bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Sno Strip Filter-Paper Wicks for Collection of Genital-Tract Samples Allows Reproducible Determination of Human Immunodeficiency Virus Type 1 (HIV-1) RNA Viral Load with a Commercial HIV-1 Viral Load Assay
Authors: Sherlock Christopher H. , Lott Paula M. , Money Deborah M. , Merrick Linda , Arikan Yasemin , Remple Valencia P. , Craib Kevin , Burdge David R. 
Published: March 2006

ABSTRACT

To assess the reproducibility of measurements of cervical and vaginal human immunodeficiency virus (HIV) viral load, 92 duplicate cervical and 88 duplicate vaginal samples were collected from 13 HIV-infected women using Sno Strip filter-paper wicks. RNA was eluted from the strips, extracted, and assayed using a modified protocol for the Roche Cobas Amplicor HIV-1 Monitor assay. Pearson's correlation coefficient (
R
), coefficient of determination (
D
), and Bland-Altman plots (BA) were used to compare paired log
10
-transformed viral loads. Analysis of duplicate same-site samples showed good reproducibility (cervix:
R
= 0.72,
D
= 52%, BA = 89% within range; vagina:
R
= 0.72,
D
= 51%, BA = 87% within range); paired cervix/vagina measurements showed moderate correlation only (
R
= 0.56;
D
= 31.3%). Standardized sample collection and simple modification of the Roche Cobas Amplicor HIV-1 Monitor assay allows reproducible measurement of genital viral load.
Identification of Human H1N2 and Human-Swine Reassortant H1N2 and H1N1 Influenza A Viruses among Pigs in Ontario, Canada (2003 to 2005)
Authors: Karasin Alexander I. , Carman Suzanne , Olsen Christopher W. 
Published: March 2006

ABSTRACT
Since 2003, three novel genotypes of H1 influenza viruses have been recovered from Canadian pigs, including a wholly human H1N2 virus and human-swine reassortants. These isolates demonstrate that human-lineage H1N2 viruses are infectious for pigs and that viruses with a human PB1/swine PA/swine PB2 polymerase complex can replicate in pigs.
Consecutive Use of Two Multiplex PCR-Based Assays for Simultaneous Identification and Determination of Capsular Status of Nine Common
Neisseria meningitidis
Serogroups Associated with Invasive Disease
Authors: Bennett Désirée E. , Cafferkey Mary T. 
Published: March 2006

ABSTRACT

We developed two
Neisseria meningitidis
multiplex PCR assays to be used consecutively that allow determination of the serogroup and capsular status of serogroup A, B, C, 29E, W135, X, and Y
cnl-3
/
cnl-1
-like-containing
N. meningitidis
isolates by direct analysis of the amplicon size. These assays offer a rapid and simple method of serogrouping
N. meningitidis
.
Emergence of Linezolid Resistance in the Vancomycin-Resistant
Enterococcus faecium
Multilocus Sequence Typing C1 Epidemic Lineage
Authors: Bonora Maria Grazia , Solbiati Maurizio , Stepan Erminia , Zorzi Antonella , Luzzani Aldo , Catania Maria Rosaria , Fontana Roberta 
Published: March 2006

ABSTRACT

A relatively high rate of vancomycin-resistant
Enterococcus faecium
not susceptible to linezolid was observed in intensive care unit patients. Linezolid-resistant isolates carried the G2576T mutation in the 23S rRNA gene, belonged to different clones, and shared the same allelic profile, which clusters in the C1 multilocus sequence typing epidemic lineage.
Differentiation of Species Combined into the
Burkholderia cepacia
Complex and Related Taxa on the Basis of Their Fatty Acid Patterns
Authors: Krejčí Eva , Kroppenstedt Reiner M. 
Published: March 2006

ABSTRACT

Using the established commercial system Sherlock (MIDI, Inc.), cellular fatty acid methyl ester analysis for differentiation among
Burkholderia cepacia
complex species was proven. The identification key based on the diagnostic fatty acids is able to discern phenotypically related
Ralstonia pickettii
and
Pandoraea
spp. and further distinguish
Burkholderia pyrrocinia
,
Burkholderia ambifaria
, and
Burkholderia vietnamiensis
.
Fatal Case of Community-Acquired Bacteremia and Necrotizing Fasciitis Caused by
Chryseobacterium meningosepticum
: Case Report and Review of the Literature
Authors: Lee Ching-Chi , Chen Po-Lin , Wang Li-Rong , Lee Hsin-Chun , Chang Chia-Ming , Lee Nan-Yao , Wu Chi-Jung , Shih Hsin-I , Ko Wen-Chien 
Published: March 2006

ABSTRACT

A diabetic patient with chronic heart failure developed necrotizing fasciitis and bacteremia caused by
Chryseobacterium meningosepticum
, which rapidly evolved into death, even with fasciotomy and intensive care. A review of the English literature found 10 cases of soft tissue infection caused by
C. meningosepticum
, which is rarely acquired in the community.
Pelvic Abscess Due to
Ochrobactrum anthropi
in an Immunocompetent Host: Case Report and Review of the Literature
Authors: Vaidya Sagar A. , Citron Diane M. , Fine Marjorie B. , Murakami Georgette , Goldstein Ellie J. C. 
Published: March 2006

ABSTRACT

Ochrobactrum anthropi
infection is rare in humans and is generally associated with immunocompromised hosts with indwelling foreign bodies. We report a case of pelvic abscess with
O. anthropi
after a routine appendectomy in an immunocompetent patient and review the literature on
O. anthropi
infection in patients with normal immune function.
Endocarditis Due toKytococcus schroeteri: Case Report and Review of the Literature
Authors: Mnif Basma , Boujelbène Inès , Mahjoubi Fouzia , Gdoura Radouane , Trabelsi Imen , Moalla Sana , Frikha Imed , Kammoun Samir , Hammami Adnane 
Published: March 2006

ABSTRACTWe report the third case of endocarditis caused by the newly described micrococcal speciesKytococcus schroeteri. A 49-year-old woman was admitted to the hospital with suspected prosthetic valve endocarditis. Five blood cultures and prosthetic valve cultures grew the same type of organism, initially identified asMicrococcussp. Assignment to the genusKytococcuswas suggested by the arginine dihydrolase activity and resistance to oxacillin. After sequencing of the 16S rRNA genes, the isolate was recognized asK. schroeteri. The patient was treated first with vancomycin combined with gentamicin and later with pristinamycin and rifampin. Three cases ofK. schroeteriendocarditis described within a short period of time might indicate a specific pathogenicity of this new species. The isolation of kytococci from normally sterile sites should not be overlooked.
Recurrent Osteomyelitis Caused by Infection with Different Bacterial Strains without Obvious Source of Reinfection
Authors: Uçkay Ilker , Assal Mathieu , Legout Laurence , Rohner Peter , Stern Richard , Lew Daniel , Hoffmeyer Pierre , Bernard Louis 
Published: March 2006

ABSTRACT
Recurrence of osteomyelitis by the same bacterial strain is well known. We report three patients with a second episode of osteomyelitis at the same site caused by different strains of bacteria from the original. Formerly infected and altered bone surface might present a region of diminished resistance for a new infection.
Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions
Authors: Leaw Shiang Ning , Chang Hsien Chang , Sun Hsiao Fang , Barton Richard , Bouchara Jean-Philippe , Chang Tsung Chain 
Published: March 2006

ABSTRACT

Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as
Pichia
,
Rhodotorula
,
Trichosporon
, and
Saccharomyces
spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (
Rhodotorula glutinis
BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.
Multidrug Resistance in
Salmonella enterica
Serotype Typhimurium from Humans in France (1993 to 2003)
Authors: Weill François-Xavier , Guesnier Françoise , Guibert Véronique , Timinouni Mohammed , Demartin Marie , Polomack Lucette , Grimont Patrick A. D. 
Published: March 2006

ABSTRACT

The aim of this study was to determine the distribution of the antimicrobial resistance phenotypes (R types), the phage types and XbaI-pulsed-field gel electrophoresis (PFGE) types, the genes coding for resistance to β-lactams and to quinolones, and the class 1 integrons among a representative sample of
Salmonella enterica
serotype Typhimurium isolates collected from humans in 2002 through the French National Reference Center for
Salmonella
(NRC-Salm) network. The trends in the evolution of antimicrobial resistance of serotype Typhimurium were reviewed by using NRC-Salm data from 1993, 1997, 2000, and 2003. In 2002, 3,998 isolates of serotype Typhimurium were registered at the NRC-Salm among 11,775 serotyped
S. enterica
isolates (34%). The most common multiple antibiotic resistance pattern was resistance to amoxicillin, chloramphenicol, streptomycin and spectinomycin, sulfonamides, and tetracycline (ACSSpSuTe R type), with 156 isolates (48.8%). One isolate resistant to extended-spectrum cephalosporins due to the production of TEM-52 extended-spectrum β-lactamase was detected (0.3%), and one multidrug-resistant isolate was highly resistant to ciprofloxacin (MIC > 32 mg/liter). We found that 57.2% of the isolates tested belonged to the DT104 clone. The main resistance pattern of DT104 isolates was R type ACSSpSuTe (83.2%). However, evolutionary changes have occurred within DT104, involving both loss (variants of
Salmonella
genomic island 1) and acquisition of genes for drug resistance to trimethoprim or to quinolones. PFGE profile X1 was the most prevalent (74.5%) among DT104 isolates, indicating the need to use a more discriminatory subtyping method for such isolates. Global data from the NRC-Salm suggested that DT104 was the main cause of multidrug resistance in serotype Typhimurium from humans from at least 1997 to 2003, with a roughly stable prevalence during this period.
Analysis of Mutations within the 5′ Untranslated Region, Interferon Sensitivity Region, and PePHD Region as a Function of Response to Interferon Therapy in Hepatitis C Virus-Infected Patients in India
Authors: Gupta Romi , Subramani Murugan , Khaja Mohammed N. , Madhavi Chandra , Roy Swagata , Habibullah Chittoor M. , Das Saumitra 
Published: March 2006

ABSTRACT

Mutations in several subgenomic regions have been implicated in influencing response to interferon therapy; however, a comprehensive picture of Indian patients was lacking. Based on the viral load and clinical factors, 10 out of 15 patients were found to be complete responders, whereas 5 patients were nonresponders. The pretreatment viral RNA load of the patients was found to be between 5.20 and 6.13 log
10
IU/ml, which eventually fell to 2.77 log
10
IU/ml after 24 weeks of treatment, whereas in the case of nonresponders, the average was 5.38 log
10
IU/ml. In order to study the influence of the hepatitis C virus genotype on the response to interferon therapy, the 5′ untranslated region sequences of the samples were analyzed, which showed that genotype 3 patients responded better than genotype 1 patients. Additionally, the mutations in the interferon sensitivity-determining region (ISDR) of the NS5A protein and the double-stranded RNA-activated protein kinase-eukaryotic initiation factor 2 alpha phosphorylation homology domain (PePHD) of the E2 envelope protein, before and after treatment, were compared with nonresponder prototype J. Although, no clear correlation was found in the case of the mutated ISDR, some significant changes in residues were observed in the PePHD region, which could be helpful in understanding the molecular basis of resistance to therapy. Interestingly, analysis of the quasispecies variations showed a change in genotype in one sample during treatment, which might have contributed to the resistance. The results suggest that the mutations in different regions of the viral genome might have a concerted effect on the response to interferon therapy.
Performance Assessment of the DR. MTBC Screen Assay and the BD ProbeTec ET System for Direct Detection of
Mycobacterium tuberculosis
in Respiratory Specimens
Authors: Wang Jann-Yuan , Lee Li-Na , Hsu Hsiao-Leng , Hsueh Po-Ren , Luh Kwen-Tay 
Published: March 2006

ABSTRACT

The performance of the DR. MTBC PCR-based assay and the BD ProbeTec ET
Mycobacterium tuberculosis
Complex Direct Detection (DTB) assay for the direct detection of
Mycobacterium tuberculosis
was evaluated using 1,066 consecutive clinical respiratory samples collected from 494 patients who did not have old cases of pulmonary tuberculosis and were not receiving antituberculosis treatment at National Taiwan University Hospital from January to February 2005. The results of both assays were compared to the “gold standard” of combined culture results and clinical diagnosis. The overall sensitivity and specificity of the DR. MTBC Screen assay were 56.6% and 98.9%, respectively, and of the DTB assay were 63.2% and 98.4%, respectively. The positive and negative predictive values for the DR. MTBC Screen assay were 84.5% and 95.4%, respectively, and for the DTB assay were 81.7% and 96.0%, respectively. The DR. MTBC Screen assay produced 11 false-positive results for 11 patients, including three samples yielding non-
M. tuberculosis
mycobacteria (one each for
M. abscessus
, a mixture of
M. abscessus
and
M. chelonae
, and unidentified non-tuberculosis mycobacteria). The DTB assay produced 15 false-positive results for 13 patients, including five samples from four patients yielding non-tuberculosis mycobacteria (two for
M. abscessus
, one for a mixture of
M. abscessus
and
M. chelonae
, and two for unidentified non-tuberculosis mycobacteria). This study demonstrated that the DR. MTBC Screen assay has a similar diagnostic value but fewer false-positive results than the DTB assay for respiratory specimens.
Comparison between Two Amplification Sets for Molecular Diagnosis of Toxoplasmosis by Real-Time PCR
Authors: Cassaing S. , Bessières M. H. , Berry A. , Berrebi A. , Fabre R. , Magnaval J. F. 
Published: March 2006

ABSTRACT
PCR is now commonly applied to the diagnosis of toxoplasmosis. Although several methods are available, comparative studies are few, making it difficult to compare the performance of each technique. We compared the sensitivities of two real-time PCR assays through a prospective study on fetuses, neonates, and immunocompromised patients and on the ocular diagnosis of toxoplasmosis. The first system targeted the widely used B1 gene (GenBank accession number AF179871) while the second (RE) targeted a more recently described sequence repeated roughly 200 to 300 times (GenBank accession number AF146527). We demonstrated that molecular diagnosis requires the duplication of PCR assays, especially with the B1 system, as only one PCR was positive in 33.3% of cases. Our study showed that the RE target was more sensitive for all biological samples (amniotic fluid, placenta, aqueous humor, whole blood, and cerebrospinal and bronchoalveolar fluids) and significantly improved the performance of the diagnosis of toxoplasmosis. Taking into consideration all clinical samples, the mean gain in the crossing point value was 4.2 ± 1.7 cycles and was even more significant for amniotic fluid (5.8 ± 1.7 cycles).
Molecular Genotyping of
Candida parapsilosis
Group I Clinical Isolates by Analysis of Polymorphic Microsatellite Markers
Authors: Lasker Brent A. , Butler Geraldine , Lott Timothy J. 
Published: March 2006

ABSTRACT

Candida parapsilosis
, a pathogenic yeast, is composed of three newly designated genomic species that are physiologically and morphologically indistinguishable. Nosocomial infections caused by group I
C. parapsilosis
are often associated with the breakdown of infection control practices and the contamination of medical devices, solutions, and indwelling catheters. Due to the low levels of nucleotide sequence variation that are observed, an investigation of the size polymorphisms in loci harboring microsatellite repeat sequences was applied for the typing of
C. parapsilosis
group I isolates. PCR primer sets that flank the microsatellite repeats for seven loci were designed. Following amplification by PCR, the size of each amplification product was determined automatically by capillary electrophoresis. A total of 42
C. parapsilosis
group I isolates were typed by microsatellite analysis, and their profiles were compared to the hybridization profiles obtained by use of the Cp3-13 DNA probe. A high degree of discrimination (discriminatory power = 0.971) was observed by microsatellite analysis. The number of different alleles per locus ranged from 14 for locus B to 5 for locus C. Microsatellite analysis detected 30 different microsatellite genotypes, with 24 genotypes represented by a single isolate. Comparison of the genotypes obtained by microsatellite analysis and those obtained by analysis of the Cp3-13 hybridization profiles showed that they were similar, and these methods were able to identify related and unrelated isolates. Some discrepancies were observed between the methods and may be due to higher mutation rates and/or homoplasy by microsatellite markers. Identical results were observed between microsatellite analysis and Cp3-13 DNA hybridization profile analysis for
C. parapsilosis
isolates obtained from two patients, demonstrating the reproducibilities of the methods in vivo. Identical microsatellite profiles were observed for isolates displaying different phenotypic switching morphologies. Indistinguishable Cp3-13 DNA hybridization profiles were observed for six epidemiologically related isolates; however, only three of six primary isolates had identical microsatellite profiles. Size variation at a single locus was observed for three of six isolates obtained either after the outbreak period or from a different body site, suggesting the potential of the method to detect microevolutionary events. Interestingly, for most loci a single allele per strain was observed; in contrast, two alleles per locus were observed for some strains, and consistent with the findings for natural isolates, some isolates may be aneuploid. Due to the potential for high throughput, reproducibility, and discrimination, microsatellite analysis may provide a robust and efficient method for the genotyping of large numbers of
C. parapsilosis
group I isolates.
Effects ofMoraxella(Branhamella)ovisCulture Filtrates on Bovine Erythrocytes, Peripheral Mononuclear Cells, and Corneal Epithelial Cells
Authors: Cerny Henry E. , Rogers Douglas G. , Gray Jeffrey T. , Smith David R. , Hinkley Susanne 
Published: March 2006

ABSTRACTInfectious bovine keratoconjunctivitis (IBK) is a highly contagious ocular disease that affects cattle of all ages and that occurs worldwide. Piliated hemolyticMoraxella bovisis recognized as the etiologic agent of IBK. According to data from the Nebraska Veterinary Diagnostic Laboratory System, however,Moraxella(Branhamella)ovishas been isolated with increasing frequency from cattle affected with IBK. The objective of this study was, therefore, to examineM. ovisfield isolates for the presence of the putative virulence factors ofM. bovis. Culture filtrates from selectedM. ovisfield isolates demonstrated hemolytic activity on bovine erythrocytes and cytotoxic activity on bovine peripheral blood mononuclear cells and corneal epithelial cells. The hemolytic activity of the culture filtrates was attenuated after heat treatment. Polyclonal antibodies raised against theM. bovishemolysin-cytotoxin also recognized a protein of approximately 98 kDa in a Western blot assay. These data indicate that theM. ovisfield isolates examined produce one or more heat-labile exotoxins and may suggest thatM. ovisplays a role in the pathogenesis of IBK.
Isolation of the Genome Sequence StrainMycobacterium avium104 from Multiple Patients over a 17-Year Period
Authors: Horan Kathleen L. , Freeman Robert , Weigel Kris , Semret Makeda , Pfaller Stacy , Covert Terry C. , van Soolingen Dick , Leão Sylvia C. , Behr Marcel A. , Cangelosi Gerard A. 
Published: March 2006

ABSTRACTThe genome sequence strain 104 of the opportunistic pathogenMycobacterium aviumwas isolated from an adult AIDS patient in Southern California in 1983. Isolates of non-paratuberculosisM. aviumfrom 207 other patients in Southern California and elsewhere were examined for genotypic identity to strain 104. This process was facilitated by the use of a novel two-step approach. In the first step, all 208 strains in the sample were subjected to a high-throughput, large sequence polymorphism (LSP)-based genotyping test, in which DNA from each strain was tested by PCR for the presence or absence of 4 hypervariable genomic regions. Nineteen isolates exhibited an LSP type that resembled that of strain 104. This subset of 19 isolates was then subjected to high-resolution repetitive sequence-based PCR typing, which identified 10 isolates within the subset that were genotypically identical to strain 104. These isolates came from 10 different patients at 5 clinical sites in the western United States, and they were isolated over a 17-year time span. Therefore, the sequenced genome ofM. aviumstrain 104 has been associated with disease in multiple patients in the western United States. AlthoughM. aviumis known for its genetic plasticity, these observations also show that strains of the pathogen can be genotypically stable over extended time periods.
Genetic Heterogeneity of Shiga Toxin-Producing
Escherichia coli
Strains Isolated in São Paulo, Brazil, from 1976 through 2003, as Revealed by Pulsed-Field Gel Electrophoresis
Authors: Vaz Tânia Mara I. , Irino Kinue , Nishimura Lucilia S. , Cergole-Novella Maria Cecília , Guth Beatriz Ernestina C. 
Published: March 2006

ABSTRACT

The pulsed-field gel electrophoresis (PFGE) patterns of 46 Shiga toxin-producing
Escherichia coli
(STEC) strains isolated in São Paulo, Brazil, during the period from 1976 to 2003 were compared with those found among 30 non-STEC strains that carried
eae
and that belonged to the same serogroups as the STEC strains. All except two of the STEC and non-STEC strains of human origin were from sporadic and unrelated cases of infection; two O111 strains originated from the same patient. Multiple PFGE patterns were found among STEC strains of distinct serotypes. Moreover, the PFGE restriction patterns of STEC strains differed substantially from those observed among non-STEC strains of the same serogroup except serotype O26 strains. Based on the indistinguishable PFGE pattern for two O157:H7 STEC strains isolated in the same geographic area at an interval of approximately 15 days and toxin profile data, the first occurrence of an O157:H7 outbreak in Brazil during that period can be suggested. In general, a close relationship between types of intimin, serotypes, and diarrheagenic groups of
E. coli
was observed. This is the first time that a large collection of STEC strains from Brazil has been analyzed, and a great genetic diversity was shown among O157:H7 and non-O157:H7 STEC strains isolated in São Paulo, Brazil.