bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison between Prototype Hybrid Capture 3 and Hybrid Capture 2 Human Papillomavirus DNA Assays for Detection of High-Grade Cervical Intraepithelial Neoplasia and Cancer
Authors: Castle Philip E. , Lorincz Attila T. , Scott David R. , Sherman Mark E. , Glass Andrew G. , Rush Brenda B. , Wacholder Sholom , Burk Robert D. , Manos M. Michele , Schussler John E. , Macomber Paul , Schiffman Mark 
Published: September 2003

ABSTRACT

We compared the performance of a prototype version of the Hybrid Capture 3 (HC3) human papillomavirus (HPV) DNA assay to the current generation Hybrid Capture 2 (HC2) assay, both of which target 13 oncogenic HPV types, for the detection of cervical intraepithelial neoplasia grade 3 and cancer (CIN3+) with cervicovaginal lavage specimens collected at enrollment into a 10-year cohort study at Kaiser Permanente (Portland, Oreg.). HC3 results for a risk-stratified sample (
n
= 4,364) were compared to HC2 results for the entire cohort (
n
= 20,810) with receiver operating characteristics curves, and the optimal cut points for both tests (relative light units [RLU]/positive control [PC]) for the detection of CIN3+ were determined. Specimens were also tested for HPV16 and HPV18 with separate HC3 type-specific probes. The optimal cut point for detecting CIN3+ was 1.0 RLU/PC for HC2, as previously shown, and was 0.6 RLU/PC for HC3. At the optimal cut points, HC3 and HC2 had similar screening performance characteristics for CIN3+ diagnosed at the enrollment visit. In analyses that included cases CIN3+ at enrollment and those diagnosed during early follow-up, HC3 had nonsignificantly higher sensitivity and equal specificity for the detection of CIN3+ compared to HC2; this increase in sensitivity was primarily the result of increased detection of CIN3+ in women who were 30 years of age or older and were cytologically negative (
P
= 0.006). We also compared the performance of the hybrid capture tests to MY09/11 L1 consensus primer PCR results (
n
= 1,247). HC3 was less likely than HC2 to test positive for specimens that tested positive by PCR for any untargeted types (
P
< 0.001). HC3 was less likely than HC2 to test positive for untargeted PCR-detected single infections with HPV53 (
P
= 0.001) and HPV66 (
P
= 0.01). There was good agreement between test positivity by PCR and by single type-specific HC3 probes for HPV16 (kappa = 0.76; 95% confidence interval [CI] = 0.71 to 0.82) and for HPV18 (kappa = 0.73; 95% CI = 0.68 to 0.79). In conclusion, we suggest that HC3 (≥0.6 RLU/PC) may be slightly more sensitive than and equally specific test as HC2 (≥1.0 RLU/PC) for the detection of CIN3+ over the duration of typical screening intervals.
Epidemiology and Molecular Characterization of
Clostridium difficile
Strains from Patients with Diarrhea: Low Disease Incidence and Evidence of Limited Cross-Infection in a Swedish Teaching Hospital
Authors: Svenungsson Bo , Burman Lars G. , Jalakas-Pörnull Kirsti , Lagergren Åsa , Struwe Johan , Åkerlund Thomas 
Published: September 2003

ABSTRACT

We prospectively studied the epidemiology of
Clostridium difficile-
associated diarrhea (CDAD) in a 900-bed hospital over the course of 12 months by PCR-ribotyping of
C. difficile
isolates. A total of 304 cases were diagnosed, corresponding to an overall incidence of 7/1,000 admissions, with higher rates in nephrology, hematology, and organ transplantation wards (37, 30, and 21/1,000), and 72% were classified as hospital associated (onset in hospital or onset at home but after a hospital stay within 2 months). All 382 isolates from 227 of 304 (75%) patients available for PCR-ribotyping were typeable, yielding 70 PCR-ribotypes. The three most common types comprised 30% of hospital-associated and 34% of community-associated cases, indicating import via admitted patients as a major source of
C. difficile
strains occurring in the hospital. Of the 227 patients studied, 38% each contributed 2 to 13 fecal samples positive for
C. difficile
over the course of the study period. Repeat isolates of the same PCR-ribotype as the first isolate were found in 79% of these patients and in 95% of specimens delivered within 30 days, compared to 63% of those obtained at 31 to 204 days. Nosocomial acquisition of CDAD, defined as the proportion of cases sharing
C. difficile
type and admitted to the same ward within 2 or 12 months, was 20% and 32% of hospital-associated cases and 14% and 23% of all cases, respectively. Thus, most CDAD cases diagnosed over the course of the study period, including those associated with hospitalization, appeared to be caused by endogenous
C. difficile
strains rather than by strains truly being acquired in the hospital.
Unexpected Decrease with Age of
Helicobacter pylori
Seroprevalence among Swedish Blood Donors
Authors: Sörberg M. , Nyrén O. , Granström M. 
Published: September 2003

ABSTRACT

Blood donors are often used as proxies for the general population in studies of
Helicobacter pylori
epidemiology. Our aim was to test if the age-specific seroprevalence rates among blood donors match with the corresponding rates in a random population sample. This descriptive study was based on sera obtained from 3,502 blood donors representing all Swedish counties and cities. An age-stratified random population sample of 1,030 from Stockholm County served as comparison. Sera were analyzed by an in-house enzyme-linked immunosorbent assay for
H. pylori
immunoglobulin G antibodies. In the population sample, we found the expected increase with age in the seroprevalence of
H. pylori
infection. This was true also among young blood donors, while the prevalence-by-age curve showed a deflection downward among blood donors who are ≥ 50 years of age. In this age group, the probability of being seropositive was reduced by 73% (95% confidence interval [CI], 63 to 81%) relative to the population sample. Overall, the adjusted odds ratio for
H. pylori
seropositivity among blood donors was decreased by 43% (95% CI, 28 to 55%). Thus, it appears that blood donors who are
H. pylori
seropositive selectively disappear from the blood donor cohort. We speculate that
H. pylori
-seropositive blood donors may tolerate repeated bleedings less well than do noninfected individuals and/or that the general well-being among those who are infected may be somewhat impaired. Our unexpected observation indicates that blood donors may be less suitable as proxies for the general population in analytic studies of
H. pylori
infection and that the underlying cause needs further study.
Biofilm Formation by Group A Streptococci: Is There a Relationship with Treatment Failure?
Authors: Conley Joslyn , Olson Merle E. , Cook Linda S. , Ceri Howard , Phan Van , Davies H. Dele 
Published: September 2003

ABSTRACT
Group A streptococcus (GAS) is the primary cause of bacterial pharyngitis in children and adults. Up to one-third of patients treated for GAS pharyngitis fail to respond to antibiotic therapy. The objective of this cohort study was to evaluate GAS biofilm formation as a mechanism for antibiotic treatment failure using previously collected GAS isolates and penicillin treatment outcome data. The minimum biofilm eradication concentration (MBEC) assay device was used to determine the biofilm-forming capabilities, efficiencies, and antibiotic susceptibilities of GAS isolates. The MBECs and MICs of several antibiotics for GAS were determined. All 99 GAS isolates available for this study formed biofilms, with various efficiencies. Antibiotic MBECs were consistently higher than MICs for all of the GAS isolates. MBECs indicated penicillin insensitivity in 60% of GAS isolates, producing the first report of in vitro GAS insensitivity to penicillin. Using MBECs to predict penicillin treatment failure had better sensitivity (56%) but lower specificity (36%) than the sensitivity (0%) and specificity (100%) when MICs were used. However, the positive predictive value of the MBEC was superior to that of the MIC (56 versus 0%), while the negative predictive values (42 and 47%) were similar. More studies are needed to understand the roles of biofilms and the MBEC assay in predicting GAS treatment failure. In addition, further investigations are necessary to determine if non-biofilm-forming strains of GAS exist and the roles of in vivo monospecies and multispecies biofilms in streptococcal pharyngitis treatment failure.
Importance of Methodology in Determination of
Chlamydia pneumoniae
Seropositivity in Healthy Subjects and in Patients with Coronary Atherosclerosis
Authors: Hoymans V. Y. , Bosmans J. M. , Van Renterghem L. , Mak R. , Ursi D. , Wuyts F. , Vrints C. J. , Ieven M. 
Published: September 2003

ABSTRACT

Enzyme immunoassays (EIAs) for the detection of
Chlamydia pneumoniae
antibodies were compared to the microimmunofluorescence (MIF) test, the reference method. Furthermore, we assessed the hypothesis that a possible relationship between
Chlamydia pneumoniae
immunoglobulin G (IgG) antibodies and coronary artery disease is dependent on the type of EIA. Sera from 112 healthy men (mean age, 50.1 years) were tested for antibodies against
Chlamydia pneumoniae
by five commercial test kits: Focus Chlamydia MIF IgG test, Labsystems
Chlamydia pneumoniae
IgG EIA (LS EIA), R-Biopharm Elegance
Chlamydia pneumoniae
IgG EIA (RB EIA), Medac
Chlamydia pneumoniae
IgG sandwich enzyme-linked immunosorbent assay ELISA (MCp sELISA) and Medac Chlamydia IgG recombinant enzyme-linked immunosorbent assay ELISA (MC rELISA). Sera from 106 consecutive male patients (mean age, 63.6 years) undergoing diagnostic coronary angiography were also examined using the Focus MIF, LS EIA, MCp sELISA, and MC rELISA techniques. The agreement between LS EIA (65 to 83% [controls-patients]) or MC rELISA (49 to 61%) and Focus MIF (78 to 83%) was average to fair (κ = 0.597 and 0.234, respectively). MCp sELISA and RB EIA showed good agreement with MIF (κ = 0.686 and 0.665, respectively), with 80 to 89 and 79% of individuals reacting positively. A significant difference in seroprevalence between patients and healthy subjects was observed with the LS EIA, while seropositivities in the two study groups appeared equal when the Focus MIF assay was applied. The MC rELISA and MCp sELISA gave statistically significant differences in antibody seroprevalence in patients with two-vessel disease or when the patient group combined individuals with a two- or a three-vessel disease, respectively. The concordance between MIF and other commonly used serological assays for
C. pneumoniae
IgG antibody detection is good to fair. The choice of serological assay has important implications for
C. pneumoniae
antibody seroprevalence, as well as for the relationship between
C. pneumoniae
seropositivity and coronary artery disease.
Characterization of a Herpesvirus Associated with Tracheitis in Gouldian Finches (
Erythrura
[
Chloebia
]
gouldiae
)
Authors: Wellehan James F. X. , Gagea Mihai , Smith Dale A. , Taylor W. Michael , Berhane Yohannes , Bienzle Dorothee 
Published: September 2003

ABSTRACT

Severe tracheitis and bronchitis were identified in two fatal cases of respiratory disease affecting a flock of Gouldian finches (
Erythrura
[
Chloebia
]
gouldiae
). Intranuclear inclusion bodies in epithelial cells of the upper respiratory tract were identified in samples from two birds. Electron microscopic examination showed that the inclusions consisted of viral particles consistent in appearance with
Herpesviridae
. Degenerate PCR primers targeting a conserved region of the herpesviral-DNA-dependent DNA polymerase were used to amplify a region of DNA isolated from tissues with lesions from each animal. Nucleotide sequencing of the PCR products yielded identical viral sequences that were distinct from known herpesviruses. An analysis of sequence homology indicated that these gene segments appear to belong to a member of the subfamily
Alphaherpesvirinae
.
Clonal Complexes of
Campylobacter jejuni
Identified by Multilocus Sequence Typing Correlate with Strain Associations Identified by Multilocus Enzyme Electrophoresis
Authors: Sails Andrew D. , Swaminathan Bala , Fields Patricia I. 
Published: September 2003

ABSTRACT

Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) with
Sma
I were used to subtype 55 isolates of
Campylobacter jejuni
from a diverse range of human and animal sources previously characterized by multilocus enzyme electrophoresis (MEE). MEE and MLST targeted 11 and 7 loci, respectively, and all loci were unique to each method. MEE, MLST, and PFGE identified 40, 37, and 48 discrete subtypes, respectively, with many of the subtypes occurring only once within the data set. Simpson's indices of diversity were calculated to be 0.979, 0.966, and 0.994 for MEE, MLST, and PFGE, respectively, demonstrating that MEE and MLST had similar discriminatory powers but that PFGE was more discriminatory. Allele diversity was higher in the MLST loci; individual single-locus diversities for the 11 MEE loci and the 7 MLST loci were 0.491 and 0.854, respectively. The clonal complexes recognized by MLST correlated with the strain associations previously recognized by MEE and contained some isolates indistinguishable by PFGE. Many clusters contained isolates from diverse geographical regions and from both humans and animals. These results demonstrate the usefulness of MLST for investigation of the global epidemiology of this important pathogen and illustrate its potential to identify indistinguishable strains or clones in geographically distinct regions.
Smallpox: Residual Antibody after Vaccination
Authors: Gallwitz Stephanie , Schutzbank Ted , Heberling Richard L. , Kalter S. S. , Galpin Jeffrey E. 
Published: September 2003

ABSTRACT

Of all the microorganisms and toxins, poxviruses (
Orthopoxvirus
) have the greatest potential for use by terrorists. These viruses can spread rapidly through the environment following initial infection. In 1980, the World Health Organization Eradication Program discontinued vaccination for smallpox and declared that the disease had been eliminated. With the threat of smallpox virus as a bioterrorism weapon, questions have been asked about the persistence of protection (as offered by antibodies) following vaccination with vaccinia virus vaccine. To address this, sera from 204 adults vaccinated as children were tested by enzyme immunoassay (EIA) for the presence of vaccinia virus antibody. Of the 204 individuals whose sera were examined for the presence of vaccinia antibody, 165 (80.9%) had been vaccinated once and 39 (19.1%) had been vaccinated at least twice. Of the 165 sera from individuals vaccinated once, 112 (67.9%) were positive. Of the 39 sera from individuals vaccinated more than once, 31 (79.5%) were positive. The presence of a vaccination scar at the time of blood collection was not determined. Fifty-six nonvaccinated individuals, under 30 years of age, were tested by EIA; four of these (7.1%) were positive for vaccinia virus antibody by EIA. Forty-four EIA-positive and 16 EIA-negative sera were also tested by serum neutralization (SN) as a comparison with the EIA test results; one serum (negative by EIA) was SN positive. No attempt was made to ascertain any demographics other than age (date of birth) and “remembered” times of vaccination.
Microarray-BasedIdentification of Thermophilic
Campylobacter jejuni
,
C.coli
,
C. lari
, and
C.upsaliensis
Authors: Volokhov Dmitriy , Chizhikov Vladimir , Chumakov Konstantin , Rasooly Avraham 
Published: September 2003

ABSTRACT

DNA
microarrays are an excellent potential tool for clinical microbiology,
since this technology allows relatively rapid identification and
characterization of microbial and viral pathogens. In the present
study, an oligonucleotide microarray was developed and used for the
analysis of thermophilic
Campylobacter
spp., the primary
food-borne pathogen in the United States. We analyzed four
Campylobacter
species:
Campylobacter jejuni
,
C.
coli
,
C. lari
, and
C. upsaliensis.
Our assay
relies on the PCR amplification of specific regions in five target
genes (
fur
,
glyA
,
cdtABC
,
ceuB-C
,
and
fliY
) as a first step, followed by microarray-based
analysis of amplified DNAs. Alleles of two genes,
fur
and
glyA
, which are found in all tested thermophilic
Campylobacter
spp., were used for identification and
discrimination among four bacterial species, the
ceuB-C
gene
was used for discrimination between
C. jejuni
and
C.
coli
, and the
fliY
and
cdt
genes were used as
additional genetic markers specific either for
C. upsaliensis
and
C. lari
or for
C. jejuni.
The array was developed
and validated by using 51 previously characterized
Campylobacter
isolates. All isolates were unambiguously
identified on the basis of hybridization patterns with 72 individual
species-specific oligoprobes. Microarray identification of
C.
jejuni
and
C. coli
was confirmed by PCR amplification of
other genes used for identification (
hipO
and
ask
).
Our results demonstrate that oligonucleotide microarrays are suitable
for rapid and accurate simultaneous differentiation among
C.
jejuni
,
C. coli
,
C. lari
, and
C.
upsaliensis
.
Detection of Infectious Human Immunodeficiency Virus Type 1 in Female Genital Secretions by a Short-Term Culture Method
Authors: Cummins James E. , Villanueva Julie M. , Evans-Strickfaden Tammy , Sesay Shekou M. , Abner Sheila R. , Bush Timothy J. , Green Timothy A. , Lennox Jeffrey L. , Wright Thomas , Folks Thomas M. , Hart Clyde E. , Dezzutti Charlene S. 
Published: September 2003

ABSTRACT

Infectious human immunodeficiency virus type 1 (HIV-1) is difficult to detect in female genital secretions by standard virus culture techniques. To improve detection of cell-free HIV-1 in female genital secretions, we adapted a short-term assay that uses the multinuclear-activation galactosidase indicator (MAGI) assay. When vaginal lavages from HIV-1-infected women were tested with the adapted MAGI assay, 25 (64%) of 39 lavages with detectable, cell-free HIV-1 RNA were shown to have infectious virus. No infectious virus was found in 10 vaginal lavages from HIV-1-infected women with undetectable vaginal viral loads. Significantly (
P
< 0.01) more lavages from HIV-1-infected women tested positive for infectious virus by the MAGI assay than by standard peripheral blood mononuclear cell (PBMC) coculture, which detected infectious virus in only 6 (17%) of 35 vaginal lavages. Lavages with viral loads of >10,000 copies per lavage yielded significantly (
P
< 0.01) more positive cultures than those with <10,000 copies by using the MAGI assay. Detection of infectious HIV-1 in vaginal lavages was not associated with the presence of genital tract infections or CD4
+
-T-cell counts. However, although the results were not significant (
P
= 0.08), the MAGI assay detected infectious virus from more vaginal lavages at a vaginal pH of ≥4.5 than at a pH of <4.5. These results indicate that the MAGI assay is more sensitive than PBMC culture methods for detecting infectious virus in female genital secretions. Accurate measurements of infectious virus in genital secretions will improve studies that evaluate sexual transmission of HIV-1.
Multiplex PCR Assay for Simultaneous Detection of Nine Clinically Relevant Antibiotic Resistance Genes inStaphylococcus aureus
Authors: Strommenger Birgit , Kettlitz Christiane , Werner Guido , Witte Wolfgang 
Published: September 2003

ABSTRACTIn this study we describe a multiplex PCR assay for the detection of nine clinically relevant antibiotic resistance genes ofStaphylococcus aureus.Conditions were optimized to amplify fragments ofmecA(encoding methicillin resistance),aacA-aphD(aminoglycoside resistance),tetK,tetM(tetracycline resistance),erm(A),erm(C) (macrolide-lincosamide-streptogramin B resistance),vat(A),vat(B), andvat(C) (streptogramin A resistance) simultaneously in one PCR amplification. An additional primer pair for the amplification of a fragment of the staphylococcal 16S rDNA was included as a positive control. The multiplex PCR assay was evaluated on 30 differentS. aureusisolates, and the PCR results correlated with the phenotypic antibiotic resistance data obtained by the broth microdilution assay. The multiplex PCR assay offers a rapid, simple, and accurate identification of antibiotic resistance profiles and could be used in clinical diagnosis as well as for the surveillance of the spread of antibiotic resistance determinants in epidemiological studies.
Evaluation of a Multiplex PCR Test for Simultaneous Identification and Serotyping of
Actinobacillus pleuropneumoniae
Serotypes 2, 5, and 6
Authors: Jessing Stine G. , Angen Øystein , Inzana Tomas J. 
Published: September 2003

ABSTRACT

Serotype-specific DNA regions involved in the biosynthesis of capsular polysaccharides (
cps
region) were used to develop a multiplex PCR test for the simultaneous species identification and serotyping of
Actinobacillus pleuropneumoniae
serotypes 2, 5, and 6. Primers specific for serotypes 2, 5, and 6 were combined with the already existing species-specific primers used in a PCR test based on the
omlA
gene. The PCR test was evaluated with serotype reference strains of
A. pleuropneumoniae
as well as 182 Danish field isolates previously serotyped by latex agglutination or immunodiffusion. For all serologically typeable strains, a complete correspondence was found between the results obtained by the multiplex PCR test and the results obtained by the traditional serotyping methods. Six of eight serologically nontypeable strains could be allocated to a serotype on the basis of the multiplex PCR results. The species specificity of the assay was evaluated with a collection of 93 strains representing 29 different species within the family
Pasteurellaceae
, as well as species normally found in the respiratory tracts of swine. All of these strains were negative by the multiplex PCR test, including 50 field isolates of the phylogenetically closely related species
Actinobacillus lignieresii
. When the multiplex PCR test was used to test Danish field strains, it was able to identify the serotypes of approximately 94% of all strains isolated from swine with clinical disease. More than 90% of the isolates that cross-reacted by the latex agglutination test were of serotype 2, 5, or 6. Determination of the serotype by PCR represents a convenient and specific method for the serotyping of
A. pleuropneumoniae
in diagnostic laboratories.