bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of Universal Sample Processing Methodology, Combining Smear Microscopy, Culture, and PCR, for Diagnosis of Pulmonary Tuberculosis
Authors: Chakravorty Soumitesh , Dudeja Mridu , Hanif M. , Tyagi Jaya Sivaswami 
Published: June 2005

ABSTRACT

The universal sample processing (USP) multipurpose methodology was developed for the diagnosis of tuberculosis (TB) and other mycobacterial diseases by using smear microscopy, culture, and PCR (S. Chakravorty and J. S. Tyagi, J. Clin. Microbiol. 43:2697-2702, 2005). Its performance was evaluated in a blinded study of 571 sputa and compared with that of the direct and
N
-acetyl
l
-cysteine (NALC)-NaOH methods of smear microscopy and culture. With culture used as the gold standard, USP smear microscopy demonstrated a sensitivity and specificity of 98.2% and 91.4%, respectively, compared to 68.6% and 92.6%, respectively, for the direct method. For a subset of 325 specimens, the USP method recorded a 97.1% sensitivity and 83.2% specificity compared to the NALC-NaOH method, which had a sensitivity and specificity of 80.0% and 89.7%, respectively, with culture used as the gold standard. Thus, the USP method exhibited a highly significant enhancement in sensitivity (
P
< 0.0001) compared to the direct and NALC-NaOH methods of smear microscopy. The USP culture sensitivity was 50.1% and was not significantly different from that of conventional methods (53.6%). The sensitivity and specificity of IS
6110
PCR were 99.1% and 71.2%, respectively, with culture used as the gold standard, and increased to 99.7% and 78.8%, respectively, when compared with USP smear microscopy. Thus, the USP methodology was highly efficacious in diagnosing TB by smear microscopy, culture, and PCR in a clinical setting.
Comparison ofCampylobacter jejuniLipooligosaccharide Biosynthesis Loci from a Variety of Sources
Authors: Parker Craig T. , Horn Sharon T. , Gilbert Michel , Miller William G. , Woodward David L. , Mandrell Robert E. 
Published: June 2005

ABSTRACTCampylobacter jejunistrains exhibit significant variation in the genetic content of the lipooligosaccharide (LOS) biosynthesis loci with concomitant differences in LOS structure. TheC. jejuniLOS loci have been grouped into six classes based on gene content and organization. Utilizing PCR amplifications of genes from these loci, we were able to classify a majority (80%) of the LOS biosynthesis loci from 123 strains ofC. jejunithat included 39 of the Penner serotype reference strains. We found that a particular LOS class was not always associated with a specific Penner serotype, and 14 of 16 Guillain-Barré syndrome-associated isolates tested in this study shared the same LOS class. The remaining isolates that could not be classified were often distinguishable from each other based on the results of gene-specific PCR and the lengths of their LOS biosynthesis loci as determined by long (XL) PCR. Sequence analysis of two of these unique XL PCR products demonstrated two new LOS classes. These results support the hypothesis that the LOS locus is a hot spot for genetic exchange and rearrangements. Analysis of the LOS biosynthesis genes by PCR assays can be used for typingC. jejuniand offers the advantage of inferring potential LOS structures.
Epidemiologic Relationship between Fluoroquinolone-ResistantSalmonella entericaSerovar Choleraesuis Strains Isolated from Humans and Pigs in Taiwan (1997 to 2002)
Authors: Chang Chao-Chin , Lin Yi-Hsuan , Chang Chao-Fu , Yeh Kuang-Sheng , Chiu Cheng-Hsun , Chu Chishih , Chien Maw-Sheng , Hsu Yuan-Man , Tsai Li-Shu , Chiou Chien-Shun 
Published: June 2005

ABSTRACTThe emergence of ciprofloxacin-resistantSalmonella entericaserovar Choleraesuis in recent years has become an important public health issue in Taiwan. The resistant strains that cause human infections are considered to be from pigs. In this study, we characterized 157 swine and 42 humanSalmonellaserovar Choleraesuis isolates by pulsed-field gel electrophoresis (PFGE) and drug susceptibility testing to investigate the epidemiologic relationship among the isolates. By PFGE analyses, two major clusters (clusters GA and GB) were identified. Isolates in cluster GA were of both human and swine origins, while those in cluster GB were from pigs only. Among the various genotypes identified, genotype gt-1a was the most prevalent, which was found in 71% (30 of 42) and 48% (76 of 157) of human and swine isolates, respectively. The susceptibility tests for the 106 gt-1a isolates identified 44 susceptibility profiles and showed that 73% of human isolates and 34% of swine isolates were resistant to three fluoroquinolones (ciprofloxacin, enrofloxacin, and norfloxacin). Our findings indicate that a clonal group ofSalmonellaserovar Choleraesuis may have been circulating in human and swine populations in Taiwan for years and that the fluoroquinolone-resistantSalmonellaserovar Choleraesuis strains most likely evolved from a gt-1a clone that emerged in 2000 and that then caused widespread infections in humans and pigs. Nevertheless, it is still debatable whether thoseSalmonellainfections in humans are caused by isolates derived from pigs, on the basis of the higher fluoroquinolone and other antimicrobial resistance percentages in human isolates than in pig isolates.
Antifungal Activities of Tacrolimus and Azole Agents against the Eleven Currently Accepted
Malassezia
Species
Authors: Sugita Takashi , Tajima Mami , Ito Tomonobu , Saito Masuyoshi , Tsuboi Ryoji , Nishikawa Akemi 
Published: June 2005

ABSTRACT

The lipophilic yeast
Malassezia
is an exacerbating factor in atopic dermatitis (AD) and colonizes the skin surface of patients with AD. With the goal of reducing the number of
Malassezia
cells, we investigated the antifungal activities of a therapeutic agent for AD, tacrolimus, and the azole agents itraconazole and ketoconazole against
Malassezia
species in vitro. We examined 125 strains of the 11 currently accepted
Malassezia
species by using the agar dilution method. All strains of the 11
Malassezia
species were very susceptible to both azole agents, with MICs ranging from 0.016 to 0.25 μg/ml. Tacrolimus had antifungal activities against half of the strains, with MICs ranging from 16 to 32 μg/ml. Two of the major cutaneous floras,
Malassezia globosa
and
Malassezia restricta
, have several genotypes in the intergenic spacer region of the rRNA gene; the azole agents had slightly higher MICs for specific genotype strains of both microorganisms. A combination of azole agents and tacrolimus had a synergistic effect against
Malassezia
isolates, based on a fractional inhibitory index of 0.245 to 0.378. Our results provide the basis for testing these agents in future clinical trials to reduce the number of
Malassezia
cells colonizing the skin surface in patients with AD.
Species-Level Identification of Staphylococcal Isolates by Real-Time PCR and Melt Curve Analysis
Authors: Skow Áine , Mangold Kathy A. , Tajuddin Mohammed , Huntington Anne , Fritz Brett , Thomson Richard B. , Kaul Karen L. 
Published: June 2005

ABSTRACTA real-time PCR assay was developed to identify common staphylococcal species. A single set of consensus primers was designed to amplify a portion of the 16S rRNA gene, and a pair of fluorescence resonance energy transfer probes was used to identify species based on the unique melt properties of the probes resulting from sequence variations in the amplicons from each species. Nine common staphylococcal strains (S. aureus,S. capitis,S. epidermidis,S. haemolyticus,S. hominis,S. lugdunensis,S. schleiferi,S. simulans, andS. warneri) were used for assay development. The species-specific melting profiles were validated by correctly identifying 36 of 37 coagulase-negative staphylococcal (CoNS) isolates identified by ribotyping. In a study of clinical isolates, the PCR/melt curve approach correctly identified 56/56S. aureusisolates identified by coagulase/protein A latex agglutination. Fifty-four CoNS clinical isolates characterized using the API Staph assay were studied, with the PCR/melt curve approach yielding matching identifications for 32/54 (59%). The API Staph assay was unable to identify 18 CoNS isolates, and differing results were obtained for 4 isolates. Sequencing of the 22 discrepant or unidentified CoNS samples revealed that the PCR/melt curve results were correct for all but one isolate. Thus, PCR/melt curve analysis achieved a nearly 100% accuracy and performed better than biochemical testing. Performance of the PCR/melt curve approach requires less than 2 h after colony selection. This method thus provides a rapid and accurate approach to the identification of staphylococcal species in the clinical laboratory.
Use of the Genomic Subtractive Hybridization Technique To Develop a Real-Time PCR Assay for Quantitative Detection of
Prevotella
spp. in Oral Biofilm Samples
Authors: Nagashima Shiori , Yoshida Akihiro , Suzuki Nao , Ansai Toshihiro , Takehara Tadamichi 
Published: June 2005

ABSTRACT

Genomic subtractive hybridization was used to design
Prevotella nigrescens
-specific primers and TaqMan probes. Based on this technique, a TaqMan real-time PCR assay was developed for quantifying four oral black-pigmented
Prevotella
species. The combination of real-time PCR and genomic subtractive hybridization is useful for preparing species-specific primer-probe sets for closely related species.
Use of Genotypic Identification by
sodA
Sequencing in a Prospective Study To Examine the Distribution of Coagulase-Negative
Staphylococcus
Species among Strains Recovered during Septic Orthopedic Surgery and Evaluate Their Significance
Authors: Sivadon V. , Rottman M. , Chaverot S. , Quincampoix J.-C. , Avettand V. , de Mazancourt P. , Bernard L. , Trieu-Cuot P. , Féron J.-M. , Lortat-Jacob A. , Piriou P. , Judet T. , Gaillard J.-L. 
Published: June 2005

ABSTRACT

A total of 212 coagulase-negative
Staphylococcus
strains recovered prospectively during 119 surgeries for proven or suspected bone and joint infection (BJI) were identified by
sodA
sequencing. These strains were identified as 151
Staphylococcus epidermidis
isolates, 15
S. warneri
isolates, 14
S. capitis
isolates, 9
S. hominis
isolates, 6
S. lugdunensis
isolates, 5
S. haemolyticus
isolates, 4
S. caprae
isolates, 4
S. pasteuri
isolates, 3
S. simulans
isolates, and 1
S. cohnii
isolate. Only
S. epidermidis
,
S. lugdunensis
,
S. capitis
, and
S. caprae
were found to be infecting organisms and were involved, respectively, in 35 (81.4%), 3 (7.0%), 3 (7.0%), and 2 (4.6%) cases of BJI.
Survey of Methicillin-Resistant
Staphylococcus aureus
Strains from Two Hospitals in El Paso, Texas
Authors: O'Brien Frances G. , Lim Tien Tze , Winnett David C. , Coombs Geoffrey W. , Pearson Julie C. , Delgado Alejandro , Langevin Mark J. , Cantore Stephanie A. , Gonzalez Leti , Gustafson John E. 
Published: June 2005

ABSTRACT

Seventy-one percent of 76 methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from two medical centers in El Paso, Texas, represent three similar pulsed-field gel electrophoresis types. Overall, six pulsed-field types were identified represented by multilocus sequence/staphylococcal chromosomal cassette DNA
mec
(SCC
mec
) types: ST5-MRSA-II; ST36-MRSA-II; ST8 (untypeable SCC
mec
); and a newly described clonal cluster 8 strain, ST507-MRSA-IV. This study demonstrates the presence of multiple-antibiotic-resistant epidemic MRSA clones in El Paso.
Molecular Diagnosis of Lymphogranuloma Venereum in Patients with Genital Ulcer Disease
Authors: Sturm Patrick D. J. , Moodley Prashini , Govender Keshnie , Bohlken Louise , Vanmali Trusha , Sturm A. Willem 
Published: June 2005

ABSTRACT
The detection of herpes, chancroid, and syphilis in genital ulcers is done by PCR. This is not so for lymphogranuloma venereum (LGV). We report on the use of a PCR with digestion that differentiates the LGV biovar from the trachoma biovar. Our findings suggest that the clinical description of LGV in current textbooks is incomplete.
Isolation and Characterization of
Mycoplasma sphenisci
sp. nov. from the Choana of an Aquarium-Reared Jackass Penguin (
Spheniscus demersus
)
Authors: Frasca Salvatore , Weber E. Scott , Urquhart Heather , Liao Xiaofen , Gladd Martha , Cecchini Katharine , Hudson Paul , May Meghan , Gast Rebecca J. , Gorton Timothy S. , Geary Steven J. 
Published: June 2005

ABSTRACT

Strain UCMJ was isolated from the choana of a jackass penguin (
Spheniscus demersus
) with recurrent mucocaseous choanal discharge. Isolation of this mycoplasma expands the known range of species hosting mycoplasmas. The name
Mycoplasma sphenisci
sp. nov. is proposed for this new species, for which strain UCMJ is the type strain.
Recurrent Breast Abscess Caused by
Gordonia bronchialis
in an Immunocompetent Patient
Authors: Werno Anja M. , Anderson Trevor P. , Chambers Stephen T. , Laird Heather M. , Murdoch David R. 
Published: June 2005

ABSTRACT

We present the first reported case of a recurrent breast infection caused by
Gordonia bronchialis
. The infection occurred in a 43-year-old immunocompetent female, and species level identification was obtained with 16S rRNA sequencing.
Atypical Serological Response Marked by a Lack of Detectable Anti-gp43 Antibodies in a Patient with Disseminated Paracoccidioidomycosis
Authors: Vidal Mônica S. M. , Benard Gil , de Brito Thales , Dantas Kátia C. , Pereira Cristiane N. , França Francisco O. S. , da Silva Ana M. G. , Martins José E. C. 
Published: June 2005

ABSTRACT
Serological tests are frequently used to diagnosis paracoccidioidomycosis. A glycoprotein of 43 kDa is considered to be the main diagnostic antigen, being recognized by virtually all patients' sera. A case of atypical serological response, consisting of a lack of detectable anti-gp43 antibodies, in a patient with disseminated paracoccidioidomycosis is presented.
Compartmentalized Human Immunodeficiency Virus Type 1 Present in Cerebrospinal Fluid Is Produced by Short-Lived Cells
Authors: Harrington Patrick R. , Haas David W. , Ritola Kimberly , Swanstrom Ronald 
Published: June 2005

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) invades the central nervous system (CNS) during primary infection and persists in this compartment by unknown mechanisms over the course of infection. In this study, we examined viral population dynamics in four asymptomatic subjects commencing antiretroviral therapy to characterize cellular sources of HIV-1 in the CNS. The inability to monitor viruses directly in the brain poses a major challenge in studying HIV-1 dynamics in the CNS. Studies of HIV-1 in cerebrospinal fluid (CSF) provide a useful surrogate for the sampling of virus in the CNS, but they are complicated by the fact that infected cells in local CNS tissues and in the periphery contribute to the population pool of HIV-1 in CSF. We utilized heteroduplex tracking assays to differentiate CSF HIV-1 variants that were shared with peripheral blood plasma from those that were compartmentalized in CSF and therefore presumably derived from local CNS tissues. We then tracked the relative decline of individual viral variants during the initial days of antiretroviral therapy. We found that HIV-1 variants compartmentalized in CSF declined rapidly during therapy, with maximum half-lives of approximately 1 to 3 days. These kinetics emulate the decline in HIV-1 produced from short-lived CD4+T cells in the periphery, suggesting that a similarly short-lived, HIV-infected cell population exists within the CNS. We propose that short-lived CD4+T cells trafficking between the CNS and the periphery play an important role in amplifying and maintaining HIV-1 populations in the CNS during the asymptomatic phase of infection.
A Cellular
Drosophila melanogaster
Protein with Similarity to Baculovirus F Envelope Fusion Proteins
Authors: Lung Oliver , Blissard Gary W. 
Published: June 2005

ABSTRACT

Baculovirus F (fusion) proteins are found in the envelopes of budded virions. Recently a
Drosophila melanogaster
gene (CG4715) that encodes a protein with sequence similarity to baculovirus F proteins was discovered. To examine similarities and differences with baculovirus F proteins, we cloned the
D. melanogaster
cellular F (
Dm-cF
) protein gene and analyzed
Dm-cF
expression and localization. The predicted Dm-cF protein sequence lacks a furin cleavage site, and transiently expressed Dm-cF showed no protein cleavage and no detectable membrane fusion activity. In cell localization studies, transiently expressed Dm-cF was localized to intracellular organelles in
D. melanogaster
S2 cells, unlike baculovirus F proteins, which localize to cellular plasma membranes. Using reverse transcriptase PCR and Western blot analysis to examine
Dm-cF
expression in animals, we detected
Dm-cF
expression in both larval and adult
D. melanogaster
cells. However,
Dm-cF
expression was detected only in third instar larvae and adults, suggesting that
Dm-cF
expression may be developmentally regulated. We also identified genes related to
Dm-cF
in the genomes of two other
Drosophila
species,
Drosophila yakuba
and
Drosophila pseudoobscura
, and the mosquito
Anopheles gambiae
. These observations suggest that
f
genes may be present in the genomes of many insects. Conservation within and between 22 baculovirus and 4 insect F proteins was examined in detail. These studies demonstrate that
Dm-cF
is expressed in
D. melanogaster
and suggest that if baculovirus
f
genes are derived from a host cellular
f
gene, the function appears to have changed substantially upon adaptation to the baculovirus infection cycle.
Inhibition of Alpha/Beta Interferon Signaling by the NS4B Protein of Flaviviruses
Authors: Muñoz-Jordán Jorge L. , Laurent-Rolle Maudry , Ashour Joseph , Martínez-Sobrido Luis , Ashok Mundrigi , Lipkin W. Ian , García-Sastre Adolfo 
Published: June 2005

ABSTRACT
Flaviviruses are insect-borne, positive-strand RNA viruses that have been disseminated worldwide. Their genome is translated into a polyprotein, which is subsequently cleaved by a combination of viral and host proteases to produce three structural proteins and seven nonstructural proteins. The nonstructural protein NS4B of dengue 2 virus partially blocks activation of STAT1 and interferon-stimulated response element (ISRE) promoters in cells stimulated with interferon (IFN). We have found that this function of NS4B is conserved in West Nile and yellow fever viruses. Deletion analysis shows that that the first 125 amino acids of dengue virus NS4B are sufficient for inhibition of alpha/beta IFN (IFN-α/β) signaling. The cleavable signal peptide at the N terminus of NS4B, a peptide with a molecular weight of 2,000, is required for IFN antagonism but can be replaced by an unrelated signal peptide. Coexpression of dengue virus NS4A and NS4B together results in enhanced inhibition of ISRE promoter activation in response to IFN-α/β. In contrast, expression of the precursor NS4A/B fusion protein does not cause an inhibition of IFN signaling unless this product is cleaved by the viral peptidase NS2B/NS3, indicating that proper viral polyprotein processing is required for anti-interferon function.
Extensive Syncytium Formation Mediated by the Reovirus FAST Proteins Triggers Apoptosis-Induced Membrane Instability
Authors: Salsman Jayme , Top Deniz , Boutilier Julie , Duncan Roy 
Published: June 2005

ABSTRACT

The fusion-associated small transmembrane (FAST) proteins of the fusogenic reoviruses are the only known examples of membrane fusion proteins encoded by nonenveloped viruses. While the involvement of the FAST proteins in mediating extensive syncytium formation in virus-infected and -transfected cells is well established, the nature of the fusion reaction and the role of cell-cell fusion in the virus replication cycle remain unclear. To address these issues, we analyzed the syncytial phenotype induced by four different FAST proteins: the avian and Nelson Bay reovirus p10, reptilian reovirus p14, and baboon reovirus p15 FAST proteins. Results indicate that FAST protein-mediated cell-cell fusion is a relatively nonleaky process, as demonstrated by the absence of significant [
3
H]uridine release from cells undergoing fusion and by the resistance of these cells to treatment with hygromycin B, a membrane-impermeable translation inhibitor. However, diminished membrane integrity occurred subsequent to extensive syncytium formation and was associated with DNA fragmentation and chromatin condensation, indicating that extensive cell-cell fusion activates apoptotic signaling cascades. Inhibiting effector caspase activation or ablating the extent of syncytium formation, either by partial deletion of the avian reovirus p10 ectodomain or by antibody inhibition of p14-mediated cell-cell fusion, all resulted in reduced membrane permeability changes. These observations suggest that the FAST proteins do not possess intrinsic membrane-lytic activity. Rather, extensive FAST protein-induced syncytium formation triggers an apoptotic response that contributes to altered membrane integrity. We propose that the FAST proteins have evolved to serve a dual role in the replication cycle of these fusogenic nonenveloped viruses, with nonleaky cell-cell fusion initially promoting localized cell-cell transmission of the infection followed by enhanced progeny virus release from apoptotic syncytia and systemic dissemination of the infection.
Preliminary Physical Mapping of RNA-RNA Linkages in the Genomic RNA of Moloney Murine Leukemia Virus
Authors: Hibbert Catherine S. , Rein Alan 
Published: June 2005

ABSTRACT
Retrovirus particles contain two copies of their genomic RNA, held together in a dimer by linkages which presumably consist of a limited number of base pairs. In an effort to localize these linkages, we digested deproteinized RNA from Moloney murine leukemia virus (MLV) particles with RNase H in the presence of oligodeoxynucleotides complementary to specific sites in viral RNA. The cleaved RNAs were then characterized by nondenaturing gel electrophoresis. We found that fragments composed of nucleotides 1 to 754 were dimeric, with a linkage as thermostable as that between dimers of intact genomic RNA. In contrast, there was no stable linkage between fragments consisting of nucleotides 755 to 8332. Thus, the most stable linkage between monomers is on the 5′ side of nucleotide 754. This conclusion is in agreement with earlier electron microscopic analyses of partially denatured viral RNAs and with our study (C. S. Hibbert, J. Mirro, and A. Rein, J. Virol. 78:10927-10938, 2004) of encapsidated nonviral mRNAs containing inserts of viral sequence. We obtained similar results with RNAs from immature MLV particles, in which the dimeric linkage is different from that in mature particles and has not previously been localized. The 5′ and 3′ fragments of cleaved RNA are all held together by thermolabile linkages, indicating the presence of tethering interactions between bases 5′ and bases 3′ of the cleavage site. When RNAs from mature particles were cleaved at nucleotide 1201, we detected tethering interactions spanning the cleavage site which are intramonomeric and are as strong as the most stable linkage between the monomers.