bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Phenotyping of Leukocytes in Bovine Bronchoalveolar Lavage Fluid
Authors: Soethout E. C. , Müller K. E. , van den Belt A. J. M. , Rutten V. P. M. G. 
Published: July 2004

ABSTRACTA method is proposed to identify leukocyte subpopulations in bovine bronchoalveolar lavage fluid by dual-laser flow cytometry. The technique uses several parameters, i.e., exclusion of highly autofluorescent alveolar macrophages and inclusion of leukocytes on the basis of labeling by specific antibodies and light scatter characteristics.
Evaluation of a Monoclonal Antibody-Based Test for Detection of
Helicobacter pylori
-Specific Antigen in Stool Samples from Mice
Authors: Crone Julia , Symonds Erin , Campbell Fiona , Butler Ross 
Published: July 2004

ABSTRACT

A test using monoclonal antibodies for detection of antigen in stool samples was compared with culture and histology for noninfected (
n
= 25),
Helicobacter pylori
-infected (
n
= 25), and
Helicobacter felis
-infected (
n
= 6) mice. Sensitivity and specificity were 96%. The monoclonal antibody-based test is therefore a noninvasive technique that is able to diagnose
H. pylori
infection in mice.
Clinical Evaluation of a Chemiluminescence Immunoassay for Determination of Immunoglobulin G Avidity to Human Cytomegalovirus
Authors: Revello Maria Grazia , Gorini Giovanna , Gerna Giuseppe 
Published: July 2004

ABSTRACT
Clinical evaluation of a novel fully automated chemiluminescence immunoassay for determination of immunoglobulin G avidity to human cytomegalovirus (HCMV) showed 92.8% sensitivity and 84.7% specificity in detecting a recent (≤90 days) primary HCMV infection. The assay appears useful for accurately diagnosing recent primary HCMV infections.
Long-Term Effects of Immunization with Recombinant Lipoprotein Outer Surface Protein A on Serologic Test for Lyme Disease
Authors: Fawcett Paul T. , Rose Carlos D. , Maduskuie Victoria 
Published: July 2004

ABSTRACT
Immunization with recombinant lipoprotein outer surface protein A vaccine is known to interfere with some serologic tests for Lyme disease. We tested sera from 152 vaccine recipients by using in-house and commercial Western blot assays and found that vaccination caused interference in up to 25% of recipients and can persist for over 6 years.
Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein in SARS Patients by Enzyme-Linked Immunosorbent Assay
Authors: Lau Susanna K. P. , Woo Patrick C. Y. , Wong Beatrice H. L. , Tsoi Hoi-Wah , Woo Gibson K. S. , Poon Rosana W. S. , Chan Kwok-Hung , Wei William I. , Peiris J. S. Malik , Yuen Kwok-Yung 
Published: July 2004

ABSTRACT

We report the development of an enzyme-linked immunosorbent assay (ELISA) for the detection of severe acute respiratory syndrome (SARS) coronavirus (CoV) nucleocapsid protein. The assay was carried out with hyperimmune polyclonal nucleocapsid-specific antibodies from guinea pigs and rabbits immunized with recombinant His
6
-tagged SARS CoV nucleocapsid protein. The assay was used for the detection of SARS CoV nucleocapsid protein in nasopharyngeal aspirate, urine, and fecal samples collected from patients with confirmed SARS between days 2 and 33 after the onset of illness. The ELISA was capable of detecting this protein in SARS CoV cell culture lysates at 15 50% tissue culture infective doses/ml but did not produce positive signals when tested with cell culture lysates of human coronaviruses OC43 and 229E. When tested with 120 nasopharyngeal aspirate, 100 urine, and 100 fecal specimens from hospitalized patients without SARS, the assay was shown to have high specificities—96.7, 99, and 96%, respectively. In an evaluation of clinical specimens from SARS patients, 34 (52%) of 66 nasopharyngeal aspirate samples from 50 patients, 5 (5%) of 94 urine samples from 94 patients, and 36 (55%) of 65 fecal samples from 65 patients tested positive for SARS CoV nucleocapsid protein. Nucleocapsid protein could be detected from days 6 to 24 in nasopharyngeal aspirate specimens, from days 11 to 31 in urine specimens, and from days 8 to 32 in fecal specimens after the onset of illness. Moreover, the protein could be detected in 25 (83%) of 30 nasopharyngeal aspirate specimens obtained from days 11 to 15 and in all 7 fecal specimens obtained from days 21 to 32. Since the present ELISA is more convenient and economical than reverse transcription-PCR, it may serve as an alternative tool for the early diagnosis of SARS CoV infection in laboratories with limited resources and expertise and for mass screening for the reservoir of SARS CoV. Further studies on serial clinical specimens should reveal the duration of nucleocapsid protein shedding and may reveal a higher detection rate in SARS patients.
Detection of Human Immunodeficiency Virus Type 1 Antiretroviral Resistance Mutations by High-Density DNA Probe Arrays
Authors: Gonzalez R. , Masquelier B. , Fleury H. , Lacroix B. , Troesch A. , Vernet G. , Telles J. N. 
Published: July 2004

ABSTRACT
Genotypic resistance testing has become an important tool in the clinical management of patients infected with human immunodeficiency virus type 1 (HIV-1). Standard sequencing methodology and hybridization-based technology are the two principal methods used for HIV-1 genotyping. This report describes an evaluation of a new hybridization-based HIV-1 genotypic test of 99 clinical samples from patients infected mostly with HIV-1 subtype B and receiving treatment. This test combines RNA extraction with magnetic silica particles, amplification by nested reverse transcriptase PCR, and detection with high-density probe arrays designed to detect 204 antiretroviral resistance mutations simultaneously in Gag cleavage sites, protease, reverse transcriptase, integrase, and gp41. The nested reverse transcriptase PCR success rates at viral loads exceeding 1,000 copies/ml were 98% for the 2.1-kb amplicon that covers the Gag cleavage sites and the protease and reverse transcriptase genes, 92% for the gp41 amplicon, and 100% for the integrase amplicon. We analyzed 4,465 relevant codons with the HIV-1 DNA chip genotyping assay and the classic sequence-based method. Key resistance mutations in protease and reverse transcriptase were identified correctly 95 and 92% of the time, respectively. This test should be a valuable alternative to the standard sequence-based system for HIV-1 drug resistance monitoring and a useful diagnostic tool for simultaneous multiple genetic analyses.
Prospective Study of a Real-Time PCR That Is Highly Sensitive, Specific, and Clinically Useful for Diagnosis of Meningococcal Disease in Children
Authors: Bryant Penelope A. , Li Hua Yi , Zaia Angelo , Griffith Julia , Hogg Geoff , Curtis Nigel , Carapetis Jonathan R. 
Published: July 2004

ABSTRACT
Due to the early administration of antibiotics, meningococcal disease is increasingly difficult to diagnose by culturing. Laboratory studies have shown PCR to be sensitive and specific, but there have been few clinical studies. The objectives of this study were to determine the diagnostic accuracy and clinical usefulness of meningococcal PCR through a prospective comparison of real-time PCR, nested PCR, and standard culturing of blood and cerebrospinal fluid (CSF). The setting was a tertiary-care pediatric hospital in Australia, and the participans were 118 children admitted with possible septicemia or meningitis. The main outcome measures—sensitivity, specificity, and positive and negative predictive values—were compared to a “gold standard ” fulfilling clinical and laboratory criteria. For 24 cases of meningococcal disease diagnosed by the gold standard, culturing of blood or CSF was positive for 15 (63%), nested PCR was positive for 21 (88%), and real-time PCR was positive for 23 (96%). The sensitivity, specificity, and positive and negative predictive values of real-time PCR (the most sensitive test) for all specimens were, respectively, 96% (95% confidence interval, 79 to 99%), 100% (95% confidence interval, 96 to100%), 100% (95% confidence interval, 85 to 100%), and 99% (95% confidence interval, 94 to 100%). Of 54 patients with suspected meningococcal disease at admission, 23 had positive PCR results. Only one PCR specimen was positive in a patient thought unlikely to have meningococcal disease at admission. Blood PCR remained positive for 33% of patients tested at up to 72 h. Real-time PCR has high positive and negative predictive values in this clinical setting, with better confirmation of cases than nested PCR. Targeting patients for PCR based on admission criteria appears to be practical, and the test may remain useful for several days after the start of antibiotic administration.
Combination of PCR Targeting the VD2 of
omp1
and Reverse Line Blot Analysis for Typing of Urogenital
Chlamydia trachomatis
Serovars in Cervical Scrape Specimens
Authors: Molano Monica , Meijer Chris J. L. M. , Morré Servaas A. , Pol Rene , van den Brule Adriaan J. C. 
Published: July 2004

ABSTRACT

In this study we developed and evaluated a new PCR-based typing assay, directed to the VD2 region of the
omp1
gene, for the detection and typing of urogenital
Chlamydia trachomatis
infections. A nested VD2 PCR-reverse line blot (RLB) assay was developed for the typing of nine different urogenital serovars of
C. trachomatis
. The assay developed was tested with reference strains of
C. trachomatis
serovars and cervical scrapes of 86 Colombian women previously found to be positive for
C. trachomatis
by using plasmid PCR. Two sets of primers directed to the VD2 region of the
omp1
gene of
C. trachomatis
were designed, and fragments of 220 and 166 bp were generated in the primary and nested PCRs, respectively. In addition, an RLB assay was developed to identify nine different urogenital serovars of
C. trachomatis
(Ba, D, E, F, G, H, I, J, and K) and group controls, including group B (Ba, D, and E), group C (I, J, K, and H), and an intermediate group (F and G). Using this assay, we were able to type 81 of the 86 samples (94.2%). Of these samples, 91.3% were single
C. trachomatis
infections, and 8.7% were multiple infections. The most common serovars identified were serovars D (22.2%), F (18.5%), G (13.6%), and E (12.3%). Of the women with multiple
C. trachomatis
infections, >50% contained both serovars D and E. The nested VD2 PCR-RLB developed is a simple, fast, and specific method for the identification of individual urogenital
C. trachomatis
serovars previously detected by using plasmid PCR. Moreover, it is an appropriate method for studying multiple
C. trachomatis
infections and for use in large epidemiological studies.
Performance of a New, Rapid Assay for Detection of
Trichomonas vaginalis
Authors: Kurth Ann , Whittington William L. H. , Golden Matthew R. , Thomas Katherine K. , Holmes King K. , Schwebke Jane R. 
Published: July 2004

ABSTRACT

Trichomonas vaginalis
infection is highly prevalent, may have serious health consequence, and is readily treatable. However, screening has been limited by currently available tests, which tend to be insensitive, expensive, or require a delay before results are reported. The XenoStrip-Tv (Xenotope Diagnostics, Inc., San Antonio, Tex.) was evaluated on vaginal swab specimens from 936 women attending sexually transmitted disease clinics in Seattle, Wash. (
n
= 497), and Birmingham, Ala. (
n
= 439).
T. vaginalis
prevalence by culture (InPouch; Biomed) was 8.7% in Seattle and 21.0% in Birmingham. Compared to culture, the XenoStrip assay in Seattle was 76.7% (95% confidence interval [95% CI] = 61.4 to 88.2) sensitive and 99.8% (95% CI = 98.8 to 99.9) specific, and in Birmingham it was 79.4% (95% CI = 69.6 to 87.1) sensitive and 97.1% (95% CI = 94.8 to 98.6) specific. The positive predictive values were 97.1% in Seattle and 87.9% in Birmingham; the negative predictive values were 97.8 and 94.7%, respectively. Rapid test performance did not vary by vaginal symptoms or by the presence of other vaginal or cervical syndromes or infections. The sensitivity did vary by day of culture-positive result, with a 71% decline in XenoStrip sensitivity for every additional day delay until
T. vaginalis
was first detected in cultures (odds ratio = 0.29, 95% CI = 0.18 to 0.49). The rapid assay was more sensitive than wet preparation microscopy (78.5% versus 72.4% [
P
= 0.04]) but was less specific (98.6% versus 100% [
P
= 0.001]). The XenoStrip rapid assay is well suited for use in settings with a moderately high prevalence of
T. vaginalis
infection, particularly when microscopy is not practical.
Isolation of Recombinant Antibodies against EspA and Intimin of
Escherichia coli
O157:H7
Authors: Kühne Sarah A. , Hawes William S. , La Ragione Roberto M. , Woodward Martin J. , Whitelam Garry C. , Gough Kevin C. 
Published: July 2004

ABSTRACT

Intimin, Tir, and EspA proteins are expressed by attaching-effacing
Escherichia coli
, which include enteropathogenic and enterohemorrhagic
E. coli
pathotypes. EspA proteins are part of the type three secretion system needle complex that delivers Tir to the host epithelial cell, while surface arrayed intimin docks the bacterium to the translocated Tir. This intimate attachment leads to attaching and effacing lesions. Recombinant forms of these effector proteins from enterohemorrhagic
E. coli
O157:H7 were produced by using
E. coli
expression vectors. Binding of intimin and Tir fragments in enzyme-linked immunosorbent assay (ELISAs) demonstrated the interaction of intimin fragments containing the C-terminal 282 or 188 amino acids to a Tir fragment containing amino acid residues 258 to 361. Recombinant intimin and EspA proteins were used to elicit immune responses in rabbits and immune phage-display antibody libraries were produced. Screening of these immune libraries by conventional phage-antibody panning and colony filter screening produced a panel of antibodies with specificity for EspA or intimin. Antibodies recognizing different C-terminal epitopes on intimin bound specifically to the gamma intimin of O157:H7 and not to other classes of intimin. Antibodies recognizing EspA from
E. coli
O157 also recognized the protein from the
eae
-deficient O157 mutant DM3 and from
E. coli
O111. Anti-intimin antibodies were also produced as fusion proteins coupled to the reporter molecule alkaline phosphatase, allowing the one-step detection of γ intimin. The isolated recombinant monoclonal antibodies were functional in a range of assay formats, including ELISA, Western blotting, and dot blots, thus demonstrating their diagnostic potential.
Intra- and Interlaboratory Study of a Method for Testing the Antifungal Susceptibilities of Dermatophytes
Authors: Ghannoum M. A. , Chaturvedi V. , Espinel-Ingroff A. , Pfaller M. A. , Rinaldi M. G. , Lee-Yang W. , Warnock D. W. 
Published: July 2004

ABSTRACT

The National Committee for Clinical Laboratory Standards (NCCLS) M38-A standard for the susceptibility testing of conidium-forming filamentous fungi does not explicitly address the testing of dermatophytes. This multicenter study, involving six laboratories, investigated the MIC reproducibility of seven antifungal agents tested against 25 dermatophyte isolates (5 blinded pairs of five dermatophyte species per site for a total of 300 tests), using the method of dermatophyte testing developed at the Center for Medical Mycology, Cleveland, Ohio. The dermatophytes tested included
Trichophyton rubrum
,
Trichophyton mentagrophytes
,
Trichophyton tonsurans
,
Epidermophyton floccosum
, and
Microsporum canis
. Seven antifungals with activity against dermatophytes were tested, including ciclopirox, fluconazole, griseofulvin, itraconazole, posaconazole, terbinafine, and voriconazole. Interlaboratory MICs for all isolates were in 92 to 100% agreement at a visual endpoint reading of 50% inhibition as compared to the growth control and 88 to 99% agreement at a visual endpoint reading of 80% inhibition as compared to the growth control. Intralaboratory MICs between blinded pairs were in 97% agreement at a visual endpoint reading of 50% inhibition as compared to the growth control and 96% agreement at a visual endpoint reading of 80% inhibition as compared to the growth control. Data from this study support consideration of this method as an amendment to the NCCLS M38-A standard for the testing of dermatophytes.
Coexistence of Multiple Genotypes, Including Newly Identified Genotypes, in Outbreaks of Gastroenteritis Due to
Norovirus
in Japan
Authors: Kageyama Tsutomu , Shinohara Michiyo , Uchida Kazue , Fukushi Shuetsu , Hoshino Fuminori B. , Kojima Shigeyuki , Takai Reiko , Oka Tomoichiro , Takeda Naokazu , Katayama Kazuhiko 
Published: July 2004

ABSTRACT

Norovirus
(NV) (formerly called Norwalk-like virus) is the most common cause of acute nonbacterial gastroenteritis in humans. Recently, we reported an NV genotyping scheme based on variability in the capsid N-terminal/shell (N/S) domain gene (Katayama et al., Virology
299:
225-239, 2002). We found 19 genotypes, including nine of genogroup I and 10 of genogroup II. In the present study, we investigated the molecular epidemiology of NV from 66 outbreaks that occurred in Saitama Prefecture, Japan, from 1997 to 2002. We screened 416 stool specimens by a real-time reverse transcription (RT)-PCR method (Kageyama et al., J. Clin. Microbiol.
41:
1548-1557, 2003) and detected 156 NV-positive specimens, from which we amplified the capsid N/S domain gene by RT-PCR and then cloned the PCR products. After sequencing these clones, we obtained 368 sequence variants (strains). By applying our classification scheme to the strains from Saitama and other published strains, we identified a total of 31 genotypes, including an additional five genotypes for genogroup I and seven for genogroup II. Of the 31 genotypes, 26 were present in the Saitama area during that time period. These results provide additional evidence for the great diversity of human NV genotypes. Specimens from all shellfish-related infections contained multiple genotypes, including several new genotypes. On the other hand, single genotypes were observed mostly in outbreaks that originated in semiclosed communities. Thus, the number of NV genotypes in each outbreak depended on the route of transmission.
Comparison of Three Nucleic Acid Amplification Tests for Detection of
Chlamydia trachomatis
in Urine Specimens
Authors: Gaydos Charlotte A. , Theodore Mellisa , Dalesio Nicholas , Wood Billie Jo , Quinn Thomas C. 
Published: July 2004

ABSTRACT

Traditionally, culture and immunoassays have been performed for the detection of sexually transmitted diseases, including
Chlamydia trachomatis
. However, these assays may often require invasive specimen collection methods, such as female cervical and male urethral swabs. Recently, nucleic acid amplification tests (NAATs) have been approved for testing for the presence of
C. trachomatis
in urine samples. Our objective was to compare the sensitivities and specificities of
C. trachomatis
detection in urine samples with three NAATs: the Abbott LCx (LCx), BD ProbeTec ET (ProbeTec), and Gen-Probe APTIMA Combo 2 (AC2). Urine specimens (
n
= 506) were collected from both symptomatic and asymptomatic males and females from various high school health clinics. Specimens were tested for
C. trachomatis
with the three NAATs, and a true-positive result was defined as any two positive NAATs. The
C. trachomatis
prevalence was 14.8% (75 of 506 samples). Of the 75 urine samples defined as true positives, LCx detected 72, ProbeTec 72, and AC2 detected 75. The sensitivities of LCx, ProbeTec, and AC2 for
C. trachomatis
detection were 96.0, 96.0, and 100%, and the specificities were 99.1, 100, and 98.8%, respectively. Four of five samples that were positive with AC2 and negative with LCx and ProbeTec were found to be positive with an alternative target TMA-based NAAT, APTIMA
C. trachomatis
, suggesting that they may have been true positives. Two of four uniquely positive LCx samples available for subsequent testing were both found to be positive by Roche PCR. We found that the LCx, ProbeTec, and AC2 NAATs are highly sensitive and specific methods for the detection of
C. trachomatis
in urine specimens and can be recommended for noninvasive screening of
C. trachomatis
in urine.
Studies on the Involvement of the Exopolysaccharide Produced by Cystic Fibrosis-Associated Isolates of the
Burkholderia cepacia
Complex in Biofilm Formation and in Persistence of Respiratory Infections
Authors: Cunha Mónica V. , Sousa Sílvia A. , Leitão Jorge H. , Moreira Leonilde M. , Videira Paula A. , Sá-Correia Isabel 
Published: July 2004

ABSTRACT

Bacteria belonging to the
Burkholderia cepacia
complex (BCC) are important opportunistic pathogens that lead to respiratory infections in patients with cystic fibrosis (CF). The clinical outcome following colonization with BCC bacteria is highly variable, and so far, unpredictable. A large percentage (80 to 90%) of BCC isolates from CF patients produce the exopolysaccharide (EPS) cepacian, which has been hypothesized to play a role in the colonization and persistence of these bacteria in the CF lung. In this work, we demonstrate that although it is not required for the initiation of biofilm formation, cepacian plays a role in the establishment of thick biofilms. This conclusion was based on a comparison of the abilities of EPS-defective mutants derived from a
B. cepacia
mucoid CF isolate by random plasposon insertion mutagenesis and the ability of the parental strain to form biofilms. However, the systematic characterization of 108 CF isolates, corresponding to 15 distinct strains, indicated that other strain-dependent factors are also involved in the development of thick, mature biofilms. The isolates examined belonged to the species
B. cepacia
,
B. multivorans
,
B. cenocepacia
, and
B. stabilis
and were obtained during a 7-year period of surveillance from 21 CF patients receiving care at the major Portuguese CF center. Most of them (90%) were serial isolates from 12 persistently infected patients. In spite of the concept that bacteria growing in biofilms display more resistance to antibiotics and to host phagocyte killing than do planktonically growing cells, no clear correlation could be established between the ability of the various strains examined to produce EPS and/or to form biofilms in vitro and the persistence or virulence of the respiratory infections they caused in different patients.
Prevalence of the
hifBC
,
hmw1A
,
hmw2A
,
hmwC
, and
hia
Genes in
Haemophilus influenzae
Isolates
Authors: Ecevit I. Zafer , McCrea Kirk W. , Pettigrew Melinda M. , Sen Ananda , Marrs Carl F. , Gilsdorf Janet R. 
Published: July 2004

ABSTRACT

Adherence of
Haemophilus influenzae
to respiratory epithelial cells is the first step in the pathogenesis of
H. influenzae
infection and is facilitated by the action of several adhesins located on the surface of the bacteria. In this study, prevalences of
hifBC
, which represent the pilus gene cluster;
hmw1A
,
hmw2A
, and
hmwC
, which represent high-molecular-weight (HMW) adhesin genes; and
hia
, which represents
H. influenzae
adhesin (Hia) genes were determined among clinical isolates of encapsulated type b (Hib) and nonencapsulated (NTHi)
H. influenzae. hifBC
genes were detected in 109 of 170 (64%) Hib strains and in 46 of 162 (28%) NTHi isolates (
P
= 0.0001) and were more prevalent among the invasive type b strains than invasive NTHi strains (
P
= 0.00003). Furthermore,
hifBC
genes were significantly more prevalent (
P
= 0.0398) among NTHi throat isolates than NTHi middle ear isolates.
hmw1A
,
hmw2A
,
hmwC
, and
hia
genes were not detected in Hib strains. Among NTHi isolates, the prevalence of
hmw1A
was 51%, the prevalence of
hmw2A
was 23%, the prevalence of
hmwC
was 48%, and the prevalence of
hia
was 33%. The
hmw
genes were significantly more prevalent among middle ear than throat isolates, while
hia
did not segregate with a respiratory tract site. These results show the variability of the presence of adhesin genes among clinical
H. influenzae
isolates and suggest that hemagglutinating pili may play a larger role in
H. influenzae
nasopharyngeal colonization than in acute otitis media whereas the HMW adhesins may be virulence factors for acute otitis media.