bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of New Vitek 2 Card and Disk Diffusion Method for Determining Susceptibility of
Staphylococcus aureus
to Oxacillin
Authors: Roisin Sandrine , Nonhoff Claire , Denis Olivier , Struelens Marc J. 
Published: June 2008

ABSTRACT

Detection of methicillin resistance in
Staphylococcus aureus
is a challenge, especially low-level resistance, which is often misdiagnosed. The aim of this study was to compare the diagnostic accuracies of the automated Vitek 2 system and disk diffusion tests, using cefoxitin and moxalactam, for the detection of methicillin resistance in
S. aureus
strains. Four sets of genotypically diverse isolates were selected from a national reference collection, including
mecA
-negative
S. aureus
isolates (
n
= 56), hospital-acquired (
n
= 88) and community-acquired (
n
= 40)
S. aureus
isolates, and heterogeneous methicillin-resistant
S. aureus
isolates (
n
= 29). Oxacillin susceptibility was tested by the Vitek 2 system with the AST P549 card and by disk diffusion methods using 10, 30, and 60 μg cefoxitin and 30 μg moxalactam. Oxacillin resistance was confirmed by PCR for the
mecA
gene. The overall sensitivities for oxacillin resistance detection were 97.5% for the Vitek 2 automated system, 98.7% for 60-μg cefoxitin and moxalactam disk diffusion, and 99.6% for 10- and 30-μg cefoxitin disks, respectively. Methicillin-susceptible
S. aureus
isolates were correctly reported as susceptible by all methods. The median times for methicillin testing were 7 h for the Vitek 2 system versus 24 h for disk diffusion methods. In conclusion, the cefoxitin and moxalactam disk diffusion methods and the Vitek 2 automated system are highly accurate methods for methicillin resistance detection, including a range of representative Belgian methicillin-resistant
S. aureus
strains and unusual strains exhibiting cryptic or low-level oxacillin resistance.
Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification ofMycobacterium tuberculosisComplex Isolates
Authors: Allix-Béguec Caroline , Harmsen Dag , Weniger Thomas , Supply Philip , Niemann Stefan 
Published: June 2008

ABSTRACTBecause of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing has become a major method for the epidemiological tracking ofMycobacterium tuberculosiscomplex (MTBC) clones. However, no public MIRU-VNTR database based on well-characterized reference strains has been available hitherto for easy strain identification. Therefore, a collection of 186 reference strains representing the primary MTBC lineages was used to build a database, which is freely accessible athttp://www.MIRU-VNTRplus.org. The geographical origin and the drug susceptibility profile of each strain were stored together with comprehensive genetic lineage information, including the 24-locus MIRU-VNTR profile, the spoligotyping pattern, the single-nucleotide- and large-sequence-polymorphism profiles, and the IS6110restriction fragment length polymorphism fingerprint. Thanks to flexible import functions, a single or multiple user strains can be analyzed, e.g., for lineage identification with or without the use of reference strains, by best-match or tree-based analyses with single or combined marker data sets. The results can easily be exported. In the present study, we evaluated the database consistency and various analysis parameters both by testing the reference collection against itself and by using an external population-based data set comprising 629 different strains. Under the optimal conditions found, lineage predictions based on typing by 24-locus MIRU-VNTR analysis optionally combined with spoligotyping were verified in >99% of the cases. On the basis of this evaluation, a user strategy was defined, which consisted of best-match analysis followed, if necessary, by tree-based analysis. The MIRU-VNTRplusdatabase is a powerful tool for high-resolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.
Comparison of Two Immunoassays for Detection of
Entamoeba histolytica
Authors: Buss Sarah , Kabir Mamun , Petri William A. , Haque Rashidul 
Published: June 2008

ABSTRACT

Effective diagnostic tools are essential in order to combat disease caused by the parasite
Entamoeba histolytica
. In this study, we compared the commercially available Ridascreen
Entamoeba
test (R-Biopharm) and the
E. histolytica
II test (Techlab), and we found that the
E. histolytica
II test detects
E. histolytica
infections more accurately.
Rifampin Resistance, Beijing-W Clade-Single Nucleotide Polymorphism Cluster Group 2 Phylogeny, and the Rv2629 191-C Allele inMycobacterium tuberculosisStrains
Authors: Chakravorty Soumitesh , Aladegbami Bola , Motiwala Alifiya S. , Dai Yang , Safi Hassan , Brimacombe Michael , Helb Danica , Alland David 
Published: June 2008

ABSTRACTRifampin resistance is a key prognostic marker for treatment success in tuberculosis patients. Recently, Wang et al. demonstrated that Rv2629 A191C mutations were present in 99.1% of rifampin-resistant and 0% of rifampin-susceptible clinicalMycobacterium tuberculosisisolates and that overexpression of the Rv2629 191C allele inMycobacterium smegmatisproduced an eightfold increase in rifampin resistance. These results suggested that Rv2629 could be a cause of rifampin resistance and a valuable target for rifampin resistance detection assays. We developed a molecular-beacon assay to study the association between Rv2629 191 alleles and rifampin resistance in 246 geographically and phylogenetically diverse clinicalM. tuberculosisisolates. The 191C allele was present in 30/98 (30.6%) rifampin-resistant isolates and 25/148 (16.9%) rifampin-susceptible isolates and was more common in isolates from Asia. Phylogenetic analysis demonstrated complete overlap between the 191C allele and single nucleotide polymorphism cluster group 2 (SCG-2), a phylogenetic lineage that corresponds to the Beijing-W clade ofM. tuberculosis. All 55 (100%) 191C isolates were SCG-2, while none of the 191 191A isolates were SCG-2 (P< 0.001). No association was found between the 191C allele and rifampin resistance in an analysis that included the SCG type (P= 1.0). Also, in contrast to the findings of Wang et al., we found that overexpression of either Rv2629 191 allele inM. smegmatisdid not produce an increase in rifampin resistance. We conclude that the Rv2629 191C allele is not associated with rifampin resistance and that the allele cannot be used as a molecular target to detect rifampin resistance. The allele appears to be an excellent marker for the Beijing-W clade/SCG-2 phylogenetic group.
Fourier Transform Infrared Spectroscopy for Rapid Identification of Nonfermenting Gram-Negative Bacteria Isolated from Sputum Samples from Cystic Fibrosis Patients
Authors: Bosch Alejandra , Miñán Alejandro , Vescina Cecilia , Degrossi José , Gatti Blanca , Montanaro Patricia , Messina Matías , Franco Mirta , Vay Carlos , Schmitt Juergen , Naumann Dieter , Yantorno Osvaldo 
Published: June 2008

ABSTRACT

The accurate and rapid identification of bacteria isolated from the respiratory tract of patients with cystic fibrosis (CF) is critical in epidemiological studies, during intrahospital outbreaks, for patient treatment, and for determination of therapeutic options. While the most common organisms isolated from sputum samples are
Pseudomonas aeruginosa, Staphylococcus aureus
, and
Haemophilus influenzae
, in recent decades an increasing fraction of CF patients has been colonized by other nonfermenting (NF) gram-negative rods, such as
Burkholderia cepacia
complex (BCC) bacteria,
Stenotrophomonas maltophilia, Ralstonia pickettii, Acinetobacter
spp., and
Achromobacter
spp. In the present study, we developed a novel strategy for the rapid identification of NF rods based on Fourier transform infrared spectroscopy (FTIR) in combination with artificial neural networks (ANNs). A total of 15 reference strains and 169 clinical isolates of NF gram-negative bacteria recovered from sputum samples from 150 CF patients were used in this study. The clinical isolates were identified according to the guidelines for clinical microbiology practices for respiratory tract specimens from CF patients; and particularly, BCC bacteria were further identified by
recA
-based PCR followed by restriction fragment length polymorphism analysis with HaeIII, and their identities were confirmed by
recA
species-specific PCR. In addition, some strains belonging to genera different from BCC were identified by 16S rRNA gene sequencing. A standardized experimental protocol was established, and an FTIR spectral database containing more than 2,000 infrared spectra was created. The ANN identification system consisted of two hierarchical levels. The top-level network allowed the identification of
P. aeruginosa, S. maltophilia, Achromobacter xylosoxidans, Acinetobacter
spp.,
R. pickettii
, and BCC bacteria with an identification success rate of 98.1%. The second-level network was developed to differentiate the four most clinically relevant species of BCC,
B. cepacia, B. multivorans, B. cenocepacia
, and
B. stabilis
(genomovars I to IV, respectively), with a correct identification rate of 93.8%. Our results demonstrate the high degree of reliability and strong potential of ANN-based FTIR spectrum analysis for the rapid identification of NF rods suitable for use in routine clinical microbiology laboratories.
Lewis Antigen Expression by
Helicobacter pylori
Strains Colonizing Different Regions of the Stomach of Individual Patients
Authors: González-Valencia Gerardo , Muñoz-Perez Leopoldo , Morales-Espinosa Rosario , Camorlinga-Ponce Margarita , Muñoz Onofre , Torres Javier 
Published: June 2008

ABSTRACT

The diversity in the expression of Lewis antigens (Le) of 226 single colonies of
Helicobacter pylori
isolated from four regions of the stomach of eight adults is shown. Le
y
was expressed more in strains colonizing antrum than in strains colonizing fundus, whereas Le
x
was more common in fundus strains.
cagA
+
strains were more associated with Le-negative strains.
Previously Infected Chimpanzees Are Not Consistently Protected against Reinfection or Persistent Infection after Reexposure to the Identical Hepatitis C Virus Strain
Authors: Bukh Jens , Thimme Robert , Meunier Jean-Christophe , Faulk Kristina , Spangenberg Hans Christian , Chang Kyong-Mi , Satterfield William , Chisari Francis V. , Purcell Robert H. 
Published: June 2008

ABSTRACT
Protective immunity after resolved hepatitis C virus (HCV) infection has been reported. However, the breadth of this immunity has remained controversial, and the role of neutralizing antibodies has not been well-defined. In the present study, two chimpanzees (CH96A008 and CH1494) with resolved monoclonal H77C (genotype 1a) infection were rechallenged with low-dose homologous H77C virus about 12 months after viral clearance; CH96A008 became persistently infected, and CH1494 had transient viremia lasting 2 weeks. CH1494 was subsequently either partially or completely protected following five homologous rechallenges with monoclonal H77C or polyclonal H77 and after six heterologous rechallenges with HC-J4 (genotype 1b) or HC-J6 (genotype 2a) viruses. Subsequently, a final challenge with H77C resulted in persistent HCV infection. In both chimpanzees, serum neutralizing antibodies against retroviral pseudoparticles bearing the H77C envelope proteins were not detected during the initial infection or during rechallenge. However, anamnestic cellular immune responses developed during the initial homologous rechallenge, in particular in CH96A008, which developed a persistent infection. Polyprotein sequences of viruses recovered from CH1494 after the two homologous rechallenges that resulted in transient viremia were identical with the H77C virus. In contrast, the polyprotein sequences of viruses recovered from both chimpanzees after homologous rechallenge resulting in persistent infection had numerous changes. These findings have important implications for our understanding of immunity against HCV; even in the best-case scenario with autologous rechallenge, low-level viral persistence was seen in the presence of primed T-cell responses.
Replication Properties of Clade A/C Chimeric Feline Immunodeficiency Viruses and Evaluation of Infection Kinetics in the Domestic Cat
Authors: de Rozìeres Sohela , Thompson Jesse , Sundstrom Magnus , Gruber Julia , Stump Debora S. , de Parseval Aymeric P. , VandeWoude Sue , Elder John H. 
Published: June 2008

ABSTRACT

Feline immunodeficiency virus (FIV) causes progressive immunodeficiency in domestic cats, with clinical course dependent on virus strain. For example, clade A FIV-PPR is predominantly neurotropic and causes a mild disease in the periphery, whereas clade C FIV-C36 causes fulminant disease with CD4
+
T-cell depletion and neutropenia but no significant pathology in the central nervous system. In order to map pathogenic determinants, chimeric viruses were prepared between FIV-C36 and FIV-PPR, with reciprocal exchanges involving (i) the 3′ halves of the viruses, including the Vif, OrfA, and Env genes; (ii) the 5′ end extending from the 5′ long terminal repeat (LTR) to the beginning of the capsid (CA)-coding region; and (iii) the 3′ LTR and Rev2-coding regions. Ex vivo replication rates and in vivo replication and pathologies were then assessed and compared to those of the parental viruses. The results show that FIV-C36 replicates ex vivo and in vivo to levels approximately 20-fold greater than those of FIV-PPR. None of the chimeric FIVs recapitulated the replication rate of FIV-C36, although most replicated to levels similar to those of FIV-PPR. The rates of chloramphenicol acetyltransferase gene transcription driven by the FIV-C36 and FIV-PPR LTRs were identical. Furthermore, the ratios of surface glycoprotein (SU) to capsid protein (CA) in the released particles were essentially the same in the wild-type and chimeric FIVs. Tests were performed in vivo on the wild-type FIVs and chimeras carrying the 3′ half of FIV-C36 or the 3′ LTR and Rev2 regions of FIV-C36 on the PPR background. Both chimeras were infectious in vivo, although replication levels were lower than for the parental viruses. The chimera carrying the 3′ half of FIV-C36 demonstrated an intermediate disease course with a delayed peak viral load but ultimately resulted in significant reductions in neutrophil and CD4
+
T cells, suggesting potential adaptation in vivo. Taken together, the findings suggest that the rapid-growth phenotype and pathogenicity of FIV-C36 are the result of evolutionary fine tuning throughout the viral genome, rather than being properties of any one constituent.
Structural Insights into Calicivirus Attachment and Uncoating
Authors: Bhella David , Gatherer Derek , Chaudhry Yasmin , Pink Rebecca , Goodfellow Ian G. 
Published: June 2008

ABSTRACT

The
Caliciviridae
family comprises positive-sense RNA viruses of medical and veterinary significance. In humans, caliciviruses are a major cause of acute gastroenteritis, while in animals respiratory illness, conjunctivitis, stomatitis, and hemorrhagic disease are documented. Investigation of virus-host interactions is limited by a lack of culture systems for many viruses in this family. Feline calicivirus (FCV), a member of the
Vesivirus
genus, provides a tractable model, since it may be propagated in cell culture. Feline junctional adhesion molecule 1 (fJAM-1) was recently identified as a functional receptor for FCV. We have analyzed the structure of this virus-receptor complex by cryo-electron microscopy and three-dimensional image reconstruction, combined with fitting of homology modeled high-resolution coordinates. We show that domain 1 of fJAM-1 binds to the outer face of the P2 domain of the FCV capsid protein VP1, inducing conformational changes in the viral capsid. This study provides the first structural view of a native calicivirus-protein receptor complex and insights into the mechanisms of virus attachment and uncoating.
A Simple Mathematical Model Helps To Explain the Immunodominance of CD8 T Cells in Influenza A Virus Infections
Authors: Handel Andreas , Antia Rustom 
Published: June 2008

ABSTRACT

Understanding immunodominance, the phenomenon of epitope-specific T cells expanding in an often distinctly hierarchical fashion, is important for the design of T-cell-based intervention strategies. Several recent studies have investigated immunodominance of H-2D
b
-restricted CD8
+
T cells specific for the nucleoprotein NP366 and acid polymerase PA224 epitopes during influenza A virus infection of C57BL/6 mice. CD8
+
T cells specific for these two epitopes are codominant during primary infection; NP366 dominates during secondary infection. While a number of explanations for this observation have been proposed, none of them can fully account for all the observed data. In this article, we use a simple mathematical model to explain the seemingly inconsistent data. We show that the dynamic interactions between CD8
+
T cells and antigen presentation lead to a situation where CD8
+
T cells are limiting during the initial response whereas antigen is limiting in the secondary response. This “numbers game” between antigen and CD8
+
T cells can reproduce the observed immunodominance of the NP336- and PA224-specific CD8
+
T cells, thereby explaining the reported experimental data.
Small-Molecule Inhibitor Which Reactivates p53 in Human T-Cell Leukemia Virus Type 1-Transformed Cells
Authors: Jung Kyung-Jin , Dasgupta Arindam , Huang Keven , Jeong Soo-Jin , Pise-Masison Cynthia , Gurova Katerina V. , Brady John N. 
Published: June 2008

ABSTRACT

Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of the aggressive and fatal disease adult T-cell leukemia. Previous studies have demonstrated that the HTLV-1-encoded Tax protein inhibits the function of tumor suppressor p53 through a Tax-induced NF-κB pathway. Given these attributes, we were interested in the activity of small-molecule inhibitor 9-aminoacridine (9AA), an anticancer drug that targets two important stress response pathways, NF-κB and p53. In the present study, we have examined the effects of 9AA on HTLV-1-transformed cells. Treatment of HTLV-1-transformed cells with 9AA resulted in a dramatic decrease in cell viability. Consistent with these results, we observed an increase in the percentage of cells in sub-G
1
and an increase in the number of cells positive by terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling assay following treatment of HTLV-1-transformed cells with 9AA. In each assay, HTLV-1-transformed cells C8166, Hut102, and MT2 were more sensitive to treatment with 9AA than control CEM and peripheral blood mononuclear cells. Analyzing p53 function, we demonstrate that treatment of HTLV-1-transformed cells with 9AA resulted in an increase in p53 protein and activation of p53 transcription activity. Of significance, 9AA-induced cell death could be blocked by introduction of a p53 small interfering RNA, linking p53 activity and cell death. These results suggest that Tax-repressed p53 function in HTLV-1-transformed cells is “druggable” and can be restored by treatment with 9AA. The fact that 9AA induces p53 and inhibits NF-κB suggests a promising strategy for the treatment of HTLV-1-transformed cells.
Functional Characterization of the Cleavage Specificity of the Sapovirus Chymotrypsin-Like Protease
Authors: Robel Ivonne , Gebhardt Julia , Mesters Jeroen R. , Gorbalenya Alexander , Coutard Bruno , Canard Bruno , Hilgenfeld Rolf , Rohayem Jacques 
Published: June 2008

ABSTRACT

Sapovirus is a positive-stranded RNA virus with a translational strategy based on processing of a polyprotein precursor by a chymotrypsin-like protease. So far, the molecular mechanisms regulating cleavage specificity of the viral protease are poorly understood. In this study, the catalytic activities and substrate specificities of the predicted forms of the viral protease, the 3C-like protease (NS6) and the 3CD-like protease-polymerase (NS6-7), were examined in vitro. The purified NS6 and NS6-7 were able to cleave synthetic peptides (15 to 17 residues) displaying the cleavage sites of the sapovirus polyprotein, both NS6 and NS6-7 proteins being active forms of the viral protease. High-performance liquid chromatography and subsequent mass spectrometry analysis of digested products showed a specific
trans
cleavage of peptides bearing Gln-Gly, Gln-Ala, Glu-Gly, Glu-Pro, or Glu-Lys at the scissile bond. In contrast, peptides bearing Glu-Ala or Gln-Asp at the scissile bond (NS4-NS5 and NS5-NS6, or NS6-NS7 junctions, respectively) were resistant to
trans
cleavage by NS6 or NS6-7 proteins, whereas
cis
cleavage of the Glu-Ala scissile bond of the NS5-NS6 junction was evidenced. Interestingly, the presence of a Phe at position P4 overruled the resistance to
trans
cleavage of the Glu-Ala junction (NS5-NS6), whereas substitutions at the P1 and P2′ positions altered the cleavage efficiency. The differential cleavage observed is supported by a model of the substrate-binding site of the sapovirus protease, indicating that the P4, P1, and P2′ positions in the substrate modulate the cleavage specificity and efficiency of the sapovirus chymotrypsin-like protease.
The Secondary Structure of the Human Immunodeficiency Virus Type 1 Transcript Modulates Viral Splicing and Infectivity
Authors: Jablonski Joseph A. , Buratti Emanuele , Stuani Cristiana , Caputi Massimo 
Published: June 2008

ABSTRACT
Splicing of human immunodeficiency virus type 1 (HIV-1) exon 6D is regulated by the presence of a complex splicing regulatory element (SRE) sequence that interacts with the splicing factors hnRNP H and SC35. In this work, we show that, in the context of the wild-type viral sequence, hnRNP H acts as a repressor of exon 6D inclusion independent of its binding to the SRE. However, hnRNP H binding to the SRE acts as an enhancer of exon 6D inclusion in the presence of a critical T-to-C mutation. These seemingly contrasting functional properties of hnRNP H appear to be caused by a change in the RNA secondary structure induced by the T-to-C mutation that affects the spatial location of bound hnRNP H with respect to the exon 6D splicing determinants. We propose a new regulatory mechanism mediated by RNA folding that may also explain the dual properties of hnRNP H in splicing regulation.