bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus Sequence Typing versus Pulsed-Field Gel Electrophoresis for Characterization of Extended-Spectrum Beta-Lactamase-Producing
Escherichia coli
Isolates
Authors: Nemoy Lucia L. , Kotetishvili Mamuka , Tigno Justine , Keefer-Norris Ananda , Harris Anthony D. , Perencevich Eli N. , Johnson Judith A. , Torpey Dave , Sulakvelidze Alexander , Morris J. Glenn , Stine O. Colin 
Published: April 2005

ABSTRACT

Extended-spectrum beta-lactamase (ESBL)-producing
Escherichia coli
strains are emerging pathogens. Molecular typing of ESBL-producing
E. coli
is useful for surveillance purposes, to monitor outbreaks and track nosocomial spread. Although pulsed-field gel electrophoresis (PFGE) is the current “gold standard” for bacterial molecular typing, multilocus sequence typing (MLST) may offer advantages. Forty ESBL-producing
E. coli
isolates were selected at random from a cohort of intensive care unit patients who had active surveillance perirectal cultures done. PFGE identified 19 unique PFGE types (PT) among the 40 isolates; MLST identified 22 unique sequence types. MLST had greater discriminatory ability than PFGE for ESBL-producing
E. coli
. Simpson's indices of diversity for PFGE and MLST were 0.895 and 0.956, respectively. There were five clonal complexes (CCs) (isolates with differences of no more than two loci) that each contained multiple PT, but each PT was found in only one CC, indicating genetic consistency within a CC. MLST has clear utility in studies of ESBL-producing
E. coli
, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains.
Analysis ofMycobacterium tuberculosisGenotypes in Madrid and Identification of Two New Families Specific to Spain-Related Settings
Authors: García de Viedma Darío , Bouza Emilio , Rastogi Nalin , Sola Christophe 
Published: April 2005

ABSTRACTIn Spain, tuberculosis (TB) patterns are changing because of the recent increase in the number of cases among immigrants. To establish the composition of circulatingMycobacterium tuberculosisstrains before the effects of foreign strains appear, this study focused on molecular characterization of 233 patient isolates using spoligotyping. The spoligotyping data were further analyzed using an international database, SpolDB4. The results obtained showed that the general features of theM. tuberculosispopulation in Spain are coherent with those of other European countries, with the Latin American and Mediterranean group, and with the Haarlem 3 and T1 families as the most prevalent genotypes. The Spanish isolates clustered mostly with genotypes which had previously been isolated in countries linked with Spain. We also describe and fully characterize two novelM. tuberculosisfamilies, Madrid1 and Madrid2, which are specific to Spain-related settings. The data reported here provide a solid reference when monitoring changes in the composition of theM. tuberculosispopulation in Spain as a consequence of the increasing rate of TB in the foreign population.
System To Assess Genome Sequencing Needs for Viral Protein Diagnostics and Therapeutics
Authors: Gardner Shea N. , Kuczmarski Thomas A. , Zhou Carol E. , Lam Marisa W. , Slezak Tom R. 
Published: April 2005

ABSTRACTComputational analyses of genome sequences may elucidate protein signatures unique to a target pathogen. We constructed a Protein Signature Pipeline to guide the selection of short peptide sequences to serve as targets for detection and therapeutics. In silico identification of good target peptides that are conserved among strains and unique compared to other species generates a list of peptides. These peptides may be developed in the laboratory as targets of antibody, peptide, and ligand binding for detection assays and therapeutics or as targets for vaccine development. In this paper, we assess how the amount of sequence data affects our ability to identify conserved, unique protein signature candidates. To determine the amount of sequence data required to select good protein signature candidates, we have built a computationally intensive system called the Sequencing Analysis Pipeline (SAP). The SAP performs thousands of Monte Carlo simulations, each calling the Protein Signature Pipeline, to assess how the amount of sequence data for a target organism affects the ability to predict peptide signature candidates. Viral species differ substantially in the number of genomes required to predict protein signature targets. Patterns do not appear based on genome structure. There are more protein than DNA signatures due to greater intraspecific conservation at the protein than at the nucleotide level. We conclude that it is necessary to use the SAP as a dynamic system to assess the need for continued sequencing for each species individually and to update predictions with each additional genome that is sequenced.
Epidemiology and Predictors of Mortality in Cases of
Candida
Bloodstream Infection: Results from Population-Based Surveillance, Barcelona, Spain, from 2002 to 2003
Authors: Almirante Benito , Rodríguez Dolors , Park Benjamin J. , Cuenca-Estrella Manuel , Planes Ana M. , Almela Manuel , Mensa Jose , Sanchez Ferran , Ayats Josefina , Gimenez Montserrat , Saballs Pere , Fridkin Scott K. , Morgan Juliette , Rodriguez-Tudela Juan L. , Warnock David W. , Pahissa Albert 
Published: April 2005

ABSTRACT

We conducted population-based surveillance for
Candida
bloodstream infections in Spain to determine its incidence, the extent of antifungal resistance, and risk factors for mortality. A case was defined as the first positive blood culture for any
Candida
spp. in a resident of Barcelona, from 1 January 2002 to 31 December 2003. We defined early mortality as occurring between days 3 to 7 after candidemia and late mortality as occurring between days 8 to 30. We detected 345 cases of candidemia, for an average annual incidence of 4.3 cases/100,000 population, 0.53 cases/1,000 hospital discharges, and 0.73 cases/10,000 patient-days. Outpatients comprised 11% of the cases, and 89% had a central venous catheter (CVC) at diagnosis. Overall mortality was 44%.
Candida albicans
was the most frequent species (51% of cases), followed by
Candida parapsilosis
(23%),
Candida tropicalis
(10%),
Candida glabrata
(8%),
Candida krusei
(4%), and other species (3%). Twenty-four isolates (7%) had decreased susceptibility to fluconazole (MIC ≥ 16 μg/ml). On multivariable analysis, early death was independently associated with hematological malignancy (odds ratio [OR], 3.5; 95% confidence interval [CI], 1.1 to 10.4). Treatment with antifungals (OR, 0.05; 95% CI, 0.01 to 0.2) and removal of CVCs (OR, 0.3; 95% CI, 0.1 to 0.9) were protective factors for early death. Receiving adequate treatment, defined as having CVCs removed and administration of an antifungal medication (OR, 0.2; 95% CI, 0.08 to 0.8), was associated with lower odds of late mortality; intubation (OR, 7.5; 95% CI, 2.6 to 21.1) was associated with higher odds. The incidence of candidemia and prevalence of fluconazole resistance are similar to other European countries, indicating that routine antifungal susceptibility testing is not warranted. Antifungal medication and catheter removal are critical in preventing mortality.
Sequencing and Resolution of Amplified Herpes Simplex Virus DNA with Intermediate Melting Curves as Genotype 1 or 2 by LightCycler PCR Assay
Authors: Issa Nicolas C. , Espy Mark J. , Uhl James R. , Smith Thomas F. 
Published: April 2005

ABSTRACT
DNA from 101 specimens containing herpes simplex virus (HSV) produced atypical intermediate melting curves compared with those expected for HSV type 1 or HSV type 2 subsequent to real-time PCR. Nucleic acid sequence analysis of amplified target DNA revealed 1- or 3-bp polymorphisms in the probe region which allowed designation of these viruses as HSV genotype 1 or HSV genotype 2. These two subpopulations of HSV were also identified as HSV genotype 1 or HSV genotype 2 using another commercially available PCR method. Amplified HSV target DNA producing intermediate melting curves could be designated as HSV genotype 1 or HSV genotype 2 without performing sequencing or another PCR method with 96/101 (95%) specimens by adding known intermediate HSV DNA characteristic for the two subpopulations as controls.
Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay
Authors: Luo Wei , Yang Hua , Rathbun Kimberly , Pau Chou-Pong , Ou Chin-Yih 
Published: April 2005

ABSTRACTA dried blood spot (DBS) is a well-accepted means for the collection, transport, and storage of blood samples for various epidemiologic, serologic, and molecular assays for human immunodeficiency virus (HIV) studies. It is particularly important for mother-to-infant-transmission studies of affected individuals living in remote areas. We have developed a real-time PCR method to detect HIV type 1 (HIV-1) DNA in dried blood spots. A cellular gene, RNase P, was coamplified with the HIV-1 DNA in the same tube to monitor the DNA extraction efficiency and the overall assay performance. Our assay is a one-tube, single-step closed-system assay and uses a dUTP/uracil DNA glycosidase anti-PCR contamination control. The HIV-1 primers and probe were derived from a conserved region of the long terminal repeat. The detection of RNase P is attenuated by lowering the forward and reverse primer concentrations so that its amplification will not overwhelm the HIV-1 amplification and yet will provide a semiquantitative measurement of the quality of the isolated DBS DNA. We examined 103 HIV-1-seropositive and 56 seronegative U.S. adults and found that our assay has a sensitivity of 98.1% (95% confidence interval [CI], 95.5% to 100%) and specificity of 100% (95% CI, 99% to 100%). The positive and negative predictive values are 100% and 96.6%, respectively. This duplex PCR assay may be useful in identifying HIV-1-infected persons, particularly infants born to seropositive mothers in remote areas of the world.
Molecular Evidence for Multiple Host-Specific Strains in the Genus
Rhinosporidium
Authors: Silva Victor , Pereira Cristiane N. , Ajello Libero , Mendoza Leonel 
Published: April 2005

ABSTRACT

The taxonomic relationship of
Rhinosporidium seeberi
with other organisms remained controversial for over a century. Recently, molecular studies have shown
R. seeberi
to be a protistal microbe in the newly described class
Mesomycetozoea
at the animal-fungal boundary. Phylogenetic analyses of
R. seeberi
using 18S small-subunit (SSU) rRNA genes from several hosts suggested
Rhinosporidium
as a monotypic genus. To test this hypothesis, the internal transcribed spacer 1 (ITS1), 5.8S, and ITS2 from eight humans, two swans, and a dog with rhinosporidiosis were sequenced. The ITS regions were amplified by PCR using a primer designed from a unique region of
R. seeberi
's 18S SSU rRNA genes in combination with the ITS4 universal primer. In addition, the universal ITS4 and ITS5 primers were also used.
R. seeberi
's ITS sequences showed differences in the numbers of nucleotides among strains. For instance, the eight human ITS sequences were uniformly similar with only a few mismatches and ∼1,060 bp long. In contrast, sequences from one of the swans and the dog were 1,356 bp and ∼1,147 bp long, respectively. Clustal analysis of all of the ITS sequences showed multiple 50- to 60-bp gaps and several mismatches among them. Parsimony analysis placed the
Rhinosporidium
ITS sequences in three well-supported sister groups according to the hosts' identities. This analysis strongly suggests that the genus
Rhinosporidium
may possess multiple host-specific strains. No correlation was found between this finding and the phenotypic features of
R. seeberi
in the studied samples.
Nucleic Acid Amplification Assays for Detection of La Crosse Virus RNA
Authors: Lambert Amy J. , Nasci Roger S. , Cropp Bruce C. , Martin Denise A. , Rose Becky C. , Russell Brandy J. , Lanciotti Robert S. 
Published: April 2005

ABSTRACT
We report the development of nucleic acid sequence-based amplification (NASBA) and quantitative real-time reverse transcription (RT)-PCR assays for the detection of La Crosse (LAC) virus in field-collected vector mosquito samples and human clinical samples. The sensitivities of these assays were compared to that of a standard plaque assay in Vero cells. The NASBA and quantitative real-time RT-PCR assays demonstrated sensitivities greater than that of the standard plaque assay. The specificities of these assays were determined by testing a battery of reference strain viruses, including representative strains of LAC virus and other arthropod-borne viruses. Additionally, these assays were used to detect LAC viral RNA in mosquito pool samples and human brain tissue samples and yielded results within less than 4 h. The NASBA and quantitative real-time RT-PCR assays detect LAC viral RNA in a sensitive, specific, and rapid manner; these findings support the use of these assays in surveillance and diagnostic laboratory systems.
Molecular Epidemiology of Hepatitis C Virus Genotype 4 Isolates in Egypt and Analysis of the Variability of Envelope Proteins E1 and E2 in Patients with Chronic Hepatitis
Authors: Genovese D. , Dettori S. , Argentini C. , Villano U. , Chionne P. , Angelico M. , Rapicetta M. 
Published: April 2005

ABSTRACTWe analyzed hepatitis C virus (HCV) genotype 4 isolates circulating in the Alexandria District (Egypt) in terms of genetic divergence and the presence of different subtypes. Hypervariable region 1 (HVR1) and the NH2 region of the E2 protein were characterized, and the heterogeneity of subtype 4a isolates was evaluated by analyzing epitope frequencies, immunoproteasome prediction, and possible glycosylation patterns. The heterogeneity of the nucleotide sequences was greater than that found in previous studies, which reported only subtype 4a. Subtype 4a was most common (78% of cases), yet four new subtypes were found, with subtype 4m representing 11% of the cases and the other three subtypes representing another 11%. Substantial heterogeneity was also found when the intrasubtype 4a sequences were analyzed. Differences in the probability of glycosylation and in the positions of the different sites were also observed. The analysis of the predicted cytotoxic-T-lymphocyte epitopes showed differences in both the potential proteosome cleavage and the prediction score. The Egyptian isolates in our study also showed high variability in terms of the HVR1 neutralization epitope. Five of these isolates showed amino acid substitutions never previously observed (a total of six positions). Four of these residues (in four different isolates) were in positions involved in anchoring to the E2 glycoprotein core and in maintaining the HVR1 conformation. The results of this study indicate that HCV genotype 4 in Egypt is extremely variable, not only in terms of sequence, but also in terms of functional and immunological determinants. These data should be taken into account in planning the development of vaccine trials in Egypt.
Comparison of the Quantitative Formalin Ethyl Acetate Concentration Technique and Agar Plate Culture for Diagnosis of Human Strongyloidiasis
Authors: Intapan P. M. , Maleewong W. , Wongsaroj T. , Singthong S. , Morakote N. 
Published: April 2005

ABSTRACT

The quantitative formalin ethyl acetate concentration technique (QFEC) was compared to agar plate culture (APC) for the detection of
Strongyloides stercoralis
larvae. QFEC could substitute for APC only when the parasite load was higher than 50 larvae per g of stool. This study serves as a good reminder to those conducting stool exams about the sensitivity and specificity limitations of both techniques.
Multiplex PCR for Typing Strains of
Toxoplasma gondii
Authors: Ajzenberg Daniel , Dumètre Aurélien , Dardé Marie-Laure 
Published: April 2005

ABSTRACT

A multiplex PCR assay was designed for multilocus strain typing of
Toxoplasma gondii
based on length polymorphism of five microsatellite markers. Eight
T. gondii
strains already sequenced at these five markers were used as control isolates. This method is simple, rapid, reproducible, and adapted to a large set of isolates.
Improvement of the Specificity of an Enzyme-Linked Immunosorbent Assay for Diagnosis of Paracoccidioidomycosis
Authors: Albuquerque C. F. , Silva S. H. Marques da , Camargo Z. P. 
Published: April 2005

ABSTRACTIn an attempt to improve the specificity of an enzyme-linked immunosorbent assay (ELISA) for the diagnosis of paracoccidioidomycosis (PCM), sera from patients with PCM were tested using various approaches, such as sodium metaperiodate antigen (gp43) treatment, a serum absorption process withCandida albicansorHistoplasma capsulatumantigens, and dilution of serum in galactose, the main common epitope among pathogenic fungi. The maximum specificity found in this ELISA was 84%. All of these procedures proved inefficient for eliminating all cross-reacting antibodies and obtaining an ELISA specific for PCM diagnosis.
Evaluation of Two Chromogenic Agar Media for Recovery and Identification of
Staphylococcus aureus
Small-Colony Variants
Authors: Kipp Frank , Kahl Barbara C. , Becker Karsten , Baron Ellen J. , Proctor Richard A. , Peters Georg , von Eiff Christof 
Published: April 2005

ABSTRACT

To identify the most rapid and reliable technique for recovery and identification of
Staphylococcus aureus
small-colony variants (SCVs), the colonial appearance of 106 isolates representing SCVs and the normal phenotype were evaluated on two newly described chromogenic agar media. Although almost all of the SCVs grew on the chromogenic agar media, they did not exhibit a change of color. In comparison with conventional media,
S. aureus
ID agar (SAID; bioMérieux, La Balme Les Grottes, France) showed the most reliable results, with 49 of 53 SCVs tested growing either as an SCV colony or with a normal phenotype after only 24 h of incubation. Growth of SCVs was often not detected before 72 h of incubation on some of the media tested. In conclusion, the most accurate and rapid method to detect both the species
S. aureus
and the SCV phenotype is to inoculate specimens onto both Columbia blood agar and SAID.
Controlled Clinical Comparison of Plastic and Glass Bottles of BacT/ALERT FA Medium for Culturing Organisms from Blood of Adult Patients
Authors: Petti Cathy A. , Mirrett Stanley , Woods Christopher W. , Reller L. Barth 
Published: April 2005

ABSTRACT
A new, clear-plastic nonvented aerobic FA bottle, designed to prevent breakage, has been developed for the BacT/ALERT blood culture system. We assessed the new plastic FA bottle by comparing its performance with that of the current glass FA bottle for recovery of microorganisms and time to detection of growth in blood samples obtained for culture from adult patients with suspected bloodstream infections. We conclude that the BacT/ALERT plastic and glass FA bottles are comparable for recovery of microorganisms and that the safety advantage of plastic bottles can be achieved without compromising performance.
Evidence for
icaADBC
-Independent Biofilm Development Mechanism in Methicillin-Resistant
Staphylococcus aureus
Clinical Isolates
Authors: Fitzpatrick Fidelma , Humphreys Hilary , O'Gara James P. 
Published: April 2005

ABSTRACT

Synthesis of a polysaccharide adhesin by
icaADBC
-encoded enzymes is currently the best-understood mechanism of staphylococcal biofilm development. In four methicillin-resistant
Staphylococcus aureus
isolates, environmental activation of
icaADBC
did not always correlate with increased biofilm production. Moreover, glucose-mediated biofilm development in these isolates was
icaADBC
independent. Apparently, an environmentally regulated,
ica
-independent mechanism(s) of biofilm development exists in
S. aureus
clinical isolates.
Evaluation of a Rapid Assay as an Alternative to Conventional Enzyme Immunoassays for Detection of Hepatitis C Virus-Specific Antibodies
Authors: Daniel Hubert Darius J. , Abraham Priya , Raghuraman Sukanya , Vivekanandan Perumal , Subramaniam Thenmozhi , Sridharan Gopalan 
Published: April 2005

ABSTRACT
A rapid membrane flow-through immunoassay to detect antibodies to hepatitis C virus was compared with a commercial enzyme immunoassay (EIA) and microparticle enzyme immunoassay (MEIA) using 2,590 serum samples. Sensitivity and specificity of the “rapid assay” in comparison to the EIA/MEIA were 99.3 and 99.0%; the correlation coefficient being 0.91. This assay is suitable where infrastructure and laboratory expertise are limited.
First Report of Infection with Community-Acquired Methicillin-Resistant
Staphylococcus aureus
in South America
Authors: Ribeiro Apoena , Dias Cícero , Silva-Carvalho Maria Cícera , Berquó Laura , Ferreira Fabienne Antunes , Santos Raquel Neves Soares , Ferreira-Carvalho Bernadete Teixeira , Figueiredo Agnes Marie 
Published: April 2005

ABSTRACT

Community-acquired methicillin-resistant
Staphylococcus aureus
(CA-MRSA) has recently emerged in the southwestern Pacific, North America, and Europe. These
S. aureus
isolates frequently shared some genetic characteristics, including the SCC
mec
type IV and
lukS-lukF
genes. In this paper we show that typical CA-MRSA isolates have spread to South America (Brazil).
Characterization of a
Bacillus anthracis
Isolate Causing a Rare Case of Fatal Anthrax in a 2-Year-Old Boy from Hong Kong
Authors: Cheung Danny T. L. , Kam Kai Man , Hau Kong Lung , Au Tak Kong , Marston Chung K. , Gee Jay E. , Popovic Tanja , Van Ert Matthew N. , Kenefic Leo , Keim Paul , Hoffmaster Alex R. 
Published: April 2005

ABSTRACT

We used multiple-locus variable-number tandem repeat analysis (MLVA) and
pagA
sequencing to genotype a
Bacillus anthracis
isolate from a fatal case of human anthrax in Hong Kong. The isolate has a unique MLVA genotype, is related to the Sterne and Ames strains, and is consistent with genotypes identified in China.
Use of Single Nucleotide Polymorphisms in theplcRGene for Specific Identification ofBacillus anthracis
Authors: Easterday W. Ryan , Van Ert Matthew N. , Simonson Tatum S. , Wagner David M. , Kenefic Leo J. , Allender Christopher J. , Keim Paul 
Published: April 2005

ABSTRACTA TaqMan-minor groove binding assay designed around a nonsense mutation in theplcRgene was used to genotypeBacillus anthracis,B. cereus, andB. thuringiensisisolates. The assay differentiatedB. anthracisfrom these genetic near-neighbors and determined that the nonsense mutation is ubiquitous across 89 globally and genetically diverseB. anthracisstrains.
Fusarium verticillioides
Abscess of the Nasal Septum in an Immunosuppressed Child: Case Report and Identification of the Morphologically Atypical Fungal Strain
Authors: Dornbusch Hans Jürgen , Buzina Walter , Summerbell Richard C. , Lass-Flörl Cornelia , Lackner Herwig , Schwinger Wolfgang , Sovinz Petra , Urban Christian 
Published: April 2005

ABSTRACT

Morphologically atypical
Fusarium verticillioides
causing a nasal abscess in a severely immunosuppressed child was successfully treated with repeated surgical intervention and liposomal amphotericin B, despite amphotericin B resistance in vitro. Definitive identification was achieved by sequencing the translation elongation factor α gene after ribosomal sequencing proved inadequate.
Multilocus Sequence Typing Directly on DNA from Clinical Samples and a Cultured Isolate To Investigate Linked Fatal Pneumococcal Disease in Residents of a Shelter for Homeless Men
Authors: Birtles Andrew , McCarthy Noel , Sheppard Carmen L. , Rutter Harry , Guiver Malcolm , Haworth Elizabeth , George Robert C. 
Published: April 2005

ABSTRACT

Two apparently linked fatal cases of pneumococcal meningitis were investigated. Pneumolysin PCR performed on blood and cerebrospinal fluid was positive in a culture-negative case. A second case yielded
Streptococcus pneumoniae
from blood culture. Multilocus sequence typing performed on DNA extracted from case 1 (specimens) and case 2 (isolate) revealed identical sequence types (ST53) substantiating the link between them.