bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endemic, Epidemic Clone of
Salmonella enterica
Serovar Typhi Harboring a Single Multidrug-Resistant Plasmid in Vietnam between 1995 and 2002
Authors: Le Thi Anh Hong , Lejay-Collin Monique , Grimont Patrick A. D. , Hoang Thuy Long , Nguyen Thi Vinh , Grimont Francine , Scavizzi Maurice R. 
Published: July 2004

ABSTRACT

Salmonella enterica
serovar Typhi strains resistant to ampicillin, chloramphenicol, tetracyclines, streptomycin, and cotrimoxazole, isolated from sporadic cases and minor outbreaks in Vietnam between 1995 and 2002, were typed and compared. Plasmid fingerprinting, Vi bacteriophage typing, XbaI pulsed-field gel electrophoresis, and PstI ribotyping showed that endemic, epidemic multidrug-resistant typhoid fever was due, for at least 74.1% of the isolates, to one or two clones of serovar Typhi harboring a single resistance plasmid. PstI ribotyping was used as a basic technique to ensure that a serovar Typhi expansion was clonal.
Quantitative Analysis of Diverse
Lactobacillus
Species Present in Advanced Dental Caries
Authors: Byun Roy , Nadkarni Mangala A. , Chhour Kim-Ly , Martin F. Elizabeth , Jacques Nicholas A. , Hunter Neil 
Published: July 2004

ABSTRACT

Our previous analysis of 65 advanced dental caries lesions by traditional culture techniques indicated that lactobacilli were numerous in the advancing front of the progressive lesion. Production of organic acids by lactobacilli is considered to be important in causing decalcification of the dentinal matrix. The present study was undertaken to define more precisely the diversity of lactobacilli found in this environment and to quantify the major species and phylotypes relative to total load of lactobacilli by real-time PCR. Pooled DNA was amplified by PCR with
Lactobacillus
genus-specific primers for subsequent cloning, sequencing, and phylogenetic analysis. Based on 16S ribosomal DNA sequence comparisons, 18 different phylotypes of lactobacilli were detected, including strong representation of both novel and gastrointestinal phylotypes. Specific PCR primers were designed for nine prominent species, including
Lactobacillus gasseri
,
L. ultunensis
,
L. salivarius
,
L. rhamnosus
,
L. casei
,
L. crispatus
,
L. delbrueckii
,
L. fermentum
, and
L. gallinarum
. More than three different species were identified as being present in most of the dentine samples, confirming the widespread distribution and numerical importance of various
Lactobacillus
spp. in carious dentine. Quantification by real-time PCR revealed various proportions of the nine species colonizing carious dentine, with higher mean loads of
L. gasseri
and
L. ultunensis
than of the other prevalent species. The findings provide a basis for further characterization of the pathogenicity of
Lactobacillus
spp. in the context of extension of the carious lesion.
Molecular and Ultrastructural Characterization of Porcine Hippurate-Negative
Brachyspira pilosicoli
Authors: Fossi Marja , Pohjanvirta Tarja , Sukura Antti , Heinikainen Sirpa , Lindecrona Rikke , Pelkonen Sinikka 
Published: July 2004

ABSTRACT

Brachyspira pilosicoli
, the causative agent of porcine intestinal spirochetosis, usually has hippurate-cleaving capacity. We have regularly isolated hippurate-negative
B. pilosicoli
from cases of porcine diarrhea. In this study, we show that these biochemically atypical
B. pilosicoli
isolates can be classified as
B. pilosicoli
. 16S ribosomal DNA was partially sequenced from eight hippurate-negative and two hippurate-positive
B. pilosicoli-
like isolates from seven herds. The differences in nucleotide sequence with
B. pilosicoli
P43/6/78 type strain were not associated with hippurate cleavage. In 877 bp, the hippurate-negative isolates had a similarity of 98.63 to 100% to the type strain, with the corresponding figures for the two hippurate-positive isolates being 98.86 and 100%. The nucleotide sequences of hippurate-positive isolates were identical to the respective sequences of hippurate-negative isolates from one herd. The DNA macrorestriction patterns of a total of 20 hippurate-negative and -positive
B. pilosicoli
isolates were diverse, and no clustering in conjunction with the hippurate reaction was found. In two herds, hippurate-positive and -negative
B. pilosicoli
isolates had a common macrorestriction pattern. The ultrastructure of hippurate-negative isolates was similar to the type strain. In conclusion,
B. pilosicoli
can be either hippurate positive or negative and, thus, the scheme for biochemical differentiation of porcine
Brachyspira
should be revised to include identification of hippurate-negative
B. pilosicoli
.
Use of Swabs without Transport Media for the Gen-Probe Group A Strep Direct Test
Authors: Bourbeau Paul P. , Heiter Barbara J. 
Published: July 2004

ABSTRACT
For several years we used rayon or Dacron swabs with liquid transport media for collection and transport of throat swab specimens for testing with the Gen-Probe Group A Strep Direct Test (GASDT). A report of favorable results with a Dacron swab without any transport media for GASDT by another laboratory prompted us to compare detection of group A streptococci (GAS) with and without transport media (referred to as “wet” and “dry” swabs, respectively). Phase one of this study used swabs seeded with GAS. Initially, six recent clinical isolates of GAS were inoculated onto wet and dry swabs and stored at room temperature (RT). After 1, 2, and 3 days of storage, colony counting and GASDT were performed with the swabs. The results, expressed as the mean percentage of the results at zero time, were as follows: for GASDT with wet swabs at 1, 2, and 3 days, 62, 51, and 56%, respectively; for GASDT with dry swabs at 1, 2, and 3 days, 105, 80, and 85%, respectively; for colony counts with wet swabs at 1, 2, and 3 days, 52, 26, and 13%, respectively; for colony counts with dry swabs at 1, 2, and 3 days, 10, 0, and 0%, respectively. An additional six strains of GAS were tested in a similar manner, except that extracts of pharyngeal flora (PF) were added to the inocula. The results obtained with extracts of PF were comparable to those obtained with GAS alone. We also compared the performance of GASDT with wet and dry swabs stored at RT and 4°C. Ten strains of GAS were inoculated onto wet and dry swabs, and GASDT was performed each day for 9 days. The GASDT results for swabs on day 9, expressed as the mean percentage of the results obtained at zero time, were as follows: dry swab and 4°C, 59%; wet swab and 4°C, 31%; dry swab and RT, 33%; and wet swab and RT, 19%. In phase two of this study we conducted a clinical evaluation to determine whether the differences observed with seeded specimens would also be evident with patient specimens. We used a single dry Dacron swab paired with a single rayon Bacti-Swab with liquid Stuart transport medium for the clinical evaluation. Specimens were collected from 1,005 outpatients, plated onto a Strep Selective Agar plate, and then tested within 30 min by GASDT. If culture of GAS from the same swab is used to define a true-positive test result, the sensitivities and specificities were as follows: GASDT with wet swabs, 86.2 and 98.5%, respectively; GASDT with dry swabs, 90.7 and 98.1%, respectively. However, the use of culture as the “gold standard” may understate the actual performance characteristics of GASDT, particularly for the dry swabs. In conclusion, for GASDT the use of swabs without transport media may be preferable to the use of swabs with transport media.
Amplicon Sequencing and Improved Detection of Human Rhinovirus in Respiratory Samples
Authors: Deffernez Christelle , Wunderli Werner , Thomas Yves , Yerly Sabine , Perrin Luc , Kaiser Laurent 
Published: July 2004

ABSTRACT

Improved knowledge of the genotypic characteristics of human rhinovirus (HRV) is required, as are nucleic detection assays with the capacity to overcome both the similarities between members of the family
Picornaviridae
and the wide diversity of different HRV serotypes. The goal of the present study was to investigate the variability and the genotypic diversity of clinical strains circulating in the community. Since most reverse transcription (RT)-PCR assays available cannot differentiate HRV from other members of the family
Picornaviridae
, we also validated an assay specific for HRV detection. The 5′ noncoding regions of 87 different HRV serotypes and clinical isolates were sequenced. On the basis of sequence analysis and phylogenetic determination, we first confirmed that all clinical isolates were HRV. We then validated a real-time RT-PCR assay that was able not only to detect all HRV serotypes and all clinical isolates tested but also to accurately discriminate between rhinovirus and other viruses from the family
Picornaviridae
. This assay was negative with isolates of coxsackievirus (types A and B), echovirus, enterovirus, parechovirus, and poliovirus, as well as nonpicornaviruses. Among a series of bronchoalveolar lavage specimens, 4% (7 of 161) were positive by culture, whereas 13% (21 of 161) were positive by RT-PCR. In the present study we showed that to specifically identify HRV in clinical specimens, diagnostic assays need to overcome both the diversities and the similarities of picornaviruses. By sequencing the 5′ noncoding regions of rhinoviruses recovered from clinical specimens, we designed probes that could specifically detect rhinovirus.
Molecular Genotyping of a Large, Multicentric Collection of Tubercle Bacilli Indicates Geographical Partitioning of Strain Variation and Has Implications for Global Epidemiology of
Mycobacterium tuberculosis
Authors: Ahmed Niyaz , Alam Mahfooz , Rao K. Rajender , Kauser Farhana , Kumar N. Ashok , Qazi Nazia N. , Sangal Vartul , Sharma V. D. , Das Ram , Katoch V. M. , Murthy K. J. R. , Suneetha Sujai , Sharma S. K. , Sechi Leonardo A. , Gilman Robert H. , Hasnain Seyed E. 
Published: July 2004

ABSTRACT

Tuberculosis continues to be a major killer disease, despite an all-out effort launched against it in the postgenomic era. We describe here the population structure of
Mycobacterium tuberculosis
strains, as revealed by a chromosome-wide scan of fluorescent amplified fragment length polymorphisms (FAFLPs), for more than 1,100 independent isolates from 11 different countries. The bacterial strains were genotyped based on a total of 136
±
1 different FAFLP markers at the genome sequence interface, with details on IS
6110
profiles, drug resistance status, clinicopathological observations, and host status integrated into the analysis process. The strains were found to cluster with possible geographic affinities, including the parameters of host species type, IS
6110
profile, and drug susceptibility status. Of the five most commonly amplified fragment sets (or amplitypes), type A predominated in strains of mixed origin, deposited in The Netherlands; type B was exclusively observed for Indian isolates; type C was found mainly in strains from Peru and Australia; and types D and E predominated in European strains from France and Italy. The amplitypes were independent of certain large sequence polymorphisms representing two important deletions, TbD1 and Rd9. It appears that
M. tuberculosis
has a high genomic diversity with a possible geographic evolution. This may have occurred due to specific genomic deletions and synonymous substitutions selected rigorously against host defenses and environmental stresses on an evolutionary timescale. The genotypic data reported here are additionally significant for genotype-phenotype correlations and for determining whether pathogen diversity is a reflection f the host population diversity.
High Genetic Diversity Revealed by Variable-Number Tandem Repeat Genotyping and Analysis ofhsp65Gene Polymorphism in a Large Collection of “Mycobacterium canettii” Strains Indicates that theM. tuberculosisComplex Is a Recently Emerged Clone of “M. canettii”
Authors: Fabre Michel , Koeck Jean-Louis , Le Flèche Philippe , Simon Fabrice , Hervé Vincent , Vergnaud Gilles , Pourcel Christine 
Published: July 2004

ABSTRACTWe have analyzed, using complementary molecular methods, the diversity of 43 strains of “Mycobacterium canettii” originating from the Republic of Djibouti, on the Horn of Africa, from 1998 to 2003. Genotyping by multiple-locus variable-number tandem repeat analysis shows that all the strains belong to a single but very distant group when compared to strains of theMycobacterium tuberculosiscomplex (MTBC). Thirty-one strains cluster into one large group with little variability and five strains form another group, whereas the other seven are more diverged. In total, 14 genotypes are observed. The DR locus analysis reveals additional variability, some strains being devoid of a direct repeat locus and others having unique spacers. Thehsp65gene polymorphism was investigated by restriction enzyme analysis and sequencing of PCR amplicons. Four new single nucleotide polymorphisms were discovered. One strain was characterized by three nucleotide changes in 441 bp, creating new restriction enzyme polymorphisms. As no sequence variability was found forhsp65in the whole MTBC, and as a single point mutation separatesM. tuberculosisfrom the closest “M. canettii” strains, this diversity within “M. canettii” subspecies strongly suggests that it is the most probable source species of the MTBC rather than just another branch of the MTBC.
Purification of
Enterocytozoon bieneusi
Spores from Stool Specimens by Gradient and Cell Sorting Techniques
Authors: Kucerova Zuzana , Moura Hercules , Leitch Gordon J. , Sriram Rama , Bern Caryn , Kawai Vivian , Vargas Daniel , Gilman Robert H. , Ticona Eduardo , Vivar Aldo , Visvesvara Govinda S. 
Published: July 2004

ABSTRACT

A three-step method for the purification of
Enterocytozoon bieneusi
spores from stool specimens was developed. The primary process of purification of the spores from bacterial contaminants involved Percoll gradient centrifugation followed by additional separation using cesium chloride density gradient centrifugation. The cesium chloride-isolated spores were further purified using a flow cytometer with cell sorting capabilities. Sorting was performed without the use of antibodies, fluorochromes, or dyes, leaving the sorted spores in their native state, which appears to be less destructive for spores. When quantified by flow cytometry using tubes with known numbers of highly fluorescent polystyrene beads, the sorted material showed a slight decrease in light scatter characteristics compared with the slightly larger
Encephalitozoon
species spores. Although the overall recovery of the
E. bieneusi
spores was low, calcofluor and Gram chromotrope staining, indirect immunofluorescence assay, and transmission electron microscopy revealed that the sorted material was highly purified and contained large numbers of
E. bieneusi
spores and relatively few bacteria and other debris. The sorted material appeared to be sufficiently pure and could be used for in vitro culture and for the development of a variety of diagnostic reagents as well as in studying the genome of
E. bieneusi
and host-parasite interactions.
Detection and Genotyping of
Entamoeba histolytica
,
Entamoeba dispar
,
Giardia lamblia
, and
Cryptosporidium parvum
by Oligonucleotide Microarray
Authors: Wang Zheng , Vora Gary J. , Stenger David A. 
Published: July 2004

ABSTRACT

Entamoeba histolytica
,
Giardia lamblia
, and
Cryptosporidium parvum
are the most frequently identified protozoan parasites causing waterborne disease outbreaks. The morbidity and mortality associated with these intestinal parasitic infections warrant the development of rapid and accurate detection and genotyping methods to aid public health efforts aimed at preventing and controlling outbreaks. In this study, we describe the development of an oligonucleotide microarray capable of detecting and discriminating between
E. histolytica
,
Entamoeba dispar
,
G. lamblia
assemblages A and B, and
C. parvum
types 1 and 2 in a single assay. Unique hybridization patterns for each selected protozoan were generated by amplifying six to eight diagnostic sequences/organism by multiplex PCR; fluorescent labeling of the amplicons via primer extension; and subsequent hybridization to a set of genus-, species-, and subtype-specific covalently immobilized oligonucleotide probes. The profile-based specificity of this methodology not only permitted for the unequivocal identification of the six targeted species and subtypes, but also demonstrated its potential in identifying related species such as
Cryptosporidium meleagridis
and
Cryptosporidium muris
. In addition, sensitivity assays demonstrated lower detection limits of five trophozoites of
G. lamblia
. Taken together, the specificity and sensitivity of the microarray-based approach suggest that this methodology may provide a promising tool to detect and genotype protozoa from clinical and environmental samples.
Use of Applied Biosystems 7900HT Sequence Detection System and Taqman Assay for Detection of Quinolone-Resistant
Neisseria gonorrhoeae
Authors: Giles Julie , Hardick Justin , Yuenger Jeffrey , Dan Michael , Reich Karl , Zenilman Jonathan 
Published: July 2004

ABSTRACT

Mutations in quinolone resistance-determining regions (QRDRs) have been associated with quinolone-resistant
Neisseria gonorrhoeae
(QRNG). Since diagnostic nucleic acid amplification tests for gonococci are now in frequent use, molecular detection of QRNG could facilitate surveillance in the absence of culture. Here we describe a real-time molecular assay for detecting QRDR mutations in gonococci.
Identification of the Severe Acute Respiratory Syndrome Coronavirus by Simultaneous Multigene DNA Sequencing
Authors: Vinayagamoorthy T. , Mulatz Kirk , Hodkinson Roger 
Published: July 2004

ABSTRACT
The recent severe acute respiratory syndrome (SARS) outbreak resulted in calls for an accurate diagnostic test that can be used not only for routine testing but also for generating nucleotide sequences to monitor the epidemic. Although the identity of the SARS coronavirus (SARS-CoV) genome was confirmed by DNA sequencing, it is impractical to sequence the entire 29-kb SARS-CoV genome on a routine basis. Therefore, alternative assay methods such as the enzyme-linked immunosorbent assay and PCR have been pursued for routine testing, primarily to resolve probable cases. We report here a modification of standard DNA sequencing technology for accurate identification of SARS-CoV in routine testing. Instead of requiring the sequencing of the whole SARS-CoV genome, our modification enables the simultaneous sequencing of three regions of the SARS-CoV genome, the spike protein-encoding gene (35 nucleotides), gene M (43 nucleotides), and gene N (45 nucleotides), in a single electropherogram. Comparing these nucleotide sequences to DNA databank entries (National Institutes of Health) conclusively identified them as SARS-CoV sequences.
A Novel Multiplex Real-Time PCR Assay for Rapid Typing of Major Staphylococcal Cassette Chromosome
mec
Elements
Authors: Francois Patrice , Renzi Gesuele , Pittet Didier , Bento Manuela , Lew Daniel , Harbarth Stephan , Vaudaux Pierre , Schrenzel Jacques 
Published: July 2004

ABSTRACT

We describe a novel procedure for rapid typing of the staphylococcal cassette chromosome
mec
element, a molecular marker allowing discrimination between community- and hospital-acquired methicillin-resistant
Staphylococcus aureus
(MRSA) strains. Oligonucleotides targeting the recombinase genes were type specific and used to type a collection of 399 MRSA isolates recovered during patient screening at admission. This novel assay constitutes a valuable tool for evaluating the molecular epidemiology of MRSA and adjusting infection control strategies against MRSA.
Genotypic Profile of Human Herpesvirus 8 (Kaposi's Sarcoma-Associated Herpesvirus) in Urine
Authors: Beyari M. M. , Hodgson T. A. , Kondowe W. , Molyneux E. M. , Scully C. M. , Porter S. R. , Teo C. G. 
Published: July 2004

ABSTRACT
Human herpesvirus 8 (HHV-8) open reading frame K1 sequences amplified from the urine of 5 of 78 (6.4%) infected people in Malawi were monotypic. In two people, urinary and oral sequences were genotypically different. Comprehensive evaluation of HHV-8 transmission may require characterization of HHV-8 shed both in urine and orally.
Genetic Relatedness and Quinolone Resistance of
Campylobacter jejuni
Strains Isolated in 2002 in Hong Kong
Authors: Chu Yiu-Wai , Chu Man-Yu , Luey Kit-Yee , Ngan Yin-Wa , Tsang Ka-Lok , Kam Kai-Man 
Published: July 2004

ABSTRACT

Pulsed-field gel electrophoresis fingerprints of 98
Campylobacter jejuni
isolates from patients (85) and chicken carcasses (13) in Hong Kong in 2002 demonstrated high genetic diversity. The prevalence of quinolone resistance among the isolates was 85.9%, and replacement of the threonine-86 residue in the gyrase subunit A was the major resistance mechanism.
Direct Identification of
Mycobacterium haemophilum
in Skin Lesions of Immunocompromised Patients by PCR-Restriction Endonuclease Analysis
Authors: Wang S. X. , Sng L. H. , Leong H. N. , Tan B. H. 
Published: July 2004

ABSTRACT

PCR-restriction endonuclease analysis (PRA) was used for direct identification of
Mycobacterium haemophilum
in clinical specimens from immunocompromised patients. PRA correctly identified
M. haemophilum
in four smear-positive specimens. Direct identification by PRA takes 2 to 3 working days compared to the 3 to 5 weeks required for culture isolation and identification by conventional methods.
Diagnostic Utility and Clinical Significance of Naso- and Oropharyngeal Samples Used in a PCR Assay To Diagnose
Mycoplasma pneumoniae
Infection in Children with Community-Acquired Pneumonia
Authors: Michelow Ian C. , Olsen Kurt , Lozano Juanita , Duffy Lynn B. , McCracken George H. , Hardy R. Doug 
Published: July 2004

ABSTRACT

PCR assays of naso- and oropharyngeal samples among hospitalized children appear equally effective for the diagnosis of serologically confirmed community-acquired mycoplasmal pneumonia. However, the combination of results from both sites yields optimal sensitivity (57%), specificity (98%), and positive (92%) and negative (82%) predictive values when compared with
Mycoplasma pneumoniae
enzyme-linked immunosorbent assay.
First Comprehensively Documented Case of
Paracoccus yeei
Infection in a Human
Authors: Funke Guido , Frodl Reinhard , Sommer Hartmut 
Published: July 2004

ABSTRACT

Paracoccus yeei
was isolated in pure culture from an aerobic blood culture and bulla fluid from a 67-year-old male. The biochemical identification scheme for this recently described species is outlined. Because of its reaction pattern it is not unlikely that
P. yeei
is underdiagnosed.
Analysis of Composite Bonded/Bolted Joints Used in Repairing
Authors: Chan Wen S. , Vedhagiri S. 
Published: July 2004

The performance of composite repairing using single lapped joints is sensitive to factors such as ply stacking sequence of laminate, bonding surface preparation, anisotropic nature of adherend, as well as bearing and load transfer from one adherend to the other. This research is focused to investigate the stress distributions in laminated composite joints with multiple pin loads using finite element analysis. The structural response of various configurations of single lap joints, namely bonded, bolted and bonded-bolted joints, are analyzed by three-dimensional finite element method. A comparison of the results obtained using finite element analysis is conducted with experimental results and the results are validated. Parametric study is conducted to investigate the effect of stress distribution and load transfer due to ply stacking sequence of laminate.