bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnosis of Schistosomiasis by Reagent Strip Test for Detection of Circulating Cathodic Antigen
Authors: van Dam G. J. , Wichers J. H. , Ferreira T. M. Falcao , Ghati D. , van Amerongen A. , Deelder A. M. 
Published: December 2004

ABSTRACT

A newly developed reagent strip assay for the diagnosis of schistosomiasis based on parasite antigen detection in urine of infected individuals was evaluated. The test uses the principle of lateral flow through a nitrocellulose strip of the sample mixed with a colloidal carbon conjugate of a monoclonal antibody specific for
Schistosoma
circulating cathodic antigen (CCA). The strip assay to diagnose a group of highly infected schoolchildren in Mwanza, Tanzania, demonstrated a high sensitivity and association with the intensity of infection as measured both by egg counts, and by circulating anodic antigen and CCA levels determined by enzyme-linked immunosorbent assay. A specificity of ca. 90% was shown in a group of schistosome-negative schoolchildren from Tarime, Tanzania, an area where schistosomiasis is not endemic. The test is easy to perform and requires no technical equipment or special training. The stability of the strips and the conjugate in the dry format lasts for at least 3 months at ambient temperature in sealed packages, making it suitable for transport and use in areas where schistosomiasis is endemic. This assay can easily be developed to an end-user format.
Burkholderia cepaciaIs Associated with Pulmonary Hypertension and Increased Mortality among Cystic Fibrosis Patients
Authors: Fauroux Brigitte , Hart Nicholas , Belfar Samira , Boulé Michèle , Tillous-Borde Isabelle , Bonnet Damien , Bingen Edouard , Clément Annick 
Published: December 2004

ABSTRACTThe aim of the study was to evaluate the impact ofBurkholderia cepaciaon cardiovascular status and mortality in cystic fibrosis. Seven patients infected withB. cepaciawere matched with 31 patients not infected with this organism for gender, age, height, weight, genotype, and percent predicted forced expiratory volume in one second, partial arterial oxygen pressure, and pancreatic sufficiency status. The pulmonary artery systolic pressure, as assessed by transthoracic echocardiography, was significantly higher in patients infected withB. cepacia(61.3 ± 17.2 mm Hg) than in controls (37.3 ± 13.9 mm Hg;P= 0.02), and the mean acceleration time was significantly lower (77 ± 33 ms versus 108 ± 25 ms;P= 0.02). The 6-month mortality was significantly higher in patients infected withB. cepacia(57% versus 16%;P= 0.02). Six of the seven patients infected withB. cepaciaharbored the same ribotype (genomovar II,B. multivorans). Pulmonary hypertension was significantly more frequent in patients infected byB. cepaciaand could contribute to the increased mortality rate.
Differentiation of
Campylobacter coli
,
Campylobacter jejuni
,
Campylobacter lari
, and
Campylobacter upsaliensis
by a Multiplex PCR Developed from the Nucleotide Sequence of the Lipid A Gene
lpxA
Authors: Klena John D. , Parker Craig T. , Knibb Krista , Ibbitt J. Claire , Devane Phillippa M. L. , Horn Sharon T. , Miller William G. , Konkel Michael E. 
Published: December 2004

ABSTRACT

We describe a multiplex PCR assay to identify and discriminate between isolates of
Campylobacter coli
,
Campylobacter jejuni
,
Campylobacter lari
, and
Campylobacter upsaliensis
. The
C. jejuni
isolate F38011
lpxA
gene, encoding a UDP-
N
-acetylglucosamine acyltransferase, was identified by sequence analysis of an expression plasmid that restored wild-type lipopolysaccharide levels in
Escherichia coli
strain SM105 [
lpxA
(Ts)]. With oligonucleotide primers developed to the
C. jejuni lpxA
gene, nearly full-length
lpxA
amplicons were amplified from an additional 11 isolates of
C. jejuni
, 20 isolates of
C. coli
, 16 isolates of
C. lari
, and five isolates of
C. upsaliensis
. The nucleotide sequence of each amplicon was determined, and sequence alignment revealed a high level of species discrimination. Oligonucleotide primers were constructed to exploit species differences, and a multiplex PCR assay was developed to positively identify isolates of
C. coli
,
C. jejuni
,
C. lari
, and
C. upsaliensis.
We characterized an additional set of 41 thermotolerant isolates by partial nucleotide sequence analysis to further demonstrate the uniqueness of each species-specific region. The multiplex PCR assay was validated with 105 genetically defined isolates of
C. coli
,
C. jejuni
,
C. lari
, and
C. upsaliensis
, 34 strains representing 12 additional
Campylobacter
species, and 24 strains representing 19 non-
Campylobacter
species. Application of the multiplex PCR method to whole-cell lysates obtained from 108 clinical and environmental thermotolerant
Campylobacter
isolates resulted in 100% correlation with biochemical typing methods.
Pulsed-Field Gel Electrophoresis Study of
Mycobacterium abscessus
Isolates Previously Affected by DNA Degradation
Authors: Zhang Yansheng , Yakrus Mitchell A. , Graviss Edward A. , Williams-Bouyer Natalie , Turenne Christine , Kabani Amin , Wallace Richard J. 
Published: December 2004

ABSTRACT

DNA degradation (which results in a smear pattern) occurs with almost 50% of
Mycobacterium abscessus
strains during pulsed-field gel electrophoresis (PFGE). We assessed the potential benefit of using thiourea-containing buffer with
M. abscessus
by studying 69 isolates not previously typeable by PFGE (i.e., those with a smear pattern). Random (epidemiologically unrelated) isolates that were typeable (no smear pattern) were included as controls. Genomic DNA was digested with DraI, XbaI, and AseI. PFGE gels were run in regular gel buffer with and without 100 μM thiourea. All 69 isolates that generated smear patterns had clear band profiles when the thiourea buffer was used. These isolates were divided into only 30 patterns with DraI, 20 patterns with XbaI, and 20 patterns with AseI. The molecular profiles were all closely or possibly related, and the differences between the isolates ranged from zero to six bands. By multilocus enzyme electrophoresis (MEE), 45 of 53 smear isolates (85%) belonged to two closely related electrophoretic types. These isolates contained at least one enzyme allele seen almost exclusively in this group. Isolates without smear patterns were unaffected by thiourea and produced unrelated PFGE profiles, as well as multiple MEE types. The
hsp65
and 16S rRNA gene sequences of the isolates with smear patterns were identical to those of
M. abscessus
type strain ATCC 19977, which had a nonsmear pattern, suggesting that this clone is a subgroup within
M. abscessus
. This demonstrates that the inability to type
M. abscessus
by PFGE is associated with a single clone of organisms.
Detection of Virulence-Associated Genes Not Useful for Discriminating between Invasive and Commensal
Staphylococcus epidermidis
Strains from a Bone Marrow Transplant Unit
Authors: Rohde Holger , Kalitzky Matthias , Kröger Nicolaus , Scherpe Stefanie , Horstkotte Matthias A. , Knobloch Johannes K.-M. , Zander Axel R. , Mack Dietrich 
Published: December 2004

ABSTRACT

Because of their biofilm-forming capacity, invasive
Staphylococcus epidermidis
isolates, which cause the majority of nosocomial catheter-related bloodstream infections (BSIs), are thought to be selected at the time of catheter insertion from a population of less virulent commensal strains. This fact allows the prediction that invasive and contaminating strains can be differentiated via detection of virulence-associated genes. However, the hospital environment may pave the way for catheter-related infections by promoting a shift in the commensal bacterial population toward strains with enhanced virulence. The distribution of virulence-associated genes (
icaADBC
,
aap
,
atlE
,
bhp
,
fbe
,
embp
,
mecA
, IS
256
, and
IS257
), polysaccharide intercellular adhesin synthesis, and biofilm formation were investigated in
S. epidermidis
strains from independent episodes of catheter-related BSIs in individuals who have received bone marrow transplantation (BMT). The results were compared with those obtained for commensal
S. epidermidis
isolates from hospitalized patients after BMT and from healthy individuals, respectively. The clonal relationships of the strains were investigated by pulsed-field gel electrophoresis.
icaADBC
,
mecA
, and IS
256
were significantly more prevalent in BSI isolates than in commensal isolates from healthy individuals. However, the prevalence of any of the genes in clonally independent, endogenous commensal strains from BMT patients did not differ from that in invasive BSI strains.
icaADBC
and methicillin resistance, factors important for the establishment of catheter-related infections, already ensure survival of the organisms in their physiological habitat in the hospital environment, resulting in a higher probability of contamination of indwelling medical devices with virulent
S. epidermidis
strains. The dynamics of
S. epidermidis
populations reveal that detection of
icaADBC
and
mecA
is not suitable for discriminating invasive from contaminating
S. epidermidis
strains.
Development of a Multilocus Sequence Typing Scheme for the Opportunistic Pathogen
Pseudomonas aeruginosa
Authors: Curran Barry , Jonas Daniel , Grundmann Hajo , Pitt Tyrone , Dowson Christopher G. 
Published: December 2004

ABSTRACT

A multilocus sequence typing (MLST) scheme has been developed for
Pseudomonas aeruginosa
which provides molecular typing data that are highly discriminatory and electronically portable between laboratories. MLST data confirm the data from previous studies that suggest that
P. aeruginosa
is best described as nonclonal but as having an epidemic population. The index of association was 0.17, indicating a freely recombining population; however, there was evidence of clusters of closely related strains or clonal complexes among the members of this population. It is apparent that the sequence types (STs) from single isolates, representing each of the present epidemic clones in the United Kingdom from Liverpool, Manchester, and the West Midlands, are not closely related to each other. This suggests distinct evolutionary origins for each of these epidemic clones in the United Kingdom. Furthermore, these clones are distinct from European clone C. Comparison of the results of MLST with those of
toxA
typing and serotyping revealed that strains with identical STs may possess different
toxA
types and diverse serotypes. Given that recombination is important in the population of
P. aeruginosa
, the lack of a linkage between
toxA
type and serotype is not surprising and reveals the strength of the MLST approach for obtaining a better understanding of the epidemiology of
P. aeruginosa
.
Variable Number of Tandem Repeats in
Salmonella enterica
subsp.
enterica
for Typing Purposes
Authors: Ramisse Vincent , Houssu Perrine , Hernandez Eric , Denoeud France , Hilaire Valérie , Lisanti Olivier , Ramisse Françoise , Cavallo Jean-Didier , Vergnaud Gilles 
Published: December 2004

ABSTRACT

The genomic sequences of
Salmonella enterica
subsp.
enterica
strains CT18, Ty2 (serovar Typhi), and LT2 (serovar Typhimurium) were analyzed for potential variable number tandem repeats (VNTRs). A multiple-locus VNTR analysis (MLVA) of 99 strains of
S. enterica
supsp.
enterica
based on 10 VNTRs distinguished 52 genotypes and placed them into four groups. All strains tested were independent human isolates from France and did not reflect isolates from outbreak episodes. Of these 10 VNTRs, 7 showed variability within serovar Typhi, whereas 1 showed variability within serovar Typhimurium. Four VNTRs showed high Nei's diversity indices (DIs) of 0.81 to 0.87 within serovar Typhi (
n
= 27). Additionally, three of these more variable VNTRs showed DIs of 0.18 to 0.58 within serovar Paratyphi A (
n
= 10). The VNTR polymorphic site within multidrug-resistant (MDR) serovar Typhimurium isolates (
n
= 39; resistance to ampicillin, chloramphenicol, spectinomycin, sulfonamides, and tetracycline) showed a DI of 0.81. Cluster analysis not only identified three genetically distinct groups consistent with the present serovar classification of salmonellae (serovars Typhi, Paratyphi A, and Typhimurium) but also discriminated 25 subtypes (93%) within serovar Typhi isolates. The analysis discriminated only eight subtypes within serovar Typhimurium isolates resistant to ampicillin, chloramphenicol, spectinomycin, sulfonamides, and tetracycline, possibly reflecting the emergence in the mid-1990s of the DT104 phage type, which often displays such an MDR spectrum. Coupled with the ongoing improvements in automated procedures offered by capillary electrophoresis, use of these markers is proposed in further investigations of the potential of MLVA in outbreaks of salmonellosis, especially outbreaks of typhoid fever.
Phylogenetic Analysis and PCR-Restriction Fragment Length Polymorphism Identification of
Campylobacter
Species Based on Partial
groEL
Gene Sequences
Authors: Kärenlampi R. I. , Tolvanen T. P. , Hänninen M.-L. 
Published: December 2004

ABSTRACT

The phylogeny of 12
Campylobacter
species and reference strains of
Arcobacter butzleri
and
Helicobacter pylori
was studied based on partial 593-bp
groEL
gene sequences. The topology of the phylogenetic neighbor-joining tree based on the
groEL
gene was similar to that of the tree based on the 16S rRNA gene. However,
groEL
was found to provide a better resolution for
Campylobacter
species, with lower interspecies sequence similarities (range, 65 to 94%) compared with those for the 16S rRNA gene (range, 90 to 99%) and high intraspecies sequence similarities (range, 95 to 100%; average, 99%). A new universal reverse primer that amplifies a 517-bp fragment of the
groEL
gene was developed and used for PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of 68 strains representing 11
Campylobacter
species as well as reference strains of
A. butzlerii
and
H. pylori
. Digestion with the AluI enzyme discriminated all
Campylobacter
species included in the study but showed more intraspecies diversity than digestion with the ApoI enzyme. A hippurate-negative variant of
Campylobacter jejuni
with a high level of
groEL
sequence similarity to both
C. jejuni
(96%) and
C. coli
(94%) gave a unique AluI profile and an ApoI profile identical to those of other
C. jejuni
strains. In conclusion,
groEL
gene sequencing and PCR-RFLP analysis are recommended as valuable tools for the identification of
Campylobacter
species.
Direct Comparison of the BD ProbeTec ET System with In-House LightCycler PCR Assays for Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
from Clinical Specimens
Authors: Koenig Michael G. , Kosha Sandra L. , Doty Brandon L. , Heath David G. 
Published: December 2004

ABSTRACT

The commercial BD ProbeTec ET (BDPT) system for the detection of
Neisseria gonorrhoeae
and
Chlamydia trachomatis
from clinical specimens was compared with our in-house LightCycler real-time PCR (LC-PCR) assays. Specimens initially positive by the BDPT system were retested by our LC-PCR assays. Our results for
C. trachomatis
testing indicate a 91.2% agreement when the results of 114 clinical specimens, initially positive by BDPT over a wide range of method-other-than-acceleration (MOTA) scores, were retested by our LC-PCR assay. The agreement between the two systems improved to 96% when only MOTA scores of >30,000 were retested by the LC-PCR assay. The overall agreement between the two systems for
Neisseria gonorrhoeae
detection from 155 clinical specimens was only 77.4%, with agreement particularly low (24.1%) for MOTA scores ranging from 2,000 to 19,999. Repeat testing of specimens with the BDPT only closely correlated with that seen by others demonstrating that reproducibility of the BDPT system for specimens initially within the MOTA score range from 2,000 to 9,999 is problematic, especially for
Neisseria gonorrhoeae
testing. With our study, we proposed an algorithm for
C. trachomatis
and
N. gonorrhoeae
testing which involves screening with the BDPT system followed by selective use of our in-house LC-PCR assays.
Emergence of Extended-Spectrum-β-Lactamase (CTX-M-9)-Producing Multiresistant Strains of
Salmonella enterica
Serotype Virchow in Poultry and Humans in France
Authors: Weill François-Xavier , Lailler Renaud , Praud Karine , Kérouanton Annaëlle , Fabre Laëtitia , Brisabois Anne , Grimont Patrick A. D. , Cloeckaert Axel 
Published: December 2004

ABSTRACT

During 2002 to 2003, eight
Salmonella enterica
serotype Virchow poultry and poultry product isolates from various sources (chicken farms, poultry slaughterhouse, or retail store) and one
S. enterica
rough strain isolated from human feces were found to produce extended-spectrum β-lactamase CTX-M-9. Poultry and poultry product isolates were recovered from different locations in the southwest of France. The human rough isolate had sequences of flagellin genes (
fliC
and
fljB
) typical of serotype Virchow and ribotyping and pulsed-field gel electrophoresis (PFGE) patterns closely similar to those of serotype Virchow strains. PFGE confirmed the clonal relationship between the poultry isolates, while the human isolate displayed a pattern with 94% homology. The
bla
CTX-M-9
gene was located on a conjugative plasmid and was shown to be linked to orf513. Plasmid profiling found a very similar EcoRI restriction pattern in six transconjugants studied, including transconjugants obtained from the human isolate. A single hatchery, supplying chicks to the six farms, was identified. Emergence of extended-spectrum β-lactamase-producing
S. enterica
strains in food animals is a major concern, as such strains could disseminate on a large scale and lead to antibiotic therapy difficulties.
Mapping of Genomic Segments of Influenza B Virus Strains by an Oligonucleotide Microarray Method
Authors: Ivshina Anna V. , Vodeiko Galina M. , Kuznetsov Vladimir A. , Volokhov Dmitry , Taffs Rolf , Chizhikov Vladimir I. , Levandowski Roland A. , Chumakov Konstantin M. 
Published: December 2004

ABSTRACT
Similar to other segmented RNA viruses, influenza viruses can exchange genome segments and form a wide variety of reassortant strains upon coreplication within a host cell. Therefore, the mapping of genome segments of influenza viruses is essential for understanding their phenotypes. In this work, we have developed an oligonucleotide microarray hybridization method for simultaneous genotyping of all genomic segments of two highly homologous strains of influenza B virus. A few strain-specific oligonucleotide probes matching each of the eight segments of the viral genomes of the B/Beijing/184/93 and B/Shangdong/7/97 strains were hybridized with PCR-amplified fluorescently labeled single-stranded DNA. Even though there were a few mismatches among the genomes of the studied virus strains, microarray hybridization showed highly significant and reproducible discrimination ability and allowed us to determine the origins of individual genomic segments in a series of reassortant strains prepared as vaccine candidates. Additionally, we were able to detect the presence of at least 5% of mixed genotypes in virus stocks even when conventional sequencing methods failed, for example, for the NS segment. Thus, the proposed microarray method can be used for (i) rapid and reliable genome mapping of highly homologous influenza B viruses and (ii) extensive monitoring of influenza B virus reassortants and the mixed genotypes. The array can be expanded by adding new oligoprobes and using more quantitative assays to determine the origin of individual genomic segments in series of reassortant strains prepared as vaccine candidates or in mixed virus populations.
DNA Microarrays for Virus Detection in Cases of Central Nervous System Infection
Authors: Boriskin Yury S. , Rice Philip S. , Stabler Richard A. , Hinds Jason , Al-Ghusein Hasan , Vass Keith , Butcher Philip D. 
Published: December 2004

ABSTRACT
A low-density, high-resolution diagnostic DNA microarray comprising 38 gene targets for 13 viral causes of meningitis and encephalitis was constructed. The array has been used for the detection of multiplex PCR-amplified viruses in cerebrospinal fluid (CSF) and non-CSF specimens. A total of 41 clinical specimens were positive for echoviruses (23 samples), herpes simplex virus type 2 (4 samples), varicella-zoster virus (4 samples), human herpesvirus 7 (1 sample), human herpesvirus 6A (1 sample) and 6B (2 samples), Epstein-Barr virus (three samples), polyomavirus JC (1 sample), and cytomegalovirus (2 samples). Probes for herpes simplex virus type 1, polyomavirus BK, and mumps and measles viruses were also included on the array. Three samples were false negative by the microarray assay due to discordant results between the multiplex PCR for all 13 viruses simultaneously and the virus-specific PCR alone. Fifteen CSF specimens were true negative. The clinical sensitivity, specificity, and negative and positive predictive values of the assay were 93, 100, 100, and 83%, respectively, when the results were compared to those of the single-virus PCR, which was used as the “gold standard.” The microarray-based virus detection assay is qualitative and provides a single-format diagnostic tool for the detection of panviral CNS infections.
Clinical and Serological Variation between Patients Infected with Different Hepatitis B Virus Genotypes
Authors: Kidd-Ljunggren Karin , Myhre Erling , Bläckberg Jonas 
Published: December 2004

ABSTRACTHepatitis B virus (HBV) has eight genotypes which have distinct geographical distributions. Studies comparing differences in the clinical outcomes of infections caused by strains with genotype-related variations in the HBV genome have largely compared genotypes B and C and genotypes A and D but not all four genotypes. The present study included 196 HBV-infected patients attending an infectious diseases outpatient clinic in Sweden. The age and geographic origin, liver function, HBeAg and anti-HBe status, and the presence or absence of HBV DNA were analyzed for each patient. HBV DNA was detected in 144 patients, and the HBV genotype and the core promoter and precore sequences were determined for the isolates from 101 of these patients. Among the patients who might be considered most likely to be nonviremic, namely, anti-HBe-positive HBV carriers with normal alanine aminotransferase (ALT) levels, 65% had detectable HBV DNA and were thus viremic. Among the viremic patients, HBeAg-positive patients were more likely to have elevated ALT levels than anti-HBe-positive patients. HBV genotypes A to F were represented in the study, and their distributions coincided accurately with the origin of the patient. A significantly higher number of genotype D-infected patients were anti-HBe positive and had elevated ALT levels (42% of genotype D-infected patients but 0% of patients infected with genotypes B and C). Genotype D strains with mutations in the core promoter and precore regions were significantly correlated with elevated ALT levels in the patients. The differences were not age related. Therefore, in this large-scale cross-sectional study, genotype D appears to be associated with more active disease.
Azithromycin Retards
Pseudomonas aeruginosa
Biofilm Formation
Authors: Gillis Richard J. , Iglewski Barbara H. 
Published: December 2004

ABSTRACT

Using a flow cell biofilm model, we showed that a sub-MIC of azithromycin (AZM) can delay but not inhibit
Pseudomonas aeruginosa
biofilm formation and results in the development of a stable AZM resistance phenotype. Furthermore, mature biofilms were not affected by AZM.
Identification and Discrimination of
Burkholderia pseudomallei
,
B. mallei
, and
B. thailandensis
by Real-Time PCR Targeting Type III Secretion System Genes
Authors: Thibault F. M. , Valade E. , Vidal D. R. 
Published: December 2004

ABSTRACT

Burkholderia pseudomallei
and
B. mallei
are two highly pathogenic bacteria, responsible for melioidosis and glanders, respectively. The two are closely related and can also be mistaken for
B. thailandensis
, a nonpathogenic species. To improve their differential identification, we describe a hydrolysis probe-based real-time PCR method using the uneven distribution of type III secretion system genes among these three species.