bluuebunny/crossref_metadata_2025_split huggingface dataset:
tRNA Is the Source of Low-Level
trans-
Zeatin Production in
Methylobacterium
spp
Authors: Koenig Robbin L. , Morris Roy O. , Polacco Joe C. 
Published: July 2002

ABSTRACT

Pink-pigmented facultatively methylotrophic bacteria (PPFMs), classified as
Methylobacterium
spp., are persistent colonizers of plant leaf surfaces. Reports of PPFM-plant dialogue led us to examine cytokinin production by PPFMs. Using immunoaffinity and high-performance liquid chromatography (HPLC) purification, we obtained 22 to 111 ng of
trans
-zeatin per liter from culture filtrates of four PPFM leaf isolates (from
Arabidopsis
, barley, maize, and soybean) and of a
Methylobacterium extorquens
type culture originally recovered as a soil isolate. We identified the zeatin isolated as the
trans
isomer by HPLC and by a radioimmunoassay in which monoclonal antibodies specific for
trans
-hydroxylated cytokinins were used. Smaller and variable amounts of
trans
-zeatin riboside were also recovered.
trans
-Zeatin was recovered from tRNA hydrolysates in addition to the culture filtrates, suggesting that secreted
trans
-zeatin resulted from tRNA turnover rather than from de novo synthesis. The product of the
miaA
gene is responsible for isopentenylation of a specific adenine in some tRNAs. To confirm that the secreted zeatin originated from tRNA, we mutated the
miaA
gene of
M. extorquens
by single exchange of an internal
miaA
fragment into the chromosomal gene. Mutant exconjugants, confirmed by PCR, did not contain zeatin in their tRNAs and did not secrete zeatin into the medium, findings which are consistent with the hypothesis that all zeatin is tRNA derived rather than synthesized de novo. In germination studies performed with heat-treated soybean seeds, cytokinin-null (
miaA
) mutants stimulated germination as well as wild-type bacteria. While cytokinin production may play a role in the plant-PPFM interaction, it is not responsible for stimulation of germination by PPFMs.
Construction of an Integration-Proficient Vector Based on the Site-Specific Recombination Mechanism of Enterococcal Temperate Phage φFC1
Authors: Yang Hee-Youn , Kim Young-Woo , Chang Hyo-Ihl 
Published: July 2002

ABSTRACTThe genome of temperate phage φFC1 integrates into the chromosome ofEnterococcus faecalisKBL 703 via site-specific recombination. In this study, an integration vector containing theattPsite and putative integrase genemj1of phage φFC1 was constructed. A 2,744-bp fragment which included theattPsite andmj1was inserted into a pUC19 derivative containing thecatgene to construct pEMJ1-1.E. faecalisKBL 707, which does not contain the bacteriophage but which has a putativeattBsite within its genome, could be transformed by pEMJ1-1. Southern hybridization, PCR amplification, and DNA sequencing revealed that pEMJ1-1 was integrated specifically at the putativeattBsite within theE. faecalisKBL 707 chromosome. This observation suggested that the 2,744-bp fragment carryingmj1and theattPsite of phage φFC1 was sufficient for site-specific recombination and that pEMJ1-1 could be used as a site-specific integration vector. The transformation efficiency of pEMJ1-1 was as high as 6 × 103transformants/μg of DNA. In addition, a vector (pATTB1) containing the 290-bpattBregion was constructed. pATTB1 was transformed intoEscherichia colicontaining a derivative of the pET14b vector carryingattPandmj1.This resulted in the formation of chimeric plasmids by site-specific recombination between the clonedattBandattPsequences. The results indicate that the integration vector system based on the site-specific recombination mechanism of phage φFC1 can be used for genetic engineering inE. faecalisand in other hosts.
Molecular Epidemiology of the Integron-Located VEB-1 Extended-Spectrum β-Lactamase in Nosocomial Enterobacterial Isolates in Bangkok, Thailand
Authors: Girlich Delphine , Poirel Laurent , Leelaporn Amornrut , Karim Amal , Tribuddharat Chanwitt , Fennewald Michael , Nordmann Patrice 
Published: July 2002

ABSTRACTOver a 2½-month period in 1999, 37 ceftazidime-resistant nonrepetitive enterobacterial isolates were collected from 37 patients in a Bangkok hospital, Thailand. Eighty-one percent of these strains expressed a clavulanic acid-inhibited extended-cephalosporin resistance profile. An identical extended-spectrum β-lactamase (ESBL), VEB-1, was found in 16 unrelated enterobacterial isolates (Escherichia coli,n= 10;Enterobacter cloacae,n= 2;Enterobacter sakazakii,n= 1; andKlebsiella pneumoniae,n= 3) and in two clonally relatedE. cloacaeisolates. TheblaVEB-1gene was located on mostly self-conjugative plasmids (ca. 24 to 200 kb) that conferred additional non-β-lactam antibiotic resistance patterns. Additionally, theblaVEB-1gene cassette was part of class 1 integrons varying in size and structure. TheblaVEB-1-containing integrons were mostly associated withblaOXA-10-like andarr-2-like gene cassettes, the latter conferring resistance to rifampin. These data indicated the spread ofblaVEB-1in Bangkok due to frequent transfer of different plasmids and class 1 integrons and rarely to clonally related strains. Plasmid- and integron-mediated resistance to rifampin was also found in enterobacterial isolates.
Detection and Initial Characterization of Novel Capsular Polysaccharide among Diverse
Campylobacter jejuni
Strains Using Alcian Blue Dye
Authors: Karlyshev Andrey V. , Wren Brendan W. 
Published: July 2002

ABSTRACT

We have recently demonstrated that most strains of
Campylobacter jejuni
produce capsular polysaccharide (CPS), which can be detected by immunoblotting with homologous Penner antisera on polyvinylidene difluoride membranes (A. V. Karlyshev, D. Linton, N. A. Gregson, A. J. Lastovica, and B. W. Wren, Mol. Microbiol. 35:529–541, 2000). In this report, we describe a universal and rapid staining procedure using Alcian blue for
C. jejuni
CPS, which does not rely on the availability of antisera and identifies CPS in untypeable strains. Furthermore, Alcian blue staining identified CPS in its lipid-free form directly on Tricine gels, and we demonstrate that CPS is thermostable and is accumulated in the culture supernatant in a lipid-free form. The identification of a newly described CPS and its lipid-free form in
C. jejuni
should prove invaluable in studying the pathogenesis and epidemiology of this important pathogen.
Outbreak of Necrotizing Enterocolitis Associated with
Enterobacter sakazakii
in Powdered Milk Formula
Authors: van Acker Jos , de Smet Francis , Muyldermans Gaëtan , Bougatef Adel , Naessens Anne , Lauwers Sabine 
Published: July 2002

ABSTRACT

We describe an outbreak of necrotizing enterocolitis (NEC) that occurred in the neonatal intensive care unit of our hospital. A total of 12 neonates developed NEC in June-July 1998. For two of them, twin brothers, the NEC turned out to be fatal.
Enterobacter sakazakii
, a known contaminant of powdered milk formula, was isolated from a stomach aspirate, anal swab, and/or blood sample for 6 of the 12 neonates. A review of feeding procedures revealed that 10 of the 12 patients were fed orally with the same brand of powdered milk formula.
E. sakazakii
was isolated from the implicated prepared formula milk as well as from several unopened cans of a single batch. Molecular typing by arbitrarily primed PCR (AP-PCR) confirmed, although partially, strain similarity between milk and patient isolates. No further cases of NEC were observed after the use of the contaminated milk formula was stopped. With this outbreak we show that intrinsic microbiological contamination of powdered milk formula can be a possible contributive factor in the development of NEC, a condition encountered almost exclusively in formula-fed premature infants. The use of sterilized liquid milk formula in neonatal care could prevent problems with intrinsic and extrinsic contamination of powdered milk formula.
Contamination of Transplantable Human Tumor-Bearing Lines by
Helicobacter hepaticus
and Its Elimination
Authors: Goto Kazuo , Ishihara Ken-Ichi , Kuzuoka Ayako , Ohnishi Yasuyuki , Itoh Toshio 
Published: July 2002

ABSTRACT

Helicobacter hepaticus
contaminating nonfrozen tumors was transmissible to severe combined immunodeficient (SCID) mice, but the organism in cryopreserved samples was not. This suggests that
H. hepaticus
has the ability to spread via biomaterials and that freezing-thawing is able to reduce the numbers of organisms to levels insufficient for subcutaneous infection of SCID mice.
Analysis of Microsatellite Markers of
Candida albicans
Used for Rapid Typing
Authors: Botterel Françoise , Desterke Christophe , Costa Catherine , Bretagne Stéphane 
Published: July 2002

ABSTRACT

To obtain a rapid genotyping method of
Candida albicans
, three polymorphic microsatellite markers were investigated by multiplex PCR. The three loci, called
CDC3
,
EF3
, and
HIS3
, were chosen because they are on different chromosomes so as to improve the chances of finding polymorphisms. One set of primers was designed for each locus, and one primer of each set was dye-labeled to read PCR signals by using an automatic sequencer. Amplifications were performed directly from the colonies harvested on the agar plate without a sophisticated DNA extraction step. At total of 27 reference strains and 73 clinical independent isolates were tested. The numbers of allelic associations were 10, 22, and 25 for the loci
CDC3
,
EF3
, and
HIS3
, respectively. The combined discriminatory power of the three microsatellites markers was 0.97. The markers were stable after 25 subcultures, and the amplifications were specific for
C. albicans
. An initial study of 17 clinical isolate pairs, including blood culture and peripheral sites, showed a similar genotype for 15 of them, confirming that candidemia usually originates from the colonizing isolate. Therefore, microsatellite marker analysis with multiplex PCR and automated procedures has a high throughput and should be suitable for large epidemiologic studies of
C. albicans
.
Risk Factors for Antibiotic-Resistant
Escherichia coli
Isolated from Hospitalized Patients with Urinary Tract Infections: a Prospective Study
Authors: Sotto Albert , De Boever Corinne Merle , Fabbro-Peray Pascale , Gouby Anne , Sirot Danielle , Jourdan Jacques 
Published: July 2002

ABSTRACT

From November 1998 to February 1999 we prospectively evaluated the prevalence of resistance to penicillins, cephalosporins, carbapenem, quinolones, aminoglycosides, and trimethoprim-sulfamethoxazole (SXT) in 320
Escherichia coli
isolates isolated from hospitalized patients with acute urinary tract infections (UTIs). We also studied for these strains risk factors for resistance to amoxicillin-clavulanic acid (AMC), fluoroquinolones (FQs), and SXT. Resistance rates were consistent with those from major recent studies reported in the literature. Multivariate analyses selected the following factors as being significantly associated with
E. coli
resistance: (i) for resistance to AMC, prior (1 year) UTI (odds ratio [OR] = 2.71,
P
= 0.006), prior (1 year) urinary catheter (OR = 2.98,
P
= 0.0025), and prior (6 months) antibiotic exposure (OR = 2.68,
P
= 0.005); (ii) for resistance to FQs male sex (OR = 3.87,
P
= 0.03), with a trend toward significance for age >65 years (OR = 7.67,
P
= 0.06) and prior (1 year) UTI (OR = 2.98,
P
= 0.07); and (iii) for resistance to SXT, male sex (OR = 1.91,
P
= 0.046), hospitalization in an intermediate-term-care unit (OR = 2.18,
P
= 0.008), and prior (1 year) UTI (OR = 2.03,
P
= 0.03). Ours results suggest that prior UTI is a common risk factor for resistance to the different antibiotics tested. Although few studies on risk factors for
E. coli
resistance to antibiotics have been published, careful interpretation of their findings, taking into consideration the population, infection site, and period studied, should contribute to the formulation of a better strategy that can be used to overcome antibiotic resistance.
Kaposi's Sarcoma Associated with Previous Human Herpesvirus 8 Infection in Kidney Transplant Recipients
Authors: Cattani Paola , Capuano Maria , Graffeo Rosalia , Ricci Rosalba , Cerimele Francesca , Cerimele Decio , Nanni Giuseppe , Fadda Giovanni 
Published: July 2002

ABSTRACT
This study investigates the prevalence of human herpesvirus 8 (HHV-8) infection in kidney transplant patients, evaluating the risk of HHV-8 transmission via transplantation and the association between pre- and posttransplantation HHV-8 infection and the subsequent development of Kaposi's sarcoma (KS). Immunofluorescence and an enzyme immunoassay were used to determine HHV-8 seroprevalence in 175 patients awaiting kidney transplantation and 215 controls who were attending our clinic for other reasons. All patients in the study came from central or southern Italy. Seroprevalence was similar in both groups (14.8 versus 14.9%), with no significant difference between the rates for male and female patients. Of the 175 patients, 100 were tested for anti-HHV-8 antibodies at various times during follow-up. During follow-up, seroprevalence increased from 12% on the date of transplantation to 26%. This increase was paralleled by an age-related increase in seroprevalence in the control group. During follow-up from 3 months to 10 years after transplantation, KS was diagnosed in seven patients (4.0%). Six of these patients were positive for HHV-8 prior to transplantation. Overall, 23.0% of patients who were HHV-8 positive before transplantation developed KS, whereas only 0.7% of seronegative patients developed the disease (relative risk, 34.4; 95% confidence interval, 4.31 to 274.0). This finding suggests that the key risk factor for KS is infection prior to transplantation and that antibody detection in patients awaiting transplantation could be useful in identifying patients at high risk for KS. In patients from geographic areas with a high prevalence of HHV-8, serological tests on donors may be less important.
Breast Milk Transmission of a Panton-Valentine Leukocidin-Producing
Staphylococcus aureus
Strain Causing Infantile Pneumonia
Authors: Le Thomas Isabelle , Mariani-Kurkdjian Patricia , Collignon Anne , Gravet Alain , Clermont Olivier , Brahimi Naı̈ma , Gaudelus Joël , Aujard Yannick , Navarro Jean , Beaufils François , Bingen Edouard 
Published: July 2002

ABSTRACT

We report on a 38-day-old infant who developed pleuropneumonia due to a
Staphylococcus aureus
strain responsible for familial furunculosis, which was acquired by maternal breast-feeding. All isolates from the infant and parents were genetically related by randomly amplified polymorphic DNA analysis and produced Panton-Valentine leukocidin.
Fatal Pulmonary Infection Due to Multidrug-Resistant
Mycobacterium abscessus
in a Patient with Cystic Fibrosis
Authors: Sanguinetti Maurizio , Ardito Fausta , Fiscarelli Ersilia , La Sorda Marilena , D'Argenio Patrizia , Ricciotti Gabriella , Fadda Giovanni 
Published: July 2002

ABSTRACT

We report a case of fatal pulmonary infection caused by
Mycobacterium abscessus
in a young patient with cystic fibrosis, who underwent bipulmonary transplantation after a 1-year history of severe lung disease. Fifteen days after surgery he developed septic fever with progressive deterioration in lung function.
M. abscessus
, initially isolated from a pleural fluid specimen, was then recovered from repeated blood samples, suggesting a disseminated nature of the mycobacterial disease. Drug susceptibility testing assay, performed on two sequential isolates of the microorganism, showed a pattern of multidrug resistance. Despite aggressive therapy with several antimycobacterial drugs, including clarithromycin, the infection persisted, and the patient died.
Diagnostics of
Neisseriaceae
and
Moraxellaceae
by Ribosomal DNA Sequencing: Ribosomal Differentiation of Medical Microorganisms
Authors: Harmsen Dag , Singer Christian , Rothgänger Jörg , Tønjum Tone , Sybren de Hoog Gerrit , Shah Haroun , Albert Jürgen , Frosch Matthias 
Published: July 2002

ABSTRACT

Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the
Neisseriaceae
and
Moraxellaceae
. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera
Acinetobacter, Moraxella
, and
Neisseria
, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to
Escherichia coli
positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600).
Neisseria macacae
and
Neisseria mucosa
subsp.
mucosa
(ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of
Acinetobacter lwoffii, Moraxella lacunata
, and
N. mucosa. Neisseria meningitidis
isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of
Neisseriaceae
and
Moraxellaceae
and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (
http://www.ridom.hygiene.uni-wuerzburg.de/
). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes.
Classification and Identification of Enterococci: a Comparative Phenotypic, Genotypic, and Vibrational Spectroscopic Study
Authors: Kirschner C. , Maquelin K. , Pina P. , Ngo Thi N. A. , Choo-Smith L.-P. , Sockalingum G. D. , Sandt C. , Ami D. , Orsini F. , Doglia S. M. , Allouch P. , Mainfait M. , Puppels G. J. , Naumann D. 
Published: July 2002

ABSTRACT

Rapid and accurate identification of enterococci at the species level is an essential task in clinical microbiology since these organisms have emerged as one of the leading causes of nosocomial infections worldwide. Vibrational spectroscopic techniques (infrared [IR] and Raman) could provide potential alternatives to conventional typing methods, because they are fast, easy to perform, and economical. We present a comparative study using phenotypic, genotypic, and vibrational spectroscopic techniques for typing a collection of 18
Enterococcus
strains comprising six different species. Classification of the bacteria by Fourier transform (FT)-IR spectroscopy in combination with hierarchical cluster analysis revealed discrepancies for certain strains when compared with results obtained from automated phenotypic systems, such as API and MicroScan. Further diagnostic evaluation using genotypic methods—i.e., PCR of the species-specific ligase and glycopeptide resistance genes, which is limited to the identification of only four
Enterococcus
species and 16S RNA sequencing, the “gold standard” for identification of enterococci—confirmed the results obtained by the FT-IR classification. These results were later reproduced by three different laboratories, using confocal Raman microspectroscopy, FT-IR attenuated total reflectance spectroscopy, and FT-IR microspectroscopy, demonstrating the discriminative capacity and the reproducibility of the technique. It is concluded that vibrational spectroscopic techniques have great potential as routine methods in clinical microbiology.
Development of Reverse Transcriptase PCR Assays for Detection of Active Human Herpesvirus 6 Infection
Authors: Van den Bosch Glenn , Locatelli Giuseppe , Geerts Lieve , Fagà Giovanni , Ieven Margareta , Goossens Herman , Bottiger Disa , Öberg Bo , Lusso Paolo , Berneman Zwi N. 
Published: July 2002

ABSTRACT
We developed reverse transcriptase (RT) PCR assays for the detection of mRNA from three spliced genes of human herpesvirus 6 (HHV-6), the immediate-early genes U16/U17 and U89/U90 and the late gene U60/U66. Sequence analysis determined the splicing sites of these genes. The new assays may be instrumental in investigating the association between HHV-6 and disease.
Effects of Two Different Growth Media on the Postantifungal Effect Induced by Polyenes on
Candida
Species
Authors: Shu M. , Ellepola A. N. B. , Samaranayake L. P. 
Published: July 2002

ABSTRACT

There are no data on the effects of different growth media on polyene-induced postantifungal effect (PAFE) in
Candida
species. Hence, the nystatin- and amphotericin B-induced PAFEs in six
Candida
species (26 isolates) grown in Sabouraud's dextrose broth (SAB) and RPMI broth were evaluated, following limited exposure to the MICs of the two polyenes, using an automated turbidometric method. For nystatin, PAFE varied between 1.88 and 4.87 h in SAB and 0.66 and 6.89 h in RPMI, and for amphotericin B, the equivalent values were 3.13 to 10.98 h in SAB and 0.97 to 7.01 h in RPMI. These highly significant (
P
< 0.001) variations in the PAFE with both drugs, noted with most
Candida
strains grown in different media, call for standardization of intralaboratory methodology in measuring this parameter in order to obtain universally comparable data.
Genetic Variation among Hospital Isolates of Methicillin-Sensitive
Staphylococcus aureus
: Evidence for Horizontal Transfer of Virulence Genes
Authors: Moore P. C. L. , Lindsay J. A. 
Published: July 2002

ABSTRACT

Staphylococcus aureus
strains often carry in their genomes virulence genes that are not found in all strains and that may be carried on discrete genetic elements. Strains also differ in that they carry one of four classes of an accessory gene regulator (
agr
) locus, an operon that regulates virulence factor expression and that has been proposed to be a therapeutic target. To look at their distribution among hospital strains, we investigated 38 methicillin-sensitive
S. aureus
isolates, classifying the isolates by
agr
class and screening them for the presence and restriction fragment length polymorphisms (RFLPs) of 12 core and 14 accessory virulence genes. Twenty-three (61%) were
agr
class I, 10 (26%) were
agr
class II, and 5 (13%) were
agr
class III. None were
agr
class IV. The
S. aureus
strains had distinguishable RFLP profiles, although clusters of isolates with clearly related core gene profiles were found among our strains, including all five
agr
class III strains, two sets of six strains within
agr
class I, and six strains within
agr
class II. Within these clusters there was evidence of horizontal acquisition and/or loss of multiple accessory virulence genes. Furthermore, two isolates from the same patient were identical except for the presence of the
sea
gene, indicating that movement of mobile elements may occur in vivo. Several strong correlations with the carriage of virulence genes between strains were seen, including a positive correlation between
tst
and
agr
class III and negative correlations between
tst
and
lukE-splB
and between
lukE-splB
and
seg-sei
. This suggests that the core genome or the presence of accessory genetic elements within a strain may influence acquisition and loss of other elements encoding virulence genes.