bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Antifungal MICs by a Rapid Susceptibility Assay
Authors: Riesselman Marcia H. , Hazen Kevin C. , Cutler Jim E. 
Published: May 2021

ABSTRACT
A novel microtiter assay for antifungal susceptibility testing was developed. This method has several potential advantages over the M27-A assay of the National Committee for Clinical Laboratory Standards. These include provision of MIC results within 6 to 19 h, graphical display of data, and the availability of objective quantitative endpoints. We refer to the method as the rapid susceptibility assay (RSA). RSA is based on substrate utilization by fungi in the presence of antifungal drugs. Substrate uptake is determined by a colorimetric method, which can be scored by analysis of data obtained from a microplate reader. Variables evaluated in the development of the RSA included inoculum size, incubation period, and efficacy with different classes of antifungal drugs and different yeast isolates. With the rapidly available and quantitative endpoints of the RSA, correlation of MICs and therapeutic drug doses can be evaluated more successfully than they can be evaluated by existing assays.
Improved Sensitivity of PCR for Diagnosis of Human Granulocytic Ehrlichiosis Using
epank1
Genes of
Ehrlichia phagocytophila
-Group Ehrlichiae
Authors: Walls Jennifer J. , Caturegli Patrizio , Bakken Johan S. , Asanovich Kristin M. , Dumler J. Stephen 
Published: May 2021

ABSTRACT

The agent of human granulocytic ehrlichiosis (HGE),
Ehrlichia phagocytophila
, and
Ehrlichia equi
probably comprise variants of a single
Ehrlichia
species now called the
Ehrlichia phagocytophila
genogroup. These variants share a unique 153-kDa protein antigen with ankyrin repeat motifs encoded by the
epank1
gene. The
epank1
gene was investigated as an improved target for PCR diagnosis of HGE compared with the currently used 16S rRNA gene target. Primers for
epank1
flanking a region that spans part of the 5′ ankyrin repeat coding region and part of the unique 3′ region were synthesized. Blood samples from 31 patients with suspected HGE who were previously tested by 16S rRNA gene (16S) PCR and indirect immunofluorescent antibody test (IFA) were retrospectively tested with the
epank1
primers. Eleven patients were 16S PCR positive and had a seroconversion detected by IFA (group A), 10 patients were 16S PCR negative but had a seroconversion detected by IFA (group B), and 10 patients were 16S PCR negative and seronegative (group C). Ten of the 11 group A patients were
epank1
PCR positive, all 10 of the group B patients were
epank1
PCR positive, and all of the PCR-negative and seronegative patients (group C) were
epank1
PCR negative. The
epank1
primers are more sensitive than the previously used 16S rRNA gene primers and therefore may be more useful in diagnostic testing for HGE.
Improved Amplification of Genital Human Papillomaviruses
Authors: Gravitt P. E. , Peyton C. L. , Alessi T. Q. , Wheeler C. M. , Coutlée F. , Hildesheim A. , Schiffman M. H. , Scott D. R. , Apple R. J. 
Published: May 2021

ABSTRACT

Genital human papillomaviruses (HPVs) are commonly detected from clinical samples by consensus PCR methods. Two commonly used primer systems, the MY09-MY11 (MY09/11) primers and the GP5+-GP6+ (GP5+/6+) primers, amplify a broad spectrum of HPV genotypes, but with various levels of sensitivity among the HPV types. Analysis of the primer-target sequence homology for the MY09/11 primers showed an association between inefficient amplification of HPV types and the number and position of mismatches, despite accommodation of sequence variation by inclusion of degenerate base sites. The MY09/11 primers were redesigned to increase the sensitivity of amplification across the type spectrum by using the same primer binding regions in the L1 open reading frame. Sequence heterogeneity was accommodated by designing multiple primer sequences that were combined into an upstream pool of 5 oligonucleotides (PGMY11) and a downstream pool of 13 oligonucleotides (PGMY09), thereby avoiding use of degenerate bases that yield irreproducible primer syntheses. The performance of the PGMY09-PGMY11 (PGMY09/11) primer system relative to that of the standard MY09/11 system was evaluated with a set of 262 cervicovaginal lavage specimens. There was a 91.5% overall agreement between the two systems (kappa = 0.83;
P
< 0.001). The PGMY09/11 system appeared to be significantly more sensitive than the MY09/11 system, detecting an additional 20 HPV-positive specimens, for a prevalence of 62.8% versus a prevalence of 55.1% with the MY09/11 system (McNemar's χ
2
= 17.2;
P
< 0.001). The proportion of multiple infections detected increased with the PGMY09/11 system (40.0 versus 33.8% of positive infections). HPV types 26, 35, 42, 45, 52, 54, 55, 59, 66, 73, and MM7 were detected at least 25% more often with the PGMY09/11 system. The PGMY09/11 primer system affords an increase in type-specific amplification sensitivity over that of the standard MY09/11 primer system. This new primer system will be useful in assessing the natural history of HPV infections, particularly when the analysis requires HPV typing.
A Polymorphic Multigene Family Encoding an Immunodominant Protein from
Babesia microti
Authors: Homer M. J. , Bruinsma E. S. , Lodes M. J. , Moro M. H. , Telford S. , Krause P. J. , Reynolds L. D. , Mohamath R. , Benson D. R. , Houghton R. L. , Reed S. G. , Persing D. H. 
Published: May 2021

ABSTRACT

Human babesiosis in the United States is caused predominantly by
Babesia microti
, a tick-transmitted blood parasite. Improved testing methods for the detection of infection with this parasite are needed, since asymptomatic
B. microti
infection represents a potential threat to the blood supply in areas where
B. microti
is endemic. We performed immunoscreening of an expression library of genomic DNA from a human isolate of
B. microti
(strain MN1). Among 17 unique immunoreactive clones, we identified 9 which represent a related family of genes with little sequence homology to other known sequences but with an architecture resembling that of several surface proteins of
Plasmodium
. Within this family, a tandem array of a degenerate six-amino-acid repeat (SEAGGP, SEAGWP, SGTGWP, SGTVGP) was found in various lengths between relatively well conserved segments at the N and C termini. In order to examine within-clone variation, we developed a PCR protocol for direct recovery of a specific
bmn1-6
homologue directly from 30 human blood isolates, 4 corresponding hamster isolates, and 5 geographically corresponding
Peromyscus leucopus
(white-footed mouse) isolates. Isolates from the hamsters had the same sequences as those found in the corresponding human blood, suggesting that genetic variation of
bmn1-6
does not occur during passage. However, clones from different patients were often substantially different from each other with regard to the number and location of the degenerate repeats within the
bmn1-6
homologue. Moreover, we found that strains that were closely related geographically were also closely related at the sequence level; nine patients, all from Nantucket Island, Mass., harbored clones that were indistinguishable from each other but that were distinct from those found in other northeastern or upper midwestern strains. We conclude that considerable genetic and antigenic diversity exists among isolates of
B. microti
from the United States and that geographic clustering of subtypes may exist. The nature of the
bmn1-6
gene family suggests a mechanism of antigenic variation in
B. microti
that may occur by recombination, differential expression, or a combination of both mechanisms.
Molecular Cloning and Characterization of the 120-Kilodalton Protein Gene of
Ehrlichia canis
and Application of the Recombinant 120-Kilodalton Protein for Serodiagnosis of Canine Ehrlichiosis
Authors: Yu Xue-jie , McBride Jere W. , Diaz C. Marcela , Walker David H. 
Published: May 2021

ABSTRACT

The 120-kDa outer membrane protein (p120) is a potential adhesin of
Ehrlichia chaffeensis
, and recombinant p120 is very useful for serodiagnosis of human monocytotropic ehrlichiosis. The analogous gene of p120 in
Ehrlichia canis
was cloned, sequenced, and expressed. Like the
E. chaffeensis
p120, the
E. canis
p120 contains tandem repeat units. However, neither the repeat number nor the amino acid sequences in the repeats are identical in the two
Ehrlichia
species. The repeat units are hydrophilic and by probability analysis are predicted to be surface exposed in both species. The repeat regions of the p120s of the two species have common amino acid sequences that are predicted to be surface exposed. The overall amino acid sequence of the
E. canis
p120 is 30% homologous to that of
E. chaffeensis
p120. Protein immunoblotting demonstrated that the recombinant
E. canis
p120 reacted with convalescent sera from dogs with canine ehrlichiosis. These results indicate that the recombinant p120 is a potential antigen for the serodiagnosis of canine ehrlichiosis.
Distribution and Antigenicity of Fibronectin Binding Proteins (SfbI and SfbII) of
Streptococcus pyogenes
Clinical Isolates from the Northern Territory, Australia
Authors: Goodfellow Alison M. , Hibble Megan , Talay Susanne R. , Kreikemeyer Bernd , Currie Bart J. , Sriprakash Kadaba S. , Chhatwal Gursharan S. 
Published: May 2021

ABSTRACT

Fibronectin binding proteins play an important role in the adherence and invasion of group A streptococci (GAS). Genotypically distinct GAS isolates were screened for the presence and expression of two streptococcal fibronectin binding protein genes,
sfbI
and
sfbII
. Of the tested strains, 64 and 36% were shown to harbor and express the
sfbI
and
sfbII
genes, respectively. All
sfbII
-positive strains tested were also positive for
sfbI
, but only 28% of the
sfbII
-negative strains were positive for
sfbI
. High levels of immunoglobulin G antibodies to both SfbI and SfbII were found in sera from 80 subjects with defined streptococcal infections.
Microascus cinereus
(Anamorph
Scopulariopsis
) Brain Abscess in a Bone Marrow Transplant Recipient
Authors: Baddley John W. , Moser Stephen A. , Sutton Deanna A. , Pappas Peter G. 
Published: May 2021

ABSTRACT

We report the first documented case of brain abscess due to the dematiaceous fungus
Microascus cinereus
, an organism common in soil and stored grain.
M. cinereus
was isolated from brain abscess material from a bone marrow transplant recipient. The patient responded well to treatment by amphotericin B lipid complex, itraconazole, and a craniotomy but later died from secondary complications caused by graft-versus-host disease.
Mink Lung Cells and Mixed Mink Lung and A549 Cells for Rapid Detection of Influenza Virus and Other Respiratory Viruses
Authors: Huang Yung T. , Turchek Brian M. 
Published: May 2021

ABSTRACT
Mink lung cells were more sensitive than the commonly used MDCK or pRhMK cells for rapid detection of influenza virus A from clinical specimens. Mixed Mv1Lu and A549 cells in a single shell vial were synergistic for detection of influenza virus A and were as sensitive as individual cells for detection of other respiratory viruses.
Pulsed-Field Gel Electrophoresis-Based Molecular Comparison of
Vibrio cholerae
O1 Isolates from Domestic and Imported Cases of Cholera in Japan
Authors: Arakawa Eiji , Murase Toshiyuki , Matsushita Shigeru , Shimada Toshio , Yamai Shiro , Ito Takeshi , Watanabe Haruo 
Published: May 2021

ABSTRACT

Sixty-seven
Vibrio cholerae
O1 El Tor isolates (36 domestic and 31 imported) were classified into 19 subtypes by
Not
I- and
Sfi
I-digested pulsed-field gel electrophoresis. Twenty-five of 36 domestic and 4 imported isolates were assigned to a
Not
I-A1–
Sfi
I-A1 subtype, suggesting that this pulse type is widely distributed in Asia and Japan.
Aspergillus fumigatus
Antigen Detection in Sera from Patients at Risk for Invasive Aspergillosis
Authors: Chumpitazi Bernabé F. F. , Pinel Claudine , Lebeau Bernadette , Ambroise-Thomas Pierre , Grillot Renee 
Published: May 2021

ABSTRACT

We have developed an inhibition enzyme immunoassay (inhibition-EIA) to monitor for the occurrence of invasive aspergillosis (IA) in sera from 45 immunocompromised (IC) patients. The test uses rabbit polyclonal antibodies and a mixture of components from
Aspergillus fumigatus
, containing three predominant antigens with molecular weights of 18,000, 33,000, and 56,000. Circulating antigens were found in five of seven proven cases of IA due to
A. fumigatus
. In two of the five positive cases, antigenemia was detected with inhibition-EIA earlier than with X ray or other biological methods. No antigens were detected in the sera from two patients with proven IA due to
Aspergillus flavus
and
Aspergillus terreus
nor in the sera from four patients with probable IA. Circulating antigens were not detected in the control group, composed of 30 healthy adult blood donors. Four of the 32 at-risk patients examined, though they displayed no definite evidence of IA, gave a positive result in this test. The sensitivity, specificity, and positive predictive value of inhibition-EIA were 71.4, 94.4, and 71.2%, respectively. The data were compared with those obtained by a latex agglutination assay of galactomannan (GM) that was positive in only one patient with probable IA. The higher sensitivity obtained by inhibition-EIA may well be due to its ability to detect circulating antigens other than GM in the sera of IC patients with IA. Detecting these antigens may improve the diagnosis of IA, as they may serve as markers of this infection.
Natural Infection of Domestic Goats withEhrlichia chaffeensis
Authors: Dugan Vivien G. , Little Susan E. , Stallknecht David E. , Beall Ashley D. 
Published: May 2021

ABSTRACTThirty-eight domestic goats from an area ofEhrlichia chaffeensisendemicity were tested for antibodies reactive toE. chaffeensisand forE. chaffeensis-specific 16S rRNA gene fragments by an indirect fluorescent antibody test and a nested PCR assay, respectively. Twenty-eight of 38 (73.7%) goats had antibodies reactive toE. chaffeensis(≥1:128), and 6 of 38 (15.8%) goats were positive by diagnostic PCR;E. chaffeensiswas isolated in cell culture from one goat. Our data indicate that goats in areas of endemicity are naturally exposed to and infected withE. chaffeensis.
A Clonal Subpopulation of
Leptospira interrogans
Sensu Stricto Is the Major Cause of Leptospirosis Outbreaks in Brazil
Authors: Pereira M. M. , Matsuo M. G. S. , Bauab A. R. , Vasconcelos S. A. , Moraes Z. M. , Baranton G. , Saint Girons I. 
Published: May 2021

ABSTRACT

Leptospira
is a highly diverse genus comprising many species and serogroups in Brazil as well as all over the world. However, a study by arbitrarily primed PCR of 44 leptospiral strains isolated from humans during three different outbreaks in Brazilian urban centers reveals that 43 of 44 isolates exhibit very similar fingerprints. Analysis of these isolates indicates that they belong to a clonal subpopulation of
Leptospira interrogans
sensu stricto.
Peritonitis Due to
Roseomonas fauriae
in a Patient Undergoing Continuous Ambulatory Peritoneal Dialysis
Authors: Bibashi Evangelia , Sofianou Danai , Kontopoulou Konstantina , Mitsopoulos Efstathios , Kokolina Elisabeth 
Published: May 2021

ABSTRACT

Roseomonas
is a newly described genus of pink-pigmented, nonfermentative, gram-negative bacteria that have been recognized as a cause of human infections.
Roseomonas fauriae
is a species rarely isolated from clinical specimens. We report the first known case of peritonitis caused by
R. fauriae
in a patient receiving continuous ambulatory peritoneal dialysis.
Isolation of
Pantoea agglomerans
in Two Cases of Septic Monoarthritis after Plant Thorn and Wood Sliver Injuries
Authors: De Champs C. , Le Seaux S. , Dubost J. J. , Boisgard S. , Sauvezie B. , Sirot J. 
Published: May 2021

ABSTRACT

Arthritis after plant injury is often apparently aseptic. We report two cases due to
Pantoea agglomerans
. In one case, the bacterium was isolated only from the pediatric blood culture media, BACTEC Peds Plus, monitored in BACTEC 9240, and not from the other media inoculated with the joint fluid. This procedure could help improve the diagnosis of septic arthritis.
Streptococcus bovis
Meningitis in an Infant
Authors: Grant Russell J. , Whitehead Terence R. , Orr James E. 
Published: May 2021

ABSTRACT

Streptococcus bovis
is a nonenterococcal, group D streptococcus which has been identified as a causative agent for serious human infections, including endocarditis, bacteremia, and septic arthritis. Several cases of adult
S. bovis
meningitis have been reported, usually in association with underlying disease. In the neonatal period, it is an uncommon agent of meningitis. We report, to our knowledge, the third documented case of neonatal
S. bovis
meningitis in the English language literature. As in the previous cases, this neonate showed no anatomical or congenital immunologic lesion which might be expected to predispose the patient to meningitis. Sequencing of the 16S ribosomal DNA gene was performed and a new PCR test was used to secure a more reliable identification of the strain.
Neutralization Assay for Human Group C Rotaviruses Using a Reverse Passive Hemagglutination Test for Endpoint Determination
Authors: Fujii Ritsushi , Kuzuya Mitsutaka , Hamano Masako , Ogura Hajime , Yamada Masao , Mori Tadashige 
Published: May 2021

ABSTRACT
A novel neutralization assay for human group C rotavirus (CHRV) was developed by using a reverse passive hemagglutination (RPHA) test for endpoint determination. In this assay, the neutralization (N)-RPHA test, serial twofold dilutions of sera were mixed with a solution of CHRV that yielded an RPHA test titer of 8 at 3 days after infection. The mixtures were incubated at 37°C for 1 h and were inoculated onto CaCo-2 cell monolayers in a 96-well microplate. Maintenance medium containing 100 μg of pancreatin per ml was placed in each well. The plate was sealed with sticky plastic film and was incubated at 37°C for 3 days under continuous rotation. Then, the RPHA test titer of each well was determined. The neutralization titer was expressed as the reciprocal of the maximum dilution of the serum that exhibited a fourfold (75%) or greater reduction in the RPHA test titer (8 to 2 or less). Seroconversion of neutralizing antibody was demonstrated by this method in four sets of paired serum specimens from patients with diarrheal disease caused by CHRV. The seroprevalence of CHRV in the general population in Okayama Prefecture was 26.8% by immunofluorescence and 25.5% by the N-RPHA test. The N-RPHA test described here is the first system used to assay for a neutralization antibody against CHRV and is applicable in both clinical and epidemiological settings.
New Monoclonal Antibody Specific for
Candida albicans
Germ Tube
Authors: Marot-Leblond Agnes , Grimaud Linda , Nail Sandrine , Bouterige Sandrine , Apaire-Marchais Veronique , Sullivan Derek J. , Robert Raymond 
Published: May 2021

ABSTRACT

Hydrophobic components of the germ tube of the dimorphic pathogenic fungus
Candida albicans
were used as immunogens to prepare monoclonal antibodies (MAbs). Among the resulting MAbs, one (MAb 16B1-F10) was shown by indirect immunofluorescence to be specific to the surface of the mycelium phase of the
C. albicans
and
C. stellatoidea
species. No labeling of any other genera and
Candida
species tested was observed, including
C. dubliniensis
, a newly described species which has many phenotypic similarities to
C. albicans
. This phase-specific epitope resides on a protein moiety. The molecular mass of the antigen released by Zymolyase digestion was determined by gel filtration and ranges from 25 to 166 kDa. The antigen was also shown to be highly hydrophobic. This anti-
C. albicans
cell wall surface-specific MAb may be a good candidate for use in tests for the rapid differentiation of the two closely related species
C. albicans
and
C. dubliniensis
.
Revealing microstructural properties of shocked and tectonically deformed zircon from the Vredefort impact structure: Raman spectroscopy combined with SEM microanalyses
Authors: Kovaleva Elizaveta , Zamyatin Dmitry A. 
Published: May 2021

ABSTRACT
Finite deformation patterns of accessory phases can indicate the tectonic regime and deformation history of the host rocks and geological units. In this study, tectonically deformed, seismically deformed, and shocked zircon grains from a granite sample from the core of the Vredefort impact structure were analyzed in situ, using a combination of Raman spectroscopy, backscatter electron (BSE) imaging, electron backscattered diffraction (EBSD) mapping, electron probe microanalyses (EPMA), energy-dispersive X-ray spectroscopy (EDS) qualitative chemical mapping, and cathodoluminescence (CL) imaging. We aimed to reveal the effects of marginal grain-size reduction, planar deformation bands (PDBs), and shock microtwins on the crystal structure and microchemistry of zircon.
Deformation patterns such as PDBs, microtwins, and subgrains did not show any significant effect on zircon crystallinity/metamictization degree or on the CL signature. However, the ratio of Raman band intensities B1g (1008 cm–1) to Eg (356 cm–1) slightly decreased within domains with low misorientation. The ratio values were affected in shocked grains, particularly in twinned domains with high misorientation. B1g/Eg ratio mapping combined with metamictization degree mapping (full width at half maximum of B1g peak) suggest the presence of shock deformation features in zircon; however, due to the lower spatial resolution of the method, they must be used in combination with the EBSD technique. Additionally, we discovered anatase, quartz, goethite, calcite, and hematite micro-inclusions in the studied zircon grains, with quartz and anatase specifically being associated with strongly deformed domains of shocked zircon crystals.
Shock deformation microstructures in xenotime from the Spider impact structure, Western Australia
Authors: Cox* Morgan A. , Cavosie Aaron J. , Poelchau Michael , Kenkmann Thomas , Bland Phil A. , Miljković Katarina 
Published: May 2021

ABSTRACT
The rare earth element–bearing phosphate xenotime (YPO4) is isostructural with zircon, and therefore it has been predicted that xenotime forms similar shock deformation microstructures. However, systematic characterization of the range of microstructures that form in xenotime has not been conducted previously. Here, we report a study of 25 xenotime grains from 10 shatter cones in silicified sandstone from the Spider impact structure in Western Australia. We used electron backscatter diffraction (EBSD) in order to characterize deformation and microstructures within xenotime. The studied grains preserve multiple sets of planar fractures, lamellar {112} deformation twins, high-angle planar deformation bands (PDBs), partially recrystallized domains, and pre-impact polycrystalline grains. Pressure estimates from microstructures in coexisting minerals (quartz and zircon) allow some broad empirical constraints on formation conditions of ~10–20 GPa to be placed on the observed microstructures in xenotime; at present, more precise formation conditions are unavailable due to the absence of experimental constraints. Results from this study indicate that the most promising microstructures in xenotime for recording shock deformation are lamellar {112} twins, polycrystalline grains, and high-angle PDBs. The {112} deformation twins in xenotime are likely to be a diagnostic shock indicator, but they may require a different stress regime than that of {112} twinning in zircon. Likewise, polycrystalline grains are suggestive of impact-induced thermal recrystallization; however, in contrast to zircon, the impact-generated polycrystalline xenotime grains here appear to have formed in the solid state, and, in some cases, they may be difficult to distinguish from diagenetic xenotime with broadly similar textures.