bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicobacter pylori
Growth and Urease Detection in the Chemically Defined Medium Ham's F-12 Nutrient Mixture
Authors: Testerman Traci L. , McGee David J. , Mobley Harry L. T. 
Published: July 2002

ABSTRACT

Obstacles continue to hinder in vitro studies of the gastric human pathogen
Helicobacter pylori
, including difficulty culturing the organism in the absence of serum or blood, rapid loss of viability following exponential growth due to autolysis, and the necessity for using high starting inocula. We demonstrate that
H. pylori
grows in the chemically defined broth medium Ham's F-12 nutrient mixture (F-12) in the absence of fetal bovine serum (FBS); this represents a breakthrough for studies in which serum components or proteins interfere with interpretation of results. Cultures can be continually passaged in fresh, FBS-free F-12 medium at an initial inoculum of only ∼10
3
CFU/ml. All
H. pylori
strains (
n
= 21), including fresh clinical isolates, grew in serum-free F-12.
H. pylori
grew poorly in the related medium, F-10, unless additional zinc was supplied. Enhanced growth of
H. pylori
in F-12 broth was obtained by addition of bovine serum albumin (BSA) (1 mg/ml), β-cyclodextrin (200 μg/ml), or cholesterol (50 μg/ml).
H. pylori
also grew in several simplified versions of F-12 broth lacking glucose and most vitamins but containing hypoxanthine, pyruvate, and all 20 amino acids. On F-12 medium solidified with agar,
H. pylori
only grew when BSA (98% pure; 1 mg/ml), cholesterol (50 μg/ml), β-cyclodextrin (200 μg/ml), or FBS (2 to 4%) was added; addition of urea and phenol allowed colorimetric detection of urease activity. Thus, F-12 agar plus cholesterol or β-cyclodextrin represents the first transparent chemically defined agar and the first urease indicator agar for
H. pylori
. Several lines of evidence suggested that BSA itself is not responsible for
H. pylori
growth enhancement in F-12 containing BSA or FBS. Taken together, these innovations represent significant advances in the cultivation and recovery of
H. pylori
using chemically defined media. Use of F-12 or its derivatives may lead to improved understanding of
H. pylori
metabolism, virulence factors, and transmission, and result in improved recovery and identification of
H. pylori
from clinical specimens.
Chlamydia trachomatis
Serology: Diagnostic Value of Outer Membrane Protein 2 Compared with That of Other Antigens
Authors: Bas S. , Muzzin P. , Vischer T. L. 
Published: July 2002

ABSTRACT

Different immunoassays using recombinant antigens or synthetic peptides were evaluated for the serodiagnosis of
Chlamydia trachomatis
infections. Antigens used included cysteine-rich outer membrane protein 2 (OMP2), heat shock protein 60, the polypeptide encoded by open reading frame 3 of the plasmid (pgp3), synthetic peptides derived from species-specific epitopes in variable domain IV of the major OMP (MOMP) (Labsystems, Helsinki, Finland), and a fragment of the total lipopolysaccharide (Medac, Hamburg, Germany). Because cross-reactions between chlamydial species have been reported,
Chlamydia pneumoniae
-specific antibodies were also determined by immunoassays (Labsystems). Responses obtained with serum samples from patients with well-defined diseases (i.e., urethral or endocervical samples from which
C. trachomatis
DNA was amplified) were compared to those obtained with samples from healthy blood donors. The best sensitivity (79%) associated with the best specificity (82%) was obtained when immunoglobulin G (IgG) responses to both MOMP and pgp3 were considered. The highest sensitivity (89%) was obtained with anti-OMP2 IgG, but the lowest specificity (57%) was obtained with this antibody, due to probable cross-reactivity with
C. pneumoniae
OMP2.
Quantification of Human Cytomegalovirus DNA in Bone Marrow Transplant Recipients by Real-Time PCR
Authors: Griscelli Frank , Barrois Michel , Chauvin Sylvie , Lastere Stephane , Bellet Dominique , Bourhis Jean-Henri 
Published: July 2002

ABSTRACT

A real-time PCR assay was developed to quantify human cytomegalovirus (CMV) DNA in peripheral blood leukocytes (PBLs) of bone marrow transplantation patients. Unlike other teams, we quantified CMV and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene using a plasmid containing both sequences as an external standard. Tenfold serial dilutions of this plasmid yielded overlapping standard curves that allowed the quantification of CMV and GAPDH gene copies in an efficient and accurate manner. Sequential blood samples (164 specimens) were collected from 16 patients. PBLs were tested by the pp65 antigenemia assay and quantitative CMV and GAPDH gene PCRs. CMV DNA was detected by PCR in 13 patients a mean of 15 days prior to the appearance of antigenemia. The administration of anti-CMV drugs led to a rapid decrease in the numbers of viral copies and positive nuclei. Real-time PCR assay results correlated with those of the CMV pp65 antigenemia assay (
P
< 0.00001). The TaqMan assay may be a useful tool for rapid quantification of CMV infection and for monitoring of CMV reactivation in bone marrow transplantation recipients.
Polymorphism of
Bordetella pertussis
Isolates Circulating for the Last 10 Years in France, Where a Single Effective Whole-Cell Vaccine Has Been Used for More than 30 Years
Authors: Weber Christian , Boursaux-Eude Caroline , Coralie Gilberte , Caro Valérie , Guiso Nicole 
Published: July 2002

ABSTRACT

We compared
Bordetella pertussis
isolates collected in France over the last 10 years, the vaccine strains used for more than 30 years, and isolates collected before the introduction of generalized vaccination. The analysis included serotyping, pulsed-field gel electrophoresis of chromosomal DNA after digestion with
Xba
I and
Spe
I, and sequencing of the
pt
S1 gene, encoding the S1 subunit of pertussis toxin, and the
prn
gene, encoding the adhesin pertactin. We found that the incidence of infection increases every 3 years. Ninety-five per cent of the isolates analyzed express type 3 fimbriae. Most of the isolates circulating since 1991, unlike the vaccinal strains, express a type A pertussis toxin and a type 2 pertactin. The isolates could be classified into five major groups by pulsed-field gel electrophoresis. Most of these groups correlated with the pertactin type expressed by the isolates. Pulsed-field gel electrophoresis is more discriminative than sequencing particular genes since it could differentiate isolates expressing type 2 pertactin into two subgroups: those circulating in 1993 to 1997 and those circulating in 1997 to 2001. This observation suggests that there has been continuous evolution of the
B. pertussis
population.
Nosocomial Fungemia Due to
Exophiala jeanselmei
var.
jeanselmei
and a
Rhinocladiella
Species: Newly Described Causes of Bloodstream Infection
Authors: Nucci Marcio , Akiti Tiyomi , Barreiros Gloria , Silveira Fernanda , Revankar Sanjay G. , Sutton Deanna A. , Patterson Thomas F. 
Published: July 2002

ABSTRACT

Fungi have become increasingly important causes of nosocomial bloodstream infections. The major cause of nosocomial fungemia has been
Candida
spp, but increasingly molds and other yeasts have caused disease.
Exophiala jeanselmei
and members of the genus
Rhinocladiella
are dematiaceous moulds, which have been infrequently associated with systemic infection and have not been described as causes of fungemia. In this paper, the occurrence of 23 cases of fungemia due to these organisms over a 10-month period is reported and the clinical characteristics of patients and outcomes are described. The majority of patients were immunosuppressed; 21 of 23 (91%) had received blood products and 78% had a central venous catheter. All patients had at least one manifestation of fever, but only one patient had signs or symptoms suggesting deep-seated infection. Antifungal therapy was given to 19 of the 23 patients; of those who did not receive therapy, 3 died prior to the culture result and 1 had been discharged without therapy. Antifungal susceptibility of the organisms showed activity of amphotericin B, itraconazole, and the new triazole antifungals voriconazole and posaconazole.
E. jeanselmei
and
Rhinocladiella
species are potential causes of nosocomial fungemia and may be associated with systemic infection.
Genetic Variability and Prevalence of
Bartonella henselae
in Cats in Berlin, Germany, and Analysis of Its Genetic Relatedness to a Strain from Berlin That Is Pathogenic for Humans
Authors: Arvand Mardjan , Klose Alexander J. , Schwartz-Porsche Dorothea , Hahn Helmut , Wendt Constanze 
Published: July 2002

ABSTRACT

Nineteen
Bartonella henselae
strains and one
Bartonella clarridgeiae
strain were isolated from blood samples of 97 pet cats and 96 stray cats from Berlin, Germany, indicating prevalence rates of 1 and 18.7%, respectively, for
B. henselae
and 0 and 1%, respectively, for
B. clarridgeiae
. Eighteen of 19
B. henselae
isolates corresponded to 16S rRNA type II. Pulsed-field gel electrophoresis (PFGE) analysis revealed seven different PFGE types among the feline
B. henselae
strains. Interestingly, all feline isolates displayed low genetic relatedness to
B. henselae
strain Berlin-1, which is pathogenic for humans.
Molecular Epidemiology of
Mycobacterium tuberculosis
Infection in Israel
Authors: Ravins M. , Bercovier H. , Chemtob D. , Fishman Y. , Rahav G. 
Published: July 2002

ABSTRACT

Restriction fragment length polymorphism analysis with IS
6110
and DR-r probes was used to study 69
Mycobacterium tuberculosis
isolates obtained from Israeli patients and new immigrants from the former Soviet Union and Ethiopia. DNA fingerprinting identified unique patterns for almost all isolates, indicating that most patients were infected with a unique strain imported from their country of origin and that their latent infection was reactivated in Israel.
Phenotypic and Genotypic Characterization of
Pediococcus
Strains Isolated from Human Clinical Sources
Authors: Barros Rosana R. , Carvalho Maria Da Glória S. , Peralta José Mauro , Facklam Richard R. , Teixeira Lúcia M. 
Published: July 2002

ABSTRACT

Seventy-two strains of pediococci isolated from human clinical sources were characterized by conventional physiological tests, chromogenic enzymatic tests, analysis of whole-cell protein profiles (WCPP) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and analysis of chromosomal DNA restriction profiles by pulsed-field gel electrophoresis (PFGE). Conventional tests allowed identification of 67 isolates: 52 strains were identified as
Pediococcus acidilactici
, 15 strains were identified as
Pediococcus pentosaceus
, and 5 strains were not identified because of atypical reactions. Analysis of WCPP identified all isolates since each species had a unique WCPP. By the WCPP method, the atypical strains were identified as
P. acidilactici
(two strains) and
P. pentosaceus
(three strains). The chromogenic substrate test with
o
-nitrophenyl-β-
d
-glucopyranoside differentiated all 54 strains of
P. acidilactici
(negative reactions) and 13 (72%) of 18 strains of
P. pentosaceus
(positive reactions). Isolates of both species were shown to be nonclonal as revealed by the genetic diversity when chromosomal DNA was analyzed by PFGE. Using WCPP as the definitive identification procedure,
P. acidilactici
(28 of 54 strains; 51.8%) was more likely than
P. pentosaceus
(4 of 18 strains; 22.3%) to be isolated from blood cultures.
Molecular Characteristic-Based Epidemiology of Hepatitis B, C, and E Viruses and GB Virus C/Hepatitis G Virus in Myanmar
Authors: Nakai Kazuhiko , Win Khin Maung , Oo San San , Arakawa Yasuyuki , Abe Kenji 
Published: July 2002

ABSTRACT
We carried out a molecular characteristic-based epidemiological survey of various hepatitis viruses, including hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and GB virus C (GBV-C)/hepatitis G virus (HGV), in Myanmar. The study population of 403 subjects consisted of 213 healthy individuals residing in the city of Yangon, Myanmar, and the surrounding suburbs and 190 liver disease patients (155 virus-related liver disease patients and 35 nonviral disease patients). The infection rates of the viruses among the 213 healthy subjects were as follows: 8% for HBV (16 patients), 2% for HCV (4 patients), and 8% for GBV-C/HGV (17 patients). In contrast, for 155 patients with acute hepatitis, chronic hepatitis, liver cirrhosis, or hepatocellular carcinoma, the infection rates were 30% for HBV (46 patients), 27% for HCV (41 patients), and 11% for GBV-C/HGV (17 patients). In the nonviral liver disease group of 35 patients with alcoholic liver disease, fatty liver, liver abscess, and biliary disease, the infection rates were 6% for HBV (2 patients), 20% for HCV (7 patients), and 26% for GBV-C/HGV (9 patients). The most common viral genotypes were type C of HBV (77%), type 3b of HCV (67%), and type 2 of GBV-C/HGV (67%). Moreover, testing for HEV among 371 subjects resulted in the detection of anti-HEV immunoglobulin G (IgG) in 117 patients (32%). The age prevalence of anti-HEV IgG was 3% for patients younger than 20 years and 30% or more for patients 20 years of age or older. Furthermore, a high prevalence of anti-HEV IgG (24%) was also found in swine living together with humans in Yangon. These results suggest that these hepatitis virus infections are widespread in Myanmar and have led to a high incidence of acute and chronic liver disease patients in the region.
B-Cell Epitope Mapping of the VapA Protein of
Rhodococcus equi
: Implications for Early Detection of
R. equi
Disease in Foals
Authors: Vanniasinkam Thiru , Barton Mary D. , Heuzenroeder Michael W. 
Published: July 2002

ABSTRACT

Linear B-cell epitopes of the
Rhodococcus equi
virulence-associated protein (VapA) were mapped using a synthetic peptide bank in this study. The peptides were screened in an enzyme-linked immunosorbent assay (ELISA) with a total of 70 sera from foals with current
R. equi
disease (51 sera), as well as from foals that had either recovered from
R. equi
infection 10 months previously (3 sera) or that had no known history of
R. equi
disease (16 sera). An epitope with the sequence NLQKDEPNGRA was identified and was universally recognized by all 51 sera from foals with
R. equi
disease and was not recognized by any of the other sera. There was poor reactivity between all sera and peptides relating to other areas of the VapA protein. It is proposed that an ELISA based upon a defined peptide epitope may be used in an improved serological diagnostic test for
R. equi
infection in foals.
Antifungal Susceptibilities, Varieties, and Electrophoretic Karyotypes of Clinical Isolates of
Cryptococcus neoformans
from Brazil, Chile, and Venezuela
Authors: Calvo Belinda M. , Colombo Arnaldo L. , Fischman Olga , Santiago A. , Thompson L. , Lazera Marcia , Telles Flavio , Fukushima Kazutaka , Nishimura Kazuko , Tanaka Reiko , Myiajy Makoto , Moretti-Branchini M. Luiza 
Published: July 2002

ABSTRACT

One hundred clinical isolates of
Cryptococcus neoformans
from human immunodeficiency virus (HIV)-infected and non-HIV-infected patients from Brazil, Chile, and Venezuela were separated according to varieties and tested for antifungal susceptibility. A high susceptibility to antifungal agents was observed among all the isolates. The electrophoretic karyotyping of 51 strains revealed good discrimination among
Cryptococcus neoformans
var.
neoformans
strains.
Diagnosis of Oropouche Virus Infection Using a Recombinant Nucleocapsid Protein-Based Enzyme Immunoassay
Authors: Saeed Mohammad F. , Nunes Marcio , Vasconcelos Pedro F. , Travassos Da Rosa Amelia P. A. , Watts Douglas M. , Russell Kevin , Shope Robert E. , Tesh Robert B. , Barrett Alan D. T. 
Published: July 2002

ABSTRACT
Oropouche (ORO) virus is an emerging infectious agent that has caused numerous outbreaks of an acute febrile (dengue-like) illness among humans in Brazil, Peru, and Panama. Diagnosis of ORO virus infection is based mainly on serology. Two different antigens, hamster serum antigen (HSA) and Vero cell lysate antigen (VCLA), are currently used in enzyme immunoassays (EIAs) in Brazil and Peru, respectively, to investigate the epidemiology of ORO virus infection. Both antigens involve use of infectious virus, and for this reason their use is restricted. Consequently, the frequency and distribution of ORO virus infection are largely unexplored in other countries of South America. This report describes the use of a bacterially expressed recombinant nucleocapsid (rN) protein of ORO virus in EIAs for the diagnosis of ORO virus infection. The data revealed that the purified rN protein is comparable to the authentic viral N protein in its antigenic characteristics and is highly sensitive and specific in EIAs. Among 183 serum samples tested, a high degree of concordance was found between rN protein-based EIA and HSA- and VCLA-based EIAs for the detection of both ORO virus-specific immunoglobulin M (IgM) and IgG antibodies. The high sensitivity, specificity, and safety of the rN protein-based EIA make it a useful diagnostic technique that can be widely used to detect ORO virus infection in South America.
Evaluation of COBAS AMPLICOR (Roche): Accuracy in Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
by Coamplification of Endocervical Specimens
Authors: Livengood Charles H. , Wrenn Jane W. 
Published: July 2002

ABSTRACT

We evaluated further the accuracy of the COBAS AMPLICOR (Roche) (CA) PCR-based system in detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in endocervical specimens. Endocervical specimens collected for any indication for testing for
C. trachomatis
and
N. gonorrhoeae
among a university hospital health system population were included. Testing for
C. trachomatis
was done by two PCR methods, CA and manual microwell AMPLICOR (Roche) (MWA), and by culture; testing for
N. gonorrhoeae
was done by CA and culture. Discrepancy resolution was performed. Reproducibility testing and hands-on labor time measurements for CA were done. Among 654
C. trachomatis
samples, the prevalence of true positivity was 9.2%, and among the 618
N. gonorrhoeae
samples, the prevalence of true positivity was 4.4%. For detection of
C. trachomatis
, the sensitivity, specificity, and negative and positive predictive values were, respectively, as follows for each test: CA, 93.3, 99.7, 99.3, and 96.4%; MWA, 91.7, 99.7, 99.2, and 96.5%; and culture, 65.0, 100, 96.6, and 100%. For detection of
N. gonorrhoeae
those values were as follows: CA, 96.3, 100, 99.8, and 100%; and culture, 92.6, 100, 99.7, and 100%. Hands-on labor time for each clinical result was estimated to be at 7.5 min. The prevalence of inhibitory specimens was 3.5%, including two positive
C. trachomatis
samples which would have been missed otherwise. The direct cost of each clinical result with CA was estimated to be $9.09. Our methods include a diverse range of indications for testing among women, using endocervical swabbing samples, 2 M sucrose phosphate transport medium, and discrepancy resolution for comparison. Under our test conditions, the CA system is an accurate, rapid, and cost- and labor-efficient method for detection of
C. trachomatis
and
N. gonorrhoeae
.
Identification of
Mycobacterium
Species by Multiple-Fluorescence PCR–Single-Strand Conformation Polymorphism Analysis of the 16S rRNA Gene
Authors: Gillman Lawrence M. , Gunton James , Turenne Christine Y. , Wolfe Joyce , Kabani Amin M. 
Published: July 2002

ABSTRACT
Identification of mycobacteria to the species level by growth-based methodologies is a process that has been fraught with difficulties due to the long generation times of mycobacteria. There is an increasing incidence of unusual nontuberculous mycobacterial infections, especially in patients with concomitant immunocompromised states, which has led to the discovery of new mycobacterial species and the recognition of the pathogenicity of organisms that were once considered nonpathogens. Therefore, there is a need for rapid and sensitive techniques that can accurately identify all mycobacterial species. Multiple-fluorescence-based PCR and subsequent single-strand conformation polymorphism (SSCP) analysis (MF-PCR-SSCP) of four variable regions of the 16S rRNA gene were used to identify species-specific patterns for 30 of the most common mycobacterial human pathogens and environmental isolates. The species-specific SSCP patterns generated were then entered into a database by using BioNumerics, version 1.5, software with a pattern-recognition capability, among its multiple uses. Patient specimens previously identified by 16S rRNA gene sequencing were subsequently tested by this method and were identified by comparing their patterns with those in the reference database. Fourteen species whose SSCP patterns were included in the database were correctly identified. Five other test organisms were correctly identified as unique species or were identified by their closest relative, as they were not in the database. We propose that MF-PCR-SSCP offers a rapid, specific, and relatively inexpensive identification tool for the differentiation of mycobacterial species.
Use of a Heteroduplex Mobility Assay To Detect Differences in the Fusion Protein Cleavage Site Coding Sequence among Newcastle Disease Virus Isolates
Authors: Berinstein Analia , Sellers Holly S. , King Daniel J. , Seal Bruce S. 
Published: July 2002

ABSTRACT
Newcastle disease virus (NDV) is an economically important pathogen of poultry that may cause clinical disease that ranges from a mild respiratory syndrome to a virulent form with high mortality, depending on an isolate's pathotype. Infections with virulent NDV strains are required to be reported by member nations to the Office of International Epizootes (OIE). The primary determinant for virulence among NDV isolates is the presence or absence of dibasic amino acids in the fusion (F) protein cleavage activation site. Along with biological virulence determinations as the definitive tests, OIE accepts reporting of the F protein cleavage site sequence of NDV isolates as a virulence criterion. Nucleotide sequence data for many NDV isolates recently isolated from infected chickens and other avian species worldwide have been deposited in GenBank. Consequently, viral genomic information surrounding the F protein cleavage site coding sequence was used to develop a heteroduplex mobility assay (HMA) to aid in further identification of molecular markers as predictors of NDV virulence. Using common vaccine strains as a reference, we were able to distinguish virulent viruses among NDV isolates that correlated with phylogenetic analysis of the nucleotide sequence. This technique was also used to examine NDV isolates not previously characterized. We were able to distinguish vaccine-like viruses from other isolates potentially virulent for chickens. This technique will help improve international harmonization of veterinary biologics as set forth by the OIE and the Veterinary International Cooperation on Harmonization of Technical Requirements of Veterinary Medicinal Products. Ultimately, the HMA could be used for initial screening among a large number of isolates and rapid identification of potentially virulent NDV that continue to threaten commercial poultry worldwide.