bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-Specific Single-Nucleotide Polymorphism Assays for the
Bacillus anthracis
Ames Strain
Authors: Van Ert Matthew N. , Easterday W. Ryan , Simonson Tatum S. , U'Ren Jana M. , Pearson Talima , Kenefic Leo J. , Busch Joseph D. , Huynh Lynn Y. , Dukerich Megan , Trim Carla B. , Beaudry Jodi , Welty-Bernard Amy , Read Timothy , Fraser Claire M. , Ravel Jacques , Keim Paul 
Published: November 2006

ABSTRACT

Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In
Bacillus anthracis
, whole-genome sequencing efforts revealed ca. 3,500 single-nucleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of
B. anthracis
makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of
B. anthracis
that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across
B. anthracis
strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the
B. anthracis
Ames strain from the 88 unique
B. anthracis
strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in
B. anthracis
.
Evaluation of Commercial Rubella Immunoglobulin G Avidity Assays
Authors: Mubareka Samira , Richards Hannah , Gray Michael , Tipples Graham A. 
Published: November 2006

ABSTRACT

We compared the performances of five commercial rubella virus immunoglobulin G (IgG) avidity assays. The Adaltis (kappa = 0.28) and Diesse (kappa = 0.33) assays showed poor correlation, the Behring assay (kappa = 0.68) showed good correlation, and the Euroimmun (kappa = 0.95) and Radim (kappa = 0.94) assays showed excellent correlation with a well-established in-house rubella virus IgG avidity assay. The Euroimmun and Radim assays were statistically significantly better than the other commercial assays (
P
< 0.01).
Nosocomial Liver Abscess Caused by Extended-Spectrum Beta-Lactamase-ProducingKlebsiella pneumoniae
Authors: Lin Jung-Chung , Siu L. K. , Fung Chang-Phone , Yeh Kao-Ming , Chang Feng-Yee 
Published: November 2006

ABSTRACTA nosocomial pyogenic liver abscess caused by an extended-spectrum beta-lactamase-producingKlebsiella pneumoniaeisolate presented in a man with adenocarcinoma of the stomach. TheK. pneumoniaestrain isolated from blood and liver aspirate cultures after antibiotic therapy for recurrent bacteremia was resistant to all extended-spectrum beta-lactams except imipenem and differed fromK. pneumoniaestrains causing community-acquired liver abscesses.
Isolation of
Bartonella quintana
from a Woman and a Cat following Putative Bite Transmission
Authors: Breitschwerdt Edward B. , Maggi Ricardo G. , Sigmon Betsy , Nicholson William L. 
Published: November 2006

ABSTRACT

We report here the detection of
Bartonella quintana
, after putative bite transmission, in pre-enrichment blood cultures from a woman and from two feral barn cats. Prospective molecular epidemiological studies are necessary to characterize the risk of human
Bartonella quintana
infection following cat bites.
Double-Locus Sequence Typing Using
clfB
and
spa
, a Fast and Simple Method for Epidemiological Typing of Methicillin-Resistant
Staphylococcus aureus
Authors: Kuhn G. , Francioli P. , Blanc D. S. 
Published: November 2006

ABSTRACT

Sequence-based epidemiological typing of methicillin-resistant
Staphylococcus aureus
(MRSA) has recently been promoted because it results in unambiguous data sets that can be organized in local and global databases. The replacement of previous typing methods, such as the highly discriminatory pulsed-field gel electrophoresis (PFGE), has been attempted with various markers and typing schemes, including
spa
typing and multilocus sequence typing. However, despite a number of advantages, none of these methods showed convincing evidence for performance in epidemiological typing comparable to that of PFGE. By using three sets of 48 MRSA strains comprising isolates that were (i) genetically highly diverse, (ii) genetically related, and (iii) obtained from long-term carriers, we analyzed the performance of the four highly polymorphic
S. aureus
markers:
clfA
,
clfB
,
fnbA
, and
spa
. Typeability, discriminatory power, in vivo stability, and evolution of these markers were compared to those of PFGE. Clearly, none of the markers alone could match the discriminatory power of PFGE (63 genotypes; index of discrimination of 0.96). Instead, this could be achieved by combining markers in pairs. We showed that by using only 3′ partial sequences of approximately 500 bp, the majority of each marker's discriminatory power was displayed, and using the partial sequences, the best performance was obtained with the combination of
clfB
and
spa
(57 genotypes; index of discrimination of 0.94). Genetic changes were not observed for any of the sequence markers over a period of 3 years and in the case of partial sequences for a period of more than 4 years. This is in contrast to PFGE where changes occurred after several months. The genetic differences found between isolate pairs of long-term carriers and among highly related isolates indicated clonal evolution. A typing scheme based on 500-bp 3′ partial sequences of
clfB
and
spa
is proposed.
Newly Developed Primers for Comprehensive Amplification of the
rpoB
Gene and Detection of Rifampin Resistance in
Mycobacterium tuberculosis
Authors: Rigouts Leen , Nolasco Oscar , de Rijk Pim , Nduwamahoro Elie , Van Deun Armand , Ramsay Andy , Arevalo Jorge , Portaels Françoise 
Published: November 2006

ABSTRACT

New
rpoB
gene primers for detecting Rif
r
in
Mycobacterium tuberculosis
complex bacteria achieved 100% specificity and 88% (fresh sputa) and 92% (ethanol-preserved sputa) diagnostic sensitivity and detected up to 4 CFU/sample. Of the 99 Rif
r
isolates examined, 97% had mutations within cluster I, 2% at codon 176, and 1% at codon 497.
Identification ofVibrioIsolates by a Multiplex PCR Assay andrpoBSequence Determination
Authors: Tarr Cheryl L. , Patel Jayna S. , Puhr Nancy D. , Sowers Evangeline G. , Bopp Cheryl A. , Strockbine Nancy A. 
Published: November 2006

ABSTRACTVibrio, a diverse genus of aquatic bacteria, currently includes 72 species, 12 of which occur in human clinical samples. Of these 12, three species—Vibrio cholerae,Vibrio parahaemolyticus, andVibrio vulnificus—account for the majority ofVibrioinfections in humans. Rapid and accurate identification ofVibriospecies has been problematic because phenotypic characteristics are variable within species and biochemical identification requires 2 or more days to complete. To facilitate the identification of human-pathogenic species, we developed a multiplex PCR that uses species-specific primers to amplify gene regions in four species (V. cholerae,V. parahaemolyticus,V. vulnificus, andV. mimicus). The assay was tested on a sample of 309Vibrioisolates representing 26 named species (including 12 human pathogens) that had been characterized by biochemical methods. A total of 190 isolates that had been identified as one of the four target species all yielded results consistent with the previous classification. The assay identified an additional fourV. parahaemolyticusisolates among the other 119 isolates. Sequence analysis based onrpoBwas used to validate the multiplex results for these four isolates, and all clustered with otherV. parahaemolyticussequences. TherpoBsequences for 12 of 15 previously unidentified isolates clustered with otherVibriospecies in a phylogenetic analysis, and three isolates appeared to represent unnamedVibriospecies. The PCR assay provides a simple, rapid, and reliable tool for identification of the majorVibriopathogens in clinical samples, andrpoBsequencing provides an additional identification tool for other species in the genusVibrio.
Multicenter Studies of Tigecycline Disk Diffusion Susceptibility Results for
Acinetobacter
spp
Authors: Jones Ronald N. , Ferraro Mary Jane , Reller L. Barth , Schreckenberger Paul C. , Swenson Jana M. , Sader Helio S. 
Published: November 2006

ABSTRACT

Acinetobacter
sp. isolates having multidrug resistance (MDR) patterns have become common in many medical centers worldwide, limiting therapeutic options. A five-center study tested 103 contemporary clinical
Acinetobacter
spp., including MDR strains, by reference broth microdilution and disk diffusion (15-μg disk content) methods against tigecycline. Applying U.S. Food and Drug Administration tigecycline breakpoint criteria for
Enterobacteriaceae
(susceptibility at ≤2 μg/ml [≤1 μg/ml by the European Committee on Antimicrobial Susceptibility Testing]; disk diffusion breakpoints at ≥19 mm and ≤14 mm) to
Acinetobacter
spp. led to an unacceptable error rate (23.3%). However, an adjustment of tigecycline disk diffusion breakpoints (susceptible/resistant) to ≥16/≤12 mm reduced intermethod errors to an acceptable level (only 9.7%, all minor).
Age-Related Urinary Excretion of BK Polyomavirus by Nonimmunocompromised Individuals
Authors: Zhong Shan , Zheng Huai-Ying , Suzuki Motofumi , Chen Qin , Ikegaya Hiroshi , Aoki Naoto , Usuku Shuzo , Kobayashi Nobuyoshi , Nukuzuma Souichi , Yasuda Yukiharu , Kuniyoshi Noboru , Yogo Yoshiaki , Kitamura Tadaichi 
Published: November 2006

ABSTRACT
Two polyomaviruses, BK virus (BKV) and JC virus (JCV), are ubiquitous in the human population, generally infecting children asymptomatically and then persisting in renal tissue. It is generally thought that reactivation leads to productive infection for both viruses, with progeny shed in the urine. Several studies have shown that the rate of JC viruria increases with the age of the host, but a systematic approach to examine the shedding of BKV has not been developed. To elucidate the relationship between BK viruria and host age, we obtained urine from donors (healthy volunteers or nonimmunocompromised patients) who were divided into nine age groups, each containing 50 members. A high-sensitivity PCR was used to detect BKV and JCV DNA from urinary samples, and the specificity of amplification was confirmed by sequencing or restriction analysis of the amplified fragments. The rate of BK viruria was relatively low in subjects aged <30 years but gradually increased with age in subjects aged ≥30 years. However, BK viruria was less frequent than JC viruria in adults. The detected BKV isolates were classified into subtypes, and detection rates for individual subtypes were compared among age groups; this analysis showed that viruria of subtypes I (the most prevalent subtype) and IV (the second most prevalent subtype) occurred more frequently in older subjects. Therefore, our results reveal new aspects of BK viruria in nonimmunocompromised individuals.
Prevalence and Antibacterial Susceptibility of
mef
(A)-Positive Macrolide-Resistant
Streptococcus pneumoniae
over 4 Years (2000 to 2004) of the PROTEKT US Study
Authors: Farrell David J. , File Thomas M. , Jenkins Stephen G. 
Published: November 2006

ABSTRACT

In the United States, approximately 30% of
Streptococcus pneumoniae
isolates are macrolide (erythromycin [ERY]) resistant (ERSP), most commonly due to expression of the
mef
(A) gene previously associated with lower-level ERY resistance (ERY
r
; MIC = 1 to 4 μg/ml). The data from the PROTEKT US surveillance study were analyzed to evaluate the prevalence and antibacterial susceptibility of
mef
(A)-positive ERSP. In all, 26,634 isolates of
S. pneumoniae
were collected in the United States between 2000 and 2004 from centers common to all years. ERY
r
was stable at approximately 29% over the 4 years, but the proportion of ERSP isolates positive for
mef
(A) alone decreased (year 1 [2000 to 2001], 69.0%; year 4 [2003 to 2004], 60.7%), with the sharpest declines seen in isolates from patients from 0 to 2 years of age. Conversely, the proportion isolates positive for both
erm
(B) and
mef
(A) increased over the duration of the present study (year 1, 9.3%; year 4, 19.1%), a change that was again most marked in patients aged ≤2 years. The majority of ERSP isolates expressing
mef
(A) alone exhibited higher than previously reported levels of ERY
r
(MIC
90
= 16 μg/ml). However, the ketolide antibacterial telithromycin consistently demonstrated in vitro activity against these isolates over the 4 years of the study (MIC
90
= 0.5 to 1 μg/ml).
Clonal Structure of
Enterococcus faecalis
Isolated from Polish Hospitals: Characterization of Epidemic Clones
Authors: Kawalec Magdalena , Pietras Zbigniew , Daniłowicz Emilia , Jakubczak Aleksandra , Gniadkowski Marek , Hryniewicz Waleria , Willems Rob J. L. 
Published: November 2006

ABSTRACT

To study the population structure of
Enterococcus faecalis
from Polish hospitals, 291 isolates were typed by pulsed-field gel electrophoresis and a novel multilocus sequence typing scheme (P. Ruiz-Garbajosa et al., J. Clin. Microbiol. 44:2220-2228, 2006). The isolates originated from geographically widespread medical institutions and were recovered during a 10-year period (1996 to 2005) from different clinical sources. The analysis grouped the isolates into five epidemic and 71 sporadic clones. The importance of the previously identified global clonal complexes CC2 and CC9 was corroborated by our findings that two of the Polish epidemic clones, A and J, were classified into these clonal complexes (CCs). However, the two most predominant clones, C (ST40) and F (CC87), did not cluster in the aforementioned CCs and may represent novel epidemic CCs. These clones may have emerged in Central Europe. Clone F, carrying glycopeptide resistance determinants of VanA or VanB phenotypes, caused several outbreaks in hematology units and appeared to be the most prevalent clone in recent years in Poland. Antimicrobial susceptibility testing and additional tests for pathogenicity-related phenotypes (hemolysin and gelatinase production) and genes (
asa1
and
esp
) were performed to further characterize these epidemic clones. Multidrug resistance, glycopeptide resistance, presence of
asa1
, and production of hemolysin appeared to be statistically significant features related to epidemicity. Production of gelatinase was significant for two of the epidemic clones, whereas presence of the
esp
gene was not specific for the epidemic clones.
Statistical Analyses of Correlation between Fluconazole MICs for
Candida
spp. Assessed by Standard Methods Set Forth by the European Committee on Antimicrobial Susceptibility Testing (E.Dis. 7.1) and CLSI (M27-A2)
Authors: Rodriguez-Tudela Juan Luis , Donnelly J. Peter , Pfaller Michael A. , Chryssantou Erja , Warn Peter , Denning David W. , Espinel-Ingroff Ana , Barchiesi Francesco , Cuenca-Estrella Manuel 
Published: November 2006

ABSTRACT
The European Committee on Antimicrobial Susceptibility Testing (EUCAST) Subcommittee on Antifungal Susceptibility Testing recently published a standard for determining the susceptibility of fermentative yeasts to antifungals. From the beginning, the EUCAST and its North American counterpart, the CLSI, decided to work together in order to establish common standards. As part of this exercise, the susceptibility of a set of 475 yeast isolates was tested by both standards. The intraclass correlation coefficient and the equations defining the linear regression between both methods were estimated. Both methods produced very similar results, with an intraclass correlation coefficient of 0.954 (0.945 to 0.962), although linear regression analysis shows that the EUCAST standard resulted in slightly lower MICs. There were only eight isolates showing at least four twofold dilution MIC differences between both standards. After 24 h of incubation, the MICs obtained by the CLSI method were equivalent to those obtained by the EUCAST standard. In summary, both methods produce very similar MICs, indicating that methodology does not pose any obstacle to obtaining uniform standards for antifungal susceptibility testing of yeasts.
The Adenovirus L4 33-Kilodalton Protein Binds to Intragenic Sequences of the Major Late Promoter Required for Late Phase-Specific Stimulation of Transcription
Authors: Ali Humayra , LeRoy Gary , Bridge Gemma , Flint S. J. 
Published: November 2006

ABSTRACT

The adenovirus late IVa
2
protein is required for maximally efficient transcription from the viral major late (ML) promoter, and hence, the synthesis of the majority of viral late proteins. This protein is a sequence-specific DNA-binding protein that also promotes the assembly of progeny virus particles. Previous studies have established that a IVa
2
protein dimer (DEF-B) binds specifically to an intragenic ML promoter sequence necessary for late phase-specific stimulation of ML transcription. However, activation of transcription from the ML promoter correlates with binding of at least one additional infected-cell-specific protein, termed DEF-A, to the promoter. Using an assay for the DNA-binding activity of DEF-A, we identified the unknown protein by using conventional purification methods, purification of FLAG-tagged IVa
2
-protein-containing complexes, and transient synthesis of viral late proteins. The results of these experiments established that the viral L4 33-kDa protein is the only component of DEF-A: the IVa
2
and L4 33-kDa proteins are necessary and sufficient for formation of all previously described complexes in the intragenic control region of the ML promoter. Furthermore, the L4 33-kDa protein binds to the promoter with the specificity characteristic of DEF-A and stimulates transcription from the ML promoter in transient-expression assays.
Loss of Naïve Cells Accompanies Memory CD4
+
T-Cell Depletion during Long-Term Progression to AIDS in Simian Immunodeficiency Virus-Infected Macaques
Authors: Nishimura Yoshiaki , Igarashi Tatsuhiko , Buckler-White Alicia , Buckler Charles , Imamichi Hiromi , Goeken Robert M. , Lee Wendy R. , Lafont Bernard A. P. , Byrum Russ , Lane H. Clifford , Hirsch Vanessa M. , Martin Malcolm A. 
Published: November 2006

ABSTRACT

Human immunodeficiency virus and simian immunodeficiency virus (SIV) induce a slow progressive disease, characterized by the massive loss of memory CD4
+
T cells during the acute infection followed by a recovery phase in which virus replication is partially controlled. However, because the initial injury is so severe and virus production persists, the immune system eventually collapses and a symptomatic fatal disease invariably occurs. We have assessed CD4
+
T-cell dynamics and disease progression in 12 SIV-infected rhesus monkeys for nearly 2 years. Three macaques exhibiting a rapid progressor phenotype experienced rapid and irreversible loss of memory, but not naïve, CD4
+
T lymphocytes from peripheral blood and secondary lymphoid tissues and died within the first 6 months of virus inoculation. In contrast, SIV-infected conventional progressor animals sustained marked but incomplete depletions of memory CD4
+
T cells and continuous activation/proliferation of this T-lymphocyte subset. This was associated with a profound loss of naïve CD4
+
T cells from peripheral blood and secondary lymphoid tissues, which declined at rates that correlated with disease progression. These data suggest that the persistent loss of memory CD4
+
T cells, which are being eliminated by direct virus killing and activation-induced cell death, requires the continuous differentiation of naïve into memory CD4
+
T cells. This unrelenting replenishment process eventually leads to the exhaustion of the naïve CD4
+
T-cell pool and the development of disease.
Identification of the FHL2 Transcriptional Coactivator as a New Functional Target of the E7 Oncoprotein of Human Papillomavirus Type 16
Authors: Campo-Fernández Beatriz , Morandell Dieter , Santer Frédéric R. , Zwerschke Werner , Jansen-Dürr Pidder 
Published: November 2006

ABSTRACT
We identified the transcriptional coactivator FHL2 as a novel target of the human papillomavirus type 16 (HPV-16) E7 oncoprotein, which plays a major role in cell transformation. The interaction with FHL2 is abolished by mutations in conserved regions 1 and 2 and in the C-terminal zinc finger domain of E7, all required for its transforming potential. We found that E7 impairs the coactivator function of FHL2 on both β-catenin/LCF-dependent and AP-1-dependent promoters. Thus, the interaction with HPV-16 E7 leads to a promoter-specific impairment of FHL2 function and this may contribute to cell transformation.
Role of the Amphipathic Peptide of Semliki Forest Virus Replicase Protein nsP1 in Membrane Association and Virus Replication
Authors: Spuul Pirjo , Salonen Anne , Merits Andres , Jokitalo Eija , Kääriäinen Leevi , Ahola Tero 
Published: November 2006

ABSTRACT

Semliki Forest virus RNA replication takes place in association with specific cytoplasmic vacuoles, derived from the endosomal apparatus. Of the four virus-encoded replicase proteins, nsP1 serves as the membrane anchor of the replication complex. An amphipathic peptide segment, G
245
STLYTESRKLLRSWHLPSV
264
, has been implicated in the membrane binding of nsP1. nsP1 variants with changes within the peptide were studied after protein expression and in the context of virus infection. Proteins with mutations R253E and W259A accumulated in the cytoplasm and were very poorly palmitoylated. The same mutations also drastically affected the localization of the precursor polyprotein P123, and they were lethal when introduced into the virus genome. Mutations R253A and L255A+L256A partially changed the localization of nsP1, and the respective viruses acquired compensatory changes. L255A+L256A only yielded virus encoding L255A+L256V, indicating the importance of a hydrophobic residue in the central 256 position. When fused to green fluorescent protein, the peptide was required in at least two tandem copies to effect a change in localization, but even then the fusion protein was associated with membranes in a nonspecific manner. Thus, the amphipathic peptide is a crucial element for the membrane association of nsP1 and the replication complex. It provides essential affinity for membranes, and other regions of nsP1 also appear to contribute to the localization of the protein.
Lysis of Human Immunodeficiency Virus Type 1 by a Specific Secreted Human Phospholipase A2
Authors: Kim Jae-Ouk , Chakrabarti Bimal K. , Guha-Niyogi Anuradha , Louder Mark K. , Mascola John R. , Ganesh Lakshmanan , Nabel Gary J. 
Published: November 2006

ABSTRACTPhospholipase A2(PLA2) proteins affect cellular activation, signal transduction, and possibly innate immunity. A specific secretory PLA2, sPLA2-X, is shown here to neutralize human immunodeficiency virus type 1 (HIV-1) through degradation of the viral membrane. Catalytic function was required for antiviral activity, and the target cells of infection were unaffected. sPLA2-X potently reduced gene transfer of HIV-1 Env-pseudotyped lentivirus vectors and inhibited the replication of both CCR5- and CXCR4-tropic HIV-1 in human CD4+T cells. Virions resistant to damage by antibody and complement were sensitive to lysis by sPLA2-X, suggesting a novel mechanism of antiviral surveillance independent of the acquired immune system.