bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the Phenotype and Functionality of Porcine CD8 T Cell Responses following Vaccination with Live Attenuated Classical Swine Fever Virus (CSFV) and Virulent CSFV Challenge
Authors: Franzoni Giulia , Kurkure Nitin V. , Edgar Daniel S. , Everett Helen E. , Gerner Wilhelm , Bodman-Smith Kikki B. , Crooke Helen R. , Graham Simon P. 
Published: August 2013

ABSTRACTVaccination with live attenuated classical swine fever virus (CSFV) induces solid protection after only 5 days, which has been associated with virus-specific T cell gamma interferon (IFN-γ) responses. In this study, we employed flow cytometry to characterize T cell responses following vaccination and subsequent challenge infections with virulent CSFV. The CD3+CD4−CD8hiT cell population was the first and major source of CSFV-specific IFN-γ. A proportion of these cells showed evidence for cytotoxicity, as evidenced by CD107a mobilization, and coexpressed tumor necrosis factor alpha (TNF-α). To assess the durability and recall of these responses, a second experiment was conducted where vaccinated animals were challenged with virulent CSFV after 5 days and again after a further 28 days. While virus-specific CD4 T cell (CD3+CD4+CD8α+) responses were detected, the dominant response was again from the CD8 T cell population, with the highest numbers of these cells being detected 14 and 7 days after the primary and secondary challenges, respectively. These CD8 T cells were further characterized as CD44hiCD62L−and expressed variable levels of CD25 and CD27, indicative of a mixed effector and effector memory phenotype. The majority of virus-specific IFN-γ+CD8 T cells isolated at the peaks of the response after each challenge displayed CD107a on their surface, and subpopulations that coexpressed TNF-α and interleukin 2 (IL-2) were identified. While it is hoped that these data will aid the rational design and/or evaluation of next-generation marker CSFV vaccines, the novel flow cytometric panels developed should also be of value in the study of porcine T cell responses to other pathogens/vaccines.
All-trans-Retinoic Acid Imprints Expression of the Gut-Homing Marker α4β7 while Suppressing Lymph Node Homing of Dendritic Cells
Authors: Evans Tristan I. , Reeves R. Keith 
Published: August 2013

ABSTRACTTissue-directed trafficking of dendritic cells (DCs) as natural adjuvants and/or direct vaccine carriers is highly attractive for the next generation of vaccines and immunotherapeutics. Since these types of studies would undoubtedly be first conducted using nonhuman primate models, we evaluated the ability of all-trans-retinoic acid (ATRA) to induce gut-homing α4β7 expression on rhesus macaque plasmacytoid and myeloid DCs (pDCs and mDCs, respectively). Induction of α4β7 occurred in both a time-dependent and a dose-dependent manner with up to 8-fold increases for mDCs and 2-fold increases for pDCs compared to medium controls. ATRA treatment was also specific in inducing α4β7 expression, but not expression of another mucosal trafficking receptor, CCR9. Unexpectedly, upregulation of α4β7 was associated with a concomitant downregulation of CD62L, a marker of lymph node homing, indicating an overall shift in the trafficking repertoire. These same phenomena occurred with ATRA treatment of human and chimpanzee DCs, suggesting a conserved mechanism among primates. Collectively, these data serve as a first evaluation forex vivomodification of primate DC homing patterns that could later be used in reinfusion studies for the purposes of immunotherapeutics or mucosa-directed vaccines.
Comparison of 14 Molecular Assays for Detection of Mycobacterium tuberculosis Complex in Bronchoalveolar Lavage Fluid
Authors: Akkerman Onno W. , van der Werf Tjip S. , de Boer Maria , de Beer Jessica L. , Rahim Zeaur , Rossen John W. A. , van Soolingen Dick , Kerstjens Huib A. M. , van der Zanden Adri G. M. 
Published: August 2013

ABSTRACT

We compared 14 molecular assays for their ability to detect the
Mycobacterium tuberculosis
complex in bronchoalveolar lavage fluid samples. Three approaches were followed. First, by using DNA from
Mycobacterium bovis
BCG, we determined the detection limits of the assays using routine molecular methods. Second, in order to determine the analytical sensitivities of the assays, we added one of four
M. tuberculosis
isolates with various numbers of the insertion sequence IS
6110
to
N
-acetyl-
l
-cysteine (NALC)-NaOH-treated bronchoalveolar lavage fluid samples in dilutions of 1:10 to 1:10,000,000. Third, intertest variabilities were measured and defined by the standard deviations for the quantitation cycle (Cq) values of three positive test results per dilution per assay. The 14 assays tested had similar analytical sensitivities, except for GeneXpert, which had an analytical sensitivity that was 10- to 100-fold lower than that of the other assays. The MP MTB/NTM test and the in-house TaqMan-10 revealed the best performances for the detection limit and had the highest analytical sensitivities. Most of the tests performed well regarding detection limit and analytical sensitivity for the detection of the
M. tuberculosis
complex in serial dilutions, and the differences were small. The MP MTB/NTM and the in-house TaqMan-10 assays revealed the best, and GeneXpert the worst, overall performances.
Rapid Detection of Gram-Positive Organisms by Use of the Verigene Gram-Positive Blood Culture Nucleic Acid Test and the BacT/Alert Pediatric FAN System in a Multicenter Pediatric Evaluation
Authors: Sullivan K. V. , Turner N. N. , Roundtree S. S. , Young S. , Brock-Haag C. A. , Lacey D. , Abuzaid S. , Blecker-Shelly D. L. , Doern C. D. 
Published: August 2013

ABSTRACT

Assays that expedite the reporting of organism identification and antibiotic susceptibility status in positive blood cultures can fast track interventions that improve clinical outcomes. We evaluated the Verigene Gram-positive blood culture nucleic acid test (BC-GP) in two pediatric hospitals. Positive BacT/Alert Pediatric FAN blood cultures with Gram-positive organisms were tested using the BC-GP in tandem with routine laboratory procedures. To test organisms underrepresented in the clinical blood culture evaluation, blood culture bottles were spiked with diluted organism suspensions at concentrations of 10 to 100 CFU per milliliter. A total of 249 Gram-positive bacterial isolates were recovered from 242 blood cultures. The BC-GP detected
Staphylococcus aureus
, methicillin-susceptible
S. aureus
, and methicillin-resistant
S. aureus
with sensitivities of 100%, 99%, and 100% and specificities of 100%, 100%, and 99.5%, respectively. The BC-GP detected
Staphylococcus epidermidis
, methicillin-susceptible
S. epidermidis
, and methicillin-resistant
S. epidermidis
with sensitivities of 95%, 80%, and 96%, respectively, and 100% specificity. The BC-GP correctly identified 14/15 cases of
Enterococcus faecalis
and
Enterococcus faecium
bacteremia and 9 cases of
Streptococcus pneumoniae
. It misidentified 5/15 clinical blood cultures with
Streptococcus mitis
/
Streptococcus oralis
and 1/3 blood cultures spiked with
Streptococcus anginosus
group as
S. pneumoniae
. The BC-GP detected a case of
Streptococcus pyogenes
bacteremia but failed to detect 2/3 clinical blood cultures with
Streptococcus agalactiae
. BC-GP's rapid accurate detection of
Staphylococcus
spp.,
E. faecium
, and
E. faecalis
and its ability to ascertain
mecA
,
vanA
, and
vanB
status may expedite clinical decisions pertaining to optimal antibiotic use. False-positive
S. pneumoniae
results may warrant reporting of only “
Streptococcus
spp.” when this organism is reported by the BC-GP.
Emergence, Circulation, and Spatiotemporal Phylogenetic Analysis of Coxsackievirus A6- and Coxsackievirus A10-Associated Hand, Foot, and Mouth Disease Infections from 2008 to 2012 in Shenzhen, China
Authors: He Ya-Qing , Chen Long , Xu Wen-Bo , Yang Hong , Wang Han-Zhong , Zong Wen-Ping , Xian Hui-Xia , Chen Hui-Ling , Yao Xiang-Jie , Hu Zhang-Li , Luo Min , Zhang Hai-Long , Ma Han-Wu , Cheng Jin-Quan , Feng Qian-Jin , Zhao De-Jian 
Published: August 2013

ABSTRACTSporadic hand, foot, and mouth disease (HFMD) outbreaks and other infectious diseases in recent years have frequently been associated with certain human enterovirus (HEV) serotypes. This study explored the prevalences and genetic characteristics of non-HEV71 and non-coxsackievirus A16 (CV-A16) human enterovirus-associated HFMD infections in Shenzhen, China. A total of 2,411 clinical stool specimens were collected from hospital-based surveillance for HFMD from 2008 to 2012. The detection of HEV was performed by real-time reverse transcription-PCR (RT-PCR) and RT-seminested PCR, and spatiotemporal phylogenetic analysis was performed based on the VP1 genes. A total of 1,803 (74.8%) strains comprising 28 different serotypes were detected. In the past 5 years, the predominant serotypes were HEV71 (60.0%), followed by CV-A16 (21.2%) and two uncommon serotypes, CV-A6 (13.0%) and CV-A10 (3.3%). However, CV-A6 replaced CV-A16 as the second most common serotype between 2010 and 2012. As an emerging pathogen, CV-A6 became as common a causative agent of HFMD as HEV71 in Shenzhen in 2012. Phylogenetic analysis revealed that little variation occurred in the Chinese HEV71 and CV-A16 strains. The genetic characteristics of the Chinese CV-A6 and CV-A10 strains displayed geographic differences. The CV-A6 and CV-A10 strains circulating in Shenzhen likely originated in Europe. It was found that human enteroviruses have a high mutation rate due to evolutionary pressure and frequent recombination (3.2 × 10−3to 6.4 ×10−3substitutions per site per year for HEV71, CV-A6, CV-A16, and CV-A10). Since certain serotypes are potential threats to the public health, this study provides further insights into the significance of the epidemiological surveillance of HFMD.
Development of a Loop-Mediated Isothermal Amplification Assay Targeting the
mpb64
Gene for Diagnosis of Intraocular Tuberculosis
Authors: Balne Praveen Kumar , Barik Manas Ranjan , Sharma Savitri , Basu Soumyava 
Published: August 2013

ABSTRACT

A loop-mediated isothermal amplification (LAMP) assay targeting the
mpb64
gene for the diagnosis of intraocular tuberculosis was highly specific (100%), sensitive (85.7%), rapid, and easy to perform. The LAMP assay can be an alternative to conventional PCR for the diagnosis of ocular tuberculosis in resource-limited settings.
Pharmacodynamics of Doxycycline and Tetracycline against Staphylococcus pseudintermedius: Proposal of Canine-Specific Breakpoints for Doxycycline
Authors: Maaland Marit Gaastra , Papich Mark G. , Turnidge John , Guardabassi Luca 
Published: August 2013

ABSTRACT

Doxycycline is a tetracycline that has been licensed for veterinary use in some countries, but no clinical breakpoints are available for veterinary pathogens. The objectives of this study were (i) to establish breakpoints for doxycycline and (ii) to evaluate the use of tetracycline as a surrogate to predict the doxycycline susceptibility of
Staphylococcus pseudintermedius
isolates. MICs and inhibition zone diameters were determined for 168 canine
S. pseudintermedius
isolates according to Clinical and Laboratory Standards Institute (CLSI) standards. Tetracycline resistance genes were detected by PCR, and time-kill curves were determined for representative strains.
In vitro
pharmacodynamic and target animal pharmacokinetic data were analyzed by Monte Carlo simulation (MCS) for the development of MIC interpretive criteria. Optimal zone diameter breakpoints were defined using the standard error rate-bounded method. The two drugs displayed bacteriostatic activity and bimodal MIC distributions. Doxycycline was more active than tetracycline in non-wild-type strains. MCS and target attainment analysis indicated a certainty of ≥90% for attaining an area under the curve (AUC)/MIC ratio of >25 with a standard dosage of doxycycline (5 mg/kg of body weight every 12 h) for strains with MICs of ≤0.125 μg/ml. Tetracycline predicted doxycycline susceptibility, but current tetracycline breakpoints were inappropriate for the interpretation of doxycycline susceptibility results. Accordingly, canine-specific doxycycline MIC breakpoints (susceptible, ≤0.125 μg/ml; intermediate, 0.25 μg/ml; resistant, ≥0.5 μg/ml) and zone diameter breakpoints (susceptible, ≥25 mm; intermediate, 21 to 24 mm; resistant, ≤20 mm) and surrogate tetracycline MIC breakpoints (susceptible, ≤0.25 μg/ml; intermediate, 0.5 μg/ml; resistant, ≥1 μg/ml) and zone diameter breakpoints (susceptible, ≥23 mm; intermediate, 18 to 22 mm; resistant, ≤17 mm) were proposed based on the data generated in this study.
Tuberculosis-Spoligo-Rifampin-Isoniazid Typing: an All-in-One Assay Technique for Surveillance and Control of Multidrug-Resistant Tuberculosis on Luminex Devices
Authors: Gomgnimbou Michel Kiréopori , Hernández-Neuta Iván , Panaiotov Stefan , Bachiyska Elizabeta , Palomino Juan Carlos , Martin Anandi , del Portillo Patricia , Refregier Guislaine , Sola Christophe 
Published: August 2013

ABSTRACT

As a follow-up of the “spoligoriftyping” development, we present here an extension of this technique which includes the detection of isoniazid resistance-associated mutations in a new 59-plex assay, i.e., tuberculosis-spoligo-rifampin-isoniazid typing (TB-SPRINT), running on microbead-based multiplexed systems. This assay improves the synergy between clinical microbiology and epidemiology by providing (i) mutation-based prediction of drug resistance profiles for patient treatment and (ii) genotyping data for tuberculosis (TB) surveillance. This third-generation microbead-based high-throughput assay for TB runs on the Luminex 200 system and on the recently launched MagPix system (Luminex, Austin, TX). Spoligotyping patterns obtained by the TB-SPRINT method were 100% (
n
= 85 isolates; 3,655/3,655 spoligotype data points) concordant with those obtained by microbead-based and membrane-based spoligotyping. Genetic drug susceptibility typing provided by the TB-SPRINT method was 100% concordant with resistance locus sequencing (
n
= 162 for
rpoB
gene sequencing and
n
= 76 for
katG
and
inhA
sequencing). Considering phenotypic drug susceptibility testing (DST) as the reference method, the sensitivity and specificity of TB-SPRINT regarding
Mycobacterium tuberculosis
complex (
n
= 162 isolates) rifampin resistance were both 100%, and those for isoniazid resistance were 90.4% (95% confidence interval, 85 to 95%) and 100%, respectively. Used routinely in national TB reference and specialized laboratories, the TB-SPRINT assay should simultaneously improve personalized medicine and epidemiological surveillance of multidrug-resistant (MDR) TB. This assay is expected to play an emerging role in public health in countries with heavy burdens of MDR TB and/or HIV/TB coinfection. Application of this assay directly to biological samples, as well as development for extensively drug-resistant (XDR) TB detection by inclusion of second-line antituberculosis drug-associated mutations, is under development. With bioinformatical methods and data mining to reduce the number of targets to the most informative ones, locally adapted formats of this technique can easily be developed everywhere.
Impact of Blood Volume, Tube Shaking, and Incubation Time on Reproducibility of QuantiFERON-TB Gold In-Tube Assay
Authors: Gaur Rajiv L. , Pai Madhukar , Banaei Niaz 
Published: August 2013

ABSTRACT

Gamma interferon (IFN-γ) release assays (IGRAs) are functional assays used serially to measure the efficacy of novel tuberculosis (TB) vaccines and to screen health care workers for latent tuberculosis infection (LTBI). However, studies have shown nonreproducible IGRA results. In this study, we investigated the effects of blood volume (0.8, 1.0, and 1.2 ml), tube shaking (gentle versus vigorous), and incubation duration (16, 20, and 24 h) on the reproducibility of QuantiFERON-TB Gold In-Tube (QFT-GIT) results for 50 subjects (33 uninfected and 17 infected). The median IFN-γ TB response (TB antigen [Ag] minus nil value) was significantly higher with 0.8 ml blood (1.04 IU/ml) than with 1.0 ml (0.85 IU/ml;
P
= 0.002) or 1.2 ml (0.49 IU/ml;
P
< 0.001) for subjects with LTBI. Compared with 0.8 ml (11.8%), there were larger proportions of false-negative results with 1.0 ml (29.4%;
P
= 0.2) and 1.2 ml (41.2%;
P
= 0.05) of blood for infected subjects. Blood volume did not significantly change the proportions of positive results in uninfected controls. Compared with gentle shaking, vigorous shaking increased the median IFN-γ response in nil (0.04 versus 0.06 IU/ml;
P
< 0.001) and TB Ag (0.12 versus 0.24 IU/ml;
P
= 0.004) tubes and increased TB responses (TB Ag
vigorous
minus nil
gentle
) (0.02 versus 0.08 IU/ml;
P
= 0.004). The duration of incubation did not have a significant impact on the proportion of positive results in uninfected or infected subjects. This study identified blood volume and tube shaking as novel preanalytical sources of variability which require further standardization in order to improve the quality and reproducibility of QFT-GIT results.
Gallibacterium anatis Bacteremia in a Human
Authors: Aubin Guillaume Ghislain , Haloun Alain , Treilhaud Michèle , Reynaud Alain , Corvec Stéphane 
Published: August 2013

ABSTRACT

We describe the first case of bacteremia due to
Gallibacterium anatis
. The patient, a 26-year-old woman, developed bacteremia and diarrhea. The origin of infection was possibly due to a diet contaminated by
G. anatis
in this highly immunocompromised patient.
Molecular Characterization of Herpes Simplex Virus 2 Strains by Analysis of Microsatellite Polymorphism
Authors: Burrel Sonia , Ait-Arkoub Zaïna , Voujon Delphine , Deback Claire , Abrao Emiliana P. , Agut Henri , Boutolleau David 
Published: August 2013

ABSTRACT
The complete 154-kbp linear double-stranded genomic DNA sequence of herpes simplex virus 2 (HSV-2), consisting of two extended regions of unique sequences bounded by a pair of inverted repeat elements, was published in 1998 and since then has been widely employed in a wide range of studies. Throughout the HSV-2 genome are scattered 150 microsatellites (also referred to as short tandem repeats) of 1- to 6-nucleotide motifs, mainly distributed in noncoding regions. Microsatellites are considered reliable markers for genetic mapping to differentiate herpesvirus strains, as shown for cytomegalovirus and HSV-1. The aim of this work was to characterize 12 polymorphic microsatellites within the HSV-2 genome by use of 3 multiplex PCR assays in combination with length polymorphism analysis for the rapid genetic differentiation of 56 HSV-2 clinical isolates and 2 HSV-2 laboratory strains (gHSV-2 and MS). This new system was applied to a specific new HSV-2 variant recently identified in HIV-1-infected patients originating from West Africa. Our results confirm that microsatellite polymorphism analysis is an accurate tool for studying the epidemiology of HSV-2 infections.
Detection of Influenza H7N9 Virus: All Molecular Tests Are Not Equal
Authors: Hatchette Todd F. , Drews Steven J. , Bastien Nathalie , Li Yan , German Gregory , Antonishyn Nick , Charest Hugues , Mazzulli Tony , Fonseca Kevin , Krajden Mel , Petric Martin , Dust Kerry , LeBlanc Jason J. 
Published: August 2013

ABSTRACT
The recent emergence of influenza A virus (H7N9) emphasizes the need for its rapid detection. While commercial nucleic acid amplification tests (NAATs) are commonly used to detect seasonal influenza virus, this study demonstrated that the analytical sensitivity of commercial assays is highly variable compared to that of CDC-based in-house NAATs for the detection of H7N9.
Is Hydrogen Cyanide a Marker of Burkholderia cepacia Complex?
Authors: Gilchrist Francis J. , Sims Hayley , Alcock Alice , Jones Andrew M. , Bright-Thomas Rowland J. , Smith David , Španĕl Patrik , Webb A. Kevin , Lenney Warren 
Published: August 2013

ABSTRACT

Biofilm cultures of
Burkholderia cepacia
complex (BCC) infection have been found to generate the nonvolatile cyanide ion. We investigated if gaseous hydrogen cyanide (HCN) was a marker of BCC infection. Selected ion flow tube mass spectrometry analysis showed HCN was not elevated in the headspace of planktonic or biofilm cultures or in the exhaled breath of adult cystic fibrosis patients with chronic BCC infection. HCN is therefore not an
in vitro
or
in vivo
marker of BCC.
Refrex-1, a Soluble Restriction Factor against Feline Endogenous and Exogenous Retroviruses
Authors: Ito Jumpei , Watanabe Shinya , Hiratsuka Takahiro , Kuse Kyohei , Odahara Yuka , Ochi Haruyo , Kawamura Maki , Nishigaki Kazuo 
Published: August 2013

ABSTRACT

The host defense against viral infection is acquired during the coevolution or symbiosis of the host and pathogen. Several cellular factors that restrict retroviral infection have been identified in the hosts. Feline leukemia virus (FeLV) is a gammaretrovirus that is classified into several receptor interference groups, including a novel FeLV-subgroup D (FeLV-D) that we recently identified. FeLV-D is generated by transduction of the
env
gene of feline endogenous gammaretrovirus of the domestic cat (ERV-DCs) into FeLV. Some ERV-DCs are replication competent viruses which are present and hereditary in cats. We report here the determination of new viral receptor interference groups and the discovery of a soluble antiretroviral factor, termed Refrex-1. Detailed analysis of FeLV-D strains and ERV-DCs showed two receptor interference groups that are distinct from other FeLV subgroups, and Refrex-1 specifically inhibited one of them. Refrex-1 is characterized as a truncated envelope protein of ERV-DC and includes the N-terminal region of surface unit, which is a putative receptor-binding domain, but lacks the transmembrane region. Refrex-1 is efficiently secreted from the cells and appears to cause receptor interference extracellularly. Two variants of Refrex-1 encoded by provirus loci, ERV-DC7 and DC16, are expressed in a broad range of feline tissues. The host retains Refrex-1 as an antiretroviral factor, which may potentially prevent reemergence of the ERVs and the emergence of novel ERV-related viruses in cats. Refrex-1 may have been acquired during endogenization of ERV-DCs and may play an important role in retroviral restriction and antiviral defense in cats.