bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of the OraQuick HCV Rapid Antibody Test for Screening Exposed Patients in a Hepatitis C Outbreak Investigation
Authors: Gao Fengxiang , Talbot Elizabeth A. , Loring Carol H. , Power Jill J. , Dionne-Odom Jodie , Alroy-Preis Sharon , Jackson Patricia , Bean Christine L. 
Published: May 2014

ABSTRACT
During a nosocomial hepatitis C outbreak, emergency public clinics employed the OraQuick HCV rapid antibody test on site, and all results were verified by a standard enzyme immunoassay (EIA). Of 1,157 persons, 1,149 (99.3%) exhibited concordant results between the two tests (16 positive, 1,133 negative). The sensitivity, specificity, positive predictive value, and negative predictive value were 94.1%, 99.5%, 72.7%, and 99.9%, respectively. OraQuick performed well as a screening test during an outbreak investigation and could be integrated into future hepatitis C virus (HCV) outbreak testing algorithms.
Next-Generation Sequencing for Typing and Detection of Resistance Genes: Performance of a New Commercial Method during an Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli
Authors: Veenemans J. , Overdevest I. T. , Snelders E. , Willemsen I. , Hendriks Y. , Adesokan A. , Doran G. , Bruso S. , Rolfe A. , Pettersson A. , Kluytmans J. A. J. W. 
Published: May 2014

ABSTRACT

Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131)
Escherichia coli
infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL)
E. coli
isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of
E. coli
isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.
Evaluation of Curetis Unyvero, a Multiplex PCR-Based Testing System, for Rapid Detection of Bacteria and Antibiotic Resistance and Impact of the Assay on Management of Severe Nosocomial Pneumonia
Authors: Jamal Wafaa , Al Roomi Ebtehal , AbdulAziz Lubna R. , Rotimi Vincent O. 
Published: May 2014

ABSTRACT

Health care-associated pneumonia due to multidrug-resistant organisms represents a major therapeutic challenge. Unfortunately, treatment is dependent on empirical therapy, which often leads to improper and inadequate antimicrobial therapy. A rapid multiplex PCR-based Unyvero pneumonia application (UPA) assay that assists in timely decision-making has recently become available. In this study, we evaluated the performance of UPA in detecting etiological pathogens and resistance markers in patients with nosocomial pneumonia (NP). The impact of this assay on the management of severe nosocomial pneumonia was also assessed. Appropriate specimens were processed by UPA according to the manufacturer's protocol in parallel with conventional culture methods. Of the 56 patients recruited into the study, 49 (87.5%) were evaluable. Of these, 27 (55.1%) and 4 (8.2%) harbored multiple bacteria by the PCR assay and conventional culture, respectively. A single pathogen was detected in 8 (16.3%) and 4 (8.2%) patients, respectively. Thirteen different genes were detected from 38 patients, including the
ermB
gene (40.8%), the
bla
OXA-51
-like gene (28.6%), the
sul1
(28.6%) and
int1
(20.4%) integrase genes, and the
mecA
and
bla
CTX-M
genes (12.3% each). The time from sample testing to results was 4 h versus 48 to 96 h by UPA and culture, respectively. Initial empirical treatment was changed within 5 to 6 h in 33 (67.3%) patients based on the availability of UPA results. Thirty (62.2%) of the patients improved clinically. A total of 3 (6.1%) patients died, mainly from their comorbidities. These data demonstrate the potential of a multiplex PCR-based assay for accurate and timely detection of etiological agents of NP, multidrug-resistant (MDR) organisms, and resistance markers, which can guide clinicians in making early antibiotic adjustments.
Development and Clinical Evaluation of
sdaA
Loop-Mediated Isothermal Amplification Assay for Detection of Mycobacterium tuberculosis with an Approach To Prevent Carryover Contamination
Authors: Nimesh Manoj , Joon Deepali , Varma-Basil Mandira , Saluja Daman 
Published: May 2014

ABSTRACT

A rapid and sensitive loop-mediated isothermal amplification assay for the
sdaA
gene of
Mycobacterium tuberculosis
was developed using a dUTP-uracil-
N
-glycosylase (dUTP-UNG) strategy to prevent carryover contamination. Evaluation of the assay using clinical specimens (
n
= 648) showed high specificity (97.2%) and sensitivity (100%), demonstrating its potential as a diagnostic test for tuberculosis, especially in resource-limited settings.
Predicted Configurations of Oligosaccharide Extensions in the Lipooligosaccharide of Nontypeable Haemophilus influenzae Isolates
Authors: McCrea Kirk W. , Xie Jingping , Daniel Deborah , Ulrich-Lewis Justin Theophilus , Zhang Lixin 
Published: May 2014

ABSTRACT

Lipooligosaccharide configurations were predicted in nontypeable
Haemophilus influenzae
isolates based on the presence of seven oligosaccharide extension-initiating genes (or alleles). Predicted configurations with 2 to 3 oligosaccharide extensions were more prevalent among middle ear than throat strains. In addition, strains with these configurations averaged higher levels of serum resistance than strains with other configurations.
Mixed Mycobacterium tuberculosis Complex Infections and False-Negative Results for Rifampin Resistance by GeneXpert MTB/RIF Are Associated with Poor Clinical Outcomes
Authors: Zetola Nicola M. , Shin Sanghyuk S. , Tumedi Kefentse A. , Moeti Keletso , Ncube Ronald , Nicol Mark , Collman Ronald G. , Klausner Jeffrey D. , Modongo Chawangwa 
Published: May 2014

ABSTRACT

The Xpert MTB/RIF (Xpert) assay is becoming a principal screening tool for diagnosing rifampin-resistant
Mycobacterium tuberculosis
complex (MTBC) infection. However, little is known about the performance of the Xpert assay in infections with both drug-sensitive and drug-resistant strains (mixed MTBC infections). We assessed the performance of the Xpert assay for detecting rifampin resistance using phenotypic drug sensitivity testing (DST) as the reference standard in 370 patients with microbiologically proven pulmonary tuberculosis. Mixed MTBC infections were identified genetically through 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) analysis. Logistic regression was used to identify the factors associated with poor (defined as treatment failure, default, and death from any cause) or good (defined as cure or successful treatment completion) clinical outcomes. The analytic sensitivity of the Xpert assay for detecting rifampin resistance was assessed
in vitro
by testing cultures containing different ratios of drug-sensitive and drug-resistant organisms. Rifampin resistance was detected by the Xpert assay in 52 (14.1%) and by phenotypic DST in 55 (14.9%) patients. Mixed MTBC infections were identified in 37 (10.0%) patients. The Xpert assay was 92.7% (95% confidence interval [CI], 82.4% to 97.9%) sensitive for detecting rifampin resistance and 99.7% (95% CI, 98.3% to 99.9%) specific. When restricted to patients with mixed MTBC infections, Xpert sensitivity was 80.0% (95% CI, 56.3 to 94.3%). False-negative Xpert results (adjusted odds ratio [aOR], 6.6; 95% CI,1.2 to 48.2) and mixed MTBC infections (aOR, 6.5; 95% CI, 2.1 to 20.5) were strongly associated with poor clinical outcome. The Xpert assay failed to detect rifampin resistance
in vitro
when <90% of the organisms in the sample were rifampin resistant. Our study indicates that the Xpert assay has an increased false-negative rate for detecting rifampin resistance with mixed MTBC infections. In hyperendemic settings where mixed infections are common, the Xpert results might need further confirmation.
Multicenter Feasibility Study To Assess External Quality Assessment Panels for Xpert MTB/RIF Assay in South Africa
Authors: Scott Lesley , Albert Heidi , Gilpin Chris , Alexander Heather , DeGruy Kyle , Stevens Wendy 
Published: May 2014

ABSTRACT

External quality assessment (EQA) for the Xpert MTB/RIF assay is part of the quality system required for clinical and laboratory practice. Five newly developed EQA panels that use different matrices, including a lyophilized sample (Vircell, Granada, Spain), a dried tube specimen (CDC), liquid (Maine Molecular Quality Control, Inc. [MMQCI], Scarborough, ME), artificial sputum (Global Laboratory Initiative [GLI]), and a dried culture spot (National Health Laboratory Services [NHLS]), were evaluated at 11 GeneXpert testing sites in South Africa. The panels comprised
Mycobacterium tuberculosis
complex (MTBC)-negative, MTBC-positive (including rifampin [RIF] susceptible and RIF resistant), and nontuberculosis mycobacterial material that was inactivated and safe for transportation. Twelve qualitative and quantitative variables were scored as acceptable (1) or unacceptable (0); the overall panel performance score for the Vircell, CDC, GLI, and NHLS panels was 9 of 12, while the MMQCI panel scored 6 of 12 (owing to the need for cold chain maintenance). All panels showed good compatibility with Xpert MTB/RIF testing, and none showed PCR inhibition. The use of a liquid or dry matrix did not appear to be a distinguishing criterion, as both matrices had reduced scores on insufficient volumes, a need for extra consumables, and the ability to transfer to the Xpert MTB/RIF cartridge. EQA is an important component of the quality system required for diagnostic testing programs, but it must be complemented by routine monitoring of performance indicators and instrument verification. This study aims to introduce EQA concepts for Xpert MTB/RIF testing and evaluates five potential EQA panels.
Capture of syncytin-Mar1, a Fusogenic Endogenous Retroviral Envelope Gene Involved in Placentation in the Rodentia Squirrel-Related Clade
Authors: Redelsperger François , Cornelis Guillaume , Vernochet Cécile , Tennant Bud C. , Catzeflis François , Mulot Baptiste , Heidmann Odile , Heidmann Thierry , Dupressoir Anne 
Published: May 2014

ABSTRACT

Syncytin
genes are fusogenic envelope protein (
env
) genes of retroviral origin that have been captured for a function in placentation. Within rodents, two such genes have previously been identified in the mouse-related clade, allowing a demonstration of their essential role via knockout mice. Here, we searched for similar genes in a second major clade of the Rodentia order, the squirrel-related clade, taking advantage of the complete sequencing of the ground squirrel
Ictidomys tridecemlineatus
genome.
In silico
search for
env
genes with full coding capacity identified several candidate genes with one displaying placenta-specific expression, as revealed by quantitative reverse transcription-PCR analysis of a large panel of tissues. This gene belongs to a degenerate endogenous retroviral element, with recognizable hallmarks of an integrated provirus. Cloning of the gene in an expression vector for
ex vivo
cell-cell fusion and pseudotype assays demonstrated fusogenicity on a large panel of mammalian cells.
In situ
hybridization on placenta sections showed specific expression in domains where trophoblast cells fuse into a syncytiotrophoblast at the fetomaternal interface, consistent with a role in syncytium formation. Finally, we show that the gene is conserved among the tribe Marmotini, thus dating its capture back to about at least 25 million years ago, with evidence for purifying selection and conservation of fusogenic activity. This gene that we named
syncytin-Mar1
is distinct from all seven
Syncytin
genes identified to date in eutherian mammals and is likely to be a major effector of placentation in its related clade.

IMPORTANCE
Syncytin
genes are fusogenic envelope genes of retroviral origin, ancestrally captured for a function in placentation. Within rodents, two such genes had been previously identified in the mouse-related clade. Here, in the squirrel-related rodent clade, we identified the envelope gene of an endogenous retrovirus with all the features of a
Syncytin
: it is specifically expressed in the placenta of the woodchuck
Marmota monax
, at the level of cells fusing into a syncytium; it can trigger cell-cell and virus-cell fusion
ex vivo
; and it has been conserved for >25 million years of evolution, suggesting an essential role in its host physiology. Remarkably,
syncytin-Mar1
is unrelated to all other
Syncytin
genes identified thus far in mammals (primates, muroids, carnivores, and ruminants). These results extend the range of retroviral envelope gene “domestication” in mammals and show that these events occurred independently, on multiple occasions during evolution to improve placental development in a process of convergent evolution.
Specificities of Human CD4
+
T Cell Responses to an Inactivated Flavivirus Vaccine and Infection: Correlation with Structure and Epitope Prediction
Authors: Schwaiger Julia , Aberle Judith H. , Stiasny Karin , Knapp Bernhard , Schreiner Wolfgang , Fae Ingrid , Fischer Gottfried , Scheinost Ondrej , Chmelik Vaclav , Heinz Franz X. 
Published: May 2014

ABSTRACT

Tick-borne encephalitis (TBE) virus is endemic in large parts of Europe and Central and Eastern Asia and causes more than 10,000 annual cases of neurological disease in humans. It is closely related to the mosquito-borne yellow fever, dengue, Japanese encephalitis, and West Nile viruses, and vaccination with an inactivated whole-virus vaccine can effectively prevent clinical disease. Neutralizing antibodies are directed to the viral envelope protein (E) and an accepted correlate of immunity. However, data on the specificities of CD4
+
T cells that recognize epitopes in the viral structural proteins and thus can provide direct help to the B cells producing E-specific antibodies are lacking. We therefore conducted a study on the CD4
+
T cell response against the virion proteins in vaccinated people in comparison to TBE patients. The data obtained with overlapping peptides in interleukin-2 (IL-2) enzyme-linked immunosorbent spot (ELISpot) assays were analyzed in relation to the three-dimensional structures of the capsid (C) and E proteins as well as to epitope predictions based on major histocompatibility complex (MHC) class II peptide affinities. In the C protein, peptides corresponding to two out of four alpha helices dominated the response in both vaccinees and patients, whereas in the E protein concordance of immunodominance was restricted to peptides of a single domain (domain III). Epitope predictions were much better for C than for E and were especially erroneous for the transmembrane regions. Our data provide evidence for a strong impact of protein structural features that influence peptide processing, contributing to the discrepancies observed between experimentally determined and computer-predicted CD4
+
T cell epitopes.

IMPORTANCE
Tick-borne encephalitis virus is endemic in large parts of Europe and Asia and causes more than 10,000 annual cases of neurological disease in humans. It is closely related to yellow fever, dengue, Japanese encephalitis, and West Nile viruses, and vaccination with an inactivated vaccine can effectively prevent disease. Both vaccination and natural infection induce the formation of antibodies to a viral surface protein that neutralize the infectivity of the virus and mediate protection. B lymphocytes synthesizing these antibodies require help from other lymphocytes (helper T cells) which recognize small peptides derived from proteins contained in the viral particle. Which of these peptides dominate immune responses to vaccination and infection, however, was unknown. In our study we demonstrate which parts of the proteins contribute most strongly to the helper T cell response, highlight specific weaknesses of currently available approaches for their prediction, and demonstrate similarities and differences between vaccination and infection.
Investigating the Role of F-Actin in Human Immunodeficiency Virus Assembly by Live-Cell Microscopy
Authors: Rahman Sheikh Abdul , Koch Peter , Weichsel Julian , Godinez William J. , Schwarz Ulrich , Rohr Karl , Lamb Don C. , Kräusslich Hans-Georg , Müller Barbara 
Published: May 2014

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) particles assemble at the plasma membrane, which is lined by a dense network of filamentous actin (F-actin). Large amounts of actin have been detected in HIV-1 virions, proposed to be incorporated by interactions with the nucleocapsid domain of the viral polyprotein Gag. Previous studies addressing the role of F-actin in HIV-1 particle formation using F-actin-interfering drugs did not yield consistent results. Filamentous structures pointing toward nascent HIV-1 budding sites, detected by cryo-electron tomography and atomic force microscopy, prompted us to revisit the role of F-actin in HIV-1 assembly by live-cell microscopy. HeLa cells coexpressing HIV-1 carrying fluorescently labeled Gag and a labeled F-actin-binding peptide were imaged by live-cell total internal reflection fluorescence microscopy (TIR-FM). Computational analysis of image series did not reveal characteristic patterns of F-actin in the vicinity of viral budding sites. Furthermore, no transient recruitment of F-actin during bud formation was detected by monitoring fluorescence intensity changes at nascent HIV-1 assembly sites. The chosen approach allowed us to measure the effect of F-actin-interfering drugs on the assembly of individual virions in parallel with monitoring changes in the F-actin network of the respective cell. Treatment of cells with latrunculin did not affect the efficiency and dynamics of Gag assembly under conditions resulting in the disruption of F-actin filaments. Normal assembly rates were also observed upon transient stabilization of F-actin by short-term treatment with jasplakinolide. Taken together, these findings indicate that actin filament dynamics are dispensable for HIV-1 Gag assembly at the plasma membrane of HeLa cells.

IMPORTANCE
HIV-1 particles assemble at the plasma membrane of virus-producing cells. This membrane is lined by a dense network of actin filaments that might either present a physical obstacle to the formation of virus particles or generate force promoting the assembly process. Drug-mediated interference with the actin cytoskeleton showed different results for the formation of retroviral particles in different studies, likely due to general effects on the cell upon prolonged drug treatment. Here, we characterized the effect of actin-interfering compounds on the HIV-1 assembly process by direct observation of virus formation in live cells, which allowed us to measure assembly rate constants directly upon drug addition. Virus assembly proceeded with normal rates when actin filaments were either disrupted or stabilized. Taken together with the absence of characteristic actin filament patterns at viral budding sites in our analyses, this indicates that the actin network is dispensable for HIV-1 assembly.
Repertoire of Epitopes Recognized by Serum IgG from Humans Vaccinated with Herpes Simplex Virus 2 Glycoprotein D
Authors: Whitbeck J. Charles , Huang Zhen-Yu , Cairns Tina M. , Gallagher John R. , Lou Huan , Ponce-de-Leon Manuel , Belshe Robert B. , Eisenberg Roselyn J. , Cohen Gary H. 
Published: May 2014

ABSTRACT

The results of a clinical trial of a subunit vaccine against genital herpes were recently reported (R. B. Belshe, P. A. Leone, D. I. Bernstein, A. Wald, M. J. Levin, J. T. Stapleton, I. Gorfinkel, R. L. Morrow, M. G. Ewell, A. Stokes-Riner, G. Dubin, T. C. Heineman, J. M. Schulte, C. D. Deal, N. Engl. J. Med.
366:
34–43, 2012, doi:10.1056/NEJMoa1103151). The vaccine consisted of a soluble form of herpes simplex virus 2 (HSV-2) glycoprotein D (gD2) with adjuvant. The goal of the current study was to examine the composition of the humoral response to gD2 within a selected subset of vaccinated individuals. Serum samples from 30 vaccine recipients were selected based upon relative enzyme-linked immunosorbent assay (ELISA) titers against gD2; 10 samples had high titers, 10 had medium titers, and the remaining 10 had low ELISA titers. We employed a novel, biosensor-based monoclonal antibody (MAb)-blocking assay to determine whether gD2 vaccination elicited IgG responses against epitopes overlapping those of well-characterized MAbs. Importantly, IgGs from the majority of gD2-immunized subjects competed for gD binding with four antigenically distinct virus-neutralizing MAbs (MC2, MC5, MC23, and DL11). Screening of patient IgGs against overlapping peptides spanning the gD2 ectodomain revealed that about half of the samples contained antibodies against linear epitopes within the N and C termini of gD2. We found that the virus-neutralizing abilities of the 10 most potent samples correlated with overall gD-binding activity and to an even greater extent with the combined content of IgGs against the epitopes of MAbs MC2, MC5, MC23, and DL11. This suggests that optimal virus-neutralizing activity is achieved by strong and balanced responses to the four major discontinuous neutralizing epitopes of gD2.

IMPORTANCE
Several herpes simplex virus 2 (HSV-2) subunit vaccine studies have been conducted in human subjects using a recombinant form of HSV-2 glycoprotein D (gD2). Although several distinct, well-characterized virus-neutralizing epitopes on gD2 are targeted by murine monoclonal antibodies, it is not known whether the same epitopes are targeted by the humoral response to gD2 in humans. We have developed a novel, biosensor-based competition assay to directly address this important question. Using this approach, we identified epitopes that elicit strong humoral responses in humans, as well as other epitopes that elicit much weaker responses. These data provide new insight into the human response to known neutralizing gD2 epitopes and reveal characteristics of this response that may guide future vaccine development.