bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Two Culture Media and Three Sampling Techniques for Sensitive and Rapid Screening of Vaginal Colonization by Group B Streptococcus in Pregnant Women
Authors: Gupta Chakshu , Briski Laurence Edward 
Published: September 2004

ABSTRACT
The Centers for Disease Control and Prevention (CDC) recommend universal screening of all pregnant women between 35 and 37 weeks of gestation for group B streptococci (GBS) by use of a selective broth medium. Recent reports suggest that Granada medium can be used for rapid and direct visual identification of GBS colonies. However, studies comparing the Granada medium method to the selective broth method are few, and while some report comparable sensitivities, others have found significant differences in detection rates between the two methods. This prospective study compared a method using Granada agar to a Todd-Hewitt broth method with subculture to blood agar in order to determine which GBS detection method is more sensitive and less labor-intensive and has a more rapid turnaround time. Detection rates for three sampling techniques (rectovaginal, vaginal only, and cervical only) were also compared. Consecutive specimens for GBS screening received over a 6-month period from 1,635 pregnant women were included. Overall, GBS was detected in 390 (23.8%) women. The Granada medium gave positive results for 348 of these women, and the selective broth gave positive results for 385, indicating sensitivities of 89.2% for the Granada medium and 98.7% for the selective broth. These findings show that the Granada medium method is less sensitive than the selective broth method and should not replace it as the only method for screening pregnant women for GBS. However, the Granada medium method reduced detection time to 1 day and also reduced the use of ancillary tests in approximately 90% of positive cases. Additionally, no significant differences were noted in the detection rates with rectovaginal, vaginal, and cervical specimens.
Nosocomial Transmission of CTX-M-2 β-Lactamase-Producing
Acinetobacter baumannii
in a Neurosurgery Ward
Authors: Nagano Noriyuki , Nagano Yukiko , Cordevant Christophe , Shibata Naohiro , Arakawa Yoshichika 
Published: September 2004

ABSTRACT

Three strains of cefotaxime (CTX)-resistant
Acinetobacter baumannii
, FM0209680, FM0300106, and FM0301433, were isolated from transtracheal aspirate cultures of three patients with probable nosocomial infections in a neurosurgery ward in Japan. The CTX MICs for these isolates were greater than 128 μg/ml but were drastically reduced in the presence of 4 μg of clavulanic acid per ml. These strains were also resistant to ceftriaxone, cefpodoxime, and aztreonam but were susceptible to ceftazidime and imipenem. The profile of resistance to various broad-spectrum β-lactams was transferred by conjugation. Strain FM0209680 was not eradicated from case patient 1 by administration of imipenem, ceftazidime, and levofloxacin, even after a 6-month hospitalization period. Strains FM0300106 and FM0301433 were isolated from case patients 2 and 3 during the sixth week following admission, respectively, and then each patient was colonized for 3 weeks. Eradication of FM0300106 was successfully obtained from case patient 2 by imipenem treatment, while administration of imipenem was continued to prevent pneumonia. Prophylactic antimicrobial therapy was discontinued in case patient 3 because of the lack of pneumonic symptoms, and FM0301433 disappeared after the discontinuation of antimicrobial chemotherapy. All three strains carried the
bla
CTX-M-2
gene, and the appearance of colonies in the growth-inhibitory zones around disks of CTX and aztreonam in double-disk synergy tests suggested inducible β-lactamase production in these
A. baumannii
strains. The ribotyping investigation suggested that all these strains belong to the same clonal lineage. The plasmids harbored by
A. baumannii
had the same restriction profile as those harbored by
Proteus mirabilis
strains previously isolated in a urology ward of the Funabashi Medical Center.
Use of Culture, PCR Analysis, and DNA Microarrays for Detection of
Campylobacter jejuni
and
Campylobacter coli
from Chicken Feces
Authors: Keramas Georgios , Bang Dang Duong , Lund Marianne , Madsen Mogens , Bunkenborg Henrik , Telleman Pieter , Christensen Claus Bo Vöge 
Published: September 2004

ABSTRACT

A DNA microarray for detection of
Campylobacter
spp. was recently developed and applied to detect
Campylobacter
spp. directly from chicken feces. Sixty-five pooled chicken cloacal swab samples from 650 individual broiler chickens were included in the study. The results of
Campylobacter
sp. detection obtained with DNA microarrays were compared to those obtained by conventional culture and gel electrophoresis. By conventional culture, 60% of the samples were positive for either
Campylobacter jejuni
or
Campylobacter coli
. By PCR and capillary electrophoresis, 95% of the samples were positive for
Campylobacter
spp., whereas with DNA microarrays all samples were positive for
Campylobacter
spp. By application of DNA microarray analysis, the isolates in 4 samples (6%) could not be identified to the species level, whereas by PCR-capillary electrophoresis, the isolates in 12 samples (19%) remained unidentified. Interestingly, PCR-capillary electrophoresis analysis revealed that two (3%) of the samples were positive for both
C. jejuni
and
C. coli
, while DNA microarray analysis revealed that nine (14%) of the samples were positive for both species. Of 65 samples, 2 samples were identified to contain
C. coli
by conventional culture but were positive for
C. jejuni
by both PCR-capillary electrophoresis and DNA microarray analysis. The discrepancy between the methods is discussed.
Enumeration and Isolation ofcpe-PositiveClostridium perfringensSpores from Feces
Authors: Heikinheimo Annamari , Lindström Miia , Korkeala Hannu 
Published: September 2004

ABSTRACTA hydrophobic grid membrane filter-colony hybridization (HGMF-CH) method for the enumeration and isolation ofcpegene-carrying (cpe-positive)Clostridium perfringensspores from feces was developed. A 425-bp DNA probe specific for thecpegene was sensitive and specific when tested with bacterial DNA and pure cultures. The enumeration ofcpe-positiveC. perfringensby the HGMF-CH method proved to be as sensitive as nested PCR combined with the most-probable number technique when tested with fecal samples from healthy individuals. With the aid of the HGMF-CH method, positive hybridization signals were detected from two out of seven fecal samples obtained from healthy individuals. Furthermore,cpe-positiveC. perfringenswas successfully isolated from both of these samples. The detection ofcpe-positiveC. perfringensby the HGMF-CH method is dependent on the ratio ofcpe-positiveC. perfringenscolonies to totalC. perfringenscolonies growing on the HGMF-tryptose-sulfite-cycloserine plate.cpe-positiveC. perfringenscould be isolated if the ratio ofcpe-positiveC. perfringensspores to totalC. perfringensspores was 6 × 10−5or higher. The HGMF-CH method provides an aid in the investigation of fecal samples of patients suffering from food poisoning or other diseases caused bycpe-positiveC. perfringens. The method also offers a new approach in the investigation of the epidemiology ofcpe-positiveC. perfringensstrains.
Epidemiology and Molecular Characterization ofStreptococcus pyogenesRecovered from Scarlet Fever Patients in Central Taiwan from 1996 to 1999
Authors: Chiou Chien-Shun , Liao Tsai-Ling , Wang Tzu-Hui , Chang Hsiu-Li , Liao Jui-Cheng , Li Chun-Chin 
Published: September 2004

ABSTRACTOne hundred seventy-nineStreptococcus pyogenesisolates recovered from scarlet fever patients from 1996 to 1999 in central Taiwan were characterized byemm, Vir, and pulsed-field gel electrophoresis (PFGE) typing methods. The protocols for Vir and PFGE typing were standardized. A database of the DNA fingerprints for the isolates was established. Nineemmoremm-like genes, 19 Vir patterns, and 26 SmaI PFGE patterns were detected among the isolates. Among the three typing methods, PFGE was the most discriminatory. However, it could not completely replace Vir typing because some isolates with identical PFGE patterns could be further differentiated into several Vir patterns. The prevalentemmtypes wereemm4 (n= 81 isolates [45%]),emm12 (n= 64 [36%]),emm1 (n= 14 [8%]), andemm22 (n= 13 [7%]). Someemmtype isolates could be further differentiated into severalemm-Vir-PFGE genotypes; however, only one genotype in eachemmgroup was usually predominant. DNA from nine isolates was resistant to SmaI digestion. Further PFGE analysis with SgrAI showed that the SmaI digestion-resistant strains could be derived from indigenous strains by horizontal transfer of exogenous genetic material. The emergence of the new strains could have resulted in an increase in scarlet fever cases in central Taiwan since 2000. Theemmsequences, Vir, and PFGE pattern database will serve as a basis for information for the long-term evolutionary study of localS. pyogenesstrains.
Phage Types and Genotypes of Shiga Toxin-Producing
Escherichia coli
O157:H7 Isolates from Humans and Animals in Spain: Identification and Characterization of Two Predominating Phage Types (PT2 and PT8)
Authors: Mora Azucena , Blanco Miguel , Blanco Jesús E. , Alonso M. Pilar , Dhabi Ghizlane , Thomson-Carter Fiona , Usera Miguel A. , Bartolomé Rosa , Prats Guillermo , Blanco Jorge 
Published: September 2004

ABSTRACT

Phage
typing and DNA macrorestriction fragment analysis by
pulsed-field electrophoresis (PFGE) were used for the epidemiological
subtyping of a collection of Shiga toxin-producing
Escherichia
coli
(STEC) O157:H7 strains isolated in Spain between 1980 and
1999. Phage typing distinguished a total of 18 phage types among 171
strains isolated from different sources (67 humans, 82 bovines, 12
ovines, and 10 beef products). However, five phage types, phage type 2
(PT2; 42 strains), PT8 (33 strains), PT14 (14 strains), PT21/28 (11
strains), and PT54 (16 strains), accounted for 68% of the study
isolates. PT2 and PT8 were the most frequently found among strains from
both humans (51%) and bovines (46%). Interestingly, we
detected a significant association between PT2 and PT14 and the
presence of acute pathologies. A group of 108 of the 171 strains were
analyzed by PFGE, and 53 distinct XbaI macrorestriction
patterns were identified, with 38 strains exhibiting unique PFGE
patterns. In contrast, phage typing identified 15 different phage
types. A total of 66 phage type-PFGE subtype combinations were
identified among the 108 strains. PFGE subtyping differentiated between
unrelated strains that exhibited the same phage type. The most common
phage type-PFGE pattern combinations were PT2-PFGE type 1 (1 human and
11 bovine strains), PT8-PFGE type 8 (2 human, 6 bovine, and 1 beef
product strains), PT2-PFGE subtype 4A (1 human, 3 bovine, and 1 beef
product strains). Nine (29%) of 31 human strains showed phage
type-PFGE pattern combinations that were detected among the bovine
strains included in this study, and 26 (38%) of 68 bovine
strains produced phage type-PFGE pattern combinations observed among
human strains included in this study, confirming that cattle are a
major reservoir of strains pathogenic for humans. PT2 and PT8 strains
formed two groups which differed from each other in their motilities,
stx
genotypes, PFGE patterns, and the severity of the
illnesses that they
caused.
Identification to the Species Level and Differentiation between Strains of
Aspergillus
Clinical Isolates by Automated Repetitive-Sequence-Based PCR
Authors: Healy M. , Reece K. , Walton D. , Huong J. , Shah K. , Kontoyiannis D. P. 
Published: September 2004

ABSTRACT

A commercially available repetitive-sequence-based PCR (rep-PCR) DNA fingerprinting assay adapted to an automated format, the DiversiLab system, enables rapid microbial identification and strain typing. We explored the performance of the DiversiLab system as a molecular typing tool for 69
Aspergillus
isolates (38
A. fumigatus
, 15
A. flavus
, and 16
A. terreus
isolates) had been previously characterized by morphological analysis. Initially, 27
Aspergillus
isolates (10
A. fumigatus
, 9
A. flavus
, and 8
A. terreus
isolates) were used as controls to create a rep-PCR-based DNA fingerprint library with the DiversiLab software. Then, 42 blinded
Aspergillus
isolates were typed using the system. The rep-PCR-based profile revealed 98% concordance with morphology-based identification. rep-PCR-based DNA fingerprints were reproducible and were consistent for DNA from both hyphae and conidia. DiversiLab dendrogram reports correctly identified all
A. fumigatus
(
n
= 28),
A. terreus
(
n
= 8), and
A. flavus
(
n
= 6) isolates in the 42 blinded
Aspergillus
isolates. rep-PCR-based identification of all isolates was 100% in agreement with the contiguous internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) sequence-based identification of the respective isolates. Additionally, the DiversiLab system could demonstrate strain-level differentiation of
A. flavus
and
A. terreu
s. Automated rep-PCR may be a time-efficient, effective, easy-to-use, novel genotyping tool for identifying and determining the strain relatedness of fungi. This system may be useful for epidemiological studies, molecular typing, and surveillance of
Aspergillus
species.
Microevolution of
Candida albicans
Strains during Catheter-Related Candidemia
Authors: Shin Jong Hee , Park Mi-Ra , Song Jeong Won , Shin Dong Hyeon , Jung Sook-In , Cho Duck , Kee Seung Jung , Shin Myung Geun , Suh Soon Pal , Ryang Dong Wook 
Published: September 2004

ABSTRACT

We examined microevolution in a series of
Candida albicans
strains isolated from patients with catheter-related candidemia. Sixty-one isolates (29 from blood, 18 from catheters, 10 from urine, and 4 from other sites) were obtained from 15 patients who were admitted to the same hospital over a 3-year period. Isolates were analyzed by using Southern hybridization with the C1 fragment of Ca3 as a probe (C1 fingerprinting) and pulsed-field gel electrophoresis (PFGE). PFGE typing consisted of electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA (REAG) by using SfiI (REAG-S) and BssHII (REAG-B). When catheter isolates were compared with blood isolates from the same patient, catheter isolates from 5 of 14 patients (36%) exhibited minor band differences (microevolution) relative to blood isolates in either C1 fingerprinting (
n
= 4), REAG-S (
n
= 3), or REAG-B (
n
= 5) profiles, although they had identical EK patterns. However, the other sequential isolates from each patient, which had identical EK patterns, showed the same REAG and C1 fingerprinting patterns. Both fingerprinting methods revealed that two distinct genotypes were shared by isolates from seven patients in a neonatal intensive care unit, suggesting two nosocomial clusters. Except for two catheter isolates from the index patients of each cluster, no consecutive isolates collected from each of the two clusters showed any microevolution during the 2- or 7-month cluster periods. The findings suggest that in catheter-related candidemia, some
C. albicans
strains undergo microevolution during catheter colonization.
Characterizations of Adenovirus Type 41 Isolates from Children with Acute Gastroenteritis in Japan, Vietnam, and Korea
Authors: Li Lei , Shimizu Hideaki , Doan Lan Thi Phuong , Tung Phan Gia , Okitsu Shoko , Nishio Osamu , Suzuki Eiko , Seo Jeong Kee , Kim Kyo Sun , Müller Werner E. G. , Ushijima Hiroshi 
Published: September 2004

ABSTRACT
Genetic and antigenic characterizations of 70 strains of adenovirus type 41 (Ad41), isolated between 1998 and 2001 from children in Japan, Vietnam, and Korea, were done by DNA restriction enzyme (RE) analysis, sequencing analysis, and monoclonal antibody (MAb)-based enzyme-linked immunosorbent assay (ELISA). Eight genome types were observed in the present study, among which D25, D26, D27, and D28 were novel genome types. These eight genome types were divided into two genome-type clusters (GTCs) based on phylogenetic analysis of the hypervariable regions (HVRs) of the hexon. GTC1 includes D1, D25, D26, D27, and D28, and the GTC2 contains D4, D12, and D22. The amino acid homologies among the members within a GTC were 97 to 100%, whereas between the members of different GTCs the homologies were 92 to 94%. The specificity of the GTC classification was confirmed by ELISA with MAb 1F, which was selected by the Ad41 prototype Tak strain. It was found that only the isolates of GTC1 but not of GTC2 reacted with MAb 1F. These results suggest that Ad41 isolates from the three countries should be classified into two subtypes. The accumulation of amino acid mutations located in HVRs of hexon are indicative for the classification of Ad41 subtype.
Definition of the Beijing/W Lineage of
Mycobacterium tuberculosis
on the Basis of Genetic Markers
Authors: Kremer Kristin , Glynn Judith R. , Lillebaek Troels , Niemann Stefan , Kurepina Natalia E. , Kreiswirth Barry N. , Bifani Pablo J. , van Soolingen Dick 
Published: September 2004

ABSTRACT

Mycobacterium tuberculosis
Beijing genotype strains are highly prevalent in Asian countries and in the territory of the former Soviet Union. They are increasingly reported in other areas of the world and are frequently associated with tuberculosis outbreaks and drug resistance. Beijing genotype strains, including W strains, have been characterized by their highly similar multicopy IS
6110
restriction fragment length polymorphism (RFLP) patterns, deletion of spacers 1 to 34 in the direct repeat region (Beijing spoligotype), and insertion of IS
6110
in the genomic
dnaA-dnaN
locus. In this study the suitability and comparability of these three genetic markers to identify members of the Beijing lineage were evaluated. In a well-characterized collection of 1,020
M. tuberculosis
isolates representative of the IS
6110
RFLP genotypes found in The Netherlands, strains of two clades had spoligotypes characteristic of the Beijing lineage. A set of 19 Beijing reference RFLP patterns was selected to retrieve all Beijing strains from the Dutch database. These reference patterns gave a sensitivity of 98.1% and a specificity of 99.7% for identifying Beijing strains (defined by spoligotyping) in an international database of 1,084 strains. The usefulness of the reference patterns was also assessed with large DNA fingerprint databases in two other European countries and for identification strains from the W lineage found in the United States. A standardized definition for the identification of
M. tuberculosis
strains belonging to the Beijing/W lineage, as described in this work, will facilitate further studies on the spread and characterization of this widespread genotype family of
M. tuberculosis
strains.
Risk Factors for Community-Associated Methicillin-Resistant
Staphylococcus aureus
Infections in an Outbreak of Disease among Military Trainees in San Diego, California, in 2002
Authors: Campbell Katherine M. , Vaughn Andrew F. , Russell Kevin L. , Smith Besa , Jimenez Dinice L. , Barrozo Christopher P. , Minarcik John R. , Crum Nancy F. , Ryan Margaret A. K. 
Published: September 2004

ABSTRACT

An outbreak of community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) skin infections was observed in a population of U.S. military trainees in the summer of 2002. A questionnaire was developed and administered to 206 trainees, 22 of whom had MRSA infections. Factors associated with infection were described by multivariable logistic regression modeling and included having a roommate in training with a prior skin infection (odds ratio [OR] = 3.44) or having a family member or friend who worked in a health care setting (OR = 2.79). Previous antibiotic use, hospitalization, or health problems were not associated with MRSA infection. This outbreak of MRSA skin infections in an otherwise-healthy, well-defined, military population provided an opportunity to describe risk factors for CA-MRSA which may help focus prevention efforts in this and other communities.
Evaluation of the Core Antigen Assay as a Second-Line Supplemental Test for Diagnosis of Active Hepatitis C Virus Infection
Authors: Krajden Mel , Shivji Rishma , Gunadasa Kingsley , Mak Annie , McNabb Gail , Friesenhahn Michel , Hendricks David , Comanor Lorraine 
Published: September 2004

ABSTRACT
The British Columbia Center for Disease Control laboratory performs approximately 95% of all hepatitis C virus (HCV) antibody tests for the province's 4 million inhabitants. In 2002, the laboratory tested 96,000 specimens for anti-HCV antibodies, of which 4,800 (5%) were seroreactive and required confirmation of active infection. Although HCV RNA assays with a sensitivity of 50 IU/ml or less are recommended for the confirmation of active HCV infection, given the large number of seroreactive specimens tested annually, we evaluated the Ortho trak-C assay (OTCA) as a second-line confirmatory test and determined its limit of detection (LoD). Of 502 specimens from treatment-naïve anti-HCV-positive individuals, 478 had sufficient volumes for evaluation by the OTCA and HCV RNA tests. Core antigen was not detected in 147 of 478 (30.8%) of these specimens, of which 37 of 147 (25.2%) were shown to be viremic by the VERSANT HCV (version 3.0) (branched-DNA) assay and/or the VERSANT HCV qualitative assay. Testing of 144 replicates of a World Health Organization standard dilution series indicated that the LoD of OTCA was ∼27,000 IU/ml. This LoD is consistent with the inability of OTCA to detect core antigen in clinical specimens with low viral loads. We conclude that OTCA has limited value as a confirmatory test for the diagnosis of active HCV infection because 37 of 367 (10%) of viremic specimens had undetectable core antigen. Qualitative HCV RNA testing remains the present standard for the confirmation of active HCV infection in the diagnostic setting.
Evaluation of the New VITEK 2 Card for Identification of Clinically Relevant Gram-Negative Rods
Authors: Funke Guido , Funke-Kissling Pascale 
Published: September 2004

ABSTRACT

The
VITEK 2 card for gram-negative bacteria (bioMérieux,Marcy-l′Etoile, France) has been redesigned to improve the
identification of fermenting and nonfermenting bacilli. Forty-seven
biochemical tests, including 19 enzymatic tests, are present in the new
card and interpreted in a kinetic mode. Final identification results
are available within 10 h. The database allows the
identification of 159 different taxa. Six hundred fifty-five
gram-negative rods (GNR; 511 fermenters and 144 nonfermenters),
representing 54 taxa, were tested. Strains were taken from fresh
routine primary isolation plates (
n
= 157), from
stored routine plates (
n
= 301), and from stock
cultures (
n
= 197). Six hundred thirty-seven strains
(97.3%) were correctly identified to the species level, 14
strains (2.1%) gave low discrimination results requiring
additional tests, and 4 strains (0.6%) gave discordant results;
not a single strain remained unidentified. Nearly 92% of all
isolates were correctly identified within 7 h of incubation.
The robustness of the system was demonstrated by the fact that strains
were grown on four different agar media before testing. The system may
also have the potential to be applied directly to primary isolation
plates, since in this instance 96.2% of 157 GNR were correctly
identified and 3.8% gave low discrimination results. The new
VITEK 2 card for gram-negative bacteria seems to be a promising new
tool for routine, rapid identification of
GNR.