bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequency of Decreased Susceptibility and Resistance to Echinocandins among Fluconazole-Resistant Bloodstream Isolates of Candida glabrata
Authors: Pfaller M. A. , Castanheira M. , Lockhart S. R. , Ahlquist A. M. , Messer S. A. , Jones R. N. 
Published: January 2012

ABSTRACT

The echinocandin class of antifungal agents is considered to be the first-line treatment of bloodstream infections (BSI) due to
Candida glabrata
. Recent reports of BSI due to strains of
C. glabrata
resistant to both fluconazole and the echinocandins are of concern and prompted us to review the experience of two large surveillance programs, the SENTRY Antimicrobial Surveillance Program for the years 2006 through 2010 and the Centers for Disease Control and Prevention population-based surveillance conducted in 2008 to 2010. The
in vitro
susceptibilities of 1,669 BSI isolates of
C. glabrata
to fluconazole, voriconazole, anidulafungin, caspofungin, and micafungin were determined by CLSI broth microdilution methods. Fluconazole MICs of ≥64 μg/ml were considered resistant. Strains for which anidulafungin and caspofungin MICs were ≥0.5 μg/ml and for which micafungin MICs were ≥0.25 μg/ml were considered resistant. A total of 162 isolates (9.7%) were resistant to fluconazole, of which 98.8% were nonsusceptible to voriconazole (MIC > 0.5 μg/ml) and 9.3%, 9.3%, and 8.0% were resistant to anidulafungin, caspofungin, and micafungin, respectively. There were 18 fluconazole-resistant isolates that were resistant to one or more of the echinocandins (11.1% of all fluconazole-resistant isolates), all of which contained an acquired mutation in
fks1
or
fks2
. By comparison, there were no echinocandin-resistant strains detected among 110 fluconazole-resistant isolates of
C. glabrata
tested in 2001 to 2004. These data document the broad emergence of coresistance over time to both azoles and echinocandins in clinical isolates of
C. glabrata
.
ϕ
2
GFP10, a High-Intensity Fluorophage, Enables Detection and Rapid Drug Susceptibility Testing of Mycobacterium tuberculosis Directly from Sputum Samples
Authors: Jain Paras , Hartman Travis E. , Eisenberg Nell , O'Donnell Max R. , Kriakov Jordan , Govender Karnishree , Makume Mantha , Thaler David S. , Hatfull Graham F. , Sturm A. Willem , Larsen Michelle H. , Moodley Preshnie , Jacobs William R. 
Published: January 2012

ABSTRACT

The difficulty of diagnosing active tuberculosis (TB) and lack of rapid drug susceptibility testing (DST) at the point of care remain critical obstacles to TB control. This report describes a high-intensity mycobacterium-specific-fluorophage (ϕ
2
GFP10) that for the first time allows direct visualization of
Mycobacterium tuberculosis
in clinical sputum samples. Engineered features distinguishing ϕ
2
GFP10 from previous reporter phages include an improved vector backbone with increased cloning capacity and superior expression of fluorescent reporter genes through use of an efficient phage promoter. ϕ
2
GFP10 produces a 100-fold increase in fluorescence per cell compared to existing reporter phages. DST for isoniazid and oxofloxacin, carried out in cultured samples, was complete within 36 h. Use of ϕ
2
GFP10 detected
M. tuberculosis
in clinical sputum samples collected from TB patients. DST for rifampin and kanamycin from sputum samples yielded results after 12 h of incubation with ϕ
2
GFP10. Fluorophage ϕ
2
GFP10 has potential for clinical development as a rapid, sensitive, and inexpensive point-of-care diagnostic tool for
M. tuberculosis
infection and for rapid DST.
Detection of Toxigenic Clostridium difficile: Comparison of the Cell Culture Neutralization, Xpert C. difficile, Xpert C. difficile/Epi, and Illumigene C. difficile Assays
Authors: Pancholi P. , Kelly C. , Raczkowski M. , Balada-Llasat J. M. 
Published: January 2012

ABSTRACT

Clostridium difficile
is the most important cause of nosocomial diarrhea. Several laboratory techniques are available to detect
C. difficile
toxins or the genes that encode them in fecal samples. We evaluated the Xpert
C. difficile
and Xpert
C. difficile
/Epi (Cepheid, CA) that detect the toxin B gene (
tcdB
) and
tcdB
,
cdt
, and a deletion in
tcdC
associated with the 027/NAP1/BI strain, respectively, by real-time PCR, and the Illumigene
C. difficile
(Meridian Bioscience, Inc.) that detects the toxin A gene (
tcdA
) by loop-mediated isothermal amplification in stool specimens. Toxigenic culture was used as the reference method for discrepant stool specimens. Two hundred prospective and fifty retrospective diarrheal stool specimens were tested simultaneously by the cell cytotoxin neutralization assay (CCNA) and the Xpert
C. difficile
, Xpert
C. difficile
/Epi, and Illumigene
C. difficile
assays. Of the 200 prospective stools tested, 10.5% (
n
= 23) were determined to be positive by CCNA, 17.5% (
n
= 35) were determined to be positive by Illumigene
C. difficile
, and 21.5% (
n
= 43) were determined to be positive by Xpert
C. difficile
and Xpert
C. difficile
/Epi. Of the 50 retrospective stools, previously determined to be positive by CCNA, 94% (
n
= 47) were determined to be positive by Illumigene
C. difficile
and 100% (
n
= 50) were determined to be positive by Xpert
C. difficile
and Xpert
C. difficile
/Epi. Of the 11 discrepant results (i.e., negative by Illumigene
C. difficile
but positive by Xpert
C. difficile
and Xpert
C. difficile
/Epi), all were determined to be positive by the toxigenic culture. A total of 21% of the isolates were presumptively identified by the Xpert
C. difficile
/Epi as the 027/NAP1/BI strain. The Xpert
C. difficile
and Xpert
C. difficile
/Epi assays were the most sensitive, rapid, and easy-to use assays for the detection of toxigenic
C. difficile
in stool specimens.
Evaluation of Several Biochemical and Molecular Techniques for Identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and Their Detection in Respiratory Samples
Authors: Wessels Els , Schelfaut Jacqueline J. G. , Bernards Alexandra T. , Claas Eric C. J. 
Published: January 2012

ABSTRACT

The identification and detection of mitis group streptococci, which contain
Streptococcus pneumoniae
, have been hampered by the lack of sensitive and specific assays. In this study, we evaluated several biochemical and molecular assays for the identification of
S. pneumoniae
and
Streptococcus pseudopneumoniae
and their distinction from other mitis group streptococci using a collection of 54 isolates obtained by the routine culturing of 53 respiratory specimens from patients with community-acquired pneumonia. The combined results of the biochemical and molecular assays indicated the presence of 23
S. pneumoniae
, 2
S. pseudopneumoniae
, and 29 other mitis group streptococcal isolates. The tube bile solubility test that is considered gold standard for the identification of
S. pneumoniae
showed concordant results with optochin susceptibility testing (CO
2
atmosphere) and a real-time multiplex PCR assay targeting the Spn9802 fragment and the autolysin gene. Optochin susceptibility testing upon incubation in an O
2
atmosphere, bile solubility testing by oxgall disk, matrix-assisted laser desorption ionization–time of flight mass spectrometry, and sequence analysis of the
tuf
and
rpoB
genes resulted in several false-positive, false-negative, or inconclusive results. The
S. pseudopneumoniae
isolates could be identified only by molecular assays, and the multiplex real-time PCR assay was concluded to be most convenient for the identification of
S. pneumoniae
and
S. pseudopneumoniae
isolates. Using this method,
S. pneumoniae
and
S. pseudopneumoniae
DNA could be detected in the respiratory samples from which they were isolated and in an additional 11 samples from which only other streptococci were isolated.
Species Specificity of Protein Kinase R Antagonism by Cytomegalovirus TRS1 Genes
Authors: Child Stephanie J. , Brennan Greg , Braggin Jacquelyn E. , Geballe Adam P. 
Published: January 2012

ABSTRACT
The host antiviral protein kinase R (PKR) has rapidly evolved during primate evolution, likely in response to challenges posed by many different viral antagonists, such as the TRS1 gene of cytomegaloviruses (CMVs). In turn, viral antagonists have adapted to changes in PKR. As a result of this “arms race,” modern TRS1 alleles in CMVs may function differently in cells derived from alternative species. We have previously shown that human CMV TRS1 (HuTRS1) blocks the PKR pathway and rescues replication of a vaccinia virus mutant lacking its major PKR antagonist in human cells. We now demonstrate that HuTRS1 does not have these activities in Old World monkey cells. Conversely, the rhesus cytomegalovirus homologue of HuTRS1 (RhTRS1) fulfills these functions in African green monkey cells, but not rhesus or human cells. Both TRS1 proteins bind to double-stranded RNA and, in the cell types in which they can rescue VVΔE3L replication, they also bind to PKR and prevent phosphorylation of the α-subunit of eukaryotic initiation factor 2. However, while HuTRS1 binds to inactive human PKR and prevents its autophosphorylation, RhTRS1 binds to phosphorylated African green monkey PKR. These studies reveal that evolutionary adaptations in this critical host defense protein have altered its binding interface in a way that has resulted in a qualitatively altered mechanism of PKR antagonism by viral TRS1 alleles from different CMVs. These results suggest that PKR antagonism is likely one of the factors that contributes to species specificity of cytomegalovirus replication.
Canine Distemper Virus Epithelial Cell Infection Is Required for Clinical Disease but Not for Immunosuppression
Authors: Sawatsky Bevan , Wong Xiao-Xiang , Hinkelmann Sarah , Cattaneo Roberto , von Messling Veronika 
Published: January 2012

ABSTRACT
To characterize the importance of infection of epithelial cells for morbillivirus pathogenesis, we took advantage of the severe disease caused by canine distemper virus (CDV) in ferrets. To obtain a CDV that was unable to enter epithelial cells but retained the ability to enter immune cells, we transferred to its attachment (H) protein two mutations shown to interfere with the interaction of measles virus H with its epithelial receptor, human nectin-4. As expected for an epithelial receptor (EpR)-blind CDV, this virus infected dog and ferret epithelial cells inefficiently and did not cause cell fusion or syncytium formation. On the other hand, the EpR-blind CDV replicated in cells expressing canine signaling lymphocyte activation molecule (SLAM), the morbillivirus immune cell receptor, with similar kinetics to those of wild-type CDV. While ferrets infected with wild-type CDV died within 12 days after infection, after developing severe rash and fever, animals infected with the EpR-blind virus showed no clinical signs of disease. Nevertheless, both viruses spread rapidly and efficiently in immune cells, causing similar levels of leukopenia and inhibition of lymphocyte proliferation activity, two indicators of morbillivirus immunosuppression. Infection was documented for airway epithelia of ferrets infected with wild-type CDV but not for those of animals infected with the EpR-blind virus, and only animals infected with wild-type CDV shed virus. Thus, epithelial cell infection is necessary for clinical disease and efficient virus shedding but not for immunosuppression.
Cell Entry-Associated Conformational Changes in Reovirus Particles Are Controlled by Host Protease Activity
Authors: Madren Jillann A. , Sarkar Payel , Danthi Pranav 
Published: January 2012

ABSTRACT

Membrane penetration by reovirus requires successive formation of two cell entry intermediates, infectious subvirion particles (ISVPs) and ISVP*s.
In vitro
incubation of reovirus virions with high concentration of chymotrypsin (CHT) results in partial digestion of the viral outer capsid to form ISVPs. When virions are instead digested with low concentrations of chymotrypsin, the outer capsid is completely proteolyzed to form cores. We investigated the basis for the inverse relationship between CHT activity and protease susceptibility of the reovirus outer capsid. We report that core formation following low-concentration CHT digestion proceeds via formation of particles that contain a protease-sensitive form of the μ1C protein, a characteristic of ISVP*s. In addition, we found that both biochemical features and viral genetic requirements for ISVP* formation and core formation following low-concentration CHT digestion are identical, suggesting that core formation proceeds via a particle resembling ISVP*s. Furthermore, we determined that intermediates generated following low-concentration CHT digestion are distinct from ISVPs and convert to ISVP*-like particles much more readily than ISVPs. These results suggest that the activity of host proteases used to generate ISVPs can influence the efficiency with which the next step in reovirus cell entry, namely, ISVP-to-ISVP* conversion, occurs.
Roles of the Coding and Noncoding Regions of Rift Valley Fever Virus RNA Genome Segments in Viral RNA Packaging
Authors: Murakami Shin , Terasaki Kaori , Narayanan Krishna , Makino Shinji 
Published: January 2012

ABSTRACT
We characterized the RNA elements involved in the packaging of Rift Valley fever virus RNA genome segments, L, M, and S. The 5′-terminal 25 nucleotides of each RNA segment were equally competent for RNA packaging and carried an RNA packaging signal, which overlapped with the RNA replication signal. Only the deletion mutants of L RNA, but not full-length L RNA, were efficiently packaged, implying the possible requirement of RNA compaction for L RNA packaging.
Timely Synthesis of the Adenovirus Type 5 E1B 55-Kilodalton Protein Is Required for Efficient Genome Replication in Normal Human Cells
Authors: Chahal Jasdave S. , Flint S. J. 
Published: January 2012

ABSTRACT
Previous studies have indicated that the adenovirus type 5 E1B 55-kDa protein facilitates viral DNA synthesis in normal human foreskin fibroblasts (HFFs) but not in primary epithelial cells. To investigate this apparent difference further, viral DNA accumulation was examined in primary human fibroblasts and epithelial cells infected by the mutant AdEasyE1Δ2347, which carries the Hr6 frameshift mutation that prevents production of the E1B 55-kDa protein, in an E1-containing derivative of AdEasy. Impaired viral DNA synthesis was observed in normal HFFs but not in normal human bronchial epithelial cells infected by this mutant. However, acceleration of progression through the early phase, which is significantly slower in HFFs than in epithelial cells, eliminated the dependence of efficient viral DNA synthesis in HFFs on the E1B 55-kDa protein. These observations suggest that timely synthesis of the E1B 55-kDa protein protects normal cells against a host defense that inhibits adenoviral genome replication. One such defense is mediated by the Mre11-Rad50-Nbs1 complex. Nevertheless, examination of the localization of Mre11 and viral proteins by immunofluorescence suggested that this complex is inactivated similarly in AdEasyE1Δ2347 mutant-infected and AdEasyE1-infected HFFs.
The Multibasic Cleavage Site in H5N1 Virus Is Critical for Systemic Spread along the Olfactory and Hematogenous Routes in Ferrets
Authors: Schrauwen Eefje J. A. , Herfst Sander , Leijten Lonneke M. , van Run Peter , Bestebroer Theo M. , Linster Martin , Bodewes Rogier , Kreijtz Joost H. C. M. , Rimmelzwaan Guus F. , Osterhaus Albert D. M. E. , Fouchier Ron A. M. , Kuiken Thijs , van Riel Debby 
Published: January 2012

ABSTRACT
The route by which highly pathogenic avian influenza (HPAI) H5N1 virus spreads systemically, including the central nervous system (CNS), is largely unknown in mammals. Especially, the olfactory route, which could be a route of entry into the CNS, has not been studied in detail. Although the multibasic cleavage site (MBCS) in the hemagglutinin (HA) of HPAI H5N1 viruses is a major determinant of systemic spread in poultry, the association between the MBCS and systemic spread in mammals is less clear. Here we determined the virus distribution of HPAI H5N1 virus in ferrets in time and space—including along the olfactory route—and the role of the MBCS in systemic replication. Intranasal inoculation with wild-type H5N1 virus revealed extensive replication in the olfactory mucosa, from which it spread to the olfactory bulb and the rest of the CNS, including the cerebrospinal fluid (CSF). Virus spread to the heart, liver, pancreas, and colon was also detected, indicating hematogenous spread. Ferrets inoculated intranasally with H5N1 virus lacking an MBCS demonstrated respiratory tract infection only. In conclusion, HPAI H5N1 virus can spread systemically via two different routes, olfactory and hematogenous, in ferrets. This systemic spread was dependent on the presence of the MBCS in HA.
Draft Genome Sequence of the Coccolithovirus Emiliania huxleyi Virus 202
Authors: Nissimov Jozef I. , Worthy Charlotte A. , Rooks Paul , Napier Johnathan A. , Kimmance Susan A. , Henn Matthew R. , Ogata Hiroyuki , Allen Michael J. 
Published: January 2012

ABSTRACT

Emiliania huxleyi
virus 202 (EhV-202) is a member of the
Coccolithoviridae
, a group of viruses that infect the marine coccolithophorid
Emiliania huxleyi
. EhV-202 has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 407 kbp, consisting of 485 coding sequences (CDSs). Here we describe the genomic features of EhV-202, together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.
Structural Basis for Broad Detection of Genogroup II Noroviruses by a Monoclonal Antibody That Binds to a Site Occluded in the Viral Particle
Authors: Hansman Grant S. , Taylor David W. , McLellan Jason S. , Smith Thomas J. , Georgiev Ivelin , Tame Jeremy R. H. , Park Sam-Yong , Yamazaki Makoto , Gondaira Fumio , Miki Motohiro , Katayama Kazuhiko , Murata Kazuyoshi , Kwong Peter D. 
Published: January 2012

ABSTRACT
Human noroviruses are genetically and antigenically highly divergent. Monoclonal antibodies raised in mice against one kind of norovirus virus-like particle (VLP), however, were found to have broad recognition. In this study, we present the crystal structure of the antigen-binding fragment (Fab) for one of these broadly reactive monoclonal antibodies, 5B18, in complex with the capsid-protruding domain from a genogroup II genotype 10 (GII.10) norovirus at 3.3-Å resolution and, also, the cryo-electron microscopy structure of the GII.10 VLP at ∼10-Å resolution. The GII.10 VLP structure was more similar in overall architecture to the GV.1 murine norovirus virion than to the prototype GI.1 human norovirus VLP, with the GII.10 protruding domain raised ∼15 Å off the shell domain and rotated ∼40° relative to the GI.1 protruding domain. In the crystal structure, the 5B18 Fab bound to a highly conserved region of the protruding domain. Based on the VLP structure, this region is involved in interactions with other regions of the capsid and is buried in the virus particle. Despite the occluded nature of the recognized epitope in the VLP structure, enzyme-linked immunosorbent assay (ELISA) binding suggested that the 5B18 antibody was able to capture intact VLPs. Together, the results provide evidence that the norovirus particle is capable of extreme conformational flexibility, which may allow for antibody recognition of conserved surfaces that would otherwise be buried on intact particles.
Recombinant Dengue Type 2 Viruses with Altered E Protein Domain III Epitopes Are Efficiently Neutralized by Human Immune Sera
Authors: Wahala Wahala M. P. B. , Huang Claire , Butrapet Siritorn , White Laura J. , de Silva Aravinda M. 
Published: January 2012

ABSTRACT
Humans develop polyclonal, serotype-specific neutralizing antibody responses after dengue virus (DENV) infection. Many mouse antibodies that neutralize DENV bind to the lateral ridge or A strand epitopes on domain III of the viral envelope (EDIII) protein. It has been assumed that these epitopes are also the main target of human neutralizing antibodies. Using recombinant dengue serotype 2 viruses with altered EDIII epitopes, we demonstrate that EDIII epitopes are not the main target of human neutralizing antibody.
Distinct Transformation Tropism Exhibited by Human T Lymphotropic Virus Type 1 (HTLV-1) and HTLV-2 Is the Result of Postinfection T Cell Clonal Expansion
Authors: Kannian Priya , Yin Han , Doueiri Rami , Lairmore Michael D. , Fernandez Soledad , Green Patrick L. 
Published: January 2012

ABSTRACT

Human T lymphotropic virus type 1 (HTLV-1) and HTLV-2 are related but pathogenically distinct viruses. HTLV-1 mainly causes adult T cell leukemia, while HTLV-2 is not associated with leukemia.
In vitro
, HTLV-1 and HTLV-2 predominantly transform CD4
+
and CD8
+
T cells, respectively: the genetic determinant maps to the viral envelope. Herein, we investigate whether this transformation tropism occurs during initial infection or subsequently during the cellular transformation process. Since most individuals are chronically infected at the time of detection, we utilized an established rabbit model to longitudinally measure the early HTLV-1 and HTLV-2 infection and replication kinetics in purified CD4
+
and CD8
+
T cells. HTLV-1 and HTLV-2 were detected in both CD4
+
and CD8
+
T cells within 1 week postinoculation. In HTLV-1-infected rabbit CD4
+
T cells, proviral burden and
tax
/
rex
mRNA expression peaked early, and expression levels were directly proportional to each other. The late expression of the antisense transcript (
Hbz
or
Aph-2
) correlated directly with a late proviral burden peak in HTLV-1- or HTLV-2-infected rabbit CD8
+
T cells, respectively. This study provides the first
in vivo
evidence that these viruses do not exhibit cellular preference during initial infection. We further evaluated the transformation tropism of HTLV-1 and HTLV-2 over a 9-week period using
in vitro
cell growth/immortalization assays. At the early weeks, both HTLV-1 and HTLV-2 showed proportionate growth of CD4
+
and CD8
+
T cells. However, beyond week 5, the predominance of one particular T cell type emerged, supporting the conclusion that transformation tropism is a postinfection event due to selective clonal expansion over time.
Hepatitis C Virus Infection of Human T Lymphocytes Is Mediated by CD5
Authors: Sarhan Mohammed A. , Pham Tram N. Q. , Chen Annie Y. , Michalak Tomasz I. 
Published: January 2012

ABSTRACT
Hepatitis C virus (HCV) is one of the main causes of chronic liver disease. Although infection of hepatocytes is mainly responsible for manifestations of hepatitis C, the virus also invades the immune system by a yet-to-be-identified mechanism. Using human T cell lines and primary T lymphocytes as targets and patient-derived HCV as inocula, we aimed to identify how HCV gains entry into these cells. HCV replication was determined by detection of the HCV RNA replicative (negative) strand and viral proteins, while specific antibodies, knocking down gene expression and making otherwise-resistant cells prone to HCV, were employed to identify a receptor molecule determining T lymphocyte permissiveness to HCV infection. The results revealed that T cell susceptibility to HCV requires CD5, a lymphocyte-specific glycoprotein belonging to the scavenger receptor cysteine-rich family. Blocking of T cell CD5 with antibody or silencing with specific short hairpin RNA (shRNA) decreased cell susceptibility to HCV, while increasing CD5 expression by mitogen stimulation had the opposite effect. Moreover, transfection of naturally CD5-deficient HEK-293 fibroblasts with CD5 facilitated infection of these otherwise HCV-resistant cells. In contrast to T cells, hepatocytes do not express CD5. The data revealed that CD5 is a molecule important for HCV entry into human T lymphocytes. This finding provides direct insight into the mechanism of HCV lymphotropism and defines a target for potential interventions against HCV propagating in this extrahepatic compartment.