bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene (
clfB
) for Resolution within Clonal Groups of
Staphylococcus aureus
Authors: Koreen Larry , Ramaswamy Srinivas V. , Naidich Steven , Koreen Irina V. , Graff Gavin R. , Graviss Edward A. , Kreiswirth Barry N. 
Published: August 2005

ABSTRACT

Molecular
techniques such as
spa
typing and multilocus sequence typing
use DNA sequence data for differentiating
Staphylococcus
aureus
isolates. Although
spa
typing is capable of
detecting both genetic micro- and macrovariation, it has less
discriminatory power than the more labor-intensive pulsed-field gel
electrophoresis (PFGE) and costly genomic DNA microarray analyses. This
limitation hinders strain interrogation for newly emerging clones and
outbreak investigations in hospital or community settings where robust
clones are endemic. To overcome this constraint, we developed a typing
system using DNA sequence analysis of the serine-aspartate (SD)
repeat-encoding region within the gene encoding the
keratin- and fibrinogen-binding clumping factor B (
clfB
typing) and tested whether it is capable of discriminating within
clonal groups. We analyzed 116
S. aureus
strains, and the
repeat region was present in all isolates, varying in sequence and in
length from 420 to 804 bp. In a sample of 36 well-characterized
genetically diverse isolates,
clfB
typing subdivided identical
spa
and PFGE clusters which had been discriminated by
whole-genome DNA microarray mapping. The combination of
spa
typing and
clfB
typing resulted in a discriminatory power
(99.5%) substantially higher than that of
spa
typing alone and
closely approached that of the whole-genome microarray (100.0%).
clfB
typing also successfully resolved genetic differences
among isolates differentiated by PFGE that had been collected over
short periods of time from single hospitals and that belonged to the
most prevalent
S. aureus
clone in the United States.
clfB
typing demonstrated in vivo, in vitro, and interpatient
transmission stability yet revealed that this locus may be
recombinogenic in a primarily clonal population structure. Taken
together, these data show that the SD repeat-encoding region of
clfB
is a highly stable marker of microvariation, that in
conjunction with
spa
typing it may serve as a DNA
sequence-based alternative to PFGE for investigating genetically
similar strains, and that it is useful for analyzing collections of
isolates in both long-term population-based and local epidemiologic
studies.
Regulated Expression of the Beta2-Toxin Gene (
cpb2
) in
Clostridium perfringens
Type A Isolates from Horses with Gastrointestinal Diseases
Authors: Waters Michael , Raju Deepa , Garmory Helen S. , Popoff Michel R. , Sarker Mahfuzur R. 
Published: August 2005

ABSTRACT

Recent epidemiological studies suggested that
cpb2
-positive
Clostridium perfringens
isolates are associated with gastrointestinal (GI) diseases in horses. These putative relationships, indicated by PCR genotyping, were tested in the present study by further genotyping and phenotyping of 23
cpb2
-positive
C. perfringens
isolates from horses with GI disease (referred to hereafter as horse GI disease isolates). Our beta2-toxin (CPB2) Western blot analyses demonstrated that all of the tested isolates were unable to produce detectable levels of CPB2. However, Southern blot and nucleotide sequencing analyses identified intact
cpb2
open reading frames in all of our surveyed horse GI disease isolates. Furthermore, reverse transcriptase PCR and Northern blot analyses showed that
cpb2
genes in all of our surveyed horse GI disease isolates were transcriptionally active, i.e., an ∼1.2-kb
cpb2
-specific mRNA was identified in total RNA from our surveyed isolates. The levels of
cpb2
mRNA in CWC245 (a high-CPB2-producing pig strain) and our surveyed horse GI disease isolates differed to such an extent (35-fold) that this difference could be considered as a major cause of the difference in levels of CPB2 production by CWC245 and horse GI disease isolates. This finding received further support from our observation that the complementing strain 106902(pMRS140), which produced significantly higher levels of mRNA than strain 106902, produced high levels of CPB2. Collectively, our results indicated that there is a positive correlation between
cpb2
transcription levels and the amount of CPB2 produced by a
C. perfringens
cell and that decreased transcription and/or message instability may be involved, at least in part, in the low CPB2 production noted for horse GI disease isolates in comparison to that noted for pig GI disease isolate CWC245.
Use of the Roche LightCycler Strep B Assay for Detection of Group B Streptococcus from Vaginal and Rectal Swabs
Authors: Uhl James R. , Vetter Emily A. , Boldt Kristi L. , Johnston Bruce W. , Ramin Kirk D. , Adams Marla J. , Ferrieri Patricia , Reischl Udo , Cockerill Franklin R. 
Published: August 2005

ABSTRACT
The
results for a real-time PCR assay, using the LightCycler Strep B
analyte-specific reagents (Roche Diagnostics Corporation, Indianapolis,
Ind.), were compared to a direct plate method combined with a broth
enrichment culture method for detection of group B streptococcus
colonization in pregnant women. Two separate evaluations
were conducted using two different automated nucleic extraction
instruments, the MagNA Pure LC instrument (Roche Diagnostics
Corporation) and the lower-capacity MagNA Pure Compact instrument
(Roche Diagnostics Corporation). The sensitivities, specificities, and
positive and negative predictive values for the different evaluation
methods were as follow: for the LightCycler Strep B assay with MagNA
Pure LC, 100, 97, 90, and 100%, respectively; for the LightCycler Strep
B assay with MagNA Pure Compact, 92.5, 99, 97, and 97.5%, respectively.
The LightCycler Strep B assay combined with either MagNA Pure LC or
MagNA Pure Compact extraction is a suitable method for detecting group
B streptococcus colonization in pregnant women. An advantage of the
LightCycler assay over culture is the considerably reduced turnaround
time for
results.
Phenotypic and Molecular Characterization of
Candida nivariensis
sp. nov., a Possible New Opportunistic Fungus
Authors: Alcoba-Flórez Julia , Méndez-Álvarez Sebastián , Cano Josep , Guarro Josep , Pérez-Roth Eduardo , del Pilar Arévalo María 
Published: August 2005

ABSTRACT

The new species
Candida nivariensis
, isolated from the clinical samples of three patients in Spain over a 3-year period, is presented here. This species can be easily differentiated from
Candida glabrata
, the closest genetic species, by different colony color on CHROMagar and by its ability to ferment trehalose. The analyses of the internal transcribed spacer region and the D1-D2 region of the 26S rRNA gene sequences support a new species designation.
Photorhabdus asymbiotica
, a Pathogen Emerging on Two Continents That Proves that There Is No Substitute for a Well-Trained Clinical Microbiologist
Authors: Weissfeld Alice S. , Halliday Rhonda J. , Simmons Dawn E. , Trevino Ernest A. , Vance Paula H. , O'Hara Caroline M. , Sowers Evangeline G. , Kern Rebecca , Koy R. Dudley , Hodde Kathy , Bing M. , Lo Carson , Gerrard John , Vohra Renu , Harper Jacqueline 
Published: August 2005

ABSTRACT

A 54-year-old ranch hand presented to the emergency room with an alleged spider bite and multiple abscesses. Both wound and blood cultures grew
Photorhabdus asymbiotica
, an enteric gram-negative rod that was initially misidentified by the hospital's rapid identification system. Clinical laboratories should be aware of the limitations of their rapid identification systems and always use them as an adjunct to analysis of morphological and phenotypic traits.
Septic Arthritis Caused by Vancomycin-Intermediate
Staphylococcus aureus
Authors: Lu Jang-Jih , Lee Shih-Yi , Hwa Su-Yang , Yang An-Hang 
Published: August 2005

ABSTRACT

Four methicillin-resistant
Staphylococcus aureus
isolates were consecutively isolated from synovial fluid and a knee wound of a patient with septic arthritis. Determination of the MIC of vancomycin and population analysis confirmed these isolates as vancomycin-intermediate
S. aureus
(VISA). Results of this study also revealed that cell wall thickness and reduced susceptibility to Triton X-100 were characteristic features of VISA.
Inhibitor-Based Methods for Detection of Plasmid-Mediated AmpC β-Lactamases in
Klebsiella
spp.,
Escherichia coli
, and
Proteus mirabilis
Authors: Coudron Philip E. 
Published: August 2005

ABSTRACT

Non-beta-lactam inhibitor-based methods were evaluated for detecting plasmid-mediated AmpC β-lactamases in
Klebsiella
spp.,
Escherichia coli
, and
Proteus mirabilis
. Using CLSI methodology and disks containing cefotetan alone and in combination with 400 μg of boronic acid, 9 of 10 positive control strains and 54 of 55 AmpC-PCR-positive clinical isolates were detected. Importantly 71% and 40% of these clinical isolates were susceptible by routine testing to ceftriaxone and ceftazidime, respectively. Boronic acid disks also enhanced detection of expanded-spectrum β-lactamases in AmpC producers.
Evaluation of β-Lactamase Inhibitors in Disk Tests for Detection of Plasmid-Mediated AmpC β-Lactamases in Well-Characterized Clinical Strains of
Klebsiella
spp
Authors: Black Jennifer A. , Thomson Kenneth S. , Buynak John D. , Pitout Johann D. D. 
Published: August 2005

ABSTRACT

The diagnostic utility of the AmpC β-lactamase inhibitors LN-2-128, 48-1220, and Syn 2190 in combination with cefotetan (CTT) or cefoxitin in a disk test for the detection of clinical isolates of
Klebsiella
spp. producing plasmid-mediated AmpC β-lactamases (pAmpCs) was evaluated. The combination of Syn 2190 and CTT had a sensitivity of 91%, a specificity of 100%, and a reproducibility of 100% and showed the best potential of using an inhibitor for detection of
Klebsiella
spp. producing pAmpCs.
Reduced Rate of Diagnostic Positive Detection of JC Virus DNA in Cerebrospinal Fluid in Cases of Suspected Progressive Multifocal Leukoencephalopathy in the Era of Potent Antiretroviral Therapy
Authors: Marzocchetti Angela , Di Giambenedetto Simona , Cingolani Antonella , Ammassari Adriana , Cauda Roberto , De Luca Andrea 
Published: August 2005

ABSTRACT
Fifty-nine human immunodeficiency virus (HIV)-infected patients with suspected progressive multifocal leukoencephalopathy and 224 controls were tested for JC virus (JCV) DNA in cerebrospinal fluid by PCR. The diagnostic positive detection rate dropped from 89.5% (95% confidence intervals of 75.5 to 103.5%) in the pre-highly active antiretroviral therapy (HAART) era to 57.5% (95% confidence intervals of 42.1 to 72.9%) in the HAART era; the specificity remained unchanged. Predictors of failure to detect JCV DNA were exposure to HAART at disease onset and higher CD4 counts.
Partial Excision of the Chromosomal Cassette Containing the Methicillin Resistance Determinant Results in Methicillin-SusceptibleStaphylococcus aureus
Authors: Donnio Pierre-Yves , Oliveira Duarte C. , Faria Nuno A. , Wilhelm Nathalie , Le Coustumier Alain , de Lencastre Herminia 
Published: August 2005

ABSTRACTWe report a detailed characterization of methicillin-susceptibleStaphylococcus aureusisolates from five French hospitals negative for both themecAand theccrABloci but positive for the IS431::pUB110::IS431::dcsstructure, present in someStaphylococcuscassette chromosomemec(SCCmec) types. The presence of SCCmec-associated elements suggests that this unusual resistant phenotype is due to a partial excision of SCCmecfrom epidemic methicillin-resistantS. aureus. The hypothesis of a genetic relatedness is strengthened by common sequence andspatypes and similar susceptibility patterns.
Performance of a Rapid Immunochromatographic Screening Test for Detection of Antibodies to Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2: Experience at a Tertiary Care Hospital in South India
Authors: Vijayakumar Theophilus-Sunder , David Shoba , Selvaraj Kavitha , Viswanathan Thiruppavai , Kannangai Rajesh , Sridharan Gopalan 
Published: August 2005

ABSTRACT
The performance characteristics of a rapid immunochromatographic-screening test, SD Bioline HIV-1/2 3.0 (Standard Diagnostics Inc., Kyonggi-do, South Korea) on 23,754 sera and 30 plasma samples are reported. The sensitivity and specificity for the assay on serum samples are 100% and 99.4%, respectively. The assay detected antibodies in individuals infected with human immunodeficiency virus type 1 (HIV-1) genotypes A and C and HIV-2. This straightforward assay is a reliable diagnostic tool for screening HIV in resource-poor settings.
Use of the MGB Eclipse System and SmartCycler PCR for Differentiation of
Mycobacterium chelonae
and
M. abscessus
Authors: Cloud Joann L. , Hoggan Karen , Belousov Evgeniy , Cohen Samuel , Brown-Elliott Barbara A. , Mann Linda , Wilson Rebecca , Aldous Wade , Wallace Richard J. , Woods Gail L. 
Published: August 2005

ABSTRACT

Although accurate in the identification of
Mycobacterium
species, partial 16S rRNA gene sequencing does not distinguish
Mycobacterium chelonae
from
M. abscessus
. Thus, we designed a SmartCycler PCR assay targeting the 16S-to-23S internal transcribed spacer (ITS) region with use of MGB Eclipse probes to distinguish each species. Comparison with PCR-restriction enzyme analysis of a 441-bp fragment of the
hsp65
gene resulted in 100% correlation with 25 isolates of
M. chelonae
and 25 isolates of
M. abscessus
. ITS PCR performed on 90 consecutive isolates identified by partial 16S rRNA gene sequencing (26 isolates of the
M. chelonae
-
M. abscessus
complex and 64 remaining isolates, including
Mycobacterium
species,
Nocardia
species, and other aerobic actinomycetes) showed 100% specificity and sensitivity. The ITS PCR assay is accurate and specific, easy to perform, and a good supplemental test when using partial 16S rRNA gene sequencing to identify
M. chelonae
and
M. abscessus
.
Variation of the Conserved Neutralizing Epitope in Influenza B Virus Victoria Group Isolates in Japan
Authors: Nakagawa Naoko , Kubota Ritsuko , Okuno Yoshinobu 
Published: August 2005

ABSTRACT
For almost 20 years, the neutralizing-epitope site specific for influenza B virus Victoria group isolates was conserved at the “tip” of the hemagglutinin molecule; however, it was not detected in half of the isolates from the 2002-2003 epidemic in Japan. Amino acid substitutions (D164E or N165K) were observed at the “tip,” and the epitope was altered. The viral antigenicities were affected, and human antibodies did not substantially inhibit the hemagglutination in the hemagglutination inhibition tests. It is suspected that such variants will be important in future epidemics.
Decreased Prevalence of Virulence Factors among Ciprofloxacin-Resistant Uropathogenic
Escherichia coli
Isolates
Authors: Drews S. J. , Poutanen S. M. , Mazzulli T. , McGeer A. J. , Sarabia A. , Pong-Porter S. , Rzayev Y. , Willey B. , Green K. , Low D. E. 
Published: August 2005

ABSTRACT

Ciprofloxacin resistance was identified in 18% and 6% of consecutively collected, clinically significant urinary tract isolates of
Escherichia coli
from inpatients and outpatients, respectively. In comparison to ciprofloxacin-susceptible isolates, there were fewer resistant isolates that expressed beta-hemolysis (outpatient, 9% versus 87%,
P
< 0.0001; inpatient, 4% versus 76%,
P
< 0.0001) and that had a
papEF
genotype, genes encoding P fimbriae (outpatient, 30% versus 70%,
P
= 0.0004; inpatient, 26% versus 70%,
P
< 0.0001).
Genetic Diversity of
Campylobacter
sp. Isolates from Retail Chicken Products and Humans with Gastroenteritis in Central Michigan
Authors: Fitch Brooke R. , Sachen Kacey L. , Wilder Stacey R. , Burg Matthew A. , Lacher David W. , Khalife Walid T. , Whittam Thomas S. , Young Vincent B. 
Published: August 2005

ABSTRACT

Multilocus sequencing was used to compare
Campylobacter
sp. strains isolated from retail chicken products and humans with gastroenteritis in central Michigan. Sequence comparisons demonstrated overlapping diversity between chicken and human isolates.
Campylobacter jejuni
isolates from clinical sources had a greater diversity of flagellin alleles and a higher rate of quinolone resistance than isolates from retail chicken products.
Molecular Profiling and Phenotype Analysis of
Escherichia coli
O26:H11 and O26:NM: Secular and Geographic Consistency of Enterohemorrhagic and Enteropathogenic Isolates
Authors: Bielaszewska Martina , Zhang Wenlan , Tarr Phillip I. , Sonntag Anne-Katharina , Karch Helge 
Published: August 2005

ABSTRACT

Fifty-eight enterohemorrhagic
Escherichia coli
O26:H11 or O26:NM (nonmotile) strains and 44 atypical enteropathogenic
E. coli
O26:H11 or O26:NM strains isolated from patients in 11 countries during 52 years share a common pool of non-
stx
virulence genes, fitness loci, and genotypic and phenotypic diagnostic markers. These findings indicate close relatedness between these pathotypes and provide a basis for their clinical laboratory diagnosis.
Monoclonal Antibody Routinely Used To Identify Avirulent Strains of Newcastle Disease Virus Binds to an Epitope at the Carboxy Terminus of the Hemagglutinin-Neuraminidase Protein and Recognizes Individual Mesogenic and Velogenic Strains
Authors: Alamares Judith G. , Li Jianrong , Iorio Ronald M. 
Published: August 2005

ABSTRACTNewcastle disease virus (NDV) strains are classified as having high (velogenic), intermediate (mesogenic), or low (lentogenic) pathogenesis and virulence in chickens. Recent studies have established that the hemagglutinin-neuraminidase (HN) protein plays an important role in viral tropism and virulence. A monoclonal antibody (AVS-I) has previously been shown to be specific for lentogenic strains of NDV (Srinivasappa et al., Avian Dis.30:562-567, 1986) and is routinely used to identify these strains. We have used competition antibody binding assays with a previously characterized panel of monoclonal antibodies, binding to chimeric HN proteins, and the characterization of an escape mutant to localize the binding site of AVS-I to the extreme carboxy terminus of the protein. In addition, we have shown that AVS-I does recognize at least one mesogenic strain and one velogenic strain of the virus, calling into question the potential of this antibody as a diagnostic reagent for avirulent NDV strains.
Evaluation of Two New Chromogenic Media, CHROMagar MRSA and S. aureus ID, for Identifying
Staphylococcus aureus
and Screening Methicillin-Resistant
S. aureus
Authors: Hedin Göran , Fang Hong 
Published: August 2005

ABSTRACT

Thirty-nine methicillin-resistant
Staphylococcus aureus
(MRSA) isolates with diverse genetic backgrounds and two reference strains were correctly identified as
S. aureus
on CHROMagar MRSA and S. aureus ID media. Growth inhibition on CHROMagar MRSA was noted. A combination of cefoxitin disk and S. aureus ID was found suitable for rapid MRSA screening.
Stability of Human Immunodeficiency Virus Type 1 Proviral DNA in Whole-Blood Samples
Authors: Jennings Cheryl , Danilovic Aleksandra , Scianna Salvatore , Brambilla Donald J. , Bremer James W. 
Published: August 2005

ABSTRACT
The Roche Amplicor HIV-1 Test requires that whole blood be processed within four days of collection. However, this requirement may be too limiting for use in international settings. Thus, we demonstrate that blood may be processed up to 10 days after collection if maintained under ambient conditions (2 to 25°C).
Dynamic Range and Reproducibility of Hepatitis B Virus (HBV) DNA Detection and Quantification by Cobas Taqman HBV, a Real-Time Semiautomated Assay
Authors: Lindh Magnus , Hannoun Charles 
Published: August 2005

ABSTRACT

The Cobas Taqman assay for hepatitis B virus (HBV) DNA showed linear detection over 7 logs for genotypes A to D. The coefficient of variation was 1.2% at ≥1,000 IU/ml and 22.0% at 10 IU/ml. In 97 clinical samples, the log HBV DNA/ml differed by 0.11 between Cobas Amplicor and Cobas Taqman (
r
2
= 0.97).
Performance of Single-Step Gel-Based Reverse Transcription-PCR (RT-PCR) Assays Equivalent to That of Real-Time RT-PCR Assays for Detection of the Severe Acute Respiratory Syndrome-Associated Coronavirus
Authors: Inoue Masafumi , Barkham Timothy , Keong Lee Kok , Gee Lim Seng , Wanjin Hong 
Published: August 2005

ABSTRACT
Simple gel-based one-step reverse transcription-PCR (RT-PCR) assays, used to investigate patients during the 2003 severe acute respiratory syndrome (SARS) outbreak in Singapore, were found to be as sensitive as commercial and in-house real-time RT-PCR assays. The detection limit was approximately 1 genome equivalent (GE) per 5 μl PCR mixture. One PFU of SARS coronavirus was estimated to be 258 ± 46 GE.
Phenotypic and Genotypic Mupirocin Resistance among Staphylococci Causing Prosthetic Joint Infection
Authors: Rotger Margalida , Trampuz Andrej , Piper Kerryl E. , Steckelberg James M. , Patel Robin 
Published: August 2005

ABSTRACT

Mupirocin MICs and
mupA
presence were determined in 108 staphylococci causing prosthetic joint infection. Zero of 35 isolates (0%) of methicillin-susceptible
Staphylococcus aureus
, 4/15 (27%) methicillin-resistant
S. aureus
isolates, 3/16 (19%) methicillin-susceptible coagulase-negative staphylococci, and 11/42 (26%) methicillin-resistant coagulase-negative staphylococci were mupirocin resistant.
mupA
was detected in all five high-level mupirocin-resistant staphylococci and one mupirocin-susceptible staphylococcus.
Clindamycin-Resistant
Fusobacterium varium
Bacteremia and Decubitus Ulcer Infection
Authors: Legaria M. C. , Lumelsky G. , Rodriguez V. , Rosetti S. 
Published: August 2005

ABSTRACT

Bacteremia due to
Fusobacterium
spp. is unusual (<10% of cases of anaerobic bacteremia), and the isolation of
Fusobacterium varium
is especially uncommon. The most probable sources of
Fusobacterium
bacteremia are the respiratory, the gastrointestinal, and the genitourinary tracts. A.-M. Bourgault et al. (Clin. Infect. Dis. 25[Suppl. 2]:181-183) described 40 patients with
Fusobacterium
bacteremia; only 3 had
Fusobacterium varium
, and no one had decubitus scars as the portal of entry. In another published series (S. Henry, A. De Maria, and W. R. McCabe, Am. J. Med. 75:225-231, 1983) of 26 cases, two patients had concomitant pulmonary lesions and decubitus ulcers but there was no identification to the species level mentioned. We report a case of
Fusobacterium varium
bacteremia and infected sacral decubitus ulcer in an elderly patient.
Unintentional injury depictions in popular children’s television programs
Authors: Glik D , Kinsler J , Todd W A , Clarke L , Fazio K , Miyashiro R , Perez M , Vielmetter E , Flores R C 
Published: August 2005

Objectives:The frequency and magnitude of depictions of risky events and unintentional injuries in top ranked children’s animated and live action television programs was assessed.Methods:Qualitative and quantitative media content analysis were used. Scenes from television episodes were examined for the depiction of risky events and unintentional injuries.Results:A total of 201 actual and potential injury related events were tabulated in 99 episodes aired in 2003 and 2004. Only 26% of the risky events depicted led to an injury or physical consequence. More than 80% of the events involved behavioral or environmental risk factors. Safety factors were not present in over 90% of risky events depicted. The general tone and context of events was humor or indifference rather than concern or action, with little or no relevance to the plot.Conclusion:Unintentional injuries are the leading cause of death and disability for children, yet animated and live action television programs marketed to children continue to portray injury risk inaccurately. Working with the children’s television production industry to improve injury depiction is a much needed advocacy activity.