bluuebunny/crossref_metadata_2025_split huggingface dataset:
Streptococcus pneumoniae Serotype 1 Burden in the African Meningitis Belt: Exploration of Functionality in Specific Antibodies
Authors: Blumental S. , Moïsi J. C. , Roalfe L. , Zancolli M. , Johnson M. , Burbidge P. , Borrow R. , Yaro S. , Mueller J. E. , Gessner B. D. , Goldblatt D. 
Published: February 2015

ABSTRACTStreptococcus pneumoniaeserotype 1 (Sp1) constitutes an important cause of seasonal endemic meningitis in all age groups in the African meningitis belt. Despite a higher meningitis incidence, the Burkinabé population has an Sp1-specific antibody seroprevalence similar to that reported in the United Kingdom (UK). We aimed to establish whether the opsonophagocytic activity (OPA) of pneumococcal IgG naturally present in Burkina Faso differs from that seen in individuals in the UK and to compare the OPAs generated by natural and vaccine-induced immunity. Samples collected from pneumococcal vaccine-naive Burkinabé and UK subjects were matched for age (1 to 39 years) and anti-Sp1 IgG level, analyzed for OPA to 3S. pneumoniaeserotypes (1, 5, and 19A), and compared to postvaccine samples. Furthermore, the Burkinabé samples were assessed for IgG avidity and serotype-specific IgM concentrations. One hundred sixty-nine matched serum samples from both populations were selected. A greater proportion of Burkinabé subjects aged 1 to 19 years had functional Sp1 activity (OPA ≥ 8) compared to UK subjects (12% versus 2%,P< 0.001); however, the proportions were similar among adults (9%). The correlation between Sp1 IgG concentration and OPA was good (P< 0.001), but many individuals had nonfunctional IgG, which was not related to avidity. While the Sp1 IgM concentrations correlated with OPA, not all of the function in serum samples with low IgG could be attributed to IgM. Finally, vaccine-induced Sp1-specific IgG was more functional than equivalent amounts of naturally occurring IgG. In conclusion, despite a substantially higher pneumococcal meningitis incidence, no decreased functional immunity to Sp1 could be evidenced in the Burkinabé population compared to that in the population from the UK. Furthermore, the naturally induced antibodies were less functional than vaccine-induced antibodies.
Detection of Pathogen-Specific Antibodies by Loop-Mediated Isothermal Amplification
Authors: Burbulis Ian E. , Yamaguchi Kumiko , Nikolskaia Olga V. , Prigge Sean T. , Magez Stefan , Bisser Sylvie , Reller Megan E. , Grab Dennis J. 
Published: February 2015

ABSTRACTLoop-mediated isothermal amplification (LAMP) is a method for enzymatically replicating DNA that has great utility for clinical diagnosis at the point of care (POC), given its high sensitivity, specificity, speed, and technical requirements (isothermal conditions). Here, we adapted LAMP for measuring protein analytes by creating a protein-DNA fusion (referred to here as a “LAMPole”) that attaches oligonucleotides (LAMP templates) to IgG antibodies. This fusion consists of a DNA element covalently bonded to an IgG-binding polypeptide (protein L/G domain). In our platform, LAMP is expected to provide the most suitable means for amplifying LAMPoles for clinical diagnosis at the POC, while quantitative PCR is more suitable for laboratory-based quantification of antigen-specific IgG abundance. As proof of concept, we measured serological responses to a protozoan parasite by quantifying changes in solution turbidity in real time. We observed a >6-log fold difference in signal between sera from vaccinated versus control mice and in a clinical patient sample versus a control. We assert that LAMPoles will be useful for increasing the sensitivity of measuring proteins, whether it be in a clinical laboratory or in a field setting, thereby improving acute diagnosis of a variety of infections.
Fusobacterium nucleatum Subspecies Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Nie Shuping , Tian Baoyu , Wang Xiaowei , Pincus David H. , Welker Martin , Gilhuley Kathleen , Lu Xuedong , Han Yiping W. , Tang Yi-Wei 
Published: February 2015

ABSTRACT

We explored the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for identification of
Fusobacterium nucleatum
subspecies. MALDI-TOF MS spectra of five
F. nucleatum
subspecies (
animalis
,
fusiforme
,
nucleatum
,
polymorphum
, and
vincentii
) were analyzed and divided into four distinct clusters, including subsp.
animalis
,
nucleatum
,
polymorphum
, and
fusiforme
/
vincentii
. MALDI-TOF MS with the modified SARAMIS database further correctly identified 28 of 34
F. nucleatum
clinical isolates to the subspecies level.
Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis
Authors: Scaltriti Erika , Sassera Davide , Comandatore Francesco , Morganti Marina , Mandalari Carmen , Gaiarsa Stefano , Bandi Claudio , Zehender Gianguglielmo , Bolzoni Luca , Casadei Gabriele , Pongolini Stefano 
Published: February 2015

ABSTRACT

We retrospectively analyzed a rare
Salmonella enterica
serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (
n
= 15) and food, feed, animal, and environmental sources (
n
= 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system.
Diagnostic Accuracy of Presepsin (sCD14-ST) for Prediction of Bacterial Infection in Cerebrospinal Fluid Samples from Children with Suspected Bacterial Meningitis or Ventriculitis
Authors: Stubljar David , Kopitar Andreja Natasa , Groselj-Grenc Mojca , Suhadolc Kristina , Fabjan Teja , Skvarc Miha 
Published: February 2015

ABSTRACTChildren with temporary external ventricular drains (EVD) are prone to nosocomial infections. Diagnosis of bacterial meningitis and ventriculitis in these children is challenging due to frequent blood contamination of cerebrospinal fluid (CSF) and the presence of chemical ventriculitis. The aim of this study was to compare diagnostic accuracy of presepsin (sCD14-ST), a novel biomarker of bacterial infection in CSF, to predict bacterial infection in comparison to the accuracy of established biomarkers like those demonstrated in biochemical analysis of CSF. We conducted a prospective study with 18 children with suspected bacterial meningitis or ventriculitis who had 66 episodes of disease. CSF samples were taken from external ventricular drainage. We measured presepsin in CSF, as well as CSF leukocyte count, glucose, and proteins. CSF was also taken to prove bacterial infection with culture methods or with 16S rRNA gene broad-range PCR (SepsiTest; Molzym, Germany). Infection was clinically confirmed in 57 (86%) episodes of suspected meningitis or ventriculitis. Chemical ventriculitis was diagnosed in 9 (14%) episodes of suspected meningitis or ventriculitis. Diagnostic accuracies presented as area under the curve (AUC) for sCD14-ST, leukocytes, and proteins measured in CSF were 0.877 (95% confidence interval [CI], 0.793 to 0.961), 0.798 (95% CI, 0.677 to 0.920), and 0.857 (95% CI, 0.749 to 0.964), respectively. With CSF culture, we detected bacteria in 17 samples, compared to 37 detected with broad-range PCR. It was found that presepsin was present at a significantly higher level in children with clinically proven ventriculitis than in those without meningitis or ventriculitis. Diagnostic accuracies of presepsin were superior to those of leukocytes or proteins in CSF. Presepsin-guided 16S rRNA gene PCR could be used in everyday clinical practice to improve etiological diagnosis of meningitis and ventriculitis and to prescribe more appropriate antibiotics.
Development of a Peptide Nucleic Acid-Based Multiprobe Real-Time PCR Method Targeting the
hsp65
Gene for Differentiation among Mycobacterium abscessus Strains
Authors: Kim Kijeong , Kim Byoung-Jun , Shim Tae Sun , Hong Seok-Hyun , Kook Yoon-Hoh , Kim Bum-Joon 
Published: February 2015

ABSTRACT

Recently, the need to distinguish between members of the
Mycobacterium abscessus
group has gained increasing attention. Here, we introduced a novel peptide nucleic acid (PNA) real-time PCR method targeting the
hsp65
gene in order to distinguish between four subspecies within the
M. abscessus
group (
M. abscessus
and 3 types of
M. massiliense
).
Comparison of Human Papillomavirus Detection by Aptima HPV and cobas HPV Tests in a Population of Women Referred for Colposcopy following Detection of Atypical Squamous Cells of Undetermined Significance by Pap Cytology
Authors: Castle Philip E. , Eaton Barbara , Reid Jennifer , Getman Damon , Dockter Janel 
Published: February 2015

ABSTRACT

Few studies have compared the cobas HPV test to the Aptima HPV assay (AHPV) and the Aptima HPV 16 18/45 genotype assay (AHPV GT) for high-risk human papillomavirus (hrHPV) detection, clinical performance in detecting cervical intraepithelial neoplasia grade 2 (CIN2) or more severe (CIN2+) diagnoses, and risk stratification by partial HPV genotyping. The cobas HPV test is a DNA test that separately and concurrently detects HPV16, HPV18, and a pool of 12 other hrHPV types. AHPV is an RNA test for a pool of 14 hrHPV genotypes, and AHPV GT is an RNA test run on AHPV-positive results to detect HPV16 separately from HPV18 and HPV45, which are detected together. In a population of patients (
n
= 988) referred for colposcopy because of a cervical Pap cytology result of atypical squamous cells of undetermined significance (ASC-US), a cervical scrape specimen was taken, placed into a ThinPrep Pap test vial containing PreservCyt liquid cytology medium, and tested in a blinded fashion with cobas and AHPV and with AHPV GT for AHPV-positive results. The final diagnoses were based on a consensus panel review of the biopsy specimen histology. AHPV and cobas were equally sensitive for CIN2+ diagnoses (89.4% each;
P
= 1.000), and AHPV was more specific than cobas (63.1% versus 59.3%;
P
≤ 0.001). The percent total agreement, percent positive agreement, and kappa value were 90.9%, 81.1%, and 0.815, respectively. Risk stratification using partial HPV genotyping was similar for the two assays. AHPV and AHPV GT had similar sensitivity and risk stratification to cobas HPV, but they were more specific than cobas HPV.
Glycosylation of Mouse DPP4 Plays a Role in Inhibiting Middle East Respiratory Syndrome Coronavirus Infection
Authors: Peck Kayla M. , Cockrell Adam S. , Yount Boyd L. , Scobey Trevor , Baric Ralph S. , Heise Mark T. 
Published: February 2015

ABSTRACT
Middle East respiratory syndrome coronavirus (MERS-CoV) utilizes dipeptidyl peptidase 4 (DPP4) as an entry receptor. Mouse DPP4 (mDPP4) does not support MERS-CoV entry; however, changes at positions 288 and 330 can confer permissivity. Position 330 changes the charge and glycosylation state of mDPP4. We show that glycosylation is a major factor impacting DPP4 receptor function. These results provide insight into DPP4 species-specific differences impacting MERS-CoV host range and may inform MERS-CoV mouse model development.
Expression of Human Decay-Accelerating Factor on Intestinal Epithelium of Transgenic Mice Does Not Facilitate Infection by the Enteral Route
Authors: Pan Jieyan , Zhang Lili , Odenwald Matthew A. , Shen Le , Turner Jerrold R. , Bergelson Jeffrey M. 
Published: February 2015

ABSTRACT

In vitro
, infection of polarized human intestinal epithelial cells by coxsackievirus B3 (CVB3) depends on virus interaction with decay-accelerating factor (DAF), a receptor expressed on the apical cell surface. Although mice are highly susceptible to CVB3 infection when virus is delivered by intraperitoneal injection, infection by the enteral route is very inefficient. Murine DAF, unlike human DAF, does not bind virus, and we hypothesized that the absence of an accessible receptor on the intestinal surface is an important barrier to infection by the oral route. We generated transgenic mice that express human DAF specifically on intestinal epithelium and measured their susceptibility to infection by a DAF-binding CVB3 isolate. Human DAF permitted CVB3 to bind to the intestinal surface
ex vivo
and to infect polarized monolayers of small-intestinal epithelial cells derived from DAF transgenic mice. However, expression of human DAF did not facilitate infection by the enteral route either in immunocompetent animals or in animals deficient in the interferon alpha/beta receptor. These results indicate that the absence of an apical receptor on intestinal epithelium is not the major barrier to infection of mice by the oral route.

IMPORTANCE
CVB3 infection of human intestinal epithelial cells depends on DAF at the apical cell surface, and expression of human DAF on murine intestinal epithelial cells permits their infection
in vitro
. However, expression of human DAF on the intestinal surface of transgenic mice did not facilitate infection by the oral route. Although the role of intestinal DAF in human infection has not been directly examined, these results suggest that DAF is not the critical factor in mice.
African Green Monkey TRIM5α Restriction in Simian Immunodeficiency Virus-Specific Rhesus Macaque Effector CD4 T Cells Enhances Their Survival and Antiviral Function
Authors: Jain Sumiti , Trivett Matthew T. , Ayala Victor I. , Ohlen Claes , Ott David E. 
Published: February 2015

ABSTRACT

The expression of xenogeneic TRIM5α proteins can restrict infection in various retrovirus/host cell pairings. Previously, we have shown that African green monkey TRIM5α (AgmTRIM5α) potently restricts both human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus mac239 (SIV
mac239
) replication in a transformed human T-cell line (L. V. Coren, et al., Retrovirology 12:11, 2015,
http://dx.doi.org/10.1186/s12977-015-0137-9
). To assess AgmTRIM5α restriction in primary cells, we transduced AgmTRIM5α into primary rhesus macaque CD4 T cells and infected them with SIV
mac239
. Experiments with T-cell clones revealed that AgmTRIM5α could reproducibly restrict SIV
mac239
replication, and that this restriction synergizes with an intrinsic resistance to infection present in some CD4 T-cell clones. AgmTRIM5α transduction of virus-specific CD4 T-cell clones increased and prolonged their ability to suppress SIV spread in CD4 target cells. This increased antiviral function was strongly linked to decreased viral replication in the AgmTRIM5α-expressing effectors, consistent with restriction preventing the virus-induced cytopathogenicity that disables effector function. Taken together, our data show that AgmTRIM5α restriction, although not absolute, reduces SIV replication in primary rhesus CD4 T cells which, in turn, increases their antiviral function. These results support prior
in vivo
data indicating that the contribution of virus-specific CD4 T-cell effectors to viral control is limited due to infection.

IMPORTANCE
The potential of effector CD4 T cells to immunologically modulate SIV/HIV infection likely is limited by their susceptibility to infection and subsequent inactivation or elimination. Here, we show that AgmTRIM5α expression inhibits SIV spread in primary effector CD4 T cells
in vitro
. Importantly, protection of effector CD4 T cells by AgmTRIM5α markedly enhanced their antiviral function by delaying SIV infection, thereby extending their viability despite the presence of virus. Our
in vitro
data support prior
in vivo
HIV-1 studies suggesting that the antiviral CD4 effector response is impaired due to infection and subsequent cytopathogenicity. The ability of AgmTRIM5α expression to restrict SIV infection in primary rhesus effector CD4 T cells now opens an opportunity to use the SIV/rhesus macaque model to further elucidate the potential and scope of anti-AIDS virus effector CD4 T-cell function.
Chimeric Rhinoviruses Obtained via Genetic Engineering or Artificially Induced Recombination Are Viable Only if the Polyprotein Coding Sequence Derives from the Same Species
Authors: Schibler Manuel , Piuz Isabelle , Hao Weidong , Tapparel Caroline 
Published: February 2015

ABSTRACT

Recombination is a widespread phenomenon that ensures both the stability and variation of RNA viruses. This phenomenon occurs with different frequencies within species of the
Enterovirus
genus. Intraspecies recombination is described frequently among non-rhinovirus enteroviruses but appears to be sporadic in rhinoviruses. Interspecies recombination is even rarer for rhinoviruses and mostly is related to ancient events which contributed to the speciation of these viruses. We reported that artificially engineered 5′ untranslated region (UTR) interspecies rhinovirus/rhinovirus or rhinovirus/non-rhinovirus enterovirus recombinants are fully viable. Using a similar approach, we demonstrated in this study that exchanges of the P1-2A polyprotein region between members of the same rhinovirus species, but not between members of different species, give rise to competent chimeras. To further assess the rhinovirus intra- and interspecies recombination potential, we used artificially induced recombination by cotransfection of 5′-end-deleted and 3′-end-deleted and replication-deficient genomes. In this system, intraspecies recombination also resulted in viable viruses with high frequency, whereas no interspecies rhinovirus recombinants could be recovered. Mapping intraspecies recombination sites within the polyprotein highlighted recombinant hotspots in nonstructural genes and at gene boundaries. Notably, all recombinants occurring at gene junctions presented in-frame sequence duplications, whereas most intragenic recombinants were homologous. Taken together, our results suggest that only intraspecies recombination gives rise to viable rhinovirus chimeras in the polyprotein coding region and that recombination hotspots map to nonstructural genes with in-frame duplications at gene boundaries. These data provide new insights regarding the mechanism and limitations of rhinovirus recombination.

IMPORTANCE
Recombination represents a means to ensure both the stability and the variation of RNA viruses. While intraspecies recombination is described frequently among non-rhinovirus enteroviruses, it seems to occur more rarely in rhinoviruses. Interspecies recombination is even rarer in this virus group and is mostly related to ancient events, which contributed to its speciation. We used engineered chimeric genomes and artificially induced RNA recombination to study experimentally the recombination potential of rhinoviruses and analyze recombination sites. Our results suggest that only intraspecies recombination gives rise to viable chimeras in the polyprotein coding region. Furthermore, characterization of intraspecies chimeras provides new insight into putative recombination hotspots within the polyprotein. In summary, we applied two powerful and complementary experimental approaches to improve current knowledge on rhinovirus recombination.
Service evaluation of the GOALS family-based childhood obesity treatment intervention during the first 3 years of implementation
Authors: Watson Paula M , Dugdill Lindsey , Pickering Katie , Owen Stephanie , Hargreaves Jackie , Staniford Leanne J , Murphy Rebecca C , Knowles Zoe , Cable N Timothy 
Published: February 2015

ObjectivesTo evaluate the impact of the GOALS (Getting Our Active Lifestyles Started) family-based childhood obesity treatment intervention during the first 3 years of implementation.DesignSingle-group repeated measures with qualitative questionnaires.SettingCommunity venues in a socioeconomically deprived, urban location in the North-West of England.Participants70 overweight or obese children (mean age 10.5 years, 46% boys) and their parents/carers who completed GOALS between September 2006 and March 2009.InterventionsGOALS was a childhood obesity treatment intervention that drew on social cognitive theory to promote whole family lifestyle change. Sessions covered physical activity (PA), diet and behaviour change over 18 2 h weekly group sessions (lasting approximately 6 months). A Template for Intervention Description and Replication (TIDieR) checklist of intervention components is provided.Primary and secondary outcome measuresThe primary outcome measure was child body mass index (BMI) z-score, collected at baseline, post-intervention and 12 months. Secondary outcome measures were child self-perceptions, parent/carer BMI and qualitative changes in family diet and PA (parent/carer questionnaire).ResultsChild BMI z-score reduced by 0.07 from baseline to post-intervention (p<0.001) and was maintained at 12 months (p<0.05). There was no change in parent/carer BMI or child self-perceptions, other than an increase in perceived social acceptance from baseline to post-intervention (p<0.05). Parents/carers reported positive changes to family PA and dietary behaviours after completing GOALS.ConclusionsGOALS completion was associated with small improvements in child BMI z-score and improved family PA and dietary behaviours. Several intervention modifications were necessary during the implementation period and it is suggested childhood obesity treatment interventions need time to embed before a definitive evaluation is conducted. Researchers are urged to use the TIDieR checklist to ensure transparent reporting of interventions and facilitate the translation of evidence to practice.