bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple Subtyping Assay for Human Immunodeficiency Virus Type 1 Subtypes B, C, CRF01-AE, CRF07-BC, and CRF08-BC
Authors: Wei Min , Guan Qi , Liang Hao , Chen Jianping , Chen Zhao , Hei Faxin , Feng Yi , Hong Kunxue , Huang Hailong , Xing Hui , Shao Yiming 
Published: September 2004

ABSTRACT

After the initial development of a human immunodeficiency virus type 1 (HIV-1) subtype-screening tool by nested multiplex PCR, we further improve it through the redesign of subtype-specific primers based on subtype signature pattern (SSP) analyses and optimization of the PCR conditions. Extracted RNA from plasma samples was used in reverse transcription and the cDNA products were added to the first round PCR, in which universal primers in the
gag
region were used to detect HIV-1 M group isolates. In the second round of PCR, three pairs of subtype-specific primers, detecting subtypes B, C, and CRF01-AE, were added in one tube. Subtype determination was based on the different size of PCR products on the agarose gel electrophoresis. An additional set of primers detecting only the prevalent recombinant strains CRF07-BC and CRF08-BC was used to discriminate CRF07- and CRF08-BC from pure subtype C. Testing for all kinds of HIV subtype reference strains indicated that this assay was applicable. A panel of 252 HIV-positive samples and 30 HIV-negative samples was further used to evaluate and validate this assay. Compared to the assay of sequence-based phylogenetic analysis, the newly developed assay has an adequate designated subtype sensitivity, 93.2% (69 of 74) for subtype B, 95.1% (117 of 123) for subtype C, 94.0% (47 of 50) for CRF01-AE, and 95.0% (115 of 121) for CRF07-BC and CRF08-BC. Most importantly, the intersubtype specificity of the assay was found to be 100%. The assay specificity was also found to be 100% when used to test 30 HIV-negative samples. The average reproducibility was 96.0% for subtype B, 96.7% for subtype C, and 95.0% for CRF01-AE. We have developed a simple, rapid, and low cost assay for screening subtypes B, C, CRF01-AE, CRF07-BC, and CRF08-BC in China.
Use of an Oligonucleotide Array for Laboratory Diagnosis of Bacteria Responsible for Acute Upper Respiratory Infections
Authors: Roth Stina B. , Jalava Jari , Ruuskanen Olli , Ruohola Aino , Nikkari Simo 
Published: September 2004

ABSTRACT

We developed a diagnostic array of oligonucleotide probes targeting species-specific variable regions of the genes encoding topoisomerases GyrB and ParE of respiratory bacterial pathogens. Suitable broad-range primer sequences were designed based on alignment of
gyrB/parE
sequences from nine different bacterial species. These species included
Corynebacterium diphtheriae
,
Fusobacterium necrophorum
,
Haemophilus influenzae
,
Legionella pneumophila
,
Moraxella catarrhalis
,
Mycoplasma pneumoniae
,
Staphylococcus aureus
,
Streptococcus pneumoniae
, and
Streptococcus pyogenes
. Specific probe sequences were selected by comparative analysis against the European Bioinformatics Database, as well as
gyrB/parE
sequences generated for this study. To verify specificity, at least six initial oligonucleotide probe sequences per bacterial species were tested by hybridization on a solid glass support using culture collection strains as templates. Finally, three oligonucleotide probes per bacterial species were utilized to examine 65 middle ear fluid and 29 throat swab samples. The sensitivities of the developed assay compared to classic culture from middle ear fluid samples for
H. influenzae
,
M. catarrhalis
, and
S. pneumoniae
were 96 (93 for culture), 73 (93 for culture), and 100% (78% for culture), respectively. No cross-reactivity with bacterial species belonging to the normal oral flora was observed when the 29 throat swab samples were studied. The sensitivity of the assay to detect
S. pyogenes
from these samples was 93% (80% for culture). These results provide a proof of concept for the diagnostic use of microarray technology based on broad-range topoisomerase gene amplification, followed by hybridization and specific detection of bacterial species.
Rapid and Specific Detection of
tdh
,
trh
1, and
trh
2 mRNA of
Vibrio parahaemolyticus
by Transcription-Reverse Transcription Concerted Reaction with an Automated System
Authors: Nakaguchi Yoshitsugu , Ishizuka Tetsuya , Ohnaka Satoru , Hayashi Toshinori , Yasukawa Kiyoshi , Ishiguro Takahiko , Nishibuchi Mitsuaki 
Published: September 2004

ABSTRACT

Vibrio parahaemolyticus
strains carrying the thermostable direct hemolysin (TDH)
tdh
gene, the TDH-related hemolysin (
trh
) gene, or both genes are considered virulent strains. We previously demonstrated that the transcription-reverse transcription concerted (TRC) method could be used to quantify the amount of mRNA transcribed from the
tdh
gene by using an automated detection system. In this study, we devised two TRC-based assays to quantify the mRNAs transcribed from the
trh
1 and
trh
2 genes, the two representative
trh
genes. The TRC-based detection assays for the
tdh
,
trh
1, and
trh
2 transcripts could specifically and quantitatively detect 10
3
to 10
7
copies of the corresponding calibrator RNAs. We examined by the three TRC assays the total RNA preparations extracted from 103 strains of
Vibrio parahaemolyticus
carrying the
tdh
,
trh
1, or
trh
2 gene in various combinations. The
tdh
,
trh
1, and
trh
2 mRNAs in the total RNA preparations were specifically quantified, and the time needed for detection ranged from 9 to 19 min, from 14 to 18 min, and from 9 to 12 min, respectively. The results showed that this automated TRC assays could detect the
tdh
,
trh
1, and
trh
2 mRNAs specifically, quantitatively, and rapidly. The relative levels of TDH determined by the immunological method and that of
tdh
mRNA determined by the TRC assays for most
tdh
-positive strains correlated. Interestingly, the levels of TDH produced from the strains carrying both
tdh
and
trh
genes were lower than those carrying only the
tdh
gene, whereas the levels of mRNA did not significantly differ between the two groups.
Simple Chemical Extraction Method for DNA Isolation from
Aspergillus fumigatus
and Other
Aspergillus
Species
Authors: Jin J. , Lee Y.-K. , Wickes B. L. 
Published: September 2004

ABSTRACT

DNA was successfully isolated from numerous
Aspergillus
spp. by use of a commercial kit. DNA that was easily digested and yielded PCR products up to 8.5 kb in size was recovered from broth or agar cultures. The ease and speed of this protocol provide an alternative to physical methods of DNA isolation.
Surveillance Study (2000 to 2001) of G- and P-Type Human Rotaviruses Circulating in South Korea
Authors: Min Bok Soon , Noh Yoon Ju , Shin Jin Ho , Baek Sun Young , Kim Jae Ok , Min Kyung Il , Ryu Seung Rel , Kim Byoug Guk , Kim Do Keun , Lee Seok Ho , Min Hong Ki , Ahn Byung Yoon , Park Sue Nie 
Published: September 2004

ABSTRACT
Human
rotavirus VP4 and VP7 gene sequences were amplified by reverse
transcription-PCR from 53% (322 of 607) of fecal specimens
collected from children with severe diarrhea who visited hospitals in
six urban areas of South Korea in 2000 and 2001. G2 was the most
frequently found G type (constituted 50.6%), followed by G1
(30.1%) and G4 (13.0%). Although the P types of high
incidence were P[4] (53.1%) and P[8]
(21.4%), a significant incidence of P[6]
(20.2%) was also noticeable. The commonest G- and P-type
combination found in this study was G2P[4], rather than
G1P[8], the most prevalent type known
worldwide.
Usefulness of the GenoType MTBC Assay for Differentiating Species of the
Mycobacterium tuberculosis
Complex in Cultures Obtained from Clinical Specimens
Authors: Richter Elvira , Weizenegger Michael , Fahr Anne-Marie , Rüsch-Gerdes Sabine 
Published: September 2004

ABSTRACT

A novel DNA strip assay, GenoType MTBC, was evaluated for differentiation of
Mycobacterium tuberculosis
complex species from 77 positive liquid cultures in clinical practice. Species identification (
M. tuberculosis
[71 strains],
Mycobacterium bovis
subsp.
bovis
[5 strains], and
Mycobacterium africanum
subtype I [1 strain]) results were identical to conventional results. The sensitivity was slightly higher for this test than for the AccuProbe assay.
Comparison of the Real-Time PCR Method and the Gen-Probe Amplified
Mycobacterium tuberculosis
Direct Test for Detection of
Mycobacterium tuberculosis
in Pulmonary and Nonpulmonary Specimens
Authors: Lemaître Nadine , Armand Sylvie , Vachée Anne , Capilliez Odile , Dumoulin Christine , Courcol René J. 
Published: September 2004

ABSTRACT

Real-time PCR was compared to Amplified
Mycobacterium tuberculosis
Direct Test (AMTDII) for 100 clinical specimens. The overall sensitivities of the real-time PCR method and AMTDII were similar for respiratory and nonrespiratory specimens. However, real-time PCR seemed to be less susceptible to amplification inhibitors than AMTDII.
Fosfomycin and Rifampin Disk Diffusion Tests for Detection of
Escherichia coli
Mutator Strains
Authors: Galán Juan-Carlos , Tato Marta , Baquero María-Rosario , Turrientes Carmen , Baquero Fernando , Martinez José-Luis 
Published: September 2004

ABSTRACT

A simple method, using commercial disks to detect
Escherichia coli
mutator strains, is proposed. The breakpoint for detecting strains with a mutation frequency ≥5 × 10
−7
was established at ≥70 and ≥20 colonies in the inhibition zone of fosfomycin and rifampin disks, respectively, after seeding 100 μl of an overnight culture. Strains with <30 and <10 colonies in fosfomycin and rifampin inhibition zones are presumptively non-mutators.
Community-Acquired
Clostridium difficile
Diarrhea Caused by Binary Toxin, Toxin A, and Toxin B Gene-Positive Isolates in Hungary
Authors: Terhes Gabriella , Urbán Edit , Sóki József , Hamid Kanjo Abdul , Nagy Elisabeth 
Published: September 2004

ABSTRACT

The aim of this work was to study the toxin types of
Clostridium difficile
isolates originating from different parts of Hungary. A PCR method was used for amplification of the two major toxin genes and the binary toxin gene and to detect the deletion or insertion in the 3′ end of the toxin A gene. The findings were compared with the results of cytotoxicity assays on the HeLa cell line. One hundred twelve isolates were tested; the toxin A and toxin B genes were detected in 79 strains by the PCR method. All of the isolates that were positive by the PCR method were also positive by the cytotoxicity assay. All of the other strains (
n
= 33) were negative for the toxin A and toxin B genes; in these cases, cytopathic effects on the cell line were not observed. No
tcdA
-negative and
tcdB
-positive isolates were found by the PCR method. In two cases, the presence of a binary toxin gene was observed by PCR; both isolates that were isolated from diarrheal feces carried the
tcdA
and
tcdB
genes. No prior hospitalization had occurred in either case.
In Vitro Susceptibilities of Isolates of
Sporothrix schenckii
to Itraconazole and Terbinafine
Authors: Kohler Lidiane Meire , Monteiro Paulo César Fialho , Hahn Rosane Christine , Hamdan Júnia Soares 
Published: September 2004

ABSTRACT

Thirty isolates of the yeast form of
Sporothrix schenckii
were evaluated for in vitro susceptibility to itraconazole and terbinafine by the recommended NCCLS modified technique (M27-A2). The MICs of itraconazole obtained oscillated between 0.062 and 4.0 μg/ml, and those of terbinafine oscillated between 0.007 and 0.50 μg/ml; therefore, terbinafine showed greater in vitro activity.
Prevalence of Hepatitis C Virus Infection among Hemodialysis Patients at a Tertiary-Care Hospital in Mexico City, Mexico
Authors: Méndez-Sánchez Nahum , Motola-Kuba Daniel , Chavez-Tapia Norberto C. , Bahena Jesús , Correa-Rotter Ricardo , Uribe Misael 
Published: September 2004

ABSTRACT
We determined the prevalence of hepatitis C virus (HCV) in hemodialysis patients by antibody testing and HCV RNA determination by PCR. A total of 149 patients with kidney failure with replacement therapy were tested. The prevalence of anti-HCV was 6.7% (10 of 149 patients), and viremia was detectable in 8 of 149 (5%) patients. Three of 149 patients (2%) were anti-HCV negative with detectable HCV RNA.
Antimicrobial Susceptibilities of Invasive Pediatric
Abiotrophia
and
Granulicatella
Isolates
Authors: Zheng Xiaotian , Freeman Alexandra F. , Villafranca Jay , Shortridge Dee , Beyer Jill , Kabat William , Dembkowski Karen , Shulman Stanford T. 
Published: September 2004

ABSTRACT

Abiotrophia
and
Granulicatella
species have been associated with various infections. Antimicrobial susceptibility data for these nutritionally variant streptococcus-like organisms, especially for pediatric isolates, are very limited. Little is known about the genetic bases of their resistance mechanisms. We report the results of identification to bacterial species level, antimicrobial susceptibility testing, macrolide resistance testing, and detection of genes encoding that resistance for a collection of 15 pediatric clinical isolates from normally sterile sites. Our results indicate that the prevalence of beta-lactam and macrolide resistance is high and that both
erm
and
mef
are found in these isolates.
Evaluation of Conventional Castaneda and Lysis Centrifugation Blood Culture Techniques for Diagnosis of Human Brucellosis
Authors: Mantur Basappa G. , Mangalgi Smita S. 
Published: September 2004

ABSTRACT

We investigated the role of the lysis centrifugation blood culture technique over the conventional Castaneda technique for the diagnosis of human brucellosis. The lysis centrifugation technique has been found to be more sensitive in both acute (20% higher sensitivity;
P
< 0.00001) and chronic (40% higher sensitivity;
P
= 0.087) forms of brucellosis. The major advantage of lysis centrifugation was in the mean detection time, which was only 2.4 days in acute and 2.7 days in chronic cases, with 103 out of 110 (93.6%) and 17 out of 20 (85%) cultures from acute and chronic brucellosis, respectively, detected before the conventional culture was positive. Our results confirmed the potential usefulness of the lysis technique in diagnosis and institution of appropriate antibiotic therapy.
Detection of Hepatitis A Virus RNA in Saliva
Authors: Mackiewicz Vincent , Dussaix Elisabeth , Le Petitcorps Marie-France , Roque-Afonso Anne Marie 
Published: September 2004

ABSTRACT
Hepatitis A virus (HAV) is shed in feces but also in saliva. HAV RNA was detected in saliva in five out of six acutely infected patients with HAV viremia. Serum and saliva sequences were identical. The simplicity of obtaining material allows the recommendation of the use of saliva for investigation of outbreaks.
Multicenter Validation of the
cppB
Gene as a PCR Target for Detection of
Neisseria gonorrhoeae
Authors: Bruisten S. M. , Noordhoek G. T. , van den Brule A. J. C. , Duim B. , Boel C. H. E. , El-Faouzi K. , du Maine R. , Mulder S. , Luijt D. , Schirm J. 
Published: September 2004

ABSTRACT

The
cppB
gene is often used as a target for detection of
Neisseria gonorrhoeae
by PCR. Using a coded panel of 500 DNA samples, we determined that the
cppB
gene is missing in 5.8% of
N. gonorrhoeae
strains, and therefore we consider the
cppB
gene to be an unsuitable target.
Variability of Germinative Potential among Pathogenic Species of
Aspergillus
Authors: Araujo Ricardo , Rodrigues Acacio Gonçalves 
Published: September 2004

ABSTRACT

The objective of our study was to evaluate parameters influencing the germination of
Aspergillus
conidia. Inoculum concentration and age significantly influenced germination. Different incubation temperatures revealed significant differences among
Aspergillus
species. The internal human milieu provides the ideal conditions for the development of invasive disease by
Aspergillus fumigatus
but restricts invasion by
Aspergillus flavus
and
Aspergillus niger
.
Sequencing and Phylogenetic Analysis of Human Genotype P[6] Rotavirus Strains Detected in Hungary Provides Evidence for Genetic Heterogeneity within the P[6] VP4 Gene
Authors: Bányai Krisztián , Martella Vito , Jakab Ferenc , Melegh Béla , Szücs György 
Published: September 2004

ABSTRACT
Although rotavirus genotype P[6] is one of the three most common VP4 specificities associated with human infection, the relatively few sequence data available in public databases suggest that the genetic variability within P[6] might be presently unexplored. Thus far, two human P[6] lineages (M37-like and AU19-like) and a single porcine P[6] lineage (Gottfried-like) have been identified by phylogenetic analysis. Serologic studies demonstrated that these three lineages are antigenically distinct from each other, a finding based on which they were classified into three subtypes, P2A[6] (M37-like), P2B[6] (Gottfried-like), and P2C[6] (AU19-like). To study heterogeneity within this genotype, we selected for molecular characterization a total of six P[6] strains detected during an ongoing surveillance in Hungary. The variable region of the VP4 gene was subjected to sequencing and phylogenetic analysis. Our data indicated that these six strains fell into two phylogenetic lineages distinguishable from the human lineages M37-like and AU19-like and from the porcine lineage Gottfried-like. Further studies are needed to understand whether these two novel lineages are genuine human strains or might have originated from animal strains and to evaluate the antigenic relationship of the novel Hungarian P[6] strains to the three established subtypes.
Characterization of Avian H3N3 and H1N1 Influenza A Viruses Isolated from Pigs in Canada
Authors: Karasin Alexander I. , West Keith , Carman Suzanne , Olsen Christopher W. 
Published: September 2004

ABSTRACTH3N3 and H1N1 influenza A viruses were isolated from Canadian pigs in 2001 and 2002. These viruses are phylogenetically related to waterfowl viruses and antigenically distinct from reference swine influenza viruses. The isolation of these viruses reemphasizes the potential for interspecies transmission of influenza viruses from waterfowl to pigs in North America.
Pneumolysin Is a Key Factor in Misidentification of Macrolide-Resistant
Streptococcus pneumoniae
and Is a Putative Virulence Factor of
S. mitis
and Other Streptococci
Authors: Neeleman Chris , Klaassen Corné H. W. , Klomberg Debbie M. , de Valk Hanneke A. , Mouton Johan W. 
Published: September 2004

ABSTRACT

We evaluated the applicability of
ply
PCR for confirmation of the identification of
Streptococcus pneumoniae. lytA
PCR, 16S rRNA sequencing, and amplified-fragment length polymorphism were used as reference methods. In contrast to the
lytA
gene, the
ply
gene proved to be not specific for
S. pneumoniae
. The presence of the
ply
gene in other streptococci, in particular
Streptococcus mitis
, suggests that pneumolysin plays a pathogenic role.
Comparison of the Sensititre YeastOne Colorimetric Antifungal Panel with a Modified NCCLS M38-A Method To Determine the Activity of Voriconazole against Clinical Isolates of
Aspergillus
spp
Authors: Castro Carmen , Serrano M. Carmen , Flores Bernardo , Espinel-Ingroff Ana , Martín-Mazuelos Estrella 
Published: September 2004

ABSTRACT

The
susceptibilities of 63 isolates of
Aspergillus
spp. to
voriconazole were evaluated by a modified NCCLS M38-A method and the
Sensititre YeastOne method. The overall agreement was 82.5%,
ranging from 100% for
Aspergillus niger
and
Aspergillus terreus
to 62.5% for
Aspergillus
flavus
. Discrepancies between the methods were due to higher
Sensititre MICs. The Sensititre YeastOne method could have potential
value for susceptibility testing of
Aspergillus
spp. to
voriconazole.
Development of a Real-Time PCR Assay Using SYBR Green I for Provirus Load Quantification in a Murine Model of AIDS
Authors: Casabianca Anna , Orlandi Chiara , Fraternale Alessandra , Magnani Mauro 
Published: September 2004

ABSTRACT
A real-time PCR assay using SYBR Green I for quantification of provirus load in a murine model of AIDS (i.e., LP-BM5 infection) was developed and validated. In this method, data are normalized against the 18S rRNA gene. The method has a dynamic range of 8 logs and a sensitivity of one copy.
Differing Patterns of Liver Disease Progression and Hepatitis C Virus (HCV) Quasispecies Evolution in Children Vertically Coinfected with HCV and Human Immunodeficiency Virus Type 1
Authors: Canobio Sophie , Guilbert Cynthia M. , Troesch Myriam , Samson Johanne , Lemay Mireille , Pelletier Veronique Anne , Bernard-Bonnin Anne-Claude , Kozielski Rafal , Lapointe Normand , Martin Steven R. , Soudeyns Hugo 
Published: September 2004

ABSTRACT
Hepatitis C virus (HCV) quasispeciation was studied in two children vertically coinfected with HCV and human immunodeficiency virus type 1 (HIV-1). HCV quasispecies diversification and liver injury were more significant in patient C1, who was immunocompetent with anti-HIV therapy, than in patient C2, who was immunosuppressed, in consistency with modulation of HCV quasispeciation and liver injury by immunocompetence in coinfected children.
Pathogenic Differences between North American and Latin American Strains of
Histoplasma capsulatum
var.
capsulatum
in Experimentally Infected Mice
Authors: Durkin Michelle M. , Connolly Patricia A. , Karimi Kian , Wheat Emerson , Schnizlein-Bick Carol , Allen Stephen D. , Alves Katia , Tewari Ram P. , Keath Elizabeth 
Published: September 2004

ABSTRACT
Clinical differences in histoplasmosis between North America and Brazil prompted investigation of experimental infection with representative strains. Mortality was higher with Latin American strains, and lung pathology showed large necrotizing granuloma with prominent neutrophilic infiltration. Chronic disease was unique to the North American strain.
Cladophialophora bantiana
Brain Abscess in a Solid-Organ Transplant Recipient: Case Report and Review of the Literature
Authors: Levin Todd P. , Baty Darric E. , Fekete Thomas , Truant Allan L. , Suh Byungse 
Published: September 2004

ABSTRACT

Cerebral phaeohyphomycosis caused by
Cladophialophora bantiana
is a rare disease. We describe a heart and bilateral lung transplant recipient who was unsuccessfully treated for a
C. bantiana
brain abscess. This report compares the present case to those of other solid-organ transplant recipients with the same infection and to those of patients who did not receive transplants.
NeonatalCandida albicansSeptic Thrombosis of the Portal Vein followed by Cavernous Transformation of the Vessel
Authors: Pacifico Lucia , Panero Alessandra , Colarizi Patrizia , Matrunola Marco , Simonetti Antonella F. , Chiesa Claudio 
Published: September 2004

ABSTRACTWe report two premature neonates withCandida albicansseptic thrombosis of the portal vein who developed, in very early childhood, the sonographic appearance of cavernous transformation of the vessel and/or clinical signs of extrahepatic portal hypertension.
Pyelonephritis and Urosepsis Caused by
Streptococcus pneumoniae
Authors: Dufke Severin , Kunze-Kronawitter Heike , Schubert Sören 
Published: September 2004

ABSTRACT

This report presents the case of a patient with a massive pyelonephritis and a urosepsis caused by
Streptococcus pneumoniae
. This case is unusual as the focus was distant from the respiratory tract, the usual primary site of infection caused by this organism. No other primary site of infection was documented.
Mycobacterium heckeshornense
Infection in an Immunocompetent Patient and Identification by 16S rRNA Sequence Analysis of Culture Material and a Histopathology Tissue Specimen
Authors: van Hest Rob , van der Zanden Adri , Boeree Martin , Kremer Kristin , Dessens Mirjam , Westenend Pieter , Maraha Boulos , van Uffelen René , Schütte Ronald , de Lange Wiel 
Published: September 2004

ABSTRACT

Mycobacterium heckeshornense
is a rare isolate in clinical specimens. We performed simultaneous 16S rRNA sequence analysis of a mycobacterium culture and a histopathology specimen to determine the relevance of
M. heckeshornense
infection in an immunocompetent patient initially presenting with pneumothorax.