bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Fingerprinting of
Lactobacillus
crispatus
Strain CTV-05 by Repetitive Element Sequence-Based PCR Analysis in a Pilot Study of Vaginal Colonization
Authors: Antonio May A. D. , Hillier Sharon L. 
Published: May 2003

ABSTRACT

Lactobacillus
crispatus
is one of the predominant hydrogen peroxide (H
2
O
2
)-producing species found in the vagina and is under development as a probiotic for the treatment of bacterial vaginosis. In this study, we assessed whether DNA fingerprinting by repetitive element sequence-based PCR (rep-PCR) can be used to distinguish the capsule strain of
L
.
crispatus
(CTV-05) from other endogenous strains as well as other species of vaginal lactobacilli. Vaginal and rectal lactobacilli were identified to the species level by using whole-chromosome probe DNA hybridization. The DNAs from
L
.
crispatus
,
L
.
jensenii
,
L
.
gasseri
, and an as-yet-unnamed H
2
O
2
-negative
Lactobacillus
species designated 1086V were subjected to rep-PCR. The results of gel electrophoresis and ethidium bromide staining of the DNA fingerprints obtained were compared.
L
.
crispatus
CTV-05 had a unique DNA fingerprint compared to all other lactobacilli. DNA fingerprints for 27 production lots of
L
.
crispatus
sampled from 1994 through 2001 were identical to that of the original strain isolated in 1993, suggesting strain stability. In a pilot study of nine women, this DNA fingerprinting method distinguished CTV-05 from other endogenous vaginal lactobacilli prior to and after vaginal capsule use. rep-PCR DNA fingerprinting is useful for strain typing and for evaluating longitudinal loss or acquisition of vaginal lactobacilli used as probiotics.
Multicenter Evaluation of Use of Dried Blood and Plasma Spot Specimens in Quantitative Assays for Human Immunodeficiency Virus RNA: Measurement, Precision, and RNA Stability
Authors: Brambilla Don , Jennings Cheryl , Aldrovandi Grace , Bremer James , Comeau Anne Marie , Cassol Sharon A. , Dickover Ruth , Jackson J. Brooks , Pitt Jane , Sullivan John L. , Butcher Ann , Grosso Lynell , Reichelderfer Patricia , Fiscus Susan A. 
Published: May 2003

ABSTRACT
Eleven laboratories evaluated the use of dried blood and plasma spots for quantitation of human immunodeficiency virus (HIV) RNA by two commercially available RNA assays, the Roche Amplicor HIV-1 Monitor and the bioMerieux NucliSens HIV-1 QT assays. The recovery of HIV RNA was linear over a dynamic range extending from 4,000 to 500,000 HIV type 1 RNA copies/ml. The Monitor assay appeared to have a broader dynamic range and seemed more sensitive at lower concentrations. However, the NucliSens assay gave more consistent results and could be performed without modification of the kit. HIV RNA was stable in dried whole blood or plasma stored at room temperature or at −70°C for up to 1 year. Dried blood and dried plasma spots can be used as an easy and inexpensive means for the collection and storage of specimens under field conditions for the diagnosis of HIV infection and the monitoring of antiretroviral therapy.
Evaluation of a New Cellulose Sponge-Tipped Swab for Microbiological Sampling: a Laboratory and Clinical Investigation
Authors: Österblad Monica , Järvinen Helinä , Lönnqvist Kurt , Huikko Solja , Laippala Pekka , Viljanto Jouko , Arvilommi Heikki , Huovinen Pentti 
Published: May 2003

ABSTRACT

A new type of swab (Cellswab; Cellomeda, Turku, Finland), utilizing a highly absorbent cellulose viscose sponge material, was compared to some traditional swabs. The survival of 14 aerobic and 10 anaerobic and microaerophilic bacterial species in the Cellswab, two commercial swab transport systems (Copan, Brescia, Italy, and Orion Diagnostica, Espoo, Finland), and one Dacron swab (Technical Service Consultants Ltd. [TSC], Heywood, United Kingdom) was evaluated. Bacteria were suspended in broth, into which the swabs were dipped. The Cellswab absorbed 1.3 times more fluid and released 3.5 times more fluid upon plating than the other swabs. Aerobic bacteria were stored in dry tubes, the others in transport medium, at 4°C and room temperature (RT), for up to 14 days. Swab samples were transferred to plates at 0, 1, 2, 4, 7, and 14 days. For 10 strains the Cellswab yielded ≥10% of the original CFU for longer than all the other swabs. In the clinical study, the ability of the Cellswab to detect beta-hemolytic streptococci from throat samples (
n
= 995) was compared to that of the TSC Dacron swab. The swabs performed equally, both when their samples were transferred to plates immediately and after storage for 1 day at 4°C or RT. The changes in normal microbiota after storage were also similar. The Cellswab was found to perform at least as well as ordinary swabs. It was better at storing fastidious strains, and at keeping bacteria viable for long storage times; it might well be a useful replacement or complement to ordinary swabs.
New Enzyme Immunoassay for Detection of Hepatitis B Virus Core Antigen (HBcAg) and Relation between Levels of HBcAg and HBV DNA
Authors: Kimura Tatsuji , Rokuhara Akinori , Matsumoto Akihiro , Yagi Shintaro , Tanaka Eiji , Kiyosawa Kendo , Maki Noboru 
Published: May 2003

ABSTRACTA new enzyme immunoassay specific for hepatitis B virus (HBV) core antigen (HBcAg) was developed. In order to detect HBcAg, specimens were pretreated with detergents to release HBcAg from the HBV virion and disassemble it to dimers, and simultaneously, the treatment inactivated anti-HBc antibodies. HBcAg detected by the assay peaked with HBV DNA in density gradient fractions of HBV-positive sera. The assay showed a wide detection range from 2 to 100,000 pg/ml. We observed no interference from anti-HBc antibody or blood components, but the assay was inhibited by very high concentrations (>1 μg/ml; corresponding to 80 signal/cutoff) of HBeAg. When the cutoff value was tentatively set at 4 pg/ml, all healthy control (HBsAg and HBV DNA negative,n= 160) and anti-hepatitis C virus-positive (n= 55) sera were identified as negative. HBcAg concentrations correlated very closely with HBV DNA (r= 0.946,n= 145) in 216 samples from 72 hepatitis B patients. In seroconversion panels, HBcAg concentrations changed in parallel with HBV DNA levels. The assay, therefore, offers a simple method for monitoring hepatitis B patients. With a series of sera during lamivudine therapy, HBV DNA levels fell sharply and the HBcAg concentration also decreased, but the change in HBcAg was smaller and more gradual. The supposed mechanism of these changes and their clinical significance are discussed.
Candida dubliniensis
at a University Hospital in Saudi Arabia
Authors: Fotedar R. , Al Hedaithy S. S. A. 
Published: May 2003

ABSTRACT

Candida dubliniensis
is a newly described yeast species that is a close phylogenetic relative of
C. albicans
. Although it has been reported from different parts of the world, no detailed investigation of this species has been done in Saudi Arabia. The purpose of the present study was to identify
C. dubliniensis
isolates recovered from clinical specimens at a tertiary-care hospital in Riyadh, Saudi Arabia, and to determine the drug susceptibility profiles of those isolates. Over a period of 8 months, 823 germ tube- and chlamydospore-positive yeasts identified as
C. albicans
and recovered from different clinical specimens were screened for their ability to grow at 45°C on Sabouraud dextrose agar. Isolates which failed to grow at 45°C were presumptively identified as
C. dubliniensis.
The species identities were further confirmed by the production of pseudohyphae and chlamydospores on Staib agar and their inability to assimilate
d
-xylose and α-methyl-
d
-glucoside by using the API 20C AUX system. A total of 27 (3.3%) isolates were identified as
C. dubliniensis
. They were all recovered from 23 human immunodeficiency virus-negative patients. The prevalence of
C. dublinensis
in bronchoalveolar lavage (33.3%), oral (16.7%), and blood (16.7%) specimens was high. In addition, 33 isolates previously identified as
C. albicans
and preserved among our stock blood culture isolates were also recruited for the study. Of these, 5 isolates were found to be
C. dubliniensis
, thus making the total number of isolates identified as this species 32. Antifungal susceptibility testing of the
C. dubliniensis
isolates showed 100% sensitivity to amphotericin B, 97% sensitivity to each of fluconazole and ketoconazole, and 87.5% sensitivity to itraconazole. However, in contrast to other studies, the majority of the isolates (65.6%) showed high levels of resistance to flucytosine (MIC > 64 μg/ml). Further studies are warranted to investigate the cause of this unusually high rate of resistance to flucytosine of the
C. dubliniensis
isolates in this region.
Quality Control for β-Lactam Susceptibility Testing with a Well-Defined Collection of
Enterobacteriaceae
and
Pseudomonas aeruginosa
Strains in Spain
Authors: Cantón Rafael , Loza Elena , Del Carmen Conejo María , Baquero Fernando , Martínez-Martínez Luis 
Published: May 2003

ABSTRACT

Eighteen
Enterobacteriaceae
and
Pseudomonas aeruginosa
strains, 16 of them with well-defined β-lactam re sistance mechanisms, were sent to 52 Spanish microbiology laboratories. Interpretative categories for 8 extended-spectrum β-lactams were collected. Participating laboratories used their own routine susceptibility testing procedures (88% automatic systems, 10% disk diffusion, and 2% agar dilution). Control results were established by two independent reference laboratories by applying the NCCLS microdilution method and interpretative criteria. Interpretative discrepancies were observed in 16% of the results (4.4% for cefepime, 3.0% for aztreonam, 2.8% for piperacillin-tazobactam, 1.7% for cefotaxime [CTX] and ceftazidime, 1.1% for ceftriaxone, 0.9% for meropenem, and 0.3% for imipenem). High consistency with reference values (<5% of major plus very major errors) was observed with (i) American Type Culture Collection quality control strains; (ii) strains with low-efficiency mechanisms inactivating extended-spectrum β-lactams, such as OXA-1-producing
Escherichiacoli
or SHV-1-hyperproducing
Klebsiella pneumoniae
; (iii) strains with highly efficient mechanisms, such as SHV-5 porin-deficient
K. pneumoniae
, CTX-M-10 in
Enterobacter cloacae
hyperproducing AmpC, and
P. aeruginosa
with the MexAB OprM efflux phenotype or hyperproducing AmpC. Low consistency (>30% major plus very major errors) was detected in K1-producing
Klebsiella oxytoca
, CTX-M-9-producing
E. coli
, and in OprD
−
P. aeruginosa
strains. Extended-spectrum β-lactamase (ESBL)-producing strains accounted for 86% of very major errors. Recognition of the ESBL phenotype was particularly low in
Enterobacter cloacae
strains (<35%), due to the lack of NCCLS-specific rules in this genus. A K1-producing
K. oxytoca
was misidentified by 10% of laboratories as an ESBL producer. The use of well-defined resistant strains is useful for improving proficiency in susceptibility testing in clinical laboratories.
Antimicrobial Resistance and Genetic Diversity of
Shigella sonnei
Isolates from Western Ireland, an Area of Low Incidence of Infection
Authors: DeLappe Niall , O'Halloran Fiona , Fanning Seamus , Corbett-Feeney G. , Cheasty T. , Cormican M. 
Published: May 2003

ABSTRACT

Shigella sonnei
is a significant cause of gastroenteritis in both developing and industrialized countries. Definition of the diversity and antimicrobial susceptibility of
S. sonnei
isolates may be helpful in the management of individual cases and outbreaks. Antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) were performed with 67 isolates of
S. sonnei
predominantly (
n
= 59) from three counties in the west of Ireland. Phage typing (
n
= 17), plasmid profiling (
n
= 28), and integron analysis (
n
= 24) were performed with subsets of strains. PFGE typing permitted recognition of two major clusters: PFGE type A (
n
= 53) and PFGE type B (
n
= 14). PFGE type A was associated with resistance to ampicillin, streptomycin, and sulfonamides (51 of 53 isolates), and those that were phage typed (
n
= 6) were phage type 3. PFGE type B was associated with resistance to streptomycin, sulfonamides, tetracycline, and trimethoprim (11 of 14 isolates) and phage type 6 (9 of 11 isolates). Fifteen different plasmid profiles were identified among the 28 isolates analyzed. A class 2 integron was present in all 14 PFGE type B isolates. One of these isolates also contained a class 1 integron and showed a unique variant of the PFGE type B pattern. Sequence analysis of the gene cassette structures contained within these integrons identified distinct open reading frames that encoded determinants of resistance to trimethoprim, streptomycin, and streptothricin. Our data demonstrate two predominant PFGE types among
S. sonnei
isolates circulating in this region. The limited diversity of the
S. sonnei
isolates in this region means that detection of isolates indistinguishable by PFGE and according to their antibiograms in two or more patients is not persuasive evidence of a common-source food- or waterborne outbreak. Indistinguishable plasmid profiles in addition to indistinguishable PFGE and antibiogram types may be more suggestive of an epidemiologically relevant link between cases.
BVBlue Test for Diagnosis of Bacterial Vaginosis
Authors: Myziuk Linda , Romanowski Barbara , Johnson Stephen C. 
Published: May 2003

ABSTRACT

Bacterial vaginosis (BV) is a disorder of the vaginal ecosystem characterized by a shift in the vaginal flora from the normally predominant
Lactobacillus
to one dominated by sialidase enzyme-producing mixed flora. It is the most common cause of abnormal vaginal discharge in adult women. The BVBlue system (Gryphus Diagnostics, L.L.C.) is a chromogenic diagnostic test based on the presence of elevated sialidase enzyme in vaginal fluid samples. BVBlue was compared to the standard method for diagnosing BV (Amsel criteria and Nugent score). Fifty-seven nonmenstruating women of ≥16 years of age who presented for a pelvic examination were recruited. Demographic features were collected via a self-administered questionnaire. The Amsel criteria were assessed based on three of four of the following characteristics of vaginal discharge: consistency, odor, pH, and presence of clue cells on Gram stain. BVBlue was compared to the Gram stain and Amsel criteria. The sensitivity, specificity, positive predictive value, and negative predictive value for BVBlue versus the Gram stain and Amsel criteria were 91.7, 97.8, 91.7, and 97.8% and 50.0, 100, 100, and 88.2%, respectively. A significantly greater proportion of patients with a vaginal pH of >4.5, a positive amine test, or with clue cells on vaginal Gram smear were found to have a positive BVBlue test (
P
< 0.001). Women previously treated for BV were 2.98 times more likely to have another episode of BV. BVBlue is a useful point-of-care diagnostic tool to provide a presumptive diagnosis of BV, especially in situations where microscopic capabilities are unavailable.
Escherichia coli
Strains from Pregnant Women and Neonates: Intraspecies Genetic Distribution and Prevalence of Virulence Factors
Authors: Watt Stéphane , Lanotte Philippe , Mereghetti Laurent , Moulin-Schouleur Maryvonne , Picard Bertrand , Quentin Roland 
Published: May 2003

ABSTRACT

To determine the extent to which the vagina, endocervix, and amniotic fluid screen the
Escherichia coli
strains responsible for neonatal infections, we studied the genetic relationships among 105
E. coli
strains isolated from all of the ecosystems involved in this infectious process. Twenty-four strains were isolated from the intestinal flora, and 25 strains were isolated from the vaginas of pregnant women. Twenty-seven strains were isolated from the amniotic fluid, blood, and cerebrospinal fluid (CSF) of infected neonates. The intraspecies genetic characteristics of all of the isolates were determined by random amplified polymorphic DNA (RAPD) analysis, PCR ECOR (E. coli reference) grouping, and PCR virulence genotyping. A correlation was found between the intraspecies distributions of the strains in the A, B1, B2, and D ECOR groups and in the two major RAPD groups (I and II). Nevertheless, the distribution of the
E. coli
strains in the RAPD groups according to their anatomical origins was more significant than their distribution in the ECOR groups. This may be explained by the existence of an
E. coli
subpopulation, defined by the RAPD I group, within the ECOR B2 group. This RAPD I group presents a major risk for neonates: 75% of the strains isolated from patients with meningitis and 100% of the strains isolated from patients with bacteremia were in this group. The vagina and the amniotic fluid are two barriers that favor colonization by highly infectious strains. Indeed, only 17% of fecal strains belonged to the RAPD I group, whereas 52% of vaginal strains and 67% of amniotic fluid strains belonged to this subpopulation. The
ibeA
and
iucC
genes were significantly associated with CSF strains, whereas the
hly
and
sfa/foc
genes were more frequent in blood strains. These findings could serve as a basis for developing tools to recognize vaginal strains, which present a high risk for neonates, for use in prophylaxis programs.
Comparison of the Pathogenesis of Two Genetically Different H3N2 Influenza A Viruses in Pigs
Authors: Landolt Gabriele A. , Karasin Alexander I. , Phillips Lynette , Olsen Christopher W. 
Published: May 2003

ABSTRACT

In 1997 and 1998, H3N2 influenza A viruses emerged among pigs in North America. Genetic analyses of the H3N2 isolates demonstrated that they had distinctly different genotypes. The most commonly isolated viruses in the United States have a triple-reassortant genotype, with the hemagglutinin, neuraminidase, and PB1 polymerase genes being of human influenza virus origin, the nucleoprotein, matrix, and nonstructural genes being of classical swine influenza virus origin, and the PA and PB2 polymerase genes being of avian influenza virus origin. In contrast, a wholly human H3N2 virus was isolated from a single baby pig in Ontario, Canada, in 1997, but it did not spread within the swine population. Genetic differences between this wholly human virus and the triple-reassortant viruses may affect their replication efficiencies in pigs. In the present study we compared the pathogenicities and replication kinetics of the wholly human virus and a triple-reassortant virus in 7-week-old pigs that were infected intranasally with 2 × 10
3
to 2 × 10
6
50% tissue culture infective doses of virus. Our results demonstrate that the wholly human virus replicated to significantly lower titers and that the onset of virus shedding was delayed compared to the replication titers and the time of onset of virus shedding in triple-reassortant viruses. In addition, infection with the triple-reassortant virus was associated with moderate to severe gross pathological and histological pulmonary lesions, while infection with the wholly human virus induced only mild pulmonary changes.
Regional Variation amongvacAAlleles ofHelicobacter pyloriin China
Authors: Wang Jingtong , van Doorn Leen-Jan , Robinson Philip A. , Ji Xuhuai , Wang Dong , Wang Yu , Ge Lianying , Telford John L. , Crabtree Jean E. 
Published: May 2003

ABSTRACTAllelic variation amongHelicobacter pylori vacAoccurs in the signal and middle region of the gene. The aim of the study was to investigate alleleic variation ofvacAamongH. pyloristrains from three regional areas of China and the relationship betweenvacAalleles and PUD. DNA extracted from 88 clinical isolates ofH. pyloriwas analyzed by type-specific PCR and reverse hybridization line probe assay (LiPA) to determine the genotype ofvacAand presence ofcagA.In 87 isolates, all of thevacAalleles could be classified as either type s1c or type s1a, and all could be classified as m1, m2a, or m2b. One strain could not be typed. In all, 41% of patients were infected with multiplevacAgenotypes, with the highest level being observed in Shanghai (63%). In strains from Beijing, s1a was dominant; by contrast, s1c was dominant in Guangxi and Shanghai. The prevalence of m2b strains in Shanghai (63%) was significantly higher than that in Beijing (83%) or Guangxi (0%). Thirty of the 87 patients had peptic ulcers. However, there was no association betweenvacAgenotype and PUD. This study demonstrates that there is significant geographic diversity of genotype ofvacAwithin China. The absence ofvacAs2 genotypes precluded analysis of an association ofvacAs genotypes and clinical disease.
Genomic Diversity of Clinical and Environmental
Vibrio cholerae
Strains Isolated in Brazil between 1991 and 2001 as Revealed by Fluorescent Amplified Fragment Length Polymorphism Analysis
Authors: Thompson Fabiano L. , Thompson Cristiane C. , Vicente Ana C. P. , Theophilo Grace N. D. , Hofer Ernesto , Swings Jean 
Published: May 2003

ABSTRACT

Vibrio cholerae
is a ubiquitous and abundant organism in aquatic environments, particularly in coastal areas, estuaries, and rivers. This organism was the cause of a considerable number of deaths in Brazil during the last decade. In this study we applied the genomic fingerprinting technique fluorescent amplified fragment length polymorphism (FAFLP) to analyze 106
V. cholerae
O1 and non-O1 and non-O139 strains isolated from clinical specimens and the environment between 1991 and 2001. Numerical analysis of the FAFLP patterns disclosed seven main groups of genomes, all of them originated from a variety of different places in different years, suggesting that
V. cholerae
is a very diverse species. O1 and non-O1 and non-O139 strains were distinguishable by FAFLP, although clinical and environmental strains clustered together in a few cases. The persistence of some strains of highly related genomes during several years and in completely different geographical regions suggests that these strains are highly successful in adapting to changing environmental conditions.
Validation of the Automated Reading and Incubation System with Sensititre Plates for Antimicrobial Susceptibility Testing
Authors: Chapin Kimberle C. , Musgnug Michael C. 
Published: May 2003

ABSTRACT
The present study compared the antimicrobial susceptibility testing (AST) results generated by the Automated Incubation and Reading System (ARIS) with custom Sensititre plates (TREK Diagnostic Systems, Cleveland, Ohio) and MicroScan PC10 GP and NUMIC10 GN plates interpreted with the WalkAway-96 system (Dade Behring, West Sacramento, Calif.) for gram-positive (GP) and gram-negative (GN) organisms as part of an in-house validation. A total of 326 isolates (3,689 antimicrobial agent-organism combinations) were evaluated. Sensititre plates were inoculated according to the instructions of the manufacturer with a suspension adjusted to a 0.5 McFarland standard, while the Prompt Inoculation System was used for the MicroScan plates. ARIS and the WalkAway system were used for automated reading of the Sensititre and MicroScan plates, respectively, at 18 to 24 h. The results were analyzed for essential (±1 twofold dilution) and categorical (sensitive, intermediate, or resistant) agreements. Plates that resulted in ARIS interpretations with major (falsely resistant) or very major (falsely susceptible) errors compared to the results obtained with the WalkAway system were read manually to corroborate instrument readings. Isolates for which very major or major errors were obtained and for which the results were not resolved by manual reading were retested in parallel. Isolates for which very major or major errors were obtained and for which the results were not resolved upon repeat testing were tested by the National Committee for Clinical Laboratory Standards M7-A5 frozen reference microdilution method. Essential agreement was 95.8% for 246 GN isolates. The following categorical error rates were obtained for the GN isolates: 1.3% minor errors, 0% major errors, and 0.4% very major errors. For 95 GP isolates, there was 93.5% essential agreement. Categorical error rates for GP isolates were 0.9% minor errors, 0.6% major errors, and 0.4% very major errors. ARIS-Sensititre is a diagnostic system feasible for use for automated AST in a clinical laboratory.