bluuebunny/crossref_metadata_2025_split huggingface dataset:
Etiology of Diarrhea in Young Children in Denmark: a Case-Control Study
Authors: Olesen Bente , Neimann Jacob , Böttiger Blenda , Ethelberg Steen , Schiellerup Peter , Jensen Charlotte , Helms Morten , Scheutz Flemming , Olsen Katharina E. P. , Krogfelt Karen , Petersen Eskild , Mølbak Kåre , Gerner-Smidt Peter 
Published: August 2005

ABSTRACT

Infectious gastroenteritis is one of the most common diseases in young children. To clarify the infectious etiology of diarrhea in Danish children less than 5 years of age, we conducted a 2-year prospective case-control study. Stools from 424 children with diarrhea and 870 asymptomatic age-matched controls were examined, and their parents were interviewed concerning symptoms. Rotavirus, adenovirus, and astrovirus were detected by enzyme-linked immunosorbent assay, and norovirus and sapovirus were detected by PCR.
Salmonella
, thermotolerant
Campylobacter
,
Yersinia
,
Shigella
, and
Vibrio
spp. were detected by standard methods. Shiga toxin-producing (STEC), attaching-and-effacing (A/EEC), enteropathogenic (EPEC), enterotoxigenic, enteroinvasive, and enteroaggregative
Escherichia coli
were detected by using colony hybridization with virulence gene probes and serotyping. Parasites were detected by microscopy. Overall, a potential pathogen was found in 54% of cases. More cases than controls were infected with rotavirus,
Salmonella
, norovirus, adenovirus,
Campylobacter
, sapovirus, STEC, classical EPEC,
Yersinia
, and
Cryptosporidium
strains, whereas A/EEC, although common, was not associated with illness. The single most important cause of diarrhea was rotavirus, which points toward the need for a childhood vaccine for this pathogen, but norovirus, adenovirus, and sapovirus were also major etiologies.
Salmonella
sp. was the most common bacterial pathogen, followed by
Campylobacter
, STEC,
Yersinia
, and classical EPEC strains. A/EEC not belonging to the classical EPEC serotypes was not associated with diarrhea, underscoring the importance of serotyping for the definition of EPEC.
Identification of Immunodominant Epitopes on the Membrane Protein of the Severe Acute Respiratory Syndrome-Associated Coronavirus
Authors: He Yuxian , Zhou Yusen , Siddiqui Pamela , Niu Jinkui , Jiang Shibo 
Published: August 2005

ABSTRACT
Similar to other coronaviruses, the membrane (M) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a major transmembrane glycoprotein with multiple biological functions. To date, limited information is available about its antigenic properties. In this study, we identified two major immunodominant epitopes on the M protein located in the extreme N-terminal region (residues 1 to 31) and the interior C-terminal region (residues 132 to 161), respectively, by Pepscan analyses against convalescent-phase sera from SARS patients and antisera from virus-immunized mice and rabbits. Synthetic peptides M1-31 derived from the N-terminal epitope and M132-161 derived from the C-terminal epitope were highly reactive with all of the convalescent-phase sera from 40 SARS patients but not with 30 control serum samples from healthy blood donors, suggesting their potential application for serologic diagnosis of SARS. We showed that both peptides (M1-31 and M132-161) were able to induce high titers of antibody responses in the immunized rabbits, highlighting their antigenicity and immunogenicity. These findings provide important information for developing SARS diagnostics and vaccines.
Molecular Subtyping of
Treponema pallidum
from North and South Carolina
Authors: Pope Victoria , Fox Kimberley , Liu Hsi , Marfin Anthony A. , Leone Peter , Seña Arlene C. , Chapin Johanna , Fears Martha B. , Markowitz Lauri 
Published: August 2005

ABSTRACT

Patients from five clinics in North and South Carolina who had lesions suggestive of primary or secondary syphilis were evaluated using molecular techniques that allow the differentiation of
Treponema pallidum
strains on the basis of two variable genes,
tpr
and
arp
. Lesion samples were screened for the presence of
T. pallidum
DNA using PCR for
polA
, which represents a segment of the polymerase I gene that is unique to the spirochete. Twenty-seven of 154 lesion samples were found to contain
T. pallidum
, 23 of which had typeable DNA. Seven molecular subtypes were found (10f, 12f, 13f, 14f, 14g, 15f, and 16f); one to four subtypes were identified at each clinic. Subtype 14f was found in 52% of the typeable specimens and was distributed in four of the five clinics. Subtype 16f was found in 22% of specimens and was concentrated at one clinic. Further data are needed to define the role of this technique in examining the epidemiology of syphilis.
International and Multicenter Comparison of EUCAST and CLSI M27-A2 Broth Microdilution Methods for Testing Susceptibilities of
Candida
spp. to Fluconazole, Itraconazole, Posaconazole, and Voriconazole
Authors: Espinel-Ingroff A. , Barchiesi F. , Cuenca-Estrella M. , Pfaller M. A. , Rinaldi M. , Rodriguez-Tudela J. L. , Verweij P. E. 
Published: August 2005

ABSTRACT

The aim of this study was to compare MICs of fluconazole, itraconazole, posaconazole, and voriconazole obtained by the European Committee on Antibiotic Susceptibility Testing (EUCAST) and CLSI (formerly NCCLS) methods in each of six centers for 15
Candida albicans
(5 fluconazole-resistant and 4 susceptible-dose-dependent [S-DD] isolates), 10
C. dubliniensis
, 7
C. glabrata
(2 fluconazole-resistant isolates), 5
C. guilliermondii
(2 fluconazole-resistant isolates), 10
C. krusei
, 9
C. lusitaniae
, 10
C. parapsilosis
, and 5
C. tropicalis
(1 fluconazole-resistant isolate) isolates. CLSI MICs were obtained visually at 24 and 48 h and spectrophotometric EUCAST MICs at 24 h. The agreement (within a 3-dilution range) between the methods was species, drug, and incubation time dependent and due to lower EUCAST than CLSI MICs: overall, 94 to 95% with fluconazole and voriconazole and 90 to 91% with posaconazole and itraconazole when EUCAST MICs were compared against 24-h CLSI results. The agreement was lower (85 to 94%) against 48-h CLSI endpoints. The overall interlaboratory reproducibility by each method was ≥92%. When the comparison was based on CLSI breakpoint categorization, the agreement was 68 to 76% for three of the four species that included fluconazole-resistant and S-DD isolates; 9% very major discrepancies (≤8 μg/ml versus ≥64 μg/ml) were observed among fluconazole-resistant isolates and 50% with voriconazole (≤1 μg/ml versus ≥4 μg/ml). Similar results were observed with itraconazole for seven of the eight species evaluated (28 to 77% categorical agreement). Posaconazole EUCAST MICs were also substantially lower than CLSI MIC modes (0.008 to 1 μg/ml versus 1 to ≥8 μg/ml) for some of these isolates. Therefore, the CLSI breakpoints should not be used to interpret EUCAST MIC data.
Bifidobacterial Lipoglycan as a New Cause for False-Positive Platelia
Aspergillus
Enzyme-Linked Immunosorbent Assay Reactivity
Authors: Mennink-Kersten Monique A. S. H. , Ruegebrink Dorien , Klont Rocus R. , Warris Adilia , Gavini Françoise , Op den Camp Huub J. M. , Verweij Paul E. 
Published: August 2005

ABSTRACT

We previously hypothesized that a lipoglycan of
Bifidobacterium bifidum
subsp.
pennsylvanicum
cross-reacts with the Platelia
Aspergillus
(PA) enzyme-linked immunosorbent assay (ELISA) based on the presence of galactofuranosyl epitopes in the cell wall (M. A. S. H. Mennink-Kersten, R. R. Klont, A. Warris, H. J. M. Op den Camp, and P. E. Verweij, Lancet 363:325-327, 2004). We tested this hypothesis by testing bacterial suspensions of different bifidobacterial species and other gram-positive and -negative bacteria with the PA ELISA, which is used to detect circulating galactomannan for the serodiagnosis of invasive aspergillosis. Furthermore, neonatal fecal samples were enumerated for bifidobacteria by fluorescence in situ hybridization (FISH) and tested for PA ELISA reactivity. All bifidobacteria, except
B. infantis
and
B. adolescentis
, showed reactivity 6- to 600-fold higher compared to the controls (i.e.,
Micrococcus luteus
and
Propionibacterium freudenreichii
, which contain a cell wall lipomannan).
Eggerthella lenta
showed a 25-fold-higher reactivity. ELISA reactivity was clearly shown to be associated with bacterial lipoglycans containing a β-1,5-galactofuranosyl chain. All neonatal feces showed PA ELISA reactivity and associated numbers of bifidobacteria. Since high concentrations of bifidobacteria are present in the human gut, these bacteria or excreted lipoglycan may cause false serum PA ELISA reactivity in selected patient groups, especially neonates.
In Vitro Cultivation of a ZoonoticBabesiasp. Isolated from Eastern Cottontail Rabbits (Sylvilagus floridanus) on Nantucket Island, Massachusetts
Authors: Holman Patricia J. , Spencer Angela M. , Droleskey Robert E. , Goethert Heidi K. , Telford Samuel R. 
Published: August 2005

ABSTRACTABabesiasp. found in eastern cottontail rabbits (Sylvilagus floridanus) on Nantucket Island, Massachusetts, is the same organism that caused human babesiosis in Missouri and Kentucky, on the basis of morphology and identical small-subunit rRNA (SSU rRNA) gene sequences. Continuous cultures of the rabbit parasite were established from infected blood samples collected from two cottontail rabbits livetrapped on Nantucket Island. HL-1 medium or minimal essential medium alpha medium supplemented with 20% human serum best supported in vitro propagation of the parasite in human or cottontail erythrocytes, respectively. Parasite growth was not sustained in domestic-rabbit erythrocytes or in medium supplemented with domestic-rabbit serum. The cultured parasites were morphologically indistinguishable from the Kentucky human isolate. Transmission electron microscopy revealed similar fine structures of the parasite regardless of the host erythrocyte utilized in the cultures. Two continuous lines of the zoonoticBabesiasp. were established and confirmed to share identical SSU rRNA gene sequences with each other and with the Missouri and Kentucky humanBabesiaisolates.
Molecular Evolutionary History of Tubercle Bacilli Assessed by Study of the Polymorphic Nucleotide within the Nitrate Reductase (
narGHJI
) Operon Promoter
Authors: Goh Khye Seng , Rastogi Nalin , Berchel Mylène , Huard Richard C. , Sola Christophe 
Published: August 2005

ABSTRACT

A well-characterized collection of
Mycobacterium tuberculosis
complex (MTC) isolates, representing all known subspecies as well as some relevant genotypic families of
M. tuberculosis
, was analyzed for the newly discovered
narGHJI
−215 C-to-T promoter single-nucleotide polymorphism (SNP). This point mutation has been shown in earlier studies to be responsible for the differential nitrate reductase activity of
M. tuberculosis
versus
M. bovis
. As previously defined by the presence or the absence of the TbD1 genetic locus, the group included both the “modern” W-Beijing, Haarlem, and Central-Asian1 (CAS1) families as well as the “ancestral” East-African-Indian (EAI) clade. Interestingly, among “modern”
M. tuberculosis
isolates, those previously classified as Principal Genetic Group 1 (PGG1) organisms by
katG

463

-gyrA

95

polymorphism analysis did not present the two-banded
narGHJI
restriction fragment length polymorphism analysis of PCR products pattern common to the other PGG1 MTC members, including the “ancestral”
M. tuberculosis
isolates. Instead, they showed a one-banded pattern, aligning them with other evolutionarily recent
M. tuberculosis
isolates of the PGG2 and PGG3 groups, such as Haarlem, Latin-American and Mediterranean (LAM), and X families. The presence of a nitrate reductase producer phenotype in “
Mycobacterium canettii”
and some “ancestral”
M. tuberculosis
isolates, despite a two-band −215C genotype, argues in favor of an alternate mechanism to explain the differential nitrate reductase activity of certain PGG1 subspecies of the MTC. Overall, these findings may help to establish the precise evolutionary history of important genotype families such as W-Beijing and suggest that the −215T genotype may have contributed the virulence, spread, and evolutionary success of “modern”
M. tuberculosis
strains compared to the remaining MTC organisms.
Simultaneous Visual Detection of Multiple Viral Amplicons by Dipstick Assay
Authors: Dineva Magda Anastassova , Candotti Daniel , Fletcher-Brown Fiona , Allain Jean-Pierre , Lee Helen 
Published: August 2005

ABSTRACT
A sensitive, simple, and instrument-independent method for the visual detection and identification of multiple nucleic acid amplicons by dipstick has been developed. This method is based on nucleic acid hybridization on the dipstick membrane and a signal amplification system to allow visual detection. With hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus type 1 (HIV-1) as model analytes, it is demonstrated that the visual dipstick test combined with multiplex reverse transcription (RT)-PCR for the amplification of viral nucleic acid provides a specific and sensitive detection method. The RT-PCR products were detected by the dipstick with an efficiency similar to that of a complex, expensive, and instrument-dependent method based on fluorogenic oligonucleotide probes. The detection limits of the dipstick combined with multiplex RT-PCR were 50, 125, and 500 IU/ml for HBV DNA, HCV RNA, and HIV-1 RNA, respectively. The dipstick assay detected with similar efficiencies amplicons derived from strains of HBV genotypes A through F, HCV genotypes 1 to 6, and HIV-1 subtypes A through H as well as CRF02 circulating recombinant forms of HIV-1. Analysis of 295 clinical samples and 19 pools of 10 plasma specimens from blood donors revealed that multiplex dipstick detection was reproducible, sensitive, and specific. The visual dipstick detection of multiple amplicons thus provides an attractive alternative to complex, instrument-dependent detection methods currently in use for nucleic acid testing. This new and sensitive method for nucleic acid detection should increase the availability of genomic screening in resource-limited settings and its applicability to near-patient testing.
Value of Serological Testing for Diagnosis of Legionellosis in Outbreak Patients
Authors: Rojas Almudena , Navarro M. Dolores , Fornés Francisca E. , Serra Estefanía , Simarro Encarnación , Rojas José , Ruiz Joaquín 
Published: August 2005

ABSTRACT

Serum antibody detection tests and a urine antigen detection technique were compared in samples from 116 patients epidemiologically characterized as belonging to a legionellosis outbreak. Sera were tested by enzyme-linked immunosorbent assays (ELISAs) for immunoglobulin M (IgM) and IgG plus IgM and by immunofluorescent assays (IFAs) for IgG, IgM, IgA, and polyimmunoglobulin using commercial kits (Vircell); concentrated urines were tested with the Binax NOW
Legionella
test. ELISA for IgM, ELISA for IgG plus IgM, antigenuria detection, and IFA for IgM were able to diagnose 72.3%, 60.5%, 53.3%, and 51.4%, respectively, of patients. Antigenuria was present in 53.8% of first samples, ELISA detected IgM in 29.7%, ELISA detected IgG plus IgM in 7.9%, and IFA detected IgM in 3.9%. Ten antigenuria-negative first samples tested serologically positive, 9 of them to IgM by ELISA. Despite the single source of the samples included in the study, detection of IgM using a sensitive technique such as ELISA seems to be a suitable complement to antigenuria detection for the diagnosis of legionellosis.
Novel 5-Flucytosine-Resistant Clade of
Candida dubliniensis
from Saudi Arabia and Egypt Identified by Cd25 Fingerprinting
Authors: Al Mosaid Asmaa , Sullivan Derek J. , Polacheck Itzhack , Shaheen Faisal A. , Soliman Osama , Al Hedaithy Saleh , Al Thawad Sahar , Kabadaya Motaz , Coleman David C. 
Published: August 2005

ABSTRACT

DNA fingerprinting of
Candida dubliniensis
isolates using the species-specific probe Cd25 previously showed that this species consists of two distinct groups, termed Cd25 group I and Cd25 group II. The present study investigated the population structure of 30
C. dubliniensis
oral isolates from Saudi Arabia and Egypt using Cd25 fingerprinting and rRNA gene internal transcribed spacer region-based genotyping. Cd25 fingerprinting analysis of these isolates revealed two distinct populations, the first of which consisted of 10 closely related genotype 1 isolates (average similarity coefficient [
S
AB
] value, 0.86). The second population of 20 isolates was much more heterogeneous (average
S
AB
value, 0.35) and consisted of two distinct subpopulations, one of which consisted of genotype 3 isolates (
n
= 13) and the other of genotype 4 isolates (
n
= 7). A mixed dendrogram generated from the fingerprint data from the 30 Saudi Arabian and Egyptian isolates, 5 Israeli isolates, and 51 previously characterized international isolates (32 of Cd25 group I and 19 of Cd25 group II) revealed the presence of three distinct main clades. The first corresponded to the previously described Cd25 group I and contained all the Saudi Arabian, Egyptian, and Israeli genotype 1 isolates mixed with international isolates. The second clade corresponded to the previously described Cd25 group II and contained three Israeli isolates, one genotype 2 isolate, one genotype 3 isolate, and a genotype 4 variant isolate, which were mixed with international isolates. The third clade has not been described before and consisted solely of the 20 Saudi Arabian and Egyptian genotype 3 and 4 isolates identified in this study and a previously described genotype 4 Israeli isolate. All 20 Cd25 group III isolates exhibited high-level resistance to 5-flucytosine (MIC ≥ 128 μg/ml), whereas all Cd25 group I and Cd25 group II isolates tested (10 Saudi Arabian and Egyptian, 16 Israeli, and 24 international) were susceptible to 5-flucytosine (MIC ≤ 0.125 μg/ml). The results of this study show for the first time the presence of a novel 5-flucytosine-resistant clade of
C. dubliniensis
(Cd25 group III) that is predominant among isolates from Saudi Arabia and Egypt and absent from a previously characterized international collection of 98 isolates from 15 countries.
Evaluation of the ReSSQ Assay in Relation to the COBAS AMPLICOR CMV MONITOR Test and an In-House Nested PCR Method for Detection of Cytomegalovirus DNA
Authors: Wirgart Benita Zweygberg , Andersson Pia , Grillner Lena 
Published: August 2005

ABSTRACT

The ReSSQ CMV assay is a novel commercially available kit for quantification of cytomegalovirus (CMV), based on real-time PCR with a peptide nucleic acid probe coupled with a single dye. In combination with the LightCycler, the ReSSQ CMV assay was evaluated with respect to specificity, PCR inhibition, linearity, reproducibility, and sensitivity. All nontested CMV materials were negative, and the assay was not inhibited by the use of different anticoagulants or other factors that may influence blood samples. The dynamic range was between 10 and 5 × 10
8
copies/PCR, and intra- and interassay variabilities were below 0.10 and 0.12 log
10
standard deviations, respectively. Assay sensitivity was validated by analysis of 24 samples from a proficiency panel and by comparison to a nested in-house CMV PCR and the COBAS AMPLICOR CMV MONITOR test, using 159 clinical samples. Results from the proficiency panel were well in accordance with input values over the entire range of viral concentrations tested (50 to 31,250 copies/ml). The association between the ReSSQ CMV assay and the in-house PCR was in agreement in 90% of the clinical samples, and discordant results were found for all types of sample materials analyzed. The ReSSQ CMV and COBAS AMPLICOR assays showed no significant differences for samples containing >1,000 CMV copies/ml, but results differed to a greater extent at lower viral concentrations. The results demonstrate that the ReSSQ CMV assay is a CMV-specific, robust, and reproducible method and hence is well suited for routine use in clinical virology laboratories.
Use of a Novel Panel of Nine Short Tandem Repeats for Exact and High-Resolution Fingerprinting of
Aspergillus fumigatus
Isolates
Authors: de Valk Hanneke A. , Meis Jacques F. G. M. , Curfs Ilse M. , Muehlethaler Konrad , Mouton Johan W. , Klaassen Corné H. W. 
Published: August 2005

ABSTRACT

Here we describe a new panel of short tandem repeats (STRs) for a novel exact typing assay that can be used to discriminate between
Aspergillus fumigatus
isolates. A total of nine STR markers were selected from available genomic
A. fumigatus
sequences and were divided into three multicolor multiplex PCRs. Each multiplex reaction amplified three di-, tri-, or tetranucleotide repeats, respectively. All nine STR markers were used to analyze 100 presumably unrelated
A. fumigatus
isolates. For each marker, between 11 and 37 alleles were found in this population. One isolate proved to be a mixture of at least two different isolates. With the remaining 99 isolates, 96 different fingerprinting profiles were obtained. The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. In theory, this panel of markers is able to discriminate between no less than 27 × 10
9
different genotypes. The multicolor multiplex approach allows large numbers of markers to be tested in a short period of time. The exact nature of the assay combines high reproducibility with the easy exchange of results and makes it a very suitable tool for large-scale epidemiological studies.
Simultaneous Detection of Four Human Pathogenic Microsporidian Species from Clinical Samples by Oligonucleotide Microarray
Authors: Wang Zheng , Orlandi Palmer A. , Stenger David A. 
Published: August 2005

ABSTRACT

Microsporidian species have been rapidly emerging as human enteric pathogens in immunocompromised and immunocompetent individuals in recent years. Routine diagnostic techniques for microsporidia in clinical laboratories are laborious and insensitive and tend to underestimate their presence. In most instances, they are unable to differentiate species of spores due to their small sizes and similar morphologies. In this study, we report the development of another protozoan oligonucleotide microarray assay for the simultaneous detection and identification to the species level of four major microsporidian species:
Enterocytozoon bieneusi
,
Encephalitozoon cuniculi
,
Encephalitozoon hellem
, and
Encephalitozoon intestinalis
. The 18S small-subunit rRNA gene was chosen as the amplification target, labeled with fluorescence dye, and hybridized to a series of species-specific oligonucleotide probes immobilized on a microchip. The specificity and sensitivity of the microarray were clearly demonstrated by the unique hybridization profiles exhibited by each species of microsporidian tested and its ability to detect as few as 10 spores. In order to assess the applicability of this microarray in a clinical setting, we conducted microarray assays of 20 fecal samples from AIDS patients. Twelve of these samples were positive for the presence of microsporidia and could be confidently identified; 11 of them were positive for more than one species. Our results suggested that this microarray-based approach represents an attractive diagnostic tool for high-throughput detection and identification of microsporidian species in clinical and epidemiological investigations.