bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Comparative Workflow and Performance Characteristics of the VITEK 2 and Phoenix Systems
Authors: Eigner U. , Schmid A. , Wild U. , Bertsch D. , Fahr A.-M. 
Published: August 2005

ABSTRACT

The VITEK 2 (bioMérieux, Marcy L′Ètoile, France) and the Phoenix systems (BD Diagnostic Systems, Sparks, Md.) are automated instruments for rapid organism identification and susceptibility testing. We evaluated the workflow, the time to result, and the performance of identification and susceptibility testing of both instruments. A total of 307 fresh clinical isolates were tested: 141
Enterobacteriaceae
, 22 nonfermenters, 93
Staphylococcus
spp., and 51
Enterococcus
spp. Manipulation time was measured in batches, each with seven isolates, for a total of 39 batches. The mean (± standard deviation [SD]) manipulation time per batch was 20.9 ± 1.8 min for Phoenix and 10.6 ± 1.0 min for VITEK 2 (
P
< 0.001). Mean (±SD) time to result for all bacterial groups was 727 ± 162 min for Phoenix and 506 ± 120 min for VITEK 2 (
P
< 0.001). Concerning identification, Phoenix and VITEK 2 yielded the same results for nonfermenters (100%), staphylococci (97%), and enterococci (100%). For 140
Enterobacteriaceae
strains evaluated, 135 (96%) were correctly identified by Phoenix and 137 (98%) by VITEK 2 (
P
= 0.72). The overall category agreement for all isolates was 97.0% for both instruments. The minor error rate, major error rate, and very major error rate for all bacterial isolates tested were 3.0, 0.3, and 0.6 and 2.8, 0.2, and 1.7 for Phoenix and VITEK 2, respectively (
P
values of 0.76, 0.75, and 0.09). The VITEK 2 system required less manual manipulation time and less time than the Phoenix system to yield results.
Identification of Four Fimbria-Encoding Genomic Islands That Are Highly Specific for Verocytotoxin-Producing
Escherichia coli
Serotype O157 Strains
Authors: Shen Songhai , Mascarenhas Mariola , Morgan Robyn , Rahn Kris , Karmali Mohamed A. 
Published: August 2005

ABSTRACT

Verocytotoxin-producing
Escherichia coli
causes zoonotic food- or waterborne infection that may be associated with massive outbreaks and with the serious complication of hemolytic uremic syndrome (HUS). Serotypes O157:H7 and O157:NM are more commonly associated with HUS and outbreaks than other serotypes, such as O26:H11. To determine whether a genetic basis exists for why serotype O157:H7/NM causes HUS and outbreaks more often than other serotypes, such as O26:H11, we conducted suppression subtractive hybridization (SSH) between the genomes of the sequenced O157:H7 strain EDL933 and CL1, a clinical serotype O26:H11 isolate. Genes from four EDL933 fimbria-encoding genomic O islands (OIs) (OI-1, -47, -141, and -154) were identified in the SSH library. OI-47 encodes several additional putative virulence factors, including secreted and signaling proteins, a hemolysin locus, a lipoprotein, an ABC transport system, and a lipid biosynthesis locus. The distribution of the OIs was investigated by PCR and Southern hybridization (when PCR was negative) with 69 VTEC strains belonging to 39 different serotypes corresponding to 5 seropathotypes that differ in their disease and epidemic potential. The four OIs described here were distributed almost exclusively in serotypes O157:H7 and O157:NM, which indicates that they may be associated with the ability of these strains to colonize human and/or animal intestinal tracts and to cause epidemic and serious disease more frequently than other serotypes. The occurrence of the four OIs in enteropathogenic
E. coli
O55:H7 strains is consistent with their vertical inheritance by VTEC O157:H7/NM from this clonally related ancestor.
Phylogenetic Analysis of the SpirochetesBorrelia parkeriandBorrelia turicataeand the Potential for Tick-Borne Relapsing Fever in Florida
Authors: Schwan Tom G. , Raffel Sandra J. , Schrumpf Merry E. , Policastro Paul F. , Rawlings Julie A. , Lane Robert S. , Breitschwerdt Edward B. , Porcella Stephen F. 
Published: August 2005

ABSTRACTIsolates ofBorrelia turicatae,Borrelia parkeri, and the Florida canine borrelia (FCB) were examined to further phylogenetically characterize the identities of these spirochetes in the United States. DNA sequences of four chromosomal loci (the 16S rRNA gene,flaB,gyrB, andglpQ) were determined for eight isolates ofB. turicataeand six isolates ofB. parkeri, which grouped the spirochetes into two distinct but closely related taxa (>98% sequence identity) separate fromBorrelia hermsii. The FCB was clearly separated with the group identified asB. turicatae, confirming this bacterium as a relapsing fever spirochete. Therefore, the potential for tick-borne relapsing fever in humans and other animals exists in Florida and future efforts are needed to determine the enzootic hosts and distribution of this spirochete in the southeastern United States. Analysis of plasmids demonstrated both linear and circular forms inB. turicataebut only linear plasmids inB. parkeri, which should be of interest to investigators concerned with plasmid diversity and evolution within this group of spirochetes.
Simultaneous Detection of Hepatitis C Virus (HCV) Core Antigen and Anti-HCV Antibodies Improves the Early Detection of HCV Infection
Authors: Laperche Syria , Le Marrec Nadine , Girault Annie , Bouchardeau Françoise , Servant-Delmas Annabelle , Maniez-Montreuil Michèle , Gallian Pierre , Levayer Thierry , Morel Pascal , Simon Nicole 
Published: August 2005

ABSTRACTTo evaluate whether a new enzyme immunoassay developed for the simultaneous detection of hepatitis C virus (HCV) core antigen (Ag) and anti-HCV antibodies (anti-HCV Ab) (Monolisa HCV Ag/Ab ULTRA; Bio-Rad) could improve the early detection of HCV infection, we compared its sensitivity to that of anti-HCV, HCV core Ag, and HCV RNA assays. The populations studied included 12 blood donor samples positive for HCV RNA and HCV core Ag but negative for anti-HCV antibodies and 23 hemodialysis patients who developed anti-HCV Ab (seroconversion) during the follow-up. From these 23 individuals, 83 samples sequentially collected prior to seroconversion and 108 samples collected after seroconversion were tested. Six of 12 blood donations were positive by the HCV Ag/Ab assay. In the hemodialysis cohort, the 24 HCV RNA-negative samples were negative by the HCV Ag/Ab assay and 23 of the 59 HCV RNA-positive samples (39%) were positive. The HCV Ag/Ab assay detected HCV infection on average 21.6 days before the most sensitive antibody assay. The HCV Ag/Ab assay did not detect HCV infection as early as the HCV RNA assay (mean delay, 30.3 days) or HCV Ag assay (mean delays, 27.9, and 16.3 days by the HCV core Ag quantification assay and the HCV Ag blood screening assay, respectively). This new assay provides a notable improvement for the early detection of HCV infection during the so-called window period compared with anti-HCV Ab assays and could be a useful alternative to HCV RNA detection or HCV core Ag assays for diagnosis or blood screening when nucleic acid technologies or HCV core Ag detection are not implemented.
Use of a Heminested Reverse Transcriptase PCR Assay for Detection of Astrovirus in Environmental Swabs from an Outbreak of Gastroenteritis in a Pediatric Primary Immunodeficiency Unit
Authors: Gallimore Chris I. , Taylor Clive , Gennery Andrew R. , Cant Andrew J. , Galloway Angela , Lewis David , Gray Jim J. 
Published: August 2005

ABSTRACT
An outbreak of astrovirus gastroenteritis occurred in the Primary Immunodeficiency Unit at Newcastle General Hospital in March 2004. Environmental swabbing of the unit was undertaken after the outbreak, with multiple sites swabbed pre- and postcleaning. Astroviruses were detected in four environmental swabs and from two patient fecal samples using heminested reverse transcriptase PCR. An astrovirus genotype 3 strain was identified in both environmental swabs and fecal specimens and was the strain identified as being responsible for the outbreak. Environmental transmission of the virus was thought to have occurred by contamination of a syringe pump outside the laminar-flow curtain of a patient who was admitted with astrovirus gastroenteritis. This was subsequently transmitted to a cubicle next door and to a television/games console in a parents' room in the ward. Environmental monitoring of surfaces/equipment, using PCR assays for gastroenteric viruses in hospital situations where infection can give rise to serious clinical complications, may have a role in controlling and monitoring cleaning and the subsequent prevention of nosocomial transmission of gastroenteritis.
Association of Tumor Necrosis Factora-2anda-8Microsatellite Alleles with Human Papillomavirus and Squamous Intraepithelial Lesions among Women in Brazil
Authors: Simões R. T. , Gonçalves M. A. G. , Donadi E. A. , Simões A. L. , Bettini J. S. R. , Duarte G. , Quintana S. M. , Carvalho M. W. P. , Soares E. G. 
Published: August 2005

ABSTRACTInfection with oncogenic human papillomavirus (HPV) is considered to be the major risk factor for cervical cancer. Tumor necrosis factor (TNF) is a pluripotent cytokine that plays an important role in inhibiting the action of microbial agents, andTNFmicrosatellite polymorphisms have been associated with several diseases, including cancer and viral infections. This study analyzed the associations betweenTNFato -emicrosatellite polymorphisms and the severity of squamous intraepithelial lesions (SIL), according to the presence of the oncogenic HPV16 and HPV18 types. Samples from 146 HPV-positive women with low-grade SIL (LSIL) and high-grade SIL (HSIL) and samples from 101 healthy women were studied.TNFmicrosatellite polymorphism typing and HPV detection and typing were performed using PCR-amplified DNA hybridized with sequence-specific primers. Data were analyzed by Fisher's exact test using the GENEPOP software. Significant associations were observed between LSIL and theTNFa-8allele (4/166;P= 0.04), as well as betweenTNFa-2with HPV18 only (16/44;P= 0.002) andTNFa-2with HPV18 coinfection with HPV16 (16/44;P= 0.001). Patients exhibiting theTNFa-2allele and harboring HPV18, in the presence or absence of coinfection with HPV16, had an increased risk of HSIL occurrence (13/38;P= 0.04; 5/10;P= 0.04) compared to patients with other HPV types. These results suggest that theTNFa-8allele is associated with increased susceptibility to the occurrence of LSIL and that despite the presence of a high TNF-α production allele, the ability of HPV18 to resist the inhibitory effects of TNF-α may contribute to the occurrence of infection and consequently to HSIL in women with cervical HPV18 infection.
Clinical and Microbiological Features ofInquilinussp. Isolates from Five Patients with Cystic Fibrosis
Authors: Chiron Raphaël , Marchandin Hélène , Counil François , Jumas-Bilak Estelle , Freydière Anne-Marie , Bellon Gabriel , Husson Marie-Odile , Turck Dominique , Brémont François , Chabanon Gérard , Segonds Christine 
Published: August 2005

ABSTRACTPatients with cystic fibrosis (CF) may be colonized with unusual gram-negative bacilli whose identification is difficult and clinical impact unclear. We describe the clinical and microbiological features of five colonizations with organisms belonging to the recently described genusInquilinusin CF patients. Isolates were identified fromBurkholderia cepaciaselective medium by means of 16S rRNA analysis. All of them were resistant to colistin, penicillins, cephalosporins, and monobactams but exhibited a remarkable susceptibility to imipenem. One of the five patients was transiently colonized with a nonmucoid isolate, whereas the four other patients were persistently colonized over the period of follow-up (8 to 21 months) with mucoid isolates. Pulsed-field gel electrophoresis of SpeI-digested genomic DNA was powerful for strain genotyping and demonstrated the clonality ofInquilinussp. colonization for the two patients tested. Clinical evolution after the onset ofInquilinuswas heterogeneous, but for at least one patient the lung function worsened and eradication ofInquilinussp. was unsuccessful despite several imipenem courses. Finally,Inquilinusspp. may represent a new threat for CF patients due to their mucoid characteristic, their multiresistant pattern to antibiotics, and their ability to persist in the respiratory tract.
Early Immune Response to the Components of the Type III System of
Pseudomonas aeruginosa
in Children with Cystic Fibrosis
Authors: Corech R. , Rao A. , Laxova A. , Moss J. , Rock M. J. , Li Z. , Kosorok M. R. , Splaingard M. L. , Farrell P. M. , Barbieri J. T. 
Published: August 2005

ABSTRACT

The lungs of patients with cystic fibrosis (CF) are colonized initially by
Pseudomonas aeruginosa
, which is associated with progressive lung destruction and increased mortality. The pathogenicity of
P. aeruginosa
is caused by a number of virulence factors, including exotoxin A (ETA) and the type III cytotoxins (ExoS, ExoT, ExoU, and ExoY).
P. aeruginosa
contacts the plasma membrane to deliver type III cytotoxins through a channel formed by PopB, PopD, and PcrV; ETA enters mammalian cells via receptor-mediated endocytosis. The Wisconsin CF Neonatal Screening Project is a longitudinal investigation to assess the potential benefits and risks of newborn screening for CF; the project was the source of serum samples used in this study. Past studies evaluated the longitudinal appearance of antibodies to ETA and elastase and
P. aeruginosa
infections in patients with CF. The current study characterized the longitudinal appearance of antibodies to components of the type III system in children with CF. Western blot analyses showed that serum antibodies to PopB, PcrV, and ExoS were common. Longitudinal enzyme-linked immunosorbent assays determined that the first detection of antibodies to pooled ExoS/PopB occurred at a time similar to those of detection of antibodies to a
P. aeruginosa
cell lysate and the identification of oropharyngeal cultures positive for
P. aeruginosa
. This indicates that children with CF are colonized early with
P. aeruginosa
expressing the type III system, implicating it in early pathogenesis, and implies that surveillance of clinical symptoms, oropharyngeal cultures, and seroconversion to type III antigens may facilitate early detection of
P. aeruginosa
infections.
Detection of
Streptococcus pneumoniae
Antigen in Bronchoalveolar Lavage Fluid Samples by a Rapid Immunochromatographic Membrane Assay
Authors: Jacobs Jan A. , Stobberingh Ellen E. , Cornelissen Elisa I. M. , Drent Marjolein 
Published: August 2005

ABSTRACT

We conducted a retrospective study to evaluate an immunochromatographic membrane test (ICT), applied to bronchoalveolar lavage (BAL) fluid samples obtained in patients with suspected pneumonia, for the detection of
Streptococcus pneumoniae
antigen. The NOW
Streptococcus pneumoniae
test was assessed on 96 BAL fluid samples. Sensitivity was tested in 20 samples obtained from patients diagnosed as having pneumococcal pneumonia (growth of
S. pneumoniae
in blood cultures and/or in BAL fluid samples of ≥10
4
CFU/ml). Specificity was tested in BAL fluid samples of nonpneumococcal etiology (
n
= 41) and in samples with no respiratory pathogen and a total bacterial count of <10
4
CFU/ml (
n
= 35). Using the ICT, pneumococcal antigen was detected in 29 (30.2%) BAL fluid samples, with a sensitivity of 95.0% (95% confidence interval [CI], 90.6% to 99.4%) and a specificity of 86.8% (95% CI, 80.1% to 93.8%). The ICT was easy to perform and revealed unequivocal and reproducible results. No interference was observed with high cell counts, red blood cells, or elevated protein levels. Four out of 10 false-positive readings occurred in samples with
S. pneumoniae
counts below the 10
4
CFU/ml threshold limit of pneumonia. In BAL fluid samples obtained after pneumococcal bacteremia, positive test results were found for up to 35 days after bacteremia. The ICT test applied to BAL fluid specimens is reproducible and accurate in the diagnosis of pneumococcal antigen. Further studies are required to establish the impact of the ICT on patient care.
Predominance of Rotavirus Genotype G9 during the 1999, 2000, and 2002 Seasons among Hospitalized Children in the City of Salvador, Bahia, Brazil: Implications for Future Vaccine Strategies
Authors: Santos Norma , Volotão Eduardo M. , Soares Caroline C. , Campos Gúbio S. , Sardi Silvia Ines , Hoshino Yasutaka 
Published: August 2005

ABSTRACT
Two hundred eight of 648 (32%) diarrheal stool samples collected from hospitalized children under 5 years of age during a 3-year period (1999, 2000, and 2002) in the city of Salvador, in the state of Bahia, Brazil, were rotavirus positive. One hundred sixty-four of 208 (78.8%) rotavirus-positive samples had genotype G9 specificity, predominantly in association with P[8]. Other specificities detected were G1 (12.0%) and G4 (1.4%). Viruses with G2, G3, or P[4] specificity were not detected. Rotavirus genotype G9 predominated during each of the three seasons studied; it represented 89.2% of rotavirus strains detected in 1999, 85.3% in 2000, and 74.5% in 2002. G1 viruses (the globally most common G type) have a unique epidemiological characteristic of maintaining predominance during multiple consecutive rotavirus seasons. We have shown in this study for the first time that the G9 viruses also have a similar epidemiological characteristic, albeit for a shorter period of surveillance. The next generation of rotavirus vaccines will need to provide adequate protection against disease caused by G9 viruses.
Distribution of the Serine Protease Autotransporters of the
Enterobacteriaceae
among Extraintestinal Clinical Isolates of
Escherichia coli
Authors: Parham Nick J. , Pollard Samantha J. , Desvaux Mickaël , Scott-Tucker Anthony , Liu Chengjie , Fivian Amanda , Henderson Ian R. 
Published: August 2005

ABSTRACT

Urinary tract infections continue to be among the most common extraintestinal diseases. Cystitis in women is by far the most common urinary tract infection; pyelonephritis in both sexes and prostatitis in men are more severe but less frequent complaints.
Escherichia coli
is by far the most common cause of urinary tract infection. It is believed that uropathogenic
E. coli
is adept at colonizing the urinary tract via the production of specific virulence factors. Recently, a novel virulence determinant, Vat, was described for the prototypical uropathogenic
E. coli
strain CFT073. Vat is a member of the SPATE (serine protease autotransporters of the
Enterobacteriaceae
) subfamily of the autotransporters. Previously, SPATEs have been described for all pathovars of
E. coli
, but until recently their presence had been noticeably absent in nonpathogenic
E. coli
. In this report we describe the prevalence and phylogenetic distribution of the SPATEs among uropathogenic
E. coli
and the ECOR collection, demonstrating an association between the presence of the SPATEs, including Vat, and uropathogenic
E. coli
phylogroups. In addition, we describe the distribution of SPATEs among nonpathogenic
E. coli
.
Genetic Diversity among Type
emm28
Group A
Streptococcus
Strains Causing Invasive Infections and Pharyngitis
Authors: Green Nicole M. , Beres Stephen B. , Graviss Edward A. , Allison James E. , McGeer Allison J. , Vuopio-Varkila Jaana , LeFebvre Rance B. , Musser James M. 
Published: August 2005

ABSTRACT

Genome sequencing of group A
Streptococcus
(GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the
emm
gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the
emm28
gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the
emm28
gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (
mefA
,
ermB
, and
ermTR
) was analyzed by PCR, and less than 2% of the strains were positive.
Pilot Study To Evaluate Microarray Hybridization as a Tool forSalmonella entericaSerovar Typhimurium StrainDifferentiation
Authors: Pelludat C. , Prager R. , Tschäpe H. , Rabsch W. , Schuchhardt J. , Hardt W.-D. 
Published: August 2005

ABSTRACTIn developed countries,Salmonella entericasubspecies 1 serovars Enteritidis and Typhimurium range among the most common causes of bacterial food-borne infections. The surveillance and typing of epidemicSalmonellastrains are important tools in epidemiology. Usually,Salmonella entericasubspecies 1 serovars are differentiated by serotyping for diagnostic purposes. Further differentiation is done by phage typing as well as molecular typing techniques. Here we have designed and evaluated a prototype DNA microarray as a tool for serovar Typhimurium strain differentiation. It harbors 83 serovar Typhimurium probes obtained by differential subtractive hybridization and from the public database. The microarray yielded reproducible hybridization patterns in repeated hybridizations with chromosomal DNA of the same strain and could differentiate five serovar Typhimurium reference strains (DT204, DT104, DT208, DT36, and LT2). Furthermore, the microarray identified two distinct groups among 13 serovar Typhimurium DT104 strains. This correlated with observations from pulsed-field gel electrophoresis analysis. Twenty-three further serovar Typhimurium strains were analyzed to explore future directions for optimization of the simple 83-probe DNA microarray. The data presented here demonstrate that DNA microarrays harboring small numbers of selected probes are promising tools for serovar Typhimurium strain typing.
OralCandidaIsolates Colonizing or Infecting Human Immunodeficiency Virus-Infected and Healthy Persons in Mexico
Authors: Sánchez-Vargas Luis Octavio , Ortiz-López Natalia Guadalupe , Villar María , Moragues María Dolores , Aguirre José Manuel , Cashat-Cruz Miguel , Lopez-Ribot Jose Luis , Gaitán-Cepeda Luis Alberto , Quindós Guillermo 
Published: August 2005

ABSTRACTOral yeast carriage was studied in 312 Mexican subjects.Candida albicanswas the most frequent species, but otherCandidaspp. were isolated from 16.5 to 38.5% of patients. Colonization did not correlate with CD4+number or viral load, but highly active antiretroviral therapy reduced the frequency of candidiasis. Most isolates were susceptible to fluconazole, but 10.8% were resistant to one or more azoles.