bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-Year Evaluation of
Borrelia burgdorferi
Culture and Supplemental Tests for Definitive Diagnosis of Lyme Disease
Authors: Coulter Peggy , Lema Clara , Flayhart Diane , Linhardt Amy S. , Aucott John N. , Auwaerter Paul G. , Dumler J. Stephen 
Published: October 2005

ABSTRACT

Lyme disease is usually diagnosed and treated based on clinical manifestations. However, laboratory testing is useful for patients with confusing presentations and for validation of disease in clinical studies. Although cultivation of
Borrelia burgdorferi
is definitive, prior investigations have shown that no single test is optimal for Lyme disease diagnosis. We applied high-volume blood culture, skin biopsy culture, PCR, and serodiagnosis to a cohort of patients with suspected Lyme disease acquired in Maryland and southern Pennsylvania. The study was performed to confirm the relative utility of culture and to identify laboratory testing algorithms that will supplement clinical diagnosis. Overall, 30 of 86 patients (35%) were culture positive, whereas an additional 15 of 84 (18%) were seropositive only (51% total sero- and culture positive), and PCR on skin biopsy identified 4 additional patients who were neither culture nor seropositive. Among 49 laboratory test-positive patients, the highest sensitivity (100%) for diagnosis was obtained when culture, skin PCR, and serologic tests were used, although serologic testing with skin PCR was almost as sensitive (92%). Plasma PCR was infrequently positive and provided no additional diagnostic value. Although culture is definitive and has a relatively high sensitivity, the results required a mean of 3.5 weeks to recovery. The combination of acute-phase serology and skin PCR was 75% sensitive, offering a practical and relatively rapid alternative for confirming clinical impression. The full battery of tests could be useful for patients with confusing clinical signs or for providing strong laboratory support for clinical studies of Lyme disease.
Delineation of
Campylobacter concisus
Genomospecies by Amplified Fragment Length Polymorphism Analysis and Correlation of Results with Clinical Data
Authors: Aabenhus Rune , On Stephen L. W. , Siemer Berit L. , Permin Henrik , Andersen Leif P. 
Published: October 2005

ABSTRACT

Campylobacter concisus
has been as frequently isolated from human diarrhea as the important enteropathogen
Campylobacter jejuni
, but it also occurs in the feces of healthy individuals. The role of
C. concisus
in human disease has been difficult to determine, since the species comprises at least two phenotypically indistinguishable but genetically distinct taxa (i.e., genomospecies) that may vary in pathogenicity. We examined 62
C. concisus
strains by amplified fragment length polymorphism (AFLP) profiling and correlated the results with clinical data. All
C. concisus
strains gave unique AFLP profiles, and numerical analysis of these data distributed the strains among four clusters. The clustering was of taxonomic significance: two clusters contained, respectively, the type strain (of oral origin) and a reference strain (from diarrhea) of each of the known genomospecies. Genomospecies 2 strains were more frequently isolated from immunocompetent patients and/or patients without concomitant infections that presented with fever, chronic diarrhea, and gut inflammation than was genomospecies 1, clustering with the type strain of oral origin. Bloody diarrhea was recorded only with
C. concisus
genomospecies 2 infections. We identified two additional
C. concisus
genomospecies: genomospecies 3 comprised a single strain from an immunocompetent patient, and genomospecies 4 contained five isolates from severely immunodeficient patients, i.e., organ transplantation recipients or those with hematological malignancies. All genomospecies 4 strains were of the same protein profile group and failed to react with a
C. concisus
species-specific PCR assay based on 23S rRNA gene sequences: the taxonomic position of this group requires closer investigation.
Campylobacter concisus
is genetically and taxonomically diverse and contains at least four distinct genomospecies that may exhibit differences in their spectra of virulence potential.
Development of Multiplex PCRs for Detection of Common Viral Pathogens and Agents of Congenital Infections
Authors: McIver C. J. , Jacques C. F. H. , Chow S. S. W. , Munro S. C. , Scott G. M. , Roberts J. A. , Craig M. E. , Rawlinson W. D. 
Published: October 2005

ABSTRACT

Potential
causes of congenital infection include
Toxoplasma gondii
and
viruses such as cytomegalovirus (CMV), enterovirus, hepatitis C virus,
herpes simplex virus types 1 and 2 (HSV-1 and -2), human herpesvirus
types 6, 7, and 8, lymphocytic choriomeningitis virus, parvovirus,
rubella virus, and varicella-zoster virus. Testing for each of these
agents using nucleic acid tests is time consuming and the availability
of clinical samples such as amniotic fluid or neonatal blood is often
limited. The aim of this study was to develop multiplex PCRs (mPCRs)
for detection of DNA and RNA agents in the investigation of congenital
infection and an mPCR for the viruses most commonly requested in a
diagnostic virology laboratory (CMV, Epstein-Barr virus, enterovirus,
HSV-1, HSV-2, and varicella-zoster virus). The assays were assessed
using known pathogen-positive tissues (cultures, placentae, plasma, and
amniotic fluid) and limits of detection were determined for all the
agents studied using serial dilutions of plasmid targets. Nested PCR
was performed as the most sensitive assay currently available, and
detection of the amplicons using hybridization to labeled probes and
enzyme-linked immunosorbent assay detection was incorporated into three
of the four assays. This allowed detection of 10 to 10
2
copies of each agent in the samples processed. In several patients, an
unexpected infection was diagnosed, including a case of encephalitis
where HSV was the initial clinical suspicion but CMV was detected. In
the majority of these cases the alternative agent could be confirmed
using reference culture, serology, or fluorescence methods and was of
relevance to clinical care of the patient. The methods described here
provide useful techniques for diagnosing congenital infections and a
paradigm for assessment of new multiplex PCRs for use in the diagnostic
laboratory.
Individual Donor Nucleic Acid Amplification Testing for Detection of West Nile Virus
Authors: Lee Dong-Hun , Mathew John , Pfahler Wolfram , Ma Dongling , Valinsky Jay , Prince Alfred M. , Andrus Linda 
Published: October 2005

ABSTRACT
We have developed an economical, high-throughput nucleic acid amplification test (NAT) for blood-borne viruses, suitable for use in the screening of plasma samples from individual blood donors. This assay system includes a semiautomated procedure, using 96-well glass fiber plates for the extraction of viral nucleic acids from plasma and “universal beacon” technology which permits the detection of all genotypes of highly variable viruses (e.g., human immunodeficiency virus and hepatitis C virus). In this detection system, two fluorescent- detection technologies were employed successfully in a single tube: molecular beacon for West Nile virus (WNV) detection using a 6-carboxyfluorescein fluorophore and TaqMan for internal control detection using a VIC fluorophore. To establish proof of concept, we focused on the development of a robust individual donor NAT for WNV. The assay showed no reactivity to 15 other viruses tested or to 420 blood donor samples from the WNV pre-epidemic season. No cross-contamination was observed on an alternating positive-/negative-well test. The sensitivity (limit of detection, 95%) of the assay for WNV is between 3.79 and 16.3 RNA copies/ml, depending on which material was used as a standard. The assay detected all positive blood donation samples identified by the Roche WNV NAT. The assay can be performed qualitatively for screening and quantitatively for confirmation.
Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR
Authors: Fredricks David N. , Smith Caitlin , Meier Amalia 
Published: October 2005

ABSTRACT

The detection of fungal pathogens in clinical samples by PCR requires the use of extraction methods that efficiently lyse fungal cells and recover DNA suitable for amplification. We used quantitative PCR assays to measure the recovery of DNA from two important fungal pathogens subjected to six DNA extraction methods.
Aspergillus fumigatus
conidia or
Candida albicans
yeast cells were added to bronchoalveolar lavage fluid and subjected to DNA extraction in order to assess the recovery of DNA from a defined number of fungal propagules. In order to simulate hyphal growth in tissue,
Aspergillus fumigatus
conidia were allowed to form mycelia in tissue culture media and then harvested for DNA extraction. Differences among the DNA yields from the six extraction methods were highly significant (
P
< 0.0001) in each of the three experimental systems. An extraction method based on enzymatic lysis of fungal cell walls (yeast cell lysis plus the use of GNOME kits) produced high levels of fungal DNA with
Candida albicans
but low levels of fungal DNA with
Aspergillus fumigatus
conidia or hyphae. Extraction methods employing mechanical agitation with beads produced the highest yields with
Aspergillus
hyphae. The MasterPure yeast method produced high levels of DNA from
C. albicans
but only moderate yields from
A. fumigatus
. A reagent from one extraction method was contaminated with fungal DNA, including DNA from
Aspergillus
and
Candida
species. In conclusion, the six extraction methods produce markedly differing yields of fungal DNA and thus can significantly affect the results of fungal PCR assays. No single extraction method was optimal for all organisms.
Molecular Epidemiology of Methicillin-Resistant
Staphylococcus aureus
in Zürich, Switzerland (2003): Prevalence of Type IV SCC
mec
and a New SCC
mec
Element Associated with Isolates from Intravenous Drug Users
Authors: Qi Wei , Ender Miriam , O'Brien Frances , Imhof Alexander , Ruef Christian , McCallum Nadine , Berger-Bächi Brigitte 
Published: October 2005

ABSTRACT

The majority of methicillin-resistant
Staphylococcus aureus
(MRSA) isolates, recovered in 2003 at the Department of Medical Microbiology in Zürich, Switzerland, belonged to major clones that are circulating worldwide. Staphylococcal cassette chromosome
mec
type IV (SCC
mec
-IV), harbored by half of the isolates, was found in sequence type 217 (ST217), which is an allelic variant of epidemic MRSA-15 (designated EMRSA-15), in a new local ST617 descending from clonal complex CC8 and in low-level oxacillin-resistant strains of multiple genetic lineages characteristic of community-onset MRSA. SCC
mec
-I, SCC
mec-
II, and SCC
mec
-III were in the minority, and four MRSA isolates had complex, rearranged SCC
mec
elements. A novel SCC
mec
-N1 of approximately 30 kb, associated with a
dfrA
gene and a
ccr4
-related recombinase complex, was identified in a large number of low-level oxacillin-resistant isolates, which descended from the successful clonal complex CC45 and are spreading among intraveneous drug users. In contrast, the SCC
mec
types of oxacillin-resistant coagulase-negative staphylococci (MRCNS) were of completely different composition. SCC
mec
type I (SCC
mec
-I) and SCC
mec
-II were more frequent than in the MRSA, while fewer contained SCC
mec
-IV. The other MRCNS displayed 11 different, complex patterns, suggesting frequent recombination between different SCC
mec
elements. With one
ccr
-negative exception, these strains amplified between one and three different
ccr
products, indicating either new varied complexes or multiple
ccr
loci. This suggests the presence of novel SCC
mec
types in MRCNS and no extensive interspecies SCC
mec
transfer between MRSA and MRCNS.
Molecular Phylogenetics of the Genus
Trichosporon
Inferred from Mitochondrial Cytochrome
b
Gene Sequences
Authors: Biswas Swarajit Kumar , Wang Li , Yokoyama Koji , Nishimura Kazuko 
Published: October 2005

ABSTRACT

Mitochondrial cytochrome
b
(cyt
b
) genes of 42 strains representing 23 species of the genus
Trichosporon
were partially sequenced to determine their molecular phylogenetic relationships. Almost half of the 22 strains investigated (from 11 different species) contained introns in their sequences. Analysis of a 396-bp coding sequence from each strain of
Trichosporon
under investigation showed a total of 141 (35.6%) variable nucleotide sites. A phylogenetic tree based on the cyt
b
gene sequences revealed that all species of
Trichosporon
except
Trichosporon domesticum
and
Trichosporon montevideense
had species-specific cyt
b
genes.
Trichosporon
sp. strain CBS 5581 was identified as
Trichosporon pullulans
, and one clinical isolate, IFM 48794, was identified as
Trichosporon faecale
. Analysis of 132-bp deduced amino acid sequences showed a total of 34 (25.75%) variable amino acid sites.
T. domesticum
and
T. montevideense
,
Trichosporon asahii
and
Trichosporon asteroides
, and
Trichosporon gracile
and
Trichosporon guehoae
had identical amino acid sequences. A phylogenetic tree constructed with the ascomycetes
Saccharomyces douglasii
and
Candida glabrata
taken as outgroup species and including representative species from closely related genera species of
Trichosporon
clustered with other basidiomycetous yeasts that contain xylose in their cell wall compositions. These results indicate the effectiveness of mitochondrial cyt
b
gene sequences for both species identification and the phylogenetic analysis of
Trichosporon
species.
First Case of Septicemia Due to a Strain Belonging to Enteric Group 58 (
Enterobacteriaceae
) and Its Designation as
Averyella dalhousiensis
gen. nov., sp. nov., Based on Analysis of Strains from 20 Additional Cases
Authors: Johnson Andrew S. , Tarr Cheryl L. , Brown B. H. , Birkhead Karen M. , Farmer J. J. 
Published: October 2005

ABSTRACT

When enteric group 58 was first described as a distinct new group of
Enterobacteriaceae
in 1985, there were only five known human isolates: four from wounds and one from feces. In 1996, we investigated the first blood isolate of enteric group 58, a case of sepsis in a 33-year-old woman receiving total parenteral nutrition. Fifteen additional clinical isolates have since been identified at CDC, including several recognized from a collection of “unidentified” strains dating back to 1973. All strains were characterized with a standard set of 49 biochemical tests used for
Enterobacteriaceae
, and the results were analyzed to determine phenotypic relatedness and best taxonomic fit. Antibiograms were determined as a taxonomic tool. Original identifications provided by submitting laboratories encompassed a wide variety of
Enterobacteriaceae
, including 14 species in eight genera, the most common being
Enterobacter
spp.,
Salmonella
spp.,
Serratia
spp.,
Kluyvera
spp., or
Escherichia
spp. Enteric group 58 strains have been most frequently isolated from traumatic injuries, fractures, and wounds and rarely from feces. Defining its clinical significance and distinguishing infection from colonization requires further study, but our case report indicates that serious systemic infection can occur. The vernacular name enteric group 58 was used from 1985 to 2004. In this paper, we formally name it
Averyella dalhousiensis
gen. nov., sp. nov., on the basis of its unique phenotype and its unique 16S rRNA gene sequence. These data indicate that enteric group 58 is not closely related to any of the existing genera or species of
Enterobacteriaceae
. The type strain is designated CDC9501-97, and a phenotypic definition is given based on all 21 strains.
Trichophyton eboreumsp. nov. Isolated from Human Skin
Authors: Brasch Jochen , Gräser Yvonne 
Published: October 2005

ABSTRACTAn unusual dermatophyte was isolated from the plantar scales of a human immunodeficiency virus-positive man with tinea pedis. Morphology, physiology, and molecular data provided evidence to support the new speciesTrichophyton eboreum.This dermatophyte is characterized by rapid growth on common mycological media, a flat powdery off-white colony, formation of clavate microconidia, smooth- and thin-walled cylindrical or club-shaped macroconidia with two to nine cells, the presence of hook-shaped hyphae, the production of cleistothecium-like structures and spiral hyphae in older cultures, positive hair perforation, the absence of pigmentation on potato glucose agar, the absence of a requirement for vitamins, a weak positive urease reaction, no growth at 37°C, resistance to 5% NaCl, resistance to fluconazole, good growth on human epidermal keratin, and the production of various enzymes on different media by the API-ZYM test. More than 5% divergence from any known species of dermatophyte was revealed by sequence analysis of the internal transcribed spacer of the rRNA gene.
Contribution of Systematic Serological Testing in Diagnosis of Infective Endocarditis
Authors: Raoult D. , Casalta J. P. , Richet H. , Khan M. , Bernit E. , Rovery C. , Branger S. , Gouriet F. , Imbert G. , Bothello E. , Collart F. , Habib G. 
Published: October 2005

ABSTRACT

Despite progress with diagnostic criteria, the type and timing of laboratory tests used to diagnose infective endocarditis (IE) have not been standardized. This is especially true with serological testing. Patients with suspected IE were evaluated by a standard diagnostic protocol. This protocol mandated an evaluation of the patients according to the modified Duke criteria and used a battery of laboratory investigations, including three sets of blood cultures and systematic serological testing for
Coxiella burnetii
,
Bartonella
spp.,
Aspergillus
spp.,
Legionella pneumophila
, and rheumatoid factor. In addition, cardiac valvular materials obtained at surgery were subjected to a comprehensive diagnostic evaluation, including PCR aimed at documenting the presence of fastidious organisms. The study included 1,998 suspected cases of IE seen over a 9-year period from April 1994 to December 2004 in Marseilles, France. They were evaluated prospectively. A total of 427 (21.4%) patients were diagnosed as having definite endocarditis. Possible endocarditis was diagnosed in 261 (13%) cases. The etiologic diagnosis was established in 397 (93%) cases by blood cultures, serological tests, and examination of the materials obtained from cardiac valves, respectively, in 348 (81.5%), 34 (8%), and 15 (3.5%) definite cases of IE. Concomitant infection with streptococci and
C. burnetii
was seen in two cases. The results of serological and rheumatoid factor evaluation reclassified 38 (8.9%) possible cases of IE as definite cases. Systematic serological testing improved the performance of the modified Duke criteria and was instrumental in establishing the etiologic diagnosis in 8% (34/427) cases of IE.
Mycobacterium avium
subsp.
paratuberculosis
, Genetic Susceptibility to Crohn's Disease, and Sardinians: the Way Ahead
Authors: Sechi Leonardo A. , Gazouli Maria , Ikonomopoulos John , Lukas John C. , Scanu Antonio M. , Ahmed Niyaz , Fadda Giovanni , Zanetti Stefania 
Published: October 2005

ABSTRACT

The
present study was performed to determine what proportion of people in
Sardinia with or without Crohn's disease were infected with
Mycobacterium avium
subspecies
paratuberculosis
and
had a preponderance of allelic variants of Nod2, an intracellular
protein involved in Crohn's disease susceptibility. Genetic analysis of
the alleles of the NOD2/CARD15 gene (
insC3020
,
G908R, and R702W alleles), linked to susceptibility or
genetic predisposition to Crohn's disease in humans, was
carried out on specimens from 37 Crohn's disease patients and 34
patients without Crohn's disease. Our results show that more than 70
percent of people in Sardinia with Crohn's disease carry at least one
of the susceptibility-associated NOD2/CARD15 alleles and
were infected with
Mycobacterium avium
subspecies
paratuberculosis
.
Development of Daptomycin Resistance In Vivo in Methicillin-Resistant
Staphylococcus aureus
Authors: Hayden M. K. , Rezai K. , Hayes R. A. , Lolans K. , Quinn J. P. , Weinstein R. A. 
Published: October 2005

ABSTRACT

Daptomycin is a new lipopeptide antibiotic that is rapidly bactericidal against
Staphylococcus aureus
. We report daptomycin resistance and treatment failure in 2 patients with osteomyelitis due to methicillin-resistant
S. aureus
. Disk diffusion susceptibility testing failed to detect resistance. Daptomycin at high concentration retained bactericidal activity against resistant isolates.
Rapid Screening of Urine Specimens for Bacteriuria by the Cellenium System
Authors: Pancholi Preeti , Pavletich Kathleen , Della-Latta Phyllis 
Published: October 2005

ABSTRACT
This study evaluated the performance of the Cellenium 160US urine screening system in comparison to that of the semiquantitative culture method. The performance characteristics of the Cellenium system for all clinically significant uropathogens were 89.5% sensitivity, 94.4% specificity, 97.1% negative predictive value, and 81% positive predictive value.
Multi-Virulence-Locus Sequence Typing Clarifies Epidemiology of Recent Listeriosis Outbreaks in the United States
Authors: Chen Yi , Zhang Wei , Knabel Stephen J. 
Published: October 2005

ABSTRACT
Multi-virulence-locus sequence typing (MVLST) was used to analyze isolates from two major listeriosis outbreaks in the United States in 1998 and 2002 that were due to consumption of contaminated hot dogs and turkey deli meat, respectively. MVLST demonstrated high epidemiological relevance and indicated that the two outbreaks were the result of one epidemic.
Changes in Serum Immunoglobulin G Levels as a Marker for
Cryptosporidium
sp. Infection in Peruvian Children
Authors: Priest Jeffrey W. , Bern Caryn , Roberts Jacquelin M. , Kwon James P. , Lescano Andres G. , Checkley William , Cabrera Lilia , Moss Delynn M. , Arrowood Michael J. , Sterling Charles R. , Gilman Robert H. , Lammie Patrick J. 
Published: October 2005

ABSTRACT
In a retrospective analysis, we assessed the usefulness of two serologic enzyme-linked immunosorbent assays as epidemiologic tools for the detection of cryptosporidiosis episodes in children from a Peruvian community. The incidence rate determined by the serologic assay was higher than the rate determined by stool microscopy (0.77 versus 0.41 infection/child-year of surveillance).
Oligonucleotide Ligation Assay for Detection of Mutations Associated with Reverse Transcriptase and Protease Inhibitor Resistance in Non-B Subtypes and Recombinant Forms of Human Immunodeficiency Virus Type 1
Authors: Vega Yolanda , Pérez-Alvárez Lucía , Delgado Elena , Muñoz Mercedes , Casado Gema , Carmona Rocío , Sierra María , Vázquez de Parga Elena , Pinilla Milagros , García Valentina , Medrano Leandro , Contreras Gerardo , Thomson Miguel , Nájera Rafael 
Published: October 2005

ABSTRACTThe oligonucleotide ligation assay is a genotypic assay for the detection of resistance-associated mutations to reverse transcriptase and protease inhibitors in human immunodeficiency virus type 1 subtype B. This assay has been modified and developed for non-B subtypes and recombinant strains and has been evaluated with sequencing, resulting in a more sensitive assay than sequencing for non-B subtypes.
Use of a Selective Enrichment Broth To Recover
Clostridium difficile
from Stool Swabs Stored under Different Conditions
Authors: Arroyo Luis G. , Rousseau Joyce , Willey Barbara M. , Low Don E. , Staempfli Henry , McGeer Allison , Weese J. Scott 
Published: October 2005

ABSTRACT

The recovery of
Clostridium difficile
from the stools of patients with
C. difficile-
associated diarrhea was evaluated by use of an enrichment broth (cycloserine-cefoxitin fructose broth supplemented with 0.1% sodium taurocholate [TCCFB]) and was compared to that from selective agar (cycloserine-cefoxitin fructose agar [CCFA]) and alcohol shock followed by inoculation onto blood agar (AS-BA). TCCFB was superior to CCFA and AS-BA, and neither the storage time nor the storage temperature affected the recovery rate.