bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Novel DNA Probe for Strain Typing
Mycobacterium bovis
by Restriction Fragment Length Polymorphism Analysis
Authors: O'Brien Rory , Flynn Orla , Costello Eamon , O'Grady Don , Rogers Mark 
Published: December 2019

ABSTRACT

Bovine tuberculosis caused by
Mycobacterium bovis
remains a significant disease of farmed cattle in many countries despite ongoing tuberculosis eradication programs. Molecular typing methods such as restriction fragment length polymorphism (RFLP) analysis and spoligotyping have been used to identify related herd breakdowns in an attempt to identify more precisely the route of infection into cattle herds and to trace the transmission of bovine tuberculosis. A recent geographical survey of Irish
M. bovis
isolates demonstrated that a significant proportion of isolates (∼20%) exhibit a common strain type, limiting the value of current strain typing methods as an epidemiological tool. We have identified and cloned a region of the
M. bovis
genome, pUCD, which generates a clear, highly polymorphic banding pattern when used as an RFLP probe on
Alu
I restriction-digested
M. bovis
genomic DNA and which effectively subdivides this common strain type. When used to type 60 Irish
M. bovis
isolates, pUCD exhibited greater discriminatory power than the commonly used mycobacterial RFLP probes IS
6110
, PGRS, and DR and detected an equivalent number of strain types to a combination of these three probes. pUCD also detected significantly more strain types than the spoligotyping technique, while maintaining a high level of concordance between epidemiologically related and unrelated herd breakdowns. The polymorphic element within pUCD remains to be fully characterized, however the potential for this probe to greatly decrease the workload necessary to genotype
M. bovis
by RFLP analysis is compelling.
Oxygen and Carbon Dioxide Regulation of Toxic Shock Syndrome Toxin 1 Production by
Staphylococcus aureus
MN8
Authors: Yarwood Jeremy M. , Schlievert Patrick M. 
Published: December 2019

ABSTRACT

The production of toxic shock syndrome toxin 1 (TSST-1) by
Staphylococcus aureus
MN8 exposed to a range of oxygen concentrations (0 to 21% [vol/vol]) was examined in batch and thin-film cultures. The response of
S. aureus
to this range of oxygen concentrations was studied in the absence and in the presence of 7% (vol/vol) carbon dioxide. In the absence of carbon dioxide, TSST-1 production in batch cultures increased from negligible levels in the presence of oxygen concentrations of 1% or less to 500 ng/ml in the presence of 2% oxygen and then decreased to 70 ng/ml or less in the presence of oxygen concentrations of 6% and higher. In the presence of carbon dioxide, however, toxin production increased from negligible levels in the presence of 1% oxygen to 1,900 ng/ml in the presence of 21% oxygen. In thin-film cultures, TSST-1 production increased from nearly undetectable levels under anaerobic conditions to 1 and 10 μg/ml under 21% oxygen in the absence and presence of carbon dioxide, respectively. This study demonstrates the controlling effects of both oxygen and carbon dioxide on TSST-1 production.
Molecular Differentiation of Seven
Malassezia
Species
Authors: Gupta Aditya K. , Kohli Yatika , Summerbell Richard C. 
Published: December 2019

ABSTRACT

A system based on PCR and restriction endonuclease analysis was developed to distinguish the seven currently recognized
Malassezia
species. Seventy-eight strains, including authentic culture collection strains and routine clinical isolates, were investigated for variation in the ribosomal DNA repeat units. Two genomic regions, namely, the large subunit of the ribosomal gene and the internal transcribed spacer (ITS) region, were amplified by PCR, and products were digested with restriction endonucleases. The patterns generated were useful in identification of five out of seven
Malassezia
species.
M. sympodialis
was readily distinguishable in that its ITS region yielded a 700-bp amplified fragment, whereas the other six species yielded an 800-bp fragment.
M. globosa
and
M. restricta
were very similar in the regions studied and could be distinguished only by performing a hot start-touchdown PCR on primers for the β-tubulin gene. Primers based on the conserved areas of the
Candida cylindracea
lipase gene, which were used in an attempt to amplify
Malassezia
lipases, yielded an amplification product after annealing at 55°C only with
M. pachydermatis
. This specific amplification may facilitate the rapid identification of this organism.
Computer-Assisted Analysis and Epidemiological Value of Genotyping Methods for
Campylobacter jejuni
and
Campylobacter coli
Authors: de Boer Paulo , Duim Birgitta , Rigter Alan , van der Plas Jan , Jacobs-Reitsma Wilma F. , Wagenaar Jaap A. 
Published: December 2019

ABSTRACT

For epidemiological tracing of the thermotolerant
Campylobacter
species
C. jejuni
and
C. coli
, reliable and highly discriminatory typing techniques are necessary. In this study the genotyping techniques of flagellin typing (
flaA
typing), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and amplified fragment length polymorphism (AFLP) fingerprinting were compared. The following aspects were compared: computer-assisted analysis, discriminatory power, and use for epidemiological typing of campylobacters. A set of 50 campylobacter poultry isolates from The Netherlands and neighboring countries was analyzed. Computer-assisted analysis made cluster analysis possible and eased the designation of different genotypes. AFLP fingerprinting was the most discriminatory technique, identifying 41 distinct genotypes, while PFGE identified 38 different types,
flaA
typing discriminated 31 different types, and ribotyping discriminated 26 different types. Furthermore, AFLP analysis was the most suitable method for computer-assisted data analysis. In some cases combining the results of AFLP fingerprinting, PFGE, and
flaA
typing increased our ability to differentiate strains that appeared genetically related. We conclude that AFLP is a highly discriminatory typing method and well suited for computer-assisted data analysis; however, for optimal typing of campylobacters, a combination of multiple typing methods is needed.
Sensitive Method for Detection of Human Herpesviruses 6 and 7 in Saliva Collected in Field Studies
Authors: Zerr Danielle M. , Huang Meei-Li , Corey Lawrence , Erickson Matthew , Parker Heather L. , Frenkel Lisa M. 
Published: December 2019

ABSTRACT
To facilitate studies of the epidemiology and natural history of human herpesviruses 6 and 7 in infants, a practical method for collecting and quantifying the DNA of these viruses was developed. Saliva was collected using small strips of filter paper, and virus was detected using a real-time quantitative fluorescent-probe PCR assay. The sensitivity and specificity of this method even after prolonged drying of the specimens compared favorably to those of our traditional method of collecting and assaying saliva.
Growth Supplements for
Helicobacter pylori
Authors: Jiang Xiuping , Doyle Michael P. 
Published: December 2019

ABSTRACT

The growth response of
Helicobacter pylori
in broth was determined in the presence of ferrous sulfate, sodium pyruvate, and mucin (porcine stomach). The addition of either ferrous sulfate and sodium pyruvate or mucin to brain heart infusion broth with 7% horse serum (BHI-HS) enhanced the growth of
H. pylori
. The best growth of strain NB2-1, which was the slowest growing of 10
H. pylori
strains evaluated, occurred in the presence of 0.05% ferrous sulfate and 0.05% sodium pyruvate. The addition of 0.3% mucin to BHI-HS reduced the lag time of
H. pylori
by 48 h and enhanced the growth. On the basis of the results for 10
H. pylori
strains, the combination of ferrous sulfate (0.025%), sodium pyruvate (0.025%), and mucin (0.15%) in BHI-HS counteracted the inhibitory effects of the antibiotics used in culture media for selective growth of
H. pylori
. Results suggest that these supplements may be useful for enhancement of the growth of
H. pylori
in enrichment media.
A Three-Year Study of
Campylobacter jejuni
Genotypes in Humans with Domestically Acquired Infections and in Chicken Samples from the Helsinki Area
Authors: Hänninen Marja-Liisa , Perko-Mäkelä Päivikki , Pitkälä Anna , Rautelin Hilpi 
Published: December 2019

ABSTRACT

Campylobacter jejuni
isolates from stool samples of patients with domestically acquired sporadic infections and from chicken from retail shops were studied during seasonal peaks from June to September over a 3-year period from 1996 to 1998. A large number of pulsed-field gel electrophoresis (PFGE) genotypes (a combined
Sma
I-
Sac
II pattern) were identified each year. Certain genotypes persisted for the whole study period, and predominant genotypes represented 28 to 52% of the strains during a restricted period of time. The peak level of positive chicken samples was between July and August of each study year, when 10 to 33% of the samples were positive for campylobacter. The same PFGE genotypes found in humans were also detected in the chicken samples. This suggests that common genotypes were circulating in the area.
Brucella abortus
Infection Acquired in Microbiology Laboratories
Authors: Fiori Pier Luigi , Mastrandrea Scilla , Rappelli Paola , Cappuccinelli Piero 
Published: December 2019

ABSTRACT

We report an outbreak of laboratory-acquired
Brucella abortus
infection originating in the accidental breakage of a centrifuge tube. A total of 12 laboratory workers were infected (attack rate of 31%), with an incubation time ranging from 6 weeks to 5 months. Antibody titers were evaluated weekly in all personnel exposed, allowing the diagnosis of the infection in most cases before the onset of clinical symptoms, so that specific therapy could be administrated.
Infective Endocarditis Complicated with Progressive Heart Failure due to β-Lactamase-Producing
Cardiobacterium hominis
Authors: Lu Po-Liang , Hsueh Po-Ren , Hung Chien-Ching , Teng Lee-Jene , Jang Tsrang-Neng , Luh Kwen-Tay 
Published: December 2019

ABSTRACT

We describe a 66-year-old woman with infective endocarditis due to
Cardiobacterium hominis
whose condition, complicated by severe aortic regurgitation and congestive heart failure, necessitated aortic valve replacement despite treatment with ceftriaxone followed by ciprofloxacin. The blood isolate of
C. hominis
produced β-lactamase and exhibited high-level resistance to penicillin (MIC, ≧256 μg/ml) and reduced susceptibility to vancomycin (MIC, 8 μg/ml).
Genetic Characterization of Type 2 Porcine Circovirus (PCV-2) from Pigs with Postweaning Multisystemic Wasting Syndrome in Different Geographic Regions of North America and Development of a Differential PCR-Restriction Fragment Length Polymorphism Assay To Detect and Differentiate between Infections with PCV-1 and PCV-2
Authors: Fenaux Martijn , Halbur Patrick G. , Gill Mike , Toth Thomas E. , Meng Xiang-Jin 
Published: December 2019

ABSTRACT
Postweaning multisystemic wasting syndrome (PMWS) is an emerging disease in swine. Increasing evidence indicates that a variant strain of porcine circovirus (PCV), designated type 2 PCV (PCV-2), is responsible for PMWS. To determine the extent of genetic heterogeneity of PCV-2 isolates, the complete genomes of six PCV-2 isolates from different regions of North America were amplified by PCR and sequenced. Sequence and phylogenetic analyses confirmed that two distinct genotypes of PCV exist: nonpathogenic genotype PCV-1 and PMWS-associated genotype PCV-2. However, within the PCV-2 genotype, several minor branches that have been identified appear to be associated with geographic origins. The genomic sequences of two French PCV-2 isolates diverge the most from those of other PCV-2 isolates and form a distinct branch. Other minor but distinguishable branches have also been identified for a Taiwan PCV-2 isolate and two of the Canadian PCV-2 isolates. All the U.S. PCV-2 isolates are closely related, but the Canadian isolates vary, to some extent, in their genomic sequences. The data from this study indicate that although the genome of PCV-2 is generally stable among different isolates, PCV-2 isolates from different geographic regions vary in their genomic sequences. This variation may have important implications for PCV-2 diagnosis and research. On the basis of genetic analyses of available PCV strains, a universal PCR-restriction fragment length polymorphism (PCR-RFLP) assay was developed to detect and differentiate between infections with PCV-1 and PCV-2. This PCR-RFLP assay should be useful for studying the pathogenesis of PCV-2, for detecting PCV-2 infection in pigs from different geographic regions, and for screening donor pigs for use in xenotransplantation.
Helicobacter canadensis
sp. nov. Isolated from Humans with Diarrhea as an Example of an Emerging Pathogen
Authors: Fox James G. , Chien Chih Ching , Dewhirst Floyd E. , Paster Bruce J. , Shen Zeli , Melito Pasquale L. , Woodward David L. , Rodgers Frank G. 
Published: December 2019

ABSTRACT

We recently analyzed 11 helicobacter isolates cultured from diarrhea patients in Canada. These isolates had been characterized biochemically by restriction fragment length polymorphism (RFLP;
Alu
I,
Hha
I) analysis and by fatty-acid analysis as
Helicobacter pullorum
. However, four of the isolates differed biochemically from
H. pullorum
by their inability to hydrolyze indoxyl acetate and their resistance to nalidixic acid. Using complete 16S rRNA analysis, we determined that these four strains clustered near
H. pullorum
but had a sequence difference of 2% and therefore represent a novel helicobacter,
Helicobacter canadensis
. This novel helicobacter could also be distinguished from
H. pullorum
by RFLP analysis using
Apa
LI. The number of novel
Helicobacter
spp. associated with gastrointestinal disease in humans and animals is rapidly increasing. There are now six
Helicobacter
spp. isolated from diarrheic humans, the other five being
H. pullorum
,
H. canis
, “
H. rappini
,”
H. fennelliae
, and
H. cinaedi
. This finding highlights the importance of careful molecular analysis in addition to standard biochemical tests in identifying the increasing number of
Helicobacter
spp. isolated from humans and animals.
Failure To Detect
Chlamydia pneumoniae
in the Late-Onset Alzheimer's Brain
Authors: Ring Robert H. , Lyons Joseph M. 
Published: December 2019

ABSTRACT

Epidemiological studies have yet to identify a single cause for the most common late-onset form of Alzheimer's disease. The common respiratory pathogen
Chlamydia pneumoniae
recently has been implicated as a risk factor for this form of Alzheimer's disease. Were this true, there would be a dramatic shift in current paradigms of Alzheimer's disease research and treatment. In the absence of published confirmation, we obtained postmortem brain tissue from late-onset Alzheimer's disease patients (
n
= 15) and representative controls (
n
= 5) and extracted DNA from up to six separate brain regions in each instance, including those areas particularly relevant to Alzheimer's disease neuropathology. Each sample of DNA (
n
= 101) was assayed five times or more for the presence of
C. pneumoniae
DNA using a nested-PCR protocol targeting a species-specific gene sequence coding for the major outer membrane protein of this organism. We were unable unequivocally to detect
C. pneumoniae
in any of the 101 samples tested by PCR and failed to culture the organism from tissue samples. We conclude that
C. pneumoniae
is neither strongly nor uniquely associated with the neuropathology seen in late-onset Alzheimer's disease.
Detection of Herpes Simplex Virus DNA by Real-Time PCR
Authors: Kessler Harald H. , Mühlbauer Gerhard , Rinner Beate , Stelzl Evelyn , Berger Annemarie , Dörr Hans-Wilhelm , Santner Brigitte , Marth Egon , Rabenau Holger 
Published: December 2019

ABSTRACT

Molecular detection of herpes simplex virus (HSV) DNA is recognized as the reference standard assay method for the sensitive and specific diagnosis of central nervous system infections caused by HSV. In this study, a molecular assay based on real-time PCR on the LightCycler (LC) instrument was evaluated and compared with a home-brew molecular assay. The detection limit of the LC assay was determined with 10-fold dilutions of plasmid pS4 with the
Sal
I restriction fragment of the DNA polymerase gene and with the First European Union Concerted Action HSV Proficiency Panel. A total of 59 cerebrospinal fluid (CSF) specimens were investigated for the comparative study. With plasmid pS4, the detection limit of the LC assay was found to be 10
4
copies per ml, i.e., 12.5 copies per run. When samples of the First European Union Concerted Action HSV Proficiency Panel were tested, 2 × 10
3
to 5 × 10
3
HSV type 1 genome equivalents (GE) per ml, i.e., 2.5 to 6.3 GE per run, could consistently be detected. There was a correlation between the LC assay and the home-brew assay in 55 of 59 specimens. In conclusion, the LC assay allows very rapid detection of HSV DNA in CSF. It was found to be laborsaving and showed sufficient sensitivity.
Comparison of Two Amplification Technologies for Detection and Quantitation of Human Immunodeficiency Virus Type 1 RNA in the Female Genital Tract
Authors: Bremer James , Nowicki Marek , Beckner Suzanne , Brambilla Donald , Cronin Mike , Herman Steven , Kovacs Andrea , Reichelderfer Patricia 
Published: December 2019

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) RNA levels in female genital tract and peripheral blood samples were compared using two commercial amplification technologies: the Roche AMPLICOR HIV-1 MONITOR test and either the Organon Teknika nucleic acid sequence-based amplification (NASBA-QT) assay or the NucliSens assay. Estimates of HIV-1 RNA copy number were derived from internal kit standards and analyzed unadjusted and adjusted to a common set of external standards. We found a discordance rate of approximately 18% between the two technologies for the detection of HIV-1 in either the genital tract or peripheral blood samples. Detection discordance was not consistent among specimens or among women. There were no significant differences in adjusted or unadjusted estimates of HIV-1 RNA copy number in the genital tract samples using the AMPLICOR HIV-1 MONITOR test and either the NASBA-QT assay or the NucliSens assay. In addition, the estimated HIV-1 RNA copy number in peripheral blood samples did not differ when tested with the NucliSens assay and the AMPLICOR HIV-1 MONITOR test using kit standards. However, there was a significant difference in estimated RNA copy number between the NASBA-QT assay and the AMPLICOR HIV-1 MONITOR test for internal kit standards, which, as we have previously shown, was eliminated after adjustment with the external standards. Our results suggest that the Roche and Organon Teknika assays are equivalent for quantifying HIV-1 RNA in female genital tract specimens, although variation in detection does exist.
Genetic Characteristics ofBorrelia coriaceaeIsolates from the Soft TickOrnithodoros coriaceus(Acari: Argasidae)
Authors: Hendson Mavis , Lane Robert S. 
Published: December 2019

ABSTRACTTwoBorreliaisolates (CA434 and CA435) cultured from the soft tickOrnithodoros coriaceuswere analyzed by contour-clamped homogeneous electric field gel electrophoresis of unrestricted andApaI-restricted DNA, standard electrophoresis ofBamHI- andHindIII-restricted DNA, Southern hybridization, restriction fragment length polymorphism and sequencing of the 16S rRNA gene, and amplification of the 5S-23S intergenic spacer region. These isolates were compared withBorrelia coriaceaetype strain Co53,B. burgdorferisensu stricto strain CA4, and the relapsing-fever spirocheteB. parkeri(undesignated). The 16S rRNA region of CA434 and CA435 differed from that ofB. coriaceaetype strain Co53 by the presence of 1 base (C) at position 367 (GenBank accession no.U42286). The linear plasmid profile of CA434 was similar to that of Co53, and theApaI,BamHI, andHindIII restriction fingerprints of the total cellular DNA of CA434 and Co53 were similar. In contrast, CA435 differed somewhat from CA434 and Co53, which demonstrates thatB. coriaceaeis genetically diverse. Southern hybridization showed that the DNAs of CA434 and CA435 hybridized strongly with the digoxigenin-labeled DNA of Co53. Low homology was found between the DNA of Co53 and that ofB. parkeri. The 16S rRNA sequence ofB. parkeriwas identical to previously published results forB. parkeristrain M3001 (GenBank accession numberU42296). CA434 and CA435 represent only the second and third isolates ofB. coriaceaeobtained from any source since its initial isolation from anO. coriaceustick in 1985. All threeB. coriaceaeisolates were derived from adult ticks collected from the same locality in northwestern California. Difficulties encountered in detectingB. coriaceaein, and isolating this spirochete from, the tissues ofO. coriaceusare discussed. The lack of concordance between different detection or isolation methods suggests that reliance upon a single technique may grossly underestimate the true prevalence of spirochetal infection in wild-caughtO. coriaceusticks.
PCR Amplification and Phylogenetic Analysis of
groESL
Operon Sequences from
Ehrlichia ewingii
and
Ehrlichia muris
Authors: Sumner John W. , Storch Gregory A. , Buller Richard S. , Liddell Allison M. , Stockham Steven L. , Rikihisa Yasuko , Messenger Sharon , Paddock Christopher D. 
Published: December 2019

ABSTRACT

Broad-range PCR primers were used to amplify part of the
groESL
operon of the canine pathogen
Ehrlichia ewingii
, recently recognized as a human pathogen, and the murine pathogen
Ehrlichia muris
. Phylogenetic analysis supported the relationships among
Ehrlichia
species previously determined by comparison of 16S rRNA gene sequences. These sequences provide additional PCR targets for species for which few gene sequences have been determined.
Comparison of Polymorphism of Thymidine Kinase Gene and Restriction Fragment Length Polymorphism of Genomic DNA in Herpes Simplex Virus Type 1
Authors: Nagamine Masayoshi , Suzutani Tatsuo , Saijo Masayuki , Hayashi Kozaburo , Azuma Masanobu 
Published: December 2019

ABSTRACT
The polymorphism of the thymidine kinase (TK) gene of herpes simplex virus type 1 (HSV-1) was analyzed and was compared with the restriction fragment length polymorphism (RFLP) of the whole genome to evaluate the relative efficiency of the TK gene as a potential probe for identification and discrimination of HSV-1. The effectiveness of using the polymorphism of the TK gene in classifying HSV-1 strains was comparable to that of RFLP analysis of 66 sites, suggesting that TK gene sequencing may have important applications in epidemiological studies of HSV-1.
Evaluation of the Binax and Biotest Urinary Antigen Kits for Detection of Legionnaires' Disease Due to Multiple Serogroups and Species of
Legionella
Authors: Benson Robert F. , Tang Patrick W. , Fields Barry S. 
Published: December 2019

ABSTRACT

The Binax and the Biotest urinary antigen kits for the detection of Legionnaires' disease caused by organisms other than
Legionella pneumophila
were compared by testing 45 urine samples from non-
Legionella pneumophila
serogroup 1 patients previously positive in a broad-spectrum enzyme-linked immunosorbent assay (ELISA). Eighteen were positive with the Binax kit, and 13 were positive with the Biotest. Although neither kit is as sensitive as ELISA, these results extend the number of serogroups and species of
Legionella
that can be diagnosed with the Binax or Biotest kit.
Recurrent Infections and Chronic Colonization by an
Escherichia coli
Clone in the Respiratory Tract of a Patient with Severe Cystic Bronchiectasis
Authors: Wang Jann-Yuan , Hsueh Po-Ren , Wang Jann-Tay , Lee Li-Na , Yang Pan-Chyr , Luh Kwen-Tay 
Published: December 2019

ABSTRACT

A 39-year-old woman with cystic bronchiectasis had repeated pulmonary infections from 1996 to 1999, and 6 of a total of 28 isolates of
Escherichia coli
from sputum specimens were studied. Their identical antibiotype and randomly amplified polymorphic DNA patterns indicated a single clone of
E. coli
, which persistently colonized the respiratory tract, causing recurrent infections.