bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic Potential and Antigenic Properties of Recombinant Tick-Borne Encephalitis Virus Subviral Particles Expressed in Mammalian Cells from Semliki Forest Virus Replicons
Authors: Levanov Lev , Kuivanen Suvi , Matveev Andrey , Swaminathan Sathyamangalam , Jääskeläinen-Hakala Anu , Vapalahti Olli 
Published: December 2013

ABSTRACT
The precursor membrane envelope (prME) proteins of all three tick-borne encephalitis virus (TBEV) subtypes were produced based on expression from Semliki Forest virus (SFV) replicons transcribed from recombinant plasmids. Vero E6 cells transfected by these plasmids showed specific reactivities in immunofluorescence and immunoblot assays by monoclonal antibodies against European and Far-Eastern subtype strains of TBEV, indicating proper folding of the expressed glycoproteins. The prME glycoproteins were secreted into the cell culture supernatant, forming TBEV subviral particles of 20 to 30 nm in diameter. IgM μ-capture and IgG monoclonal antibody (MAb)-capture enzyme immunoassays (EIAs) were developed based on prME Karelia-94 (Siberian subtype) particles. Altogether, 140 human serum samples were tested using these assays, and the results were compared to those obtained with a commercial IgM EIA, an in-house μ-capture IgM assay based on baculovirus-expressed antigen, a commercial IgG EIA, and a hemagglutination inhibition test. Compared to reference enzyme-linked immunosorbent assays (ELISAs), the sensitivities of the generated μ-capture IgM SFV-prME and IgG MAb-capture SFV-prME EIAs were 97.4 to 100% and 98.7%, respectively, and the specificities of the two assays were 100%. IgM and IgG immunofluorescence assays (IFAs) were created based on Vero E6 cells transfected with the recombinant plasmid carrying the TBEV Karelia-94 prME glycoproteins. The IgM IFA was 100% concordant with the μ-capture IgM bac-prME ELISA. The IgG IFA sensitivity and specificity were 98.7% and 100%, respectively, compared to those of the commercial ELISA. In conclusion, the tests developed based on SFV replicon-driven expression of TBEV glycoproteins provide safe and robust alternatives for conducting TBEV serology.
Intermediate Susceptibility to Ciprofloxacin among Salmonella enterica Serovar Typhi Isolates in Lima, Peru
Authors: García Coralith , Lejon Veerle , Horna Gertrudis , Astocondor Lizeth , Vanhoof Raymond , Bertrand Sophie , Jacobs Jan 
Published: December 2013

ABSTRACT

Thirty-three
Salmonella enterica
serovar Typhi blood isolates from Lima, Peru (2008 to 2012), were fully susceptible to trimethoprim-sulfamethoxazole, chloramphenicol, ceftriaxone, and tetracycline; 8/33 (24.2%) showed intermediate susceptibility to ciprofloxacin carrying mutations in the quinolone resistance-determining region of the
gyrA
gene (Ser83-Phe and Asp87-Asn) and in the
gyrB
gene (Ser464-Phe).
Loop-Mediated Isothermal Amplification for Rickettsia typhi (the Causal Agent of Murine Typhus): Problems with Diagnosis at the Limit of Detection
Authors: Dittrich Sabine , Castonguay-Vanier Josée , Moore Catrin E. , Thongyoo Narongchai , Newton Paul N. , Paris Daniel H. 
Published: December 2013

ABSTRACT

Murine typhus is a flea-borne disease of worldwide distribution caused by
Rickettsia typhi
. Although treatment with tetracycline antibiotics is effective, treatment is often misguided or delayed due to diagnostic difficulties. As the gold standard immunofluorescence assay is imperfect, we aimed to develop and evaluate a loop-mediated isothermal amplification (LAMP) assay. LAMP assays have the potential to fulfill the WHO ASSURED criteria (
a
ffordable,
s
ensitive,
s
pecific,
u
ser friendly,
r
obust and rapid,
e
quipment free,
d
eliverable to those who need them) for diagnostic methodologies, as they can detect pathogen-derived nucleic acid with low technical expenditure. The LAMP assay was developed using samples of bacterial isolates (
n
= 41), buffy coat specimens from
R. typhi
PCR-positive Lao patients (
n
= 42), and diverse negative controls (
n
= 47). The method was then evaluated prospectively using consecutive patients with suspected scrub typhus or murine typhus (
n
= 266). The limit of detection was ∼40 DNA copies/LAMP reaction, with an analytical sensitivity of <10 DNA copies/reaction based on isolate dilutions. Despite these low cutoffs, the clinical sensitivity was disappointing, with 48% (95% confidence interval [95% CI], 32.5 to 62.7%) (specificity, 100% [95% CI, 100 to 100%]) in the developmental phase and 33% (95% CI, 9.2 to 56.8%) (specificity, 98.5% [95% CI, 97.0% to 100%]) in the prospective study. This low diagnostic accuracy was attributed to low patient
R. typhi
bacterial loads (median, 210 DNA copies/ml blood; interquartile range, 130 to 500). PCR-positive but LAMP-negative samples demonstrated significantly lower bacterial loads than LAMP-positive samples. Our findings highlight the diagnostic challenges for diseases with low pathogen burdens and emphasize the need to integrate pathogen biology with improved template production for assay development strategies.
Panton-Valentine Leukocidin-Positive Staphylococcus aureus in Ireland from 2002 to 2011: 21 Clones, Frequent Importation of Clones, Temporal Shifts of Predominant Methicillin-Resistant S. aureus Clones, and Increasing Multiresistance
Authors: Shore Anna C. , Tecklenborg Sarah C. , Brennan Gráinne I. , Ehricht Ralf , Monecke Stefan , Coleman David C. 
Published: December 2013

ABSTRACTThere has been a worldwide increase in community-associated (CA) methicillin-resistantStaphylococcus aureus(MRSA) infections. CA-MRSA isolates commonly produce the Panton-Valentine leukocidin toxin encoded by thepvlgeneslukF-PVandlukS-PV. This study investigated the clinical and molecular epidemiologies ofpvl-positive MRSA and methicillin-susceptibleS. aureus(MSSA) isolates identified by the Irish National MRSA Reference Laboratory (NMRSARL) between 2002 and 2011. Allpvl-positive MRSA (n= 190) and MSSA (n= 39) isolates underwent antibiogram-resistogram typing,spatyping, and DNA microarray profiling for multilocus sequence type, clonal complex (CC) and/or sequence type (ST), staphylococcal cassette chromosomemectype assignment, and virulence and resistance gene detection. Where available, patient demographics and clinical data were analyzed. The prevalence ofpvl-positive MRSA increased from 0.2% to 8.8%, and that ofpvl-positive MSSA decreased from 20% to 2.5% during the study period. Thepvl-positive MRSA and MSSA isolates belonged to 16 and 5 genotypes, respectively, with CC/ST8-MRSA-IV, CC/ST30-MRSA-IV, CC/ST80-MRSA-IV, CC1/ST772-MRSA-V, CC30-MSSA, CC22-MSSA, and CC121-MSSA predominating. Temporal shifts in the predominantpvl-positive MRSA genotypes and a 6-fold increase in multiresistantpvl-positive MRSA genotypes occurred during the study period. An analysis of patient data indicated thatpvl-positiveS. aureusstrains, especially MRSA strains, had been imported into Ireland several times. Two hospital and six family clusters ofpvl-positive MRSA were identified, and 70% of the patient isolates for which information was available were from patients in the community. This study highlights the increased burden and changing molecular epidemiology ofpvl-positiveS. aureusin Ireland over the last decade and the contribution of international travel to the influx of genetically diversepvl-positiveS. aureusisolates into Ireland.
Bacteremia Caused by Comamonaskerstersii in a Patient with Diverticulosis
Authors: Opota Onya , Ney Barbara , Zanetti Giorgio , Jaton Katia , Greub Gilbert , Prod'hom Guy 
Published: December 2013

ABSTRACT

We report for the first time a case of bacteremia caused by
Comamonas
kerstersii
in a 65-year-old patient with sign of diverticulosis. In addition, we review the isolation of
Comamonas
sp. and related organisms in our hospital over 25 years.
Identification and Clinical Significance of Helcococcus species, with Description of Helcococcus seattlensis sp. nov. from a Patient with Urosepsis
Authors: Chow Siu-Kei , Clarridge Jill E. 
Published: December 2013

ABSTRACT

Helcococcus
spp. are Gram-positive, catalase-negative, facultatively anaerobic cocci that are associated with wound and prosthetic joint infections as well bacteremia and empyema. Five
Helcococcus
spp. strains were isolated from our patient population, including 2 strains of
Helcococcus kunzii
from trauma-associated wounds, 2
Helcococcus sueciensis
strains from blood and abscess, and a novel
Helcococcus
spp. strain from blood associated with urosepsis. Based on the phenotypic and phylogenetic evidence, we propose that the unknown bacterium be classified as
Helcococcus seattlensis
sp. nov. We found that all 5 tested
Helcococcus
strains grew as satellite colonies around
Staphylococcus aureus
and, interestingly, both
H. kunzii
strains were isolated together with
S. aureus
. In addition to 16S rRNA gene sequencing, conventional methods for leucine aminopeptidase (LAP) and pyrrolidonyl arylamidase (PYR) testing can be cost-effective and efficient for differentiation of
Helcococcus
spp. from
Abiotrophia
and
Granulicatella
species. Using nonstandard methods, we found that all tested
Helcococcus
spp. had high MICs of >4/76 μg/ml for trimethoprim-sulfamethoxazole, an antibiotic commonly used to treat urinary tract infections. High MICs for erythromycin, azithromycin, and clindamycin, and intermediate to high MICs for moxifloxacin, levofloxacin, and gentamicin were also observed among the
Helcococcus
strains.
Evaluation of Three Live Attenuated H2 Pandemic Influenza Vaccine Candidates in Mice and Ferrets
Authors: Chen Grace L. , Lamirande Elaine W. , Cheng Xing , Torres-Velez Fernando , Orandle Marlene , Jin Hong , Kemble George , Subbarao Kanta 
Published: December 2013

ABSTRACT

H2 influenza viruses have not circulated in humans since 1968, and therefore a significant portion of the population would be susceptible to infection should H2 influenza viruses reemerge. H2 influenza viruses continue to circulate in avian reservoirs worldwide, and these reservoirs are a potential source from which these viruses could emerge. Three reassortant cold-adapted (ca) H2 pandemic influenza vaccine candidates with hemagglutinin (HA) and neuraminidase (NA) genes derived from the wild-type A/Japan/305/1957 (H2N2) (Jap/57), A/mallard/6750/1978 (H2N2) (mal/78), or A/swine/MO/4296424/2006 (H2N3) (sw/06) viruses and the internal protein gene segments from the A/Ann Arbor/6/60 ca virus were generated by plasmid-based reverse genetics (Jap/57 ca, mal/78 ca, and sw/06 ca, respectively). The vaccine candidates exhibited the
in vitro
phenotypes of temperature sensitivity and cold adaptation and were restricted in replication in the respiratory tract of ferrets. In mice and ferrets, the vaccines elicited neutralizing antibodies and conferred protection against homologous wild-type virus challenge. Of the three candidates, the sw/06 ca vaccine elicited cross-reactive antibodies and provided significant protection against the greatest number of heterologous viruses. These observations suggest that the sw/06 ca vaccine should be further evaluated in a clinical trial as an H2 pandemic influenza vaccine candidate.

IMPORTANCE
Influenza pandemics arise when novel influenza viruses are introduced into a population with little prior immunity to the new virus and often result in higher rates of illness and death than annual seasonal influenza epidemics. An influenza H2 subtype virus caused a pandemic in 1957, and H2 viruses circulated in humans till 1968. H2 influenza viruses continue to circulate in birds, and the development of an H2 influenza vaccine candidate is therefore considered a priority in preparing for future pandemics. However, we cannot predict whether a human H2 virus will reemerge or a novel avian H2 virus will emerge. We identified three viruses as suitable candidates for further evaluation as vaccines to protect against H2 influenza viruses and evaluated the immune responses and protection that these three vaccines provided in mice and ferrets.
Vaccinia Virus Inhibits NF-κB-Dependent Gene Expression Downstream of p65 Translocation
Authors: Sumner Rebecca P. , Maluquer de Motes Carlos , Veyer David L. , Smith Geoffrey L. 
Published: December 2013

ABSTRACT
The transcription factor nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) plays a critical role in host defense against viral infection by inducing the production of proinflammatory mediators and type I interferon. Consequently, viruses have evolved many mechanisms to block its activation. The poxvirus vaccinia virus (VACV) encodes numerous inhibitors of NF-κB activation that target multiple points in the signaling pathway. A derivative of VACV strain Copenhagen, called vv811, lacking 55 open reading frames in the left and right terminal regions of the genome was reported to still inhibit NF-κB activation downstream of tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β), suggesting the presence of one or more additional inhibitors. In this study, we constructed a recombinant vv811 lacking the recently described NF-κB inhibitor A49 (vv811ΔA49), yielding a virus that lacked all currently described inhibitors downstream of TNF-α and IL-1β. Unlike vv811, vv811ΔA49 no longer inhibited degradation of the phosphorylated inhibitor of κBα and p65 translocated into the nucleus. However, despite this translocation, vv811ΔA49 still inhibited TNF-α- and IL-1β-induced NF-κB-dependent reporter gene expression and the transcription and production of cytokines induced by these agonists. This inhibition did not require late viral gene expression. These findings indicate the presence of another inhibitor of NF-κB that is expressed early during infection and acts by a novel mechanism downstream of p65 translocation into the nucleus.
Rotavirus Infection Increases Intestinal Motility but Not Permeability at the Onset of Diarrhea
Authors: Istrate Claudia , Hagbom Marie , Vikström Elena , Magnusson Karl-Eric , Svensson Lennart 
Published: December 2013

ABSTRACT
The disease mechanisms associated with onset and secondary effects of rotavirus (RV) diarrhea remain to be determined and may not be identical. In this study, we investigated whether onset of RV diarrhea is associated with increased intestinal permeability and/or motility. To study the transit time, fluorescent fluorescein isothiocyanate (FITC)-dextran was given to RV-infected adult and infant mice. Intestinal motility was also studied with an opioid receptor agonist (loperamide) and a muscarinic receptor antagonist (atropine). To investigate whether RV increases permeability at the onset of diarrhea, fluorescent 4- and 10-kDa dextran doses were given to infected and noninfected mice, and fluorescence intensity was measured subsequently in serum. RV increased transit time in infant mice. Increased motility was detected at 24 h postinfection (h p.i.) and persisted up to 72 h p.i in pups. Both loperamide and atropine decreased intestinal motility and attenuated diarrhea. Analysis of passage of fluorescent dextran from the intestine into serum indicated unaffected intestinal permeability at the onset of diarrhea (24 to 48 h p.i.). We show that RV-induced diarrhea is associated with increased intestinal motility via an activation of the myenteric nerve plexus, which in turn stimulates muscarinic receptors on intestinal smooth muscles.

IMPORTANCE
We show that RV-infected mice have increased intestinal motility at the onset of diarrhea, and that this is not associated with increased intestinal permeability. These new observations will contribute to a better understanding of the mechanisms involved in RV diarrhea.
The
MYC
,
TERT
, and
ZIC1
Genes Are Common Targets of Viral Integration and Transcriptional Deregulation in Avian Leukosis Virus Subgroup J-Induced Myeloid Leukosis
Authors: Li Yuhao , Liu Xuemei , Yang Zhen , Xu Chenggang , Liu Di , Qin Jianru , Dai Manman , Hao Jianyong , Feng Min , Huang Xiaorong , Tan Liqiang , Cao Weisheng , Liao Ming 
Published: December 2013

ABSTRACT

The integration of retroviruses into the host genome following nonrandom genome-wide patterns may lead to the deregulation of gene expression and oncogene activation near the integration sites. Slow-transforming retroviruses have been widely used to perform genetic screens for the identification of genes involved in cancer. To investigate the involvement of avian leukosis virus subgroup J (ALV-J) integration in myeloid leukosis (ML) in chickens, we utilized an ALV-J insertional identification platform based on hybrid capture target enrichment and next-generation sequencing (NGS). Using high-definition mapping of the viral integration sites in the chicken genome, 241 unique insertion sites were obtained from six different ALV-J-induced ML samples. On the basis of previous statistical definitions,
MYC
,
TERT
, and
ZIC1
genes were identified as common insertion sites (CIS) of provirus integration in tumor cells; these three genes have previously been shown to be involved in the malignant transformation of different human cell types. Compared to control samples, the expression levels of all three CIS genes were significantly upregulated in chicken ML samples. Furthermore, they were frequently, but not in all field ML cases, deregulated at the mRNA level as a result of ALV-J infection. Our findings contribute to the understanding of the relationship between multipathotypes associated with ALV-J infection and the molecular background of tumorigenesis.

IMPORTANCE
ALV-Js have been successfully eradicated from chicken breeding flocks in the poultry industries of developed countries, and the control and eradication of ALV-J in China are now progressing steadily. To further study the pathogenesis of ALV-J infections, it will be necessary to elucidate the
in vivo
viral integration and tumorigenesis mechanism. In this study, 241 unique insertion sites were obtained from six different ALV-J-induced ML samples. In addition,
MYC
,
TERT
, and
ZIC1
genes were identified as the CIS of ALV-J in tumor cells, which might be a putative “driver” for the activation of the oncogene. In addition, the CIS genes showed deregulated expression compared to nontumor samples. These results have potentially important implications for the mechanism of viral carcinogenesis.
Identifying Recombination Hot Spots in the HIV-1 Genome
Authors: Smyth Redmond P. , Schlub Timothy E. , Grimm Andrew J. , Waugh Caryll , Ellenberg Paula , Chopra Abha , Mallal Simon , Cromer Deborah , Mak Johnson , Davenport Miles P. 
Published: December 2013

ABSTRACT

HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified full-length HIV-1 genome and high-throughput sequence analysis to study recombination in
gag
and
pol
in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies.

IMPORTANCE
The ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in
gag
and
pol
and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of viral dynamics and evolution, which will be useful for the design of robust antiretroviral therapies.
Antigenic and Receptor Binding Properties of Enterovirus 68
Authors: Imamura Tadatsugu , Okamoto Michiko , Nakakita Shin-ichi , Suzuki Akira , Saito Mariko , Tamaki Raita , Lupisan Socorro , Roy Chandra Nath , Hiramatsu Hiroaki , Sugawara Kan-etsu , Mizuta Katsumi , Matsuzaki Yoko , Suzuki Yasuo , Oshitani Hitoshi 
Published: December 2013

ABSTRACT
Increased detection of enterovirus 68 (EV68) among patients with acute respiratory infections has been reported from different parts of the world in the late 2000s since its first detection in pediatric patients with lower-respiratory-tract infections in 1962. However, the underlying molecular mechanisms for this trend are still unknown. We therefore aimed to study the antigenicity and receptor binding properties of EV68 detected in recent years in comparison to the prototype strain of EV68, the Fermon strain. We first performed neutralization (NT) and hemagglutination inhibition (HI) tests using antisera generated for EV68 strains detected in recent years. We found that the Fermon strain had lower HI and NT titers than recently detected EV68 strains. The HI and NT titers were also significantly different between strains of different genetic lineages among recently detected EV68 strains. We further studied receptor binding specificities of EV68 strains for sialyloligosaccharides using glycan array analysis. In glycan array analysis, all tested EV68 strains showed affinity for α2-6-linked sialic acids (α2-6 SAs) compared to α2-3 SAs. Our study demonstrates that emergence of strains with different antigenicity is the possible reason for the increased detection of EV68 in recent years. Additionally, we found that EV68 preferably binds to α2-6 SAs, which suggests that EV68 might have affinity for the upper respiratory tract.

IMPORTANCE
Numbers of cases of enterovirus 68 (EV68) infection in different parts of the world increased significantly in the late 2000s. We studied the antigenicity and receptor binding properties of recently detected EV68 strains in comparison to the prototype strain of EV68, Fermon. The hemagglutination inhibition (HI) and neutralization (NT) titers were significantly different between strains of different genetic lineages among recently detected EV68 strains. We further studied receptor binding specificities of EV68 strains for sialyloligosaccharides using glycan array analysis, which showed affinity for α2-6-linked sialic acids (α2-6 SAs) compared to α2-3 SAs. Our study suggested that the emergence of strains with different antigenicities was the possible reason for the increased detections of EV68 in recent years. Additionally, we revealed that EV68 preferably binds to α2-6 SAs. This is the first report describing the properties of EV68 receptor binding to the specific types of sialic acids.