bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Evaluation of the New Gen-Probe
Mycobacterium tuberculosis
Amplified Direct Test and the Semiautomated Abbott LCx
Mycobacterium tuberculosis
Assay for Direct Detection of
Mycobacterium tuberculosis
Complex in Respiratory and Extrapulmonary Specimens
Authors: Piersimoni Claudio , Callegaro Annapaola , Scarparo Claudio , Penati Valeria , Nista Domenico , Bornigia Stefano , Lacchini Carla , Scagnelli Mariuccia , Santini Gianfranco , De Sio Giuseppina 
Published: December 2019

ABSTRACT

Two commercial assays that detect
Mycobacterium tuberculosis
complex (MTB) in clinical specimens by rRNA target amplification (AMTDII) and ligase chain reaction (LCx) were evaluated. The tests were applied to 457 respiratory (
n
= 273) and extrapulmonary (
n
= 184) specimens collected from 357 patients. The results were compared with those of acid-fast staining and culture. The combination of culture and clinical diagnosis was considered to be the “gold standard.” Seventy specimens were from patients with pulmonary tuberculosis and 28 specimens were from patients with extrapulmonary tuberculosis. After resolution of discrepant results, the overall sensitivities, specificities, and positive and negative predictive values for respiratory specimens were 92.8, 99.4, 98.5, and 97%, respectively, for AMTDII and 75.7, 98.8, 96.4, and 90.5%, respectively, for LCx. With extrapulmonary specimens, the overall sensitivities, specificities, and positive and negative predictive values were 78.6, 99.3, 95.6, and 96.2%, respectively, for AMTDII and 53.6, 99.3, 93.7, and 92.1%, respectively, for LCx. The level of agreement between AMTDII and LCx assay results was 78.2%. We conclude that although both nucleic acid amplification methods are rapid and specific for the detection of MTB in clinical specimens, AMTDII is significantly more sensitive than LCx with both respiratory (
P
= 0.005) and extrapulmonary (
P
= 0.048) specimens.
Variation in Electrophoretic Karyotype and Antifungal Susceptibility of Clinical Isolates of
Cryptococcus neoformans
at a University-Affiliated Teaching Hospital from 1987 to 1994
Authors: Klepser Michael E. , Pfaller Michael A. 
Published: December 2019

ABSTRACT

Ninety-eight isolates of
Cryptococcus neoformans
were collected from 30 patients at the University of Iowa Hospitals and Clinics from December 1987 through December 1994. The susceptibility of each isolate was determined against fluconazole, itraconazole, amphotericin B, and flucytosine. Of the 98 isolates, 53 were recovered from blood, 19 were recovered from cerebrospinal fluid (CSF), and 26 were recovered from other sources. Although the strains were isolated from the same institution, DNA typing by electrophoretic karyotype (EK) revealed wide genetic variation. Overall, 23 different EK profiles were identified by computer-aided analysis. An isolate exhibiting a single EK was isolated from 24 of 30 patients (80%), whereas multiple strains with unique EKs were isolated from 6 of 30 (20%) patients. Of the six patients who had multiple strains recovered, only one individual had two strains isolated from unique body sites, one strain from the blood and the other from the CSF. Six strains were isolated from multiple patients. Nine patients had multiple sequential isolates recovered over periods of time ranging from 3 days to 4 months. EK analysis revealed persistence of the same genotype in six of the cases. Three patients, however, appeared to have an isolate with a second distinct EK emerge during therapy. Of the patients with sequential positive cultures, an increase in the MICs for test agents was observed in only one case.
C. neoformans
isolates were collected over a period of 7 years, during which time MICs at our institution remained stable.
Heterogeneity of the PorB Protein in Serotype 22
Neisseria meningitidis
Authors: Urwin Rachel , Fox Andrew J. , Musilek Martin , Kriz Paula , Maiden Martin C. J. 
Published: December 2019

ABSTRACT

The genetic diversity of
porB
genes from meningococcal isolates characterized as serotype 22 was investigated by gene sequencing. This procedure identified seven distinct
porB
sequences, demonstrating variation in the PorB protein recognized by the serotype 22 monoclonal antibody. This is consistent with the genetic heterogeneity of serotype 22 meningococci reported previously.
Misleading Manifestations of
Coccidioides immitis
In Vivo
Authors: Kaufman Leo , Valero Gustavo , Padhye Arvind A. 
Published: December 2019

ABSTRACT

We describe a case of coccidioidomycosis in which several unusual morphologic forms of
Coccidioides immitis
occurred in biopsy tissue from the right lower lung of a patient. To our knowledge, this is the first case where so many diverse morphologic forms were manifested in a single patient in the absence of typical endosporulating spherules. Immature spherules demonstrating segmentation mimicked morula forms of
Prototheca
spp. Certain elements resembled budding cells of
Blastomyces dermatitidis
. These consisted of juxtaposed immature spherules without endospores, a germinating endospore, or thick-walled hyphal cells. Branched, septate hyphae and moniliform hyphae consisting of chains of thick-walled arthroconidia or immature spherules were also present. Complement fixation and immunodiffusion tests performed on the patient’s serum were negative for
C. immitis
,
B. dermatitidis
, and
Histoplasma capsulatum
antibodies. Fluorescent-antibody studies were carried out with a specific
C. immitis
conjugate. All of the diverse fungal tissue elements stained positive with a moderate to strong (2 to 3+) intensity.
Evaluation of the Auxacolor System for Biochemical Identification of Medically Important Yeasts
Authors: Sheppard Donald C. , deSouza Edwige , Hashmi Zubair , Robson Hugh G. , René Pierre 
Published: December 2019

ABSTRACT
We compared the Auxacolor yeast identification system (Sanofi Diagnostics Pasteur) with the API 20C Aux (bioMerieux-Vitek) using 105 isolates of medically important yeasts. The Auxacolor system provided more rapid, accurate results and displayed less interobserver variability than the API 20C Aux.
Evaluation of Bias in Diagnostic-Test Sensitivity and Specificity Estimates Computed by Discrepant Analysis
Authors: Green Timothy A. , Black Carolyn M. , Johnson Robert E. 
Published: December 2019

ABSTRACT

When a new diagnostic test is potentially more sensitive than the reference test used to classify persons as infected or uninfected, a substantial number of specimens from infected persons may be reference-test negative but new-test positive. Discrepant analysis involves the performance of one or more additional tests with these specimens, reclassification as infected those persons for whom the new-test-positive results are confirmed, and recalculation of the estimates of new-test sensitivity and specificity by using the revised classification. This approach has been criticized because of the bias introduced by the selective use of confirmation testing. Under conditions appropriate for evaluating a nucleic acid amplification (NAA) test for
Chlamydia trachomatis
infection with cell culture as the reference test, we compared the bias in estimates based on the discrepant-analysis classification of persons as infected or uninfected with that in estimates based on the culture classification. We concluded that the bias in estimates of NAA-test specificity based on discrepant analysis is small and generally less than that in estimates based on culture. However, the accuracy of discrepant-analysis-based estimates of NAA-test sensitivity depends critically on whether culture specificity is equal to or is slightly less than 100%, and it is affected by competing biases that are not fully taken into account by discrepant analysis.
Effects of Decontamination Methods and Culture Conditions on Viability of
Mycobacterium ulcerans
in the BACTEC System
Authors: Palomino J. C. , Portaels F. 
Published: December 2019

ABSTRACT

We used the BACTEC system to evaluate the effects of several decontamination methods and the addition of antibiotics on the viability of
Mycobacterium ulcerans
. The effects of polyoxyethylene stearate or egg yolk as supplements were also evaluated to determine their impact on the growth of
M. ulcerans
. Strains of different geographic origins were subjected to Petroff, reversed Petroff, oxalic acid, and mild HCl treatments. After treatment, the viability of each strain was assessed in the BACTEC system. All of the decontamination methods tested adversely affected bacterial viability. Treatment with mild HCl gave the best results, allowing better growth rates with some strains and causing a delay in growth with others, depending on the geographic origin of the strain. A mixture of polymyxin B, amphotericin B, nalidixic acid, trimethoprim, and azlocillin did not significantly inhibit growth. Supplementing BACTEC medium with egg yolk markedly improved the recovery of
M. ulcerans
following the use of each of the decontamination methods. Our findings demonstrate a detrimental impact on the viability of
M. ulcerans
by all of the decontamination methods currently in common use. This explains, at least in part, the difficulty often experienced in cultivating this organism from clinical specimens. Egg yolk should be added to enhance the rate of successful primary cultivation of
M. ulcerans
in the BACTEC system.
Molecular Analysis of Tn
1546
in
Enterococcus faecium
Isolated from Animals and Humans
Authors: Jensen Lars Bogø , Ahrens Peter , Dons Lone , Jones Ronald N. , Hammerum Anette M. , Aarestrup Frank Møller 
Published: December 2019

ABSTRACT

The internal areas and the position of integration of the glycopeptide resistance element Tn
1546
were characterized by using PCR fragment length polymorphism, sequencing, and DNA hybridization techniques with 38 high-level vancomycin-resistant
Enterococcus faecium
isolates of human and animal origins from Europe and the United States. Only minor variations in the coding regions within Tn
1546
were found, suggesting high genetic stability. The isolates originated from broilers (
n
= 5), a chicken (
n
= 1), a duck (
n
= 1), a turkey (
n
= 1), pigs (
n
= 8), a pony (
n
= 1), and humans (
n
= 23). A total of 13 different types were defined based on a single-nucleotide difference in the
vanX
gene, the presence of insertion sequences, and hybridization patterns. For some types more than one isolate were found. For type 1, 10 isolates of both human and animal origins were 1found. All were indistinguishable from the reference strain, BM4147. For type 2, 11 isolates of human and animal origins were found. Six human isolates from England were all of type 3. Two human isolates from the United States, indistinguishable from each other, were type 9. These results showed that vancomycin-resistant
E. faecium
of animal and human origins can contain indistinguishable genetic elements coding for vancomycin resistance, indicating either horizontal gene transfer between
E. faecium
organisms of human and animal origins or the existence of a common reservoir for glycopeptide resistance.
Value of Examining Multiple Sputum Specimens in the Diagnosis of Pulmonary Tuberculosis
Authors: Nelson Susan M. , Deike Marcia A. , Cartwright Charles P. 
Published: December 2019

ABSTRACT

To objectively assess the value of examining multiple sputum specimens in maximizing the sensitivity of detection of
Mycobacterium tuberculosis
, we retrospectively reviewed the acid-fast bacillus smear and culture results of patients diagnosed with culture-proven pulmonary tuberculosis (TB) at Hennepin County Medical Center between 1986 and 1996. Two hundred and forty six persons were diagnosed with pulmonary TB in the time period analyzed. In 93% of these cases (229 of 246) the laboratory diagnosis was made by detection of
M. tuberculosis
in sputum specimens; however, only 52% (120 of 229) of these patients had at least three sputum specimens submitted to the laboratory at the time of diagnosis. Of the patients from whom at least three specimens were collected, 47% (56 of 120) had at least one smear-positive specimen; the third or later specimen submitted was the first smear-positive specimen for 13% (7 of 56) of these persons but was the first culture-positive specimen for only 7% (4 of 56). Of the 64 patients with smear-negative specimens, for only 5% (3 of 64) was the third or subsequent specimen submitted the first from which
M. tuberculosis
was recovered. This data indicates that, in our institution, the overwhelming majority of culture-proven pulmonary TB cases are diagnosed from the first or second sputum specimen submitted to the laboratory and that only rarely is a third specimen of diagnostic value.
Molecular Approaches to Diagnosis of Pulmonary Diseases Due to
Mycoplasma pneumoniae
Authors: Abele-Horn Marianne , Busch Ulrich , Nitschko Hans , Jacobs Enno , Bax Ralph , Pfaff Friederike , Schaffer Beatrix , Heesemann Jürgen 
Published: December 2019

ABSTRACT

In this prospective study, the use of a culture-enhanced PCR assay for the detection of
Mycoplasma pneumoniae
, followed by hybridization with a specific probe (MP-HPCR) or without hybridization (MP-PCR), and the use of a nested PCR (MP-NPCR) were evaluated. Clinical samples (190 specimens) from 190 patients with respiratory complaints were incubated in culture broth overnight and then subjected to PCR. The results of the PCR were compared to those obtained by culture, the direct antigen test, and serologic testing by microparticle agglutination and by immunoblotting in unclear cases. The sensitivities were 19 CFU for MP-PCR, 1.9 CFU for MP-HPCR, and 0.019 CFU for MP-NPCR. PCR amplification of the β-globin gene was possible in 98% of cases: after dilution of the β-globin-negative samples, all samples were reactive. Correlation between negative MP-NPCR results and negative serology results was found in 89% of cases; a positive correlation was found with 10% of the patients. Samples from three immunocompromised patients were MP-NPCR positive but serologically negative. High respiratory colonization by
M. pneumoniae
(>10
5
CFU/ml) in patients with acute respiratory disease could be detected by culture, MP-PCR, and MP-NPCR. These results indicate that MP-PCR and MP-NPCR are reliable methods for the detection of
M. pneumoniae
in respiratory tract samples of patients with respiratory complaints.
Multicenter Evaluation of the New Automated Enzymun-Test Anti-HIV 1 + 2 + Subtyp O
Authors: Weber Bernard 
Published: December 2019

ABSTRACT
An international multicenter study was performed to evaluate a new, automated human immunodeficiency virus (HIV) third-generation antibody assay. The Enzymun-Test Anti-HIV 1 + 2 + Subtyp O showed 100% sensitivity and 99.8% specificity among 11,172 samples from hospitalized patients and blood donors. For early HIV antibody detection in seroconversion panels, Enzymun-Test showed a sensitivity equivalent to that of the Abbott Recomb. HIV-1/HIV-2 3rd Gen. assay.
Quality Control Limits for Dilution and Disk Diffusion Susceptibility Tests of Trovafloxacin against Eight Quality Control Strains
Authors: Fuchs Peter C. , Barry Arthur L. , Brown Steven D. 
Published: December 2019

ABSTRACT
A 10-laboratory collaborative effort was designed to generate data to propose quality control limits for susceptibility tests of trovafloxacin. Broth microdilution, agar dilution, and disk diffusion tests were evaluated with eight different control strains. All tests were reproducible, and control limits are proposed.
Rapid Cytomegalovirus pp65 Antigenemia Assay by Direct Erythrocyte Lysis and Immunofluorescence Staining
Authors: Ho Stephen K. N. , Lo Chi-Yuen , Cheng Ignatius K. P. , Chan Tak-Mao 
Published: December 2019

ABSTRACT

A rapid cytomegalovirus (CMV) pp65 antigenemia assay with direct erythrocyte lysis (DL) with 0.8% NH
4
Cl, followed by indirect immunofluorescence staining (IF), was evaluated with 82 blood samples from renal transplant recipients, and the results were compared to those of the conventional antigenemia assay with dextran sedimentation and two-cycle alkaline phosphatase, anti-alkaline phosphatase staining (DS-APAAP). The DL-IF modification gave a higher leukocyte yield compared to DS-APAAP (75.4 versus 54.9%;
P
< 0.05), with similar leukocyte viability rates of >95%. The DL-IF methodology involved fewer technical steps, and the assay time was shortened from 5 h to less than 3 h. Nineteen of the 82 samples concordantly tested positive for pp65 antigenemia by both assays, and the readings showed a good correlation (
r
= 0.996;
P
< 0.01). No discordant results were observed. We conclude that the CMV pp65 antigenemia assay by this novel DL-IF modification is technically simpler, cheaper, and less time-consuming but yields results comparable to those of the conventional DS-APAAP assay. The shortened assay time and increased capacity to handle more samples confer distinct advantages in the rapid diagnosis and prompt treatment of CMV disease in immunosuppressed patients.
Reduction of Carriage of EnterohemorrhagicEscherichia coliO157:H7 in Cattle by Inoculation with Probiotic Bacteria
Authors: Zhao Tong , Doyle Michael P. , Harmon Barry G. , Brown Cathy A. , Mueller P. O. Eric , Parks Andrew H. 
Published: December 2019

ABSTRACTBacteria inhibitory toEscherichia coliO157:H7 were isolated from cattle and evaluated for their potential for reducing carriage ofE. coliO157:H7 in calves. Eighteen of 1,200 bacterial isolates from cattle feces and intestinal tissue samples were screened and determined to inhibit the growth ofE. coliO157:H7 in vitro. Seventeen of the isolates wereE. coliand one wasProteus mirabilis. None produced Shiga toxin. Genomic DNA fingerprinting by pulsed-field gel electrophoresis revealed 13 distinguishable profiles among the 18 isolates. Two calves inoculated perorally with a mixture of all 18 isolates (1010CFU) appeared to be normal and did not develop signs of clinical disease throughout a 25- to 27-day observation period. These bacteria colonized segments of the gastrointestinal tract and were in feces at the termination of the experiment (25 and 27 days postinoculation) at levels of 50 to 200 CFU/g. Fifteen cannulated calves were studied to determine the efficiency of the probiotic bacteria in reducing or eliminating the carriage ofE. coliO157:H7. Nine calves served as controls, with each animal receiving perorally 1010CFU ofE. coliO157:H7.E. coliO157:H7 was detected intermittently in the rumen samples from all control animals throughout 3 weeks postinoculation, whereasE. coliO157:H7 was shed at various levels in feces continuously throughout the experiment (mean, 28 days).E. coliO157:H7 was isolated from the rumens and colons of eight of nine and nine of nine calves, respectively, at the termination of the study. Six calves each received perorally 1010CFU of probiotic bacteria and then 2 days later received 1010CFU ofE. coliO157:H7.E. coliO157:H7 was detected in the rumen for only 9 days postinoculation in two animals, for 16 days in one animal, for 17 days in two animals, and for 29 days in one animal.E. coliO157:H7 was detected in feces for only 11 days postinoculation in one animal, for 15 days in one animal, for 17 days in one animal, for 18 days in one animal, for 19 days in one animal, and for 29 days in one animal. At the end of the experiment (mean, 30 days),E. coliO157:H7 was not recovered from the rumen of any of the six animals treated with probiotic bacteria; however,E. coliO157:H7 was recovered from the feces of one of the animals. This animal was fasted twice postinoculation. These studies indicate that selected probiotic bacteria administered to cattle prior to exposure toE. coliO157:H7 can reduce the level of carriage ofE. coliO157:H7 in most animals.
Antigenic Diversity of Hepatitis B Virus Strains of Genotype F in Amerindians and Other Population Groups from Venezuela
Authors: Blitz Linda , Pujol Flor H. , Swenson Paul D. , Porto Leticia , Atencio Ricardo , Araujo Mary , Costa Luciana , Monsalve Diana Callejas , Torres Jaime R. , Fields Howard A. , Lambert Steve , Van Geyt Caroline , Norder Helene , Magnius Lars O. , Echevarría José M. , Stuyver Lieven 
Published: December 2019

ABSTRACT
The adw4 subtype of hepatitis B virus (HBV) belongs to a unique genomic group (genotype F) representing the original HBV strains from the New World. Data regarding the prevalence of this subtype among HBV carriers in South America are, however, scarce, and those concerning HBV genotype F are based on only a few samples from Latin America. In this study, serum samples were obtained from 141 hepatitis B surface antigen (HBsAg) carriers from Amerindians and urban populations from Venezuela. The HBsAg subtype was identified with monoclonal antibodies in 105 samples, and the HBV genotype was identified by reverse-phase hybridization with DNA fragments in 58 samples. The adw4 subtype was highly prevalent in the population studied (75%); among the Amerindians, the prevalence was 97%. The adw2 subtype was also present (10%), while other subtypes (ayw3 and ayw4) were only occasionally found. The HBV subtype was associated with the expected genotype in most cases (80%), and thus genotype F was highly prevalent. Sequencing of viral strains that gave genotypes unpredicted by the HBsAg subtyping confirmed seven of them as belonging to not previously described genotype-subtype associations: namely, adw2 and ayw4 within genotype F.
Epidemiological Study of a Food-Borne Outbreak of Enterotoxigenic
Escherichia coli
O25:NM by Pulsed-Field Gel Electrophoresis and Randomly Amplified Polymorphic DNA Analysis
Authors: Mitsuda Toshihiro , Muto Tetsunori , Yamada Mikiko , Kobayashi Nobuyoshi , Toba Masanori , Aihara Yukoh , Ito Akira , Yokota Shumpei 
Published: December 2019

ABSTRACT

This study investigated the applicability of molecular epidemiological techniques to the identification of the causal agent of an outbreak of diarrhea caused by ingestion of food contaminated with enterotoxigenic
Escherichia coli
(ETEC). The outbreak occurred at four elementary schools in July 1996 and affected more than 800 people. Illness was most strongly associated with eating tuna paste (relative risk, 1.79; 95% confidence interval = 1.16 to 2.79;
P
= 0.0001). To evaluate the epidemiological characteristics of the pathogen, the DNAs from numerous isolated ETEC strains were subjected to randomly amplified polymorphic DNA analysis, pulsed-field gel electrophoresis of nuclease S1-treated plasmid DNA, and analysis of genomic DNA restriction fragment length polymorphisms. All ETEC isolates were of the O25:NM (nonmotile) serotype, which carries a heat-stable enterotoxin Ib gene. Genotypic analysis demonstrated that the strains isolated from the patients at all four schools were identical. The isolates of ETEC O25:NM obtained from the tuna paste that had been served for lunch at these schools were genetically indistinguishable from those isolated from the patients. Results suggest that this outbreak was food borne. The molecular biology-based epidemiological techniques used in this study were useful in characterizing the causal agent in this food-borne epidemic.