bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Involvement of an Electron Shuttle in Electricity Generation byGeothrix fermentans
Authors: Bond Daniel R. , Lovley Derek R. 
Published: April 2005

ABSTRACTIn experiments performed using graphite electrodes poised by a potentiostat (+200 mV versus Ag/AgCl) or in a microbial fuel cell (with oxygen as the electron acceptor), the Fe(III)-reducing organismGeothrix fermentansconserved energy to support growth by coupling the complete oxidation of acetate to reduction of a graphite electrode. Other organic compounds, such as lactate, malate, propionate, and succinate as well as components of peptone and yeast extract, were utilized for electricity production. However, electrical characteristics and the results of shuttling assays indicated that unlike previously described electrode-reducing microorganisms,G. fermentansproduced a compound that promoted electrode reduction. This is the first report of complete oxidation of organic compounds linked to electrode reduction by an isolate outside of theProteobacteria.
Quantitative Detection of
Listeria monocytogenes
in Biofilms by Real-Time PCR
Authors: Guilbaud Morgan , de Coppet Pierre , Bourion Fabrice , Rachman Cinta , Prévost Hervé , Dousset Xavier 
Published: April 2005

ABSTRACT

A quantitative method based on a real-time PCR assay to enumerate
Listeria monocytogenes
in biofilms was developed. The specificity for
L. monocytogenes
of primers targeting the listeriolysin gene was demonstrated using a SYBR Green I real-time PCR assay. The number of
L. monocytogenes
detected growing in biofilms was 6 × 10
2
CFU/cm
2
.
Pathways for Methanogenesis and Diversity of Methanogenic Archaea in Three Boreal Peatland Ecosystems
Authors: Galand P. E. , Fritze H. , Conrad R. , Yrjälä K. 
Published: April 2005

ABSTRACT

The main objectives of this study were to uncover the pathways used for methanogenesis in three different boreal peatland ecosystems and to describe the methanogenic populations involved. The mesotrophic fen had the lowest proportion of CH
4
produced from H
2
-CO
2
. The oligotrophic fen was the most hydrogenotrophic, followed by the ombrotrophic bog. Each site was characterized by a specific group of methanogenic sequences belonging to
Methanosaeta
spp. (mesotrophic fen), rice cluster-I (oligotrophic fen), and fen cluster (ombrotrophic bog).
por
Variable-Region Typing by DNA Probe Hybridization Is Broadly Applicable to Epidemiologic Studies of
Neisseria gonorrhoeae
Authors: Bash Margaret C. , Zhu Peixuan , Gulati Sunita , McKnew Durrie , Rice Peter A. , Lynn Freyja 
Published: April 2005

ABSTRACT

The porin gene (
porB
) of
Neisseria gonorrhoeae
encodes the major outer membrane protein identified as PI or Por. To examine the utility of
por
variable-region (VR) typing,
porB
from 206 isolates was characterized by using oligonucleotide probes in a checkerboard hybridization assay that identifies the sequence types of five VRs of both PIA and PIB
porB
alleles. The strains represented temporally and geographically distinct isolates, isolates from a large cluster, epidemiologically linked partner isolates, and a collection of strains from disseminated gonococcal infections. By using rigorous epidemiologic criteria for transmission of infection between sex partners,
por
VR typing was more discriminatory than serovar typing in classifying isolates from both members of 43 epidemiologically linked pairs: 39 of 43 pairs were classified as coinciding by
por
VR typing compared to 43 of 43 by serovar determination (
P
= 0.058).
porB
sequence data confirmed the accuracy of the
por
VR method. Relationships between VR type and serovar typing monoclonal antibodies were observed for all six PIB and three of six PIA antibodies.
por
VR typing is a molecular tool that appears to have broad applicability. This method can be adapted to a wide range of technologies from simple hybridization to microarray and may allow for typing from noncultured clinical specimens.
Genetic Analysis of Enteropathogenic and Enterohemorrhagic
Escherichia coli
Serogroup O103 Strains by Molecular Typing of Virulence and Housekeeping Genes and Pulsed-Field Gel Electrophoresis
Authors: Beutin Lothar , Kaulfuss Stefan , Herold Sylvia , Oswald Eric , Schmidt Herbert 
Published: April 2005

ABSTRACT

We investigated the genetic relationships of 54
Escherichia coli
O103 strains from humans, animals, and meat by molecular typing of housekeeping and virulence genes and by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) of seven housekeeping genes revealed seven profiles, I through VII. MLST profiles I plus III cover 45 Shiga toxin-producing
E. coli
(STEC) O103:H2 strains from Australia, Canada, France, Germany, and Northern Ireland that are characterized by the intimin (
eae
) epsilon gene and carry enterohemorrhagic
E. coli
(EHEC) virulence plasmids. MLST profile II groups five human and animal enteropathogenic
E. coli
(EPEC) O103:H2 strains that were positive for intimin (
eae
) beta. Although strains belonging to MLST groups II and I plus III are closely related to each other (92.6% identity), major differences were found in the housekeeping
icdA
gene and in the virulence-associated genes
eae
and
escD. E. coli
O103 strains with MLST patterns IV to VII are genetically distant from MLST I, II, and III strains, as are the non-O103
E. coli
strains EDL933 (O157), MG1655 (K-12), and CFT073 (O6). Comparison of MLST results with those of PFGE and virulence typing demonstrated that
E. coli
O103 STEC and EPEC have recently acquired different virulence genes and DNA rearrangements, causing alterations in their PFGE patterns. PFGE typing was very useful for identification of genetically closely related subgroups among MLST I strains, such as Stx2-producing STEC O103 strains from patients with hemolytic uremic syndrome. Analysis of virulence genes contributed to grouping of
E. coli
O103 strains into EPEC and STEC. Novel virulence markers, such as
efa
(EHEC factor for adherence),
paa
(porcine adherence factor), and
cif
(cell cycle-inhibiting factor), were found widely associated with
E. coli
O103 EPEC and STEC strains.
Loop-Mediated Isothermal Amplification Method Targeting the
lytA
Gene for Detection of
Streptococcus pneumoniae
Authors: Seki Mitsuko , Yamashita Yoshihisa , Torigoe Hirotaka , Tsuda Hiromasa , Sato Setsuko , Maeno Masao 
Published: April 2005

ABSTRACT

It is difficult to separate
Streptococcus pneumoniae
from the genotypically similar species
Streptococcus mitis
and
Streptococcus oralis
, which are commensals of the human oral cavity. A novel nucleic acid amplification technique, loop-mediated isothermal amplification (LAMP), which amplifies DNA under isothermal conditions (63°C) with high specificity, efficiency, and rapidity, was examined regarding its applicability for detecting
S. pneumoniae
. An
S. pneumoniae
-specific LAMP primer targeting the
lytA
gene was designed. The primer specificity was validated using 10
Streptococcus
and 7 non-
Streptococcus
species. Within 60 min, the assay could detect 10 or more copies of purified
S. pneumoniae
DNA with a sensitivity 1,000 times that of conventional PCR. Clinical isolates of 21 other strains (3
S. oralis
, 17
S. mitis
, and 1
Streptococcus
species) that harbor virulence-factor-encoding genes (
lytA
or
ply
) were tried to differentiate
S. pneumoniae
. The detection of
S. pneumoniae
in clinical isolates was more selective using the LAMP method than using conventional PCR. Therefore, LAMP appears to be a sensitive and reliable means of diagnosing
S. pneumoniae
infection.
Characterization of
Borrelia lusitaniae
Isolates Collected in Tunisia and Morocco
Authors: Younsi Hend , Sarih M'Hammed , Jouda Fatima , Godfroid Edmond , Gern Lise , Bouattour Ali , Baranton Guy , Postic Daniele 
Published: April 2005

ABSTRACT

Borrelia lusitaniae
is a species within the complex
Borrelia burgdorferi
sensu lato and is infrequently isolated in Europe. In contrast, this species is by far the most predominant in North Africa and in Portugal. In this study, we analyzed the genetic diversity, at several loci, of a large population of isolates from free-living
Ixodes ricinus
ticks collected in Tunisia and Morocco. We found a moderate diversity of the whole genome by using pulsed-field gel electrophoresis as well as in the
ospA
gene sequences, compared to a high level of strain homogeneity in the small noncoding ribosomal spacer. In contrast, a high diversity of this locus has been previously reported for Portuguese isolates. We hypothesize that
B. lusitaniae
strains isolated in North Africa constitute a clone of Portuguese origin.
Colonization of Human Immunodeficiency Virus-Infected Outpatients in Taiwan with
Candida
Species
Authors: Hung Chien-Ching , Yang Yun-Liang , Lauderdale Tsai-Ling , McDonald L. Clifford , Hsiao Chin-Fu , Cheng Hsiao-Hsu , Ho Yong An , Lo Hsiu-Jung 
Published: April 2005

ABSTRACT

To understand the
Candida
colonization of human immunodeficiency virus (HIV)-infected outpatients in Taiwan, we have conducted a prospective cohort study of
Candida
colonization and its risk factors at the National Taiwan University Hospital from 1999 to 2002. More than 50% of the patients were colonized with
Candida
species, and 12% developed symptomatic candidiasis. Patients colonized with fluconazole-resistant strains of
Candida
species had a higher prevalence of candidiasis than those colonized with susceptible strains. Our analysis found that antibiotic treatment and lower CD4
+
counts (<200 cells/mm
3
) increased the rate of oropharyngeal candidiasis in HIV-infected patients, while antiretroviral therapy protected patients from the development of candidiasis.
Species-Level Identification of Isolates of the
Acinetobacter calcoaceticus
-
Acinetobacter baumannii
Complex by Sequence Analysis of the 16S-23S rRNA Gene Spacer Region
Authors: Chang Hsien Chang , Wei Yu Fang , Dijkshoorn Lenie , Vaneechoutte Mario , Tang Chung Tao , Chang Tsung Chain 
Published: April 2005

ABSTRACT

The species
Acinetobacter calcoaceticus
,
A. baumannii
, genomic species 3, and genomic species 13TU included in the
Acinetobacter calcoaceticus
-
Acinetobacter baumannii
complex are genetically highly related and difficult to distinguish phenotypically. Except for
A. calcoaceticus
, they are all important nosocomial species. In the present study, the usefulness of the 16S-23S rRNA gene intergenic spacer (ITS) sequence for the differentiation of (genomic) species in the
A. calcoaceticus
-
A. baumannii
complex was evaluated. The ITSs of 11 reference strains of the complex and 17 strains of other (genomic) species of
Acinetobacter
were sequenced. The ITS lengths (607 to 638 bp) and sequences were highly conserved for strains within the
A. calcoaceticus
-
A. baumannii
complex. Intraspecies ITS sequence similarities ranged from 0.99 to 1.0, whereas interspecies similarities varied from 0.86 to 0.92. By using these criteria, 79 clinical isolates identified as
A. calcoaceticus
(18 isolates) or
A. baumannii
(61 isolates) with the API 20 NE system (bioMérieux Vitek, Marcy l'Etoile, France) were identified as
A. baumannii
(46 isolates), genomic species 3 (19 isolates), and genomic species 13TU (11 isolates) by ITS sequencing. An identification rate of 96.2% (76 of 79 isolates) was obtained by using ITS sequence analysis for identification of isolates in the
A. calcoaceticus
-
A. baumannii
complex, and the accuracy of the method was confirmed for a subset of strains by amplified rRNA gene restriction analysis and genomic DNA analysis by AFLP analysis by using libraries of profiles of reference strains. In conclusion, ITS sequence-based identification is reliable and provides a promising tool for elucidation of the clinical significance of the different species of the
A. calcoaceticus
-
A. baumannii
complex.
Clonal Dissemination of Macrolide-Resistant and Penicillin-Susceptible Serotype 3 and Penicillin-Resistant Taiwan 19F-14 and 23F-15
Streptococcus pneumoniae
Isolates in Japan: a Pilot Surveillance Study
Authors: Kasahara Kei , Maeda Koichi , Mikasa Keiichi , Uno Kenji , Takahashi Ken , Konishi Mitsuru , Yoshimoto Eiichiro , Murakawa Koichi , Kita Eiji , Kimura Hiroshi 
Published: April 2005

ABSTRACT

Large-scale surveillance studies using molecular techniques such as pulsed-field gel electrophoresis (PFGE) have revealed that the spread of antibiotic-resistant pneumococci is due to clonal spread. However, in Japan, surveillance studies using such molecular techniques have never been done. Therefore, we conducted a pilot surveillance study to elucidate the present situation in Japan. Among the 145 isolates examined, the most prevalent serotype was type 19F (20%), for which most isolates were not susceptible to penicillin (86.2%) but were positive for the
mef
(A)/
mef
(E) gene (89.7%). The secondmost prevalent was serotype 3 (16.6%), for which most isolates were susceptible to penicillin (87.5%) and positive for the
erm
(B) gene (91.7%). PFGE analysis showed that both serotypes consisted mainly of clonally identical or related isolates and, in particular, 38% of the type 19F isolates were indistinguishable from or closely related to the Taiwan 19F-14 clone. In addition, some of the Japanese type 23F isolates with the
erm
(B) gene were indistinguishable from or related to the Taiwan 23F-15 clone as analyzed by PFGE. Based on the results of our pilot study performed in a single institution, it is likely that international antibiotic-resistant clones have already spread in Japan; therefore, a nationwide surveillance study should be urgently conducted.
Loop-Mediated Isothermal Amplification for Rapid Detection of Newcastle Disease Virus
Authors: Pham Hang Minh , Nakajima Chie , Ohashi Kazuhiko , Onuma Misao 
Published: April 2005

ABSTRACT
We have evaluated a diagnostic system based on the loop-mediated isothermal amplification (LAMP) assay for the rapid, simple, and sensitive detection of Newcastle disease virus (NDV) directly from culture isolates as well as clinical samples. By using one set of specific primers targeting the fusion protein gene, the LAMP assay rapidly amplified the target gene within 2 h, requiring only a regular laboratory water bath or heat block for reaction. The results obtained from testing the genomes of 38 NDV strains, other different viruses, and clinical samples of experimentally infected chickens showed that LAMP was as sensitive and specific as nested PCR. All LAMP-positive samples were positive by nested PCR. The LAMP assay is faster than nested PCR, cost-effective, and easy to perform. Our results clearly demonstrate that the LAMP-based assay is a useful tool for the rapid and sensitive diagnosis of NDV infection.
Laboratory-Based Surveillance and Molecular Epidemiology of Influenza Virus in Taiwan
Authors: Shih Shin-Ru , Chen Guang-Wu , Yang Ching-Chun , Yang Weng-Zhi , Liu Ding-Ping , Lin Jih-Hui , Chiu Shu-Chun , Chen Haur-Young , Tsao Kuo-Chien , Huang Chung-Guei , Huang Ya-Ling , Mok Chee-Keng , Chen Chi-Jene , Lin Tzou-Yien , Wang Jen-Ren , Kao Chuan-Liang , Lin Kwei-Hsian , Chen Li-Kuang , Eng Hock-Liew , Liu Yung-Ching , Chen Po-Yen , Lin Jen-Shiou , Wang Jen-Hsien , Lin Cheng-Wen , Chan Yu-Jiun , Lu Jang-Jih , Hsiung Chao A. , Chen Pei-Jer , Su Ih-Jen 
Published: April 2005

ABSTRACT
A laboratory-based surveillance network of 11 clinical virological laboratories for influenza viruses was established in Taiwan under the coordination of the Center for Disease Control and Prevention (CDC), Taiwan. From October 2000 to March 2004, 3,244 influenza viruses were isolated, including 1,969 influenza A and 1,275 influenza B viruses. The influenza infections usually occurred frequently in winter in the northern hemisphere. However, the influenza seasonality in Taiwan was not clear during the four seasons under investigation. For example, the influenza A viruses peaked during the winters of 2001, 2002, and 2003. However, some isolated peaks were also found in the summer and fall (June to November) of 2001 and 2002. An unusual peak of influenza B also occurred in the summer of 2002 (June to August). Phylogenetic analysis shows that influenza A isolates from the same year were often grouped together. However, influenza B isolates from the year 2002 clustered into different groups, and the data indicate that both B/Victoria/2/87-like and B/Yamagata/16/88-like lineages of influenza B viruses were cocirculating. Sequence comparison of epidemic strains versus vaccine strains shows that many vaccine-like Taiwanese strains were circulating at least 2 years before the vaccine strains were introduced. No clear seasonality of influenza reports in Taiwan occurred in contrast to other more continental regions.
Dynamic Range of Hepatitis C Virus RNA Quantification with the Cobas Ampliprep-Cobas Amplicor HCV Monitor v2.0 Assay
Authors: Gourlain Karine , Soulier Alexandre , Pellegrin Bertrand , Bouvier-Alias Magali , Hézode Christophe , Darthuy Françoise , Rémiré Jocelyne , Pawlotsky Jean-Michel 
Published: April 2005

ABSTRACTAccurate quantification of hepatitis C virus (HCV) RNA is needed in clinical practice to decide whether to continue or stop pegylated interferon-α-ribavirin combination therapy at week 12 of treatment for patients with chronic hepatitis C. Currently the HCV RNA quantification assay most widely used worldwide is the Amplicor HCV Monitor v2.0 assay (Roche Molecular Systems, Pleasanton, Calif.). The HCV RNA extraction step can be automated in the Cobas Ampliprep device. In this work, we show that the dynamic range of HCV RNA quantification of the Cobas Ampliprep/Cobas Amplicor HCV Monitor v2.0 procedure is 600 to 200,000 HCV RNA IU/ml (2.8 to 5.3 log IU/ml), which does not cover the full range of HCV RNA levels in infected patients. Any sample containing more than 200,000 IU/ml (5.3 log IU/ml) must thus be retested after dilution for accurate quantification. These results emphasize the need for commercial HCV RNA quantification assays with a broader range of linear quantification, such as real-time PCR-based assays.
Identification of Genotype 3 Hepatitis E Virus (HEV) in Serum and Fecal Samples from Pigs in Thailand and Mexico, Where Genotype 1 and 2 HEV Strains Are Prevalent in the Respective Human Populations
Authors: Cooper K. , Huang F. F. , Batista L. , Rayo C. D. , Bezanilla J. C. , Toth T. E. , Meng X. J. 
Published: April 2005

ABSTRACT
Hepatitis E virus (HEV), the causative agent of hepatitis E, is an important public health concern in many developing countries. Increasing evidence indicates that hepatitis E is a zoonotic disease. There exist four major genotypes of HEV, and HEV isolates identified in samples from pigs belong to either genotype 3 or 4. Genotype 1 and 2 HEVs are found exclusively in humans. To determine whether genotype 1 and 2 HEVs also exist in pigs, a universal reverse transcription-PCR assay that is capable of detecting all four HEV genotypes was used to test for the presence of HEV RNA in serum and/or fecal samples from pigs in Thailand, where genotype 1 human HEV is prevalent, and from pigs in Mexico, where genotype 2 human HEV was epidemic. In Thailand, swine HEV RNA was detected in sera from 10/26 pigs of 2 to 4 months of age but not in sera from 50 pigs of other ages. In Mexico, swine HEV RNA was detected in 8/125 sera and 28/92 fecal samples from 2- to 4-month-old pigs. Antibodies to swine HEV were also detected in about 81% of the Mexican pigs. A total of 44 swine HEV isolates were sequenced for the open reading frame 2 gene region. Sequence analyses revealed that all swine HEV isolates identified in samples from pigs in Thailand and Mexico belong to genotype 3. Phylogenetic analyses revealed that minor branches associated with geographic origin exist among the swine HEV isolates. The results indicated that genotype 1 or 2 swine HEV does not exist in pigs from countries where the respective human HEV genotype 1 or 2 is prevalent. It is likely that only genotype 3 and 4 HEV strains have zoonotic potential.
Analysis of the Genetic Structure of Nontypeable Pneumococcal Strains Isolated from Conjunctiva
Authors: Berrón Sonsoles , Fenoll Asunción , Ortega Montserrat , Arellano Noemí , Casal Julio 
Published: April 2005

ABSTRACT
More than 50% of the nontypeable (NT) pneumococcal strains received in our laboratory for reference purposes are isolated in sporadic cases of conjunctivitis. To determine the genetic structure of the population of these NT conjunctival strains, we analyzed 75 pneumococci (40 NT and 35 typeable) isolated from conjunctivas and 30 (15 NT and 15 typeable) isolated from other sources. The NT and typeable conjunctival strains grouped in separate clusters, whereas NT and typeable pneumococci isolated from other sources were similarly distributed. NT conjunctival strains belonged to two well-differentiated clonal lineages. The first, represented by three newly described sequence types, featured fully antibiotic susceptible strains and appeared to be characteristic of conjunctival tissue; the second, represented by the previously described ST344, had a pattern of multiresistance to penicillin, tetracycline, and erythromycin and shared a genetic background with some NT strains isolated from other sources.
Usefulness of the Hepatitis C Virus Core Antigen Assay for Screening of a Population Undergoing Routine Medical Checkup
Authors: Gaudy Catherine , Thevenas Catherine , Tichet Jean , Mariotte Nicole , Goudeau Alain , Dubois Frédéric 
Published: April 2005

ABSTRACT

We studied the usefulness of the recently designed Trak-C assay for the detection and quantification of the hepatitis C virus (HCV) core antigen (Ag) for the screening of HCV infection in 4,201 subjects selected from 74,150 consecutive volunteers undergoing routine medical checkups. Subjects were selected for screening because they had risk factors (group II,
n
= 321) and/or elevated alanine transaminase activity (group I,
n
= 3847). Initially, the anti-HCV antibody assay and the Trak-C assay were performed on each patient. Subsequently, the Trak-C assay was performed only when the anti-HCV enzyme immune assay (EIA) was positive. Positive samples were further evaluated for anti-HCV antibodies by a third-generation strip immunoblot assay and for HCV RNA. Four samples (1.2%) from group II and 113 (2.9%) from group I were anti-HCV EIA positive. We also tested 33 subjects who previously tested positive for anti-HCV in our medical center. Among the 150 anti-HCV EIA-positive samples, the HCV core Ag result was in accord with the HCV RNA result in 146 cases (97.3%). When the EIA result was positive, the HCV core Ag concentration and the HCV RNA load were correlated (
r
2
= 0.78;
P
< 0.001). Four samples with low viral loads were Trak-C negative but HCV RNA positive. Among the 2,395 anti-HCV EIA-negative serum samples collected during the first part of the study, 17 (0.7%) were found to contain very low levels of HCV core Ag (<8.5 pg/ml, the cutoff value being 1.5 pg/ml). All these samples were HCV RNA negative and considered to be false positives. This was confirmed by HCV core Ag neutralization analysis. The HCV core Ag assay is a useful method in the screening strategy of HCV infection and provides a reliable means of distinguishing between current and cleared HCV infections that is well correlated with HCV RNA testing.