bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic Selection and Phase Variation Occur during Alfalfa Root Colonization by
Pseudomonas fluorescens
F113
Authors: Sánchez-Contreras María , Martín Marta , Villacieros Marta , O'Gara Fergal , Bonilla Ildefonso , Rivilla Rafael 
Published: July 2002

ABSTRACT

During colonization of the alfalfa rhizosphere,
Pseudomonas fluorescens
F113 undergoes phenotypic variation, resulting in the appearance of colonies with different morphology. Among phenotypic variants, three isolates, C, F, and S were selected, with the C variant showing colony morphology identical to that of the inoculated wild-type strain and F and S having a translucent and diffuse morphology. Phenotypic variants F and S were shown to preferentially colonize distal parts of the roots and showed alterations in motility, swimming faster than the C variant and swarming under conditions that did not allow swarming of the C variant. The motility behavior correlated with overproduction of the
fliC-
encoded protein flagellin but not with hyperflagellation. Flagella of the F and S variants were several times longer than those of the C variant, and overproduction of flagellin was regulated at the transcriptional level. Variant F showed alterations in traits that have been shown to be important for rhizosphere colonization, such as siderophore, cyanide, and exoprotease production, and these phenotypes were complemented by a cloned
gacA
. Sequence analysis of the
gacA
alelle in variant F suggested selection of the phenotype in the rhizosphere. Variant F was also affected in other phenotypes, such as lipopolysaccharide structure and flocculation in unshaken liquid medium, which were not complemented by the
gacA
or
gacS
gene. Mutation of the F113
sss
gene, encoding a site-specific recombinase, showed that most of the phenotypic variation was due to the activity of this recombinase, indicating that phase variation occurs during rhizosphere colonization.
Differential Effects of Mutations intonB1on Intrinsic Multidrug Resistance and Iron Acquisition inPseudomonas aeruginosa
Authors: Zhao Qixun , Poole Keith 
Published: July 2002

ABSTRACTLoss oftonB1adversely affects iron acquisition and intrinsic multidrug resistance inPseudomonas aeruginosa. Several mutations intonB1compromised the protein's contribution to both processes, although TonB1 derivatives altered in residues C35, Q268, R287, Q292, R300, and R304 were compromised vis-à-vis their contribution to drug resistance only.
Conserved Serine/Threonine Kinase Encoded by
CBK1
Regulates Expression of Several Hypha-Associated Transcripts and Genes Encoding Cell Wall Proteins in
Candida albicans
Authors: McNemar Mark D. , Fonzi William A. 
Published: July 2002

ABSTRACT

The opportunistic fungal pathogen,
Candida albicans
, is reported to have several potential virulence factors. A potentially significant factor is the ability to undergo morphological transition from yeast to hypha. This alteration of form is accompanied by many changes within the cell, including alterations in gene expression and cell wall composition. We have isolated a gene that encodes a highly conserved serine/threonine kinase that appears to be involved in the regulation of proteins associated with the cell wall. We have assigned the designation
CBK1
(cell wall biosynthesis kinase 1) to this gene. Mutants lacking
CBK1
form large aggregates of round cells under all growth conditions and lack the ability to undergo morphological differentiation. Additionally, these mutants show an altered pattern of expression of several transcripts encoding proteins associated with the cell wall. The results suggest that the kinase encoded by
CBK1
plays a general role in the maintenance and alteration of the cell wall of
C. albicans
in all morphologies.
Rapid Identification of Clinically Relevant
Legionella
spp. by Analysis of Transfer DNA Intergenic Spacer Length Polymorphism
Authors: De Gheldre Yves , Maes Nicole , Presti François Lo , Etienne Jerome , Struelens Marc 
Published: July 2002

ABSTRACT

Analysis of PCR-amplified transfer DNA (tDNA) intergenic spacers was evaluated as a rapid method for identification to the species level of 18 species of
Legionella
known as human pathogens. Type strains (
n
= 19), reference strains (
n
= 16), environmental strains (
n
= 31), and clinical strains (
n
= 32) were tested. PCR products using outwardly directed tDNA consensus primers were separated on polyacrylamide gels and analyzed with automated laser fluorescence. Test results were obtained in 8 h starting with 72-h-old bacterial growth on solid medium. Species-specific patterns were obtained for all 18
Legionella
species tested:
Legionella anisa
,
L. bozemanii
serogroups 1 and 2,
L. cincinnatiensis
,
L. dumoffii
,
L. feeleii
serogroups 1 and 2,
L. gormanii
,
L. hackeliae
serogroups 1 and 2,
L. jordanis
,
L. lansingensis
,
L. longbeachae
serogroups 1 and 2,
L. lytica
,
L. maceachernii
,
L. micdadei
,
L. oakridgensis
,
L. parisiensis
,
L. pneumophila
serogroups 1 to 14,
L. sainthelensi
serogroup 2,
L. tucsonensis
, and
L. wadsworthii
. Computer-assisted matching of tDNA-intergenic length polymorphism (ILP) patterns identified all 63 environmental and clinical strains to the species level and to serogroup for some strains. tDNA-ILP analysis is proposed as a routinely applicable method which allows rapid identification of environmental and clinical isolates of
Legionella
spp. associated with legionellosis.
Molecular Characterization of Rifampin-Resistant Isolates of
Mycobacterium tuberculosis
from Hungary by DNA Sequencing and the Line Probe Assay
Authors: Bártfai Zoltán , Somoskövi Ákos , Ködmön Csaba , Szabó Nóra , Puskás Erzsébet , Kosztolányi Lászlóné , Faragó Eszter , Mester Judit , Parsons Linda M. , Salfinger Max 
Published: July 2002

ABSTRACT

Two regions of
rpoB
associated with rifampin resistance were sequenced in 29 rifampin-resistant (determined by the proportion method) isolates of
Mycobacterium tuberculosis
obtained from patients from three counties in Hungary. Of the 29 resistant strains, 27 had a mutation in either the 81-bp region (26 strains) or the N-terminal region (1 strain), while the other 2 strains had no mutations in either region. The locations and frequencies of the mutations differed from those previously reported. The most common mutation in this study, D516V, was found in 38% of the Hungarian strains, a frequency 2 to 10 times higher than that found in studies from other countries. These same 29 isolates were also evaluated with the Inno-LiPA Rif. TB test (LiPA), a reverse hybridization assay for the rapid detection of rifampin resistance. Although LiPA detected the presence of an
rpoB
mutation in 26 of the resistant isolates, the type of mutation could not be determined in 4 isolates because the mutations present were not among those included on the LiPA strip. In addition, a silent mutation in one of the rifampin-susceptible control strains was interpreted as rifampin resistant by LiPA. These findings demonstrate the importance of validating this rapid molecular test by comparison with DNA sequence results in each geographic location before incorporating the test into routine diagnostic work.
Longitudinal Variability of Human Immunodeficiency Virus Type 1 RNA Viral Load Measurements by Nucleic Acid Sequence-Based Amplification and NucliSens Assays in a Large Multicenter Study
Authors: Nowicki Marek J. , Benning Lorie , Bremer James W. , Meyer William A. , Hanson Carl , Brambilla Donald , Silver Sylvia , Kovacs Andrea ,   the Women's Interagency HIV-1 Study Collaborative Study Group
Published: July 2002

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) RNA measurements were evaluated within an externally controlled multilaboratory program. Three external standards (1.5 × 10
3
to 1.5 × 10
6
copies/ml) were included in 814 assay runs by four laboratories. Results indicate that HIV-1 RNA levels can be measured with a precision equal to that of the pre-highly active antiretroviral therapy era (standard deviations, ±0.16 to 0.25 log
10
units).
Genome Sequence-Based Fluorescent Amplified Fragment Length Polymorphism of
Campylobacter jejuni
, Its Relationship to Serotyping, and Its Implications for Epidemiological Analysis
Authors: Desai Meeta , Logan Julie M. J. , Frost Jennifer A. , Stanley John 
Published: July 2002

ABSTRACT

The published genome sequence of
Campylobacter jejuni
strain NCTC 11168 was used to model an accurate and highly reproducible fluorescent amplified fragment length polymorphism (FAFLP) analysis. Predicted and experimentally observed amplified fragments (AFs) generated with the primer pair
Hin
dIII+A and
Hha
I+A were compared. All but one of the 61 predicted AFs were reproducibly detected, and no unpredicted fragments were amplified. This FAFLP analysis was used to genotype 74
C. jejuni
strains belonging to the nine heat-stable (HS) serotypes most prevalent in human disease in England and Wales. The 74
C. jejuni
strains exhibited 60 FAFLP profiles, and cluster analysis of them yielded a radial tree showing genetic relationships between and within 13 major clusters. Some clusters were related, and others were unrelated, to a single HS serotype. For example, all strains belonging to serotypes HS6 and HS19 grouped into corresponding single genotypic clusters, while strains of serotypes HS11 and HS18 each grouped into two genotypic clusters. Strains of HS50, the most prevalent serotype infecting humans, were found both in one large (multiserotype) cluster complex and dispersed throughout the tree. The strain genotypes within each FAFLP cluster were characterized by a particular combination of AFs, and among the cluster there were additional differential AFs. Identification of such AFs could act as a search tool to look for potential associations with disease or animal hosts, when applied to large number of human isolates. Genome-sequence based FAFLP, thus, has the potential to establish a genetic database for epidemiological investigations of
Campylobacter
.
Rotavirus Strains Bearing Genotype G9 or P[9] Recovered from Brazilian Children with Diarrhea from 1997 to 1999
Authors: Santos Norma , Volotão Eduardo M. , Soares Caroline C. , Albuquerque Maria Carolina M. , da Silva Fabiano M. , de Carvalho Tatiane R. B. , Pereira Cláudio F. A. , Chizhikov Vladimir , Hoshino Yasutaka 
Published: July 2002

ABSTRACT

Human rotavirus strains belonging to genotype G9 or P[9] were detected in a collection of stool specimens from children with diarrhea in two cities of the state of Rio de Janeiro, Brazil, between March 1997 and December 1999. G9 strains were first detected in April 1997 and remained prevalent until the end of the study, at a frequency of 15.9% (
n
= 157). A high percentage of VP7 nucleotide (99.0 to 99.5%) and deduced amino acid identity (98.6 to 99.1%) was found between three randomly selected Brazilian G9 strains and the American G9 strain US1205. A novel G9:P[4] genotype combination was detected in addition to G9:P[8] and G9:P[6], demonstrating that this G genotype may undergo constant genetic reassortment in nature. The P[9] rotavirus strains constituted 10.2%, the majority of which were detected between April and July 1997. The RNA electrophoretic migration pattern of the G3:P[9] strains resembled that of AU-1 virus (G3:P3[9]), suggesting a genetic similarity between the Brazilian G3:P[9] strains and the Japanese virus, which is similar to a feline rotavirus genetically.
Nationwide German Multicenter Study on the Prevalence of Antibiotic Resistance in Streptococcal Blood Isolates from Neutropenic Patients and Comparative In Vitro Activities of Quinupristin-Dalfopristin and Eight Other Antimicrobials
Authors: Reinert Ralf René , von Eiff Christof , Kresken Michael , Brauers Johannes , Hafner Dieter , Al-Lahham Adnan , Schorn Holger , Lütticken Rudolf , Peters Georg ,   The Multicenter Study On Antibiotic Resistance In Staphylococci and Other Gram- Positive Cocci (Mars) Study Group
Published: July 2002

ABSTRACT

In a prospective multicenter study (1996 to 1999), 156 episodes of bacteremic streptococcal infections of neutropenic patients were evaluated.
Streptococcus oralis
(26.3%),
S. pneumoniae
(26.3%),
S. agalactiae
(11.5%),
S. mitis
(9%), and
S. pyogenes
(5.8%) were the predominant species. Four strains (2.6%) were found to be intermediately resistant to penicillin. One strain (0.6%) was found to be highly resistant to penicillin (MIC, 8 mg/liter). Reduced susceptibility to penicillin was detected among
S. oralis
(14.6%),
S. mitis
(7.1%), and
S. pneumoniae
(4.9%) isolates but was not recorded among
S. agalactiae
and
S. pyogenes
. Resistance rates and intermediate resistance rates for other antimicrobials were as follows (all species): amoxicillin, 1.3 and 3.2%; erythromycin, 16 and 2.6%; clindamycin, 5.8 and 0%; ciprofloxacin, 1.9 and 7.7%. Quinupristin-dalfopristin showed good in vitro activity against most streptococcal isolates (MIC at which 50% of the isolates were inhibited [MIC
50
], 0.5 mg/liter; MIC
90
, 1 mg/liter, MIC range, 0.25 to 4 mg/liter).
Enzyme-Linked Immunosorbent Assay for Detecting Herpesvirus Exposure in Mediterranean Tortoises (Spur-Thighed Tortoise [Testudo graeca] and Hermann's Tortoise [Testudo hermanni])
Authors: Origgi F. C. , Klein P. A. , Mathes K. , Blahak S. , Marschang R. E. , Tucker S. J. , Jacobson E. R. 
Published: July 2002

ABSTRACTAn enzyme-linked immunosorbent assay (ELISA) was developed for the detection of antibodies to a herpesvirus associated with an upper respiratory tract disease in Mediterranean tortoises [spur-thighed tortoise (Testudo graeca) and Hermann's tortoise (Testudo hermanni)]. This serodiagnostic test was validated through a hyperimmunization study. The mean of theA405readings of the plasma samples collected at time zero of the hyperimmunization study plus three times the standard deviation was used as the cutoff for seropositivity in tortoises. ELISA results were compared to serum neutralization (SN) values for the same samples by using the McNemar test. The results obtained by SN and ELISA were not significantly different (P> 0.05). This new ELISA could be used as an important diagnostic tool for screening wild populations and private and zoo collections of Mediterranean tortoises.
Antifungal Effects of Lysozyme and Lactoferrin against Genetically Similar, Sequential
Candida albicans
Isolates from a Human Immunodeficiency Virus-Infected Southern Chinese Cohort
Authors: Samaranayake Y. H. , Samaranayake L. P. , Pow E. H. N. , Beena V. T. , Yeung K. W. S. 
Published: July 2002

ABSTRACT

A variety of innate defense factors in saliva such as lysozyme and lactoferrin contribute to mucosal protection and modulate
Candida
populations in the oral cavity. It is also known that in human immunodeficiency virus (HIV)-infected individuals significant variations in the concentrations of lysozyme and lactoferrin in saliva occur during disease progression. Therefore, the aim of this study was to determine the in vitro susceptibility to human lactoferrin and hen egg white lysozyme of genotypically similar oral
Candida albicans
isolates obtained from six HIV-infected ethnic Chinese during sequential visits over a 12-month period. The similarity of the genotypes (50 in total) was evaluated using a randomly amplified polymorphic DNA assay. A blastospore viability assay was performed to evaluate the sensitivity of the organisms to lysozyme and lactoferrin. Exposure to physiological concentrations of either lysozyme (30 μg/ml) or lactoferrin (20 μg/ml) caused a rapid loss of viability among all isolates to a varying extent. None of the sequential
C
.
albicans
isolates demonstrated significant differences in sensitivity to either protein from one visit to the next; similar results were noted when the different genotypes from the same individual were compared. On Spearman correlation analysis of two genotypes that were sequentially isolated from a single patient, a significant negative correlation between lysozyme (
r
= −0.88;
P
< 0.02) (but not lactoferrin) resistance and the duration of HIV disease was seen. These results imply that a minority of
C
.
albicans
isolates that persist intraorally in individuals with HIV disease develop progressive resistance to innate salivary antifungal defenses such as lysozyme, possibly as an adaptive response. However, the vast majority of the
Candida
isolates appear to succumb to these nonspecific host immune mediators abundantly present in the oral environment.
Comparative Analysis of Two Commercial Phenotypic Assays for Drug Susceptibility Testing of Human Immunodeficiency Virus Type 1
Authors: Qari Shoukat H. , Respess Richard , Weinstock Hillard , Beltrami Elise M. , Hertogs Kurt , Larder Brendan A. , Petropoulos Christos J. , Hellmann Nicholas , Heneine Walid 
Published: July 2002

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) isolates from 50 plasma specimens were analyzed for phenotypic susceptibility to licensed reverse transcriptase inhibitors and protease inhibitors by the Antivirogram and PhenoSense HIV assays. Twenty of these specimens were from recently seroconverted drug-naïve persons, and 30 were from patients who were the sources of occupational exposures to HIV-1; 16 of the specimens in the latter group were from drug-experienced patients. The phenotypic results of the Antivirogram and PhenoSense HIV assays were categorized as sensitive or reduced susceptibility on the basis of the cutoff values established by the manufacturers of each assay. Data for 12 to 15 drugs were available by both assays for 38 specimens and represented a total of 529 pairs of results. The two data sets had a 91.5% concordance by phenotypic category. The discordant results (
n
= 45) were distributed randomly among 26 specimens and included 28 results (62.2%) which were within a twofold difference of the assay cutoff values. None of the discordant results were associated with primary resistance mutations that predicted high-level (>20-fold) resistance. Discordant results were distributed equally among specimens from drug-experienced and drug-naïve individuals and were slightly higher for protease inhibitors than for nonnucleoside reverse transcriptase inhibitors or nucleoside reverse transcriptase inhibitors. The findings of the present study demonstrate that the results of the Antivirogram and PhenoSense HIV assays correlate well, despite the use of different testing strategies.
Detection of Meningococcal Carriage by Culture and PCR of Throat Swabs and Mouth Gargles
Authors: Jordens J. Zoe , Williams Jeannette N. , Jones Graeme R. , Heckels John E. 
Published: July 2002

ABSTRACT

The standard method for detecting meningococcal carriage is culture of throat swabs on selective media, but the levels of carriage determined depend heavily on the skills of the individuals taking the swab and interpreting the cultures. This study aimed to determine the most sensitive detection method for meningococcal carriage. Throat swabs and saline mouth gargles, obtained from 89 university students, were processed in parallel by conventional culture and TaqMan
ctrA
PCR. Carriage of meningococci, as detected by the combined methods, was 20%. The sensitivities of throat swab culture, throat swab PCR, gargle culture, and gargle PCR were 72, 56, 56, and 50%, respectively, and the probabilities that these techniques would correctly identify the absence of carriage (negative predictive value [NPV]) were 93.4, 89.9, 89.9, and 88.8%. Culturing both throat swabs and gargles increased the NPV to 98.6%. The further addition of throat swab PCR increased this to 100%. Testing gargles by both culture and PCR was as sensitive as testing throat swabs by both methods, suggesting that gargles may be a suitable alternative for large-scale screening studies when throat swabs are difficult to obtain, although they required more lengthy laboratory processing. PCR was a useful adjunct to culture for detecting nasopharyngeal carriage, but it failed to detect some nongroupable strains. For maximum sensitivity, a combination of techniques was required. This study indicates the confidence with which health care professionals involved in meningococcal screening can regard laboratory results.
Tiamulin Activity against Fastidious and Nonfastidious Veterinary and Human Bacterial Isolates: Initial Development of In Vitro Susceptibility Test Methods
Authors: Jones Ronald N. , Pfaller Michael A. , Rhomberg Paul R. , Walter Donald H. 
Published: July 2002

ABSTRACT

Tiamulin is a pleuromutilin derivative used in veterinary practice for the control and specific therapy of infections in swine. This report summarizes studies to establish standardized susceptibility testing methods, interpretive criteria, and reagent details for use in veterinary methods recently developed by the National Committee for Clinical Laboratory Standards (NCCLS) (standards M31-A and M37-A, NCCLS, Wayne, Pa., 1999). A total of 636 fastidious and nonfastidious animal and human pathogens were processed by using media and procedures described by the NCCLS. Tiamulin disk diffusion tests used a 30-μg disk concentration, and the proposed MIC breakpoints corresponding to levels achievable in animal target tissues (lung) were ≤4 μg/ml for susceptibility and ≥32 μg/ml for resistance. Correlate zone diameters for specific nonfastidious species were as follows: for
Pasteurella multocida
and staphylococci tested on Mueller-Hinton agar, susceptibility at ≥19 mm and resistance at ≤11 mm, and for
Actinobacillus suis
,
Erysipelothrix rhusiopathiae
, and
Streptococcus suis
tested on enriched chocolate Mueller-Hinton agar, susceptibility at ≥16 mm and resistance at ≤8 mm. When
Actinobacillus pleuropneumoniae
was tested, a susceptibility breakpoint of ≤16 μg/ml (≥9 mm) was suggested for veterinary fastidious medium broth and enriched chocolate Mueller-Hinton agar. Absolute categorical agreement between NCCLS dilution and disk diffusion test results with these criteria ranged from 90.5 to 96.2%. Tiamulin susceptibility testing methods appear to be accurate in their categorical classification for indicated species, and their availability will allow immediate testing of animal isolates to guide therapy via appropriate levels of dosing and to monitor the development of resistance for agents in this unique class.
Epidemic Strains of
Shigella sonnei
Biotype g Carrying Integrons
Authors: McIver Christopher J. , White Peter A. , Jones Louisa A. , Karagiannis Tom , Harkness Jock , Marriott Deborah , Rawlinson William D. 
Published: July 2002

ABSTRACT

Class 2 integrons (Tn
7
) were found in all randomly selected epidemic (
n
= 27) and preepidemic (
n
= 13) strains of multiresistant
Shigella sonnei
biotype g. A class 1 integron was also found in two epidemic strains. Gene cassettes within these integrons account for resistance to commonly used therapeutic agents.