bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal Shifts in the Dominance of Serotypes of
Shigella dysenteriae
from 1999 to 2002 in Dhaka, Bangladesh
Authors: Talukder Kaisar A. , Islam M. Aminul , Khajanchi Bijay K. , Dutta Dilip K. , Islam Zhahirul , Safa Ashrafus , Alam Khorshed , Hossain A. , Nair G. B. , Sack David A. 
Published: November 2003

ABSTRACT

A total of 358
Shigella dysenteriae
strains isolated from patients attending the Dhaka treatment center of the International Centre for Diarrheal Disease Research, Bangladesh, between the years 1999 and 2002 were included in this study.
S. dysenteriae
type 1, the dominant serotype in 1999 (76.4%), declined to 6.5% in 2002. On the other hand,
S. dysenteriae
types 2 to 12 were isolated with increasing frequencies of 19, 67, 73.5, and 87% in 1999, 2000, 2001, and 2002, respectively. Of these, types 2 and 4 were the most dominant serotypes, accounting for more than 18.7 and 28.5% of the total isolates, respectively. There was no isolation of serotypes 5, 7, 8, and 13 during this period. Twenty-eight (7.8%) of the isolates were atypical and agglutinated only with the polyvalent antiserum of
S. dysenteriae
. More than 98% of type 1 strains isolated between 1999 and 2001 were resistant to ampicillin, sulfamethoxazole-trimethoprim, and nalidixic acid. Among other serotypes of
S. dysenteriae
, Nal
r
type 2 strains were isolated in 2001 and 2002. Although heterogeneous plasmid profiles were obtained depending on the presence or absence of a single plasmid, core plasmids were defined for particular serotypes. On the other hand, the same plasmid profile was found to be shared by different serotypes. Interestingly, plasmid patterns of types 2 and 4 were almost identical except that a middle-range plasmid of 70 to 60 MDa was present in type 4 in addition to the core plasmids. All the strains harboring the 140-MDa plasmid were positive for the
ipaH
gene, had Congo red binding abilities, and were positive by the Sereny test, demonstrating their invasive properties.
PCR Assay for Monitoring
Trypanosoma cruzi
Parasitemia in Childhood after Specific Chemotherapy
Authors: Galvão Lúcia M. C. , Chiari Egler , Macedo Andréa M. , Luquetti Alejandro O. , Silva Simonne A. , Andrade Ana Lúcia S. S. 
Published: November 2003

ABSTRACT

Assessment of cure of
Trypanosoma cruzi
infection by antibody seroconversion usually involves several years of follow-up. Parasitological negativity is useless for cure assessment, since even untreated patients mostly show negative results; conversely, positive tests are of great value because they indicate treatment failure. Here, PCR was used to assess the rate of specific chemotherapy failure in a well-characterized Brazilian cohort of
T. cruzi
-seropositive children, who were enrolled in a field trial of benznidazole (Bz) efficacy. Paired blood samples from 111 children were taken at baseline and 36 months after treatment with either Bz (
n
= 58) or a placebo (
n
= 53). DNA extraction and PCR amplification were carried out as previously described, and hybridization was performed with all PCR products. At the end of follow-up, PCR was positive for 39.6% of the patients in the Bz group versus 64.2% in the placebo group (
P
= 0.01). Untreated patients had a 1.6-fold-higher chance of remaining positive by PCR than those in the Bz group (
P
< 0.05). We conclude that PCR is a useful tool for revealing therapeutic failure of
T. cruzi
infection on a short-term basis.
Real-Time PCR Assay for Clinical Management of Human Immunodeficiency Virus-Infected Patients with Visceral Leishmaniasis
Authors: Bossolasco Simona , Gaiera Giovanni , Olchini Davide , Gulletta Maurizio , Martello Leonardo , Bestetti Arabella , Bossi Laura , Germagnoli Luca , Lazzarin Adriano , Uberti-Foppa Caterina , Cinque Paola 
Published: November 2003

ABSTRACT

To evaluate the usefulness of a real-time PCR for
Leishmania
DNA in the diagnosis and follow-up of patients with human immunodeficiency virus type 1 (HIV-1) and
Leishmania
coinfection,
Leishmania
DNA levels were measured in whole peripheral blood from 25 HIV-infected patients with clinical features suggestive of visceral leishmaniasis.
Leishmania
DNA was detected in 10 of 25 patients with microscopically confirmed visceral leishmaniasis and in none of those without this disease. Following treatment with liposomal amphotericin B, a clinical response was observed in 9 of 10 patients, in association with significantly decreased parasite loads. Seven patients relapsed clinically a median of 110 days after the end of treatment, in association with substantial increases in
Leishmania
DNA levels.
Leishmania
DNA levels correlated with the clinical course of visceral leishmaniasis, and their measurement at diagnosis and during and after treatment seems to be useful in the clinical management of HIV-infected patients with this disease.
Evaluation and Field Validation of PCR Tests for Detection of
Actinobacillus pleuropneumoniae
in Subclinically Infected Pigs
Authors: Fittipaldi Nahuel , Broes André , Harel Josée , Kobisch Marylène , Gottschalk Marcelo 
Published: November 2003

ABSTRACT

Eight PCR tests were evaluated for their abilities to detect
Actinobacillus pleuropneumoniae
in swine tonsils. At first they were compared regarding their specificities by using
A. pleuropneumoniae
and related bacterial species and their analytical sensitivities by using tonsils experimentally infected in vitro. PCRs were carried out both directly with tonsil homogenates (direct PCR) and after culture of the sample (after-culture PCR). Most tests demonstrated good specificities; however, some tests gave false-positive results with some non-
A. pleuropneumoniae
species. High degrees of variation in the analytical sensitivities among the tests were observed for the direct PCRs (10
9
to 10
2
CFU/g of tonsil), whereas those of most of the after-culture PCRs were similar (10
2
CFU/g of tonsil). In a second phase, the effects of sample storage time and storage conditions were evaluated by using tonsils from experimentally infected animals. Storage at −20°C allowed the detection of the organism for at least 4 months. Finally, the
omlA
PCR test described by Savoye et al. (C. Savoye et al., Vet. Microbiol. 73:337-347, 2000) and the commercially available Adiavet App PCR test were further validated with field samples. Their effectiveness was compared to those of standard and immunomagnetic separation-based methods of bacterial isolation. In addition, a comparison of tonsil biopsy specimens (from living animals) and whole tonsils (collected at the slaughterhouse) was also conducted.
A. pleuropneumoniae
was neither isolated nor detected by PCR from a herd serologically negative for
A. pleuropneumoniae
. PCR was more sensitive than the standard isolation method with whole tonsils from three infected herds. After-culture PCR offered the highest degree of sensitivity (93 and 83% for the
omlA
and Adiavet App PCRs, respectively). The PCR detection rate was higher with whole tonsils than with tonsil biopsy specimens. Good agreement (κ = 0.65) was found between the presence of
A. pleuropneumoniae
in tonsils and the individual serological status of the animals.
Experience with the MicroSeq D2 Large-Subunit Ribosomal DNA Sequencing Kit for Identification of Commonly Encountered, Clinically Important Yeast Species
Authors: Hall Leslie , Wohlfiel Sherri , Roberts Glenn D. 
Published: November 2003

ABSTRACT

Experience with a MicroSeq D2 large-subunit (LSU) ribosomal DNA (rDNA) sequencing kit for identification of yeast species commonly encountered in the mycology laboratory at Mayo Clinic is described here. A total of 131 isolates of yeasts recovered from clinical specimens were included in the study. Phenotypic methods used for initial identification included germ tube formation, urease production, microscopic morphological features on cornmeal agar, and an API 20C AUX system; all isolates were sequenced using a MicroSeq D2 LSU rDNA sequencing kit. Nucleic acid sequencing identified 93.9% of the isolates to the correct genus and species. A total of 100 of the isolates (representing 19 species of
Candida
) were sequenced, and 98% gave results concordant with identifications made by the API 20C AUX system; distance scores ranged from 0 to 1.88%, with an average value of 0.23%.
Candida dubliniensis
was not included in the MicroSeq database and was identified as
Candida albicans
. A total of 32 isolates representing 9 other genera (including
Cryptococcus
,
Filobasidium
,
Kloeckera
,
Malassezia
,
Pichia
,
Sporidiobolus
,
Rhodotorula
,
Zygosaccharomyces
, and
Trichosporon
) were included, and 81.3% showed concordant results when phenotypic and sequencing results were compared. Most discrepancies were attributed to the lack of inclusion of the species in the MicroSeq or API 20C AUX database. The MicroSeq D2 LSU rDNA sequencing kit appears to be accurate and useful for the identification of yeasts that might be seen in a clinical laboratory.
Use of O-Antigen Gene Cluster-Specific PCRs for the Identification and O-Genotyping of
Yersinia pseudotuberculosis
and
Yersinia pestis
Authors: Bogdanovich Tatiana , Carniel Elisabeth , Fukushima Hiroshi , Skurnik Mikael 
Published: November 2003

ABSTRACT

Yersinia pestis
is a very recently evolved clone of
Yersinia pseudotuberculosis
serotype O:1b. This close relationship causes potential difficulties in DNA-based diagnostic methods. Analysis of the O-antigen gene clusters in these two organisms identified two regions that were used to specifically identify
Y. pestis
-
Y. pseudotuberculosis
as a group or
Y. pestis
alone. Both PCR assays were found to be 100% specific when tested on a large collection of
Yersinia
species and other
Enterobacteriaceae
. Furthermore, advantage was taken of the different setups of the O-antigen gene clusters of the 21 known
Y. pseudotuberculosis
serotypes to develop a multiplex PCR assay to replace the conventional serotyping method of
Y. pseudotuberculosis
by O-genotyping. The multiplex PCR assay contained nine sets of specific PCRs in a single tube and when used on
Y. pseudotuberculosis
reference strains allowed the distinction of 14 individual serotypes and two duplex serotypes (O:4a-O:8 and O:12-O:13). Serotype O:7, O:9, and O:10 strains required additional PCRs for O-genotyping. Once applied to
Y. pseudotuberculosis
strains of various origins, a very good correlation between classical serotypes and O-genotypes was observed, although some discrepancies were found. O-genotyping also proved useful to correct misidentification of some strains and to type
Y. pseudotuberculosis
isolates that had lost the expression of the O-antigen. The PCR-based O-genotyping can easily be applied in conventional laboratories, without the need for tedious preparation of a large set of specific antisera.
Duplex Real-Time SYBR Green PCR Assays for Detection of 17 Species of Food- or Waterborne Pathogens in Stools
Authors: Fukushima Hiroshi , Tsunomori Yoshie , Seki Ryotaro 
Published: November 2003

ABSTRACT

A duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction using the QIAamp DNA Stool Mini kit was evaluated with regard to detection of 8 of 17 species of food- or waterborne pathogens in five stool specimens in 2 h or less. The protocol used the same LC-PCR with 20 pairs of specific primers. The products formed were identified based on a melting point temperature (

T
m

) curve analysis. The 17 species of food- or waterborne pathogens examined were enteroinvasive
Escherichia coli
, enteropathogenic
E. coli
, enterohemorrhagic
E. coli
, enterotoxigenic
E. coli
, enteroaggregative
E. coli
,
Salmonella
spp.,
Shigella
spp.,
Yersinia enterocolitica
,
Yersinia pseudotuberculosis
,
Campylobacter jejuni
,
Vibrio cholerae
,
Vibrio parahaemolyticus
,
Vibrio vulnificus
,
Aeromonas
spp.,
Staphylococcus aureus
,
Clostridium perfringens
, and
Bacillus cereus.
No interference with the LC-PCR assay was observed when stool specimens were artificially inoculated with each bacterial species. The detection levels were approximately 10
5
food- or waterborne pathogenic bacteria per g of stool. The protocol for processing stool specimens for less than 10
4
food- or waterborne pathogenic bacteria per g of stool requires an overnight enrichment step to achieve adequate sensitivity. However, the rapid amplification and reliable detection of specific genes of greater than 10
5
food- or waterborne pathogenic bacteria per g in samples should facilitate the diagnosis and management of food- or waterborne outbreaks.
Comparison of DNA Amplification, mRNA Amplification, and DNA Hybridization Techniques for Detection of Cytomegalovirus in Bone Marrow Transplant Recipients
Authors: Diaz-Mitoma Francisco , Leger Chantal , Miller Helen , Giulivi Antonio , Frost Rita , Shaw Laura , Huebsch Lothar 
Published: November 2003

ABSTRACT
A total of 676 specimens from 63 recipients of bone marrow allografts were tested for cytomegalovirus (CMV) by the following assays: CMV pp67 NucliSens (NS), AMPLICOR CMV MONITOR (RA), and the Digene CMV DNA test (DG). In a consensus analysis, the sensitivities and specificities were 60 and 99% (NS), 96 and 98% (RA), and 90 and 76% (DG), respectively; for detection of symptomatic CMV infection, they were 60 and 97% (NS), 65 and 97% (RA), and 95 and 77% (DG), respectively. In multivariate analysis, the major risk factor for symptomatic CMV infection was an increase in the viral load in the DG assay; in univariate analyses, maximum viral loads in both DG and RA assays and a rising viral load in the RA assay were also significant. The earliest detection of CMV replication was provided by the RA assay (mean, 39 days posttransplantation), followed by the DG assay (mean, 48 days) and the NS assay (mean, 58 days).
Detection of
Gallibacterium
spp. in Chickens by Fluorescent 16S rRNA In Situ Hybridization
Authors: Bojesen Anders Miki , Christensen Henrik , Nielsen Ole Lerberg , Olsen John Elmerdahl , Bisgaard Magne 
Published: November 2003

ABSTRACT

Gallibacterium
has recently been included as a new genus of the family
Pasteurellaceae
Pohl 1981, which encompasses bacteria previously reported as
Pasteurella anatis
, “
Actinobacillus salpingitidis
,” and avian
Pasteurella haemolytica
-like organisms. So far, identification has exclusively relied on phenotypic characterization. We present a method based on a cyanine dye 3.18-labeled in situ hybridization probe targeting 16S rRNA to allow specific detection of bacteria belonging to the genus
Gallibacterium
. The probe, GAN850, showed no cross-reactivity to 25 other poultry-associated bacterial species, including members of the families
Pasteurellaceae
,
Enterobacteriaceae
, and
Flavobacteriaceae
, when cross-reactivities were evaluated by whole-cell hybridization. The probe was further evaluated by hybridization to formalin-fixed spleen and liver tissues from experimentally infected chickens, in which it proved to be useful for the detection of
Gallibacterium
. Additionally, determination of the spatial distribution and the host cell affiliation of
Gallibacterium
at various times during the infection process was possible. In conclusion, the in situ hybridization technique described may be of use as a diagnostic tool as well as for studies to elucidate the pathogenesis of
Gallibacterium
infections in chickens.
Bloodstream Isolates of
Enterococcus faecium
Enriched with the Enterococcal Surface Protein Gene,
esp
, Show Increased Adhesion to Eukaryotic Cells
Authors: Lund Bodil , Edlund Charlotta 
Published: November 2003

ABSTRACT

Infection-derived
Enterococcus faecium
strains enriched with
esp
had increased ability to adhere to Caco-2 cells (
P
< 0.05) and were less genetically diverse than
esp
-negative isolates.
esp
-negative
E. faecium
fecal isolates from healthy individuals adhered significantly better than
esp
-negative infection isolates (
P
< 0.05), indicating additional factors of importance to adhesion.
Detection and Sequence Analysis of Danish and Swedish Strains of Mink Astrovirus
Authors: Mittelholzer Christian , Englund Lena , Hedlund Kjell-Olof , Dietz Hans-Henrik , Svensson Lennart 
Published: November 2003

ABSTRACT
The sequences of mink astroviruses collected from 11 farms in Denmark and Sweden were analyzed and found to be homologous with one another but different from those of other astroviruses. A species-specific reverse transcriptase-PCR for mink astrovirus was established and shown to be suitable for the analysis of clinical samples.
Comparison of Hepatitis C Virus Genotyping by 5′ Noncoding Region- and Core-Based Reverse Transcriptase PCR Assay with Sequencing and Use of the Assay for Determining Subtype Distribution in India
Authors: Lole Kavita S. , Jha Jyotsna A. , Shrotri Sandhya P. , Tandon Badri N. , Prasad V. G. Mohan , Arankalle Vidya A. 
Published: November 2003

ABSTRACT

Phylogenetic analysis of the sequences of the 5′ noncoding regions (5′NCR) of 149 samples from hepatitis C virus (HCV) RNA-positive chronic carriers representing northern, southern, eastern, and western India showed that type 3 and type 1 are the predominant genotypes circulating in India, with an overall prevalence of 53.69 and 38.25%, respectively. Type 4 viruses (6.04%) were seen only in southern India. Sequence analysis of the core region of 51 of the above isolates enabled us to classify them further into subtypes as 1b (number of isolates [
n
] = 10), 1a (
n
= 6), 3a (
n
= 9), 3g (
n
= 14), 3f (
n
= 1), and 4d (
n
= 3). Three new subtypes were identified for the first time and designated as 3i (
n
= 5), 3j (
n
= 2), and 6l (
n
= 1). Sequencing the 5′NCR could differentiate HCV types, whereas classification at the level of subtype was possible with sequence analysis of the core region.
Isolation and Characterization of Dually Reactive Strains of Group A Rotavirus from Hospitalized Children
Authors: Ranshing Sujata S. , Kelkar Shobhana D. 
Published: November 2003

ABSTRACT
Seven rotavirus strains dually reactive to serotype G1- and G2-specific monoclonal antibodies (MAbs) from hospitalized children with rotavirus diarrhea were culture adapted. Six strains were neutralized with G1 antiserum to a higher titer than that of G2, and one was neutralized with G1 and G2 antisera to equal titers. Of these, four strains were also neutralized with G6 antiserum. Five strains with short RNA pattern could not be serotyped, and the remaining two strains with long RNA pattern were serotyped as G1 strains. In addition, two strains showing dual reactivity to G2 and G4 MAbs and one G2-like strain from a nontypeable specimen were isolated. The dual reactivity of the isolates could not be attributed to mixed infections.
Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR
Authors: Kleines Michael , Schellenberg Kirsten , Ritter Klaus 
Published: November 2003

ABSTRACT
The Chemagic Viral DNA/RNA kit was evaluated for extraction of cytomegalovirus (CMV), hepatitis B virus (HBV), and hepatitis G virus (HGV) by using the QIAamp DNA Blood Mini kit and the QIAamp Viral RNA Mini kit as reference protocols. The extraction efficiencies of the different kits for CMV DNA and HBV DNA were not distinguishable, but the extraction efficiency for HGV RNA was better with the Chemagen protocol. All clinical specimens tested HBV DNA- or HGV RNA-positive after QIAGEN protocols for extraction were confirmed by using the Chemagen protocol. The Chemagen kit failed to confirm one of 75 CMV DNA-positive specimens. Thus, a new competitive extraction method using a technology with a high potential for automation is available.
Invasive Mycotic Infections Caused by
Chaetomium perlucidum
, a New Agent of Cerebral Phaeohyphomycosis
Authors: Barron M. A. , Sutton D. A. , Veve R. , Guarro J. , Rinaldi M. , Thompson E. , Cagnoni P. J. , Moultney K. , Madinger N. E. 
Published: November 2003

ABSTRACT

We report the first two cases of invasive human mycoses caused by the phaeoid ascomycete,
Chaetomium perlucidum
, and review the English literature regarding invasive
Chaetomium
infections. Fatal disseminated disease involving the brain, heart, lungs, and spleen is described in an acute myelogenous leukemia patient. A second patient with a history of asthma and chronic bronchiectasis experiencing right-middle-lobe syndrome grew
C. perlucidum
from lung tissue. This study adds
C. perlucidum
to the list of other known neurotropic
Chaetomium
species,
C. atrobrunneum
and
C. strumarium
, and also documents this organism's ability to disseminate beyond the central nervous system.
Presumed Endocarditis Caused by BRO β-Lactamase-Producing
Moraxella lacunata
in an Infant with Fallot's Tetrad
Authors: Nagano Noriyuki , Sato Junichi , Cordevant Christophe , Nagano Yukiko , Taguchi Fumiaki , Inoue Matsuhisa 
Published: November 2003

ABSTRACT

A case of presumed endocarditis caused by
Moraxella lacunata
in a 15-month-old male infant with Fallot's tetrad is described. This infection may have occurred as the result of transmission of this organism between the father and his son. This is the first report of BRO β-lactamase-producing
M. lacunata
causing presumed endocarditis.
Allergic Fungal Sinusitis Associated with
Trichoderma longibrachiatum
Authors: Tang Patrick , Mohan Subhash , Sigler Lynne , Witterick Ian , Summerbell Richard , Campbell Iivi , Mazzulli Tony 
Published: November 2003

ABSTRACT

We describe allergic fungal sinusitis caused by
Trichoderma longibrachiatum
in a patient with a history of atopy and asthma. A Gram stain of a sinus biopsy specimen was initially thought to contain yeast cells, but when
Trichoderma
was recovered in culture, these cells were subsequently recognized as chlamydospores. The patient was successfully managed with a combination of sinus lavage, oral corticosteroids, itraconazole, and allergen immunotherapy. This case also points out that careful scrutiny of direct smears is required to ensure that fungal structures are not misinterpreted.
Outbreak of
Saccharomyces cerevisiae
Subtype
boulardii
Fungemia in Patients Neighboring Those Treated with a Probiotic Preparation of the Organism
Authors: Cassone Marco , Serra Pietro , Mondello Francesca , Girolamo Antonietta , Scafetti Sandro , Pistella Eleonora , Venditti Mario 
Published: November 2003

ABSTRACT

We report an outbreak of
Saccharomyces cerevisiae
subtype
boulardii
fungemia among three intensive care unit roommates of patients receiving lyophilized preparations of this fungus. The fungemia was probably due to central venous catheter contamination and resolved after fluconazole treatment. The need for stringent application of proper hygiene when using a probiotic preparation of this organism is emphasized.
BITS AND PIECES IN LOGARITHMIC CONFORMAL FIELD THEORY
Authors: FLOHR MICHAEL A. I. 
Published: November 2003

These are notes of my lectures held at the first School & Workshop on Logarithmic Conformal Field Theory and its Applications, September 2001 in Tehran, Iran. These notes cover only selected parts of the by now quite extensive knowledge on logarithmic conformal field theories. In particular, I discuss the proper generalization of null vectors towards the logarithmic case, and how these can be used to compute correlation functions. My other main topic is modular invariance, where I discuss the problem of the generalization of characters in the case of indecomposable representations, a proposal for a Verlinde formula for fusion rules and identities relating the partition functions of logarithmic conformal field theories to such of well known ordinary conformal field theories. The two main topics are complemented by some remarks on ghost systems, the Haldane-Rezayi fractional quantum Hall state, and the relation of these two to the logarithmic c=-2 theory.