bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an Artificial-Antigen-Presenting-Cell-Based Assay for the Detection of Low-Frequency Virus-Specific CD8+T Cells in Whole Blood, with Application for Measles Virus
Authors: Ndhlovu Zaza M. , Angenendt Monika , Heckel Diana , Schneck Jonathan P. , Griffin Diane E. , Oelke Mathias 
Published: June 2009

ABSTRACTEvaluation of the immune responses induced by childhood vaccines requires measurement of T-cell, as well as antibody, responses. However, cellular immune responses are often not analyzed because of technical hurdles and the volume of blood required. Therefore, a sensitive and specific assay for antigen-specific T cells that utilizes a small volume of blood would facilitate new vaccine evaluation. We developed a novel assay for quantifying virus-specific CD8+T cells that combines the use of HLA-A2 immunoglobulin-based artificial antigen-presenting cells (aAPCs) for stimulation of antigen-specific CD8+T cells in whole blood with quantitative real-time reverse transcription-PCR (qRT-PCR) to detect gamma interferon (IFN-γ) mRNA. This assay was optimized using a well-established cytomegalovirus (CMV) CD8+T-cell system. The aAPC-qRT-PCR assay had comparable sensitivity to intracellular cytokine staining (ICS) in detecting CMV-specific CD8+T cells with a detection limit of less than 0.004%. The assay was applied to the detection of low-frequency measles virus (MV)-specific CD8+T cells by stimulating blood from five MV-immune HLA-A*0201 donors with four different MV-specific peptides (MV peptide aAPCs). Stimulation with three of the MV peptide aAPCs resulted in significant increases in IFN-γ mRNA ranging from 3.3- to 13.5-fold. Our results show that the aAPC-qRT-PCR assay is highly sensitive and specific and can be standardized for screening MV-specific CD8+T cells in vaccine trials. The technology should be transferable to analysis of CD8+T-cell responses to other antigens.
Nosocomial Outbreak of a Non-Cefepime-Susceptible Ceftazidime-Susceptible
Pseudomonas aeruginosa
Strain Overexpressing MexXY-OprM and Producing an Integron-Borne PSE-1 ß-Lactamase
Authors: Peña C. , Suarez C. , Tubau F. , Juan C. , Moya B. , Dominguez M. A. , Oliver A. , Pujol M. , Ariza J. 
Published: June 2009

ABSTRACT

Cefepime (FEP) and ceftazidime (CAZ) are broad-spectrum cephalosporins that display similar MICs for wild-type
Pseudomonas aeruginosa
strains. Recently,
P. aeruginosa
isolates showing a discordance in susceptibility to CAZ and FEP have been noted at the Hospital de Bellvitge in Barcelona, Spain, and a clustering was suspected. During the study period (March to December 2007), 51 patients, particularly those in an intensive care units (ICUs) (
n
= 29 [57%]), infected or colonized with at least one
P. aeruginosa
non-FEP-susceptible and CAZ-susceptible (Fep
ns
Caz
s
) phenotype strain were detected. Twenty-three (45%) patients were infected, and the respiratory tract was the most frequent site of infection. Changes in the consumption of antimicrobials in the ICUs were observed over time: a progressive reduction in the levels of consumption of carbapenems (247 defined daily doses [DDD]/1,000 patient days to 66 DDD/1,000 patient days;
P
= 0.008), after restriction of its use in 2006, and an expected increase in the rate of piperacillin-tazobactam use (42 DDD/1,000 patient days in 2004 to 200 DDD/1,000 patient days in 2007;
P
< 0.001). Throughout the whole study period, only a single clone of a
P. aeruginosa
Fep
ns
Caz
s
phenotype strain was identified by pulsed-field gel electrophoresis analysis to be associated with the hyperexpression of MexXY-OprM and the production of an integron-borne PSE-1 ß-lactamase. In conclusion, we identified an epidemic
P. aeruginosa
clone of an Fep
ns
Caz
s
phenotype strain involving 51 patients, in particular, ICU patients. The combination of the overexpression of an efflux pump and PSE-1 ß-lactamase production is associated with the multidrug-resistant phenotype. The dominant use of a single class of antibiotics could have provided the selective pressure required for the emergence and spread of this
P. aeruginosa
strain.
Armored Long RNA Controls or Standards for Branched DNA Assay for Detection of Human Immunodeficiency Virus Type 1
Authors: Zhan Sien , Li Jinming , Xu Ruihuan , Wang Lunan , Zhang Kuo , Zhang Rui 
Published: June 2009

ABSTRACT
The branched DNA (bDNA) assay is a reliable method for quantifying the RNA of human immunodeficiency virus type 1 (HIV-1). The positive controls and standards for this assay for the detection of HIV-1 consist of naked RNA, which is susceptible to degradation by RNase. Armored RNA is a good candidate for an RNase-resistant positive control or standard. However, its use has been limited by the maximal length of the exogenous RNA packaged into virus-like particles by routine armored RNA technology. In the present study, we produced armored long RNA (armored L-RNA) controls or standards (AR-HIV-pol-3034b) for a bDNA assay of HIV-1 by increasing the amount and affinity of the pac sites (the pac site is a specific 19-nucleotide stem-loop region located at the 5′ terminus of the MS2 bacteriophage replicase gene) by a one-plasmid double-expression system. AR-HIV-pol-3034b was completely resistant to DNase and RNase, was stable in normal human EDTA-preserved plasma at 4°C for at least 6 months, and produced reproducible, linear results in the Versant HIV-1 RNA 3.0 assay. In conclusion, AR-HIV-pol-3034b could act as a positive control or standard in a bDNA assay for the detection of HIV-1. In addition, the one-plasmid double-expression system can be used as a better platform than the one-plasmid expression system and the two-plasmid coexpression system for expressing armored L-RNA.
Molecular Subtyping of
Treponema pallidum
subsp.
pallidum
in Lisbon, Portugal
Authors: Castro R. , Prieto E. , Águas M. J. , Manata M. J. , Botas J. , Martins Pereira F. 
Published: June 2009

ABSTRACT

The objectives of this study were to evaluate the reproducibility of a molecular method for the subtyping of
Treponema pallidum
subsp.
pallidum
and to discriminate strains of this microorganism from strains from patients with syphilis. We studied 212 specimens from a total of 82 patients with different stages of syphilis (14 primary, 7 secondary and 61 latent syphilis). The specimens were distributed as follows: genital ulcers (
n
= 9), skin and mucosal lesions (
n
= 7), blood (
n
= 82), plasma (
n
= 82), and ear lobe scrapings (
n
= 32). The samples were assayed by a PCR technique to amplify a segment of the polymerase gene I (
polA
). Positive samples were typed on the basis of the analysis of two variable genes,
tpr
and
arp
. Sixty-two of the 90 samples positive for
polA
yielded typeable
Treponema pallidum
DNA. All skin lesions in which
T. pallidum
was identified (six of six [100%]) were found to contain enough DNA for typing of the organism. It was also possible to type DNA from 7/9 (77.7%) genital ulcer samples, 13/22 (59.1%) blood samples, 20/32 (62.5%) plasma samples, and 16/21 (76.2%) ear lobe scrapings. The same subtype was identified in all samples from the same patient. Five molecular subtypes (subtypes 10a, 14a, 14c, 14f, and 14g) were identified, with the most frequently found subtype being subtype 14a and the least frequently found subtype being subtype 10a. In conclusion, the subtyping technique used in this study seems to have good reproducibility. To our knowledge, subtype 10a was identified for the first time. Further studies are needed to explain the presence of this subtype in Portugal, namely, its relationship to the
Treponema pallidum
strains circulating in the African countries where Portuguese is spoken.
Emergence of KPC-Producing
Pseudomonas aeruginosa
in Trinidad and Tobago
Authors: Akpaka Patrick E. , Swanston William H. , Ihemere Hyginus N. , Correa Adriana , Torres Julian A. , Tafur Jose D. , Montealegre Maria Camila , Quinn John P. , Villegas Maria Virginia 
Published: June 2009

ABSTRACT

In 2006, the first isolate of KPC-2-producing
Pseudomonas aeruginosa
in the world was identified in Colombia. Recently, similar strains have been reported in Puerto Rico. We now report KPC-2-producing
P. aeruginosa
in Trinidad and Tobago. Surveillance for similar strains is warranted, considering their wide geographic spread and known association with mobile genetic elements.
Assessing Human Immunodeficiency Virus Type 1 Tropism: Comparison of Assays Using Replication-Competent Virus versus Plasma-Derived Pseudotyped Virions
Authors: Hosoya Noriaki , Su Zhaohui , Wilkin Timothy , Gulick Roy M. , Flexner Charles , Hughes Michael D. , Skolnik Paul R. , Giguel Françoise , Greaves Wayne L. , Coakley Eoin , Kuritzkes Daniel R. 
Published: June 2009

ABSTRACT
Detection of CXCR4-using human immunodeficiency virus by the Trofile assay was compared to that by assays using virus isolates or replication-competent recombinants. Concordance with the Trofile assay was good, but assays using replicating viruses did not increase substantially the ability to detect the presence of CXCR4-using virus.
Expanded Multilocus Sequence Typing for
Burkholderia
Species
Authors: Spilker Theodore , Baldwin Adam , Bumford Amy , Dowson Chris G. , Mahenthiralingam Eshwar , LiPuma John J. 
Published: June 2009

ABSTRACT

PCR primers targeting loci in the current
Burkholderia cepacia
complex multilocus sequence typing scheme were redesigned to (i) more reliably amplify these loci from
B
.
cepacia
complex species, (ii) amplify these same loci from additional
Burkholderia
species, and (iii) enable the use of a single primer set per locus for both amplification and DNA sequencing.
Community-Associated Methicillin-Resistant
Staphylococcus aureus
Isolated in Finland in 2004 to 2006
Authors: Kanerva Mari , Salmenlinna Saara , Vuopio-Varkila Jaana , Lehtinen Pirkko , Möttönen Teemu , Virtanen Mikko J. , Lyytikäinen Outi 
Published: June 2009

ABSTRACT

A nationwide population-based study on community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) in Finland during 2004 to 2006 showed that both incidence (1.9/100,000 population) and strain variation increased in comparison to years 1997 to 1999. There were 7 community-associated epidemic and 25 sporadic MRSA strain types. Half of these had Panton-Valentine leukocidin genes.
Development of a Multiplex Real-Time PCR for Detection and Differentiation of Malignant Catarrhal Fever Viruses in Clinical Samples
Authors: Cunha Cristina W. , Otto Lisa , Taus Naomi S. , Knowles Donald P. , Li Hong 
Published: June 2009

ABSTRACT
A multiplex real-time PCR was developed using a single pair of primers and fluorescent probes specific for five malignant catarrhal fever viruses and an internal positive control. The assay was able to simultaneously detect and differentiate the viruses in clinical samples with high sensitivity (97.2%) and specificity (100%).
Genetic Diversity among Food-Borne and Waterborne Norovirus Strains Causing Outbreaks in Sweden
Authors: Lysén Maria , Thorhagen Margareta , Brytting Maria , Hjertqvist Marika , Andersson Yvonne , Hedlund Kjell-Olof 
Published: June 2009

ABSTRACT
A total of 101 food-borne and waterborne outbreaks that were caused by norovirus and that resulted in more than 4,100 cases of illness were reported to the Swedish Institute for Infectious Disease Control from January 2002 to December 2006. Sequence and epidemiological data for isolates from 73 outbreaks were analyzed. In contrast to health care-related outbreaks, no clear seasonality could be observed. Sequence analysis showed a high degree of genetic variation among the noroviruses detected. Genogroup II (GII) viruses were detected in 70% of the outbreaks, and of those strains, strains of GII.4 were the most prevalent and were detected in 25% of all outbreaks. The GII.4 variants detected in global outbreaks in health care settings during 2002, 2004, and 2006 were also found in the food-borne outbreaks. GI strains totally dominated as the cause of water-related (drinking and recreational water) outbreaks and were found in 12 of 13 outbreaks. In 14 outbreaks, there were discrepancies among the polymerase and capsid genotype results. In four outbreaks, the polymerase of the recombinant GII.b virus occurred together with the GII.1 or GII.3 capsids, while the GII.7 polymerase occurred together with the GII.6 and GII.7 capsids. Mixed infections were observed in six outbreaks; four of these were due to contaminated water, and two were due to imported frozen berries. Contaminated food and water serve as important reservoirs for noroviruses. The high degree of genetic diversity found among norovirus strains causing food-borne and waterborne infections stresses the importance of the use of broad reaction detection methods when such outbreaks are investigated.
Prevalence, Distribution, and Antifungal Susceptibility Profiles of
Candida parapsilosis
,
C. orthopsilosis
, and
C. metapsilosis
in a Tertiary Care Hospital
Authors: Silva Ana P. , Miranda Isabel M. , Lisboa Carmen , Pina-Vaz Cidália , Rodrigues Acácio G. 
Published: June 2009

ABSTRACT

Candida parapsilosis
, an emergent agent of nosocomial infections, was previously made up of a complex of three genetically distinct groups (groups I, II, and III). Recently, the
C. parapsilosis
groups have been renamed as distinct species:
C. parapsilosis
sensu stricto,
C. orthopsilosis
, and
C. metapsilosis
. In Portugal, no data pertaining to the distribution and antifungal susceptibility of these
Candida
species are yet available. In the present report, we describe the incidence and distribution of
C. parapsilosis
sensu stricto,
C. orthopsilosis
, and
C. metapsilosis
among 175 clinical and environmental isolates previously identified by conventional methods as
C. parapsilosis
. We also evaluated the in vitro susceptibilities of the isolates to fluconazole, voriconazole, posaconazole, amphotericin B, and two echinocandins, caspofungin and anidulafungin. Of the 175 isolates tested, 160 (91.4%) were identified as
C. parapsilosis
sensu stricto, 4 (2.3%) were identified as
C. orthopsilosis
, and 5 (2.9%) were identified as
C. metapsilosis
. Six isolates corresponded to species other than the
C. parapsilosis
group. Interestingly, all isolates from blood cultures corresponded to
C. parapsilosis
sensu stricto. Evaluation of the antifungal susceptibility profile showed that only nine (5.6%)
C. parapsilosis
sensu stricto strains were susceptible-dose dependent or resistant to fluconazole, and a single strain displayed a multiazole-resistant phenotype; two (1.3%)
C. parapsilosis
sensu stricto strains were amphotericin B resistant. All
C. orthopsilosis
and
C. metapsilosis
isolates were susceptible to azoles and amphotericin B. A high number of strains were nonsusceptible to the echinocandins (caspofungin and anidulafungin).
Performance Assessment of the GenoType MTBDR
plus
Test and DNA Sequencing in Detection of Multidrug-Resistant
Mycobacterium tuberculosis
Authors: Huang Wei-Lun , Chen Huang-Yau , Kuo Yuh-Min , Jou Ruwen 
Published: June 2009

ABSTRACT

To facilitate the management of multidrug-resistant (MDR) tuberculosis, two nucleic acid sequence-based methods, the GenoType MTBDR
plus
test and DNA sequencing, were assessed for the rapid detection of drug-resistant
Mycobacterium tuberculosis
for the first time in the Asia-Pacific region. The performances of these two assays in detecting the presence of rifampin (rifampicin) (RIF) and isoniazid (INH) resistance-associated mutations in the
rpoB
,
katG
,
inhA
regulatory region,
inhA
, and
oxyR-ahpC
genes were compared to that of a conventional agar proportion drug susceptibility test. A total of 242 MDR and 30 pansusceptible
M. tuberculosis
isolates were evaluated in this study. The sensitivities obtained for RIF-resistant detection by the GenoType MTBDR
plus
test and by resistance gene sequencing were 95.5% and 97.9%, respectively. The sensitivities for INH resistance detection by the GenoType MTBDR
plus
test and by resistance gene sequencing were 81.8% and 93.4%, respectively. Together, the sensitivity for MDR tuberculosis detection was 78.5% with the GenoType MTBDR
plus
test and 91.3% by resistance gene sequencing. The specificity for RIF resistance, INH resistance, and MDR detection was 100% by both methods. The GenoType MTBDR
plus
test has the advantage of a short turnaround time for drug-resistant
M. tuberculosis
detection. Overall, the two assays performed equally well in detecting RIF resistance (
P
= 0.13). However, DNA sequencing demonstrated superior performance in detecting INH resistance (
P
< 0.001) and MDR tuberculosis (
P
< 0.001). We suggest that new alleles of INH resistance genes should be evaluated to improve the sensitivity of the GenoType MTBDR
plus
test, especially for different geographic areas with genetically diverse
M. tuberculosis
strains.
Characterization of Atypical Isolates of
Yersinia intermedia
and Definition of Two New Biotypes
Authors: Martin Liliane , Leclercq Alexandre , Savin Cyril , Carniel Elisabeth 
Published: June 2009

ABSTRACT

The species
Yersinia intermedia
is a member of the genus
Yersinia
which belongs to the
Enterobacteriaceae
family. This species is divided into eight biotypes, according to Brenner's biotyping scheme. This scheme relies on five tests (utilization of Simmons citrate and acid production from
d
-melibiose,
d
-raffinose, α-methyl-
d
-glucoside [αMG], and
l
-rhamnose). The collection of the French
Yersinia
Reference Laboratory (Institut Pasteur, Paris, France) contained 44 strains that were originally identified as
Y. intermedia
but whose characteristics did not fit into the biotyping scheme. These 44 strains were separated into two biochemical groups: variant 1 (positive for acid production from
l
-rhamnose and αMG and positive for Simmons citrate utlization) and variant 2 (positive for acid production from
l
-rhamnose and αMG). These atypical strains could correspond to new biotypes of
Y. intermedia
, to
Y. frederiksenii
strains having the atypical property of fermenting αMG, or to new
Yersinia
species. These strains did not exhibit growth or phenotypic properties different from those of
Y. intermedia
and
Y. frederiksenii
and did not harbor any of the virulence traits usually found in pathogenic species. DNA-DNA hybridizations performed between one strain each of variants 1 and 2 and the
Y. intermedia
and
Y. frederiksenii
type strains demonstrated that these variants do belong to the
Y. intermedia
species. We thus propose that Brenner's biotyping scheme be updated by adding two new biotypes: 9 (for variant 1) and 10 (for variant 2) to the species
Y. intermedia
.
Investigation of the Mechanism by Which Herpes Simplex Virus Type 1 LAT Sequences Modulate Preferential Establishment of Latent Infection in Mouse Trigeminal Ganglia
Authors: Imai Yumi , Apakupakul Kathleen , Krause Philip R. , Halford William P. , Margolis Todd P. 
Published: June 2009

ABSTRACT

We previously demonstrated that herpes simplex virus type 1 (HSV-1) preferentially establishes latent infection in monoclonal antibody (MAb) A5-positive ganglionic neurons and that a 2.8-kb portion of the HSV-1 genome, corresponding to the 5′ end of the LAT (latency-associated transcript) coding region, is responsible for this phenotype (38, 65). In the current study we carried out further genetic mapping of this latency phenotype and investigated some of the mechanisms that might be responsible. Studies with the chimeric virus HSV-1 17syn+/LAT2, an HSV-1 virus engineered to express HSV-2 LAT, demonstrated that this virus exhibited an HSV-2 latency phenotype, preferentially establishing latency in MAb KH10-positive neurons. This result is complementary to that previously described for the chimeric virus HSV-2 333/LAT1 and indicate that the HSV-1 latency phenotype can be changed to that of HSV-2 by substitution of a 2.8-kb piece of complementary viral DNA. Sequential studies in which we evaluated the pattern of HSV-1 latent infection of the mouse trigeminal ganglion following ocular inoculation with viruses with deletions of functional thymidine kinase, glycoprotein E, ICP0, and US9 protein demonstrate that preferential establishment of HSV-1 latent infection in A5-positive neurons is not a consequence of (i) differential access of HSV-1 to A5-positive neurons,(ii) differential cell-to-cell spread of HSV-1 to A5-positive neurons, (iii) differential “round-trip” spread of HSV-1 to A5-positive neurons, or (iv) expression of ICP0. Additional mapping studies with the HSV-1 LAT deletion viruses
d
LAT371, 17ΔSty, and 17Δ348 indicate that most of the LAT 5′ exon is not required for HSV-1 to preferentially establish latent infection in A5-positive neurons.
Intrathecal Humoral Responses Are Inversely Associated with the Frequency of Simian Immunodeficiency Virus Macrophage-Tropic Variants in the Central Nervous System
Authors: Ryzhova Elena , Aye Pyone , Harvey Tom , Cao Wei , Lackner Andrew , González-Scarano Francisco 
Published: June 2009

ABSTRACT
Sustained simian immunodeficiency virus (SIV) infection of the central nervous system (CNS) depends on macrophage-tropic (M-tropic) strains that are often easily neutralizable. The CNS is often thought of as an immunologically privileged site that fosters replication of M-tropic quasispecies. Yet, there are limited data addressing the intrathecal antibody response or the role of the humoral response, in general, to control M-tropic strains. We investigated the temporal course of the intrathecal fusion inhibitory activity against an M-tropic viral variant and found an inverse relationship between the magnitude of this neutralization and the prevalence of M-tropic populations. These studies suggest a role for the humoral response in the suppression of M-tropic viral species in the CNS in experimental SIV infection.
Analysis of the Percentage of Human Immunodeficiency Virus Type 1 Sequences That Are Hypermutated and Markers of Disease Progression in a Longitudinal Cohort, Including One Individual with a Partially Defective Vif
Authors: Piantadosi Anne , Humes Daryl , Chohan Bhavna , McClelland R. Scott , Overbaugh Julie 
Published: June 2009

ABSTRACT

Hypermutation, the introduction of excessive G-to-A substitutions by host proteins in the APOBEC family, can impair replication of the human immunodeficiency virus (HIV). Because hypermutation represents a potential antiviral strategy, it is important to determine whether greater hypermutation is associated with slower disease progression in natural infection. We examined the level of HIV-1 hypermutation among 28 antiretroviral-naive Kenyan women at two times during infection. By examining single-copy
gag
sequences from proviral DNA, hypermutation was detected in 16 of 28 individuals. Among individuals with any hypermutation, a median of 15% of
gag
sequences were hypermutated (range, 5 to 43%). However, there was no association between the level of
gag
hypermutation and the viral load or CD4 count. Thus, we observed no overall relationship between hypermutation and markers of disease progression among individuals with low to moderate levels of hypermutation. In addition, one individual sustained a typical viral load despite having a high level of hypermutation. This individual had 43% of
gag
sequences hypermutated and harbored a partially defective Vif, which was found to permit hypermutation in a peripheral blood mononuclear cell culture. Overall, our results suggest that a potential antiviral therapy based on hypermutation may need to achieve a substantially higher level of hypermutation than is naturally seen in most individuals to impair virus replication and subsequent disease progression.