bluuebunny/crossref_metadata_2025_split huggingface dataset:
Susceptibility of Filamentous Fungi to Voriconazole Tested by Two Microdilution Methods
Authors: Linares Maria José , Charriel Guadalupe , Solís Francisco , Rodriguez Fernando , Ibarra Ana , Casal M. 
Published: January 2005

ABSTRACT

The growing number of fungal infections, coupled with emerging resistance to classical antifungal agents, has led to the development of new agents, among them voriconazole. Susceptibility to voriconazole was tested by two microdilution techniques: the National Committee for Clinical Laboratory Standards reference method M38-A and a colorimetric method, Sensititre YeastOne. The study tested a total of 244 isolates: 223
Aspergillus
(136
Aspergillus fumigatus
, 37
A. niger
, 26
A. terreus
, 16
A. flavus
, 7
A. nidulans
, and 1
A. ustus
), 14
Fusarium
(8
Fusarium moniliformis
, and 6
F. oxysporum
), 6
Scedosporium apiospermum
, and 1
Rhizomucor pusillus
strain and four control strains (
Candida parapsilosis
ATCC 22019,
C. krusei
ATCC 6258,
A. fumigatus
ATCC 204305, and
A. flavus
ATCC 204304). For all tested species except one
F. moniliforme
strain and
R. pusillus
, the MIC, the MIC at which 50% of the isolates are inhibited (MIC
50
), and MIC
90
ranges of ≤1 μg/ml were obtained for voriconazole, indicating excellent activity against these species. The high rate of agreement between the two methods used (97 to 99%) suggests that the Sensititre YeastOne colorimetric method may be a valuable tool for determining the susceptibility of filamentous fungi to voriconazole.
Development of a Molecular-Beacon Assay To Detect the G
1896
A Precore Mutation in Hepatitis B Virus-Infected Individuals
Authors: Waltz Therese L. , Marras Salvatore , Rochford Gemma , Nolan John , Lee Eugenia , Melegari Margherita , Pollack Henry 
Published: January 2005

ABSTRACT

The 1896 precore (PC) mutation is the most frequent cause of hepatitis B virus e-antigen (HBeAg)-negative chronic hepatitis B virus (HBV) infection. Detection of the 1896 PC mutation has application in studies monitoring antiviral therapy and the natural history of the disease. Identification of this mutation is usually performed by direct sequencing, which is both costly and laborious. The aim of this study was to develop a rapid, high-throughput assay to detect the 1896 PC mutation using real-time PCR and molecular-beacon technology. The assay was initially standardized on oligonucleotide targets and plasmids containing the wild-type (WT) and PC mutation and then tested on plasma samples from children with HBV DNA of >10
6
copies/ml. Nine individuals were HBeAg negative and suspected to harbor HBeAg mutations, while 12 children were HBeAg positive and selected as controls. Ninety percent (19 of 21) of plasma samples tested with molecular beacons were in complete agreement with sequencing results. The remaining 10% (2 of 21) of samples were identified as heterogeneous mixtures of WT and mutant virus by molecular beacons, though sequencing found only a homogeneous mutant in both cases. Overall, the 1896 PC mutation was detected by this assay in 55.5% of the children with HBeAg-negative infection. In summary, this assay is a rapid, sensitive, and specific technique that effectively discriminates WT from 1896 PC mutant HBV and may be useful in clinical and epidemiological studies.
Molecular Analysis of
Malassezia sympodialis
-Related Strains from Domestic Animals
Authors: Cabañes F. J. , Hernández J. J. , Castellá G. 
Published: January 2005

ABSTRACT

Recently, several new lipid-dependent species belonging to the genus
Malassezia
have been described. Some of them, such as
Malassezia dermatis
,
Malassezia nana
, and the tentatively named “
Malassezia equi
,” have similar phenotypes and are genetically close to
Malassezia sympodialis
Simmons et Guého 1990. DNA characterization by D1/D2 26S rRNA gene and internal transcribed spacer (ITS)-5.8S rRNA gene sequencing analysis of lipid-dependent strains from different animal species close to
M. sympodialis
is described and illustrated. Phylogenetic analysis of both the D1/D2 regions of 26S rRNA gene and ITS-5.8S rRNA gene sequences showed four distinct clusters. Cluster I included isolates from different animal species (horse, pig, and lamb) and the type culture of
M. sympodialis
. Cluster II included isolates from horses grouping close to the “
M. equi
” AJ305330 sequence. Cluster III comprised isolates mainly from goats. Cluster IV contained isolates mainly from cats grouping together with the
M. nana
AB075224 sequence. This last cluster included isolates from healthy and external otitic ears. All of these strains had identical 26S rRNA gene and ITS regions. It is not clear whether the value of these genetic differences is for the definition of species or whether they only demonstrate genetic variation among strains from different origins within
M. sympodialis
, which are in the course of differentiation and probably adaptation to specific animal hosts.
Contribution of (1→3)-β-
d
-Glucan Chromogenic Assay to Diagnosis and Therapeutic Monitoring of Invasive Aspergillosis in Neutropenic Adult Patients: a Comparison with Serial Screening for Circulating Galactomannan
Authors: Pazos Carmen , Pontón José , Palacio Amalia Del 
Published: January 2005

ABSTRACT

Two noninvasive diagnostic tests, (1→3)-β-
d
-glucan (BG) (Glucatell) and galactomannan (GM) (Platelia
Aspergillus
), were used retrospectively in a twice-weekly screening for the diagnosis of invasive aspergillosis (IA) in 40 treatment episodes (one hospital visit per patient) in 40 neutropenic adult patients at high risk for IA. Five proven IA cases, three probable IA cases, and three possible IA cases were diagnosed. Diagnostic levels of both BG and GM were detected in 100% of patients with proven IA cases and in 66% of patients with probable IA cases. The kinetics of both markers in patients with IA were similar. The sensitivity, specificity, and positive and negative predictive values for GM and BG were identical, namely, 87.5, 89.6, 70, and 96.3%, respectively. False-positive reactions occurred at a rate of 10.3% in both tests, but the patients showing false-positive results were different in each test. Both tests anticipated the clinical diagnosis, computed tomography abnormalities, and the initiation of antifungal therapy in most patients, but BG tended to become positive earlier than GM. A combination of the two tests improved the specificity (to 100%) and positive predictive value (to 100%) of each individual test without affecting the sensitivity and negative predictive values. In conclusion, BG and GM detection are useful tests for the diagnosis of IA in high-risk hematological patients, but a combination of the two tests was very useful to identify false-positive reactions by each test.
External Quality Assessment for Molecular Detection of
Bordetella pertussis
in European Laboratories
Authors: Muyldermans G. , Soetens O. , Antoine M. , Bruisten S. , Vincart B. , Doucet-Populaire F. , Fry N. K. , Olcén P. , Scheftel J. M. , Senterre J. M. , van der Zee A. , Riffelmann M. , Piérard D. , Lauwers S. 
Published: January 2005

ABSTRACT

Although the PCR for the detection of
Bordetella pertussis
is routinely performed in diagnostic laboratories, no quality assessment program has so far been described. We report on the results obtained with two external quality assessment proficiency panels sent to European laboratories. The first proficiency panel contained a series of dilutions of three previously characterized
B. pertussis
clinical isolates and two negative controls. No false-positive results were reported by six laboratories providing seven data sets. The reported limits of detection of the three
B. pertussis
strains varied between 4 and 4,000, 9 and 9,000, and 3 and 30,000 CFU/ml, respectively. The second proficiency panel, composed of a series of dilutions of reference strains of
B. pertussis
,
B. holmesii
,
B. hinzii
, and
B. bronchiseptica
, as well as negative controls, was sent to nine laboratories. One laboratory reported a negative result for a sample and reported a
B. parapertussis
-positive sample to be positive for
B. pertussis
. By using the
B. pertussis
-specific target gene pertactin, one laboratory detected
B. pertussis
with 100% specificity. All other laboratories, which used IS
481
-based assays, reported positive results for the samples containing
B. holmesii
and
B. bronchiseptica
, species that have occasionally been recovered from human respiratory samples. These data show that the choice of the target gene is particularly critical for the species specificity of
B. pertussis
PCR assays.
Utility of Mycobacterial Interspersed Repetitive Unit Typing for Differentiating Multidrug-ResistantMycobacterium tuberculosisIsolates of the Beijing Family
Authors: Kam Kai Man , Yip Chi Wai , Tse Lai Wa , Wong Kin Lai , Lam Tak Kam , Kremer Kristin , Au Betty Kam Yan , van Soolingen Dick 
Published: January 2005

ABSTRACTMycobacterial interspersed repetitive unit (MIRU) typing has been found to allow rapid, reliable, high-throughput genotyping ofMycobacterium tuberculosisand may represent a feasible approach to study globalM. tuberculosismolecular epidemiology. To evaluate the use of MIRU typing in discriminating drug-resistantM. tuberculosisstrains of the Beijing genotype family, 102 multidrug-resistant (MDR) clinical isolates and 253 randomly selected non-MDR isolates collected from 2000 to 2003 in Hong Kong were subjected to 12-locus MIRU typing, spoligotyping, and IS6110restriction fragment length polymorphism (RFLP) typing. Spoligotyping showed that 243 (68.5%) of 355 isolates belonged to Beijing family genotype. MIRU typing showed lower discrimination in differentiating between the Beijing family strains (Hunter-Gaston discriminative index [HGI] of 0.8827) compared with the IS6110RFLP method (HGI = 0.9979). For non-Beijing strains, MIRU typing provided discrimination (HGI = 0.9929) comparable to that of the RFLP method (HGI = 0.9961). There was no remarkable difference in discrimination power between the two methods in differentiating both within and between MDR and non-MDR strains ofM. tuberculosis. Dendrograms constructed with the MIRU typing data showed a clear segregation between the Beijing and non-Beijing genotype. Addition of RFLP to MIRU typing offered a higher discrimination ability (92.6%) than did addition of MIRU typing to RFLP (40.0%). This supported the potential use of this method to analyze the global genetic diversity of MDRM. tuberculosisstrains that may be at different levels of evolutionary divergence.
Use of Variable-Number Tandem-Repeat Typing To DifferentiateMycobacterium tuberculosisBeijing Family Isolates from Hong Kong and Comparison with IS6110Restriction Fragment Length Polymorphism Typing and Spoligotyping
Authors: Kremer Kristin , Au Betty Kam Yan , Yip Peter Chi Wai , Skuce Robin , Supply Philip , Kam Kai Man , van Soolingen Dick 
Published: January 2005

ABSTRACTTheMycobacterium tuberculosisBeijing family isolates may cause more than a quarter of all tuberculosis cases worldwide, are emerging in some areas, and are often associated with drug resistance. Early recognition of transmission of this genotype is therefore important. To evaluate the usefulness of variable-number tandem-repeat (VNTR) typing to discriminate and recognize strains of the Beijing family,M. tuberculosisisolates from Hong Kong were subjected to VNTR analysis, spoligotyping, and IS6110restriction fragment length polymorphism (RFLP) typing. The allelic diversity of the 14 VNTR loci included in the analysis varied from 0 to 0.618 among Beijing strains. The discriminatory power of VNTR analysis was slightly lower than that of IS6110RFLP. Our analysis shows that VNTR typing, which has many practical advantages over RFLP typing, can be used for epidemiological studies of Beijing strains. However, VNTR-defined clusters should be subtyped with IS6110RFLP for maximal resolution.
Expression and Immunological Characterization of the Carboxy-Terminal Region of the P1 Adhesin Protein of
Mycoplasma pneumoniae
Authors: Chaudhry Rama , Nisar Nazima , Hora Bhavna , Chirasani Sridhar Reddy , Malhotra Pawan 
Published: January 2005

ABSTRACT

Mycoplasma pneumoniae
is the causative agent of primary atypical pneumonia in humans. Adherence of
M. pneumoniae
to host cells requires several adhesin proteins, such as P1, P30, and P116. A major limitation in developing a specific diagnostic test for
M. pneumoniae
is the inability to express adhesin proteins in heterologous expression systems due to unusual usage of the UGA stop codon, leading to premature termination of these proteins in
Escherichia coli
. In the present study, we successfully expressed the C-terminal (P1-C1) and N-terminal (P1-N1) regions of the P1 protein in
E. coli
. On screening these recombinant proteins with sera from
M. pneumoniae
-infected patients, only the P1-C1 protein was found to be immunogenic. This protein can be used as an antigen for immunodiagnosis of
M. pneumoniae
infection, as well as in adherence inhibition studies to understand the pathophysiology of the disease.
Propionibacterium acnes
Types I and II Represent Phylogenetically Distinct Groups
Authors: McDowell Andrew , Valanne Susanna , Ramage Gordon , Tunney Michael M. , Glenn Josephine V. , McLorinan Gregory C. , Bhatia Ajay , Maisonneuve Jean-Francois , Lodes Michael , Persing David H. , Patrick Sheila 
Published: January 2005

ABSTRACT

Although two phenotypes of the opportunistic pathogen
Propionibacterium acnes
(types I and II) have been described, epidemiological investigations of their roles in different infections have not been widely reported. Using immunofluorescence microscopy with monoclonal antibodies (MAbs) QUBPa1 and QUBPa2, specific for types I and II, respectively, we investigated the prevalences of the two types among 132
P. acnes
isolates. Analysis of isolates from failed prosthetic hip implants (
n
= 40) revealed approximately equal numbers of type I and II organisms. Isolates from failed prosthetic hip-associated bone (
n
= 6) and tissue (
n
= 38) samples, as well as isolates from acne (
n
= 22), dental infections (
n
= 8), and skin removed during surgical incision (
n
= 18) were predominately of type I. A total of 11 (8%) isolates showed atypical MAb labeling and could not be conclusively identified. Phylogenetic analysis of
P. acnes
by nucleotide sequencing revealed the 16S rRNA gene to be highly conserved between types I and II. In contrast, sequence analysis of
recA
and a putative hemolysin gene (
tly
) revealed significantly greater type-specific polymorphisms that corresponded to phylogenetically distinct cluster groups. All 11 isolates with atypical MAb labeling were identified as type I by sequencing. Within the
recA
and
tly
phylogenetic trees, nine of these isolates formed a cluster distinct from other type I organisms, suggesting a further phylogenetic subdivision within type I. Our study therefore demonstrates that the phenotypic differences between
P. acnes
types I and II reflect deeper differences in their phylogeny. Furthermore, nucleotide sequencing provides an accurate method for identifying the type status of
P. acnes
isolates.
Molecular Phylogenies of
Blastocystis
Isolates from Different Hosts: Implications for Genetic Diversity, Identification of Species, and Zoonosis
Authors: Noël Christophe , Dufernez Fabienne , Gerbod Delphine , Edgcomb Virginia P. , Delgado-Viscogliosi Pilar , Ho Lip-Chuen , Singh Mulkit , Wintjens René , Sogin Mitchell L. , Capron Monique , Pierce Raymond , Zenner Lionel , Viscogliosi Eric 
Published: January 2005

ABSTRACT

Small-subunit (SSU) rRNA gene sequences were obtained by PCR from 12
Blastocystis
isolates from humans, rats, and reptiles for which elongation factor 1α (EF-1α) gene sequences are already available. These new sequences were analyzed by the Bayesian method in a broad phylogeny including, for the first time, all
Blastocystis
sequences available in the databases. Phylogenetic trees identified seven well-resolved groups plus several discrete lineages that could represent newly defined clades. Comparative analysis of SSU rRNA- and EF-1α-based trees obtained by maximum-likelihood methods from a restricted sampling (13 isolates) revealed overall agreement between the two phylogenies. In spite of their morphological similarity, sequence divergence among
Blastocystis
isolates reflected considerable genetic diversity that could be correlated with the existence of potentially ≥12 different species within the genus. Based on this analysis and previous PCR-based genotype classification data, six of these major groups might consist of
Blastocystis
isolates from both humans and other animal hosts, confirming the low host specificity of
Blastocystis
. Our results also strongly suggest the existence of numerous zoonotic isolates with frequent animal-to-human and human-to-animal transmissions and of a large potential reservoir in animals for infections in humans.
Transmission of High-Risk Human Papillomavirus (HPV) between Parents and Infant: a Prospective Study of HPV in Families in Finland
Authors: Rintala Marjut A. M. , Grénman Seija E , Puranen Mirja H. , Isolauri Erika , Ekblad Ulla , Kero Pentti O. , Syrjänen Stina M. 
Published: January 2005

ABSTRACT
The Finnish HPV Family Study is a prospective cohort study assessing the dynamics of human papillomavirus (HPV) transmission between parents and infant. Serial genital and oral scrapings from 76 families, including mother, father, and infant, and semen samples were collected over 2 years of follow-up, analyzed by nested PCR, and confirmed by hybridization with 12 high-risk (HR) HPV types. The most common HPV profile was HR HPV in all family members (29%), followed by HPV-positive mother-infant pairs (26%). HPV-positive father-infant pairs were less frequent (11%), and in six (8%) families, only the infant was HR HPV positive. The prevalence of genital HR HPV in the parents ranged from 13 to 25%, and that of oral HPV ranged from 8 to 34%. In the infants, HPV DNA was detected in 15% of the genital and 10% of the oral samples at birth, reaching peaks of 18 and 21%, respectively, at 6 months, and declining to 10% at 24 months. Persistent HPV in the mother was a risk factor for oral HPV in the infant (odds ratio [OR], 5.69; 95% confidence interval [95% CI], 1.5 to 21.3), while oral HPV in the mother at 6 months was a risk factor for genital HR HPV (OR, 6.38; 95% CI, 1.15 to 35.32). No such independent risk could be attributed to subclinical HPV in the father. Persistent maternal cervical HPV and subclinical oral HPV affect the risk of infant HPV. The age of 6 months is a critical point for the infant to acquire or be free of HR HPV DNA.
Purification of
Enterocytozoon bieneusi
from Stools and Production of Specific Antibodies
Authors: Sheoran Abhineet S. , Feng Xiaochuan , Kitaka Sabrina , Green Linda , Pearson Christine , Didier Elizabeth S. , Chapman Susan , Tumwine James K. , Tzipori Saul 
Published: January 2005

ABSTRACT

Enterocytozoon bieneusi
is clinically the most significant of the microsporidia in humans, causing chronic diarrhea wasting and cholangitis in individuals with human immunodeficiency virus infection and AIDS. Little progress on this infection has been made because of the inability to propagate
E. bieneusi
in vitro and in vivo, which limits the source of parasite spores to the stools of infected human patients. Given the size and shape of the
E. bieneusi
spores (1.1 to 1.6 by 0.7 to 1.0 μm) and the lack of specific immune reagents, the identification and purification of large quantities of spores from feces are technically challenging. Consequently, diagnosis relies entirely on PCR, a labor-intensive approach that requires highly skilled personnel. We describe a method for the purification of
E. bieneusi
spores from human stools and the production of rabbit-specific antisera. Spores were purified by a combination of isopycnic Percoll gradient centrifugation and continuous sucrose gradient centrifugation. Specific polyclonal antibodies raised in mice and rabbits reacted by indirect immunofluorescence with
E. bieneusi
but not with
Encephalitozoon
spp.,
Candida albicans
,
Staphylococcus aureus
,
Escherichia coli
, or other forms present in human stools.
Real-Time Nucleic Acid Sequence-Based Amplification Is More Convenient than Real-Time PCR for Quantification of
Plasmodium falciparum
Authors: Schneider Petra , Wolters Liselotte , Schoone Gerard , Schallig Henk , Sillekens Peter , Hermsen Rob , Sauerwein Robert 
Published: January 2005

ABSTRACT

Determination of the number of malaria parasites by routine or even expert microscopy is not always sufficiently sensitive for detailed quantitative studies on the population dynamics of
Plasmodium falciparum
, such as intervention or vaccine trials. To circumvent this problem, two more sensitive assays, real-time quantitative nucleic acid sequence-based amplification (QT-NASBA) and real-time quantitative PCR (QT-PCR) were compared for quantification of
P. falciparum
parasites. QT-NASBA was adapted to molecular beacon real-time detection technology, which enables a reduction of the time of analysis and of contamination risk while retaining the specificity and sensitivity of the original assay. Both QT-NASBA and QT-PCR have a sensitivity of 20 parasites/ml of blood, but QT-PCR requires a complicated DNA extraction procedure and the use of 500 μl of venous blood to achieve this sensitivity, compared to 50 μl of finger prick blood for real-time QT-NASBA. Both techniques show a significant correlation to microscopic parasite counts, and the quantification results of the two real-time assays are significantly correlated for in vitro as well as in vivo samples. However, in comparison to real-time QT-PCR, the results of real-time QT-NASBA can be obtained 12 h earlier, with relatively easy RNA extraction and use of finger prick blood samples. The prospective development of multiplex QT-NASBA for detection of various
P. falciparum
developmental stages increases the value of QT-NASBA for malaria studies. Therefore, for studies requiring sensitive and accurate detection of
P. falciparum
parasites in large numbers of samples, the use of real-time QT-NASBA is preferred over that of real-time QT-PCR.