bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Nested PCR for Detection of
Cryptococcus neoformans
in Cerebrospinal Fluid
Authors: Rappelli Paola , Are Riccardo , Casu Giuseppe , Fiori Pier Luigi , Cappuccinelli Piero , Aceti Antonio 
Published: December 2019

ABSTRACT

We report the development of a nested-PCR-based assay for the detection of
Cryptococcus neoformans
in cerebrospinal fluid. The specificity and sensitivity of the test were assessed. The technique was then applied to 40 cerebrospinal fluid samples. We obtained positive reactions for all 21 clinical samples from patients who had been previously diagnosed as having cryptococcal meningitis by conventional techniques and negative reactions for all 19 negative controls. Nested PCR is here compared with other diagnostic methods currently used in patients’ follow-up exams during anticryptococcal therapy.
Comparison of Two Rapid Whole-Blood Tests for
Helicobacter pylori
Infection in Chinese Patients
Authors: Leung Wai Keung , Chan Francis K. L. , Falk Matthew S. , Suen Roamy , Sung Joseph J. Y. 
Published: December 2019

ABSTRACT

Consecutive Chinese patients undergoing endoscopy for dyspepsia were tested for
Helicobacter pylori
infection by two rapid whole-blood tests: FlexPack HP (Abbott Laboratories) and Helisal One-Step (Cortecs Diagnostics). Biopsy-based tests (rapid urease test and histology) and the [
13
C]urea breath test were used as the “gold standard.” One hundred sixty-one consecutive patients were studied, and 88 (54.7%) were confirmed to have
H. pylori
infection. The sensitivities, specificities, and positive and negative predictive values were 81.8%, 83.6% (
P
= 0.008), 85.7% (
P
= 0.04), and 79.2% for FlexPack HP and 84.1%, 63.0% (
P
= 0.008), 73.3% (
P
= 0.047), and 76.7% for Helisal One-Step, respectively.
Peptide-Based OspC Enzyme-Linked Immunosorbent Assay for Serodiagnosis of Lyme Borreliosis
Authors: Mathiesen Marianne J. , Christiansen Michael , Hansen Klaus , Holm Arne , Åsbrink Eva , Theisen Michael 
Published: December 2019

ABSTRACT

Sera from 210 patients with Lyme borreliosis (LB) were studied by an enzyme-linked immunosorbent assay (ELISA) based on a synthetic peptide (pepC10) comprising the C-terminal 10-amino-acid residues of OspC of
Borrelia burgdorferi
. We found that 36.3 and 45.0% of the serum samples from patients with erythema migrans (EM) and neuroborreliosis (NB), respectively, displayed immunoglobulin M (IgM) anti-pepC10 reactivities, while these samples rarely (≤8%) displayed IgG antibody reactivities. Sera from patients with acrodermatitis chronica atrophicans did not contain anti-pepC10 antibodies. The diagnostic performance of this newly developed peptide ELISA was compared with those of an ELISA based on the full-length recombinant OspC protein (rOspC) and a commercially available ELISA based on the
B. burgdorferi
flagellum (Fla). The sensitivity of the IgM pepC10 ELISA was slightly lower (P < 0.04) than that of the rOspC ELISA for EM patients (36.3 versus 43.8%), while there was no difference for NB patients (45.0 versus 48.0%). However, the optical density values obtained by the pepC10 ELISA were generally higher than those obtained by the rOspC ELISA, leading to a significantly better quantitative discrimination between seropositive patients with NB and controls (P < 0.008). The specificity of the pepC10 ELISA was similar to those of the rOspC ELISA and the Fla ELISA for relevant controls including patients with syphilis and mononucleosis. Although the overall diagnostic sensitivity of the Fla ELISA was superior, 8.8 and 12.0% of the EM and NB patients, respectively, were antibody positive only by the pepC10 ELISA. Thus, use of a diagnostic test for LB based on the detection of IgM antibodies to pepC10 and Fla has increased sensitivity for the diagnosis of early LB.
16S Ribosomal DNA Typing for Identification of Pathogens in Patients with Bacterial Keratitis
Authors: Knox C. Michele , Cevellos Vickey , Dean Deborah 
Published: December 2019

ABSTRACT
The identification of pathogens in patients with bacterial keratitis remains problematic because standard diagnostic tests are negative for 40 to 60% of patients. A cross-sectional study was undertaken to determine if PCR and sequence analysis of 16S ribosomal DNA (rDNA) could be used to detect bacterial pathogens in patients with keratitis. Corneal specimens were collected for culture and rDNA typing. Variable segments of each rDNA specimen were amplified by PCR, sequenced, and aligned with the sequences in GenBank. Eleven patients had microbiologically documented bacterial keratitis, while 17 patients had keratitis due to other causes. Nine (82%) of 11 bacterial keratitis patients were PCR positive; each sequencing result matched the culture results. Seventeen (100%) patients with nonbacterial keratitis were PCR negative. Our data suggest that 16S rDNA typing holds promise as a rapid alternative to culture for identifying pathogens in patients with bacterial keratitis.
Evaluation of Hemagglutinin Protein-Specific Immunoglobulin M for Diagnosis of Measles by an Enzyme-Linked Immunosorbent Assay Based on Recombinant Protein Produced in a High-Efficiency Mammalian Expression System
Authors: Bouche Fabienne B. , Brons Nicolaas H. C. , Houard Sophie , Schneider Francois , Muller Claude P. 
Published: December 2019

ABSTRACT
Recombinant hemagglutinin (H) of the measles virus (MV) expressed in a mammalian high-expression system based on the Semliki Forest virus replicon was used in an enzyme-linked immunosorbent assay (ELISA) for the detection of specific immunoglobulin M (IgM) and IgG in patients with acute-phase measles. One hundred twelve serum specimens from 70 patients with measles were analyzed. Case definition was based on a commercial IgM ELISA that utilizes MV-infected cells (MV-ELISA) (Enzygnost; Behring Diagnostics); the clinical criteria of the Centers for Disease Control and Prevention (Atlanta, Ga.); and/or the increase in hemagglutinin test titers, neutralization test titers, and levels of MV-specific IgG whenever paired sera were available. The initial time courses of the IgM signal after the onset of rash are similar in the H- and MV-ELISAs. On days 0 to 19, both ELISAs detected IgM in 67 of 68 (98.5%) sera. Average maximal levels of IgM seem to persist, however, about 10 days longer in the MV-ELISA (up to day 25) than in the H-ELISA (day 15). From days 20 to 29 and 30 to 59, the H-ELISA detected only 64.3 (9 of 14) and 19.2% (5 of 26), respectively, of sera that were IgM positive by MV-ELISA. At least up to day 30, the performance of the H-ELISA seemed to be similar to that reported for commercial ELISAs based on whole MV. Our results demonstrate that MV H-specific IgM can be used to diagnose most measles cases from a single serum specimen collected within 19 days after the onset of rash and that the recombinant protein used in this study is suitable for this purpose.
Differentiation between
Streptococcus gallolyticus
Strains of Human Clinical and Veterinary Origins and
Streptococcus bovis
Strains from the Intestinal Tracts of Ruminants
Authors: Devriese Luc A. , Vandamme Peter , Pot Bruno , Vanrobaeys Mia , Kersters Karel , Haesebrouck Freddy 
Published: December 2019

ABSTRACT

Strains formerly identified as
Streptococcus bovis
were allotted to two groups by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of whole-cell proteins. Strains from humans with infections, mostly patients with endocarditis, and strains from pigeons with septicemia clustered with the recently described species
Streptococcus gallolyticus
. The original
S. bovis
type strain and strains exclusively from ruminants formed the second cluster. The findings indicate that
S. gallolyticus
is more likely to be involved in human and animal infections than
S. bovis
. Growth characteristics and several biochemical reactions were found to be useful in the differentiation of
S. gallolyticus
from
S. bovis.
Rubella Virus and Chronic Joint Disease: Is There an Association?
Authors: Bosma Trent J. , Etherington John , O’Shea Siobhan , Corbett Karen , Cottam Fiona , Holt Lennox , Banatvala J. E. , Best Jennifer M. 
Published: December 2019

ABSTRACT

Synovial fluid samples and/or biopsies from 79 patients with various chronic inflammatory joint diseases or traumatic joint injury were tested for rubella virus (RV) in order to confirm or refute results from other studies that suggested RV as a cause of chronic inflammatory joint disease. Sixty-eight of the 72 patients tested had RV antibodies. RV RNA was detected by reverse transcription-PCR in the synovial fluid cells from two patients. RV was also isolated by cell culture from the synovial fluid of one of these two patients. This patient was a 42-year-old female with common variable immune deficiency and
Mycoplasma hominis
arthritis, while the other was a 68-year-old female with rheumatoid arthritis. While these results fail to confirm that RV is associated with chronic inflammatory joint disease, they suggest that RV may persist within a joint and be reactivated when cell-mediated immunity is suppressed.
Genetic Variability among Group A and Group B Respiratory Syncytial Viruses in a Children’s Hospital
Authors: Coggins Wanicha Buraphacheep , Lefkowitz Elliot J. , Sullender Wayne M. 
Published: December 2019

ABSTRACT

Respiratory syncytial (RS) viruses isolated over three epidemic periods in a children’s hospital in the United States were analyzed. The viruses (
n
= 174) were characterized as to major antigenic group (group A or B) by a PCR-based assay. Group A RS viruses were dominant the first 2 years, followed by a year with group B dominance (ratios of group A to group B viruses for epidemic periods, 56/4 for 1993–1994, 42/3 for 1994–1995, and 19/50 for 1995–1996). Genetic variability within the groups was assessed by restriction fragment analysis of PCR products; 79 isolates were also analyzed by nucleotide sequence determination of a variable region of the glycoprotein G gene. Among the group A RS virus isolates, this G-protein variable region had amino acid differences of as great as 38%. The G-protein amino acids of the group A viruses differed by up to 31% from the G-protein amino acids of a prototype (A2) group A virus. Among the group B RS virus G proteins, amino acid differences were as great as 14%. The G-protein amino acids of the group B viruses differed by up to 27% from the G-protein amino acids of a prototype (18537) group B virus. The group A and group B RS viruses demonstrated genetic variability between years and within individual years. Phylogenetic analysis revealed that there were multiple evolutionary lineages among both the group A and group B viruses. Among the recent group B isolates, variability was less than that seen for the group A viruses. However, comparisons to prototype strains revealed that the group B RS viruses may vary more extensively than was observed over the 3 years studied in the present investigation.
Standardization of the Human Cytomegalovirus Antigenemia Assay by Means of In Vitro-Generated pp65-Positive Peripheral Blood Polymorphonuclear Leukocytes
Authors: Gerna Giuseppe , Percivalle Elena , Torsellini Maria , Revello M. Grazia 
Published: December 2019

ABSTRACT
We generated in vitro human cytomegalovirus (HCMV) pp65-positive polymorphonuclear leukocytes (PMN) resembling those detected in vivo, following cocultivation of PMN from healthy donors and wild-type HCMV-infected endothelial cells or fibroblasts. After purification, PMN are suitable for preparation of cytospots which can be used for the antigenemia assay. Cytospin preparations containing a predetermined number of in vitro-generated pp65-positive PMN were used to test some of the major parameters involved in performing the antigenemia assay. The results showed or confirmed that (i) formalin fixation followed by permeabilization is the best fixation procedure developed to date, (ii) the test performance levels provided by different pools of pp65-specific monoclonal antibodies may be significantly different, and (iii) long-term storage (for an unlimited time) is best achieved by keeping fixed slides at −80°C, whereas short-term storage (for up to 1 month) is best achieved by keeping unfixed slides at room temperature. This finding signifies that slides can be shipped all over the world at room temperature. In conclusion, the newly developed procedure for in vitro generation of pp65-positive PMN will provide the basis for standardization of the HCMV antigenemia assay and development of quality control programs.
Adherence Patterns and Adherence-Related DNA Sequences in
Escherichia coli
Isolates from Children with and without Diarrhea in São Paulo City, Brazil
Authors: Gomes Tânia A. T. , Vieira Mônica A. M. , Abe Cecilia M. , Rodrigues Daleth , Griffin Patricia M. , Ramos Sônia R. T. S. 
Published: December 2019

ABSTRACT

The correlation between various adherence patterns and adherence-related DNA sequences in
Escherichia coli
isolates from 1- to 4-year-old children with and without diarrhea in São Paulo, Brazil, was evaluated. A total of 1,801 isolates obtained from 200 patients and 200 age-matched controls were studied. The adherence patterns found were classified as diffuse, aggregative, aggregative in a 6-h assay, aggregative predominantly in coverslips, localized, localized-like, and noncharacteristic. In general, the DNA sequences used as probes showed excellent specificities (>93%), but their sensitivities varied. Thus, the results of bioassays and assays with DNA probes normally used to search for adherent
E. coli
did not correlate well, and the best method for the identification of these organisms in the clinical research setting remains controversial. Isolates presenting diffuse adherence or hybridizing with the related
daaC
probe, or both, were by far the most frequent in patients (31.5, 26.0, and 23.0%, respectively), followed by isolates presenting aggregative adherence or hybridizing with the related EAEC probe, or both (21.5, 13.0, and 10.5%, respectively). None of the different combinations of adherence patterns and adherence-related DNA sequences found were associated with acute diarrhea.
Molecular Epidemiology of Ampicillin-Resistant Non-β-Lactamase-Producing
Haemophilus influenzae
Authors: Gazagne Louise , Delmas Catherine , Bingen Edouard , Dabernat Henri 
Published: December 2019

ABSTRACT

Resistance to ampicillin without β-lactamase production is not a frequent occurrence among
Haemophilus influenzae
strains. This kind of resistance is encountered in unencapsulated strains isolated from bronchial secretions and ear, nose, and throat specimens and is exceptional in
H. influenzae
type b. We studied 29 of these strains from various areas in France and 2 reference strains. Strains were compared by using ribotyping, arbitarily primed PCR with two primers, and pulsed-field gel electrophoresis. Each technique enabled the identification of 20 to 23 different patterns among the 31 strains. The combination of the different patterns for the strains obtained by the different techniques provided 27 distinct profiles. According to these results, it seems that the clonal propagation of these resistant strains does not occur.
Sequence Variation within Three Important Cytomegalovirus Gene Regions in Isolates from Four Different Patient Populations
Authors: Zweygberg Wirgart Benita , Brytting Maria , Linde Annika , Wahren Britta , Grillner Lena 
Published: December 2019

ABSTRACT
We determined the nucleotide (nt) and amino acid (aa) heterogeneities of three distinct regions of the human cytomegalovirus (CMV) genome for 46 low-passage CMV isolates from four different patient populations (congenitally infected infants, children attending day-care centers, renal transplant recipients, and human immunodeficiency virus-infected individuals) and for two laboratory strains (CMV Ad169 and Towne). The gene regions for the major immediate-early (MIE) exon 4 gene (nt positions 1702 to 1982, aa positions 152 to 244), the DNA polymerase gene (nt positions 2797 to 3046, aa positions 713 to 795), and the glycoprotein B (gB) gene (nt positions 1698 to 1884, aa positions 567 to 628) were sequenced. The sequence information was used to design sets of nested PCR primers directed against the most highly conserved regions identified. MIE was the most variable gene region compared to the variability of the DNA polymerase and gB gene regions. Comparison of the sequences of all 46 isolates with that of Ad169 revealed nt and aa sequence homologies of 87.9 and 87.2%, respectively, within the MIE gene compared to 92.8 and 100% homologies, respectively, within the DNA polymerase gene and 93 and 95.2% homologies, respectively, within the gB gene. Within the MIE gene, compared to the Ad169 nt sequence the homology at the nt level among isolates obtained from children attending day-care centers was high (96.4%), while it was lower (90%) among isolates obtained from the other three patient populations. Preliminary results of a nested PCR with oligonucleotide primers selected from the DNA polymerase gene region with a low level of nt sequence variation indicates that primers selected from this region might be more powerful for use in PCR than primers selected from the MIE gene region.
Disseminated Aspergillosis Caused by
Aspergillus ustus
in a Patient Following Allogeneic Peripheral Stem Cell Transplantation
Authors: Iwen Peter C. , Rupp Mark E. , Bishop Michael R. , Rinaldi Michael G. , Sutton Deanna A. , Tarantolo Stefano , Hinrichs Steven H. 
Published: December 2019

ABSTRACT

The first case of disseminated aspergillosis caused by
Aspergillus ustus
in an allogeneic peripheral stem cell transplant patient is described. The patient, a 46-year-old female with a history of myelodysplastic syndrome, underwent high-dose chemotherapy and total body irradiation prior to transplantation. She was released from the hospital 49 days posttransplant (p.t.) in a stable condition with an absolute neutrophil count (ANC) of 2,700 cells per μl. Multiple antimicrobial agents, including itraconazole (ITR), were prescribed during hospitalization and at the time of discharge. Three days after discharge, the patient was readmitted with hemorrhagic cystitis, persistent thrombocytopenia, and bilateral pulmonary consolidation, although no fever was present. The ANC at the time of readmission was 3,500. Upon detection of a pulmonary nodule (day 67 p.t.), a bronchoalveolar lavage was performed; the lavage fluid was positive for both cytomegalovirus and parainfluenza virus and negative for fungus. The patient was placed on ganciclovir. A biopsy specimen from a leg lesion also noted on day 67 p.t. revealed septate hyphae consistent with
Aspergillus
species, and a culture subsequently yielded
Aspergillus ustus
. Confirmation detection of
A. ustus
was made by demonstration of characteristic reproductive structures with the presence of Hülle cells. On day 67 p.t., ITR was discontinued and liposomal amphotericin B (AMB) was initiated. The patient’s condition worsened, and she died 79 days p.t. At the time of autopsy, septate hyphae were present in heart, thyroid, and lung tissues, with lung tissue culture positive for
A. ustus
. In vitro susceptibility testing indicated probable resistance to AMB but not to ITR. This case supports the need for the development of rapid methods to determine antifungal susceptibility.
Mink Lung Epithelial Cells: Unique Cell Line That Supports Influenza A and B Virus Replication
Authors: Schultz-Cherry Stacey , Dybdahl-Sissoko Naomi , McGregor Martha , Hinshaw Virginia S. 
Published: December 2019

ABSTRACT
We have demonstrated for the first time that a mink lung epithelial cell line (Mv1Lu) supports the replication of influenza A and B viruses, including the recently isolated H5N1 avian and human Hong Kong strains, to titers comparable to those in MDCK cells. These results suggest that Mv1Lu cells might serve as an alternative system for the isolation and cultivation of influenza A and B viruses and may be useful for vaccine development.
Effectiveness of Resins in Neutralizing Antibiotic Activities in Bactec Plus Aerobic/F Culture Medium
Authors: Spaargaren J. , van Boven C. P. A. , Voorn G. P. 
Published: December 2019

ABSTRACT
Incorporating resins in blood culture media can effectively reduce the activities of several antibiotics. It was shown that the activities of some generally used antibiotics decreased by 80 to 90% within 2 h in Bactec Plus Aerobic/F resin-containing culture medium. Bactec vials containing resins were still found to be positive for bacteria when antibiotics were present. The addition of β-lactamase shortened the detection time irrespective of the presence of resins.
Application of Subtype-Specific Monoclonal Antibodies for Rapid Detection and Identification of Influenza A and B Viruses
Authors: Ueda Minoru , Maeda Akiko , Nakagawa Naoko , Kase Tetsuo , Kubota Ritsuko , Takakura Hikaru , Ohshima Atsushi , Okuno Yoshinobu 
Published: December 2019

ABSTRACT
We established a rapid method for the identification of influenza A and B virus strains: the peroxidase-antiperoxidase (PAP) staining method with two subtype-specific murine monoclonal antibodies, C179 (H1 and H2 specific) and F49 (H3 specific), and an anti-influenza B virus rabbit polyclonal serum. The types and subtypes of 160 strains were examined, and 158 strains were identified to be the same by the hemagglutination-inhibition (HI) test and the PAP method. In contrast to the results by the HI test, two strains were revealed to be a mixture of two subtypes (H1 and H3) by the PAP method, which was confirmed by plaque cloning. We further analyzed clinical specimens by the PAP method by directly inoculating specimens into Madin-Darby canine kidney cells in microplates. After 40 h of incubation, the types and subtypes of viruses in 52 of 152 specimens were clearly identified. Since the reactivities of the two monoclonal antibodies are not influenced by the antigenic drift of influenza virus, the newly developed method should be applicable not only for rapid diagnosis but also for the epidemiological study of influenza.
Serotype-Specific Identification of Polioviruses by PCR Using Primers Containing Mixed-Base or Deoxyinosine Residues at Positions of Codon Degeneracy
Authors: Kilpatrick David R. , Nottay Baldev , Yang Chen-Fu , Yang Su-Ju , Da Silva Edson , Peñaranda Silvia , Pallansch Mark , Kew Olen 
Published: December 2019

ABSTRACT
We have developed a method for determining the serotypes of poliovirus isolates by PCR. Three sets of serotype-specific antisense PCR-initiating primers (primers seroPV1A, seroPV2A, and seroPV3A) were designed to pair with codons of VP1 amino acid sequences that are conserved within but that differ across serotypes. The sense polarity primers (primers seroPV1S, seroPV2S, and seroPV3S) matched codons of more conserved capsid sequences. The primers contain mixed-base and deoxyinosine residues to compensate for the high rate of degeneracy of the targeted codons. The serotypes of all polioviruses tested (48 vaccine-related isolates and 110 diverse wild isolates) were correctly identified by PCR with the serotype-specific primers. None of the genomic sequences of 49 nonpolio enterovirus reference strains were amplified under equivalent reaction conditions with any of the three primer sets. These primers are useful for the rapid screening of poliovirus isolates and for determining the compositions of cultures containing mixtures of poliovirus serotypes.