bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and Epidemiological Analyses of Human Adenovirus Type 7 Strains Isolated from the 1995 Nationwide Outbreak in Japan
Authors: Noda Mamoru , Yoshida Tetsuya , Sakaguchi Takemasa , Ikeda Yoshifumi , Yamaoka Koji , Ogino Takeo 
Published: July 2002

ABSTRACT

The adenovirus type 7 (Ad7) isolates from the 1995 nationwide outbreak in Japan were genetically and seroepidemiologically analyzed in comparison with Japanese Ad7 strains isolated before 1995 to determine their genome type and to speculate on their origin and causative factors of the outbreak. Twenty-six Ad7 isolates from the outbreak were identified by restriction enzyme analysis as the Ad7d2 genome type, while 22 Ad7 strains sporadically isolated in Japan before 1995 were identified as Ad7d. Partial nucleotide sequencing of the E3 region of Ad7d2 revealed a nucleotide substitution of G to A at position 265, resulting in the absence of the
Bst
EII site and making Ad7d2 distinct from Ad7d. In Hiroshima City, Japan, no Ad7 was isolated from 1982 to 1994, but 43 and 50 Ad7 strains were isolated in 1995 and 1996, respectively. A seroepidemiological study of 251 serum samples collected in 1989 in Hiroshima City showed that only 2.8% of the samples were positive for Ad7. These results indicate that the 1995 outbreak of Ad7 in Japan was caused by the Ad7d2 genome type, which might have been introduced from outside Japan. The results also suggest that the low mass immunity in Japan was critical for the outbreak and that the mutation in the E3 region in Ad7d2 may have influenced transmission.
Importance of Local Variations in Antibiotic Consumption and Geographical Differences of Erythromycin and Penicillin Resistance in
Streptococcus pneumoniae
Authors: García-Rey César , Aguilar Lorenzo , Baquero Fernando , Casal Julio , Dal-Ré Rafael 
Published: July 2002

ABSTRACT

A geographical analysis of how commonly prescribed oral antibiotics are quantitatively and qualitatively responsible for the different local rates of erythromycin and penicillin resistance in
Streptococcus pneumoniae
in Spain is presented. From 1998 to 1999 a multicenter surveillance study yielded 1,684 consecutive
S. pneumoniae
isolates from community-acquired respiratory infections. Data on antibiotic sales in the retail market for the same period were gathered, and the corresponding defined doses per 1,000 inhabitants per day were calculated. Macrolides and β-lactams were considered separately. Macrolides were subdivided into thrice-, twice-, and once-a-day macrolides, and β-lactams were split into aminopenicillins and cephalosporins. Univariate Spearman nonparametric coefficients (
R
) were calculated, and variables proving to be significantly associated (
P
< 0.1) were entered into several multiple lineal regression models. Ample variation in both resistance rates and antibiotic consumption was seen. Multivariate analyses showed that integrated consumption of both macrolides and β-lactams accounted well for erythromycin (
R
2
= 0.722;
P
= 0.002) and penicillin (
R
2
= 0.706;
P
= 0.002) resistance. Macrolides were more important drivers for local differences in both erythromycin and penicillin resistance than β-lactams were. Consumption of once-a-day macrolides was key for local erythromycin resistance variations. Cephalosporins were slightly more important penicillin resistance drivers than aminopenicillins were.
Identification by 16S rRNA Gene Sequencing of
Lactobacillus salivarius
Bacteremic Cholecystitis
Authors: Woo Patrick C. Y. , Fung Ami M. Y. , Lau Susanna K. P. , Yuen Kwok-Yung 
Published: July 2002

ABSTRACT

An anaerobic, nonsporulating, gram-positive bacterium was isolated from blood and bile pus cultures of a 70-year-old man with bacteremic acute cholecystitis. The API 20A system showed that it was 70%
Actinomyces naeslundii
and 30%
Bifidobacterium
species, whereas the Vitek ANI system and the ATB ID32A Expression system showed that it was “unidentified.” The 16S rRNA gene of the strain was amplified and sequenced. There were 3 base differences between the nucleotide sequence of the isolate and that of
Lactobacillus salivarius
subsp.
salivarius
or
L. salivarius
subsp.
salicinius
, indicating that the isolate was a strain of
L. salivarius
. The patient responded to cholecystectomy and a 2-week course of antibiotic treatment. Identification of the organism in the present study was important because the duration of antibiotic therapy would have been entirely different depending on the organism. If the bacterium had been identified as
Actinomyces
, penicillin for 6 months would have been the regimen of choice. However, it was
Lactobacillus
, and a 2-week course of antibiotic was sufficient.
Modeling of 5′ Nuclease Real-Time Responses for Optimization of a High-Throughput Enrichment PCR Procedure for
Salmonella enterica
Authors: Knutsson Rickard , Löfström Charlotta , Grage Halfdan , Hoorfar Jeffrey , Rådström Peter 
Published: July 2002

ABSTRACT

The performance of a 5′ nuclease real-time PCR assay was studied to optimize an automated method of detection of preenriched
Salmonella enterica
cells in buffered peptone water (BPW). The concentrations and interactions of the PCR reagents were evaluated on the basis of two detection responses, the threshold cycle (
C

T

) and the fluorescence intensity by a normalized reporter value (Δ
R

n

). The
C

T

response was identified as the most suitable for detection modeling to describe the PCR performances of different samples. DNA extracted from
S. enterica
serovar Enteritidis was studied in double-distilled H
2
O (ddH
2
O) and in two different enrichment media (brain heart infusion and BPW) with two PCR mixtures based on Ampli
Taq
Gold or r
Tth
. A descriptive model was proposed and fitted to the available experimental data. Equivalent PCR performances for the two PCR mixtures were obtained when DNA was diluted in ddH
2
O. However, the level of detection of DNA was affected when BPW was present during amplification. Use of the r
Tth
mixture generated a 1-log-unit wider linear range of amplification, and the DNA detection levels were 2 × 10
−13
g/microwell for the r
Tth
mixture and 2 × 10
−12
g/microwell for the Ampli
Taq
Gold mixture. To verify the improved amplification capacity of the r
Tth
mixture, BPW was inoculated with 1 CFU of
S. enterica
serovar Enteritidis per ml and the mixture was incubated at 30°C. Samples for PCR were withdrawn every 4 h during a 36-h enrichment. Use of the r
Tth
mixture resulted in an earlier PCR detection during enrichment than use of the Ampli
Taq
Gold mixture. For accurate detection (
C

T

≤ 30) of
S. enterica
serovar Enteritidis inoculated in BPW, the r
Tth
mixture required 8.4 h of enrichment, while the Ampli
Taq
Gold mixture needed 11.6 h. In conclusion, the principle applied can improve the methodology of 5′ nuclease real-time PCR for numerical optimization of sample pretreatment strategies to provide automated diagnostic PCR procedures.
Development and Validation of a PCR-Based Enzyme-Linked Immunosorbent Assay with Urine for Use in Clinical Research Settings To Detect
Trichomonas vaginalis
in Women
Authors: Kaydos S. Cornelia , Swygard Heidi , Wise Shelly L. , Sena Arlene C. , Leone Peter A. , Miller William C. , Cohen Myron S. , Hobbs Marcia M. 
Published: July 2002

ABSTRACT

Trichomonas vaginalis
infection is highly prevalent worldwide and is associated with poor birth outcomes and enhanced human immunodeficiency virus transmission. Traditional detection methods rely on microscopic examination of vaginal specimens (wet mount) and culture, which can be insensitive and time-consuming. More than 3,000 women attending two sexually transmitted disease clinics were enrolled in this cross-sectional study to evaluate urine-based PCR for detection of
T. vaginalis
using a combined reference standard of wet mount and culture from vaginal swab. The prevalence of trichomoniasis in the population was 16.7% (502 of 3,009 women) using the reference standard. PCR with urine combined with agarose gel-based detection was 66.9% sensitive and 98.3% specific compared to the reference standard. Detection of PCR products using an unlabeled enzyme-linked immunosorbent assay (ELISA) improved the sensitivity to 86.4%, but specificity fell to 86.1%. Using a digoxigenin-labeled ELISA for detection of amplified
T. vaginalis
DNA from urine, the sensitivity and specificity of the PCR improved to 90.8 and 93.4%, respectively, compared to wet mount or culture from vaginal swabs. For clinical research settings in which vaginal specimens are not available and culture conditions are not feasible, urine-based PCR-ELISA may be useful for the detection of trichomoniasis in women.
Experimental Infection of Domestic Cats withBartonella koehleraeand Comparison of Protein and DNA Profiles with Those of OtherBartonellaSpecies Infecting Felines
Authors: Yamamoto Kazuhiro , Chomel Bruno B. , Kasten Rickie W. , Hew Carrie M. , Weber David K. , Lee Wilson I. , Droz Sara , Koehler Jane E. 
Published: July 2002

ABSTRACTBartonella koehlerae, a recently described felineBartonellaspecies, was isolated from two naturally infected cats in northern California. We experimentally infected domestic cats withB. koehleraeto establish the microbiological and immunological characteristics of this infection in cats and to compare it to infections with those caused byB. henselaeandB. clarridgeiae. Four cats were inoculated intradermally withB. koehlerae(8.6 × 107to 3.84 × 108CFU/ml). None of the cats presented any obvious clinical signs, but all cats developed bacteremia, which peaked at 3.36 × 104to 1.44 × 106CFU/ml of blood between day 14 and day 36 postinoculation.B. koehlerae-inoculated cats had a bacteremia duration (mean, 74 days) shorter than did cats inoculated withB. clarridgeiae(mean, 324 days) (P= 0.03). None of the four cats inoculated withB. koehleraehad bacteremia relapse. As shown by enzyme-linked immunosorbent assay (ELISA) usingB. koehleraeouter membrane protein (OMP) antigens, the four cats developed a species-specific antibody response, and ELISA testing using other felineBartonellaOMP antigens showed statistically lower optical density values. All four cats developed similar antibody reactivity patterns toB. koehleraeOMP antigens as seen by Western blotting, each with at least 20 seroreactive protein bands. Using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, protein profile differences were observed for both whole-cell lysate and OMPs fromB. koehlerae, compared withB. henselaeandB. clarridgeiae. B. koehleraewas more closely related toB. henselaethan toB. clarridgeiaeby protein profile, and this relatedness was also confirmed by analysis of the genomic DNA profiles by pulsed-field gel electrophoresis.
Community-Acquired Bacteremic
Acinetobacter
Pneumonia in Tropical Australia Is Caused by Diverse Strains of
Acinetobacter baumannii
, with Carriage in the Throat in At-Risk Groups
Authors: Anstey Nicholas M. , Currie Bart J. , Hassell Marilyn , Palmer Didier , Dwyer Brian , Seifert Harald 
Published: July 2002

ABSTRACT

Acinetobacter
isolates from eight subjects with community-acquired
Acinetobacter
pneumonia (CAAP), a major cause of fatal community-acquired pneumonia in tropical Australia, were phenotypically and genotypically confirmed by pulsed-field gel electrophoresis analysis to be broadly diverse
Acinetobacter baumannii
strains. Wet-season throat carriage of
A. baumannii
was found in 10% of community residents with excess levels of alcohol consumption, the major at-risk group for CAAP.
Immune Responses to the
Mycobacterium tuberculosis
-Specific Antigen ESAT-6 Signal Subclinical Infection among Contacts of Tuberculosis Patients
Authors: Doherty T. Mark , Demissie Abebech , Olobo Joseph , Wolday Dawit , Britton Sven , Eguale Tewodros , Ravn Pernille , Andersen Peter 
Published: July 2002

ABSTRACT

Diagnosis of latent
Mycobacterium tuberculosis
infection is considered essential for tuberculosis control but is hampered by the lack of specific reagents. We report that strong recognition of tuberculosis complex-specific antigen ESAT-6 by healthy household contacts of tuberculosis patients correlates with the subsequent development of active tuberculosis during a 2-year follow-up period.
PCR Detection and Serological Evidence of Granulocytic Ehrlichial Infection in Roe Deer (
Capreolus capreolus
) and Chamois (
Rupicapra rupicapra
)
Authors: Liz Jorge S. , Sumner John W. , Pfister Kurt , Brossard Michel 
Published: July 2002

ABSTRACT

The role of wild mammals, such as roe deer (
Capreolus capreolus
) and chamois (
Rupicapra rupicapra
), in the epidemiology of granulocytic ehrlichiae in Switzerland was investigated. We tested blood samples for
Ehrlichia phagocytophila
genogroup 16S rRNA gene sequences by PCR and for immunoglobulin G antibodies against granulocytic ehrlichiae by indirect fluorescent-antibody assay (IFA). Overall means of 60.9% of 133 roe deer serum samples and 28.2% of 39 chamois serum samples were seroreactive by IFA. PCR results were positive for 18.4% of 103 roe deer serum samples as well. None of the 24 chamois blood samples tested were positive by PCR. Partial 16S rRNA gene and
groESL
heat shock operon sequences of three roe deer samples tested showed strong degrees of homology (≥99.7 and ≥98.6%, respectively) with the sequences of granulocytic ehrlichiae isolated from humans. These results confirm that chamois, and particularly roe deer, are commonly infected with granulocytic ehrlichiae and provide evidence that these wild mammals are potential reservoirs for granulocytic ehrlichiae in Switzerland.
Reactivity of Convalescent-Phase Hemolytic-Uremic Syndrome Patient Sera with the Megaplasmid-Encoded TagA Protein of Shiga Toxigenic
Escherichia coli
O157
Authors: Paton Adrienne W. , Paton James C. 
Published: July 2002

ABSTRACT

A cosmid library of Shiga toxigenic
Escherichia coli
(STEC) O157:H7 strain EDL933 DNA was screened for clones capable of reacting with convalescent-phase serum from a patient with hemolytic-uremic syndrome (HUS), in an attempt to identify candidate virulence genes. One of the immunoreactive clones contained a portion of the large plasmid pO157, and the immunoreactive gene product was identified as TagA. The function of this 898-amino-acid protein is unknown, but it exhibits 42% amino acid sequence identity and 63% similarity to a 312-amino-acid region of a ToxR-regulated lipoprotein of
Vibrio cholerae
. Antibodies to
E. coli
O157 TagA were detected in sera from other HUS patients with O157 STEC infection but not in those from patients whose illnesses were caused by other STEC types or in healthy controls. These data demonstrate that TagA is expressed in vivo and provide circumstantial evidence for a role in the pathogenesis of the disease. The
tagA
gene is present only in STEC strains belonging to serogroup O157, and so antibodies to TagA are a potentially useful serological marker for infections due to such strains.
Identification of Two Phylogenetically Related Organisms from Feces by PCR for Detection ofSalmonellaspp
Authors: Gentry-Weeks Claudia , Hutcheson H. Joel , Kim Lisa Marie , Bolte Denise , Traub-Dargatz Josie , Morley Paul , Powers Barbara , Jessen Michael 
Published: July 2002

ABSTRACTTwo previously reported PCR methods were evaluated to determine whether they are as sensitive and specific as conventional culture methods in detectingSalmonellaspp. from feces. Bovine and equine feces were enriched overnight in brain heart infusion broth and assayed using PCR methods and primer sets described by other investigators. A total of 774 fecal specimens were tested using a primer set (invE-Aprimer set) that amplifies a region spanning the invasin E and A genes ofSalmonella entericaserovar Typhimurium. A subset of these fecal specimens (306 of the 774 total) were tested using primers (hisJprimer set) that amplify a portion of the histidine transport J gene. The PCR required 24 h to obtain results, whereas it took 5 to 7 days to identifySalmonellaspp. by culture. PCR detection ofSalmonellaspp. using thehisJprimers and theinvE-Aprimers had a sensitivity of 93.3 and 80%, respectively, and a specificity of 85.6 and 98.6%, respectively, compared with bacterial culture. Amplification of 42 culture-negative fecal specimens (of 306 total specimens) generated a DNA fragment that corresponded to the molecular weight of the amplifiedhisJgene. ThehisJ-generated amplicons from six culture-negative and six culture-positive specimens were sequenced and analyzed using DNA sequence alignment and phylogenetic analysis software. A neighbor-joining dendrogram of the DNA sequences of both sets ofhisJamplicons revealed two distinct groups—one group of amplicons from culture-positive specimens identical to thehisJgene ofS. entericaserovar Typhimurium and a second group of amplicons from culture-negative specimens that were more closely related tohisJofS. entericaserovar Typhimurium than to otherhisJsequences present in nucleotide databases.
Performance of Four Chromogenic Urine Culture Media after One or Two Days of Incubation Compared with Reference Media
Authors: Aspevall Olle , Osterman Björn , Dittmer Rakel , Stén Lena , Lindbäck Emma , Forsum Urban 
Published: July 2002

ABSTRACT
Four chromogenic urine culture media were compared to culture on blood agar, MacConkey agar, and CLED (cysteine-, lactose-, and electrolyte-deficient) agar for detection of uropathogens in 1,200 urine specimens. After 2 nights of incubation, 96% of all isolates were recovered on blood agar, 96% were recovered on CLED agar, 92% were recovered on CPS ID2, 96% were recovered on CHROMagar Orientation from BBL, 95% were recovered on CHROMagar Orientation from The CHROMagar Company, and 95% were recovered on Chromogenic UTI Medium.
Probable Mother-to-Infant Transmission of
Pneumocystis carinii
f. sp.
hominis
Infection
Authors: Miller Robert F. , Ambrose Helen E. , Novelli Vas , Wakefield Ann E. 
Published: July 2002

ABSTRACT

A mother and her 4.5-week-old infant had
Pneumocystis carinii
pneumonia contemporaneously. Genotyping of
P. carinii
f. sp.
hominis
DNA at three independent loci showed the same genotype in samples from mother and infant. These data suggest transmission of
P. carinii
organisms from the mother to her infant.
Detection of Ethambutol-Resistant
Mycobacterium tuberculosis
Strains by Multiplex Allele-Specific PCR Assay Targeting
embB306
Mutations
Authors: Mokrousov Igor , Narvskaya Olga , Limeschenko Elena , Otten Tatiana , Vyshnevskiy Boris 
Published: July 2002

ABSTRACT

We describe a multiplex allele-specific (MAS)-PCR assay to detect simultaneously mutations in the first and third bases of the
embB
gene codon 306ATG. These mutations are known to confer ethambutol (EMB) resistance in the majority of clinical
Mycobacterium tuberculosis
isolates worldwide. The mutated bases are revealed depending on the presence or absence of the respective indicative fragments amplified from the
embB
306 wild-type allele. Initially optimized on purified DNA samples, the assay was tested on crude cell lysates and auramine-stained sputum slide DNA preparations with the same reproducibility and interpretability of the generated profiles in agarose gel electrophoresis. Since EMB resistance is generally linked to multiple-drug resistance (MDR), the MAS-PCR assay for EMB resistance detection can be used in clinical laboratory practice in areas with a high prevalence and a high transmission rate of MDR-EMB-resistant tuberculosis.
Calculation of the Stability of the IS
6110
Banding Pattern in Patients with Persistent
Mycobacterium tuberculosis
Disease
Authors: Warren R. M. , van der Spuy G. D. , Richardson M. , Beyers N. , Borgdorff M. W. , Behr M. A. , van Helden P. D. 
Published: July 2002

ABSTRACT

The interpretation of molecular epidemiologic data of
Mycobacterium tuberculosis
infection is dependent on the understanding of the stability and evolutionary characteristics of the DNA fingerprinting marker used to classify clinical isolates. This study investigated the stability of the IS
6110
banding pattern in serial tuberculosis isolates collected from patients resident in an area with a high incidence of tuberculosis. Evolutionary changes were observed in 4% of the strains, and a half-life (
t
1/2
) of 8.74 years was calculated, assuming a constant rate of change over time. This rate may be composed of a high rate of change seen during the early disease phase (
t
1/2
= 0.57 years) and a low rate of change seen in the late disease phase (
t
1/2
= 10.69 years). The early rate probably reflects change occurring during active growth prior to therapy, while the low late rate may reflect change occurring during or after treatment. We demonstrate that the calculation of these rates is strongly influenced by the time interval between onset of disease and sputum sampling. These calculations are further complicated by partial replacement of the original strain population, resulting in the sporadic appearance of clonal variants in sputum specimens. Therefore, the true extent of genetic diversity may be underestimated within each host, thereby influencing molecular epidemiological data used to establish transmission chains.
Random Amplified Polymorphic DNA and Amplified Fragment Length Polymorphism Analyses ofPasteurella multocidaIsolates from Fatal Fowl Cholera Infections
Authors: Huber Brad S. , Allred Darin V. , Carmen John C. , Frame David D. , Whiting David G. , Cryan Jason R. , Olson Terry R. , Jackson Paul J. , Hill Karen , Laker Miriam T. , Robison Richard A. 
Published: July 2002

ABSTRACTFowl cholera, a disease caused byPasteurella multocida, continues to be a major problem for the poultry industry. The sources of pathogenic organisms responsible for most sporadic epidemics remain unconfirmed, although attenuated vaccines that retain a low level of virulence have occasionally been implicated in outbreaks of the disease. One of the vaccines most commonly used to prevent fowl cholera is the M-9 strain. In the present study, 61 clinical isolates from turkeys that died of fowl cholera from 1997 to 1999 on 36 Utah farms were analyzed and compared to the M-9 vaccine strain. Genetic analyses of the isolates were done by random amplified polymorphic DNA (RAPD) analysis and amplified fragment length polymorphism (AFLP) fingerprinting. The results of these genetic analyses were correlated with the vaccination status of the flock, isolate serotype, and geographic location. Although both genetic techniques effectively identified similar subtle genomic differences, RAPD analysis provided only 77% of the detail provided by AFLP analysis. While a relationship between genetic profile and serotype was evident, no significant relationship indicating geographic influence was found (P= 0.351). Interestingly, organisms isolated from vaccinated flocks were significantly closer genetically to the M-9 vaccine strain than isolates from unvaccinated birds were (P= 0.020). Statistical analyses revealed that this relationship could not have been determined by serotyping alone (P= 0.320), demonstrating the value of AFLP and RAPD analyses in the characterization of disease-causing strains.