bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of
Chlamydia trachomatis
Prevalence in an Asymptomatic Screening Population: Performances of the LCx and COBAS Amplicor Tests with Urine Specimens
Authors: Morré Servaas A. , Van Valkengoed Irene G. M. , Moes Robert M. , Boeke A. Joan P. , Meijer Chris J. L. M. , Van den Brule Adriaan J. C. 
Published: December 2019

ABSTRACT

This study determined the performances of the LCx (Abbott) and COBAS Amplicor (Roche) tests with urine specimens for the detection of
Chlamydia trachomatis
in an asymptomatic screening population. Randomly selected women and men (age range, 15 to 40 years) registered in 20 general practices in Amsterdam, The Netherlands, were invited to participate in this study. Urine specimens (
n
= 2,906; 1,138 specimens from men and 1,717 specimens from women) were tested for
C. trachomatis
by the COBAS Amplicor (Roche) and LCx (Abbott) tests. Samples which were positive by only one assay were subjected to discrepant analyses by a third assay (in-house plasmid PCR). By the LCx assay
C. trachomatis
DNA was detected in urine specimens from 46 of 1,717 women and 29 of 1,138 men, while the COBAS Amplicor detected
C. trachomatis
DNA in 52 and 35 specimens, respectively. When comparing the LCx and COBAS Amplicor tests, 32 test results (20 for women and 12 for men) were discrepant. After discrepant analyses the following sensitivities, specificities, and positive predictive values were found for the LCx and COBAS Amplicor tests: 78.6 versus 98.8%, 99.7 versus 99.9%, and 88.0 versus 95.4%, respectively. No prominent differences were found between men and women with regard to the test performances. After discrepant analyses the overall prevalences of
C. trachomatis
in women and men were 3.0 and 2.8%, respectively. For both women and men the prevalence in the younger age groups was higher than that in the older age groups. In conclusion, the COBAS Amplicor tests shows better diagnostic characteristics than the LCx assay for the detection of
C. trachomatis
in urine specimens from an asymptomatic screening population. In this asymptomatic population the overall prevalence of
C. trachomatis
was 2.9%.
Development of rRNA-Based PCR Assays for Identification of
Burkholderia cepacia
Complex Isolates Recovered from Cystic Fibrosis Patients
Authors: LiPuma John J. , Dulaney Betty Jo , McMenamin Jennifer D. , Whitby Paul W. , Stull Terrence L. , Coenye Tom , Vandamme Peter 
Published: December 2019

ABSTRACT

PCR assays targeting rRNA genes were developed to identify species (genomovars) within the
Burkholderia cepacia
complex. Each assay was tested with 177 bacterial isolates that also underwent taxonomic analysis by whole-cell protein profile. These isolates were from clinical and environmental sources and included 107
B. cepacia
complex strains, 23
Burkholderia gladioli
strains, 20
Ralstonia pickettii
strains, 10
Pseudomonas aeruginosa
strains, 8
Stenotrophomonas maltophilia
strains, and 9 isolates belonging to nine other species. The sensitivity and specificity of the 16S rRNA-based assay for
Burkholderia multivorans
(genomovar II) were 100 and 99%, respectively; for
Burkholderia vietnamiensis
(genomovar V), sensitivity and specificity were 87 and 92%, respectively. An assay based on 16S and 23S rRNA gene analysis of
B. cepacia
ATCC 25416 (genomovar I) was useful in identifying genomovars I, III, and IV as a group (sensitivity, 100%, and specificity, 99%). Another assay, designed to be specific at the genus level, identified all but one of the
Burkholderia
and
Ralstonia
isolates tested (sensitivity, 99%, and specificity, 96%). The combined use of these assays offers a significant improvement over previously published PCR assays for
B. cepacia
.
Diverse Restriction Fragment Length Polymorphism Patterns of the PCR-Amplified 16S rRNA Genes in
Aeromonas veronii
Strains and Possible Misidentification of
Aeromonas
Species
Authors: Graf Joerg 
Published: December 2019

ABSTRACT

Restriction fragment length polymorphism analysis after PCR amplification (RFLP-PCR) of the 16S rRNA gene has been previously proposed as a rapid method to identify
Aeromonas
species. In the present study, the precision of RFLP-PCR was evaluated with 62
Aeromonas
reference strains. The analysis revealed that
Aeromonas veronii
biovar sobria strains produce various patterns, possibly leading to its misidentification as an environmental species. For most other
Aeromonas
species little variation was noted. This study supports the usefulness of RFLP-PCR analysis to separate three clinically important species but also reveals possible misidentifications that necessitate further biochemical tests to validate the preliminary identification.
Direct Detection of Shiga Toxigenic
Escherichia coli
Strains Belonging to Serogroups O111, O157, and O113 by Multiplex PCR
Authors: Paton Adrienne W. , Paton James C. 
Published: December 2019

ABSTRACT

Shiga toxigenic
Escherichia coli
(STEC) strains are a diverse group of organisms associated with severe gastrointestinal and systemic diseases in humans. Within the STEC family,
eae
-positive STEC strains, particularly those belonging to serogroups O157 and O111, appear to have greater virulence for humans. However, in spite of being
eae
negative, STEC strains belonging to serogroup O113 have frequently been associated with cases of severe STEC disease, including hemolytic-uremic syndrome (HUS). We have developed a modified multiplex PCR assay for detection of STEC strains belonging to these three serogroups in cultures of feces by using primers specific for portions of the genetic loci (
rfb
) encoding biosynthesis of the respective O antigen. These primers direct amplification of PCR products of 259, 406, and 593 bp for serogroups O157, O111, and O113, respectively. The assay was validated by testing 40 previously characterized STEC strains, with 100% agreement. It also detected STEC strains of the appropriate genotype in primary fecal cultures from 13 patients with HUS or bloody diarrhea. Thirty other primary fecal cultures from patients without evidence of STEC infection were negative.
Molecular Identification of a
Nocardiopsis dassonvillei
Blood Isolate
Authors: Beau Frédéric , Bollet Claude , Coton Thierry , Garnotel Eric , Drancourt Michel 
Published: December 2019

ABSTRACT

Nocardiopsis dassonvillei
is an environmental aerobic actinomycete seldom isolated in cutaneous and pulmonary infections. We herein report the first
N. dassonvillei
blood isolate in a patient hospitalized for cholangitis. Although morphological characteristics and biochemical tests allowed a presumptive identification of this isolate, cell wall fatty acid chromatographic analysis confirmed identification at the genus level, and 16S rRNA gene sequencing achieved definite identification. This study illustrates the usefulness of 16S rRNA gene sequencing as a routine method for the identification of actinomycetes.
Cloning and Expression of a 48-KilodaltonBabesia caballiMerozoite Rhoptry Protein and Potential Use of the Recombinant Antigen in an Enzyme-Linked Immunosorbent Assay
Authors: Ikadai Hiromi , Xuan Xuenan , Igarashi Ikuo , Tanaka Shigeyasu , Kanemaru Takumi , Nagasawa Hideyuki , Fujisaki Kozo , Suzuki Naoyoshi , Mikami Takeshi 
Published: December 2019

ABSTRACTA cDNA expression library prepared fromBabesia caballimerozoite mRNA was screened with a monoclonal antibody BC11D against the rhoptry protein ofB. caballimerozoite. A cDNA encoding a 48-kDa protein ofB. caballiwas cloned and designated BC48. The complete nucleotide sequence of the BC48 gene had 1,828 bp and was shown to contain no intron. Southern blotting analysis indicated that the BC48 gene contained more than two copies in theB. caballigenome. Computer analysis suggested that this sequence contained an open reading frame of 1,374 bp with a coding capacity of approximately 52 kDa. The recombinant protein expressed by the vaccinia virus vector in horse cells had an apparent molecular mass of 48 kDa, which was the same as that of the nativeB. caballi48-kDa protein. Moreover, recombinant proteins expressed by the pGEX4T expression vector inEscherichia colias glutathioneS-transferase fusion proteins were used for antigen in an enzyme-linked immunosorbent assay (ELISA). The ELISA was able to differentiate very clearly betweenB. caballi-infected horse sera andB. equi-infected horse sera or noninfected normal horse sera. These results suggest that this simple and highly sensitive test might be applicable to the detection ofB. caballi-infected horses in the field.
Comparison of Direct and Concentrated Acid-Fast Smears To Identify Specimens Culture Positive for
Mycobacterium
spp
Authors: Peterson Ellena M. , Nakasone Audrey , Platon-DeLeon J. M. , Jang Y. , de la Maza Luis M. , Desmond Edward 
Published: December 2019

ABSTRACT

Microscopic examination of respiratory specimens for acid-fast bacilli (AFB) plays a key role in the initial diagnosis of tuberculosis, monitoring of treatment, and determination of eligibility for release from isolation. The objective of this study was to compare the sensitivity obtained with smears for detection of AFB (AFB smears) made directly from respiratory specimens (direct AFB smears) to that obtained with parallel smears made from concentrates of the specimens (concentrated AFB smears). A total of 2,693 specimens were evaluated; 1,806 were from the University of California Irvine Medical Center Medical Microbiology Laboratory (UCIMC), which serves a tertiary-care hospital with outpatient clinics, and 887 were from the Microbial Disease Laboratory at the California Department of Public Health (MDL), which receives specimens from outpatient facilities and clinics on Pacific islands. Of the 353 AFB culture-positive specimens at UCIMC, there was a statistically significant difference in the sensitivity of the direct AFB smear (34%) and that of the smear made from the concentrated specimen (58%) (
P
< 0.05). This was also true for the 208 specimens positive for
Mycobacterium tuberculosis
, for which the sensitivity of the direct smear was 42% (87 of 208) and that for the smear made from the concentrated specimen was 74% (154 of 208). At MDL, where all but 1 of the 45 culture-positive specimens grew
M. tuberculosis
, the sensitivity of the smear made from the concentrated specimen was 93% (42 of 45) and was not significantly higher than the sensitivity of the direct smear, which was 82% (37 of 45). By combining the results from both laboratories, 42 patients from whom at least three specimens were received were culture positive for
M. tuberculosis
. The cumulative results for the initial three specimens from these patients showed that the direct smear detected
M. tuberculosis
in 81% of these patients, whereas the smear made from the concentrate detected
M. tuberculosis
in 91% of these patients. In summary, when all culture-positive specimens are considered, the sensitivity of the direct smear compared to that of a smear made from the concentrated specimen was significantly different overall in the two different laboratory settings. However, this difference was reduced only if the cumulative results for the initial three specimens received from patients who were culture positive for
M. tuberculosis
were evaluated.
Evaluation of the Prototype Roche DNA Amplification Kit Incorporating the New SSK145 and SKCC1B Primers in Detection of Human Immunodeficiency Virus Type 1 DNA in Zimbabwe
Authors: Zijenah Lynn S. , Humphrey Jean , Nathoo Kussum , Malaba Lucie , Zvandasara Parteson , Mahomva Agnes , Iliff Peter , Mbizvo Michael T. 
Published: December 2019

ABSTRACT
We assessed the sensitivity and specificity of a newly developed DNA PCR kit (Roche Diagnostic Corporation, Indianapolis, Ind.) that incorporates primers for all the group M viruses for the detection of human immunodeficiency virus (HIV) type 1 (HIV-1) infection in Zimbabwe. A total of 202 whole-blood samples from adults whose HIV status was known were studied. This included 100 HIV-1-positive and 102 HIV-1-negative samples selected on the basis of concordant results obtained with two enzyme-linked immunosorbent assay kits. The prototype Roche DNA PCR assay had a 100% sensitivity for the detection of HIV-1 DNA and a specificity of 100%. We conclude that the new Roche DNA PCR kit is accurate for the detection of HIV DNA in Zimbabwean samples, in which HIV-1 subtype C dominates.
Comparison of Direct Inoculation and Copan Transport Systems for Isolation of
Neisseria gonorrhoeae
from Endocervical Specimens
Authors: Olsen C. C. , Schwebke J. R. , Benjamin W. H. , Beverly A. , Waites K. B. 
Published: December 2019

ABSTRACT

Two commercial swab transport systems, Copan Amies gel agar with and without charcoal (Copan Diagnostics, Corona, Calif.), were compared to direct inoculation onto modified Thayer-Martin medium for detection of
Neisseria gonorrhoeae
in 1,490 endocervical specimens obtained from women attending a sexually transmitted disease clinic. Copan swabs were held in the transport system for 24 h at room temperature prior to inoculation onto modified Thayer-Martin medium. All cultures were incubated at 35°C in 5% CO
2
, and bacteria were identified on the basis of Gram stain, oxidase, and biochemical reactions. Copan Amies gel agar transport system without charcoal detected 77 of 81 (95%) direct inoculation culture-positive specimens, and Copan Amies gel agar transport system with charcoal detected 53 of 56 (95%) directly inoculated culture-positive specimens. Copan Amies gel agar without charcoal inoculated after 6 h supported growth of 56 (98%) positive cultures out of only 55 directly inoculated culture-positive specimens. This study demonstrates that Copan swabs represent a reasonable alternative, providing convenience, low cost, and ease of use while still maintaining a satisfactory recovery rate of
N. gonorrhoeae
from clinical specimens, if specimens can be inoculated onto selective media within a relatively short time period not involving overnight shipment.
Isolation, Identification, and Molecular Characterization of Strains of
Photorhabdus luminescens
from Infected Humans in Australia
Authors: Peel Margaret M. , Alfredson David A. , Gerrard John G. , Davis Jennifer M. , Robson Jennifer M. , McDougall Rodney J. , Scullie Barry L. , Akhurst Raymond J. 
Published: December 2019

ABSTRACT

We describe the isolation of
Photorhabdus
(
Xenorhabdus
)
luminescens
from four Australian patients: two with multiple skin lesions, one with bacteremia only, and one with disseminated infection. One of the patients had multiple skin lesions following the bite of a spider, while the lesions in the other patient were possibly associated with a spider bite. The source of infection for the remaining two patients is unknown. As a member of the family
Enterobacteriaceae
,
P. luminescens
is unusual in that it fails to reduce nitrate and ferments only glucose and mannose. It gives negative reactions for lysine decarboxylase, arginine dihydrolase, and ornithine decarboxylase (Moeller). The species is motile, utilizes citrate, hydrolyzes urea, and usually produces a unique type of annular hemolysis on sheep blood agar plates incubated at 25°C. A weak bioluminescence is the defining characteristic.
P. luminescens
is an insect pathogen and is symbiotically associated with entomopathogenic nematodes. Its isolation from human clinical specimens has been reported previously from the United States. Restriction fragment length polymorphism-PCR analysis of the 16S rRNA gene demonstrated a high level of similarity among the Australian clinical strains and significant differences between the Australian clinical strains and the U.S. clinical strains. However, numerical analyses of the data suggest that the two groups of clinical strains are more similar to each other than they are to the symbiotic strains found in nematodes. This is the first report of the isolation of
P. luminescens
from infected humans in Australia and the second report of the isolation of this species from infected humans worldwide.
Application of Different Genotyping Methods for
Pseudomonas aeruginosa
in a Setting of Endemicity in an Intensive Care Unit
Authors: Speijer Han , Savelkoul Paul H. M. , Bonten Marc J. , Stobberingh Ellen E. , Tjhie Jeroen H. T. 
Published: December 2019

ABSTRACT

Colonization with
Pseudomonas aeruginosa
was studied by taking serial swab specimens from the oropharynges and anuses and tracheal and gastric aspirates from patients in an intensive care unit during a 10-month period in a setting of endemicity. Nineteen (10%) of the 192 patients included in the study were colonized on admission, while another 30 (16%) patients acquired
P. aeruginosa
while in the hospital. Typing of 353 isolates was performed by random amplified polymorphic DNA (RAPD) analysis, and 56 strains were selected for further typing by RAPD analysis, pulsed-field gel electrophoresis (PFGE), and amplified fragment length polymorphism (AFLP) analysis. By these methods, 42, 44, and 44 genotypes were found, respectively. Computer-aided cluster analysis indicated that similar groups of related isolates were obtained by each method. By taking admission periods into account, analysis of the typing results suggested cross-acquisition of
P. aeruginosa
for five patient pairs. The small number of transfers and the large number of genotypes found indicate that most
P. aeruginosa
strains were derived from the patients themselves. The numbers of observed typing patterns and band differences between related isolates were counted for each typing method. AFLP analysis with primers without a selective base proved to be the most discriminatory method, followed by PFGE, AFLP analysis (with one selective base), and RAPD analysis. On the basis of a comparison with established strain differentiation criteria for PFGE, the criteria for differentiation of
P. aeruginosa
by AFLP analysis are presented.
Candida
Isolates from Neonates: Frequency of Misidentification and Reduced Fluconazole Susceptibility
Authors: Rowen Judith L. , Tate Judy M. , Nordoff Nicole , Passarell Lester , McGinnis Michael R. 
Published: December 2019

ABSTRACT

Systemic candidiasis affects 1.6 to 4.5% of very low birth weight (≤1,500 g) infants. A specimen archive of
Candida
strains from intensive care nurseries was created; it currently houses 98 isolates from 17 institutions. Eight isolates (8.2%) were misidentified at the referring institution. The MICs of fluconazole for seven isolates (7.1%, all non-
C. albicans
species, one misidentified initially) were >8 μg/ml.
Novel Method for Rapid Determination of Clarithromycin Sensitivity in
Helicobacter pylori
Authors: Gibson J. R. , Saunders N. A. , Burke B. , Owen R. J. 
Published: December 2019

ABSTRACT

A novel PCR-hybridization assay, performed in single closed capillaries, was developed to detect clarithromycin resistance-associated gene mutations in
Helicobacter pylori
. Mutations were detected by thermal analysis in 33 of 34 (97%) resistant isolates but not in 66 isolates determined to be sensitive by conventional antibiotic assays. The method was rapid and reproducible, and it reduced PCR product contamination risk.
Evaluation of the Revised MicroScan Dried Overnight Gram-Positive Identification Panel To Identify
Enterococcus
Species
Authors: Iwen Peter C. , Rupp Mark E. , Schreckenberger Paul C. , Hinrichs Steven H. 
Published: December 2019

ABSTRACT

The revised MicroScan Dried Overnight Gram-Positive Identification panel was evaluated for its efficacy at identifying
Enterococcus
species in comparison with conventional biochemical tests. Supplemental testing of ampicillin-susceptible
Enterococcus faecium
for motility and the ability to acidify methyl-α-
d
-glucopyranoside helped recognize
E. gallinarum
and increased the accuracy of the panel for identifying
Enterococcus
species to 98.5%.
Detection of Fluconazole-Resistant
Candida
Strains by a Disc Diffusion Screening Test
Authors: Sandven Per 
Published: December 2019

ABSTRACT

A commercial disc diffusion test has been evaluated as a screening method for the detection of
Candida
species with decreased susceptibility to fluconazole. A total of 1,407
Candida
strains of different species were tested, and the results were compared with the MIC results. The recently published National Committee for Clinical Laboratory Standards breakpoint criteria have been used. Isolates were classified as susceptible if the MIC for the isolates was ≤8 μg/ml, susceptible-dose dependent (S-DD) if the MIC was 16 to 32 μg/ml, and resistant if the MIC was ≥64 μg/ml. All 77 resistant strains and 121 of 122 S-DD strains had fluconazole zone diameters of ≤21 mm, and most of the strains (91%) had zone diameters of ≤15 mm. It was not possible to distinguish between resistant and S-DD strains by the disc test. Among a total of 1,208 strains found to be susceptible by the microdilution method, 49 (4.1%) yielded fluconazole zone sizes of ≤21 mm and would have been misclassified as resistant or S-DD strains on the basis of the disc test. For the majority (86%) of these 49 strains the fluconazole MIC was 8 μg/ml. The fluconazole disc test is recommended as a simple and reliable screening test for the detection of
Candida
strains with decreased susceptibility to fluconazole. Fluconazole MICs should be determined for strains found to be resistant by the disc test. The reason for confirmatory testing is twofold: to determine if isolates are resistant or S-DD, since the disc test does not make this distinction, and to identify fluconazole-susceptible strains that are found to be falsely resistant by the fluconazole disc test.
Large-Scale Survey of
Campylobacter
Species in Human Gastroenteritis by PCR and PCR–Enzyme-Linked Immunosorbent Assay
Authors: Lawson A. J. , Logan J. M. J. , O'neill G. L. , Desai M. , Stanley J. 
Published: December 2019

ABSTRACT

A PCR-based study of the incidence of enteropathogenic campylobacter infection in humans was done on the basis of a detection and identification algorithm consisting of screening PCRs and species identification by PCR-enzyme-linked immunosorbent assay. This was applied to DNA extracted from 3,738 fecal samples from patients with sporadic cases of acute gastroenteritis, submitted by seven regional Public Health Laboratories in England and Wales over a 2-year period. The sending laboratories had cultured “
Campylobacter
spp.” from 464 samples. The PCR methodologies detected 492
Campylobacter
-positive samples, and the combination of culture and PCR yielded 543
Campylobacter
-positive samples. There was identity (overlap) for 413 samples, but 79 PCR-positive samples were culture negative, and 51 culture-positive samples were PCR negative. While there was no statistically significant difference between PCR and culture in detection of
C. jejuni-C. coli
(PCR, 478 samples; culture, 461 samples), PCR provided unique data about mixed infections and non-
C. jejuni
and non-
C. coli
campylobacters. Mixed infections with
C. jejuni
and
C. coli
were found in 19 samples, and mixed infection with
C. jejuni
and
C. upsaliensis
was found in one sample; this was not apparent from culture. Eleven cases of gastroenteritis were attributed to
C. upsaliensis
by PCR, three cases were attributed to
C. hyointestinalis
, and one case was attributed to
C. lari
. This represents the highest incidence of
C. hyointestinalis
yet reported from human gastroenteritis, while the low incidence of
C. lari
suggests that it is less important in this context.