholera is Endemic in Bangladesh
Authors: Nusrin Suraia , Khan G. Yeahia , Bhuiyan N. A. , Ansaruzzaman M. , Hossain M. A. , Safa Ashrafus , Khan Rasel , Faruque Shah M. , Sack David A. , Hamabata T. , Takeda Yoshifumi , Nair G. Balakrish 
Published: December 2004

ABSTRACT

PCR surveillance of the
rstR
genes of CTX phages in
Vibrio cholerae
O1 and O139 showed no relationship between the incidence of disease and changes in the
rstR
but showed variations in their presence in O1 and O139 strains and the occurrence of multiple types in a few strains.
Rapid Discrimination between Human Immunodeficiency Virus Type 2 Groups A and B by Real-Time PCR
Authors: Plantier Jean-Christophe , Gueudin Marie , de Oliveira Fabienne , Damond Florence , Lemée Véronique , Brun-Vézinet Françoise , Simon François 
Published: December 2004

ABSTRACT
We studied the feasibility of genotyping human immunodeficiency virus (HIV) type 2 groups A and B by real-time PCR. Two group-specific PCRs were developed. Real-time genotyping of 22 samples of genotype A, 10 samples of genotype B, and the isolate of new group H were compared to genotyping by sequencing and phylogeny. The group-specific PCRs specifically identified 84.3% of group A or B samples; isolate H was not detected. This method allowed rapid and specific discrimination between HIV-2 groups A and B and could be a useful tool for molecular epidemiological studies.
Comparison of Five Methods for Extraction of
Legionella pneumophila
from Respiratory Specimens
Authors: Wilson Deborah , Yen-Lieberman Belinda , Reischl Udo , Warshawsky Ilka , Procop Gary W. 
Published: December 2004

ABSTRACT

The efficiencies of five commercially available nucleic acid extraction methods were evaluated for the recovery of a standardized inoculum of
Legionella pneumophila
in respiratory specimens (sputum and bronchoalveolar lavage [BAL] specimens). The concentrations of
Legionella
DNA recovered from sputa with the automated MagNA Pure (526,200 CFU/ml) and NucliSens (171,800 CFU/ml) extractors were greater than those recovered with the manual methods (i.e., Roche High Pure kit [133,900 CFU/ml], QIAamp DNA Mini kit [46,380 CFU/ml], and ViralXpress kit [13,635 CFU/ml]). The rank order was the same for extracts from BAL specimens, except that for this specimen type the QIAamp DNA Mini kit recovered more than the Roche High Pure kit.
Clinical Evaluation of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for Rapid Diagnosis of Tuberculosis Lymphadenitis
Authors: Kerleguer A. , Fabre M. , Bernatas J. J. , Gerome P. , Nicand E. , Herve V. , Koeck J. L. 
Published: December 2004

ABSTRACT
This prospective study evaluated the performance of the Amplified Mycobacterium Tuberculosis Direct Test (MTD) for the diagnosis of lymph node tuberculosis in Djibouti, Republic of Djibouti. Of 197 specimens sampled from 153 patients, 123 were from 95 tuberculous patients. The sensitivity and specificity of MTD were 93 and 100%, respectively. The sensitivity of culture was 89%.
Differential Recovery ofCandidaSpecies from Subgingival Sites in Human Immunodeficiency Virus-Positive and Healthy Children from Rio de Janeiro, Brazil
Authors: Portela M. B. , Souza I. P. R. , Costa E. M. M. B. , Hagler A. N. , Soares R. M. A. , Santos A. L. S. 
Published: December 2004

ABSTRACTThe prevalence of subgingivalCandidaspecies was studied in 52 human immunodeficiency virus (HIV)-positive and 42 HIV-negative children.Candidawas cultured from 22 (42.3%) and 3 (7.1%) HIV-infected and control children, respectively.C. albicanswas the most commonCandidaspecies isolated from HIV-infected children, followed byC. dubliniensis,C. glabrata, andC. tropicalis. In the HIV-positive group, the prevalence ofCandidaisolation was significantly higher in children who presented with low CD4+-T-lymphocyte counts, elevated viral loads, and gingivitis.
Risk of injury for occupants of motor vehicle collisions from unbelted occupants
Authors: MacLennan P A , McGwin G , Metzger J , Moran S G , Rue L W 
Published: December 2004

Objective:Unbelted occupants may increase the risk of injury for other occupants in a motor vehicle collision (MVC). This study evaluated the association between occupant restraint use and the risk of injury (including death) to other vehicle occupants.Design:A population based cohort study.Setting:United States.Subjects:MVC occupants (n = 152 191 unweighted, n = 18 426 684 weighted) seated between a belted or unbelted occupant and the line of the principal direction of force in frontal, lateral, and rear MVCs were sampled from the 1991–2002 National Automotive Sampling System General Estimates System. Offset MVCs were not included in the study.Main outcome measure:Risk ratios and 95% confidence intervals for injury (including death) for occupants seated contiguous to unbelted occupants compared to occupants seated contiguous to belted occupants. Risk ratios were adjusted for at risk occupant’s sex, age, seating position, vehicle type, collision type, travel speed, crash severity, and at risk occupants’ own seat belt use.Results:Exposure to unbelted occupants was associated with a 40% increased risk of any injury. Belted at risk occupants were at a 90% increased risk of injury but unbelted occupants were not at increased risk. Risks were similar for non-incapacitating and capacitating injuries. There was a 4.8-fold increased risk of death for exposed belted occupants but no increased risk of death for unbelted occupants.Conclusions:Belted occupants are at an increased risk of injury and death in the event of a MVC from unbelted occupants.
Water Splitting into H2 and O2 over Cs2Nb4O11 Photocatalyst
Authors: Miseki Yugo , Kato Hideki , Kudo Akihiko 
Published: December 2004

Abstract
Photophysical and photocatalytic properties of Cs2Nb4O11 consisting of NbO6 octahedra and NbO4 tetrahedra were investigated. The band gap of Cs2Nb4O11 was 3.7 eV. Broad blue photoluminescence was observed at 77 K. Pretreated NiO-loaded Cs2Nb4O11 showed a high activity for water splitting under UV-light irradiation.
Fractionally spaced blind equalization with low‐complexity concurrent constant modulus algorithm and soft decision‐directed scheme
Authors: Chen S. , Chng E. S. 
Published: December 2004

AbstractThe paper proposes a low‐complexity concurrent constant modulus algorithm (CMA) and soft decision‐directed (SDD) scheme for fractionally spaced blind equalization of high‐order quadrature amplitude modulation channels. We compare our proposed blind equalizer with the recently introduced state‐of‐art concurrent CMA and decision‐directed (DD) scheme. The proposed CMA+SDD blind equalizer is shown to have simpler computational complexity per weight update, faster convergence speed, and slightly improved steady‐state equalization performance, compared with the existing CMA+DD blind equalizer. Copyright © 2004 John Wiley & Sons, Ltd.
Torsional resistance as a principal component of the structural design of long bones: Comparative multivariate evidence in birds
Authors: De Margerie Emmanuel , Sanchez Sophie , Cubo Jorge , Castanet Jacques 
Published: December 2004

AbstractHere we study the occurrence of torsion‐resisting morphological and histological features (thin bone walls, circular shaft cross‐section, oblique collagen fibers, and laminar tissue arrangement) in a sample of 168 long bones from wings and legs of 22 bird species. These structural parameters were measured in mid diaphyseal undemineralized cross‐sections and analyzed using uni‐, bi‐, and multivariate (principal components analysis) data analysis techniques. We found that the four variables are significantly and positively correlated, and that covariation between variables accounts for as much as 58% of the total variation. These results suggest that torsion is a main determinant of the macro‐ and microstructural design of long bones in birds. Humerus, ulna, and femur generally possess torsion‐resisting features, while other bones (radius, carpometacarpus, tibiotarsus, tarsometatarsus, and foot phalanx) rather show bending/axial load‐resisting structural properties. These results are congruent with in vivo strain data from the literature, which reported high torsional loading in humerus and ulna during flapping flight, but also in the subhorizontal avian femur during terrestrial locomotion. The precise function of the laminar tissue spatial arrangement, the role of pneumatization, and the influence of flight mode are discussed. © 2004 Wiley‐Liss, Inc.