bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single Nucleotide Polymorphisms in the Toll-Like Receptor 3 and CD44 Genes Are Associated with Persistence of Vaccine-Induced Immunity to the Serogroup C Meningococcal Conjugate Vaccine
Authors: Moore Catrin E. , Hennig Branwen J. , Perrett Kirsten P. , Hoe J. Claire , Lee Sue J. , Fletcher Helen , Brocklebank Denise , O'Connor Daniel , Snape Matthew D. , Hall Andrew J. , Segal Shelley , Hill Adrian V. S. , Pollard Andrew J. 
Published: December 2011

ABSTRACTThe rate of decay of antibody concentration following serogroup C meningococcal (MenC) polysaccharide-protein conjugate vaccination varies between individuals. This depends partly on vaccination age but may be influenced by human genetics. We studied 721 single nucleotide polymorphisms (SNPs) across 131 candidate genes in a first cohort of 905 Caucasians (11 to 21 years old; mean time after vaccination, 4.9 years) and 30 SNPs across 17 genes in a replication study using 155 children, aged 6 to 12 years (mean time after vaccination, 6.7 years), and 196 infants (1 year old; mean time after vaccination, 8 months). Individuals were classified as responders or nonresponders for total MenC IgG concentration and MenC serum bactericidal antibody (SBA) measurements. Associated genes were examined further for quantitative outcome measures. Fifty-nine SNPs in 37 genes were associated with IgG persistence (adjusted for age at measurement), and 56 SNPs in 36 genes were associated with SBA persistence (adjusted for age at measurement and vaccine used). Three SNPs each within the Toll-like receptor 3 (TLR3) (rs3775291, rs3775292, and rs5743312) and CD44 (rs11033013, rs353644, and rs996076) genes were associated with IgG (adjusted for age at measurement) or SBA (adjusted for age at measurement and vaccine used) persistence in the initial genetic study (P, 0.02 to 0.04). Single SNPs within the TLR3 (rs7657186) (P= 0.004 [unadjusted]) and CD44 (rs12419062) (P= 0.01 [unadjusted]) genes were associated with IgG persistence in the replication study. These results suggest that genetic polymorphisms in the TLR3 and CD44 genes are associated with the persistence of the immune response to MenC vaccines 1 to 6 years after vaccination.
Immunological Correlates of Vaccination and Infection for Equine Herpesvirus 1
Authors: Goodman Laura B. , Wimer Christine , Dubovi Edward J. , Gold Carvel , Wagner Bettina 
Published: December 2011

ABSTRACT

Equine herpesvirus 1 (EHV-1) induces a variety of disease manifestations, including respiratory disease, abortions, and myeloencephalopathy. Several vaccines are commercially available but could not previously be distinguished by serologic testing from infection with EHV-1 (or the closely related EHV-4). Currently available vaccines are not reliably protective against the severe manifestations of the disease, including fatal myeloencephalopathy. We determined immunological parameters that can differentiate vaccinated from previously infected animals by comparing humoral and cellular EHV-1-specific responses in clinically healthy horses 10 months after vaccination. Forty-seven horses with known histories of vaccination and infection were studied, including a group of horses that survived a severe neurological outbreak 5 years prior to vaccination. Results of serum virus neutralization (SN), serum IgG isotyping, and cytokine profiling of lymphocyte subsets were compared. IgG4/7 levels strongly correlated with virus neutralization (
P
< 0.0001). IgG1/3 and SN values distinguished vaccinated/outbreak-exposed (vacc/outbreak) horses from vaccinated horses (
P
< 0.05). EHV-1-specific gamma interferon (IFN-γ)-producing CD4
+
(but not CD8
+
) T-cell numbers were also increased in vacc/outbreak horses, which distinguished them from vaccinated horses (
P
< 0.01). IFN-α secretion was similar between all groups and independent of previous exposure or vaccination. Our data suggest that IgG isotype responses to EHV-1 are more diverse under field conditions than is revealed by experimental studies and that the current modified-live virus (MLV) vaccine induces a more restricted IgG isotype response than does natural exposure to EHV-1. Since these parameters can be assessed in a high-throughput manner, they may prove useful in screening future vaccine candidates and assessing levels of protection.
Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates with Phenotypes of Polymyxin B Adaptation and Inducible Resistance
Authors: Boyle Brian , Fernandez Lucia , Laroche Jerome , Kukavica-Ibrulj Irena , Mendes Caio M. F. , Hancock Robert W. , Levesque Roger C. 
Published: December 2011

ABSTRACT

Clinical “superbug” isolates of
Pseudomonas aeruginosa
were previously observed to be resistant to several antibiotics, including polymyxin B, and/or to have a distinct, reproducible adaptive polymyxin resistance phenotype, identified by observing “skipped” wells (appearance of extra turbid wells) during broth microdilution testing. Here we report the complete assembled draft genome sequences of three such polymyxin resistant
P. aeruginosa
strains (9BR, 19BR, and 213BR).
Genome Sequencing of Bacillus subtilis SC-8, Antagonistic to the Bacillus cereus Group, Isolated from Traditional Korean Fermented-Soybean Food
Authors: Yeo In-Cheol , Lee Nam Keun , Hahm Young Tae 
Published: December 2011

ABSTRACT

Bacillus subtilis
SC-8 is a Gram-positive bacterium displaying narrow antagonistic activity for the
Bacillus cereus
group.
B. subtilis
SC-8 was isolated from Korean traditional fermented-soybean food. Here we report the draft genome sequence of
B. subtilis
SC-8, including biosynthetic genes for antibiotics that may have beneficial effects for control of food-borne pathogens.
Genetic Relationships of Phage Types and Single Nucleotide Polymorphism Typing of Salmonella enterica Serovar Typhimurium
Authors: Pang Stanley , Octavia Sophie , Reeves Peter R. , Wang Qinning , Gilbert Gwendolyn L. , Sintchenko Vitali , Lan Ruiting 
Published: December 2011

ABSTRACT

Salmonella enterica
serovar Typhimurium is one of the leading causes of gastroenteritis in humans. Phage typing has been used for the epidemiological surveillance of
S
. Typhimurium for over 4 decades. However, knowledge of the evolutionary relationships between phage types is very limited. In this study, we used single nucleotide polymorphisms (SNPs) as molecular markers to determine the relationships between common
S
. Typhimurium phage types. Forty-four SNPs, including 24 identified in a previous study and 20 from 6 available whole-genome sequences, were used to analyze 215
S
. Typhimurium isolates belonging to 45 phage types. Altogether, 215 isolates and 6 genome strains were differentiated into 33 SNP profiles and four distinctive phylogenetic clusters. Fourteen phage types, including DT9, one of the most common phage types in Australia, were differentiated into multiple SNP profiles. These SNP profiles were distributed into different phylogenetic clusters, indicating that they have arisen independently multiple times. This finding suggests that phage typing may not be useful for long-term epidemiological studies over long periods (years) and diverse localities (different countries or continents). SNP typing provided a discriminative power similar to that of phage typing. However, 12 SNP profiles contained more than one phage type, and more SNPs would be needed for further differentiation. SNP typing should be considered as a replacement for phage typing for the identification of
S
. Typhimurium strains.
Cell-Associated Hemolysis Induced by Helicobacter pylori Is Mediated by Phospholipases with Mitogen-Activated Protein Kinase-Activating Properties
Authors: Sitaraman Ramakrishnan , Israel Dawn A. , Romero-Gallo Judith , Peek Richard M. 
Published: December 2011

ABSTRACTPathogenicHelicobacter pyloristrains can selectively activate epithelial mitogen-activated protein kinase (MAPK) signaling pathways linked with disease. We now demonstrate thatH. pylori-induced hemolysis is strain specific and is mediated by phospholipases PldA1 and PldD. Inactivation of PldD inhibited activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), indicating thatH. pylorihemolytic phospholipases also harbor MAPK-activating properties.
Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China
Authors: Luo Tao , Yang Chongguang , Gagneux Sebastien , Gicquel Brigitte , Mei Jian , Gao Qian 
Published: December 2011

ABSTRACT

The standard 15- and 24-locus variable-number tandem repeat (VNTR) genotyping methods have demonstrated adequate discriminatory power and a small homoplasy effect for tracing tuberculosis (TB) transmission and predicting
Mycobacterium tuberculosis
lineages in European and North American countries. However, its validity for the definition of transmission in homogenous
M. tuberculosis
populations in settings with high TB burdens has been questioned. Here, we genotyped a population-based collection of 191 Beijing strains based on standard 15-locus VNTR (VNTR-15) and 8 single nucleotide polymorphisms (SNPs) in Shanghai, China. Limited discriminatory power and high rates of VNTR homoplasy were observed in the homogenous population of evolutionarily “modern” Beijing strains. Additional typing of three hypervariable loci (VNTR3820, VNTR4120, and VNTR3232) was performed for VNTR-15-based clusters. High variations of hypervariable alleles were observed in clusters with inconsistent SNP sublineages. We concluded that SNPs and hypervariable VNTR loci are helpful to enhance the discriminatory power and decrease the VNTR homoplasy effect for defining clusters. We recommend the combination of standard VNTR-15 and SNPs as first-line typing methods and the hypervariable loci for second-line typing of clustered strains for molecular epidemiology studies of homogenous
M. tuberculosis
populations.
Use of Illumina Deep Sequencing Technology To Differentiate Hepatitis C Virus Variants
Authors: Ninomiya Masashi , Ueno Yoshiyuki , Funayama Ryo , Nagashima Takeshi , Nishida Yuichiro , Kondo Yasuteru , Inoue Jun , Kakazu Eiji , Kimura Osamu , Nakayama Keiko , Shimosegawa Tooru 
Published: December 2011

ABSTRACT
Hepatitis C virus (HCV) is a positive-strand enveloped RNA virus that shows diverse viral populations even in one individual. Though Sanger sequencing has been used to determine viral sequences, deep sequencing technologies are much faster and can perform large-scale sequencing. We demonstrate the successful use of Illumina deep sequencing technology and subsequent analyses to determine the genetic variants and amino acid substitutions in both treatment-naïve (patient 1) and treatment-experienced (patient 7) isolates from HCV-infected patients. As a result, almost the full nucleotide sequence of HCV was detectable for patients 1 and 7. The reads were mapped to the HCV reference sequence. The coverage was 99.8% and the average depth was 69.5× for patient 7, with values of 99.4% (coverage) and 51.1× (average depth) for patient 1. In patient 7, amino acid (aa) 70 in the core region showed arginine, with methionine at aa 91, by Sanger sequencing. Major variants showed the same amino acid sequence, but minor variants were detectable in 18% (6/34 sequences) of sequences, with replacement of methionine by leucine at aa 91. In NS3, 8 amino acid positions showed mixed variants (T72T/I, K213K/R, G237G/S, P264P/S/A, S297S/A, A358A/T, S457S/C, and I615I/M) in patient 7. In patient 1, 3 amino acid positions showed mixed variants (L14L/F/V, S61S/A, and I586T/I). In conclusion, deep sequencing technologies are powerful tools for obtaining more profound insight into the dynamics of variants in the HCV quasispecies in human serum.
“Candidatus Neoehrlichia mikurensis,” Anaplasma phagocytophilum, and Lyme Disease Spirochetes in Questing European Vector Ticks and in Feeding Ticks Removed from People
Authors: Richter Dania , Matuschka Franz-Rainer 
Published: December 2011

ABSTRACT

To estimate the likelihood of people coming into contact with the recently described tick-borne agent “
Candidatus
Neoehrlichia mikurensis,” we compared its prevalence to those of Lyme disease spirochetes and
Anaplasma phagocytophilum
in questing adult
Ixodes ricinus
ticks collected in various Central European sites and examined ticks, which had been removed from people, for the presence of these pathogens. Whereas spirochetes infected questing adult ticks most frequently (22.3%), fewer than a third as many ticks were infected by “
Ca
. Neoehrlichia mikurensis” (6.2%), and about a sixth harbored
A. phagocytophilum
(3.9%). On average, every twelfth encounter of a person with an
I. ricinus
tick (8.1%) may bear the risk of acquiring “
Ca
. Neoehrlichia mikurensis.” Although a fifth of the people (20%) had removed at least one tick infected by “
Ca
. Neoehrlichia mikurensis,” none displayed symptoms described for this pathogen, suggesting that its transmission may not be immediate and/or that immunocompetent individuals may not be affected. Because immunosuppressed patients may be at a particular risk of developing symptoms, it should be considered that “
Ca
. Neoehrlichia mikurensis” appears to be the second most common pathogen in
I. ricinus
ticks. In our survey, only
Borrelia afzelii
appears to infect Central European vector ticks more frequently.
Genotype 3 Diversity and Quantification of Hepatitis E Virus RNA
Authors: Abravanel Florence , Sandres-Saune Karine , Lhomme Sebastien , Dubois Martine , Mansuy Jean-Michel , Izopet Jacques 
Published: December 2011

ABSTRACT

Genotype 3 hepatitis E viruses (HEVs) are distributed across the world and are now considered to be an emerging public health concern in industrialized countries. At least 10 genotype 3 subtypes have been identified in humans and animals worldwide. It was recently reported that the sensitivities of HEV RNA assays differ greatly. We have assessed the influence of genotype 3 diversity on the performances of two HEV RNA assays: one targeting the ORF3 gene and the other targeting the ORF2 gene. We tested a panel of 5 HEV-positive reference samples of genotypes 3a, 3b, 3c, 3e, and 3f at 10-fold serial dilutions. The HEV RNA concentrations obtained with both reverse transcription (RT)-PCRs were correlated, but the RT-PCR based on ORF2 underestimated the HEV RNA concentrations. The mean [ORF3 − ORF2] difference was 1.41 log copies/ml. We also tested 34 clinical specimens of genotypes 3c (
n
= 15), 3e (
n
= 4), and 3f (
n
= 15), representing the most prevalent subtypes in Europe. The mean [ORF3 − ORF2] differences were 1.41 log copies/ml for genotype 3c, 0.96 log copies/ml for genotype 3e, and 0.70 log copies/ml for genotype 3f. The bias between the 2 RT-PCR assays was significantly greater for genotype 3c than for genotype 3f (
P
= 0.007). We therefore recommend the use of an RT-PCR protocol based on ORF3 to quantify HEV RNA of genotype 3 strains.
Cross-Reactivity of Fusarium spp. in the Aspergillus Galactomannan Enzyme-Linked Immunosorbent Assay
Authors: Tortorano Anna Maria , Esposto Maria Carmela , Prigitano Anna , Grancini Anna , Ossi Cristina , Cavanna Caterina , Cascio Giuliana Lo 
Published: December 2011

ABSTRACT

Nine of 11 hematological patients with disseminated/deep-seated
Fusarium
infection tested at least twice for
Aspergillus
galactomannan (GM) had repeated positive results in the absence of
Aspergillus
isolation in culture. The centrifuged supernatants of 12
Fusarium
isolates were tested by a GM enzyme-linked immunosorbent assay (EIA). All the isolates produced positive reactions when tested undiluted. These results show cross-reactivity of
Fusarium
spp. with
Aspergillus
GM that may constitute a drawback with respect to the specificity of the Platelia EIA.
Recurrent Urinary Infection with Bifidobacterium scardovii
Authors: Barberis Claudia M. , Cittadini Roxana M. , Almuzara Marisa N. , Feinsilberg Alejandro , Famiglietti Angela M. , Ramírez Maria Soledad , Vay Carlos A. 
Published: December 2011

ABSTRACTBifidobacteriumspecies are difficult to identify and may be underreported or not recovered by many laboratories because of their slow growth. We emphasize the importance of the Gram stain in urine samples and the addition of enriched media and enhanced atmosphere over time for urine cultures with pyuria. This is the first report of aBifidobacterium scardoviirecurrent urinary infection in an elderly woman.
Molecular Epidemiology of Avian Leukosis Virus Subgroup J in Layer Flocks in China
Authors: Gao Yulong , Yun Bingling , Qin Liting , Pan Wei , Qu Yue , Liu Zaisi , Wang Yongqiang , Qi Xiaole , Gao Honglei , Wang Xiaomei 
Published: December 2011

ABSTRACT

Avian leukosis virus subgroup J (ALV-J) was first isolated from meat-type chickens in 1988. No field cases of ALV-J infection or tumors in layer chickens were observed worldwide until 2004. However, layer flocks in China have experienced outbreaks of this virus in recent years. The molecular epidemiology of ALV-J strains isolated from layer flocks was investigated. The
env
genes of 77.8% (21/27) of the ALV-J layer isolates with a high degree of genetic variation were significantly different from the
env
genes of the prototype strain of ALV-J (HPRS-103) and American and Chinese strains from meat-type chickens (designated ALV-J broiler isolates). A total of 205 nucleotides were deleted from the 3′ untranslated region of 89.5% (17/19) of the ALV-J layer isolates. Approximately 94.7% (16/17) of the layer isolates contained a complete E element of 146 to 149 residues. The U3 sequences of 84.2% (16/19) of the ALV-J layer isolates displayed less than 92.5% sequence homology to those of the ALV-J broiler isolates, although the transcriptional regulatory elements that are typical of avian retroviruses were highly conserved. Several unique nucleotide substitutions in the
env
gene, the U3 region, and the E element of most of the ALV-J layer isolates were detected. These results suggested that the
env
gene, E element, and U3 region in the ALV-J layer isolates have evolved rapidly and were significantly different from those of the ALV-J broiler isolates. These findings will contribute to a better understanding of the pathogenic mechanism of layer tumor diseases induced by ALV-J.
First Report of Sepsis Caused by Rhodococcus corynebacterioides in a Patient with Myelodysplastic Syndrome
Authors: Kitamura Yuka , Sawabe Etsuko , Ohkusu Kiyofumi , Tojo Naoko , Tohda Shuji 
Published: December 2011

ABSTRACTWe report a case of sepsis caused byRhodococcus corynebacterioides, identified using 16S rRNA gene sequencing, in a myelodysplastic syndrome patient who had undergone hematopoietic stem cell transplantation. This is the first report ofR. corynebacterioidesinfection in a human.
Do Differences in Panton-Valentine Leukocidin Production among International Methicillin-Resistant Staphylococcus aureus Clones Affect Disease Presentation and Severity?
Authors: Boakes Eve , Kearns Angela M. , Badiou Cederic , Lina Gerard , Hill Robert L. , Ellington Matthew J. 
Published: December 2011

ABSTRACT

Panton-Valentine leukocidin (PVL) production by methicillin-resistant
Staphylococcus aureus
(MRSA) was determined
in vitro
using the enzyme-linked immunosorbent assay (ELISA), and associations with clinical presentation and bacterial genetic characteristics were examined. PVL production ranged from 0.02 to 4.865 μg/ml and correlated with a multilocus sequence type (MLST) clonal complex associated with specific PVL phage types. A relationship between PVL production and clinical presentation or patient demographics could not be demonstrated.
Identification of a Pyridopyrimidinone Inhibitor of Orthopoxviruses from a Diversity-Oriented Synthesis Library
Authors: Dower Ken , Filone Claire Marie , Hodges Erin N. , Bjornson Zach B. , Rubins Kathleen H. , Brown Lauren E. , Schaus Scott , Hensley Lisa E. , Connor John H. 
Published: December 2011

ABSTRACT

Orthopoxviruses include the prototypical vaccinia virus, the emerging infectious agent monkeypox virus, and the potential biothreat variola virus (the causative agent of smallpox). There is currently no FDA-approved drug for humans infected with orthopoxviruses. We screened a diversity-oriented synthesis library for new scaffolds with activity against vaccinia virus. This screen identified a nonnucleoside analog that blocked postreplicative intermediate and late gene expression. Viral genome replication was unaffected, and inhibition could be elicited late in infection and persisted upon drug removal. Sequencing of drug-resistant viruses revealed mutations predicted to be on the periphery of the highly conserved viral RNA polymerase large subunit. Consistent with this, the compound had broad-spectrum activity against orthopoxviruses
in vitro
. These findings indicate that novel chemical synthesis approaches are a potential source for new infectious disease therapeutics and identify a potentially promising candidate for development to treat orthopoxvirus-infected individuals.
The Human Cytomegalovirus Protein TRS1 Inhibits Autophagy via Its Interaction with Beclin 1
Authors: Chaumorcel Magali , Lussignol Marion , Mouna Lina , Cavignac Yolaine , Fahie Kamau , Cotte-Laffitte Jacqueline , Geballe Adam , Brune Wolfram , Beau Isabelle , Codogno Patrice , Esclatine Audrey 
Published: December 2011

ABSTRACT

Human cytomegalovirus modulates macroautophagy in two opposite directions. First, HCMV stimulates autophagy during the early stages of infection, as evident by an increase in the number of autophagosomes and a rise in the autophagic flux. This stimulation occurs independently of
de novo
viral protein synthesis since UV-inactivated HCMV recapitulates the stimulatory effect on macroautophagy. At later time points of infection, HCMV blocks autophagy (M. Chaumorcel, S. Souquere, G. Pierron, P. Codogno, and A. Esclatine, Autophagy 4:1–8, 2008) by a mechanism that requires
de novo
viral protein expression. Exploration of the mechanisms used by HCMV to block autophagy unveiled a robust increase of the cellular form of Bcl-2 expression. Although this protein has an anti-autophagy effect via its interaction with Beclin 1, it is not responsible for the inhibition induced by HCMV, probably because of its phosphorylation by c-Jun N-terminal kinase. Here we showed that the HCMV TRS1 protein blocks autophagosome biogenesis and that a TRS1 deletion mutant is defective in autophagy inhibition. TRS1 has previously been shown to neutralize the PKR antiviral effector molecule. Although phosphorylation of eIF2α by PKR has been described as a stimulatory signal to induce autophagy, the PKR-binding domain of TRS1 is dispensable to its inhibitory effect. Our results show that TRS1 interacts with Beclin 1 to inhibit autophagy. We mapped the interaction with Beclin 1 to the N-terminal region of TRS1, and we demonstrated that the Beclin 1-binding domain of TRS1 is essential to inhibit autophagy.
Bovine Herpesvirus Type 4 Glycoprotein L Is Nonessential for Infectivity but Triggers Virion Endocytosis during Entry
Authors: Lété Céline , Machiels Bénédicte , Stevenson Philip G. , Vanderplasschen Alain , Gillet Laurent 
Published: December 2011

ABSTRACT

The core entry machinery of mammalian herpesviruses comprises glycoprotein B (gB), gH, and gL. gH and gL form a heterodimer with a central role in viral membrane fusion. When archetypal alpha- or betaherpesviruses lack gL, gH misfolds and progeny virions are noninfectious. However, the gL of the rhadinovirus murid herpesvirus 4 (MuHV-4) is nonessential for infection. In order to define more generally what role gL plays in rhadinovirus infections, we disrupted its coding sequence in bovine herpesvirus 4 (BoHV-4). BoHV-4 lacking gL showed altered gH glycosylation and incorporated somewhat less gH into virions but remained infectious. However, gL
−
virions showed poor growth associated with an entry deficit. Moreover, a major part of their entry defect appeared to reflect impaired endocytosis, which occurs upstream of membrane fusion itself. Thus, the rhadinovirus gL may be more important for driving virion endocytosis than for incorporating gH into virions, and it is nonessential for membrane fusion.