bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Symbiotic Performance by
Rhizobium tropici
Glycogen Synthase Mutants
Authors: Marroquı́ Silvia , Zorreguieta Angeles , Santamarı́a Carmen , Temprano Francisco , Soberón Mario , Megı́as Manuel , Downie J. Allan 
Published: July 2002

ABSTRACT

We isolated a Tn
5
-induced
Rhizobium tropici
mutant that has enhanced capacity to oxidize
N,N
-dimethyl-
p
-phenylendiamine (DMPD) and therefore has enhanced respiration via cytochrome oxidase. The mutant had increased levels of the cytochromes
c
1
and CycM and a small increase in the amount of cytochrome
aa
3
. In plant tests, the mutant increased the dry weight of
Phaseolus vulgaris
plants by 20 to 38% compared with the control strain, thus showing significantly enhanced symbiotic performance. The predicted product of the mutated gene is homologous to glycogen synthases from several bacteria, and the mutant lacked glycogen. The DNA sequence of the adjacent gene region revealed six genes predicted to encode products homologous to the following gene products from
Escherichia coli
: glycogen phosphorylase (
glgP
), glycogen branching enzyme (
glgB
), ADP glucose pyrophosphorylase (
glgC
), glycogen synthase (
glgA
), phosphoglucomutase (
pgm
), and glycogen debranching enzyme (
glgX
). All six genes are transcribed in the same direction, and analysis with
lacZ
gene fusions suggests that the first five genes are organized in one operon, although
pgm
appears to have an additional promoter;
glgX
is transcribed independently. Surprisingly, the
glgA
mutant had decreased levels of high-molecular-weight exopolysaccharide after growth on glucose, but levels were normal after growth on galactose. A deletion mutant was constructed in order to generate a nonpolar mutation in
glgA
. This mutant had a phenotype similar to that of the Tn
5
mutant, indicating that the enhanced respiration and symbiotic nitrogen fixation and decreased exopolysaccharide were due to mutation of
glgA
and not to a polar effect on a downstream gene.
snr-1
Gene Is Required for Nitrate Reduction in
Pseudomonas aeruginosa
PAO1
Authors: Kerschen Edward J. , Irani Vida R. , Hassett Daniel J. , Rowe John J. 
Published: July 2002

ABSTRACT

Pseudomonas aeruginosa
is able to use nitrate for both assimilation and anaerobic respiration. One set of genes, designated
snr
(for “shared nitrate reduction”), have been recently cloned and partially characterized. In this study, we demonstrate that the
snr-1
gene encodes a predicted 52.5-kDa protein that is 82% similar to a unique cytochrome
c
of
Desulfomonile tiedjei
DCB-1. Importantly, the Snr-1 protein sequence of
P. aeruginosa
differed from that of the cytochrome
c
of
D. tiedjei
primarily in the first 25 amino acids, which are required for membrane attachment in
D. tiedjei
. In
P. aeruginosa
, the Snr-1 protein hydropathy profile indicates that it is a soluble protein. An isogenic
snr-1
::Gm insertional mutant was unable to grow aerobically with nitrate as a sole nitrogen source or anaerobically with nitrate as an electron acceptor. Complementation of the
snr-1
::Gm mutant with the
snr-1
gene restored the wild-type phenotypes. Interestingly, anaerobic growth rates were significantly higher in the
snr-1
mutant harboring a multicopy plasmid containing
snr-1
. In contrast, aerobic growth rates of the restored mutant using nitrate as the sole nitrogen source were similar to those of the wild type. Transcriptional
lacZ
fusions demonstrated that
snr-1
was not regulated by molybdate, oxygen, or nitrate.
Comparison of Spectrophotometric and Visual Readings of NCCLS Method and Evaluation of a Colorimetric Method Based on Reduction of a Soluble Tetrazolium Salt, 2,3-Bis {2-Methoxy-4-Nitro-5-[(Sulfenylamino) Carbonyl]-2H- Tetrazolium-Hydroxide}, for Antifungal Susceptibility Testing of
Aspergillus
Species
Authors: Meletiadis Joseph , Mouton Johan W. , Meis Jacques F. G. M. , Bouman Bianca A. , Donnelly Peter J. , Verweij Paul E. ,   EUROFUNG Network
Published: July 2002

ABSTRACT

The susceptibilities of 25 clinical isolates of various
Aspergillus
species (
Aspergillus fumigatus, A. flavus, A. terreus, A. ustus
, and
A. nidulans
) to itraconazole (ITC) and amphotericin B (AMB) were determined using the standard proposed by NCCLS for antifungal susceptibility testing of filamentous fungi, a modification of this method using spectrophotometric readings, and a colorimetric method using the tetrazolium salt 2,3-bis {2-methoxy-4-nitro-5-[(sulfenylamino) carbonyl]-2H-tetrazolium-hydroxide} (XTT). Five MIC end points for ITC (MIC-0, no visible growth or ≤5% the growth control value [GC]; MIC-1, slight growth or 6 to 25% the GC; MIC-2, prominent reduction in growth or 26 to 50% the GC; MIC-3, slight reduction in growth or 51 to 75% the GC; and MIC-4, no reduction in growth or 76 to 100% the GC) and one for AMB (MIC-0) were determined visually by four observers and spectrophotometrically. The intraexperimental (between the observers) and interexperimental (between the experiments) levels of agreement of the NCCLS and XTT methods exceeded 95% for MIC-0 of AMB and MIC-0 and MIC-1 of ITC. The MIC-2 of ITC showed lower reproducibility, although spectrophotometric reading and/or incubation for 48 h increased the interexperimental reproducibility from 85 to >93%. Between visual and spectrophotometric readings, high levels of agreement were found for AMB (≈97%) and MIC-1 (≈92%) and MIC-2 (≈88%) of ITC. Poor agreement was found for MIC-0 of ITC (51% after 24 h), since the spectrophotometric readings resulted in higher MIC-0 values than the visual readings. The agreement was increased to 98% by shifting the threshold level of MIC-0 from 5 to 10% relative optical density and by establishing an optical density of greater than 0.1 for the GC as the validation criterion. No statistically significant differences were found between the NCCLS method and the XTT method, with the levels of agreement exceeding 97% for MIC-0 of AMB and 83% for MIC-0, MIC-1, and MIC-2 of ITC. The XTT method and spectrophotometric readings can increase the sensitivity and the precision, respectively, of in vitro susceptibility testing of
Aspergillus
species.
Lone Star Tick-Infecting Borreliae Are Most Closely Related to the Agent of Bovine Borreliosis
Authors: Rich Stephen M. , Armstrong Philip M. , Smith Ronald D. , Telford Sam R. 
Published: July 2002

ABSTRACTAlthoughBorrelia theileri, the agent of bovine borreliosis, was described at the turn of the century (in 1903), its relationship with borreliae causing Lyme disease or relapsing fever remains undescribed. We tested the previously published hypothesis that spirochetes infecting Lone Star ticks (Amblyomma americanum) may compriseB. theileriby analyzing the 16S ribosomal DNAs (rDNAs) and flagellin genes of these spirochetes.B. theileri, theAmblyommaagent, andB. miyamotoiformed a natural group or clade distinct from but most closely related to that of the relapsing fever spirochetes.B. theileriand theAmblyommaagent were 97 and 98% similar at the nucleotide level within the analyzed portions of the 16S rDNA and the flagellin gene respectively, suggesting a recent divergence. The agent of bovine borreliosis might be explored as a surrogate antigen for the as-yet-uncultivatableAmblyommaagent in studies designed to explore the etiology of a Lyme disease-like infection associated with Lone Star ticks.
Sequence Analysis of the Direct Repeat Region in
Mycobacterium bovis
Authors: Caimi Karina , Romano Maria I. , Alito Alicia , Zumarraga Martin , Bigi Fabiana , Cataldi Angel 
Published: July 2002

ABSTRACT

Spoligotyping is a major tool for molecular typing of
Mycobacterium bovis
. This technique is based on the polymorphism of spacers that separate direct repeats (DRs) in the
M. tuberculosis
complex DR region. Numerous
M. bovis
strains show a lack of several spacers which appears as a gap in the spoligotyping pattern. To determine whether these gaps contain alternative spacers not included in the spoligotyping membrane, PCRs using primers that hybridize to the spacers adjacent to the gaps were performed. Comparing the sizes of products obtained by PCR with those deduced from spoligotyping patterns, fragments were selected and sequenced to look for alternative spacers. Upon analysis of the sequences, five alternative spacers were detected, although deletions of spacers are mainly responsible for the observed gaps. The alternative spacers, which are more frequent in
M. bovis
than in
M. tuberculosis
, may contribute to increased
M. bovis
differentiation.
Rapid Identification of
Candida glabrata
Based on Trehalose and Sucrose Assimilation Using Rosco Diagnostic Tablets
Authors: Lopez José , Dalle Frédéric , Mantelin Pierre , Moiroux Philippe , Nierlich Anne-Charlotte , Pacot Agnès , Cuisenier Bernadette , Vagner Odile , Bonnin Alain 
Published: July 2002

ABSTRACT

We developed a simple method for the identification of
Candida glabrata
on the basis of the ability of this species to rapidly assimilate trehalose but not sucrose. After incubation of yeasts with Rosco diagnostic tablets containing sucrose or trehalose, identification of
C. glabrata
was achieved in 4 h with 100% sensitivity and specificity.
cagA
Status and Eradication Treatment Outcome of Anti-
Helicobacter pylori
Triple Therapies in Patients with Nonulcer Dyspepsia
Authors: Broutet Nathalie , Marais Armelle , Lamouliatte Hervé , de Mascarel Antoine , Samoyeau Roland , Salamon Roger , Mégraud Francis 
Published: July 2002

ABSTRACT

The differences in eradication rates reported in clinical trials aiming to cure
Helicobacter pylori
infection cannot be entirely explained by the type of regimen, bacterial resistance, or lack of compliance. Using data from a clinical trial, a logistic regression model was constructed to determine whether
cagA
status, assessed by PCR, affects the outcome of eradication. Resistance to clarithromycin (10% of the strains) predicted failure perfectly. In the model (
n
= 156), a
cagA
-lacking strain (odds ratio [OR] = 2.2; 95% confidence interval [CI], (1.1 to 4.7), tobacco smoking OR = 3.1; 95% CI, 1.3 to 7.0), and a double dose of proton pump inhibitor in the treatment regimen (OR = 0.3; 95% CI, 0.2 to 0.7) were associated with the treatment outcome. The exact role of
cagA
in the outcome of
H. pylori
eradication therapy has not been explored. However, the type of histological lesions which it causes in the gastric mucosa may be implicated. Regardless of the mechanism involved,
cagA
status is a good predictive marker of eradication outcome.
Hepatitis C Virus Genotyping Based on 5′ Noncoding Sequence Analysis (Trugene)
Authors: Halfon P. , Trimoulet P. , Bourliere M. , Khiri H. , de Lédinghen V. , Couzigou P. , Feryn J. M. , Alcaraz P. , Renou C. , Fleury H. J. A. , Ouzan D. 
Published: July 2002

ABSTRACT
Hepatitis C virus (HCV) genotyping of samples from 184 patients with chronic HCV infection by the Trugene 5′NC genotyping kit, based on sequence analysis of the 5′ noncoding region (5′ NCR), and the InnoLiPA assay was evaluated. In addition to these methods, the 184 samples were also analyzed by sequencing of part of the NS5B of the HCV genome after in-house PCR amplification, as a means of validating results obtained with the 5′ NCR. The distribution of the genotypes typed by NS5B sequence analysis was as follows: 1a, 41 samples; 1b, 58 samples; 1d, 1 sample; 2a, 5 samples; 2b, 2 samples; 2c, 7 samples; 3a, 46 samples; 4a, 7 samples; 4c, 1 samples; 4e, 9 samples; 5a, 6 samples; 6a, 1 sample. The Trugene and InnoLiPA assays gave concordant results within HCV types in 100% of cases. The ability to discriminate at the subtype level was 76 and 74% for the Trugene and the InnoLiPA assays, respectively.
Sensitivity and Specificity of Human Immunodeficiency Virus Rapid Serologic Assays and Testing Algorithms in an Antenatal Clinic in Abidjan, Ivory Coast
Authors: Koblavi-Dème Stéphania , Maurice Chantal , Yavo Daniel , Sibailly Toussaint S. , N′guessan Kabran , Kamelan-Tano Yvonne , Wiktor Stefan Z. , Roels Thierry H. , Chorba Terence , Nkengasong John N. 
Published: July 2002

ABSTRACT
To evaluate serologic testing algorithms for human immunodeficiency virus (HIV) based on a combination of rapid assays among persons with HIV-1 (non-B subtypes) infection, HIV-2 infection, and HIV-1–HIV-2 dual infections in Abidjan, Ivory Coast, a total of 1,216 sera with known HIV serologic status were used to evaluate the sensitivity and specificity of four rapid assays: Determine HIV-1/2, Capillus HIV-1/HIV-2, HIV-SPOT, and Genie II HIV-1/HIV-2. Two serum panels obtained from patients recently infected with HIV-1 subtypes B and non-B were also included. Based on sensitivity and specificity, three of the four rapid assays were evaluated prospectively in parallel (serum samples tested by two simultaneous rapid assays) and serial (serum samples tested by two consecutive rapid assays) testing algorithms. All assays were 100% sensitive, and specificities ranged from 99.4 to 100%. In the prospective evaluation, both the parallel and serial algorithms were 100% sensitive and specific. Our results suggest that rapid assays have high sensitivity and specificity and, when used in parallel or serial testing algorithms, yield results similar to those of enzyme-linked immunosorbent assay-based testing strategies. HIV serodiagnosis based on rapid assays may be a valuable alternative in implementing HIV prevention and surveillance programs in areas where sophisticated laboratories are difficult to establish.
Rapid Pulsed-Field Gel Electrophoresis Protocol for Subtyping of
Campylobacter jejuni
Authors: Ribot Efrain M. , Fitzgerald Collette , Kubota Kristy , Swaminathan Bala , Barrett Timothy J. 
Published: July 2002

ABSTRACT

We developed a rapid pulsed-field gel electrophoresis (PFGE) protocol for subtyping
Campylobacter
isolates based on the standardized protocols used by PulseNet laboratories for the subtyping of other food-borne bacterial pathogens. Various combinations of buffers, reagents, reaction conditions (e.g., cell suspension concentration, lysis time, lysis temperature, and restriction enzyme concentration), and electrophoretic parameters were evaluated in an effort to devise a protocol that is simple, rapid, and robust. PFGE analysis of
Campylobacter
isolates can be completed in 24 to 30 h using this protocol, whereas the most widely used current protocols require 3 to 4 days to complete. Comparison of PFGE patterns obtained in six laboratories showed that subtyping results obtained using this protocol are highly reproducible.
Outcome of Cephalosporin Treatment for Serious Infections Due to Apparently Susceptible Organisms Producing Extended-Spectrum β-Lactamases: Implications for the Clinical Microbiology Laboratory
Authors: Paterson David L. , Ko Wen-Chien , Von Gottberg Anne , Casellas Jose Maria , Mulazimoglu Lutfiye , Klugman Keith P. , Bonomo Robert A. , Rice Louis B. , McCormack Joseph G. , Yu Victor L. 
Published: July 2002

ABSTRACT

Although extended-spectrum beta-lactamases (ESBLs) hydrolyze cephalosporin antibiotics, some ESBL-producing organisms are not resistant to all cephalosporins when tested in vitro. Some authors have suggested that screening klebsiellae or
Escherichia coli
for ESBL production is not clinically necessary, and when most recently surveyed the majority of American clinical microbiology laboratories did not make efforts to detect ESBLs. We performed a prospective, multinational study of
Klebsiella pneumoniae
bacteremia and identified 10 patients who were treated for ESBL-producing
K. pneumoniae
bacteremia with cephalosporins and whose infecting organisms were not resistant in vitro to the utilized cephalosporin. In addition, we reviewed 26 similar cases of severe infections which had previously been reported. Of these 36 patients, 4 had to be excluded from analysis. Of the remaining 32 patients, 100% (4 of 4) patients experienced clinical failure when MICs of the cephalosporin used for treatment were in the intermediate range and 54% (15 of 28) experienced failure when MICs of the cephalosporin used for treatment were in the susceptible range. Thus, it is clinically important to detect ESBL production by klebsiellae or
E. coli
even when cephalosporin MICs are in the susceptible range (≤ 8 μg/ml) and to report ESBL-producing organisms as resistant to aztreonam and all cephalosporins (with the exception of cephamycins).
Sensitive Detection of
Borrelia burgdorferi
Sensu Lato DNA and Differentiation of
Borrelia
Species by LightCycler PCR
Authors: Mommert Susanne , Gutzmer Ralf , Kapp Alexander , Werfel Thomas 
Published: July 2002

ABSTRACT

In order to differentiate species within the
Borrelia burgdorferi
sensu lato complex, LightCyler PCR and melting-curve analysis of the amplicons of two genes with intraspecies variability, the
p66
gene and the
recA
gene, were performed. It was demonstrated that nested LightCycler PCR amplification of
p66
is more sensitive in the detection of borrelia DNA than amplification of the
recA
gene.
B. burgdorferi
sensu stricto could be differentiated from
Borrelia garinii
and
Borrelia afzelii
by melting-curve analysis of the
p66
gene amplicon.
B. garinii
could be differentiated from
B. afzelii
and
B. burgdorferi
sensu stricto by melting-curve analysis of the
recA
gene amplicon. Therefore, the PCRs complement each other in subtyping different
Borrelia
species, and combined LightCycler PCR and melting-curve analysis of both target genes is a rapid method to distinguish the three species of
B. burgdorferi
sensu lato.
Pulmonary Infection Caused by an Unusual, Slowly Growing Nontuberculous Mycobacterium
Authors: Suomalainen Sini , Koukila-Kähkölä Pirkko , Brander Eljas , Katila Marja-Leena , Piilonen Anneli , Paulin Lars , Mattson Karin 
Published: July 2002

ABSTRACT

Mycobacterium triplex
, a recently described slowly growing nontuberculous mycobacterium, was isolated from a Finnish patient with pulmonary mycobacteriosis. The disease was successfully treated with antimycobacterial drugs. The strain isolated, which was similar to the type strain but differed slightly from the species description, was regarded as a variant of
M. triplex
sensu stricto. According to present knowledge this variant of the species has never been isolated before.
PCR Detection and Molecular Identification of
Chlamydiaceae
Species
Authors: Hartley J. C. , Kaye S. , Stevenson S. , Bennett J. , Ridgway G. 
Published: July 2002

ABSTRACT

Recent taxonomic developments, based on 16s and 23s rRNA gene sequences, have divided the family
Chlamydiaceae
into two genera and nine species, of which five have been found to infect humans. Few simple methods are available to detect and identify all species sensitively and specifically. In this study the suitability of the
omp2
gene as a target for molecular identification of
Chlamydiaceae
is demonstrated. Phylogenetic analysis of partial
omp2
gene sequences from all nine species agrees with the recently published taxonomic changes based on the ribosomal genes. The use of a family-specific PCR primer pair, which is able to amplify the 5′ end of the
omp2
gene from all
Chlamydiaceae
except some
Chlamydophila pecorum
strains, is described. Identification of all nine species was achieved using restriction fragment length polymorphism analysis with a single enzyme,
Alu
I, confirmed by DNA sequencing. A PCR enzyme-linked oligonucleotide assay was developed which can detect a single chlamydial genome and may be applied to DNA extracts from any specimen or culture for the detection of single or mixed human chlamydial infection.
Six-Year Study of the Incidence of Herpes in Genital and Nongenital Cultures in a Central Kentucky Medical Center Patient Population
Authors: Ribes Julie A. , Steele Anchalee D. , Seabolt John Pat , Baker Doris J. 
Published: July 2002

ABSTRACTHerpes infections are among the most common sexually transmitted diseases and are the most common cause of genital ulcer disease in the United States. This study addresses the changing distribution of herpes simplex virus type 1 (HSV-1) and HSV-2 in patients presenting for evaluation of herpetic infections. Viral culture results from the University of Kentucky Clinical Microbiology Laboratory were reviewed for a 6-year period (1994 through 1999). Data were collected on patient sex, site of culture, and culture result. These data were analyzed statistically to identify yearly trends. Of the 4,498 cultures analyzed, nearly equal proportions of HSV-1 (13.3%) and HSV-2 (12.0%) were detected for an overall culture positivity rate of 25.3%. Approximately two-thirds of all positive cultures were from women. Although HSV-2 remained the predominant type of genital herpes, over the 6-year span of this study, there was a trend toward increasing proportions of HSV-1 genitalis, with 31.8% of male patients and 44.8% of female patients demonstrating HSV-1 genitalis by 1999. The majority of patients with HSV in nongenital sites grew HSV-1. Although there was significant yearly variation, HSV-2 was isolated from only 9.4% of patients with nongenital HSV for the entire 6-year period. This study therefore concludes that HSV-2 remains primarily a genital pathogen, while HSV-1 is taking on an increasingly important role in causing genital ulcer disease in addition to being the primary nongenital HSV.
Recombinant Assay for Serodiagnosis of Lyme Disease Regardless of OspA Vaccination Status
Authors: Gomes-Solecki Maria J. C. , Wormser Gary P. , Schriefer Martin , Neuman Glenn , Hannafey Laura , Glass John D. , Dattwyler Raymond J. 
Published: July 2002

ABSTRACTAll current seroassays using culturedBorrelia burgdorferias their antigen source have been rendered obsolete by the recombinant OspA Lyme disease vaccine. OspA is the major outer surface protein expressed in culturedB. burgdorferi, and any seroassay that uses whole organisms as its antigen source cannot differentiate between subjects who received the vaccine and those who were naturally infected. We developed a new sensitive and specific enzyme-linked immunosorbent assay (ELISA) utilizing recombinant chimeric borrelia proteins devoid of OspA (rNon-OspA) that can be used to detect antibodies to diagnostically importantB.burgdorferiantigens in both OspA-vaccinated and nonvaccinated individuals. We tested sera from patients with Lyme disease and with conditions associated with false-positive serologies, OspA-vaccinated individuals, and healthy high-risk workers from an area of endemicity and normal sera from individuals from areas of nonendemicity. The rNon-OspA test was compared with two commercially available whole-cell immunoassays. The rNon-OspA assay is as sensitive and specific as the whole-cell assay (P> 0.05) for detection of anti-B.burgdorferiantibodies. However, the rNon-OspA assay can differentiate between populations comprised of naturally infected and OspA-vaccinated individuals (P< 0.05). Our data demonstrate that this new sensitive rNon-OspA ELISA can be used for the laboratory detection ofB.burgdorferiantibodies regardless of vaccination status and could replace existing serologic assays for Lyme disease.