bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonbioluminescent Strains ofPhotobacterium phosphoreumProduce the Cell-to-Cell Communication SignalN-(3-Hydroxyoctanoyl)homoserine Lactone
Authors: Flodgaard L. R. , Dalgaard P. , Andersen J. B. , Nielsen K. F. , Givskov M. , Gram L. 
Published: April 2005

ABSTRACTBioluminescence is a common phenotype in marine bacteria, such asVibrioandPhotobacteriumspecies, and can be quorum regulated byN-acylated homoserine lactones (AHLs). We extracted a molecule that induced a bacterial AHL monitor (Agrobacterium tumefaciensNT1 [pZLR4]) from packed cod fillets, which spoil due to growth ofPhotobacterium phosphoreum. Interestingly, AHLs were produced by 13 nonbioluminescent strains ofP. phosphoreumisolated from the product. Of 177 strains ofP. phosphoreum(including 18 isolates from this study), none of 74 bioluminescent strains elicited a reaction in the AHL monitor, whereas 48 of 103 nonbioluminescent strains did produce AHLs. AHLs were also detected inAeromonasspp., but not inShewanellastrains. Thin-layer chromatographic profiles of cod extracts andP. phosphoreumculture supernatants identified a molecule similar in relative mobility (Rfvalue) and shape toN-(3-hydroxyoctanoyl)homoserine lactone, and the presence of this molecule in culture supernatants from a nonbioluminescent strain ofP. phosphoreumwas confirmed by high-performance liquid chromatography-positive electrospray high-resolution mass spectrometry. Bioluminescence (in a non-AHL-producing strain ofP. phosphoreum) was strongly up-regulated during growth, whereas AHL production in a nonbioluminescent strain ofP. phosphoreumappeared constitutive. AHLs apparently did not influence bioluminescence, as the addition of neither synthetic AHLs nor supernatants delayed or reduced this phenotype in luminescent strains ofP. phosphoreum. The phenotypes of nonbioluminescentP. phosphoreumstrains regulated by AHLs remains to be elucidated.
Opposite Enantioselectivities of Two Phenotypically and Genotypically Similar Strains of
Pseudomonas frederiksbergensis
in Bacterial Whole-Cell Sulfoxidation
Authors: Adam Waldemar , Heckel Frank , Saha-Möller Chantu R. , Taupp Marcus , Meyer Jean-Marie , Schreier Peter 
Published: April 2005

ABSTRACT

Soil samples were screened to select microorganisms with the capability to oxidize organic sulfides into the corresponding sulfoxides with differential enantioselectivities. Several bacterial strains that preferentially produced the
S-
configured sulfoxide enantiomer were isolated. Surprisingly, one bacterial strain, genotypically and phenotypically characterized as
Pseudomonas frederiksbergensis
, selectively gave the
R
enantiomer. The finding that two apparently identical organisms displayed opposite enantioselectivities is novel for non-genetically modified organisms.
Use of Specific rRNA Oligonucleotide Probes for Microscopic Detection of
Mycobacterium avium
Complex Organisms in Tissue
Authors: St. Amand Allison L. , Frank Daniel N. , De Groote Mary Ann , Pace Norman R. 
Published: April 2005

ABSTRACT

Members of the
Mycobacterium avium
complex (MAC) are important environmental pathogens that are implicated in several chronic, idiopathic diseases. Diagnosis of MAC-based diseases is compromised by the need to cultivate these fastidious and slowly growing organisms in order to identify which mycobacterial species are present. Detection is particularly difficult when MAC is intracellular or embedded within mammalian tissues. We report on the development of culture-independent, in situ hybridization (ISH) assays for the detection of MAC in culture, sputum, and tissue. This assay includes a highly reliable technique for the permeabilization of mycobacterial cells within culture and tissues. We describe a set of rRNA-based oligonucleotide probes that specifically detect either
M. intracellulare
, the two
M. avium
subspecies associated with human disease, or all members of MAC. The results call into question the validity of ISH results derived by the use of other gene loci, such as IS
900
.
Identification of Clinically Relevant Viridans Streptococci by an Oligonucleotide Array
Authors: Chen Chao Chien , Teng Lee Jene , Kaiung Seng , Chang Tsung Chain 
Published: April 2005

ABSTRACT

Viridans streptococci (VS) are common etiologic agents of subacute infective endocarditis and are capable of causing a variety of pyogenic infections. Many species of VS are difficult to differentiate by phenotypic traits. An oligonucleotide array based on 16S-23S rRNA gene intergenic spacer (ITS) sequences was developed to identify 11 clinically relevant VS. These 11 species were
Streptococcus anginosus
,
S. constellatus
,
S. gordonii
,
S. intermedius
,
S. mitis
,
S. mutans
,
S. oralis
,
S. parasanguinis
,
S. salivarius
,
S. sanguinis
, and
S. uberis
. The method consisted of PCR amplification of the ITS regions by using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species-specific oligonucleotides immobilized on a nylon membrane. After 120 strains of the 11 species of VG and 91 strains of other bacteria were tested, the sensitivity and specificity of the oligonucleotide array were found to be 100% (120 of 120 strains) and 95.6% (87 of 91 strains), respectively.
S. pneumoniae
cross-hybridized to the probes used for the identification of
S. mitis
, and simple biochemical tests such as optochin susceptibility or bile solubility should be used to differentiate
S. pneumoniae
from
S. mitis
. In conclusion, identification of species of VS by use of the present oligonucleotide array is accurate and could be used as an alternative reliable method for species identification of strains of VS.
European Multicenter Study of the LIAISON Automated Diagnostic System for Determination of
Toxoplasma gondii
-Specific Immunoglobulin G (IgG) and IgM and the IgG Avidity Index
Authors: Petersen Eskild , Borobio Maria Victoria , Guy Edward , Liesenfeld Oliver , Meroni Valeria , Naessens Anne , Spranzi Emma , Thulliez Philippe 
Published: April 2005

ABSTRACT

The LIAISON system is a fully automated system based on chemiluminescence and antigen bound to magnetic microparticles. The system allows fast and precise measurement of
Toxoplasma
-specific immunoglobulin G (IgG) and IgM antibody levels and measurement of the IgG avidity index even at low levels of
Toxoplasma
-specific IgG antibodies in a single step without manual interference. Seven European centers participated in a multicenter evaluation of the LIAISON system. The sensitivity and specificity of the LIAISON system compared to the Sabin-Feldman dye test were 99.3 and 96.8%, respectively. In a comparison of the LIAISON
Toxoplasma
-specific IgM assay with an immunosorbent agglutination assay, the LIAISON assay had a sensitivity of 96.7% and a specificity of 95.4%. The LIAISON IgG assay showed agreements of 91, 100, and 100% with the AXSYM IgG (Abbott), VIDAS IgG (bioMérieux), and Platelia IgG (Bio-Rad) assays, respectively. The LIAISON IgM assay showed agreements of 95% with the AXSYM IgM and Platelia IgM assays, 96% with the ISAGA IgM assay (bioMérieux), and 97% with the VIDAS IgM assay. The coefficient of correlation between the LIAISON system and the VIDAS
Toxoplasma
-specific IgG avidity index was 0.81. By use of the
Toxoplasma
-specific IgG avidity index assay with specific IgM-positive samples, the diagnosis of infection with
Toxoplasma gondii
in early pregnancy has been improved significantly. The LIAISON avidity assay is a valuable assay for the exclusion of recently acquired infection with
T. gondii
(less than 4 months) in pregnant women, and it decreases significantly the necessity for follow-up testing.
Rapid Detection of Ofloxacin Resistance in
Mycobacterium tuberculosis
by Two Low-Cost Colorimetric Methods: Resazurin and Nitrate Reductase Assays
Authors: Martin Anandi , Palomino Juan Carlos , Portaels Françoise 
Published: April 2005

ABSTRACT

We have evaluated the performance of two rapid, low-cost methods for the detection of ofloxacin (OFX) resistance with 95
Mycobacterium tuberculosis
isolates from countries with high multidrug-resistant tuberculosis endemicity. Results obtained by nitrate reductase and resazurin assays showed 100% agreement with those of the proportion method on 7H11 agar using 2 μg of OFX/ml. We confirmed the resistance of all isolates found to be resistant to OFX by the Mycobacterium Growth Indicator Tube system, and complete agreement among all methods was observed. Nitrate reductase and resazurin assays are rapid, simple, low-cost methods and might become inexpensive alternative procedures for rapid detection of OFX resistance in low-resource countries.
Identification and Distribution of
Acanthamoeba
Species Genotypes Associated with Nonkeratitis Infections
Authors: Booton Gregory C. , Visvesvara Govinda S. , Byers Thomas J. , Kelly Daryl J. , Fuerst Paul A. 
Published: April 2005

ABSTRACT

Acanthamoeba
is a free-living protozoan genus found in a wide variety of natural habitats, including water, soil, and air. Pathogenic isolates of
Acanthamoeba
are medically relevant as the causative agent of sight- threatening
Acanthamoeba
keratitis (AK), serious infections of other organs, and fatal granulomatous amebic encephalitis. Previous work employing DNA sequences of nuclear and mitochondrial small-subunit rRNA genes (SSU rRNA genes) determined the genotypic diversity of
Acanthamoeba
and found that many named species of
Acanthamoeba
are associated with particular genotypes. These studies also concluded that nearly all AK infections result from a single molecular genotype: T4. Here, we asked whether
Acanthamoeba
clinical isolates from non-AK infections are also associated with particular genotypes. DNA sequence determination of nuclear SSU rRNA genes was employed for genotypic identification of 29 isolates of
Acanthamoeba
from non-AK infections. Sequence analysis demonstrates that T4 is the predominant genotype in non-AK infections, including those in brain, cerebrospinal fluid, nasal passages, skin, and lung. Rare genotypes (T1, T10, and T12) have been isolated from brain infections. We conclude that genotype T4 is the primary genotype in non-AK
Acanthamoeba
infections, as was the case in AK infections. However, the genotypes that were isolated from brains have not been observed in environmental isolates of
Acanthamoeba
, and their natural ecological niche is unknown.
Evaluation of PCR Testing of Ethanol-Fixed Nasal Swab Specimens as an Augmented Surveillance Strategy for Influenza Virus and Adenovirus Identification
Authors: Krafft A. E. , Russell K. L. , Hawksworth A. W. , McCall S. , Irvine M. , Daum L. T. , Connoly J. L. , Reid A. H. , Gaydos J. C. , Taubenberger J. K. 
Published: April 2005

ABSTRACT
Viral culture isolation has been widely accepted as the “gold standard” for laboratory confirmation of viral infection; however, it requires ultralow temperature specimen storage. Storage of specimens in ethanol at room temperature could expand our ability to conduct active surveillance and retrospective screenings of viruses with rapid and inexpensive real-time PCR tests, including isolates from remote regions where freezing specimens for culture is not feasible. Molecular methods allow for rapid identification of viral pathogens without the need to maintain viability. We hypothesized that ethanol, while inactivating viruses, can preserve DNA and RNA for PCR-based methods. To evaluate the use of ethanol-stored specimens for augmenting surveillance for detection of influenza viruses A and B and adenoviruses (AdV), paired nasal swab specimens were collected from 384 recruits with febrile respiratory illness at Fort Jackson, S.C., in a 2-year study. One swab was stored at ambient temperature in 100% ethanol for up to 6 months, and the other swab was stored at −70°C in viral medium. For viral detection, frozen specimens were cultured for a variety of respiratory viruses, and ethanol-fixed specimens were tested with TaqMan (TM) probe and LightCycler SYBR green (SG) melting curve assays with at least two different PCR targets for each virus. The sensitivities of the TM and SG assays on specimens stored in ethanol for 1 month were 75% and 58% for influenza A, 89% and 67% for influenza B, and 93 to 98% and 57% for AdV, respectively. Lower specificities of the real-time assays corresponded to the increased detection of PCR-positive but culture-negative specimens. Influenza virus RNA was detected as well or better after 6 months of storage in ethanol.
Detection and Genotyping of
Mycobacterium
Species from Clinical Isolates and Specimens by Oligonucleotide Array
Authors: Park Heekyung , Jang Hyunjung , Song Eunsil , Chang Chulhun L. , Lee Minki , Jeong Seokhoon , Park Junhyung , Kang Byeongchul , Kim Cheolmin 
Published: April 2005

ABSTRACT

Identification of pathogenic
Mycobacterium
species is important for a successful diagnosis of mycobacteriosis. The purpose of this study was to develop an oligonucleotide array which could detect and differentiate mycobacteria to the species level by using the internal transcribed spacer (ITS) sequence. Using a genus-specific probe and 20 species-specific probes including two
M. avium-intracellulare
complex (MAC)-specific probes, we have developed an ITS-based oligonucleotide array for the rapid and reliable detection and discrimination of
M. tuberculosis
, MAC,
M. fortuitum
,
M. chelonae
,
M. abscessus
,
M. kansasii
,
M. gordonae
,
M. scrofulaceum
,
M. szulgai
,
M. vaccae
,
M. xenopi
,
M. terrae
,
M. flavescens
,
M. smegmatis
,
M. malmoense
,
M. simiae
,
M. marinum
,
M. ulcerans
,
M. gastri
, and
M. leprae
. All mycobacteria were hybridized with a genus-specific probe (PAN-03) for detection of the genus
Mycobacterium
. Mycobacterial species were expected to show a unique hybridization pattern with species-specific probes, except for
M. marinum
and
M. ulcerans
, which were not differentiated by ITS-based probe. Among the species-specific probes, two kinds of species-specific probes were designed for MAC in which there were many subspecies. The performance of the oligonucleotide array assay was demonstrated by using 46 reference strains, 149 clinical isolates, and 155 clinical specimens. The complete procedure (DNA extraction, PCR, DNA hybridization, and scanning) was carried out in 4.5 h. Our results indicated that the oligonucleotide array is useful for the identification and discrimination of mycobacteria from clinical isolates and specimens in an ordinary clinical laboratory.
Evaluation and Updating of the Osiris Expert System for Identification of
Escherichia coli
β-Lactam Resistance Phenotypes
Authors: Bert Frédéric , Juvin Manette , Ould-Hocine Zahia , Clarebout Gervais , Keller Emmanuelle , Lambert Nicole , Arlet Guillaume 
Published: April 2005

ABSTRACT

Osiris is a video zone size reader for disk diffusion tests that includes a built-in extended expert system (EES). We evaluated the efficacy of the Osiris EES for the identification of β-lactam susceptibility phenotypes of
Escherichia coli
isolates. Fifteen β-lactam agents and three β-lactam-β-lactamase inhibitor combinations were tested by the disk diffusion method against 50
E. coli
strains with well-characterized resistance mechanisms. The strains were screened for the production of extended-spectrum β-lactamase (ESBL) by the double-disk synergy test using a disk of amoxicillin-clavulanic acid with disks of the extended-spectrum cephalosporins and aztreonam. Overall, the EES accurately identified the phenotype for 78% of the strains, indicated an inexact phenotype for 17% of the strains, and could not find a matching phenotype for the remaining 5% of the strains. The percentage of correct identification for each resistance mechanism was 100% for inhibitor-resistant TEM and for TEM plus cephalosporinase, 88.9% for TEM and for ESBL, 70.8% for cephalosporinase overproduction, and 25% for oxacillinase. The main cause of discrepancy was the misidentification of oxacillinase as inhibitor-resistant TEM. The conventional double-disk synergy test failed to detect ESBL production in two strains (one producing VEB-1 and one producing CTX-M-14), but synergy between cefepime and amoxicillin-clavulanic acid was visible after the distance between the disks was reduced to 20 mm. After the interpretative guidelines of the EES were updated according to our results, the percentage of correct phenotype identification increased from 78 to 96%.
Use of Quantitative Real-Time PCR To Monitor the Response of
Chlamydophila felis
Infection to Doxycycline Treatment
Authors: Dean Rachel , Harley Ross , Helps Chris , Caney Sarah , Gruffydd-Jones Tim 
Published: April 2005

ABSTRACT

Fifteen cats infected with
Chlamydophila felis
were monitored for the presence of
C. felis
DNA on ocular swabs by using real-time PCR and for clinical signs of disease. The cats were assigned to three groups: oral doxycycline at 10 mg/kg of body weight/day for 7 days (six cats), oral doxycycline at 10 mg/kg/day for 14 days (five cats), and an untreated control group (four cats). The untreated cats remained positive for
C. felis
throughout the trial; clinical signs were most severe on days 14 to 21 postinfection, and then they declined. Treatment with 7 and 14 days of doxycycline decreased
C. felis
relative copy numbers and clinical signs rapidly.
C. felis
became undetectable in some of the cats during or after treatment. However, after the cessation of treatment, a recurrence of high relative copy numbers of
C. felis
and severe clinical signs in all cats was seen. Rescue treatment with 21 days of doxycycline was successful at eliminating infection in eight of the cats; a further 28 days of doxycycline was required to eliminate infection in the remaining three cats. It was concluded that 7, 14, and, in some cases, 21 days of treatment with oral doxycycline will not eliminate
C. felis
infection. At least 28 days of treatment with doxycycline is required to ensure elimination of the organism. Real-time PCR is a sensitive technique for monitoring
C. felis
infection and the response to antibiotic treatment.
Molecular Identification of
Capnocytophaga
spp. via 16S rRNA PCR-Restriction Fragment Length Polymorphism Analysis
Authors: Ciantar Marilou , Newman Hubert N. , Wilson Michael , Spratt David A. 
Published: April 2005

ABSTRACT

Capnocytophaga
spp. have been implicated as putative periodontal pathogens associated with various periodontal diseases. Although the genus is known to contain five human oral isolates, accurate identification to species level of these organisms recovered from subgingival plaque has been hampered by the lack of a reliable method. Hence, most studies to date have reported these isolates as
Capnocytophaga
spp. Previous attempts at identification were based on biochemical tests; however, the results were inconclusive. Considering the differing virulence features of the respective isolates, it is crucial to identify these isolates to species level. The universal and conservative nature of the 16S rRNA gene has provided an accurate method for bacterial identification. The aim of this study was to identify
Capnocytophaga
spp. via restriction enzyme analysis of this gene (16S rRNA PCR-restriction fragment length polymorphism). The results (backed up by 16S rRNA gene sequencing) showed that this method reliably identifies all named
Capnocytophaga
spp. to species level.
Direct Detection of
Nocardia
spp. in Clinical Samples by a Rapid Molecular Method
Authors: Couble Andrée , Rodríguez-Nava Verónica , de Montclos Michèle Pérouse , Boiron Patrick , Laurent Frédéric 
Published: April 2005

ABSTRACT

We developed a 16S PCR-based assay for the rapid detection of
Nocardia
spp. directly from human clinical samples. The applicability of the assay was confirmed by using 18 samples from patients with nocardiosis as diagnosed by conventional cultures and 20 clinical samples from patients with confirmed tuberculosis used as negative controls.
Latex Agglutination Test for Monitoring Antibodies to Avian Influenza Virus Subtype H5N1
Authors: Xu Xiaojuan , Jin Meilin , Yu Zhengjun , Li Hongchao , Qiu Dexin , Tan Yadi , Chen Huanchun 
Published: April 2005

ABSTRACT
A latex agglutination test (LAT) based on polystyrene beads sensitized with inactivated avian influenza virus H5N1 particles was developed. Compared with the hemagglutination inhibition test, the sensitivity and specificity of the LAT were 88.8 and 97.6%, respectively, in detecting 830 serum samples from vaccinated chickens. The test has application potential in field practice.
Heterogeneity among Strains of Diffusely Adherent
Escherichia coli
Isolated in Brazil
Authors: Lopes Lucia M. , Fabbricotti Sandra H. , Ferreira Antonio J. P. , Kato Maria A. M. F. , Michalski Jane , Scaletsky Isabel C. A. 
Published: April 2005

ABSTRACT

One hundred twelve diffusely adherent
Escherichia coli
strains isolated from children in a case control study were evaluated for virulence-associated characteristics, serotyping, antibiotic resistance, and plasmid profiles. Half of the strains hybridized with the probes for
icuA
(aerobactin) and
fimH
(type 1 pili);
daaE
(F1845 fimbriae),
afa
(afimbrial Dr adhesin),
agg-3A
(aggregative adhesion fimbria type III fimbriae),
pap
(P fimbriae),
astA
(EAST1 toxin), and
shET1
(
Shigella
enterotoxin 1) sequences were present in <20% of the strains. The
shET1
gene was noted most frequently in strains isolated from patients. A minority (7%) of the strains produced hemolysin or colicin or showed cytotoxic effects on Vero cells. Forty-five different serotypes were found. The majority (70%) of the strains presented multiple antibiotic resistance. Antibiotic resistance and diffuse adherence were located on the same conjugative plasmids. These results suggest that the transfer of these potential virulence markers could be important in the epidemiology of diffusely adherent
E. coli
.
Middle Eastern Migrants in the Philippines: Entrepreneurs and Cultural Brokers
Authors: Gervase Clarence-Smith William 
Published: April 2005

AbstractThe Philippines deviated from the usual Southeast Asian pattern of Hadhrami Arab dominance among Middle Easterners. Despite the influence of Muslim Arabs in the Islamic southwest, the predominant community initially consisted of Armenians, and then of immigrants from Ottoman Syria from the 1880s. Coming via Latin America, the United States, or Asian entrepôts, most of these "Syrians" were Christians from modern Lebanon. They, however, included substantial Muslim Druze and Oriental Jewish minorities, and some came from Syria proper, Palestine, and even further a field. They formed the largest twentieth-century Syro-Lebanese community in Monsoon Asia. Some Middle Easterners became Filipino citizens, speaking either Spanish or English, others emigrated to the USA or Australia, and yet others went home. Their main contribution to the Philippines was economic. Initially peddlers and small shopkeepers, they moved into real estate, agriculture, mining, the leisure industry, the professions, the import-export trade, embroidery for export to the USA and, after independence, manufacturing for the local market.
Hybridity and the "Hadhrami Diaspora" in the Indian Ocean Muslim Networks
Authors: Feener R. Michael 
Published: April 2005

AbstractThis paper addresses issues relating to the adaptation of notions of hybridity from contemporary Diaspora Studies to the study of Hadhrami migration to Southeast Asia. It also presents a series of short biographies of prominent figures in the networks of Muslim scholarship that spanned the Indian Ocean from the sixteenth through nineteenth centuries from perspectives that highlight intersections of religion, language, and ethnicity during that time. Integrating this historical data into the inter-disciplinary theoretical frameworks of contemporary Diaspora Studies approaches provides an opportunity for reflecting on changing conceptions of identity under processes of modernization.