bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Results of Voriconazole Disk Diffusion Testing for
Candida
Species with Results from a Central Reference Laboratory in the ARTEMIS Global Antifungal Surveillance Program
Authors: Pfaller M. A. , Boyken L. , Messer S. A. , Tendolkar S. , Hollis R. J. , Diekema D. J. 
Published: October 2005

ABSTRACT

The accuracy of antifungal susceptibility testing is important for reliable resistance surveillance and for the clinical management of patients with serious infections. Our primary objective was to compare the results of voriconazole disk diffusion testing of
Candida
spp. performed by centers participating in the ARTEMIS program with disk diffusion and MIC results obtained by the central reference laboratory. A total of 2,934 isolates of
Candida
spp. were tested by CLSI disk diffusion and reference broth microdilution methods in the central reference laboratory. These results were compared to the results of disk diffusion testing performed in the 54 participating centers. All tests were performed and interpreted following CLSI recommendations, as follows: susceptible (S), MIC of ≤1 μg/ml (≥17 mm); susceptible dose dependent (SDD), MIC of 2 μg/ml (14 to 16 mm); and resistant (R), MIC of ≥4 μg/ml (≤13 mm). The overall categorical agreement between participant disk diffusion test results and reference laboratory MIC results was 94.1%, with 0.1% very major errors (VME) and 3.4% major errors (ME). The categorical agreement between disk diffusion test results obtained in the reference laboratory and the MIC test results was 99.0%. Likewise, good agreement was observed between participant disk diffusion test results and reference laboratory disk diffusion test results, with an agreement of 93.8%, 0.2% VME, and 3.4% ME. The disk diffusion test was reliable for detecting those isolates of
Candida
spp. that were characterized as resistant (MIC of ≥4 μg/ml) by MIC testing. External quality assurance data obtained by surveillance programs such as the ARTEMIS Global Antifungal Surveillance Program ensure the generation of useful surveillance data and result in the continued improvement of antifungal susceptibility testing practices.
Detection of
Aspergillus
Galactomannan Antigenemia To Determine Biological and Clinical Implications of Beta-Lactam Treatments
Authors: Bart-Delabesse Emmanuelle , Basile Maria , Al Jijakli Ahmad , Souville Didier , Gay Frédérick , Philippe Bruno , Bossi Philippe , Danis Martin , Vernant Jean-Paul , Datry Annick 
Published: October 2005

ABSTRACT

Detection of
Aspergillus
galactomannan (GM) in serum with the Platelia
Aspergillus
enzyme immunoassay (EIA) is useful for diagnosing invasive aspergillosis. From May 2003 to November 2004, 65 patients who did not develop aspergillosis had at least two positive sera while receiving a beta-lactam treatment (GM index [GMI], ≥0.5). Of the 69 treatment episodes scored, 41 consisted of a beta-lactam other than piperacillin-tazobactam (
n
= 29), namely, amoxicillin-clavulanate (
n
= 25), amoxicillin (
n
= 10), ampicillin (
n
= 3), or phenoxymethylpenicillin (
n
= 2). In all cases, antigenemia became negative 24 h to 120 h upon stopping the antibiotic. Monitoring of 35 patients, including 26 with hematological malignancies, revealed three antigenemia kinetic patterns: each was observed with any drug regimen and consisted of a persistent GMI of >2.0 (65.7%), >0.5, and ≤1.5 (25.7%) or a variable GMI (14.3%) from the onset of antibiotic therapy. All available drug batches given to 26 patients cross-reacted with the EIA. Galactomannan titration in batches failed to predict the GM titers in the five patients studied at cumulative doses of ampicillin or amoxicillin-clavulanate, regardless of the time lapse between serum sampling and infusion period. Our results show that beta-lactams other than piperacillin-tazobactam may lead to false presumption of aspergillosis. The resulting kinetic patterns of GM antigenemia are variable, and sampling serum prior to the next beta-lactam dose may not decrease GMI below the threshold. Consequently, testing of suspected antibiotic batches remains the only indicator of possible false EIA positivity.
Evaluation of a Rapid Direct Assay for Identification of Bacteria and the
mecA
and
van
Genes from Positive-Testing Blood Cultures
Authors: Eigner U. , Weizenegger M. , Fahr A.-M. , Witte W. 
Published: October 2005

ABSTRACT

We performed the first evaluation of a DNA strip assay (GenoType blood culture; Hain Lifescience, Nehren, Germany) for the detection of the most relevant bacterial sepsis pathogens directly from positive BACTEC blood culture bottles (Becton Dickinson, Heidelberg, Germany). The test comprises two panels, one for the direct species identification of important gram-positive cocci and the other for gram-negative rods. Additionally, detection of the
mecA
and the
van
genes are implemented. The GenoType assay was validated regarding its analytical sensitivity with blood cultures spiked with reference strains. Approximately 10
4
CFU per ml were detected. Analytical specificity was calculated with a test panel of 212 reference strains. Of the strains tested, 99% were correctly identified. Additionally, 279 consecutive blood cultures signaled positive by BACTEC were processed directly, in comparison to conventional methods. The GenoType assays were performed according to Gram stain morphology. A total of 243 (87.1%) of the 279 organisms isolated were covered by specific probes. A total of 152 organisms were gram-positive cocci, of which 148 (97.4%) were correctly identified by the GenoType assay. Ninety-one organisms were gram-negative rods, of which 89 (97.8%) were correctly identified. Concerning
mecA
gene detection, GenoType assay correctly detected 12 of 13 methicillin-resistant
Staphylococcus aureus
isolates. One
Enterococcus faecium
isolate with a positive
vanA
gene isolated was correctly differentiated by the assay. All results were available 4 h after the results of microscopic analysis. The evaluated GenoType blood culture assay showed fast and reliable results in detecting the most important sepsis pathogens and the
mecA
and
van
genes directly from positive blood culture bottles.
Use of Sequence Data Generated in the Bayer TruGene Genotyping Assay To Recognize and Characterize Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains
Authors: Hirigoyen Diane L. , Cartwright Charles P. 
Published: October 2005

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) gene sequences obtained during antiretroviral resistance testing with a commercial genotyping assay (TruGene; Bayer Corp.) were analyzed to assess the utility of these data for detecting and characterizing non-subtype-B HIV-1 strains. A total of 125 viral sequences obtained from patients believed to have acquired their HIV-1 infection in Africa were analyzed, of which 121 were determined to belong to non-B subtypes. Utilizing TruGene sequence data alone, 92 (76%) of these viruses could be subtyped by conventional phylogenetic analysis. The addition of supplemental RT sequence data enabled a further 28 (23.1%) viruses to be classified, while one (0.9%) sample could not be classified conclusively. Two internet-accessible databases that generate HIV-1 subtypes from PR and RT sequences (HIV-SEQ and Geno2Pheno) were also evaluated, and both achieved 88% concordance (106/120) with phylogenetic analysis. Non-subtype-B and B-subtype HIV-1 sequences could be readily discriminated by tallying silent polymorphisms listed on the TruGene research report. The mean number of silent polymorphisms in the non-B HIV-1 sequences identified in this study was 58.3 (95% confidence interval [CI], 41.1 to 75.5), compared with 20.7 (95% CI, 9.9 to 31.5) for the four subtype B viruses in the study cohort and 118 case-matched B-subtype controls. Sequence data generated in the TruGene HIV-1 genotyping assay could, therefore, provide a ready means of tracking the prevalence and identity of non-B subtypes in HIV-1-infected populations undergoing routine antiretroviral resistance testing.
Use of the DiversiLab System for Species and Strain Differentiation of
Fusarium
Species Isolates
Authors: Healy M. , Reece K. , Walton D. , Huong J. , Frye S. , Raad I. I. , Kontoyiannis D. P. 
Published: October 2005

ABSTRACT
Advances in molecular typing of fusariosis would facilitate the study of its epidemiology. We tested 26 such isolates by the commercially available DiversiLab System. The system utilizes automated repetitive sequence-based PCR (rep-PCR) and web-based data analyses. rep-PCR dendrogram cluster analysis showed agreement with species sequence identification (elongation factor 1 alpha gene). Additionally, subtype differences within the same species were noted.
Ten Cases of
Actinobaculum schaalii
Infection: Clinical Relevance, Bacterial Identification, and Antibiotic Susceptibility
Authors: Reinhard Mark , Prag Jørgen , Kemp Michael , Andresen Keld , Klemmensen Belinda , Højlyng Niels , Sørensen Susan Hildebrand , Christensen Jens Jørgen 
Published: October 2005

ABSTRACT

Nine of 10 strains of
Actinobaculum schaalii
caused urinary tract infections in predisposed individuals. Identification included 16S rRNA gene sequence analysis and use of the API Coryne and Rapid ID32A test systems.
A. schaalii
is easily overlooked due to its slow growth in ambient air and its resemblance to the normal bacterial flora on skin and mucosa.
Comparison of API 50 CH Strips to Whole-Chromosomal DNA Probes for Identification of
Lactobacillus
Species
Authors: Boyd Melinda A. , Antonio May A. D. , Hillier Sharon L. 
Published: October 2005

ABSTRACT
The API 50 CH identification system was evaluated for the identification of 97 strains of commensal lactobacilli. This system agreed with the species-level identifications for none of the 7 reference strains and only 4 of 90 vaginal isolates identified using whole-chromosomal DNA probes.
Prospective Comparison of Cell Cultures and Nucleic Acid Amplification Tests for Laboratory Diagnosis of
Chlamydia trachomatis
Infections
Authors: Jespersen Deborah J. , Flatten Karen S. , Jones Mary F. , Smith Thomas F. 
Published: October 2005

ABSTRACT

Specimens submitted in M5 medium for cell culture detection of
Chlamydia trachomatis
were tested by nucleic acid amplification testing (NAAT) and in cell cultures. Of 35 (genital) and 26 (nongenital) specimens positive for
C. trachomatis
, 21 and 14 specimens, respectively, were detected exclusively by NAAT. NAAT is significantly (
P
< 0.0001) more sensitive than cell culture and should be considered the new “gold standard” for the laboratory diagnosis of
C. trachomatis
infections.
Sequence-Based Typing of
adeB
as a Potential Tool To Identify Intraspecific Groups among Clinical Strains of Multidrug-Resistant
Acinetobacter baumannii
Authors: Huys Geert , Cnockaert Margo , Nemec Alexandr , Swings Jean 
Published: October 2005

ABSTRACT

Sequence
analysis of an 850-bp fragment internal to the aspecific drug efflux
gene
adeB
revealed 11 sequence types (STs) among a collection
of 50 multidrug-resistant
Acinetobacter baumannii
(MDRAB)
strains, including members of pan-European clones I, II, and III. The
delineation of STs conformed with the intraspecific grouping of these
strains previously determined by different DNA fingerprinting methods.
Larger strain collections need to be screened to further explore the
potential of sequence-based
adeB
typing as a universal tool
for the monitoring of MDRAB
clones.
Single Multiplex PCR Assay To Identify Simultaneously the Six Categories of Diarrheagenic
Escherichia coli
Associated with Enteric Infections
Authors: Vidal Maricel , Kruger Eileen , Durán Claudia , Lagos Rosanna , Levine Myron , Prado Valeria , Toro Cecilia , Vidal Roberto 
Published: October 2005

ABSTRACT

We designed a multiplex PCR for the detection of all categories of diarrheagenic
Escherichia coli
. This method proved to be specific and rapid in detecting virulence genes from Shiga toxin-producing (
stx
1
,
stx
2
, and
eae
), enteropathogenic (
eae
and
bfp
), enterotoxigenic (
stII
and
lt
), enteroinvasive (
virF
and
ipaH
), enteroaggregative (
aafII
), and diffuse adherent (
daaE
)
Escherichia coli
in stool samples.
Endophthalmitis Caused by
Fusarium proliferatum
Authors: Ferrer Consuelo , Alio Jorge , Rodriguez Alejandra , Andreu Mariano , Colom Francisca 
Published: October 2005

ABSTRACT

Fusarium proliferatum
caused endophthalmitis after cataract surgery. Diagnosis was established by classical microbiology and molecular biology methods (PCR and DNA typing). The treatment with local amphotericin B, oral ketoconazole, and topical natamycin was successful.
Bacteremia Caused by a Metronidazole-Resistant
Prevotella
sp. Strain
Authors: Mory Francine , Carlier Jean-Philippe , Alauzet Corentine , Thouvenin Maxime , Schuhmacher Hélène , Lozniewski Alain 
Published: October 2005

ABSTRACT

Metronidazole resistance among
Prevotella
spp. is rare. We report here the first case of bacteremia due to a high-level metronidazole-resistant
Prevotella
sp. responsible for treatment failure.
First Case of Osteomyelitis Due to
Shewanella algae
Authors: Botelho-Nevers E. , Gouriet F. , Rovery C. , Paris P. , Roux V. , Raoult D. , Brouqui P. 
Published: October 2005

ABSTRACT

Shewanella
spp. are infrequently recovered from clinical specimens. We report here on the first case of osteomyelitis due to
Shewanella algae
. This bacterium, at first misidentified by phenotypic tests as
Shewanella putrefaciens
, was subsequently identified correctly as
S. algae
by 16S rRNA gene sequence analysis.
First Report of
Salmonella enterica
Serotype Panama Meningitis Associated with Consumption of Contaminated Breast Milk by a Neonate
Authors: Chen Te-Li , Thien Peck-Foong , Liaw Shu-Chin , Fung Chang-Phone , Siu L. K. 
Published: October 2005

ABSTRACT

Salmonella enterica
serotype Panama is capable of causing severe infection in children and is often transmitted via contaminated food. Here, we present the first documented case of serotype Panama infection that was acquired through the consumption of contaminated breast milk. The mother excreted the organism asymptomatically for at least 2 weeks.
Control of plant-parasitic nematodes with extracts of Quillaja saponaria
Authors: Magunacelaya Juan Carlos , Martín Ricardo San 
Published: October 2005

AbstractAqueous extracts of the tree Quillaja saponaria Molina, containing triterpenoid saponins, polyphenols, salts and sugars, were tested against the most important plant-parasitic nematodes present in Chile: Xiphinema index, X. americanum s.l., Meloidogyne hapla, M. ethiopica, Pratylenchus thornei, Tylenchorhynchus sp., Criconemoides xenoplax and Helicotylenchus sp. Three different products were tested in the laboratory: i) QL 1000® (whole extract containing saponin and non-saponin fractions); ii) QL ULTRA® (saponin fraction); and iii) QL NS® (non-saponin fraction). The results showed that QL 1000® had important nematicidal effects at economically attractive doses (e.g., 100 ppm). When used separately, QL ULTRA® and QL NS® had minimum nematicidal effects. However, the combined use of both products gave similar results to QL 1000®, suggesting a synergy between the saponin and non-saponin fractions. Based on this, QL 1000® was tested in commercial vineyards and table grapes in the Central region of Chile. The use of 30 l ha−1 showed a similar control and fruit yields to synthetic chemical nematicides.
The Thelastomatoidea (Nematoda: Oxyurida) of two sympatric Panesthiinae (Insecta: Blattodea) from southeastern Queensland, Australia: taxonomy, species richness and host specificity
Authors: Schneider Margaret , Cribb Tom , Jex Aaron ,   Harley
Published: October 2005

AbstractThe thelastomatoid fauna of two species of wood-burrowing cockroach (Blattodea, Blaberidae), Panesthia cribrata and Panesthia tryoni tryoni, from Lamington National Park, Australia, is described. The following eight new species and three new genera of thelastomatid are proposed: Bilobostoma exerovulva n. g., n. sp.; Cordonicola gibsoni n. sp.; Coronostoma australiae n. sp.; Desmicola ornata n. sp.; Hammerschmidtiella hochi n. sp.; Malaspinanema goateri n. g., n. sp.; Travassosinema jaidenae n. sp.; and Tsuganema cribratum n. g., n. sp. Additional data are given for Blattophila sphaerolaima and Leidynemella fusiformis. Of the 11 species reported, nine were found in P. cribrata and ten in P. tryoni tryoni. Such levels of thelastomatoid species richnessness in single host species are exceptional. Only the mole cricket, Gryllotalpa africana (23), and the domestic cockroach, Periplaneta americana (20), have higher reported richness. Three species, T. jaidenae, C. australiae and D. ornata, were found either exclusively or significantly more prevalently in P. tryoni tryoni than in P. cribrata. Species of Travassosinema, Coronostoma and Desmicola have been found previously only in millipedes (Diplopoda), a fact that suggests that there is a greater degree of niche overlap between P. tryoni tryoni and millipedes than for P. cribrata.
Comparison of the in-soil hatching responses of Globodera rostochiensis and G. pallida in the presence and absence of the host potato crop cv. British Queen
Authors: Devine Ken , Ryan Aileen 
Published: October 2005

AbstractExperiments were conducted in a field in Co. Cork, Ireland, to investigate the hatching behaviour of the two potato cyst nematode (PCN) species, Globodera rostochiensis and G. pallida, in soil in the presence and absence of a host potato crop cv. British Queen. In order to compare the hatching behaviour of the two PCN species in the field, standardised populations of each PCN species (produced under identical conditions for the two previous generations and extracted without desiccation) were inserted into the field in tissue-embedding cassettes by means of a novel 'harpoon' insertion tool. Inserting cassettes of both PCN species at different distances from host potato plants and destructively sampling the contents of the cassettes over the first 8 weeks after plant emergence revealed that there was no significant difference in the hatch of either PCN species around the host plant. Hatches in excess of 80% for both PCN species were recorded 8 weeks after plant emergence over a range of depths (10-40 cm) and distances (10-50 cm) around the host potato plants. Substantial hatches of G. rostochiensis (82%) and G. pallida (88%) were also recorded at a depth of 20 cm in the furrow at harvesting. Monitoring the rate of spontaneous hatching of G. rostochiensis and G. pallida in the absence of host potato plants over the spring and summer months (a 20-week period) revealed that there was a significant difference in the rate of spontaneous hatching between the two PCN species, with G. rostochiensis juveniles hatching in greater numbers over the first 14 weeks than G. pallida juveniles. However, by mid-August the mean spontaneous hatch for both PCN species within the top 30 cm of soil was found to be 37%.
Enhancing taxonomic resolution: distribution dependent genetic diversity in populations of Meloidogyne
Authors: Navas Alfonso , Flores-Romero Pilar 
Published: October 2005

AbstractRoot-knot nematodes (Meloidogyne) are one of the most damaging agricultural pests. The polyploid apomictic M. arenaria, M. javanica and M. incognita are particularly ubiquitous and exhibit an extreme polyphagy. The taxonomic position of these three species remains unclear, as does the phylogenetic relationships between them. To characterise phenotype variants among these three species, allozyme electrophoresis (α-EST, MDH, CAT, GPI, DIA, GOT, and SOD) was performed in populations from the Iberian Peninsula. A total of 50 multilocus enzyme electrophoresis (MLEE) phenotype variants were detected of which, according to the esterase pattern, 24 corresponded to M. arenaria, 15 to M. javanica and 11 to M. incognita. The phylogenetic relationships of these 50 MLEE variants were studied following the Neighbour-Joining (NJ) distance method based on an allelic frequencies matrix built using two different methodologies. In addition, Maximum-Parsimony (MP) and Maximum-Likelihood (ML) phylogenetic methods were done in order to corroborate the phylogenies obtained. Our results showed a great disparity in the NJ trees obtained, thus indicating that the monophyly of the parthenogenetic Meloidogyne spp. would seem to depend on the methodology used. Evolutionary and epidemiological implications of the recovered phylogenies are discussed.
Identification of Meloidogyne spp. from North East Libya and comparison of their inter- and intra-specific genetic variation using RAPDs
Authors: Phillips Mark , Adam Mohamed , Blok Vivian 
Published: October 2005

AbstractFour techniques, i.e., perineal patterns, isozymes, specific sequence characterised amplified region-polymerase chain reaction (SCAR-PCR) and random amplified polymorphic DNA (RAPD), were compared for the identification of species of root-knot nematode (RKN) from Libya. The RAPD technique proved superior for species diagnosis. A population from Massa that could not, because of atypical patterns, be identified using either perineal patterns or isozyme phenotypes, showed amplification patterns consistent with those of M. incognita. A new esterase phenotype is described for this population. Single egg mass lines from two other locations, Elhamma and Durnah, were identified as M. javanica, whereas those from Aun Mare were identified as M. incognita. RAPDs were used to examine the relationships between the Libyan isolates and isolates of Meloidogyne spp. from elsewhere. This technique revealed differences in the Libyan isolates of M. incognita that distinguished them from isolates from other geographic origins. The work demonstrates the potential to utilise the RAPD technique in an integrated programme to control RKN.
Some Effects of Model Resolution on Simulated Gravity Waves Generated by Deep, Mesoscale Convection
Authors: Lane Todd P. , Knievel Jason C. 
Published: October 2005

Abstract
Over the past decade, numerous numerical modeling studies have shown that deep convective clouds can produce gravity waves that induce a significant vertical flux of horizontal momentum. Such studies used models with horizontal grid spacings of O(1 km) and produced strong gravity waves with horizontal wavelengths greater than about 20 km. This paper is an examination of how simulated gravity waves and their momentum flux are sensitive to model resolution. It is shown that increases in horizontal resolution produce more power in waves with shorter horizontal wavelengths. This change in the gravity waves’ spectra influences their vertical propagation. In some cases, gravity waves that were vertically propagating in coarse simulations become vertically trapped in fine simulations, which strongly influences the vertical flux of horizontal momentum.
Downward Wave Propagation on the Polar Vortex
Authors: Scott R. K. , Dritschel D. G. 
Published: October 2005

Abstract
This paper considers the propagation of waves on the edge of a stratospheric polar vortex, represented by a three-dimensional patch of uniform potential vorticity in a compressible quasigeostrophic system. Waves are initialized by perturbing the vortex from axisymmetry in the center of the vortex, and their subsequent upward and downward propagation is measured in terms of a nonlinear, pseudomomentum-based wave activity. Under conditions typical of the winter stratosphere, the dominant direction of wave propagation is downward, and wave activity accumulates in the lower vortex levels. The reason for the preferred downward propagation arises from a recent result of Scott and Dritschel, which showed that the three-dimensional Green’s function in the compressible system contains an anisotropy that causes a general differential rotation in a finite volume vortex. The sense of the differential rotation is to stabilize the upper vortex and destabilize the lower vortex. This mechanism is particularly interesting in view of recent interest in the downward influence of the stratosphere on the troposphere and also provides a possible conservative, balanced explanation of the formation of the robust dome plus annulus potential vorticity structure observed in the upper stratosphere.