bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison between O Serotyping Method and Multiplex Real-Time PCR To Identify DiarrheagenicEscherichia coliin Taiwan
Authors: Yang Ji-Rong , Wu Fang-Tzy , Tsai Jin-Lai , Mu Jung-Jung , Lin Ling-Fen , Chen Kuang-Lo , Kuo Steve Hsu-Sung , Chiang Chuen-Sheue , Wu Ho-Sheng 
Published: August 2007

ABSTRACTTo compare the diarrheagenicEscherichia coli(DEC) identifications obtained between traditional O serotyping and modern virulence gene detection assays, we developed a multiplex real-time PCR assay by detecting six specific virulence genes for enteropathogenicE. coli(EPEC), enterohemorrhagicE. coli(EHEC), enterotoxigenicE. coli(ETEC), and enteroinvasiveE. coli(EIEC). Among 261 clinical diarrheal stool samples, a total of 137 suspected DEC (sDEC) isolates were identified by the use of commercially available antisera. The most prevalent serogroups were O1 (12/137; 8.7%), O25 (9/137; 6.5%), and O44 (9/137; 6.5%). The specific virulence genes for the 137 sDEC isolates were analyzed by the multiplex real-time PCR assay. Fifteen (10.9%) of 137 isolates were confirmed to be true DEC strains, indicating that the serotypic markers did not correlate with the specific virulence genes. ETEC (66.7%) was the most prevalent, followed by EIEC (20%) and EPEC (13.3%). No EHEC strains were identified in the specimens. Four novel serotypes were found in the study: two in EPEC strains (O111:H9 and O63:H6) and two in EIEC strains (O63:H9 and O169:H9). In conclusion, the real-time PCR assay considerably reduces the high false-positive rate from the use of serotyping alone, and thus, it is suggested that serogrouping-based methods are inadequate for the identification of DEC isolates, although they are useful for the identification of a limited number of serogroups. In addition, ETEC, EPEC, and EIEC strains were present in 5.7% (15/261) of the diarrheal patients in northern Taiwan in 2006.
Single-Nucleotide-Polymorphism Typing and Genetic Relationships of
Salmonella enterica
Serovar Typhi Isolates
Authors: Octavia Sophie , Lan Ruiting 
Published: August 2007

ABSTRACT

Salmonella enterica
serovar Typhi is a clone with a low level of variation. We developed a molecular typing method for serovar Typhi using 38 genome-wide single-nucleotide polymorphisms (SNPs) as markers detected by PCR-restriction enzyme digestion. The 73 worldwide serovar Typhi isolates studied were separated into 23 SNP profiles and four distinct genetic groups. Serovar Typhi isolates expressing the unique flagellar antigen z66 were found to cluster together and branch off from the ancestral group, suggesting that serovar Typhi was initially monophasic with only an H1 antigen and subsequently gained the z66 antigen. Typing using the 38 SNPs gave a discriminatory power of 0.87, and a minimum of 16 SNPs may be used to achieve the same level of differentiation. The SNP typing method we developed will be a valuable tool for global epidemiology studies of serovar Typhi.
Clonal Expansion and Microevolution of Quinolone-Resistant
Salmonella enterica
Serotype Typhi in Vietnam from 1996 to 2004
Authors: Le Thi Anh Hong , Fabre Laëtitia , Roumagnac Philippe , Grimont Patrick A. D. , Scavizzi Maurice R. , Weill François-Xavier 
Published: August 2007

ABSTRACT

Salmonella enterica
serotype Typhi clinical isolates (
n
= 91) resistant to nalidixic acid (Nal
r
) were collected from sporadic cases and minor outbreaks throughout Vietnam between 1996 and 2004. These isolates were typed and compared by four methods: Vi phage typing, PstI ribotyping, XbaI and SpeI pulsed-field gel electrophoresis (PFGE), and single-nucleotide polymorphism (SNP) analysis. The results indicated that 65% of the isolates were not typeable by Vi phage typing. In contrast, the ribotyping and, with more accuracy, the SNP analysis methods indicated that all Nal
r
isolates belonged to a single clone (ribotype 3a, haplotype H58) that was found previously and that largely consisted of plasmid-encoded multidrug-resistant serotype Typhi isolates. PFGE demonstrated the occurrence of microevolution within this clone. We identified two major combined PFGE profiles: X1-S1 and X3-S6. X3-S6 predominated between 1996 and 2002 but was replaced by X1-S1 after 2002. Nevertheless, PFGE, with a Simpson's index of 0.78, was not considered an optimal discriminatory method for investigating typhoid fever outbreaks in Vietnam. The rate of quinolone resistance increased and the rate of multidrug resistance decreased during the study period. From 2002 to 2004, 80.6% of the isolates from South Vietnam were resistant only to Nal. The mechanism of Nal resistance in most of the isolates (94%) was a mutation in the quinolone resistance-determining chromosomal region of
gyrA
that led to the amino acid substitution Ser83Phe. No plasmid-located
qnrA
,
qnrB
, or
qnrS
was detected.
Narrow-Spectrum Cephalosporin Susceptibility Testing of
Escherichia coli
with the BD Phoenix Automated System: Questionable Utility of Cephalothin as a Predictor of Cephalexin Susceptibility
Authors: Zhang Sean X. , Parisian Fern , Yau Yvonne , Fuller Jeffrey D. , Poutanen Susan M. , Richardson Susan E. 
Published: August 2007

ABSTRACT

The resistance of
Escherichia coli
to cephalothin was found to be overestimated when the Phoenix automated susceptibility system was used to determine resistance compared to reference broth microdilution, a finding that jeopardized the use of cephalexin for first-line treatment of urinary tract infections in children. In addition, using broth microdilution, we studied the accuracy of either cephalothin or cefazolin in predicting cephalexin susceptibility. In contrast to the recommendation of the Clinical Laboratory Standards Institute (CLSI), we found that cephalothin is not a reliable predictor of cephalexin susceptibility. Cefazolin performs no better in this role. We suggest that laboratories should consider testing and reporting cefazolin and cephalexin independently, according to clinical need.
Performance of a Pneumolysin Enzyme-Linked Immunosorbent Assay for Diagnosis of Pneumococcal Infections
Authors: del Mar García-Suárez María , Cima-Cabal María Dolores , Villaverde Roberto , Espinosa Emma , Falguera Miquel , de Los Toyos Juan R. , Vázquez Fernando , Méndez Francisco J. 
Published: August 2007

ABSTRACT

A pneumolysin-specific enzyme-linked immunosorbent assay (PLY-ELISA) for the detection of pneumolysin in urine was developed and evaluated in comparison with the commercially available Binax Now
Streptococcus pneumoniae
test (Binax, Portland, ME) for the diagnosis of pneumococcal infections. Assay sensitivity was evaluated using urine from 108 patients with culture-confirmed pneumococcal infections. In adults, the sensitivity and specificity of the PLY-ELISA were 56.6% and 92.2%, respectively. In children with nasopharyngeal pneumococcal carriage, PLY-ELISA and Binax Now
S. pneumoniae
test sensitivities were 62.5% and 87.5%, respectively, while specificities were 94.4% and 27.8%, respectively. In children with nonnasopharyngeal pneumococcal carriage, PLY-ELISA and Binax Now
S. pneumoniae
test sensitivities were 68.7% and 93.7%, respectively, and test specificities were 94.1% and 41.2%, respectively. The persistence of pneumolysin in urine of pneumococcal pneumonia patients decreased significantly after 4 to 6 days of treatment. Our data suggest that combining the high specificity of the PLY-ELISA with the high sensitivity of the Binax Now
S. pneumoniae
test would enable pneumococcal infections to be accurately diagnosed in children.
First Detection of G12 Rotaviruses in Newborns with Neonatal Rotavirus Infection at All India Institute of Medical Sciences, New Delhi, India
Authors: Ray Pratima , Sharma S. , Agarwal R. K. , Longmei K. , Gentsch J. R. , Paul V. K. , Glass R. I. , Bhan M. K. 
Published: August 2007

ABSTRACT
Rotavirus genotype G12 strains were detected for the first time among newborns with asymptomatic rotavirus infection (74% of 39 rotavirus strains isolated from the infected infants were genotype G12) in the nursery of the All India Institute of Medical Sciences during a period from 2005 to 2006. Sequence analysis of the VP7 genes from these neonatal strains indicated a high level of homology to other G12 strains reported worldwide, suggesting the recent emergence of these strains in humans. Such nosocomial infections of newborns represent a potential source of introduction of novel rotavirus serotypes into the community.
Inhibition of Foot-and-Mouth Disease Virus Infections in Cell Cultures with Antisense Morpholino Oligomers
Authors: Vagnozzi Ariel , Stein David A. , Iversen Patrick L. , Rieder Elizabeth 
Published: August 2007

ABSTRACT

Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed ungulates that can lead to severe losses in the livestock production and export industries. Although vaccines have been extensively used to control FMD, there is no antiviral therapy available to treat ongoing infections with FMD virus (FMDV). Six peptide-conjugated morpholino oligomers (PPMOs) with sequences complementary to various 21-nucleotide segments of the 5′ and 3′ untranslated regions (UTRs) of the FMDV genome (strain A
24
Cruzeiro/Brazil/1955 [A
24
Cru]) were evaluated in cell cultures. Three of the PPMOs, targeting domain 5 of the internal ribosome entry site (5D PPMO), and the two translation start codon regions (AUG1 and AUG2 PPMOs), showed high levels of anti-FMDV activity. A dose-dependent and sequence-specific reduction in viral titers of greater than 5 log
10
, with a concomitant reduction of viral protein and RNA expression, was achieved at low micromolar concentrations. Under identical conditions, three other PPMOs targeting the 5′-terminal region of the genome, the
cis
-acting replication element in the 5′ UTR, and the 3′ “ab” stem-loop showed less dramatic titer reductions of 1.5 log
10
to 2 log
10
. Treatment with 5D PPMO reduced the titers of FMDV strains representing five different serotypes by 2 log
10
to 4 log
10
compared to those of the controls. A
24
Cru-infected BHK-21 cells treated repeatedly with 5D or AUG2 PPMO generated resistant viruses for which phenotypic and genotypic properties were defined. Notably, three passages with low concentrations of the AUG1 PPMO extinguished all traces of detectable virus. The results indicate that PPMOs have potential for treating FMDV infections and that they also represent useful tools for studying picornaviral translation and evolution.
Identification of an Arsenic-Sensitive Block to Primate Lentiviral Infection of Human Dendritic Cells
Authors: Pion Marjorie , Stalder Romaine , Correa Rafael , Mangeat Bastien , Towers Greg J. , Piguet Vincent 
Published: August 2007

ABSTRACT

Dendritic cells are central to the early events of human immunodeficiency virus type 1 (HIV-1) transmission, but HIV-1 infects dendritic cells inefficiently in vitro compared to activated CD4
+
T cells. There is a strong postentry restriction of HIV-1 infection in dendritic cells, partly mediated by the cellular restriction factor APOBEC3G. Here, we reveal that arsenic trioxide markedly increases HIV infection of immature and mature dendritic cells as well as blood-derived myeloid dendritic cells in an APOBEC3G- and TRIM5α-independent way. Our data suggest the presence of powerful, arsenic-sensitive antiviral activities in primary human immune cells of the dendritic cell lineage.
Characterization of Hepatitis C Virus Deletion Mutants Circulating in Chronically Infected Patients
Authors: Noppornpanth Suwanna , Smits Saskia L. , Lien Truong Xuan , Poovorawan Yong , Osterhaus Albert D. M. E. , Haagmans Bart L. 
Published: August 2007

ABSTRACTHepatitis C virus (HCV) has a linear positive-stranded RNA genome of ∼9,600 nucleotides in length and displays a high level of sequence diversity caused by high mutation rates and recombination. However, when we performed long distance reverse transcription-PCRs on HCV RNA isolated from serum of chronic HCV patients, not only full-length HCV genomes but also HCV RNAs which varied in size from 7,600 to 8,346 nucleotides and contained large in-frame deletions between E1 and NS2 were amplified. Carefully designed control experiments indicated that these deletion mutants are a bona fide natural RNA species, most likely packaged in virions. Moreover, deletion mutants were detected in sera of patients infected with different HCV genotypes. We observed that 7/37 (18.9%) of genotype 1, 5/43 (11.6%) of genotype 3, and 4/13 (30.7%) of genotype 6 samples contained HCV deletion mutant genomes. These observations further exemplify HCV's huge genetic diversity and warrant studies to explore their biological relevance.
Recovery of
Nicotiana benthamiana
Plants from a Necrotic Response Induced by a Nepovirus Is Associated with RNA Silencing but Not with Reduced Virus Titer
Authors: Jovel Juan , Walker Melanie , Sanfaçon Hélène 
Published: August 2007

ABSTRACT

Recovery of plants from virus-induced symptoms is often described as a consequence of RNA silencing, an antiviral defense mechanism. For example, recovery of
Nicotiana clevelandii
from a nepovirus (tomato black ring virus) is associated with a decreased viral RNA concentration and sequence-specific resistance to further virus infection. In this study, we have characterized the interaction of another nepovirus, tomato ringspot virus (ToRSV), with host defense responses during symptom induction and subsequent recovery. Early in infection, ToRSV induced a necrotic phenotype in
Nicotiana benthamiana
that showed characteristics typical of a hypersensitive response. RNA silencing was also activated during ToRSV infection, as evidenced by the presence of ToRSV-derived small interfering RNAs (siRNAs) that could direct degradation of ToRSV sequences introduced into sensor constructs. Surprisingly, disappearance of symptoms was not accompanied by a commensurate reduction in viral RNA levels. The stability of ToRSV RNA after recovery was also observed in
N. clevelandii
and
Cucumis sativus
and in
N. benthamiana
plants carrying a functional RNA-dependent RNA polymerase 1 ortholog from
Medicago truncatula
. In experiments with a reporter transgene (green fluorescent protein), ToRSV did not suppress the initiation or maintenance of transgene silencing, although the movement of the silencing signal was partially hindered. Our results demonstrate that although RNA silencing is active during recovery, reduction of virus titer is not required for the initiation of this phenotype. This scenario adds an unforeseen layer of complexity to the interaction of nepoviruses with the host RNA silencing machinery. The possibility that viral proteins, viral RNAs, and/or virus-derived siRNAs inactivate host defense responses is discussed.
Human Immunodeficiency Virus Type 1 Controllers but Not Noncontrollers Maintain CD4 T Cells Coexpressing Three Cytokines
Authors: Kannanganat Sunil , Kapogiannis Bill G. , Ibegbu Chris , Chennareddi Lakshmi , Goepfert Paul , Robinson Harriet L. , Lennox Jeffrey , Amara Rama Rao 
Published: August 2007

ABSTRACTHere, we evaluate the cytokine coexpression profiles of human immunodeficiency virus (HIV)-specific CD4 T cells for the expression of the cytokines gamma interferon (IFN-γ), interleukin-2, and tumor necrosis factor alpha. In controllers, CD4 T cells producing three or two cytokines (triple producers and double producers, respectively) represented >50% of the total response. In contrast, in noncontrollers ∼75% of responding cells produced only one cytokine (single producers), mostly IFN-γ. Cells producing three cytokines were functionally superior to those producing single cytokines and showed an inverse correlation (P< 0.001) with viral load. These results demonstrate a strong association between the maintenance of highly functional CD4 T cells producing three cytokines and control of HIV-1.
Structure of Adeno-Associated Virus Serotype 8, a Gene Therapy Vector
Authors: Nam Hyun-Joo , Lane Michael Douglas , Padron Eric , Gurda Brittney , McKenna Robert , Kohlbrenner Erik , Aslanidi George , Byrne Barry , Muzyczka Nicholas , Zolotukhin Sergei , Agbandje-McKenna Mavis 
Published: August 2007

ABSTRACT
Adeno-associated viruses (AAVs) are being developed as gene therapy vectors, and their efficacy could be improved by a detailed understanding of their viral capsid structures. AAV serotype 8 (AAV8) shows a significantly greater liver transduction efficiency than those of other serotypes, which has resulted in efforts to develop this virus as a gene therapy vector for hemophilia A and familial hypercholesterolemia. Pseudotyping studies show that the differential tissue tropism and transduction efficiencies exhibited by the AAVs result from differences in their capsid viral protein (VP) amino acids. Towards identifying the structural features underpinning these disparities, we report the crystal structure of the AAV8 viral capsid determined to 2.6-Å resolution. The overall topology of its common overlapping VP is similar to that previously reported for the crystal structures of AAV2 and AAV4, with an eight-stranded β-barrel and long loops between the β-strands. The most significant structural differences between AAV8 and AAV2 (the best-characterized serotype) are located on the capsid surface at protrusions surrounding the two-, three-, and fivefold axes at residues reported to control transduction efficiency and antibody recognition for AAV2. In addition, a comparison of the AAV8 and AAV2 capsid surface amino acids showed a reduced distribution of basic charge for AAV8 at the mapped AAV2 heparin sulfate receptor binding region, consistent with an observed non-heparin-binding phenotype for AAV8. Thus, this AAV8 structure provides an additional platform for mutagenesis efforts to characterize AAV capsid regions responsible for differential cellular tropism, transduction, and antigenicity for these promising gene therapy vectors.
The Level of Friend Retrovirus Replication Determines the Cytolytic Pathway of CD8+T-Cell-Mediated Pathogen Control
Authors: Zelinskyy Gennadiy , Balkow Sandra , Schimmer Simone , Werner Tanja , Simon Markus M. , Dittmer Ulf 
Published: August 2007

ABSTRACTCytotoxic T cells (CTL) play a central role in the control of viral infections. Their antiviral activity can be mediated by at least two cytotoxic pathways, namely, the granule exocytosis pathway, involving perforin and granzymes, and the Fas-FasL pathway. However, the viral factor(s) that influences the selection of one or the other pathway for pathogen control is elusive. Here we investigate the role of viral replication levels in the induction and activation of CTL, including their effector potential, during acute Friend murine leukemia virus (F-MuLV) infection. F-MuLV inoculation results in a low-level infection of adult C57BL/6 mice that is enhanced about 500-fold upon coinfection with the spleen focus-forming virus (SFFV). Both the low- and high-level F-MuLV infections generated CD8+effector T cells that were essential for the control of viral replication. However, the low-level infection induced CD8+T cells expressing solely FasL but not the cytotoxic molecules granzymes A and B, whereas the high-level infection resulted in induction of CD8+effector T cells secreting molecules of the granule exocytosis pathway. By using knockout mouse strains deficient in one or the other cytotoxic pathway, we found that low-level viral replication was controlled by CTL that expressed FasL but control of high-level viral replication required perforin and granzymes. Additional studies, in which F-MuLV replication was enhanced experimentally in the absence of SFFV coinfection, supported the notion that only the replication level of F-MuLV was the critical factor that determined the differential expression of cytotoxic molecules by CD8+T cells and the pathway of CTL cytotoxicity.
Rapid identification ofCandidaspecies in oral rinse solutions by PCR
Authors: Liguori Giorgio , Lucariello Angela , Colella Giuseppe , De Luca Antonio , Marinelli Paolo 
Published: August 2007

Aims:To determine the sensitivity and specificity of a multiplex PCR assay for the contemporary identification of major species involved in oral candidiasis, without extraction and purification of DNA from the samples under investigation; and evaluation of this method in comparison with routine phenotypic culture identification.Methods:78 oral rinse solutions were collected. The concentrated oral rinse technique was used for a quantitative and qualitative study. Research and identification ofCandidaspp, with routine phenotypic culture identification (germ-tube test in serum at 37°C for 3 hours and sugar assimilation strip analysis), were performed. Each sample was analysed with multiplex PCR directly on oral rinse solution. Samples giving discrepant results between routine phenotypic and PCR identification methods were resubcultured on CHROMagar Candida plates. The fungus-specific primers ITS1, ITS2, CA3, and CA4 were used. For the identification of other species (C kefyr,C famataandC dubliniensis), ITS1F, ITS1K, and ITS2D primers were designed.Results:Multiplex PCR correctly identified all samples, including those with single species, or with mixed species, negative samples and positive samples which appeared to be negative from routine phenotypic methods.Conclusion:This multiplex PCR assay provides a rapid alternative to the conventional culture based technique for the identification and speciation of the most frequently isolatedCandidaspecies. The absence of an extraction method made identification of 10 species possible in a few hours.
Implications of method specific creatinine adjustments on General Medical Services chronic kidney disease classification
Authors: Reynolds Timothy M , Twomey Patrick J 
Published: August 2007

Aims:To evaluate the impact of different equations for calculation of estimated glomerular filtration rate (eGFR) on general practitioner (GP) workload.Methods:Retrospective evaluation of routine workload data from a district general hospital chemical pathology laboratory serving a GP patient population of approximately 250 000. The most recent serum creatinine result from 80 583 patients was identified and used for the evaluation. eGFR was calculated using one of three different variants of the four-parameter Modification of Diet in Renal Disease (MDRD) equation.Results:The original MDRD equation (eGFR186) and the modified equation with assay-specific data (eGFR175corrected) both identified similar numbers of patients with stage 4 and stage 5 chronic kidney disease (ChKD), but the modified equation without assay specific data (eGFR175) resulted in a significant increase in stage 4 ChKD. For stage 3 ChKD the eGFR175identified 28.69% of the population, the eGFR186identified 21.35% of the population and the eGFR175correctedidentified 13.6% of the population.Conclusions:Depending on the choice of equation there can be very large changes in the proportions of patients identified with the different stages of ChKD. Given that according to the General Medical Services Quality Framework, all patients with ChKD stages 3–5 should be included on a practice renal registry, and receive relevant drug therapy, this could have significant impacts on practice workload and drug budgets. It is essential that practices work with their local laboratories.