bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Plasmid and Chromosomal DNA of Multidrug-Resistant
Salmonella enterica
Serovar Typhi from Asia
Authors: Mirza S. , Kariuki S. , Mamun K. Z. , Beeching N. J. , Hart C. A. 
Published: December 2019

ABSTRACT

Molecular analysis of chromosomal DNA from 193 multidrug-resistant (MDR)
Salmonella enterica
serovar Typhi isolates from 1990 to 1995 from Pakistan, Kuwait, Malaysia, Bangladesh, and India produced a total of five major different pulsed-field gel electrophoresis (PFGE) patterns. Even within a particular country MDR
S. enterica
serovar Typhi DNA was found to be in different PFGE groups. Similar self-transferable 98-MDa plasmids belonging to either incompatibility group incHI1 or incHI1/FIIA were implicated in the MDR phenotype in
S. enterica
serovar Typhi isolates from all the locations except Quetta, Pakistan, where the majority were of incFIA. A total of five different PFGE genotypes with six different plasmids, based on incompatibility and restriction endonuclease analysis groups, were found among these MDR
S. enterica
serovar Typhi isolates.
Comparison of a Baculovirus-Based VP2 Enzyme Immunoassay (EIA) to an
Escherichia coli
-Based VP1 EIA for Detection of Human Parvovirus B19 Immunoglobulin M and Immunoglobulin G in Sera of Pregnant Women
Authors: Jordan Jeanne A. 
Published: December 2019

ABSTRACT

A split-sample study was conducted to evaluate the clinical performance of an enzyme immunoassay that detects the human parvovirus B19 virus (B19V) immunoglobulin M (IgM) or IgG in the sera of pregnant women. The initial study compared a baculovirus-expressed VP2 enzyme immunoassay (BVP2 EIA) (Biotrin International Inc., Dublin, Ireland) with the currently available and commonly used
Escherichia coli
-expressed VP1 enzyme immunoassay (EVP1 EIA) (MRL Diagnostics, Cypress, Calif.). There was a high degree of agreement between the two assays in the detection of IgM antibodies (283 of 307 [92.2%]) or IgG antibodies (279 of 311 [89.7%]), with the majority of discrepancies (IgM, 17 of 24 [71%]; IgG, 16 of 31 [50%]) being due to equivocal data obtained with the EVP1 EIA. Specimens with discordant BVP2 EIA and EVP1 EIA results (23 of 24 IgM and 32 of 32 IgG results) were analyzed further by baculovirus-based VP1 immunofluorescence assays (BVP1 IFAs) (Biotrin International). The BVP2 EIA and BVP1 IFA results for 20 of 23 and 28 of 32 specimens for IgM and IgG, respectively, were concordant. In contrast, the EVP1 EIA and BVP1 IFA data for only 3 of 23 and 4 of 32 specimens for IgM and IgG, respectively, were in agreement, despite the fact that the same capsid antigen was used. Both the BVP2 EIAs and BVP1 IFAs utilize a conformational viral capsid antigen, while the EVP1 EIA uses a denatured viral capsid antigen. In conclusion, the BVP2 EIAs produced far fewer equivocal results for IgM and IgG, correlating more closely to the confirmatory BVP IFAs, than did the EVP1 EIAs and proved to be more accurate for detecting B19V antibodies in the sera of pregnant women.
Development and Clinical Evaluation of a Recombinant-Antigen-Based Cytomegalovirus Immunoglobulin M Automated Immunoassay Using the Abbott AxSYM Analyzer
Authors: Maine G. T. , Stricker R. , Schuler M. , Spesard J. , Brojanac S. , Iriarte B. , Herwig K. , Gramins T. , Combs B. , Wise J. , Simmons H. , Gram T. , Lonze J. , Ruzicki D. , Byrne B. , Clifton J. D. , Chovan L. E. , Wachta D. , Holas C. , Wang D. , Wilson T. , Tomazic-Allen S. , Clements M. A. , Wright G. L. , Lazzarotto T. , Ripalti A. , Landini M. P. 
Published: December 2019

ABSTRACT

A new microparticle enzyme immunoassay (MEIA), the Cytomegalovirus (CMV) Immunoglobulin M (IgM) test, was developed on the Abbott AxSYM analyzer. This test uses recombinant CMV antigens derived from portions of four structural and nonstructural proteins of CMV: pUL32 (pp150), pUL44 (pp52), pUL83 (pp65), and pUL80a (pp38). A total of 1,608 specimens from random volunteer blood donors (
n
= 300), pregnant women (
n
= 1,118), transplant recipients (
n
= 6), and patients with various clinical conditions and disease states (
n
= 184) were tested during development and evaluation of this new assay. In a preliminary clinical evaluation we tested specimens collected prospectively from pregnant women (
n
= 799) and selected CMV IgM-positive archived specimens from pregnant women (
n
= 39). The results from the new CMV IgM immunoassay were compared to the results of a consensus interpretation of the results obtained with three commercial CMV IgM immunoassays. The results for specimens with discordant results were resolved by a CMV IgM immunoblot assay. The relative sensitivity, specificity, and agreement for the AxSYM CMV IgM assay were 94.29, 96.28, and 96.19%, respectively, and the resolved sensitivity, specificity, and agreement were 95.83, 97.47, and 97.37%, respectively. We also tested serial specimens from women who experienced seroconversion or a recent CMV infection during gestation (
n
= 17) and potentially cross-reactive specimens negative for CMV IgM antibody by the consensus tests (
n
= 184). The AxSYM CMV IgM assay was very sensitive for the detection of CMV IgM during primary CMV infection, as shown by the detection of CMV IgM at the same time as or just prior to the detection of CMV IgG. Specimens from individuals with lupus (
n
= 16) or parvovirus B19 infection (
n
= 6) or specimens containing hyper IgM (
n
= 9), hyper IgG (
n
= 8), or rheumatoid factor (
n
= 55) did not cross-react with the AxSYM assay. One specimen each from individuals infected with Epstein-Barr virus (
n
= 26), measles virus (
n
= 10), herpes simplex virus (
n
= 12), or varicella-zoster virus (
n
= 13) infection, one specimen from an influenza vaccinee (
n
= 14), and one specimen containing antinuclear antibody cross-reacted with the assay. The overall rate of cross-reactivity of the specimens with the assay was 3.3% (6 of 184). The AxSYM CMV IgM assay is a sensitive and specific assay for the detection of CMV-specific IgM.
Epidemiological Study of
pap
Genes among Diarrheagenic or Septicemic
Escherichia coli
Strains Producing CS31A and F17 Adhesins and Characterization of Pap
31A
Fimbriae
Authors: Bertin Yolande , Girardeau Jean-Pierre , Darfeuille-Michaud Arlette , Martin Christine 
Published: December 2019

ABSTRACT

The association of the
pap
operon with the CS31A and F17 adhesins was studied with 255
Escherichia coli
strains isolated from calves, lambs, or humans with diarrhea. The three classes of PapG adhesin with different receptor binding preferences were also screened. The
pap
operon was associated with 50 and 36% of human strains that produced CS31A and ovine strains that produced F17, respectively. Among the bovine isolates, the
pap
operon was detected in 61% of the CS31A-positive isolates and 72% of the strains that produce both CS31A and F17. The class II adhesin gene was present in bovine (20%) and ovine (71%) isolates. Both class II and III adhesins were genetically associated with 36% of the human strains. The highest prevalence of the
pap
operon was observed among
E. coli
strains that produce additional adhesins involved in the binding of bacteria to intestinal cells. Among the bovine isolates, the reference strain for CS31A and F17c was found to be positive for the
pap
operon. Phenotypic and genotypic characterizations were undertaken. Pap
31A
appeared as fine and flexible fimbriae surrounding the bacteria but did not mediate adhesion to calf intestinal villi. Pap
31A
production was optimal with bacteria cultured on minimal growth media and repressed by addition of exogenous leucine. The deduced amino acid sequence of the PapA
31A
structural subunit showed 57 to 97% identity with the different P-related structural subunits produced by
E. coli
strains isolated from pigs with septicemia or humans with urinary tract infections. None of the three
papG
allelic variants was detected, but a homologous
papG
gene was present in the chromosome of strain 31A.
Emergence of Resistance of
Candida albicans
to Clotrimazole in Human Immunodeficiency Virus-Infected Children: In Vitro and Clinical Correlations
Authors: Pelletier René , Peter Joanne , Antin Cynthia , Gonzalez Corina , Wood Lauren , Walsh Thomas J. 
Published: December 2019

ABSTRACT

Oropharyngeal candidiasis (OPC) is a common opportunistic infection in human immunodeficiency virus (HIV)-infected patients and other immunocompromised hosts. Clotrimazole troches are widely used in the treatment of mucosal candidiasis. However, little is known about the potential contribution of clotrimazole resistance to the development of refractory mucosal candidiasis. We therefore investigated the potential emergence of resistance to clotrimazole in a prospectively monitored HIV-infected pediatric population receiving this azole. Adapting the National Committee for Clinical Laboratory Standards M27-A reference method for broth antifungal susceptibility testing of yeasts to clotrimazole, we compared MICs in macrodilution and microdilution assays. We further analyzed the correlation between these in vitro findings and the clinical response to antifungal therapy. One isolate from each of 87 HIV-infected children was studied by the macrodilution and microdilution methods. Two inoculum sizes were tested by the macrodilution method (10
3
and 10
4
CFU/ml) in order to assess the effect of inoculum size on clotrimazole MICs. The same isolates also were tested using a noncolorimetric microdilution method. Clotrimazole concentrations ranged from 0.03 to 16 μg/ml. Readings were performed after incubation for 24 and 48 h at 35°C. For 62 (71.2%) of 87 clinical isolates, the MICs were low (≤0.06 μg/ml). The MIC for 90% of the strains tested was 0.5 μg/ml, and the highest MIC was 8 μg/ml. There was no significant difference between MICs at the two inoculum sizes. There was 89% agreement (±1 tube) between the microdilution method at 24 h and the macrodilution method at 48 h. If the MIC of clotrimazole for an isolate of
C. albicans
was ≥0.5 μg/ml, there was a significant risk (
P
< 0.001) of cross-resistance to other azoles: fluconazole, ≥64 μg/ml (relative risk [RR] = 8.9); itraconazole, ≥1 μg/ml (RR = 10). Resistance to clotrimazole was highly associated with clinically overt failure of antifungal azole therapy. Six (40%) of 15 patients for whom the clotrimazole MIC was ≥0.5 μg/ml required amphotericin B for refractory mucosal candidiasis versus 4 (5.5%) of 72 for whom the MIC was <0.5 μg/ml (
P
= 0.001; 95% confidence interval = 2.3 to 22; RR = 7.2). These findings suggest that an interpretive breakpoint of 0.5 μg/ml may be useful in defining clotrimazole resistance in
C. albicans
. The clinical laboratory's ability to determine MICs of clotrimazole may help to distinguish microbiologic resistance from the other causes of refractory OPC, possibly reducing the usage of systemic antifungal agents. We conclude that resistance to clotrimazole develops in isolates of
C. albicans
from HIV-infected children, that cross-resistance to other azoles may develop concomitantly, and that this resistance correlates with refractory mucosal candidiasis.
Evaluation of Phenotypic Markers for Selection and Identification of
Candida dubliniensis
Authors: Tintelnot Kathrin , Haase Gerhard , Seibold Michael , Bergmann Frank , Staemmler Maren , Franz Tatjana , Naumann Dieter 
Published: December 2019

ABSTRACT

Candida dubliniensis
is often associated with
C. albicans
in cultures. Easy-to-perform selective isolation procedures for these closely related species do not exist. Therefore, we evaluated previously described discriminatory phenotypic markers for
C. dubliniensis
. A total of 150 oral rinses from human immunodeficiency virus (HIV)-infected patients were cultured on CHROMagar Candida. Dark green colonies described as being indicative of
C. dubliniensis
and other green colonies, 170 in total, were isolated. Chlamydospore formation, intracellular β-
d
-glucosidase activity, ability to grow at 42°C, carbohydrate assimilation pattern obtained by the API ID 32C, and Fourier transform infrared (FT-IR) spectroscopy were used for phenotypic characterization. Sequencing of the 5′ end of the nuclear large-subunit (26S) ribosomal DNA gene was used for definitive species identification for
C. dubliniensis. C. dubliniensis
was found in 34% of yeast-colonized HIV-infected patients. The color of the colonies on CHROMagar Candida proved to be insufficient for selecting
C. dubliniensis
, since only 30 of 53 proven
C. dubliniensis
isolates showed a dark green color in primary cultures. The described typical chlamydospore formation can give only some indication of
C. dubliniensis
. The assimilation pattern proved to be insufficient to discriminate
C. dubliniensis
from
C. albicans
. All
C. dubliniensis
strains showed no or highly restricted growth at 42°C and a lack of β-
d
-glucosidase activity. Unfortunately, atypical
C. albicans
strains can also exhibit these phenotypic traits. FT-IR spectroscopy combined with hierarchical clustering proved to be as reliable as genotyping for discriminating the two species.
Long-Term Persistence of a Discotheque-Associated Invasive
Neisseria meningitidis
Group C Strain as Proven by Pulsed-Field Gel Electrophoresis and
porA
Gene Sequencing
Authors: Riesbeck Kristian , Orvelid-Mölling Paula , Fredlund Hans , Olcén Per 
Published: December 2019

ABSTRACT

A cluster of a
Neisseria meningitidis
serogroup C strain causing invasive disease was investigated. Five out of seven cases were associated with a particular discotheque. The strains were indistinguishable, as revealed by pulsed-field gel electrophoresis and sequencing of variable regions of the
porA
gene, but caused strikingly different clinical presentations during 5 months.
Molecular Typing and Exopolysaccharide Biosynthesis of
Burkholderia cepacia
Isolates from a Portuguese Cystic Fibrosis Center
Authors: Richau João A. , Leitão Jorge H. , Correia Manuela , Lito Luís , Salgado Maria José , Barreto Celeste , Cescutti Paola , Sá-Correia Isabel 
Published: December 2019

ABSTRACT

This work describes the first epidemiological survey of
Burkholderia cepacia
involved in pulmonary infections among the Portuguese population with cystic fibrosis (CF) who attended the major CF treatment Center in Lisbon at Sta. Maria Hospital from 1995 to the end of 1997. The characterization of the genomic relatedness of the isolates was based on the analysis of their ribopatterns (with
Eco
RI) followed by construction of a ribotype-based phylogenetic tree. This study was complemented with macrorestriction fragment analysis by pulsed-field gel electrophoresis. After optimization of the solid growth medium, we found that exopolysaccharide (EPS) production by
B. cepacia
CF isolates is not as rare a phenomenon as was thought before; indeed, 70% of the isolates examined were EPS producers.
Detection of and Discrimination between Gram-Positive and Gram-Negative Bacteria in Intraocular Samples by Using Nested PCR
Authors: Carroll Nora M. , Jaeger Emma E. M. , Choudhury Sarah , Dunlop Anthony A. S. , Matheson Melville M. , Adamson Peter , Okhravi Narciss , Lightman Susan 
Published: December 2019

ABSTRACT
A nested PCR protocol has been developed for the detection of and discrimination between 14 species of gram-positive and -negative bacteria in samples of ocular fluids. First-round PCR with pan-bacterial oligonucleotide primers, based on conserved sequences of the 16S ribosomal gene, was followed by a gram-negative-organism-specific PCR, which resulted in a single 985-bp amplification product, and a multiplex PCR which resulted in two PCR products: a 1,025 bp amplicon (all bacteria) and a 355 bp amplicon (gram-positive bacteria only). All products were detected by gel electrophoresis. The sensitivity of the assay was between 10 fg and 1 pg of bacterial DNA, depending on the species tested, equivalent to between 24 and 4 live bacteria spiked in water. The identification was complete in 3.5 h. The molecular techniques were subsequently applied to four samples of intraocular fluid, (three vitreous and one aqueous) from three patients with clinical signs of bacterial endophthalmitis (test samples) and two samples of vitreous from a patient with chronic intraocular inflammation (control samples). In all culture-positive samples (two of three vitreous and one of one aqueous), a complete concordance was observed between molecular methods and culture results. PCR correctly identified the gram stain classification of the organisms. The bacterial etiology was also identified in a culture-negative patient with clinical history and signs highly suggestive of bacterial endophthalmitis. Furthermore, control samples from a patient with chronic intraocular inflammation remained PCR negative. In summary, this protocol has demonstrated potential as a rapid diagnostic test in confirming the diagnosis of infection and also determining the Gram status of bacteria with high specificity and sensitivity.
Immunoblot Analysis of Humoral Immune Response to
Helicobacter pylori
in Children with and without Duodenal Ulcer
Authors: Rocha Gifone A. , Oliveira Andreia M. R. , Queiroz Dulciene M. M. , Carvalho Anfrisina S. T. , Nogueira Ana M. M. F. 
Published: December 2019

ABSTRACT

Several studies have demonstrated that enzyme-linked immunosorbent assay is not a sensitive and specific method to diagnose
Helicobacter pylori
infection in children, especially in the younger ones. Since serum immune response can also be determined by immunoblotting and it permits the detection of antibodies to virulence factors such as CagA and VacA, we evaluated the accuracy of a commercial immunoblotting test to diagnose
H. pylori
infection and to assess the humoral immune response to different
H. pylori
antigens in 122 children who underwent upper gastrointestinal endoscopy. The presence of
H. pylori
was determined in antral biopsy specimens by culture, preformed urease test, and histological analysis.
H. pylori
was identified by microbiological and histopathological methods in 66 children (including all of the 21 who had duodenal ulcer). Antibodies to
H. pylori
were detected in 63 infected children and in 8 noninfected ones. The sensitivity, specificity, and positive and negative predictive values of the immunoblotting test were 95.5, 85.7, 88.7, and 94.1%, respectively. The number of immunoreactive bands increased with age (
P
= 0.003), and the bands of 35 kDa (
P
= 0.013); 89 kDa, the VacA antigen (
P
= 0.001); and 116 kDa, the CagA antigen (
P
= 0.00004) were more frequently observed in older children. The frequency of the bands of 89 kDa (
P
= 0.001) and 116 kDa (
P
= 0.03) was higher in children with duodenal ulcer than in
H. pylori
-positive children without the disease. In conclusion, the immunoblotting test appears to be useful for the diagnosis of
H. pylori
infection in children, even in the younger ones.
Sequence Diversity of the
Escherichia coli
H7
fliC
Genes: Implication for a DNA-Based Typing Scheme for
E. coli
O157:H7
Authors: Wang Lei , Rothemund Deborah , Curd Heather , Reeves Peter R. 
Published: December 2019

ABSTRACT

Flagellar (H) antigens are mostly encoded by genes at the
fliC
locus in
E. coli
. We have sequenced 11 H7
fliC
genes from
Escherichia coli
strains that belong to seven O serotypes. These sequences, together with those of nine other H7
fliC
genes (from strains of three different O serotypes) sequenced recently (S. D. Reid, R. K. Selander, and T. S. Whittam, J. Bacteriol. 181:153–160, 1999), include 10 different sequences. The differences between these 10 sequences range from 0.06 to 3.12%. By comparison with other
E. coli
flagellin genes, we have identified primer length sequences specific for H7 genes in general and others specific for H7 genes of O157 and O55 strains: the specificity was confirmed by PCR testing the type strains for all 53
E. coli
H types. We have previously identified genes specific for the
E. coli
O157 antigen, and use of the combination of O157- and H7-specific primers allows the sensitive and rapid detection of O157:H7
E. coli
strains, which cause the majority of hemorrhagic colitis cases.
Development of a Fluorescence Polarization-Based Diagnostic Assay for Equine Infectious Anemia Virus
Authors: Tencza Sarah Burroughs , Islam Kazi R. , Kalia Vandana , Nasir Mohammad S. , Jolley Michael E. , Montelaro Ronald C. 
Published: December 2019

ABSTRACT
The control of equine infectious anemia virus (EIAV) infections of horses has been over the past 20 years based primarily on the identification and elimination of seropositive horses, predominantly by a standardized agar gel immunodiffusion (AGID) assay in centralized reference laboratories. This screening for EIAV-seropositive horses has been to date hindered by the lack of a rapid diagnostic format that can be easily employed in the field. We describe here the development of a rapid solution-phase assay for the presence of serum antibodies to EIAV based on fluorescence polarization (FP) (patent pending). Peptides derived from antigenic regions of EIAV core and envelope proteins were initially screened for their utility as probes in an FP assay to select the best peptide antigen candidates. The FP assay was optimized to detect the presence of EIAV-specific antibodies by a change in the FP of a fluorescein-labeled immunoreactive peptide diagnostic antigen. The most sensitive and specific peptide probe was a peptide corresponding to the immunodominant region of the EIAV transmembrane protein, gp45. This probe was tested for its reactivity in the optimized FP assay with 151 AGID-positive horse sera and 106 AGID-negative serum samples. The results of these studies demonstrated that the FP assay reactivity correlated with reported AGID results in 106 of 106 negative serum samples (100% specificity) and in 135 of 151 positive serum samples (89.4% sensitivity). The FP assay was also found to have a very low background reactivity and to readily detect antibodies produced early in infection (≤3 weeks postinfection). The developed EIAV FP assay is rapid (5 to 20 min) and simple to perform and is equally suitable for use both in the field and in the diagnostic laboratory, thus providing the basis of an improved commercial diagnostic assay for EIAV infection of horses.
Performance of the ImmunoCard STAT! E. coli O157:H7 Test for Detection of
Escherichia coli
O157:H7 in Stools
Authors: Mackenzie Andrew , Orrbine Elaine , Hyde Lucie , Benoit Michelle , Chan Frank , Park Choong , Alverson Jessica , Lembke Amy , Hoban Daryl , Kennedy William 
Published: December 2019

ABSTRACT

ImmunoCard STAT! E. coli O157:H7 (Meridian Diagnostics, Inc., Cincinnati, Ohio) is a novel rapid (10-min) test for the presence of
Escherichia coli
O157:H7 in stools. The test may be performed either directly on stool specimens or on an overnight broth culture of stool. In a multicenter prospective study, 14 of 14 specimens positive by culture for
E. coli
O157:H7 were positive by the ImmunoCard STAT! O157:H7 test, and there were no false positives from 263 culture-negative specimens. In a retrospective study, the test was positive in 339 (81%) of 417 stored culture-positive specimens and the specificity was 95% (98 of 103 specimens). No false positives were associated with alternate stool pathogens. The ImmunoCard STAT! O157:H7 test has high sensitivity and specificity.