bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acquisition and Colonization Stability of
Actinobacillus actinomycetemcomitans
and
Porphyromonas gingivalis
in Children
Authors: Lamell Celeste W. , Griffen Ann L. , McClellan Dawn L. , Leys Eugene J. 
Published: December 2019

ABSTRACT

The presence of
Porphyromonas gingivalis
has been shown to be a risk factor for periodontitis in adults, and
Actinobacillus actinomycetemcomitans
has been implicated as a pathogen in early-onset periodontitis. Both species have been shown to establish stable colonization in adults. In cross-sectional studies, both
A. actinomycetemcomitans
and
P. gingivalis
have been detected in over one-third of apparently healthy children. Information on the stability of colonization with these organisms in children could help to elucidate the natural history of the development of periodontitis. For this purpose, samples previously collected from a cohort of 222 children between the ages of 0 and 18 years and previously examined for the presence of
P. gingivalis
with a PCR-based assay were examined for the presence of
A. actinomycetemcomitans
. It was detected in 48% of subjects and, like
P. gingivalis
, was found at similar frequencies among children of all ages (
P
= 0.53), suggesting very early initial acquisition. One hundred one of the original subjects were recalled after 1 to 3 years to determine the continuing presence of both
A. actinomycetemcomitans
and
P. gingivalis
. The prevalence of both species remained unchanged at resampling. However, in most children both species appeared to colonize only transiently, with random concordance between the results of the first and second sampling. Stability of colonization was unrelated to age for
A. actinomycetemcomitans
, but
P. gingivalis
was more stable in the late teenage years.
Development of a Hypersensitive Detection Method for Human Parvovirus B19 DNA
Authors: Sato Kazuaki , Matsuda Eiji , Kamisango Keiichi , Iwasaki Hiroaki , Matsubara Shuzo , Matsunaga Yasuko 
Published: December 2019

ABSTRACT
A new detection method for human parvovirus B19 DNA was established using PCR coupled with a hybridization protection assay. The amplified product was detected using acridinium ester-labeled DNA probes. By this method, a few copies of B19 DNA were detected in human serum albumin.
Use of Calibrated Viral Load Standards for Group M Subtypes of Human Immunodeficiency Virus Type 1 To Assess the Performance of Viral RNA Quantitation Tests
Authors: Jagodzinski Linda L. , Wiggins Debra L. , McManis Joshua L. , Emery Sandra , Overbaugh Julie , Robb Merlin , Bodrug Sharon , Michael Nelson L. 
Published: December 2019

ABSTRACT
Optimal management of human immunodeficiency virus type 1 (HIV-1) disease requires accurate quantitation of viral RNA concentrations in plasma. Evidence for increasing geographic intermixing of HIV-1 subtypes makes equivalent quantitation of all subtypes essential. The performances of six quantitative viral RNA tests are described, for the first time, with calibrated viral isolates of diverse subtypes.
Rapid Discrimination of Monkey B Virus from Human Herpes Simplex Viruses by PCR in the Presence of Betaine
Authors: Hirano Makoto , Nakamura Shin , Okada Maki , Ueda Masahiro , Mukai Ryozaburo 
Published: December 2019

ABSTRACT
A PCR method to amplify DNA segments of the glycoprotein G gene of monkey B virus (BV) was achieved by adding betaine to the PCR mixture, in spite of the high G+C content of this gene. No product was obtained when DNA of human herpes simplex viruses (HSVs) was used as the template under the same conditions. Thus, this PCR method is useful in discriminating BV from HSVs.
Rapid Subtyping of Dengue Virus Serotypes 1 and 4 by Restriction Site-Specific PCR
Authors: Miagostovich Marize P. , dos Santos Flavia B. , Gutiérrez C. Milena , Riley Lee W. , Harris Eva 
Published: December 2019

ABSTRACT
We previously reported a simple subtyping method, restriction site-specific PCR (RSS-PCR), for dengue virus serotypes 2 and 3; here we describe its application for subtyping dengue virus serotypes 1 and 4. Three major RSS-PCR types were observed for dengue virus serotype 1 and two types were observed for dengue virus serotype 4, in agreement with previous strain classifications based on sequence analysis. Because of its simplicity, this method is amenable to rapid subtyping and application to epidemiological studies of dengue in countries where dengue is endemic.
Accelerated Detection and Identification of Mycobacteria with MGIT 960 and COBAS AMPLICOR Systems
Authors: Katila Marja-Leena , Katila Päivi , Erkinjuntti-Pekkanen Riitta 
Published: December 2019

ABSTRACT

An automated cultivation system for mycobacteria, the MGIT 960 system (MGIT system), was compared in the clinical routine with two variants of Löwenstein-Jensen (L-J) medium. A total of 152 isolates were recovered from 2,015 specimens: 139 (91%) with the MGIT system and 127 (84%) with L-J media (
P
= 0.05). These included 68 isolates of
Mycobacterium tuberculosis
, of which 88% grew in the MGIT system and 93% grew in L-J media (
P
= 0.389), and 84 isolates of mycobacteria other than
M. tuberculosis
(MOTT), of which 94% grew in the MGIT system and 76% grew in L-J media (
P
= 0.003). More
M. avium
complex isolates were detected in the MGIT system (
n
= 65) than in L-J media (
n
= 50) (
P
= 0.001). Growth in the MGIT system was detected in 2 weeks for 78% of the isolates, whereas growth was detected in the two L-J media for 17 and 25% of the isolates, respectively. The mean times to detection of
M. tuberculosis
were 12 days in the MGIT system and 20 days in L-J media, and for
M. avium
complex the mean times to detection were 8 and 22 to 25 days, respectively. The contamination rates were similar (8.7 to 8.9%) in all media. A commercial amplification system (COBAS AMPLICOR) was evaluated for its ability to rapidly identify
M. tuberculosis
,
M. avium
, and
M. intracellulare
directly from 393 samples in MGIT system broth. A correct PCR result, as evaluated by culture or clinical data, was obtained for 96% of the samples, with inhibition being detected for 2% of the samples. Of the 89 results positive for
M. tuberculosis
, 91% were regarded as true positive, 8% were regarded as inconclusive, and 2% were considered false positive. For results positive for
M. avium
and
M. intracellulare
, 97 and 79%, respectively, were regarded as true positive. Increased rapidity and enhanced isolation of MOTT were obtained with the MGIT system. COBAS AMPLICOR was suitable for rapid identification of these three common pathogens from MGIT system broth.
Evaluation of a Capacitance Method for Direct Antifungal Susceptibility Testing of Yeasts in Positive Blood Cultures
Authors: Chang Chang Hsein , Jung Chang Jui , Huey Huang Ay , Chain Chang Tsung 
Published: December 2019

ABSTRACT

The feasibility of using a capacitance method (CM) for direct antifungal susceptibility testing of yeasts in positive blood cultures was evaluated. The CM used the same test conditions as those recommended by the National Committee for Clinical Laboratory Standards. After direct inoculation of positive culture broths into module wells (Bactometer; bioMérieux, Inc., Hazelwood, Mo.), the end-point determination was made by monitoring the capacitance change in the culture broths with Bactometer. The MIC of amphotericin B was the lowest concentration at which yeast growth was completely inhibited, while the MICs of ketoconazole, flucytosine, and fluconazole were the concentrations at which a ≥80% reduction in capacitance change was observed. The MICs of the four drugs against each blood isolate obtained on subculture plates were also determined by the macrodilution method. For 51 positive blood cultures tested, the percent agreement (±2 log
2
dilutions) between the CM and the macrodilution method were as follows: amphotericin B (98%), ketoconazole (92%), flucytosine (84%), and fluconazole (96%). The CM was further used for breakpoint susceptibility testing of fluconazole (8 and 64 μg/ml) and flucytosine (4 and 32 μg/ml) against yeasts in positive blood cultures. After testing of 74 specimens by the CM, flucytosine and fluconazole produced one (1.4%) major error and two (2.8%) minor errors, respectively. All yeasts that displayed resistance to flucytosine or fluconazole were detected within 24 h after direct inoculation of the positive broths into Bactometer. The CM may be useful for the rapid detection of antifungal resistance in positive blood cultures containing yeasts.
Evaluation of Serotype Prediction by
cpsA
-
cpsB
Gene Polymorphism in
Streptococcus pneumoniae
Authors: Lawrence Elliot R. , Arias Cesar A. , Duke Brigid , Beste Dani , Broughton Karen , Efstratiou Androulla , George Robert C. , Hall Lucinda M. C. 
Published: December 2019

ABSTRACT

New pneumococcal conjugate vaccines covering a limited number of serotypes are likely to come into widespread use over the next few years. It is unknown what effect this will have on the relative importance of different serotypes as causes of pneumococcal infection. Hence, it will be important to monitor serotype prevalence before, during, and after the introduction of new vaccines. We have investigated the ability of a PCR method based on polymorphisms in two genes common to the different capsule loci to predict the serotype of 93 clinical isolates of
Streptococcus pneumoniae
submitted to the Central Public Health Laboratory in 1997. Of 70 isolates with vaccine serotypes, 65 were predicted to belong to the correct serotype; this number was improved to 69 with the inclusion of two additional patterns to the database. Of 23 isolates with other serotypes, 19 were correctly predicted as non-vaccine serotypes, the discrepancy lying with four isolates of 6A (non-vaccine serotype) that were indistinguishable from isolates of 6B (vaccine serotype). In situations in which culture of the organism is not feasible, this method could potentially be applicable directly to clinical specimens and could be a valuable aid to the surveillance of pneumococcal serotypes.
A Rapid, Automated Enzymatic Fluorometric Assay for Determination of
d
-Arabinitol in Serum
Authors: Yeo Siew Fah , Zhang Yeyan , Schafer David , Campbell Sheldon , Wong Brian 
Published: December 2019

ABSTRACT

A rapid enzymatic fluorometric assay for measuring
d
-arabinitol in serum was developed using recombinant
d
-arabinitol dehydrogenase from
Candida albicans
(rArDH). rArDH was produced in
Escherichia coli
and purified by dye-ligand affinity chromatography. rArDH was highly specific for
d
-arabinitol, cross-reacting only with xylitol (4.9%) among all polyols tested. A Cobas Fara II centrifugal autoanalyzer (Roche) was used to measure NADH fluorometrically when rArDH and NAD were added to serum extracts, and
d
-arabinitol concentrations were calculated from standard curves derived from pooled human serum containing known amounts of
d
-arabinitol. The method was precise (mean intra-assay coefficients of variation [CVs], 0.8%, and mean interassay CVs, 1.6%) and rapid (3.5 min per assay) and showed excellent recovery of added
d
-arabinitol in serum (mean recovery rate, 101%). The mean and median
d
-arabinitol/creatinine ratios were 2.74 and 2.23 μM/mg/dl, respectively, for the 11 patients with candidemia compared to 1.14 and 1.23 μM/mg/dl, respectively, for 10 healthy controls (
P
< 0.01). These results confirm earlier studies showing that serum
d
-arabinitol measurement may help to promptly diagnose invasive candidiasis. The technique shows a significant improvement in terms of accuracy, cost, simplicity, specificity, and speed compared with gas chromatography, mass spectrometry, and earlier enzymatic assays.
Incidence and Identification of
Klebsiella planticola
in Clinical Isolates with Emphasis on Newborns
Authors: Westbrook Glennis L. , O'Hara Caroline Mohr , Roman Susan B. , Miller J. Michael 
Published: December 2019

ABSTRACT

Studies conducted in France and Germany suggest that up to 19% of clinically identified
Klebsiella
sp. are actually
Klebsiella planticola
, an environmental species that has been attributed to two cases of septicemia, with a rare isolate of
Klebsiella terrigena
(0.4%) being identified. A 1-year survey of newborns on a neonatal ward, also conducted in Germany, reported that 72% of
Klebsiella
sp. were
Klebsiella oxytoca
and 8.7% were
K. planticola
. The tests necessary to identify these species are not found in most clinical identification schemes or in the database matrices of most commercial identification products. To determine the incidence of unrecognized
K. planticola
among the
Klebsiella
sp. isolates in our collection, we used the battery of seven supplemental tests amended from the work of Monnet and Freney to test 352 stock isolates and 84 fresh clinical isolates from four local hospitals. After testing 436 strains of
Klebsiella
, only one strain was identified as a possible
K. planticola
and none was identified as
K. terrigena
. We tested an additional 43 stock strains of
K. oxytoca
isolated from newborns by using eight biochemical tests and found one additional strain of
K. planticola
. The occurrence of
K. planticola
in our collection is far less frequent than that observed in other countries.
High Homogeneity of the
Yersinia pestis
Fatty Acid Composition
Authors: Leclercq Alexandre , Guiyoule Annie , El Lioui Mohamed , Carniel Elisabeth , Decallonne Jacques 
Published: December 2019

ABSTRACT

The cellular fatty acid compositions of 29 strains of
Yersinia pestis
representing the global diversity of this species have been analyzed by gas-liquid chromatography to investigate the extent of fatty acid polymorphism in this microorganism. After culture standardization, all
Y. pestis
strains studied displayed some major fatty acids, namely, the 12:0, 14:0, 3-OH-14:0, 16:0, 16:1ω9cis, 17:0-cyc, and 18:1ω9trans compounds. The fatty acid composition of the various isolates studied was extremely homogeneous (average Bousfield's coefficient, 0.94) and the subtle variations observed did not correlate with epidemiological and genetic characteristics of the strains.
Y. pestis
major fatty acid compounds were analogous to those found in other
Yersinia
species. However, when the ratios for the 12:0/16:0 and 14:0/16:0 fatty acids were plotted together, the genus
Yersinia
could be separated into three clusters corresponding to (i) nonpathogenic strains and species of
Yersinia
, (ii) pathogenic
Yersinia enterocolitica
isolates, and (iii)
Yersinia pseudotuberculosis
and
Y. pestis
strains. The grouping of the two latter species into the same cluster was also demonstrated by their high Bousfield's coefficients (average, 0.89). Therefore, our results indicate that the fatty acid composition of
Y. pestis
is highly homogeneous and very close to that of
Y. pseudotuberculosis
.
Identification of an Epitope Common to Genogroup 1 “Norwalk-Like Viruses”
Authors: Hale Antony D. , Tanaka Tomoyuki N. , Kitamoto Noritoshi , Ciarlet Max , Jiang Xi , Takeda Naokazu , Brown David W. G. , Estes Mary K. 
Published: December 2019

ABSTRACT
A panel of 10 monoclonal antibodies (MAbs) to recombinant Norwalk virus (NV) capsid protein were tested in competition enzyme-linked immunosorbent assays. Patterns of competition indicated that these MAbs recognize six to eight epitopes covering five nonoverlapping regions of the capsid protein. A single epitope, recognized by NV MAbs NV3901, NV3912, and NV2461 was found to occur in the majority of genogroup 1 (G1) but not genogroup 2 (G2) “Norwalk-like viruses” (NLVs). This observation supports the subdivision of human NLVs into two genogroups and provides an assay for the rapid identification of G1 NLVs in fecal specimens.
Relevance of Commercial Diagnostic Tests to Detection of Enteric Adenovirus Infections in South Africa
Authors: Moore P. L. , Steele A. D. , Alexander J. J. 
Published: December 2019

ABSTRACT
The prevalence of enteric adenoviruses detected by an in-house enzyme-linked immunosorbent assay (the RIVM-ELISA) ranged from 13 to 38%, and subgroup F adenoviruses comprised 86%. All subgroup F adenoviruses reacted with both RIVM anti-adenovirus type 40 (Ad40) and anti-adenovirus type 41 (Ad41) monoclonal antibodies but were not detected by Adenoclone Type 40/41 enzyme immunoassay (EIA). The correlation between the Biotrin EIA and RIVM-ELISA results was low (26%). Immunospecific tests suggest that a significant proportion of enteric adenoviruses, possibly comprising previously unidentified or emerging types, are not detected by commercial diagnostic tests in South Africa.
A Field-Suitable, Semisolid Aerobic Enrichment Medium for Isolation of
Campylobacter jejuni
in Small Numbers
Authors: Jeffrey J. S. , Hunter A. , Atwill E. R. 
Published: December 2019

ABSTRACT

The objective of this study was to produce an economical, easy to prepare, field-suitable enrichment medium for detection of
Campylobacter jejuni
in small numbers. A semisolid aerobic enrichment medium was developed. Rates of recovery from inoculated medium, sterile swabs, and mixed cultures of
C. jejuni
and coliform bacteria were tested.
G and P Genotyping of Rotavirus Strains Circulating in France over a Three-Year Period: Detection of G9 and P[6] Strains at Low Frequencies
Authors: Bon F. , Fromantin C. , Aho S. , Pothier P. , Kohli E. ,   The Azay Group
Published: December 2019

ABSTRACT
Rotavirus G and P types from 716 children with acute diarrhea in Dijon from 1995 to 1998 and throughout France during the winter of 1997-1998 were analyzed by reverse transcription-PCR. P[8],G1 predominated, followed by P[8],G4, which emerged during the last winter. G9 and P[6] strains were detected at low frequencies.
Rapid Phenotypic Characterization Method for Herpes Simplex Virus and Varicella-Zoster Virus Thymidine Kinases To Screen for Acyclovir-Resistant Viral Infection
Authors: Suzutani Tatsuo , Saijo Masayuki , Nagamine Masayoshi , Ogasawara Masahiro , Azuma Masanobu 
Published: December 2019

ABSTRACT
A rapid phenotypic screening method for herpes simplex virus (HSV) and varicella-zoster virus (VZV) thymidine kinase (TK) genes was developed for monitoring acyclovir-resistant viruses. This method determines the biochemical phenotype of the TK polypeptide, which is synthesized in vitro from viral DNA using a procedure as follows. The TK gene of each sample virus strain is amplified and isolated under the control of a T7 promoter by PCR. The PCR products are transcribed with T7 RNA polymerase and translated in a rabbit reticulocyte lysate. Using this method, enzymatic characteristics and the size of the TK polypeptides encoding HSV and VZV DNA were defined in less than 2 days without virus isolation. The assay should be a powerful tool in monitoring drug-resistant viruses, especially in cases in which virus isolation is difficult.
Rapid Identification of
Yersinia enterocolitica
in Blood by the 5′ Nuclease PCR Assay
Authors: Sen Keya 
Published: December 2019

ABSTRACT

Yersinia enterocolitica
accounts for 50% of the clinical sepsis episodes caused by the transfusion of contaminated red blood cells. A 5′ nuclease TaqMan PCR assay was developed to detect
Y. enterocolitica
in blood. Primers and a probe based on the nucleotide sequence of the 16S rRNA gene from
Y. enterocolitica
were designed. Whole-blood samples were spiked with various numbers of
Y. enterocolitica
cells, and total chromosomal DNA was extracted. When the TaqMan PCR assay was performed, as few as six bacteria spiked in 200 μl of blood could be detected. The assay was specific and did not detect other
Yersinia
species. The TaqMan assay is easy to perform, takes 2 h, and has the potential for use in the rapid detection of
Y. enterocolitica
contamination in stored blood units.
Occurrence of
Bacteroides fragilis
Enterotoxin Gene-Carrying Strains in Germany and the United States
Authors: Claros Marina C. , Claros Zaida C. , Tang Yajarayma J. , Cohen Stuart H. , Silva Joseph , Goldstein Ellie J. C. , Rodloff Arne C. 
Published: December 2019

ABSTRACT

Ninety-three
Bacteroides fragilis
isolates from different geographic locations were analyzed for the presence of an enterotoxin-encoding gene. It was shown that blood culture isolates were more likely to carry this gene than strains from other sources. All enterotoxin-positive strains belonged to the PCR fingerprint group I.
Determination of Human Immunodeficiency Virus Type 1 Subtypes in Taiwan by
vpu
Gene Analysis
Authors: Lee Chun-Nan , Wang Wei-Kung , Fan Wen-Sheng , Twu Shing-Jer , Chen Shou-Chien , Sheng Ming-Ching , Chen Mao-Yuan 
Published: December 2019

ABSTRACT

The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of the
env
and
gag
genes. Information on the
vpu
genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the
vpu
genes were analyzed, and the genetic subtypes determined by analysis of the
vpu
gene were compared with those previously determined by analysis of the
gag
and
env
genes. The
vpu
genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR products. HIV-1 subtypes were determined by sequence alignment and phylogenetic analysis with reference strains. The strains in all except one of the samples analyzed could be classified as subtype A, B, C, E, or G. The
vpu
subtype of one strain could not be determined. Of the strains analyzed, genetic subtypes of 247 (68.0%) were also determined by analysis of the
env
or
gag
gene. The genetic subtypes determined by
vpu
gene analysis were, in general, consistent with those determined by
gag
and/or
env
gene analysis except for those for two AG recombinant strains. All the strains that clustered with a Thailand subtype E strain in the
vpu
phylogenetic analyses were subtype E by
env
gene analysis and subtype A by
gag
gene analysis. In summary, our genetic typing revealed that subtype B strains, which constituted 73.8% of all strains analyzed, were most prevalent in Taiwan. While subtype E strains constituted about one-quarter of the viruses, they were prevalent at a higher proportion in the group infected by heterosexual transmission. Genetic analysis of
vpu
may provide an alternate method for determination of HIV-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.
Molecular Typing of
Mycobacterium tuberculosis
Based on Variable Number of Tandem DNA Repeats Used Alone and in Association with Spoligotyping
Authors: Filliol Ingrid , Ferdinand Severine , Negroni Laetitia , Sola Christophe , Rastogi Nalin 
Published: December 2019

ABSTRACT

Fingerprinting based on variable numbers of tandem DNA repeats (VNTR), a recently described methodology, was evaluated for molecular typing of
Mycobacterium tuberculosis
in an insular setting. In this study, VNTR fingerprinting was used alone or as a second-line test in association with spoligotyping, double-repetitive-element PCR (DRE-PCR), and IS
6110
restriction fragment length polymorphism (RFLP) analysis, and the discriminatory power for each method or the combination of methods was compared by calculating the Hunter-Gaston discriminative index (HGI). The results obtained showed that in 6 out of 12 (50%) cases, VNTR-defined clusters were further subdivided by spoligotyping, compared to 7 out of 18 (39%) cases where spoligotyping-defined clusters were further subdivided by VNTR. When used alone, VNTR was the least discriminatory method (HGI = 0.863). Although VNTR was significantly more discriminatory when used in association with spoligotyping (HGI = 0.982), the combination of spoligotyping and DRE-PCR (HGI = 0.992) was still the most efficient among rapid, PCR-based methodologies, giving results comparable to IS
6110
RFLP analysis. Nonetheless, VNTR typing may provide additional phylogenetical information that may be helpful to trace the molecular evolution of tubercle bacilli.