bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of a Three-Dimensional Microarray System for Detection of Levofloxacin Resistance and the
mecA
Gene in
Staphylococcus aureus
Authors: Nagaoka Tomonori , Horii Toshinobu , Satoh Takatomo , Ito Tomoko , Monji Akio , Takeshita Akihiro , Maekawa Masato 
Published: October 2005

ABSTRACT

We evaluated a novel three-dimensional microarray (PamChip microarray) system to detect the presence of levofloxacin-related resistance mutations and the
mecA
gene. The results were compared to those obtained for 27
Staphylococcus aureus
isolates by conventional DNA sequencing or PCR methods. Hybridization and fluorescence detection were performed using an FD10 system designed for PamChip microarray under conditions optimized for each target/probe on the array. In dilution series analysis using multiplex PCR samples, the sensitivity of the microarray was about 10 times greater than that of conventional PCR methods. A high level of data reproducibility was also confirmed in those analyses. Various point mutations in quinolone resistance-determining regions detected by our system corresponded perfectly to the results obtained by conventional DNA sequencing. The results of the
mecA
gene detection using our system also corresponded to the PCR method; that is, signal/band was detected in all isolates of methicillin-resistant
S. aureus
, and no signal/band was detected in any isolate of methicillin-susceptible
S. aureus
. In conclusion, our novel three-dimensional microarray system provided rapid, specific, easy, and reproducible results for the simultaneous detection of levofloxacin resistance and the
mecA
gene in
S. aureus
.
Diversity of Potential Short Tandem Repeats in
Mycobacterium leprae
and Application for Molecular Typing
Authors: Zhang Liangfen , Budiawan Teky , Matsuoka Masanori 
Published: October 2005

ABSTRACT

A recent advance in molecular typing for tracing the transmission of leprosy is the discovery of short tandem repeats (STRs) in
Mycobacterium leprae
. To substantiate polymorphic loci from STR as promising candidates for molecular typing tools in leprosy epidemiology, 44 STR loci including 33 microsatellites and 11 minisatellites were investigated among 27 laboratory strains by sequencing PCR products. Not all STRs were necessarily polymorphic. Thirty-two out of the 44 loci were polymorphic. Nine polymorphic loci were suitable for identifying genotypes according to the discriminatory capacity, stability, and reproducibility. All the strains were classified into independent genotypes by the selected nine loci. Three multicase households were subjected to molecular typing.
M. leprae
obtained from household cases showed identical copy numbers by TTC triplet alone, but the isolates from one family contact case were divided into different genotypes by adding eight other polymorphic loci. The combination of information from multiple loci allows increasing levels of discrimination and it is likely that the generation and documentation of data will result in the choice of a potential molecular typing tool for leprosy epidemiology.
Quality Control and Reference Guidelines for CLSI Broth Microdilution Susceptibility Method (M38-A Document) for Amphotericin B, Itraconazole, Posaconazole, and Voriconazole
Authors: Espinel-Ingroff A. , Fothergill A. , Ghannoum M. , Manavathu E. , Ostrosky-Zeichner L. , Pfaller M. , Rinaldi M. , Schell W. , Walsh T. 
Published: October 2005

ABSTRACT

Although standard conditions are available for testing the susceptibilities of filamentous fungi to antifungal agents by the Clinical and Laboratory Standards Institute (CLSI; formerly National Committee for Clinical Laboratory Standards) broth microdilution assay, quality control (QC) MIC limits have not been established for any mold-agent combination. This multicenter (eight-center) study documented the reproducibility of tests for one isolate of
Paecilomyces variotii
ATCC MYA-3630 and 11 other mold isolates (three isolates of
Aspergillus fumigatus
; two isolates of
A. terreus
; one isolate each of
A. flavus
,
A. nidulans
,
Fusarium moniliforme
, and
F. solani
; and two isolates of
Scedosporium apiospermum
) by the CLSI reference broth microdilution method (M38-A document). Control limits (amphotericin B, 1 to 4 μg/ml; itraconazole, 0.06 to 0.5 μg/ml; posaconazole, 0.03 to 0.25 μg/ml; voriconazole, 0.015 to 0.12 μg/ml) for the selected QC
P. variotii
ATCC MYA-3630 were established by the analysis of replicate MIC results. Reference isolates and corresponding MIC ranges were also established for 6 of the 12 molds evaluated. MIC limits were not proposed for the other five molds tested due to low testing reproducibility for these isolates.
Heterogeneity of Biofilms Formed by NonmucoidPseudomonas aeruginosaIsolates from Patients with Cystic Fibrosis
Authors: Lee Baoleri , Haagensen Janus A. J. , Ciofu Oana , Andersen Jens Bo , Høiby Niels , Molin Søren 
Published: October 2005

ABSTRACTBiofilms are thought to play a key role in the occurrence of lung infections byPseudomonas aeruginosain patients with cystic fibrosis (CF). In this study, 20 nonmucoidP. aeruginosaisolates collected during different periods of chronic infection from eight CF patients were assessed with respect to phenotypic changes and in vitro biofilm formation. The physiological alterations were associated with a loss of motility (35% were nonmotile) and with decreased production of virulence factors (pyocyanin, proteases) and quorum-sensing molecules (45% of the isolates were unable to produce 3-O-C12-homoserine lactone quorum-sensing molecules). Compared with wild-type strain PAO1, mostP. aeruginosaisolates demonstrated different degrees of reduction of adherence on polystyrene surfaces. The in vitro biofilm formation of isolates was investigated in a hydrodynamic flow system. Confocal laser scanning microscope analysis showed that the biofilm structures of theP. aeruginosaisolates were highly variable in biomass and morphology. Biofilm development of six genotypically identical sequential isolates recovered from a particular patient at different time points of chronic infection (20 years) and after lung transplantation demonstrated significant changes in biofilm architectures.P. aeruginosabiofilm formation followed a trend of decreased adherence with progression of the chronic lung infection. The results suggest that the adherent characteristic of in vitro biofilm development was not essential for the longitudinal survival of nonmucoidP. aeruginosaduring chronic lung colonization.
Decay of Human Immunodeficiency Virus Type 1 Unintegrated DNA Containing Two Long Terminal Repeats in Infected Individuals after 3 to 8 Years of Sustained Control of Viremia
Authors: McDermott Jennifer L. , Martini Isabella , Ferrari Davide , Bertolotti Francesca , Giacomazzi Claudio , Murdaca Giuseppe , Puppo Francesco , Indiveri Francesco , Varnier Oliviero E. 
Published: October 2005

ABSTRACT
Covert human immunodeficiency virus (HIV) replication was ongoing during the first 3 years of aviremia in 22 patients, as determined by detection of DNA containing two long terminal repeats (2LTR DNA). Although total HIV DNA was detected in 60 2LTR DNA-negative samples, the absence of 2LTR DNA in 90% of patients following 7 to 8 years of highly active antiretroviral therapy suggests suppression of cryptic viral replication.
Comparative Nucleotide Sequence Analysis of Polymorphic Variable-Number Tandem-Repeat Loci in
Mycobacterium ulcerans
Authors: Ablordey Anthony , Hilty Markus , Stragier Pieter , Swings Jean , Portaels Françoise 
Published: October 2005

ABSTRACT

We analyzed a set of variable-number tandem-repeat (VNTR) loci to assess their nucleotide sequence diversity in isolates of three
Mycobacterium ulcerans
genotypes. Sequence variants in two loci resulted in intraspecies resolution of Southeast Asian and Asian genotypes in contrast to a homogenous sequence composition among African isolates. Nucleotide sequence polymorphism in repeat units can enhance discrimination of VNTR loci.
Cervical Specimen Order and Performance Measures of
Chlamydia trachomatis
Diagnostic Testing
Authors: Ghanem Khalil G. , Johnson Robert E. , Koumans Emilia H. , Marrazzo Jeanne M. , Markowitz Lauri E. 
Published: October 2005

ABSTRACT

The orders of three endocervical specimens of 3,561 women for
Chlamydia trachomatis
testing were randomized to determine whether test performance measures of two nucleic acid amplification tests and a DNA probe were affected by swab order. Specimen collection order did not appear to affect the diagnostic accuracy of these tests.
Use of Stored Serum from Uganda for Development and Evaluation of a Human Immunodeficiency Virus Type 1 Testing Algorithm Involving Multiple Rapid Immunoassays
Authors: Singer Darrell E. , Kiwanuka Noah , Serwadda David , Nalugoda Fred , Hird Linda , Bulken-Hoover Jamie , Kigozi Godfrey , Malia Jennifer A. , Calero Eva K. , Sateren Warren , Robb Merlin L. , Wabwire-Mangen Fred , Wawer Maria , Gray Ronald H. , Sewankambo Nelson , Birx Deborah L. , Michael Nelson L. 
Published: October 2005

ABSTRACT
We report the development and evaluation of a human immunodeficiency virus type 1 testing algorithm consisting of three rapid antibody detection tests. Stored serum samples from Uganda were utilized with a final algorithm sensitivity of 100% and a specificity of 98.9% (95% confidence interval, 98.6% to 99.3%).
Pseudomonas putida
Septicemia in a Special Care Nursery Due to Contaminated Flush Solutions Prepared in a Hospital Pharmacy
Authors: Perz Joseph F. , Craig Allen S. , Stratton Charles W. , Bodner Stanley J. , Phillips Walter E. , Schaffner William 
Published: October 2005

ABSTRACT

Pseudomonas putida
bloodstream infections were reported in two preterm neonates from a special care nursery. An unopened container of preservative-free heparin flush, compounded several weeks earlier in the hospital pharmacy and from the same batch that was administered to the patients, grew
P. putida
with a pulsed-field gel electrophoresis (PFGE) pattern identical to that of the patients' isolates. Intrinsic contamination was ruled out by the absence of similar reports from other hospitals and by sterility testing of unopened stock solutions. We investigated the in vitro persistence of
P. putida
in heparinized saline: even under refrigerated conditions, inocula of 10
2
and 10
3
CFU/ml exhibited growth at 21 and 35 days, respectively. These findings highlight the need for compliance with current standards of aseptic technique and quality assurance during the preparation of compounded sterile products.
Multilocus Sequence Typing of
Escherichia coli
O26:H11 Isolates Carrying
stx
in Canada Does Not Identify Genetic Diversity
Authors: Gilmour Matthew W. , Cote Tyler , Munro Jamie , Chui Linda , Wylie John , Isaac-Renton Judith , Horsman Greg , Tracz Dobryan M. , Andrysiak Ashleigh , Ng Lai-King 
Published: October 2005

ABSTRACT

Multilocus sequence typing of 31
stx
-carrying
Escherichia coli
O26:H11 strains isolated in Canada between 1999 and 2003 revealed a high degree of genetic relatedness at 10 loci, suggesting either that this is a clonal serotype (similar to O157:H7) or that additional genetic loci need to be examined.
Evaluation of Universal Probes and Primer Sets for Assessing Total Bacterial Load in Clinical Samples: General Implications and Practical Use in Endodontic Antimicrobial Therapy
Authors: Horz H. P. , Vianna M. E. , Gomes B. P. F. A. , Conrads G. 
Published: October 2005

ABSTRACT

By reexamining 10 previously published “universal” PCR assays using the ARB phylogenetic software package and database with 41,000 16S rRNA gene sequences, we found that they differed considerably in their coverage of the domain
Bacteria
. We evaluated the broadest-range real-time quantitative PCR protocol for its efficacy in measuring the antimicrobial effects of endodontic treatments.
Prospective Multicenter Evaluation of a New Immunoassay and Real-Time PCR for Rapid Diagnosis of
Clostridium difficile
-Associated Diarrhea in Hospitalized Patients
Authors: van den Berg Renate J. , Bruijnesteijn van Coppenraet Lesla S. , Gerritsen Hendrik-Jan , Endtz Hubert P. , van der Vorm Eric R. , Kuijper Ed J. 
Published: October 2005

ABSTRACT

In a prospective multicenter study, 367 fecal samples from 300 patients with diarrhea were tested for
Clostridium difficile
-associated diarrhea (CDAD) with a new immunochromatography assay for toxins A and B (ICTAB), a real-time PCR on the toxin B gene, and the cell cytotoxicity assay. Twenty-three (6.2%) of the 367 fecal samples were positive by the cell cytotoxicity assay. With the cell cytotoxicity assay as the “gold standard,” the sensitivity, specificity, positive predictive value, and negative predictive value for the ICTAB assay and real-time PCR were 91, 97, 70, and 99%, and 87, 96, 57 and 99%, respectively. In conclusion, both the ICTAB and the real-time PCR can be implemented as rapid screening methods for patients suspected of having CDAD.
Outbreaks in Distinct Regions Due to a Single
Klebsiella pneumoniae
Clone Carrying a
bla
VIM-1
Metallo-β-Lactamase Gene
Authors: Ikonomidis Alexandros , Tokatlidou Despina , Kristo Ioulia , Sofianou Danai , Tsakris Athanassios , Mantzana Paraskevi , Pournaras Spyros , Maniatis Antonios N. 
Published: October 2005

ABSTRACT

From December 2004 to March 2005, 27
Klebsiella pneumoniae
clinical isolates that were positive by the imipenem-EDTA double-disk synergy test and that exhibited a single macrorestriction pattern were recovered in two distinct Greek hospitals. The isolates carried a transferable
bla
VIM-1
metallo-β-lactamase gene in a class 1 integron. Reverse transcriptase PCR showed that the gene was similarly expressed in low- and high-level carbapenem-resistant isolates, indicating the existence of additional resistance mechanisms. The clonal spread of VIM-1-producing
K. pneumoniae
strains in distinct regions where up to now
bla
VIM-2
and
bla
VIM-4
alleles were common is worrisome.
Comparison of Ashdown's Medium,
Burkholderia cepacia
Medium, and
Burkholderia pseudomallei
Selective Agar for Clinical Isolation of
Burkholderia pseudomallei
Authors: Peacock Sharon J. , Chieng Grace , Cheng Allen C. , Dance David A. B. , Amornchai Premjit , Wongsuvan Gumphol , Teerawattanasook Nittaya , Chierakul Wirongrong , Day Nicholas P. J. , Wuthiekanun Vanaporn 
Published: October 2005

ABSTRACT

Ashdown's medium,
Burkholderia pseudomallei
selective agar (BPSA), and a commercial
Burkholderia cepacia
medium were compared for their abilities to grow
B. pseudomallei
from 155 clinical specimens that proved positive for this organism. The sensitivity of each was equivalent; the selectivity of BPSA was lower than that of Ashdown's or
B. cepacia
medium.
Development of a Nested Qualitative Real-Time PCR Assay To Detect
Aspergillus
Species DNA in Clinical Specimens
Authors: Halliday Catriona , Wu Qi Xuan , James Gregory , Sorrell Tania 
Published: October 2005

ABSTRACT

We adapted a nested
Aspergillus
PCR to a nested qualitative real-time format on a LightCycler system. An evaluation using 134 clinical specimens showed that the real-time PCR assay significantly reduced the time for results to be made available without compromising sensitivity and was less labor-intensive. Its use will aid in the rapid diagnosis of invasive aspergillosis.
Use of Specific rRNA Oligonucleotide Probes for Microscopic Detection of
Mycobacterium tuberculosis
in Culture and Tissue Specimens
Authors: St. Amand Allison L. , Frank Daniel N. , De Groote Mary Ann , Basaraba Randall J. , Orme Ian M. , Pace Norman R. 
Published: October 2005

ABSTRACT

Mycobacterium tuberculosis
infections are a major global health problem. Fast and accurate detection of
M. tuberculosis
is clearly needed at both the clinical level and the research level. We report a rapid and reliable in situ hybridization technique using rRNA oligonucleotide probes for the identification of
M. tuberculosis
in tissues and cultures.
Mycobacterium thermoresistibile
Infection following Knee-Replacement Surgery
Authors: LaBombardi Vincent J. , Shastry Lalita , Tischler Henry 
Published: October 2005

ABSTRACT

We report a case of
Mycobacterium thermoresistibile
as a cause of infection following total knee replacement. This infection was masked by the prior isolation of a vancomycin-resistant enterococcus. The infection was resolved with long-term therapy using moxifloxacin and doxycycline.
Steinernema affine (Nematoda: Steinernematidae), a new record for North America and its distribution relative to other entomopathogenic nematodes in British Columbia
Authors: Webster John ,   Mráček, Kindlmann Pavel 
Published: October 2005

AbstractRandomly selected ecosystems in the coastal Greater Vancouver, Fraser valley and southern Vancouver Island regions, and in the interior Okanagan region of British Columbia, were sampled for the presence of entomopathogenic nematodes (EPN). Of 133 soil samples, 23 contained EPN (18 with steinernematids and five with heterorhabditids). Three identified species and one unidentified species were found. Steinernema affine and S. kraussei occurred in most EPN positive locations in the coastal regions sampled. Steinernema affine was found in open habitats and S. kraussei in all types of tree habitats. Steinernema feltiae was found in only one location, White Rock, in the Greater Vancouver region, close to an ocean beach. Heterorhabditis megidis occurred in only the drier Okanagan valley region of central, southern British Columbia, which has a more extreme climate than the moist, moderate climate of the coastal region. It occurred mostly in agricultural land represented by orchards, vineyards, and secondary woodland. In field baiting and laboratory experiments S. affine appeared to be a more successful parasite than S. kraussei.
The effect of fallow on Longidorus americanus, a nematode associated with stunting of loblolly pine seedlings in Georgia, USA
Authors: Fraedrich Stephen , Cram Michelle , Zarnoch Stanley 
Published: October 2005

AbstractStunting of loblolly pine (Pinus taeda L.) seedlings, caused by Longidorus americanus, has been a problem at a Georgia (USA) nursery. Field and growth chamber studies were conducted to determine the survivability of the nematode in fallow nursery soil. The population density of L. americanus decreased rapidly in the upper 15 cm of soil in fallow field plots during the first 101 days and the nematode was not detected after 263 days. Bioassays subsequently failed to detect the nematode in the upper 30 cm of soil in fallow plots on days 263 and 365. Population densities also decreased rapidly in fallow soil during the initial 130 days of the growth chamber study and the nematode was not detected at days 334 and 427, or in subsequent bioassays. Longidorus americanus does not survive well in the upper 15-30 cm of nursery soil in the absence of a host, and the use of fallow may be an acceptable alternative to pesticides for the management of this nematode.
Variability of the ITS rDNA and identification of Nacobbus aberrans (Thorne, 1935) Thorne & Allen, 1944 (Nematoda: Pratylenchidae) by rDNA amplification
Authors: Anthoine Géraldine , Mugniéry Didier 
Published: October 2005

AbstractIn order to identify the false root-knot nematode, Nacobbus aberrans, a nematode of quarantine importance, investigations were undertaken at the molecular level. Study of the ITS rDNA region among six South American populations showed an extremely high polymorphism. This polymorphism is due to point mutation insertions-deletions, the importance of which is increased by the presence of a degenerate microsatellite in this region. The usefulness of the ITS rDNA is therefore questionable when designing a species-specific identification tool. A study based on partial sequences of the 18S gene was carried out. A conserved part of the 18S gene, with a low level of variation when compared to Pratylenchus spp. and Meloidogyne spp., was found in all the N. aberrans populations tested. The primer set designed for this part of the 18S gene allows the amplification of a 295 bp fragment in all the N. aberrans populations tested. No amplification was obtained with other species belonging to Pratylenchidae, Heteroderidae or Hoplolaimidae. This PCR-based identification tool is effective on all N. aberrans migratory stages. From this study it is concluded that this N. aberrans specific primer set may provide a very useful tool for the identification of South American N. aberrans populations and thereby assist diagnosticians in implementing N. aberrans quarantine regulations.
Variation in the number of Bursaphelenchus xylophilus in aliquots of stock suspensions artificially inoculated on to subject pines
Authors: Yamanobe Taro 
Published: October 2005

AbstractThe procedures used to estimate the number of pine wood nematodes (Bursaphelenchus xylophilus) in stock suspensions and the variation in the number of nematodes in inocula applied to subject pine trees were examined. The findings suggest that preparing dilutions using 1 ml aliquots and making two replicate dilutions and three replicate counts of each dilution (or three dilutions and two counts) results in a precision of ±15% and an elapsed time for the majority of the population estimate procedures of less than 900 seconds. Under these conditions, the variation in the number of nematodes in the inocula was estimated to range from 55 to 156% of the intended population. This variation in the number of pine wood nematodes inoculated is unavoidable; thus, researchers should account for this variation when interpreting data from trials involving the artificial inoculation of pines.
Effects of nematode infection and mulching on the yield of plantain (Musa spp., AAB-group) ratoon crops and plantation longevity in southeastern Nigeria
Authors: Auwerkerken Annemarie , Dubois Thomas , De Schutter Bart , Speijer Paul , Rotimi Omalara , De Waele Dirk , Coyne Danny , Tenkouano Abdou 
Published: October 2005

AbstractThe effects of nematode infection and mulching on plantain cv. Agbagba (Musa spp., AAB-group, false horn) yield and plantation longevity were examined in a field experiment at the High Rainfall Station of the International Institute of Tropical Agriculture (IITA) at Onne in southeastern Nigeria. The 2nd, 3rd and 4th crop cycles (1st, 2nd and 3rd ratoon, respectively) following the plant crop cycle (mother crop) were examined in nematode inoculated or non-inoculated and mulched or non-mulched treatments. Nematodes (Radopholus similis, Helicotylenchus multicinctus and, to a lesser extent, Helicotylenchus dihystera, Hoplolaimus pararobustus and Meloidogyne spp.) were inoculated at planting of the mother plant, but were also present in relatively high population densities in the non-inoculated treatments at harvest of the 1st crop cycle. Plants inoculated with nematodes failed to reach harvest and neither did plants in the non-inoculated non-mulched treatments in any ratoon. Only non-inoculated mulched plants reached harvest, producing 0.85, 1.22 and 0.2 Mg ha−1, respectively in the 1st, 2nd and 3rd ratoon, taking toppled, broken and dead plants into consideration. Mulched plants were larger, had more suckers, survived longer and had healthier root systems compared with non-mulched plants. Damage to roots was greater in the inoculated plants compared with the non-inoculated plants for the 1st and 2nd ratoons but not for the 3rd ratoon. Radopholus similis was most strongly associated with root damage (percentage root necrosis and dead roots), although H. multicinctus population densities were also positively correlated with percentage root necrosis. At flowering of the 1st ratoon, 71% of the inoculated non-mulched plants were dead compared with only 1% of the non-inoculated mulched plants. Helicotylenchus multicinctus remained the most abundant nematode throughout the experiment. Together with R. similis, it comprised over 95% of the plant-parasitic nematode population.