bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Identification of
Candida
Species with Species-Specific DNA Probes
Authors: Elie Cheryl M. , Lott Timothy J. , Reiss Errol , Morrison Christine J. 
Published: December 2019

ABSTRACT

Rapid identification of
Candida
species has become more important because of an increase in infections caused by species other than
Candida albicans
, including species innately resistant to azole antifungal drugs. We previously developed a PCR assay with an enzyme immunoassay (EIA) format to detect amplicons from the five most common
Candida
species by using universal fungal primers and species-specific probes directed to the ITS2 region of the gene for rRNA. We designed probes to detect seven additional
Candida
species (
C. guilliermondii
,
C. kefyr
,
C. lambica
,
C. lusitaniae
,
C. pelliculosa
,
C. rugosa
, and
C. zeylanoides
) included in the API 20C sugar assimilation panel, five probes for species not identified by API 20C (
C. haemulonii
,
C. norvegica
,
C. norvegensis
,
C. utilis
, and
C. viswanathii
), and a probe for the newly described species
C. dubliniensis
, creating a panel of 18
Candida
species probes. The PCR-EIA correctly identified multiple strains of each species tested, including five identified as
C. albicans
by the currently available API 20C database but determined to be
C. dubliniensis
by genotypic and nonroutine phenotypic characteristics. Species identification time was reduced from a mean of 3.5 days by conventional identification methods to 7 h by the PCR-EIA. This method is simple, rapid, and feasible for identifying
Candida
species in clinical laboratories that utilize molecular identification techniques and provides a novel method to differentiate the new species,
C. dubliniensis
, from
C. albicans
.
Use of the BacT/Alert Blood Culture System for Culture of Sterile Body Fluids Other than Blood
Authors: Bourbeau Paul , Riley Julie , Heiter Barbara J. , Master Ron , Young Carol , Pierson Carl 
Published: December 2019

ABSTRACT

Studies have demonstrated that large-volume culture methods for sterile body fluids other than blood increase recovery compared to traditional plated-medium methods. BacT/Alert is a fully automated blood culture system for detecting bacteremia and fungemia. In this study, we compared culture in BacT/Alert standard aerobic and anaerobic bottles, BacT/Alert FAN aerobic and FAN anaerobic bottles, and culture on routine media for six specimen types, i.e., continuous ambulatory peritoneal dialysate (CAPD), peritoneal, amniotic, pericardial, synovial, and pleural fluids. Specimen volumes were divided equally among the three arms of the study. A total of 1,157 specimens were tested, with 227 significant isolates recovered from 193 specimens. Recovery by method was as follows: standard bottles, 186 of 227 (82%); FAN bottles, 217 of 227 (96%); and routine culture, 184 of 227 (81%). The FAN bottles recovered significantly more gram-positive cocci (
P
< 0.001),
Staphylococcus aureus
(
P
= 0.003), coagulase-negative staphylococci (
P
= 0.008), gram-negative bacilli (
P
< 0.001),
Enterobacteriaceae
(
P
= 0.005), and total organisms (
P
< 0.001) than the routine culture. There were no significant differences in recovery between the standard bottles and the routine culture. The FAN aerobic bottle recovered significantly more gram-positive cocci (
P
< 0.001),
S. aureus
isolates (
P
< 0.001), coagulase-negative staphyococci (
P
= 0.003), and total organisms (
P
< 0.001) than the standard aerobic bottle, while the FAN anaerobic bottle recovered significantly more gram-positive cocci (
P
< 0.001),
S. aureus
isolates (
P
< 0.001),
Enterobacteriaceae
(
P
= 0.03), and total organisms (
P
< 0.001) than the standard anaerobic bottle. For specific specimen types, significantly more isolates were recovered from the FAN bottles compared to the routine culture for synovial (
P
< 0.001) and CAPD (
P
= 0.004) fluids. Overall, the FAN bottles were superior in performance to both the standard bottles and the routine culture for detection of microorganisms from the types of sterile body fluids included in this study.
Endocarditis and Aortal Embolization Caused by
Aspergillus terreus
in a Patient with Acute Lymphoblastic Leukemia in Remission: Diagnosis by Peripheral-Blood Culture
Authors: Schett G. , Casati B. , Willinger B. , Weinländer G. , Binder T. , Grabenwöger F. , Sperr W. , Geissler K. , Jäger U. 
Published: December 2019

ABSTRACT

Disseminated infection with
Aspergillus terreus
is a rare disease that affects only the immunocompromised host. We report a case of systemic infection with
A. terreus
resulting in endocarditis, aortic embolization, and splenic infarction in a patient with acute lymphoblastic leukemia. Diagnosis through peripheral blood culture, lack of pulmonary involvement, and onset of disease during complete remission from leukemia constitute uncommon features of this case.
Distribution of Hepatitis B Virus Genotypes in Two Different Pediatric Populations from Argentina
Authors: Mbayed V. A. , López J. L. , Telenta P. F. S. , Palacios G. , Badía I. , Ferro A. , Galoppo C. , Campos R. 
Published: December 2019

ABSTRACT
Differences in pathogenesis and the probability of becoming a chronic carrier depend on the age at which hepatitis B virus (HBV) infection is acquired, ranging from 82% in infants less than 6 months of age to 15 to 30% in older children. HBV genotypes from 22 pediatric patients from two areas that differ in prevalence have been determined. Phylogenetic analysis shows a clear difference between the genotype distribution in Buenos Aires, a low-prevalence area, and that found in Gualeguay, Entre Rı́os, a high-prevalence area. While the analysis allocated the sequences in the Buenos Aires group to genotypes A (36%), D (9%), and F (55%), the Gualeguay group presented exclusively genotype A isolates with very low nucleotide divergence, which suggests a strong founder viral population. The high prevalence of genotype F in the Buenos Aires group and its high intragroup heterogeneity agree with the American origin of this genotype.
Rapid and Sensitive Assay for Detection of Enterotoxigenic
Bacteroides fragilis
Authors: Zhang Guangming , Weintraub Andrej 
Published: December 2019

ABSTRACT

Bacteroides fragilis
is an obligatory anaerobic, gram-negative bacterium found among the normal intestinal flora of humans. Enterotoxigenic strains of
B. fragilis
(ETBF) have been associated with diarrheal diseases in humans and animals. The enterotoxin of ETBF induces fluid changes in ligated intestinal segments and cytotoxic response in HT29/C1 cells. By using a pair of monoclonal antibodies (MAbs; MAb C3 and MAb 4H8) specific for the lipopolysaccharide of
B. fragilis
, an assay based on immunomagnetic separation (IMS) in combination with PCR (IMS-PCR) was developed. After DNA extraction, a 294-bp fragment was amplified. The specificity of the IMS-PCR assay was evaluated by adding previously isolated and confirmed ETBF strains to normal fecal samples. All fecal samples to which ETBF strains were added were positive, showing a 100% specificity. The spiked fecal samples were also used for evaluation of the sensitivity of the assay. The detection limit was found to be ∼50 CFU/g of feces. By this method 10 clinical fecal samples (5 from patients with diarrhea and 5 from healthy controls) were examined. The results of PCR were in accordance with the results of the HT29/C1 cell assay for all samples. The minimum time to retrieval of the final result by the IMS-PCR method is 36 h. The proposed IMS-PCR assay is rapid and sensitive for the direct detection of ETBF in stool samples.
Differentiation of
Campylobacter jejuni
Serotype O19 Strains from Non-O19 Strains by PCR
Authors: Misawa Naoaki , Allos Ban Mishu , Blaser Martin J. 
Published: December 2019

ABSTRACT

Guillain-Barré syndrome (GBS), a neurologic disease characterized by acute paralysis, is frequently preceded by
Campylobacter jejuni
infection. Serotype O19 strains are overrepresented among GBS-associated
C. jejuni
isolates. We previously showed that all O19 strains tested were closely related to one another by randomly amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism analyses. RAPD analysis demonstrated a 1.4-kb band in all O19 strains tested but in no non-O19 strains. We cloned this O19-specific band; nucleotide sequence analysis revealed a truncated open reading frame with significant homology to DNA gyrase subunit B (
gyrB
) of
Helicobacter pylori
. PCR using the random primer and a primer specific for
gyrB
showed that in non-O19 strains, the random primer did not recognize the downstream
gyrB
binding site. The regions flanking each of the random primer binding sites were amplified by degenerate PCR for further sequencing. Although the random primer had several mismatches with the downstream
gyrB
binding site, a single nucleotide polymorphism 6 bp upstream from the 3′ terminus was found to distinguish O19 and non-O19 strains. PCR using 3′-mismatched primers based on this polymorphism was designed to differentiate O19 strains from non-O19 strains. When a total of 42 (18 O19 and 24 non-O19) strains from five different countries were examined, O19 strains were distinguishable from non-O19 strains in each case. This PCR method should permit identification of O19
C. jejuni
strains.
Armored RNA Technology for Production of Ribonuclease-Resistant Viral RNA Controls and Standards
Authors: Pasloske Brittan L. , Walkerpeach Cindy R. , Obermoeller R. Dawn , Winkler Matthew , DuBois Dwight B. 
Published: December 2019

ABSTRACT

The widespread use of sensitive assays for the detection of viral and cellular RNA sequences has created a need for stable, well-characterized controls and standards. We describe the development of a versatile, novel system for creating RNase-resistant RNA. “Armored RNA” is a complex of MS2 bacteriophage coat protein and RNA produced in
Escherichia coli
by the induction of an expression plasmid that encodes the coat protein and an RNA standard sequence. The RNA sequences are completely protected from RNase digestion within the bacteriophage-like complexes. As a prototype, a 172-base consensus sequence from a portion of the human immunodeficiency virus type 1 (HIV-1)
gag
gene was synthesized and cloned into the packaging vector used to produce the bacteriophage-like particles. After production and purification, the resulting HIV-1 Armored RNA particles were shown to be resistant to degradation in human plasma and produced reproducible results in the Amplicor HIV-1 Monitor assay for 180 days when stored at −20°C or for 60 days at 4°C. Additionally, Armored RNA preparations are homogeneous and noninfectious.
Comparison of Two Measures of Human Immunodeficiency Virus (HIV) Type 1 Load in HIV Risk Groups
Authors: Lyles Cynthia M. , Vlahov David , Farzadegan Homayoon , Astemborski Jacquie , Margolick Joseph B. , Masters Beth A. , Schroeder Jennifer , Quinn Thomas C. 
Published: December 2019

ABSTRACT

Levels of viral burden were compared across risk group and gender populations among 485 human immunodeficiency virus type 1 (HIV-1)-infected participants consisting of 190 male injection drug users (IDUs), 92 female IDUs, and 203 homosexual men. Viral burden was quantified by a microculture technique to determine cell-associated infectious units per 10
6
peripheral blood mononuclear cells (IUPM) and by reverse transcriptase PCR (Amplicor) to determine plasma HIV RNA levels. Adjusting for CD4
+
cell count, females had a lower infectious HIV load than all males combined (0.33 log
10
lower;
P
= 0.004), and homosexual men had a 0.29 log
10
higher infectious viral load than all IDUs combined (
P
= 0.001). For HIV RNA levels, females had lower levels than males (0.19 log
10
lower;
P
= 0.04), but no differences were observed by risk group. After controlling for percent CD4
+
cells, no differences were found by risk group for either assay, but females still had a 0.25 log
10
lower infectious viral load than males (
P
= 0.04) and a viral RNA load similar to that of males (
P
= 0.25). The correlation between infectious viral load and HIV RNA load was 0.58 overall, which did not differ by gender or risk group. Our data suggest that differences in viral load may exist by gender and that any differences observed by risk group are driven predominantly by gender or percent CD4
+
cell differences. These data also confirm a moderate correlation between cell-associated infectious viral load and plasma HIV RNA load, which appears to be similar by gender and across risk groups.
Incidental Finding of
Myxobolus
Spores (Protozoa: Myxozoa) in Stool Samples from Patients with Gastrointestinal Symptoms
Authors: Boreham R. E. , Hendrick S. , O’Donoghue P. J. , Stenzel D. J. 
Published: December 2019

ABSTRACT

Myxozoan spores were detected in fecal samples from three patients presenting with abdominal pain and/or diarrhea. The spores were identical to those of
Myxobolus plectroplites
, a previously described pathogen from the freshwater fish
Plectroplites ambiguus
. All patients had recently eaten fish caught from local waters, and frozen fillets of such fish were found to be infected with
M. plectroplites
cysts. The passage of spores unchanged through the alimentary tract suggests they were incidental findings unrelated to clinical symptoms, especially since other enteric pathogens were present in two patients.
Detection of Specific Antibodies in Saliva during Dengue Infection
Authors: Cuzzubbo Andrea J. , Vaughn David W. , Nisalak Ananda , Suntayakorn Saroj , Aaskov John , Devine Peter L. 
Published: December 2019

ABSTRACT

Saliva was collected prospectively from patients presenting with suspected dengue infection 4 to 8 days after the onset of symptoms and assayed by a commercial dengue immunoglobulin M (IgM) and IgG capture enzyme-linked immunosorbent assay (ELISA) (PanBio Dengue Duo ELISA). Laboratory diagnosis was based on virus isolation and on hemagglutination inhibition (HAI) assay and an in-house IgM and IgG capture ELISA. With a positive result defined as either salivary IgM or IgG levels above the cutoff value, an overall sensitivity of 92% was obtained for both primary- and secondary-dengue patients (22 of 24), while no patients with non-flavivirus infections (
n
= 11) and no healthy laboratory donors (
n
= 17) showed elevation of salivary antidengue antibody (100% specificity). Salivary IgG levels correlated well with serum HAI titer (
r
= 0.78), and salivary IgG levels could be used to distinguish between primary- and secondary-dengue virus infections.
Serotyping and Genotyping of Genital
Chlamydia trachomatis
Isolates Reveal Variants of Serovars Ba, G, and J as Confirmed by
omp1
Nucleotide Sequence Analysis
Authors: Morré Servaas A. , Ossewaarde Jacobus M. , Lan Jar , van Doornum Gerard J. J. , Walboomers Jan M. M. , MacLaren David M. , Meijer Chris J. L. M. , van den Brule Adriaan J. C. 
Published: December 2019

ABSTRACT

Urogenital isolates (
n
= 93) of
Chlamydia trachomatis
were differentiated into serovars and variants by serotyping with monoclonal antibodies and genotyping by restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified
omp1
gene, respectively. The types of 87 of the 93 isolates (94%) were identical, as determined by both methods. Among these 87 isolates, 3 isolates were identified as the recently described new serovariant Ga/IOL-238 by
omp1
nucleotide sequence analysis of the variable domains. Of the remaining six isolates, three isolates serotyped as both L2 and Ba but were identified as Ba/A-7 by genotyping by RFLP analysis of
omp1
. The
omp1
nucleotide sequences of variable domains VD1, VD2, and VD4 of these urogenital Ba strains were identical to the sequences of the variable domains of Ba/J160, an ocular Ba type. The three remaining isolates were serotyped as J, but the patterns obtained by RFLP analysis of
omp1
, which were identical for the three isolates, differed from that of prototype serovar J/UW36.
omp1
nucleotide sequence analysis revealed that these strains are genovariants of serovar J/UW36. Nucleotide sequence differences between serovar J/UW36 and this J genovariant, designated Jv, were found in both variable and constant domains. In conclusion, this study shows that the PCR-based genotyping of clinical
C. trachomatis
isolates by RFLP analysis of
omp1
has a higher discriminatory power and is more convenient than serotyping. Variants of
C. trachomatis
serovars Ba, G, and J were identified and characterized.
Evaluation of a New Competitive Immunoassay (BioElisa Syphilis) for Screening for
Treponema pallidum
Antibodies at Various Stages of Syphilis
Authors: Ebel Anne , Bachelart Loïc , Alonso Jean-Michel 
Published: December 2019

ABSTRACT

The BioElisa Syphilis, a new competitive enzyme immunoassay (EIA) for
Treponema pallidum
whole antigen that uses specific human immunoglobulin G (IgG) antibodies as the competitor, was evaluated for potential use in screening for syphilis at various stages. The results obtained by this competitive EIA were compared with those obtained by the fluorescent treponemal antibody absorption (FTA-abs) test and the
T. pallidum
hemagglutination assay (TPHA). Serum samples from 434 patients with positive TPHA and FTA-abs test results, including patients with primary, latent, secondary, and tertiary syphilis and neurosyphilis, were investigated. Two samples tested negative by competitive EIA but were weakly reactive by the TPHA and the FTA-abs test. Sixteen serum samples from patients with clinically documented active syphilis, including several patients infected with human immunodeficiency virus, tested positive by the competitive EIA. There was a direct inverse correlation between EIA indices and titers in the TPHA and the FTA-abs test for all samples that tested positive. Specificity was assessed by testing 358 serum samples which tested negative for syphilis by TPHA and the FTA-abs test, including 100 serum samples from patients with documented infectious or autoimmune diseases. Only two serum samples gave a weakly positive EIA result. Thus, competitive EIA had a sensitivity of 99.5% and a specificity of 99.4% relative to the results of the FTA-abs test and TPHA. Our evaluation shows that BioElisa Syphilis is a sensitive, specific, and simple assay for screening for syphilis.
Rapid, Low-Technology MIC Determination with Clinical
Mycobacterium tuberculosis
Isolates by Using the Microplate Alamar Blue Assay
Authors: Franzblau Scott G. , Witzig Richard S. , McLaughlin James C. , Torres Patricia , Madico Guillermo , Hernandez Antonio , Degnan Michelle T. , Cook Mary B. , Quenzer Virginia K. , Ferguson Robert M. , Gilman Robert H. 
Published: December 2019

ABSTRACT

A colorimetric, microplate-based Alamar Blue assay (MABA) method was used to determine the MICs of isoniazid (INH), rifampin, streptomycin (SM), and ethambutol (EMB) for 34 Peruvian
Mycobacterium tuberculosis
isolates (including both pansensitive and multidrug-resistant strains) and the H
37
Rv strain by using bacterial suspensions prepared directly from solid media. Results for all isolates were available within 8 days. Discordant results were observed on initial tests for 3 of 16 INH-susceptible isolates, 5 of 31 EMB-susceptible isolates, and 2 of 4 SM-resistant isolates (by the BACTEC 460 system). The overall agreements between the MICs obtained by MABA and the results obtained with the BACTEC 460 system were 87.9% for initial results and 93.6% after retesting 12 of 17 samples with discrepant results. Interpretation of MABA endpoints improved with technical experience. The MABA is a simple, rapid, low-cost, appropriate technology which does not require expensive instrumentation and which makes use of a nontoxic, temperature-stable reagent.
Detection of
Chlamydia trachomatis
by the Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) in Urine Specimens from Men and Women and Endocervical Specimens from Women
Authors: Crotchfelt Kimberly A. , Pare Barbara , Gaydos Charlotte , Quinn Thomas C. 
Published: December 2019

ABSTRACT

Molecular biology-based amplification methods are significantly more sensitive than other methods for the detection of
Chlamydia trachomatis
. The performance characteristics of the new Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) with endocervical and urine specimens were compared to those of culture for patients attending two Baltimore City sexually transmitted disease clinics and a clinic for adolescents. AMP CT uses transcription-mediated amplification (TMA) and hybridization protection assay procedures to qualitatively detect
C. trachomatis
by targeting a 23S rRNA. Discrepant results between culture-negative and AMP CT-positive specimens were resolved by direct fluorescent-antibody staining of sedimented culture transport medium for elementary bodies and by TMA with 16S rRNA as a target. Following discrepant analysis, for 480 female urine specimens AMP CT had a sensitivity of 93.8% and a specificity of 100%. For 464 male urine specimens, the resolved sensitivity and specificity of AMP CT were 95.6 and 98.7%, respectively. For the 479 endocervical swab specimens the sensitivity of AMP CT was 100% and the specificity was 99.5%. Resolved culture sensitivities of AMP CT for female and male swab specimens were 52.3 and 58.9%, respectively. These results demonstrate that AMP CT is highly sensitive for the detection of
C. trachomatis
in endocervical specimens and in urine specimens from men and women.
Rapid Detection of Penicillin-Resistant
Streptococcus pneumoniae
in Cerebrospinal Fluid by a Seminested-PCR Strategy
Authors: du Plessis Mignon , Smith Anthony M. , Klugman Keith P. 
Published: December 2019

ABSTRACT

A seminested-PCR assay, based on the amplification of the pneumococcal penicillin-binding protein 2B gene (
pbp2B
), was developed for the detection of penicillin-resistant and -susceptible pneumococci in cerebrospinal fluid (CSF) specimens. Species-specific primers (P5 and P6) which amplified a 682-bp conserved region of the transpeptidase-encoding region of the
pbp2B
gene were used. Four “resistance” primers were designed to bind to altered areas of the
pbp2B
gene identified in penicillin-resistant South African wild-type strains. Together with the downstream primer P6, the upstream resistance primers amplified fragments which were used to detect the presence of penicillin resistance. This system identified all 35 of the
S. pneumoniae
isolates evaluated, including strains of 11 different serotypes and a range of penicillin-resistant and -susceptible strains. The specificity of the assay was demonstrated by its inability to amplify DNA from other bacterial species which commonly cause meningitis. It was possible to detect pneumococcal DNA from culture-negative CSF inoculated with 2.5 pg of purified DNA or 18 CFU. Analysis of 285 CSF specimens showed that PCR detected the pneumococcus in 18 samples positive by culture, including the identification of four penicillin-resistant isolates. The positive predictive value and the negative predictive value of the assay were each 100%.