bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Amplified Fragment Length Polymorphism To Identify and Type Brucella Isolates of Medical and Veterinary Interest
Authors: Whatmore Adrian M. , Murphy Terry J. , Shankster Stephen , Young Emma , Cutler Sally J. , Macmillan Alastair P. 
Published: February 2005

ABSTRACT

Amplified fragment length polymorphism (AFLP) is a whole-genome fingerprinting method that relies on the selective PCR amplification of restriction fragments. The potential of this approach for the discrimination of
Brucella
isolates at the species and intraspecies level was assessed. A number of different combinations of restriction enzymes and selective primers were examined, and one, using EcoRI and MseI with additional selective TC bases on the MseI primer, was selected for full assessment against a panel of
Brucella
isolates. The technique could readily differentiate
Brucella
spp. from all
Ochrobactrum
spp. representing the group of organisms most closely related to
Brucella
spp. Application of AFLP highlighted the genetic homogeneity of
Brucella
. In spite of this determination of AFLP profiles of large numbers of isolates of human and animal origin, including
Brucella abortus
,
B. melitensis
,
B. ovis
,
B. neotomae
, marine mammal isolates (no species name),
B. canis
, and
B. suis
, confirmed that all but the latter two species could be separated into distinct clusters based on characteristic and conserved differences in profile. Only
B. suis
and
B. canis
isolates clustered together and could not be distinguished by this approach, adding to questions regarding the validity of species assignments in this group. Under the conditions examined in the present study only limited intraspecies genomic differences were detected, and thus this AFLP approach is likely to prove most useful for identification to the species level. However, combination of several of the useful restriction enzyme-primer combinations identified in the present study could substantially add to the discriminatory power of AFLP when applied to
Brucella
and enhance the value of this approach.
Recurrent Colonization of Successively Implanted Tracheoesophageal Vocal Prostheses by a Member of theFusarium solaniSpecies Complex
Authors: Honraet K. , De Vos M. M. , Summerbell R. C. , van Kempen I. , De Saeger S. , Vermeersch H. , Van Peteghem C. , Nelis H. J. 
Published: February 2005

ABSTRACTTracheoesophageal vocal prostheses (TVP) in laryngectomized patients commonly deteriorate due to overgrowth by yeasts, particularlyCandidaspecies. We describe the first case of colonization of such devices by a member of theFusarium solanispecies complex in a patient with a history of glottal carcinoma. Three isolates, from three prostheses, were found morphologically consistent with the traditional picture ofF. solani.Ribosomal sequence analysis showed that the isolates belonged to a distinct, as yet apparently unnamed phylogenetic species within theF. solanispecies complex. This species, one of two distinct genetic types (genotype 2) traditionally considered part of the plant-pathogenic subtaxonFusarium solanif. sp.radicicola, has not previously been identified as an agent of human or animal disease, although it is closely related to a known etiologic agent of mycetoma, anAcremonium-like species recently renamedFusarium falciforme. Sequence and multisatellite M13 polymorphism analysis revealed no distinctions among the case isolates. Production of cyclosporine was detected for all three case isolates.
Self-Assembly of the Recombinant Capsid Protein of a Bovine Norovirus (BoNV) into Virus-Like Particles and Evaluation of Cross-Reactivity of BoNV with Human Noroviruses
Authors: Han M. G. , Wang Q. , Smiley J. R. , Chang K. O. , Saif L. J. 
Published: February 2005

ABSTRACT

None of the enteric caliciviruses except Po/Sapo/GIII/Cowden/80/US replicates in cell culture, which complicates efforts to develop control strategies or to study viral replication. To develop serological assays for bovine noroviruses (BoNVs) and to determine the cross-reactivity of BoNV with human noroviruses, we generated two recombinant baculoviruses, rCV186-OH and rJNCV, to express the capsid genes of Bo/CV186-OH/00/US (
Norovirus
genogroup III [GIII], genotype 2 [GIII/2]). rCV186-OH expressed the expected 57-kDa capsid protein, but rJNCV expressed a truncated capsid protein of 35 kDa. Sequence analysis of rJNCV identified a single nucleotide deletion in the P domain of the capsid gene, which introduced a stop codon at amino acid 323. The recombinant capsid protein produced by rCV186-OH but not that produced by rJNCV self-assembled into virus-like particles (VLPs) similar to native BoNV. An antibody-capture enzyme-linked immunosorbent assay (ELISA) and antigen-capture ELISA (Ag-ELISA) detected serum antibody and antigen, respectively, from calves infected with Bo/CV186-OH/00/US but not antibodies or antigens to other enteric viruses. In other tests of the GIII/2 BoNV Ag-ELISA, no cross-reactivity was observed with VLPs from one GI and four GII human noroviruses and porcine sapovirus Cowden strain. Because, like human noroviruses, BoNVs do not grow in cell culture, the BoNV VLPs will be useful in the serological assays described for the detection of BoNV antibody and antigen. Consistent with the phylogenetic analysis of the capsid genes of bovine and human noroviruses (M. G. Han, J. R. Smiley, C. Thomas, and L. J. Saif, J. Clin. Microbiol. 42:5214-5224, 2004), the results suggest that GIII/2 BoNV does not share significant antigenic relationships with the five characterized human noroviruses tested.
Tyrosine Phosphorylation of CagA from Chinese
Helicobacter pylori
Isolates in AGS Gastric Epithelial Cells
Authors: Zhang Youli , Argent Richard H. , Letley Darren P. , Thomas Rachael J. , Atherton John C. 
Published: February 2005

ABSTRACT

Helicobacter pylori
strains possessing the
cag
pathogenicity island (PaI) are associated with the development of gastroduodenal diseases, including gastric cancer.
cag
PaI products induce the secretion of interleukin-8 (IL-8) from epithelial cells and facilitate the translocation of CagA into the cell cytosol. In East Asia, where the incidence of gastric cancer is high, most strains possess the
cag
PaI. To date, however, no
cag
PaI phenotypic data have been provided for strains isolated in mainland China. Here we used 31 Chinese strains to determine the genotypic and phenotypic status of the
cag
PaI. All strains possessed
cagA
and
cagE
, and we observed a variation in the length of
cagA
variable regions. Nucleotide sequencing of the
cagA
variable region revealed that CagA was of two types, a short “Western” form with two tyrosine phosphorylation sites and a longer “East Asian” form with three tyrosine phosphorylation sites. Coculture of strains with AGS epithelial cells showed that strains could induce IL-8 secretion from the cells and that CagA with three phosphorylation sites became more phosphorylated than that with two and could induce significantly (
P
< 0.001) more cells to elongate. We hypothesize that the preponderance of the more active East Asian form of
cagA
may underlie the high rate of gastric cancer in China.
Six-Month Multicenter Study on Invasive Infections Due to
Streptococcus pyogenes
and
Streptococcus dysgalactiae
subsp.
equisimilis
in Argentina
Authors: Lopardo Horacio A. , Vidal Patricia , Sparo Monica , Jeric Paola , Centron Daniela , Facklam Richard R. , Paganini Hugo , Pagniez N. Gaston , Lovgren Marguerite , Beall Bernard 
Published: February 2005

ABSTRACT

During a 6-month period, 95 invasive infections due to
Streptococcus pyogenes
and group C or group G
Streptococcus dysgalactiae
subsp.
equisimilis
were recorded from 40 centers of 16 cities in Argentina. We describe here epidemiologic data available for 55 and 19 patients, respectively, associated with invasive infections due to
S. pyogenes
and
S. dysgalactiae
subsp.
equisimilis
. The associated isolates and 58 additional pharyngeal isolates were genotyped and subjected to serologic and/or antibiotic susceptibility testing. Group A streptococcal
emm
type distribution and strain association with toxic shock appeared to differ somewhat from results found within the United States; however, serologic characterization and
sof
sequence typing suggested that
emm
types found in both countries are reflective of shared clonal types.
Identification of Genetic Evidence for Dobrava Virus Spillover in Rodents by Nested Reverse Transcription (RT)-PCR and TaqMan RT-PCR
Authors: Weidmann Manfred , Schmidt P. , Vackova M. , Krivanec K. , Munclinger P. , Hufert F. T. 
Published: February 2005

ABSTRACT

A survey of 158 rodents caught in the Czech Republic identified Dobrava virus sequences closely related to that of the Dobrava virus type strain in
Apodemus sylvaticus
and
Mus musculus
rodents. The identity of
A. sylvaticus
was unequivocally confirmed by random amplified polymorphic DNA analysis. The data seem to indicate hantavirus spillover from
Apodemus flavicollis
to other rodents.
Sensitivity and Specificity of the ViroSeq Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping System for Detection of HIV-1 Drug Resistance Mutations by Use of an ABI PRISM 3100 Genetic Analyzer
Authors: Eshleman Susan H. , Crutcher Gillian , Petrauskene Olga , Kunstman Kevin , Cunningham Shawn P. , Trevino Christina , Davis Cheryl , Kennedy John , Fairman Jeff , Foley Brian , Kop JoAnn 
Published: February 2005

ABSTRACT
The ViroSeq human immunodeficiency virus type 1 (HIV-1) genotyping system is an integrated system for identification of drug resistance mutations in HIV-1 protease and reverse transcriptase (RT). Reagents are included for sample preparation, reverse transcription, PCR amplification, and sequencing. Software is provided to assemble and edit sequence data and to generate a drug resistance report. We determined the sensitivity and specificity of the ViroSeq system for mutation detection using an ABI PRISM 3100 genetic analyzer with a set of clinical samples and recombinant viruses. Twenty clinical plasma samples (viral loads, 1,800 to 10,500 copies/ml) were characterized by cloning and sequencing individual viral variants. Twelve recombinant-virus samples (viral loads, approximately 2,000 to 5,000 copies/ml) were also prepared. Eleven recombinant-virus samples contained drug resistance mutations as 40% mixtures. One recombinant-virus sample contained an insertion at codon 69 in RT (100% mutant). Plasma and recombinant-virus samples were analyzed using the ViroSeq system. Each sample was analyzed on three consecutive days at each of three testing laboratories. The sensitivity of mutation detection was 99.65% for the clinical plasma samples and 99.7% for the recombinant-virus preparations. The specificity of mutation detection was 99.95% for the clinical samples and 100% for the recombinant-virus mixtures. The base calling accuracy of the 3100 instrument was 99.91%. Mutations in clinical plasma samples and recombinant-virus samples were detected with high sensitivity and specificity, including mutations present as mixtures. This report supports the use of the ViroSeq system for identification of drug resistance mutations in HIV-1 protease and RT genes.
In Vitro Method To Study Antifungal Perfusion in
Candida
Biofilms
Authors: Samaranayake Y. H. , Ye J. , Yau J. Y. Y. , Cheung B. P. K. , Samaranayake L. P. 
Published: February 2005

ABSTRACT

Antimycotic perfusion through
Candida
biofilms was demonstrated by a modification of a simple in vitro diffusion cell bioassay system. Using this model, the perfusion of three commonly used antifungal agents, amphotericin B, fluconazole, and flucytosine, was investigated in biofilms of three different
Candida
species (i.e.,
Candida albicans
,
Candida parapsilosis
, and
Candida krusei
) that were developed on microporous filters. Scanning electron microscopy revealed that
C. albicans
formed a contiguous biofilm with tightly packed blastospores and occasional hyphae compared with
C. parapsilosis
and
C. krusei
, which developed confluent biofilms displaying structural heterogeneity and a lesser cell density, after 48 h of incubation on nutrient agar. Minor structural changes were also perceptible on the superficial layers of the biofilm after antifungal perfusion. The transport of antifungals to the distal biofilm-substratum interface was most impeded by
C. albicans
biofilms in comparison to
C. parapsilosis
and
C. krusei
. Fluconazole and flucytosine demonstrated similar levels of perfusion, while amphotericin B was the least penetrant through all three biofilms, although the latter appeared to cause the most structural damage to the superficial cells of the biofilm compared with the other antifungals. These results suggest that the antifungal perfusion through biofilm mode of growth in
Candida
is dependent both on the antimycotic and the
Candida
species in question, and in clinical terms, these phenomena could contribute to the failure of
Candida
biofilm-associated infections. Finally, the in vitro model we have described should serve as a useful system to investigate the complex interactions that appear to operate in vivo within the biofilm-antifungal interphase.
Outbreak of Infection Caused by
Enterobacter cloacae
Producing the Novel VEB-3 Beta-Lactamase in China
Authors: Jiang Xiaofei , Ni Yuxing , Jiang Yanqun , Yuan Feiyi , Han Lizhong , Li Ming , Liu Hong , Yang Li , Lu Yuan 
Published: February 2005

ABSTRACT

Over a 4-month period from November 2002 to February 2003, 27 ceftazidime-resistant or cefotaxime-resistant nonrepetitive
Enterobacter cloacae
isolates were collected from 27 patients hospitalized at HuaShan Hospital, Shanghai, People's Republic of China. The Etest did not detect extended-spectrum beta-lactamases (ESBLs) in those 27 isolates; however, screening by the NCCLS ESBL disk test and confirmatory tests detected ESBLs in 4 of 27 isolates and PCR detected ESBLs in 23 of 27 isolates. The majority of ESBL producers exhibited the same repetitive extragenic palindromic PCR pattern but harbored different ESBL genes. CTX-M-3 was the most prevalent ESBL in our study. Interestingly, 12 clonally related
E. cloacae
isolates possessed a novel
bla
VEB
-type beta-lactamase,
bla
VEB-3
.
Bla
VEB-3
was encoded by the chromosome and was located in an integron. Nine of the 12 isolates harbored both the
bla
VEB-3
and the
bla
CTX-M-3
-like ESBLs. This is the first report of a VEB-1-like ESBL in China and the first report of the simultaneous presence of VEB-1 and CTX-M-3-like ESBLs in an isolate.
Sequence Variation in the
porB
Gene from B:P1.4 Meningococci Causing New Zealand's Epidemic
Authors: Dyet Kristin H. , Martin Diana R. 
Published: February 2005

ABSTRACT

Since mid-1991, New Zealand has experienced an epidemic of meningococcal disease. The epidemic has been caused by serogroup B meningococci expressing PorA type P1.7-2,4, belonging to the ST-41/ST-44 complex, lineage III. Most B:P1.7-2,4 meningococci express type 4 PorB (87.0%), although case isolates with
porB
other than type 4 have been identified throughout the duration of the epidemic. To assess the genetic relatedness of case isolates with an alternative
porB
gene, multilocus restriction typing validated against multilocus sequence typing was used. This determined that B:P1.7-2,4 meningococci with a
porB
gene that was other than type 4 had the same clonal origin. It was concluded that strains with alternative
porB
genes had diverged from the original type 4
porB
. Variation in
porB
was also shown to be associated with the uptake of DNA encoding one or two of the PorB variable regions leading to mosaic
porB
. Point mutation rather than horizontal transfer and recombination was implicated as the mechanism of sequence variation in some strains. This work will serve as a reference point to determine if the administration of a strain-specific vaccine increases the level of
porB
divergence and variation already observed in New Zealand case isolates. It also complements the study undertaken of PorA stability which showed that variation in P1.7-2,4 PorA was almost exclusively due to deletions in the P1.4 epitope of the epidemic strain.
Molecular Analysis of Microbial Diversity in Advanced Caries
Authors: Chhour Kim-Ly , Nadkarni Mangala A. , Byun Roy , Martin F. Elizabeth , Jacques Nicholas A. , Hunter Neil 
Published: February 2005

ABSTRACT

Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of
Prevotella
spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included
Selenomonas
spp.,
Dialister
spp.,
Fusobacterium nucleatum
,
Eubacterium
spp., members of the
Lachnospiraceae
family,
Olsenella
spp.,
Bifidobacterium
spp.,
Propionibacterium
sp., and
Pseudoramibacter alactolyticus
. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.
Long-Term Molecular Analysis of Tuberculosis Strains in Alabama, a State Characterized by a Largely Indigenous, Low-Risk Population
Authors: Kempf Mirjam-Colette , Dunlap Nancy E. , Lok Kerry H. , Benjamin William H. , Keenan Nancy B. , Kimerling Michael E. 
Published: February 2005

ABSTRACT

With a tuberculosis case detection rate of 5.9 per 100,000 population in 2001, Alabama ranked twelfth highest in the United States. However, cases among foreign-born and human immunodeficiency virus-infected individuals remain low in Alabama. To understand the endemic statewide disease pattern, tuberculosis strains were studied for clustering in a long-term population-based study from January 1994 to May 2000. IS6
110
restriction fragment length polymorphism analysis was performed for 1,834 strains. Spoligotyping was used as a secondary typing method for the 37% of isolates displaying a restriction fragment length polymorphism pattern with <6 IS
6110
copies. A total of 721 (41%) patients provided isolates that composed 114 clusters, each containing isolates from 2 to 136 patients, suggesting that recent transmission accounted for 35% of tuberculosis cases. Demographic, behavioral, and clinical characteristics of patients with clustered versus nonclustered isolates stratified by low-copy-number strains (<6 IS
6110
copies) versus high-copy-number strains (≥6 IS
6110
copies) were evaluated. Younger age, black race, a history of alcohol abuse, and homelessness were predictors of clustering of low-copy-number, strains and younger age, urban residency, alcohol abuse, homelessness, noninjection drug use, and a history of incarceration and/or cavitary disease were predictors of clustering of high-copy-number strains. By identifying local characteristics of tuberculosis clustering through molecular fingerprinting, control programs can distribute their limited resources to impact the transmission of tuberculosis in high-risk populations and evaluate strain distribution across geographical areas.
Novel Replicon-Based Reporter Gene Assay for Detection of Rubella Virus in Clinical Specimens
Authors: Tzeng Wen-Pin , Zhou Yumei , Icenogle Joseph , Frey Teryl K. 
Published: February 2005

ABSTRACT
Proof of concept for a novel diagnostic assay for rubella virus (RUB) based on RUB replicons expressing reporter genes was demonstrated. RUB replicons have the structural protein coding region replaced with a reporter gene such as green fluorescent protein or chloramphenicol acetyltransferase. Previously, it was shown that a replicon construct with a specific in-frame deletion in the nonstructural protein coding region (NotI, approximately nucleotides 1500 to 2100 of the genome) failed to replicate and express the reporter gene unless rescued by a coinfecting wild-type helper RUB (W.-P. Tzeng et al., Virology 289:63-73, 2001). In the present study, it was found that rescue of reporter gene expression by NotI replicons occurred when coinfection was done with clinical specimens containing RUB, indicating that this system could be the basis for a diagnostic assay. The assay was sensitive, using laboratory RUB strains and as low a dose as one plaque-forming unit. The assay was specific in that it was positive for RUB strains of both genotypes and was negative for a panel of human viruses. It was also possible to genetically sequence the RUB present in positive clinical specimens detected in the assay for genotypic strain determination.
Endocarditis Due to a New Rod-Shaped
Neisseria
sp
Authors: Michaux-Charachon Sylvie , Lavigne Jean-Philippe , Le Flèche Anne , Bouziges Nicole , Sotto Albert , Grimont Patrick A. D. 
Published: February 2005

ABSTRACT

We report the first case of pacemaker endocarditis due to a new rod-shaped
Neisseria
sp. isolated from blood culture. On the basis of
rrs
sequencing, the isolate was found to be most closely related to an uncultured organism from human subgingival plaque and was identified as
Neisseria
sp. group AK105. A cure was achieved after a combination of surgical and antibiotic treatment. Oral flora-induced pacemaker endocarditis is a rare condition that reinforces the need for good oral hygiene as an important preventive measure.
Reliability of the E-Test Method for Detection of Colistin Resistance in Clinical Isolates of
Acinetobacter baumannii
Authors: Arroyo L. A. , García-Curiel A. , Pachón-Ibañez M. E. , Llanos A. C. , Ruiz M. , Pachón J. , Aznar J. 
Published: February 2005

ABSTRACT

We compared the E-test to the broth microdilution method for testing the susceptibility of 115 clinical isolates of
Acinetobacter baumannii
to colistin. Twenty-two (19.1%) strains were resistant to colistin and 93 (80.8%) strains were susceptible according to the reference broth microdilution method. A categorical agreement of 98.2% was found, with only two (1.7%) very major errors. Agreement within 1 twofold dilution between the E-test and the broth microdilution was 16.5%. Complete agreement was found for the strains for which MICs fell within the range of 0.25 to 1 μg of colistin/ml. However, there was poor concordance, particularly in extreme dilutions with higher MICs by the E-test method.
Detection of
Aspergillus fumigatus
and a Mutation That Confers Reduced Susceptibility to Itraconazole and Posaconazole by Real-Time PCR and Pyrosequencing
Authors: Trama Jason P. , Mordechai Eli , Adelson Martin E. 
Published: February 2005

ABSTRACT

A real-time PCR and pyrosequencing method was developed to detect
Aspergillus fumigatus
in whole blood by amplifying the
cyp51A
gene and sequencing the codon for glycine 54. Mutations in this codon can result in amino acid substitutions that confer reduced susceptibility to itraconazole and posaconazole.
Evaluation of Amplified Fragment Length Polymorphism for Differentiation of Avian Mycoplasma Species
Authors: Hong Yang , García Maricarmen , Levisohn Sharon , Lysnyansky Inna , Leiting Victoria , Savelkoul P. H. M. , Kleven S. H. 
Published: February 2005

ABSTRACT
Amplified fragment length polymorphism (AFLP) was used for typing avian mycoplasma species. Forty-four avian mycoplasma strains were successfully typed into eight distinct groups, with each representing a different species. Homology of AFLP patterns of 35% or less was used as a cutoff value to differentiate avian mycoplasma strains into different species.