bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vancomycin MICs for
Staphylococcus aureus
Vary by Detection Method and Have Subtly Increased in a Pediatric Population Since 2005
Authors: Mason Edward O. , Lamberth Linda B. , Hammerman Wendy A. , Hulten Kristina G. , Versalovic James , Kaplan Sheldon L. 
Published: April 2009

ABSTRACT

Vancomycin MICs for
Staphylococcus aureus
isolates in a pediatric hospital with a high rate of staphylococcal infections were examined for any increase over a 7-year period. A broth microdilution scheme allowed direct comparison of the MICs generated by this method to MICs generated by Etest. MICs generated by both methods were determined with the same inoculum suspension. One hundred sixty-five
S
.
aureus
isolates were selected on the basis of the patients having been bacteremic or having received vancomycin as the definitive therapy for their infections. Of the 165 isolates, 117 were methicillin-resistant
S
.
aureus
and 48 were methicillin-susceptible
S
.
aureus
. Forty-seven were acquired in the hospital (nosocomial), 56 were community acquired, and 62 were community onset-health care associated. All but one isolate tested by broth microdilution had MICs of <1.0 μg/ml, while 96% of these same isolates tested by Etest had MICs of ≥1 μg/ml. A significant increase in MICs that occurred after study year 4 (2004 to 2005) was demonstrated by the Etest (
P
< 0.00007) but not by broth microdilution. MICs were not different for isolates of community or health care origin, regardless of methodology. The proportion of isolates with Etest MICs of <1 and ≥1 μg/ml between children with bacteremia for ≤5 days and >5 days (
P
= 0.3) was not different. We conclude that MICs for pediatric isolates have increased slightly since 2005 and therapeutic decisions based on vancomycin MICs need to be made by considering the methodology used.
Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Hepatitis E Virus
Authors: Lan Xi , Yang Bin , Li Bao Yu , Yin Xiang Ping , Li Xue Rui , Liu Ji Xing 
Published: April 2009

ABSTRACT
The one-step single-tube betaine-free reverse transcription (RT)-loop-mediated isothermal amplification assay was developed for rapid diagnosis of hepatitis E virus. This assay amplified the target gene in less than 45 min (even as short as 20 min) under isothermal conditions at 63°C, and the sensitivity of this assay was 100-fold greater than that of RT-PCR. This assay demonstrated a detection limit of 0.045 fg (nine copies/reaction).
The First Vancomycin-Intermediate
Staphylococcus aureus
Strains Isolated from Patients in Thailand
Authors: Lulitanond Aroonlug , Engchanil Chulapan , Chaimanee Prajuab , Vorachit Malai , Ito Teruyo , Hiramatsu Keiichi 
Published: April 2009

ABSTRACT

We screened 533 and 361 methicillin (meticillin)-resistant
Staphylococcus aureus
strains isolated in a university hospital in 2002 and 2003 and in 2006 and 2007, respectively, and identified 4 (0.8%) of the strains in the first group and 8 (2.2%) of the strains in second group as heterogeneous vancomycin-resistant
S. aureus
(heterogeneous VISA) strains and 3 (0.8%) of the strains in the second group as VISA strains. This is the first report of VISA strains isolated from patients in Thailand.
Putative Adhesins of Enteropathogenic and EnterohemorrhagicEscherichia coliof Serogroup O26 Isolated from Humans and Cattle
Authors: Bardiau Marjorie , Labrozzo Sabrina , Mainil Jacques G. 
Published: April 2009

ABSTRACTEnterohemorrhagicEscherichia coli(EHEC) strains are responsible for food poisoning in developed countries via consumption of vegetal and animal food sources contaminated by ruminant feces, and some strains (O26, O111, and O118 serogroups) are also responsible for diarrhea in young calves. The prevalence of 27 putative adhesins of EHEC and of bovine necrotoxigenicE. coli(NTEC) was studied with a collection of 43 bovine and 29 human enteropathogenic (EPEC) and EHEC strains and 5 non-EPEC/non-EHEC (1 bovine and 4 human) O26 strains, using specific PCRs. Four “groups” of adhesins exist, including adhesins present in all O26 strains, adhesins present in most O26 strains, adhesins present in a few O26 strains, and adhesins not present in O26 strains. The common profile of EHEC/EPEC strains was characterized by the presence ofloc3,loc5,loc7,loc11,loc14,paa,efa1,iha,lpfAO26, andlpfAO113genes and the absence ofloc1,loc2,loc6,loc12,loc13,saa, andeibGgenes. Except for thelpfAO26gene, which was marginally associated with bovine EHEC/EPEC strains in comparison with human strains (P= 0.012), none of the results significantly differentiated bovine strains from human strains. One adhesin gene (ldaE) was statistically (P< 0.01) associated with O26 EHEC/EPEC strains isolated from diarrheic calves in comparison with strains isolated from healthy calves.ldaE-positive strains could therefore represent a subgroup possessing the specific property of producing diarrhea in young calves. This is the first time that the distribution of putative adhesins has been described for such a large collection of EHEC/EPEC O26 strains isolated from both humans and cattle.
Rapid Real-Time Nucleic Acid Sequence-Based Amplification-Molecular Beacon Platform To Detect Fungal and Bacterial Bloodstream Infections
Authors: Zhao Yanan , Park Steven , Kreiswirth Barry N. , Ginocchio Christine C. , Veyret Raphaël , Laayoun Ali , Troesch Alain , Perlin David S. 
Published: April 2009

ABSTRACT

Bloodstream infections (BSIs) are a significant cause of morbidity and mortality. Successful patient outcomes are diminished by a failure to rapidly diagnose these infections and initiate appropriate therapy. A rapid and reliable diagnostic platform of high sensitivity is needed for the management of patients with BSIs. The combination of an RNA-dependent nucleic acid sequence-based amplification and molecular beacon (NASBA-MB) detection system in multiplex format was developed to rapidly detect medically important BSI organisms. Probes and primers representing pan-gram-negative, pan-gram-positive, pan-fungal, pan-
Candida
, and pan-
Aspergillus
organisms were established utilizing 16S and 28S rRNA targets for bacteria and fungi, respectively. Two multiplex panels were developed to rapidly discriminate bacterial or fungal infections at the subkingdom/genus level with a sensitivity of 1 to 50 genomes. A clinical study was performed to evaluate the accuracy of this platform by evaluating 570 clinical samples from a tertiary-care hospital group using blood bottle samples. The sensitivity, specificity, and Youden's index values for pan-gram-positive detection and pan-gram-negative detection were 99.7%, 100%, 0.997 and 98.6%, 95.9%, 0.945, respectively. The positive predictive values (PPV) and the negative predictive values (NPV) for these two probes were 100, 90.7, and 99.4, 99.4, respectively. Pan-fungal and pan-
Candida
probes showed 100% sensitivity, specificity, PPV, and NPV, and the pan-
Aspergillus
probe showed 100% NPV. Robust signals were observed for all probes in the multiplex panels, with signal detection in <15 min. The multiplex real-time NASBA-MB assay provides a valuable platform for the rapid and specific diagnosis of bloodstream pathogens, and reliable pathogen identification and characterization can be obtained in under 3 h.
Use of Reverse Transcriptase PCR To Subtype N1 to N9 Neuraminidase Genes of Avian Influenza Viruses
Authors: Tsukamoto Kenji , Ashizawa Takayoshi , Nakanishi Koji , Kaji Noriyuki , Suzuki Kotaro , Shishido Makiko , Okamatsu Masatoshi , Mase Masaji 
Published: April 2009

ABSTRACT
Reverse transcriptase PCR designed to amplify the N1 to N9 neuraminidase (NA) genes of avian influenza viruses detected 118 of the 119 NA genes tested (99.2%) in a subtype-specific manner. This technique successfully subtyped all 167 recent avian influenza viruses isolated from birds. Subtype specificity was confirmed by sequence analyses of all 285 PCR products.
Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for TypingMycobacterium aviumwith Mycobacterial Interspersed Repetitive-Unit-VNTR and IS1245Restriction Fragment Length Polymorphism Typing
Authors: Inagaki Takayuki , Nishimori Kei , Yagi Tetsuya , Ichikawa Kazuya , Moriyama Makoto , Nakagawa Taku , Shibayama Takami , Uchiya Kei-ichi , Nikai Toshiaki , Ogawa Kenji 
Published: April 2009

ABSTRACTMycobacterium aviumcomplex (MAC) infections are increasing annually in various countries, including Japan, but the route of transmission and pathophysiology of the infection remain unclear. Currently, a variable-number tandem-repeat (VNTR) typing method using theMycobacterium aviumtandem repeat (MATR) loci (MATR-VNTR) is employed in Japan for epidemiological studies using clinical isolates ofM. avium. In this study, the usefulness of this MATR-VNTR typing method was compared with that of the IS1245-restriction fragment length polymorphism (IS1245-RFLP) typing method and a mycobacterial interspersed repetitive-unit (MIRU)-VNTR typing method reported previously (V. C. Thibault, M. Grayon, M. L. Boschiroli, C. Hubbans, P. Overduin, K. Stevenson, M. C. Gutierrez, P. Supply, and F. Biet, J. Clin. Microbiol.45:2404-2410, 2007). Seventy clinical isolates identified asM. aviumfrom human immunodeficiency virus-negative patients with MAC infections were used. MATR-VNTR typing using 15 loci distinguished 56 patterns of different allele profiles, yielding a Hunter-Gaston discriminatory index (HGDI) of 0.990. However, IS1245-RFLP and MIRU-VNTR typing yielded HGDIs of 0.960 and 0.949, respectively, indicating that MATR-VNTR has an excellent discriminatory power compared with MIRU-VNTR and IS1245-RFLP typing. Moreover, concomitant use of the MATR-VNTR method and IS1245-RFLP typing increased the HGDI to 0.999. MATR-VNTR typing is inexpensive and easy to perform and could thus be useful in establishing a digital multifacility database that will greatly contribute to the clarification of the transmission route and pathophysiology ofM. aviuminfections.
Divergent Bro1 Domains Share the Capacity To Bind Human Immunodeficiency Virus Type 1 Nucleocapsid and To Enhance Virus-Like Particle Production
Authors: Popov Sergei , Popova Elena , Inoue Michio , Göttlinger Heinrich G. 
Published: April 2009

ABSTRACT

To promote the release of infectious virions, human immunodeficiency virus type 1 (HIV-1) exploits the endosomal sorting complex required for transport (ESCRT) pathway by engaging Tsg101 and ALIX through late assembly (L) domains in p6 Gag. An LYPx
n
L motif in p6 serves as docking site for the central V domain of ALIX and is required for its ability to stimulate HIV-1 budding. Additionally, the nucleocapsid (NC) domain of Gag binds to the N-terminal Bro1 domain of ALIX, which connects ALIX to the membrane-deforming ESCRT-III complex via its CHMP4 subunits. Since the isolated Bro1 domain of ALIX is sufficient to markedly stimulate virus-like particle (VLP) production in a minimal Gag rescue assay, we examined whether the Bro1 domains of other human proteins possess a similar activity. We now show that the Bro1 domain-only protein Brox and the isolated Bro1 domains of HD-PTP and rhophilin all bind to HIV-1 NC. Furthermore, all shared the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule, and Brox in particular was as potent as the Bro1 domain of ALIX in this assay. Unexpectedly, Brox retained significant activity even if its CHMP4 binding site was disrupted. Thus, the ability to assist in VLP production may be an intrinsic property of the boomerang-shaped Bro1 domain.
Downregulation of RUNX1 by RUNX3 Requires the RUNX3 VWRPY Sequence and Is Essential for Epstein-Barr Virus-Driven B-Cell Proliferation
Authors: Brady Gareth , Whiteman Hannah J. , Spender Lindsay C. , Farrell Paul J. 
Published: April 2009

ABSTRACTCross-regulation of RUNX1 expression by RUNX3 plays a critical role in regulating proliferation of human B cells infected with Epstein-Barr virus (EBV). When EBV infection induces RUNX3, the consequent reduction in RUNX1 levels is required for the ensuing cell proliferation because forced expression of RUNX1 in an EBV lymphoblastoid cell line prevented cell proliferation. The TEL-RUNX1 fusion gene from acute B-lymphocytic leukemia retains almost all of the RUNX1 sequence but does not prevent B-cell proliferation in the same assay. B-cell maturation antigen (BCMA) was found to be induced by conditionally expressed RUNX3 in a lymphoma cell line. Chromatin immunoprecipitation assays confirmed that RUNX3 binds to the RUNX1 promoter in a lymphoblastoid cell line and a Burkitt's lymphoma cell line. The TLE binding VWRPY sequence from the C terminus of RUNX3 was found to be required for repression of the RUNX1 P1 promoter in a B-lymphoma cell line. The mechanism of repression in B-cell lines most likely involves recruitment of corepressor TLE3 or TLE4 to the RUNX1 promoter. The results demonstrate the importance of RUNX3-mediated repression of RUNX1 for EBV-driven B-cell proliferation and identify functional differences between human RUNX family proteins.
Novel MicroRNAs (miRNAs) Encoded by Herpesvirus of Turkeys: Evidence of miRNA Evolution by Duplication
Authors: Yao Yongxiu , Zhao Yuguang , Smith Lorraine P. , Watson Michael , Nair Venugopal 
Published: April 2009

ABSTRACT
Herpesviruses account for 134 out of the 140 virus-encoded microRNAs (miRNAs) known today. Here we report the identification of 11 novel miRNAs encoded by herpesvirus of turkey (HVT), a virus used as a live vaccine in poultry against the highly oncogenic Marek's disease virus type 1. Ten of these miRNAs were clustered together within the repeat long region of the viral genome, demonstrating some degree of positional conservation with other mardiviruses. Close sequence and phylogenetic relationships of some miRNAs in this cluster indicate evolution by duplication. HVT miRNAs represent the first example of virus-encoded miRNAs that show evolution by duplication.
Molecular Determinants for Subcellular Localization of the Severe Acute Respiratory Syndrome Coronavirus Open Reading Frame 3b Protein
Authors: Freundt Eric C. , Yu Li , Park Elizabeth , Lenardo Michael J. , Xu Xiao-Ning 
Published: April 2009

ABSTRACTViruses such as hepatitis C and the severe acute respiratory syndrome coronavirus (SARS-CoV) encode proteins that are distributed between mitochondria and the nucleus, but little is known about the factors that control partitioning between these sites. SARS-CoV encodes a unique accessory gene called open reading frame (ORF) 3b that, like other unique accessory genes in SARS-CoV, likely contributes to viral pathogenicity. The ORF 3b protein is 154 amino acids and is predicted to express from the second ORF in subgenomic RNA3. In this report, we have characterized the molecular components that regulate intracellular localization of the ORF 3b protein. We demonstrate unique shuttling behavior of ORF 3b, whereby the protein initially accumulates in the nucleus and subsequently translocates to mitochondria. Following nuclear localization, ORF 3b traffics to the outer membrane of mitochondria via a predicted amphipathic α-helix. Additionally, ORF 3b contains a consensus nuclear export sequence, and we demonstrate that nuclear export and thus mitochondrial translocation are dependent on a leptomycin B-sensitive nuclear export mechanism. We further show that ORF 3b inhibits induction of type I interferon induced by retinoic acid-induced gene 1 and the mitochondrial antiviral signaling protein. Our observations provide insights into the cellular localization of ORF 3b that may enhance our understanding of the mechanisms by which ORF 3b contributes to SARS-CoV pathogenesis. The findings reported here reveal that for multilocalized proteins, consideration of the spatiotemporal distribution may be crucial for understanding viral protein behavior and function.
Ebolavirus VP35 Interacts with the Cytoplasmic Dynein Light Chain 8
Authors: Kubota Toru , Matsuoka Mayumi , Chang Tsung-Hsien , Bray Mike , Jones Steven , Tashiro Masato , Kato Atsushi , Ozato Keiko 
Published: April 2009

ABSTRACT
The viral protein VP35 of ebolavirus (EBOV) is implicated to have diverse roles in the viral life cycle. We employed a yeast two-hybrid screen to search for VP35 binding partners and identified the cytoplasmic dynein light chain (DLC8) as a protein that interacts with VP35. Mapping analysis unraveled a consensus motif, SQTQT, within VP35 through which VP35 binds to DLC8. The disruption of DLC8 binding does not affect the ability of VP35 to inhibit type I IFN production. Given that VP35 from various EBOV species interacts with DLC8, this interaction may have a role in regulating the EBOV life cycle.
Human Immunodeficiency Virus Type 1 Nef Protein Targets CD4 to the Multivesicular Body Pathway
Authors: daSilva Luis L. P. , Sougrat Rachid , Burgos Patricia V. , Janvier Katy , Mattera Rafael , Bonifacino Juan S. 
Published: April 2009

ABSTRACTThe Nef protein of human immunodeficiency virus type 1 downregulates the CD4 coreceptor from the surface of host cells by accelerating the rate of CD4 endocytosis through a clathrin/AP-2 pathway. Herein, we report that Nef has the additional function of targeting CD4 to the multivesicular body (MVB) pathway for eventual delivery to lysosomes. This targeting involves theendosomalsortingcomplexrequired fortransport (ESCRT) machinery. Perturbation of this machinery does not prevent removal of CD4 from the cell surface but precludes its lysosomal degradation, indicating that accelerated endocytosis and targeting to the MVB pathway are separate functions of Nef. We also show that both CD4 and Nef are ubiquitinated on lysine residues, but this modification is dispensable for Nef-induced targeting of CD4 to the MVB pathway.
Antibodies to the Buried N Terminus of Rhinovirus VP4 Exhibit Cross-Serotypic Neutralization
Authors: Katpally Umesh , Fu Tong-Ming , Freed Daniel C. , Casimiro Danilo R. , Smith Thomas J. 
Published: April 2009

ABSTRACT
Development of a vaccine for the common cold has been thwarted by the fact that there are more than 100 serotypes of human rhinovirus (HRV). We previously demonstrated that the HRV14 capsid is dynamic and transiently displays the buried N termini of viral protein 1 (VP1) and VP4. Here, further evidence for this “breathing” phenomenon is presented, using antibodies to several peptides representing the N terminus of VP4. The antibodies form stable complexes with intact HRV14 virions and neutralize infectivity. Since this region of VP4 is highly conserved among all of the rhinoviruses, antiviral activity by these anti-VP4 antibodies is cross-serotypic. The antibodies inhibit HRV16 infectivity in a temperature- and time-dependent manner consistent with the breathing behavior. Monoclonal and polyclonal antibodies raised against the 30-residue peptide do not react with peptides shorter than 24 residues, suggesting that these peptides are adopting three-dimensional conformations that are highly dependent upon the length of the peptide. Furthermore, there is evidence that the N termini of VP4 are interacting with each other upon extrusion from the capsid. A Ser5Cys mutation in VP4 yields an infectious virus that forms cysteine cross-links in VP4 when the virus is incubated at room temperature but not at 4°C. The fact that all of the VP4s are involved in this cross-linking process strongly suggests that VP4 forms specific oligomers upon extrusion. Together these results suggest that it may be possible to develop a pan-serotypic peptide vaccine to HRV, but its design will likely require details about the oligomeric structure of the exposed termini.
Nuclear-Cytoplasmic Shuttling Is Not Required for the Epstein-Barr Virus EBNA-LP Transcriptional Coactivation Function
Authors: Ling Paul D. , Tan Jie , Peng RongSheng 
Published: April 2009

ABSTRACT
Epstein-Barr virus (EBV) EBNA-LP is a transcriptional coactivator of EBNA2 that works though interaction with the promyelocytic leukemia nuclear-body-associated protein Sp100A. EBNA-LP localizes predominantly in the nucleus through the action of nuclear localization signals in the repeated regions of the protein. EBNA-LP has also been detected in the cytoplasm, and a previous study suggested that some of the EBNA-LP coactivation function is mediated by relocalizing histone deacetylase 4 (HDAC4) from the nucleus to the cytoplasm. Although EBNA-LP can be found in the cytoplasm, it has no obvious nuclear export signal, and there is no direct evidence for active shuttling between these cellular compartments. Whether active shuttling between the nucleus and cytoplasm is required for coactivation remains to be clarified. To address these issues, we tested a variety of EBNA-LP isoforms and mutants for nuclear-cytoplasmic shuttling activity in an interspecies heterokaryon assay and for the ability to associate with HDAC4. EBNA-LP isoforms smaller than 42 kDa shuttle efficiently in the heterokaryon assay via a crm-1-independent mechanism. In addition, no specific EBNA-LP domain that mediates nuclear export could be identified. In contrast, an EBNA-LP 62-kDa isoform does not demonstrate detectable shuttling in the heterokaryon assay yet still coactivates EBNA2 similarly to the smaller EBNA-LP isoforms. All of the EBNA-LP mutants tested, including the coactivation-deficient ΔCR3 mutant and the nonshuttling 62-kDa isoform, were capable of associating with HDAC4. Taken together, our results suggest that simple diffusion may account for the nuclear export observed with smaller isoforms of EBNA-LP, that nuclear-cytoplasmic shuttling is not required for efficient EBNA-LP coactivation function, and that competence for HDAC4 association is not sufficient to mediate nuclear-cytoplasmic shuttling or EBNA-LP coactivation in the absence of a functional interaction with Sp100A.
Rhinovirus 3C Protease Can Localize in the Nucleus and Alter Active and Passive Nucleocytoplasmic Transport
Authors: Ghildyal Reena , Jordan Benjamin , Li Dongsheng , Dagher Hayat , Bardin Phillip G. , Gern James E. , Jans David A. 
Published: April 2009

ABSTRACT
The degradation of nuclear pore components and disruption of nucleocytoplasmic trafficking during rhinovirus infection have been attributed to viral 2A protease. Here we show for the first time that rhinovirus 3C protease may also have a role. Specifically, we show that 3C and its precursor, 3CD, can target green fluorescent protein to the nucleus of living cells, leading to degradation of nuclear pore components, and that incubation with recombinant 3C disrupts active and passive nucleocytoplasmic transport in a semi-intact cell nuclear transport system dependent on 3C protease activity. 3C may thus contribute to host cell shutoff in infected cells by localizing in the nucleus and facilitating nuclear pore breakdown.