bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Should Long-Term Tunneled Central Venous Catheters Be Managed in Microbiology Laboratories in Order To Provide an Accurate Diagnosis of Colonization?
Authors: Guembe M. , Martín-Rabadán P. , Echenagusia A. , Camúñez F. , Rodríguez-Rosales G. , Simó G. , Echenagusia M. , Bouza E. 
Published: December 2011

ABSTRACT

Guidelines recommend the roll-plate technique for short-term central venous catheter (CVC) tip cultures. However, the issue of whether the roll-plate technique is better than the sonication method for long-term CVCs remains unresolved. In addition, no data are available for predicting the value of direct Gram staining in anticipating catheter colonization or catheter-related bloodstream infection (CRBSI) in these long-term CVCs. Our objectives were to compare the roll-plate technique and the sonication method and to define the validity values of Gram staining for the prediction of colonization and CRBSI in patients with long-term tunneled CVCs. During the study period, all tunneled CVCs removed at our institution were prospectively and routinely sent to the microbiology laboratory for Gram staining (first) and tip culture (the Maki technique and sonication, in a random order). We received 149 tunneled CVCs, 39 (26.2%) of which were colonized and 11 (7.4%) of which were associated with CRBSI. Overall, the roll-plate method detected 94.9% of the colonized catheters, whereas sonication detected only 43.6% (
P
< 0.001). The validity values of Gram staining for the detection of colonization and CRBSI were as follows: a sensitivity of 35.9% to 60.0%, a specificity of 100% to 94.2%, a positive predictive value of 100% to 42.9%, and a negative predictive value of 81.5% to 97.0%. The roll-plate technique proved to be better than sonication for the detection of bacteria in long-term tunneled CVCs. Gram staining of the tips of tunneled CVCs can anticipate a positive culture and rule out CRBSI. In our opinion, direct Gram staining should be incorporated into routine microbiological assessments of long-term catheter tips.
Detection of Mobile-Genetic-Element Variation between Colonizing and Infecting Hospital-Associated Methicillin-Resistant Staphylococcus aureus Isolates
Authors: McCarthy Alex J. , Breathnach Aodhan S. , Lindsay Jodi A. 
Published: December 2011

ABSTRACT

Whole-genome analysis by 62-strain microarray showed variation in resistance and virulence genes on mobile genetic elements (MGEs) between 40 isolates of methicillin-resistant
Staphylococcus aureus
(MRSA) strain CC22-
SCCmecIV
but also showed (i) detection of two previously unrecognized MRSA transmission events and (ii) that 7/8 patients were infected with a variant of their own colonizing isolate.
Clinical Validation of Multiplex Real-Time PCR Assays for Detection of Bacterial Meningitis Pathogens
Authors: Wang Xin , Theodore M. Jordan , Mair Raydel , Trujillo-Lopez Elizabeth , du Plessis Mignon , Wolter Nicole , Baughman Andrew L. , Hatcher Cynthia , Vuong Jeni , Lott Lisa , von Gottberg Anne , Sacchi Claudio , McDonald J. Matthew , Messonnier Nancy E. , Mayer Leonard W. 
Published: December 2011

ABSTRACT

Neisseria meningitidis
,
Haemophilus influenzae
, and
Streptococcus pneumoniae
are important causes of meningitis and other infections, and rapid, sensitive, and specific laboratory assays are critical for effective public health interventions. Singleplex real-time PCR assays have been developed to detect
N. meningitidis ctrA
,
H. influenzae hpd
, and
S. pneumoniae lytA
and serogroup-specific genes in the
cap
locus for
N. meningitidis
serogroups A, B, C, W135, X, and Y. However, the assay sensitivity for serogroups B, W135, and Y is low. We aimed to improve assay sensitivity and develop multiplex assays to reduce time and cost. New singleplex real-time PCR assays for serogroup B
synD
, W135
synG
, and Y
synF
showed 100% specificity for detecting
N. meningitidis
species, with high sensitivity (serogroup B
synD
, 99% [75/76]; W135
synG
, 97% [38/39]; and Y
synF
, 100% [66/66]). The lower limits of detection (LLD) were 9, 43, and 10 copies/reaction for serogroup B
synD
, W135
synG
, and Y
synF
assays, respectively, a significant improvement compared to results for the previous singleplex assays. We developed three multiplex real-time PCR assays for detection of (i)
N. meningitidis ctrA
,
H. influenzae hpd
, and
S. pneumoniae lytA
(NHS assay); (ii)
N. meningitidis
serogroups A, W135, and X (AWX assay); and (iii)
N. meningitidis
serogroups B, C, and Y (BCY assay). Each multiplex assay was 100% specific for detecting its target organisms or serogroups, and the LLD was similar to that for the singleplex assay. Pairwise comparison of real-time PCR between multiplex and singleplex assays showed that cycle threshold values of the multiplex assay were similar to those for the singleplex assay. There were no substantial differences in sensitivity and specificity between these multiplex and singleplex real-time PCR assays.
Assessment on Experimental Bacterial Biofilms and in Clinical Practice of the Efficacy of Sampling Solutions for Microbiological Testing of Endoscopes
Authors: Aumeran C. , Thibert E. , Chapelle F. A. , Hennequin C. , Lesens O. , Traoré O. 
Published: December 2011

ABSTRACT

Opinions differ on the value of microbiological testing of endoscopes, which varies according to the technique used. We compared the efficacy on bacterial biofilms of sampling solutions used for the surveillance of the contamination of endoscope channels. To compare efficacy, we used an experimental model of a 48-h
Pseudomonas
biofilm grown on endoscope internal tubing. Sampling of this experimental biofilm was performed with a Tween 80-lecithin-based solution, saline, and sterile water. We also performed a randomized prospective study during routine clinical practice in our hospital sampling randomly with two different solutions the endoscopes after reprocessing. Biofilm recovery expressed as a logarithmic ratio of bacteria recovered on bacteria initially present in biofilm was significantly more effective with the Tween 80-lecithin-based solution than with saline solution (
P
= 0.002) and sterile water (
P
= 0.002). There was no significant difference between saline and sterile water. In the randomized clinical study, the rates of endoscopes that were contaminated with the Tween 80-lecithin-based sampling solution and the saline were 8/25 and 1/25, respectively (
P
= 0.02), and the mean numbers of bacteria recovered were 281 and 19 CFU/100 ml (
P
= 0.001), respectively. In conclusion, the efficiency and therefore the value of the monitoring of endoscope reprocessing by microbiological cultures is dependent on the sampling solutions used. A sampling solution with a tensioactive action is more efficient than saline in detecting biofilm contamination of endoscopes.
Sulfonamide Resistance in Isolates of Nocardia spp. from a U.S. Multicenter Survey
Authors: Brown-Elliott Barbara A. , Biehle Jon , Conville Patricia S. , Cohen Samuel , Saubolle Michael , Sussland Den , Wengenack Nancy , Kriel Kimberly , Bridge Linda , McNulty Steven , Vasireddy Ravikiran , Wallace Richard J. 
Published: December 2011

ABSTRACT

Recent reports of increasing
in vitro
sulfonamide resistance in
Nocardia
prompted us to investigate the findings. Despite the reports, there is a paucity of clinical reports of sulfonamide failure in treatment of nocardia disease. We reviewed 552 recent susceptibilities of clinical isolates of
Nocardia
from six major laboratories in the United States, and only 2% of the isolates were found to have resistant MICs of trimethoprim-sulfamethoxazole and/or sulfamethoxazole. We hypothesize that the discrepancies in the apparent sulfonamide resistance between our study and the previous findings may be associated with difficulty in the laboratory interpretation of
in vitro
MICs for trimethoprim-sulfamethoxazole and sulfamethoxazole and the lack of quality controls for
Nocardia
for these agents.
Detection of Favorable Oral Cephalosporin-Clavulanate Interactions by
In Vitro
Disk Approximation Susceptibility Testing of Extended-Spectrum-Beta-Lactamase-Producing Members of the Enterobacteriaceae
Authors: Campbell Jennifer D. , Lewis James S. , McElmeel M. Leticia , Fulcher Letitia C. , Jorgensen James H. 
Published: December 2011

ABSTRACT

Extended-spectrum-beta-lactamase (ESBL)-producing members of the
Enterobacteriaceae
are often resistant to multiple drug classes, making therapy of urinary infections with oral antibiotics difficult. Previously it was shown that amoxicillin-clavulanate can provide clavulanate inhibition of ESBLs and protect an oral cephalosporin present in combination when tested by broth microdilution. This study has shown that disk approximation testing could detect favorable cephalosporin-clavulanate interactions among a group of 101 previously characterized members of the
Enterobacteriaceae
with CTX-M, SHV, or TEM ESBLs.
Balamuthia mandrillaris and Acanthamoeba Amebic Encephalitis with Neurotoxoplasmosis Coinfection in a Patient with Advanced HIV Infection
Authors: Pietrucha-Dilanchian Paula , Chan Joseph C. , Castellano-Sanchez Amilcar , Hirzel Alicia , Laowansiri Panthipa , Tuda Claudio , Visvesvara Govinda S. , Qvarnstrom Yvonne , Ratzan Kenneth R. 
Published: December 2011

ABSTRACT

We describe a patient with advanced HIV infection and
Balamuthia mandrillaris
and
Acanthamoeba
amebic encephalitis with
Toxoplasma gondii
coinfection. A multidisciplinary effort and state-of-the-art diagnostic techniques were required for diagnosis. Our patient is the first reported case of an HIV-infected person with dual
Balamuthia mandrillaris
and
Acanthamoeba
amebic encephalitis with neurotoxoplasmosis coinfection.
Recruitment of the Nuclear Form of Uracil DNA Glycosylase into Virus Particles Participates in the Full Infectivity of HIV-1
Authors: Guenzel Carolin A. , Hérate Cécile , Le Rouzic Erwann , Maidou-Peindara Priscilla , Sadler Holly A. , Rouyez Marie-Christine , Mansky Louis M. , Benichou Serge 
Published: December 2011

ABSTRACT
The HIV-1 Vpr protein participates in the early steps of the virus life cycle by influencing the accuracy of reverse transcription. This role of Vpr was related to the recruitment of the nuclear form of the uracil DNA glycosylase (UNG2) enzyme into virus particles, but several conflicting findings have been reported regarding the role of UNG2 encapsidation on viral infectivity. Here, we report that the catalytic activity of UNG2 was not required for influencing HIV-1 mutation, and this function of UNG2 was mapped within a 60-amino-acid domain located in the N-terminal region of the protein required for direct interaction with the p32 subunit of the replication protein A (RPA) complex. Importantly, enforced recruitment of overexpressed UNG2 into virions resulted in a net increase of virus infectivity, and this positive effect on infectivity was also independent of the UNG2 enzymatic activity. In contrast, virus infectivity and replication, as well as the efficiency of the viral DNA synthesis, were significantly reduced when viruses were produced from cells depleted of either endogenous UNG2 or RPA p32. Taken together, these results demonstrate that incorporation of UNG2 into virions has a positive impact on HIV-1 infectivity and replication and positively influences the reverse transcription process through a nonenzymatic mechanism involving the p32 subunit of the RPA complex.
Inhibition of TANK Binding Kinase 1 by Herpes Simplex Virus 1 Facilitates Productive Infection
Authors: Ma Yijie , Jin Huali , Valyi-Nagy Tibor , Cao Youjia , Yan Zhipeng , He Bin 
Published: December 2011

ABSTRACT

The γ
1
34.5 protein of herpes simplex viruses (HSV) is essential for viral pathogenesis, where it precludes translational arrest mediated by double-stranded-RNA-dependent protein kinase (PKR). Paradoxically, inhibition of PKR alone is not sufficient for HSV to exhibit viral virulence. Here we report that γ
1
34.5 inhibits TANK binding kinase 1 (TBK1) through its amino-terminal sequences, which facilitates viral replication and neuroinvasion. Compared to wild-type virus, the γ
1
34.5 mutant lacking the amino terminus induces stronger antiviral immunity. This parallels a defect of γ
1
34.5 for interacting with TBK1 and reducing phosphorylation of interferon (IFN) regulatory factor 3. This activity is independent of PKR. Although resistant to IFN treatment, the γ
1
34.5 amino-terminal deletion mutant replicates at an intermediate level between replication of wild-type virus and that of the γ
1
34.5 null mutant in TBK1
+/+
cells. However, such impaired viral growth is not observed in TBK1
−/−
cells, indicating that the interaction of γ
1
34.5 with TBK1 dictates HSV infection. Upon corneal infection, this mutant replicates transiently but barely invades the trigeminal ganglia or brain, which is a difference from wild-type virus and the γ
1
34.5 null mutant. Therefore, in addition to PKR, γ
1
34.5 negatively regulates TBK1, which contributes viral replication and spread
in vivo
.
Structure of an Antibody in Complex with Its Mucin Domain Linear Epitope That Is Protective against Ebola Virus
Authors: Olal Daniel , Kuehne Ana I. , Bale Shridhar , Halfmann Peter , Hashiguchi Takao , Fusco Marnie L. , Lee Jeffrey E. , King Liam B. , Kawaoka Yoshihiro , Dye John M. , Saphire Erica Ollmann 
Published: December 2011

ABSTRACT
Antibody 14G7 is protective against lethal Ebola virus challenge and recognizes a distinct linear epitope in the prominent mucin-like domain of the Ebola virus glycoprotein GP. The structure of 14G7 in complex with its linear peptide epitope has now been determined to 2.8 Å. The structure shows that this GP sequence forms a tandem β-hairpin structure that binds deeply into a cleft in the antibody-combining site. A key threonine at the apex of one turn is critical for antibody interaction and is conserved among all Ebola viruses. This work provides further insight into the mechanism of protection by antibodies that target the protruding, highly accessible mucin-like domain of Ebola virus and the structural framework for understanding and characterizing candidate immunotherapeutics.
Viral Interferon Regulatory Factors Are Critical for Delay of the Host Immune Response against Rhesus Macaque Rhadinovirus Infection
Authors: Robinson Bridget A. , O'Connor Megan A. , Li He , Engelmann Flora , Poland Britt , Grant Richard , DeFilippis Victor , Estep Ryan D. , Axthelm Michael K. , Messaoudi Ilhem , Wong Scott W. 
Published: December 2011

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV) and the closely related gamma-2 herpesvirus rhesus macaque (RM) rhadinovirus (RRV) are the only known viruses to encode viral homologues of the cellular interferon (IFN) regulatory factors (IRFs). Recent characterization of a viral IRF (vIRF) deletion clone of RRV (vIRF-knockout RRV [vIRF-ko RRV]) demonstrated that vIRFs inhibit induction of type I and type II IFNs during RRV infection of peripheral blood mononuclear cells. Because the IFN response is a key component to a host's antiviral defenses, this study has investigated the role of vIRFs in viral replication and the development of the immune response duringin vivoinfection in RMs, the natural host of RRV. Experimental infection of RMs with vIRF-ko RRV resulted in decreased viral loads and diminished B cell hyperplasia, a characteristic pathology during acute RRV infection that often develops into more severe lymphoproliferative disorders in immune-compromised animals, similar to pathologies in KSHV-infected individuals. Moreover,in vivoinfection with vIRF-ko RRV resulted in earlier and sustained production of proinflammatory cytokines and earlier induction of an anti-RRV T cell response compared to wild-type RRV infection. These findings reveal the broad impact that vIRFs have on pathogenesis and the immune responsein vivoand are the first to validate the importance of vIRFs duringde novoinfection in the host.
Intronic Deletions That Disrupt mRNA Splicing of the
tva
Receptor Gene Result in Decreased Susceptibility to Infection by Avian Sarcoma and Leukosis Virus Subgroup A
Authors: Reinišová Markéta , Plachý Jiří , Trejbalová Kateřina , Šenigl Filip , Kučerová Dana , Geryk Josef , Svoboda Jan , Hejnar Jiří 
Published: December 2011

ABSTRACT

The group of closely related avian sarcoma and leukosis viruses (ASLVs) evolved from a common ancestor into multiple subgroups, A to J, with differential host range among galliform species and chicken lines. These subgroups differ in variable parts of their envelope glycoproteins, the major determinants of virus interaction with specific receptor molecules. Three genetic loci,
tva
,
tvb
, and
tvc
, code for single membrane-spanning receptors from diverse protein families that confer susceptibility to the ASLV subgroups. The host range expansion of the ancestral virus might have been driven by gradual evolution of resistance in host cells, and the resistance alleles in all three receptor loci have been identified. Here, we characterized two alleles of the
tva
receptor gene with similar intronic deletions comprising the deduced branch-point signal within the first intron and leading to inefficient splicing of
tva
mRNA. As a result, we observed decreased susceptibility to subgroup A ASLV
in vitro
and
in vivo
. These alleles were independently found in a close-bred line of domestic chicken and Indian red jungle fowl (
Gallus gallus murghi
), suggesting that their prevalence might be much wider in outbred chicken breeds. We identified defective splicing to be a mechanism of resistance to ASLV and conclude that such a type of mutation could play an important role in virus-host coevolution.
Specific Mutation of a Gammaherpesvirus-Expressed Antigen in Response to CD8 T Cell SelectionIn Vivo
Authors: Loh Joy , Popkin Daniel L. , Droit Lindsay , Braaten Douglas C. , Zhao Guoyan , Zhang Xin , Vachharajani Punit , Myers Nancy , Hansen Ted H. , Virgin Herbert W. 
Published: December 2011

ABSTRACTHerpesviruses are thought to be highly genetically stable, and their use as vaccine vectors has been proposed. However, studies of the human gammaherpesvirus, Epstein-Barr virus, have found viral isolates containing mutations in HLA class I-restricted epitopes. Using murine gammaherpesvirus 68 expressing ovalbumin (OVA), we examined the stability of a gammaherpesvirus antigenic locus under strong CD8 T cell selectionin vivo. OVA-specific CD8 T cells selected viral isolates containing mutations in the OVA locus but minimal alterations in other genomic regions. Thus, a CD8 T cell response to a gammaherpesvirus-expressed antigen that is not essential for replication or pathogenesis can result in selective mutation of that antigenin vivo. This finding may have relevance for the use of herpesvirus vectors for chronic antigen expressionin vivo.
Persistence of Circulating Memory B Cell Clones with Potential for Dengue Virus Disease Enhancement for Decades following Infection
Authors: Smith Scott A. , Zhou Yang , Olivarez Nicholas P. , Broadwater Anne H. , de Silva Aravinda M. , Crowe James E. 
Published: December 2011

ABSTRACTSymptomatic dengue virus infection ranges in disease severity from an influenza-like illness to life-threatening shock. One model of the mechanism underlying severe disease proposes that weakly neutralizing, dengue serotype cross-reactive antibodies induced during a primary infection facilitate virus entry into Fc receptor-bearing cells during a subsequent secondary infection, increasing viral replication and the release of cytokines and vasoactive mediators, culminating in shock. This process has been termed antibody-dependent enhancement of infection and has significantly hindered vaccine development. Much of our understanding of this process has come from studies using mouse monoclonal antibodies (MAbs); however, antibody responses in mice typically exhibit less complexity than those in humans. A better understanding of the humoral immune response to natural dengue virus infection in humans is sorely needed. Using a high-efficiency human hybridoma technology, we isolated 37 hybridomas secreting human MAbs to dengue viruses from 12 subjects years or even decades following primary or secondary infection. The majority of the human antibodies recovered were broadly cross-reactive, directed against either envelope or premembrane proteins, and capable of enhancement of infectionin vitro; few exhibited serotype-specific binding or potent neutralizing activity. Memory B cells encoding enhancing antibodies predominated in the circulation, even two or more decades following infection. Mapping the epitopes and activity of naturally occurring dengue antibodies should prove valuable in determining whether the enhancing and neutralizing activity of antibodies can be separated. Such principles could be used in the rational design of vaccines that enhance the induction of neutralizing antibodies, while lowering the risk of dengue shock syndrome.
Metagenomic Analysis of the Viral Flora of Pine Marten and European Badger Feces
Authors: van den Brand Judith M. A. , van Leeuwen Marije , Schapendonk Claudia M. , Simon James H. , Haagmans Bart L. , Osterhaus Albert D. M. E. , Smits Saskia L. 
Published: December 2011

ABSTRACT

A thorough understanding of the diversity of viruses in wildlife provides epidemiological baseline information about potential pathogens. Metagenomic analysis of the enteric viral flora revealed a new anellovirus and bocavirus species in pine martens and a new circovirus-like virus and geminivirus-related DNA virus in European badgers. In addition, sequences with homology to viruses from the families
Paramyxo
- and
Picornaviridae
were detected.
Comparative Analysis of Transforming Properties of E6 and E7 from Different Beta Human Papillomavirus Types
Authors: Cornet Iris , Bouvard Véronique , Campo Maria Saveria , Thomas Miranda , Banks Lawrence , Gissmann Lutz , Lamartine Jérôme , Sylla Bakary S. , Accardi Rosita , Tommasino Massimo 
Published: December 2011

ABSTRACT
The cutaneous beta human papillomavirus (beta HPV) types appear to be involved in skin carcinogenesis. However, only a few beta HPVs have been investigated so far. Here, we compared the properties of E6 and E7 oncoproteins from six uncharacterized beta HPVs (14, 22, 23, 24, 36, 49). Only HPV49 E6 and E7 immortalized primary human keratinocytes and efficiently deregulated the p53 and pRb pathways. Furthermore, HPV49 E6, similarly to E6 from the oncogenic HPV16, promoted p53 degradation.
Espirito Santo Virus: a New Birnavirus That Replicates in Insect Cells
Authors: Vancini Ricardo , Paredes Angel , Ribeiro Mariana , Blackburn Kevin , Ferreira Davis , Kononchik Joseph P. , Hernandez Raquel , Brown Dennis 
Published: December 2011

ABSTRACT

Espirito Santo virus (ESV) is a newly discovered virus recovered as contamination in a sample of a virulent strain of dengue-2 virus (strain 44/2), which was recovered from a patient in the state of Espirito Santo, Brazil, and amplified in insect cells. ESV was found to be dependent upon coinfection with a virulent strain of dengue-2 virus and to replicate in C6/36 insect cells but not in mammalian Vero cells. A sequence of the genome has been produced by
de novo
assembly and was not found to match to any known viral sequence. An incomplete match to the nucleotide sequence of the RNA-dependent RNA polymerase from
Drosophila
X virus (DXV), another birnavirus, could be detected. Mass spectrometry analysis of ESV proteins found no matches in the protein data banks. However, peptides recovered by mass spectrometry corresponded to the
de novo
-assembled sequence by BLAST analysis. The composition and three-dimensional structure of ESV are presented, and its sequence is compared to those of other members of the birnavirus family. Although the virus was found to belong to the family
Birnaviridae
, biochemical and sequence information for ESV differed from that of DXV, the representative species of the genus
Entomobirnavirus
. Thus, significant differences underscore the uniqueness of this infectious agent, and its relationship to the coinfecting virus is discussed.