bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apparent Culture-Negative Prosthetic Valve Endocarditis Caused by
Peptostreptococcus magnus
Authors: van der Vorm Eric R. , Dondorp Arjen M. , van Ketel Ruud J. , Dankert Jacob 
Published: December 2019

ABSTRACT

In two patients with prosthetic valve endocarditis due to
Peptostreptococcus magnus
, blood cultures in the BacT/Alert and BACTEC 9240 systems were signal negative. The capability of the BacT/Alert system to detect various
Peptostreptococcus
species was assessed.
P. magnus
and
P. anaerobius
could not be detected, and subcultures remained negative. The growth in conventional media of these two species and other
Peptostreptococcus
species was similar.
Characterization of Non-Type B
Haemophilus influenzae
Strains Isolated from Patients with Invasive Disease
Authors: Cerquetti Marina , Ciofi degli Atti Marta Luisa , Renna Giovanna , Tozzi Alberto Eugenio , Garlaschi Maria Laura , Mastrantonio Paola ,   The Hi Study Group
Published: December 2019

ABSTRACT

Forty-one non-type b
Haemophilus influenzae
isolates from cases of invasive disease were characterized. By PCR capsular genotyping, 33 nonencapsulated strains, 4 type f isolates, and 4 b
−
strains were identified. By pulsed-field gel electrophoresis, the nonencapsulated isolates exhibited great genetic heterogenicity, whereas the type f and the b
−
strains seemed to have a clonal spread. Occurrence of the
hifA
gene was found by PCR in 18% of the nonencapsulated, 50% of the b
−
, and all of the type f strains. Hemagglutinating fimbriae were generally expressed by nonencapsulated isolates when fimbrial gene
hifA
was present. Two nonencapsulated isolates not susceptible to ampicillin were detected; no strains were positive for β-lactamase production.
Identification of
Corynebacterium glucuronolyticum
Strains from the Urogenital Tract of Humans and Pigs
Authors: Devriese Luc A. , Riegel Philippe , Hommez Jozef , Vaneechoutte Mario , de Baere Thierry , Haesebrouck Freddy 
Published: December 2019

ABSTRACT

Bacterial strains isolated from the genital tracts of humans (predominantly males), semen of boars, and uterine and vaginal secretions of sows were identified as
Corynebacterium glucuronolyticum
and were compared with the type strains of the recently proposed species
Corynebacterium glucuronolyticum
and
Corynebacterium seminale
. The two type strains as well as the clinical strains were shown by DNA-DNA hybridization and sequencing of the 16S rRNA gene to be related at the species level. All strains were classified as
C. glucuronolyticum
, because this name has nomenclatural priority over
C. seminale
.
Comparison of Susceptibility Testing of
Mycobacterium tuberculosis
Using the ESP Culture System II with That Using the BACTEC Method
Authors: Ruiz P. , Zerolo F. J. , Casal M. J. 
Published: December 2019

ABSTRACT

The ESP Culture System II was evaluated for its capacity to test the susceptibility of 389 cultures of
Mycobacterium tuberculosis
to streptomycin, rifampin, ethambutol, and isoniazid. Good agreement with results with the BACTEC TB 460 was found. ESP II is a reliable, rapid, and automated method for performing susceptibility testing.
Comparison of Iodophor and Alcohol Pledgets with the Medi-Flex Blood Culture Prep Kit II for Preventing Contamination of Blood Cultures
Authors: Wilson Michael L. , Weinstein Melvin P. , Mirrett Stanley , Reimer Larry G. , Fernando Cha , Meredith Frances T. , Reller L. Barth 
Published: December 2019

ABSTRACT
Iodophor and alcohol pledgets were compared with the Medi-Flex Prep Kit II for skin disinfection before venipuncture. Of 12,367 blood cultures collected, 6,362 were done with conventional pledgets and 6,005 were done with Medi-Flex kits. Contamination occurred in 351 of 6,362 blood cultures (5.5%; range, 3.7 to 8.1%) with conventional pledgets versus 328 of 6,005 (5.5%; range, 3.5 to 7.5%) with Medi-Flex kits.
Detection of Bovine Herpesvirus 4 (BoHV-4) DNA in the Cell Fraction of Milk of Dairy Cattle with History of BoHV-4 Infection
Authors: Donofrio Gaetano , Flammini Cesidio Filippo , Scatozza Franco , Cavirani Sandro 
Published: December 2019

ABSTRACT
We have demonstrated, by PCR and restriction enzyme analysis of the PCR product, the presence of bovine herpesvirus 4 (BoHV-4) DNA in the cell fraction of milk from dairy cattle with a history of BoHV-4 infection. We next evaluated the infectious nature of BoHV-4 DNA in those cells. Cocultivation of a BoHV-4-sensitive cell line with BoHV-4 DNA-positive milk cell samples produced cytopathic effects. The same result was obtained from frozen and thawed milk cell fraction coming from the cell milk fraction PCR-positive cows, ensuring that cells were killed and only infectious virus could be recovered after cocultivation with sensitive cells. This report shows that infectious BoHV-4 can be present in milk cells and that therefore nursing may be one of the transmission routes of BoHV-4.
Salmonella enterica
Serovar Virchow with CTX-M-Like β-Lactamase in Spain
Authors: Simarro Encarna , Navarro Ferrán , Ruiz Joaquı́n , Miró Elisenda , Gómez Joaquı́n , Mirelis Beatriz 
Published: December 2019

ABSTRACT

Four
Salmonella enterica
serovar Virchow strains resistant to broad-spectrum cephalosporins were isolated from patients with gastroenteritis in 1997 and 1998 in Murcia and Barcelona, Spain. The isolates expressed a β-lactamase with a pI of about 8 and a positive PCR when specific primers for CTX-M-9 were used. These results suggest the presence of a CTX-M-9 β-lactamase in these strains.
Molecular Identification of
Pasteurella dagmatis
Peritonitis in a Patient Undergoing Peritoneal Dialysis
Authors: Wallet Frédéric , Touré Fatouma , Devalckenaere Annie , Pagniez Dominique , Courcol René J. 
Published: December 2019

ABSTRACT

Pasteurella dagmatis
was identified as the etiologic agent of peritonitis in a continuous ambulatory peritoneal dialysis patient by utilizing a molecular kit in our hospital's clinical laboratory. This method would appear a useful approach to identify a species of
Pasteurella
not included in the existing database of commercial identification kits when discrepancies exist between phenotypic tests.
Fluorometric Assessment of In Vitro Antidermatophytic Activities of Antimycotics Based on Their Keratin-Penetrating Power
Authors: Okeke C. N. , Tsuboi R. , Kawai M. , Ogawa H. 
Published: December 2019

ABSTRACT

Keratin particles impregnated with amorolfine or clotrimazole in serial doubling dilutions (64 to 0.125 μg/ml) were used to evaluate the activities of these agents against 20 isolates each of
Trichophyton mentagrophytes
and
Trichophyton rubrum
in a yeast carbon broth medium incorporating Alamar Blue dye. The proposed MIC with keratin impregnation (MIC
K
) is defined as the lowest concentration of an agent used to impregnate keratin particles that effects a fluorescence-based fungal growth quotient of 0.05 or less. The conventional colorimetric and visual MICs of amorolfine for the dermatophytes, ≤0.03 μg/ml for
T. mentagrophytes
and ≤0.063 μg/ml for
T. rubrum
, were approximately half of those of clotrimazole for the same isolates. The superiority of the MIC
K
s of amorolfine for isolates of
T. mentagrophytes
(2.0 μg/ml; range, 0.5 to 8.0 μg/ml) and
T. rubrum
(4.0 μg/ml; range, 2.0 to 8.0 μg/ml) over those of clotrimazole (32 μg/ml [range, 8.0 to >64 μg/ml] and 64 μg/ml [range, 16 to >64 μg], respectively) may indicate the strong in vivo antidermatophytic activity of amorolfine as a topical agent. The new antidermatophytic susceptibility testing procedure has potential clinical utility for the in vitro screening of agents for use in the topical treatment of superficial mycoses.
Production and Characterization of Recombinant
Aspergillus fumigatus
Cu,Zn Superoxide Dismutase and Its Recognition by Immune Human Sera
Authors: Holdom M. D. , Lechenne B. , Hay R. J. , Hamilton A. J. , Monod M. 
Published: December 2019

ABSTRACT

The Cu,Zn superoxide dismutase (SOD) of
Aspergillus fumigatus
has previously been purified and shown to be immunoreactive to the sera of patients with aspergillosis; however, the purification of large quantities of the enzyme for expanded immunological analysis is both difficult and time-consuming. Accordingly, a λEMBL3
A. fumigatus
genomic library was screened with degenerate oligonucleotides based on N-terminal amino acid sequence data; from this initial screen a 1,400-bp fragment was identified, labelled, and used to screen an
A. fumigatus
λgt11 cDNA library. A full-length cDNA encoding Cu,Zn SOD was subsequently identified and cloned. The cDNA encodes a protein of 154 amino acids, which does not have a signal peptide. The
A. fumigatus
Cu,Zn SOD possesses the typical metal binding ligands of fungal Cu,Zn SODs (six histidines and one aspartic acid) and has significant overall homology with Cu,Zn SODs in general. A recombinant
A. fumigatus
Cu,Zn SOD has been expressed in
Pichia pastoris
, is enzymatically active, and has biochemical and biophysical properties that are similar to those of the native enzyme. A sheep polyclonal antibody raised against purified native
A. fumigatus
Cu,Zn SOD was reactive to the recombinant enzyme by immunoenzyme development of Western blots. Sixty percent of serum samples from patients with
A. fumigatus
infections were reactive against the recombinant Cu,Zn SOD via immunoenzyme development of Western blots, indicating that the recombinant protein may be useful in the serodiagnostic identification of
A. fumigatus
infections.
Ability of the VITEK 2 Advanced Expert System To Identify β-Lactam Phenotypes in Isolates of
Enterobacteriaceae
and
Pseudomonas aeruginosa
Authors: Sanders Christine C. , Peyret Michel , Moland Ellen Smith , Shubert Carole , Thomson Kenneth S. , Boeufgras Jean-Marc , Sanders W. Eugene 
Published: December 2019

ABSTRACT

The Advanced Expert System (AES) was used in conjunction with the VITEK 2 automated antimicrobial susceptibility test system to ascertain the β-lactam phenotypes of 196 isolates of the family
Enterobacteriaceae
and the species
Pseudomonas aeruginosa
. These isolates represented a panel of strains that had been collected from laboratories worldwide and whose β-lactam phenotypes had been characterized by biochemical and molecular techniques. The antimicrobial susceptibility of each isolate was determined with the VITEK 2 instrument, and the results were analyzed with the AES to ascertain the β-lactam phenotype. The results were then compared to the β-lactam resistance mechanism determined by biochemical and molecular techniques. Overall, the AES was able to ascertain a β-lactam phenotype for 183 of the 196 (93.4%) isolates tested. For 111 of these 183 (60.7%) isolates, the correct β-lactam phenotype was identified definitively in a single choice by the AES, while for an additional 46 isolates (25.1%), the AES identified the correct β-lactam phenotype provisionally within two or more choices. For the remaining 26 isolates (14.2%), the β-lactam phenotype identified by the AES was incorrect. However, for a number of these isolates, the error was due to remediable problems. These results suggest that the AES is capable of accurate identification of the β-lactam phenotypes of gram-negative isolates and that certain modifications can improve its performance even further.
The Alleles of the
bft
Gene Are Distributed Differently among Enterotoxigenic
Bacteroides fragilis
Strains from Human Sources and Can Be Present in Double Copies
Authors: d'Abusco Anna Scotto , Del Grosso Maria , Censini Stefano , Covacci Antonello , Pantosti Annalisa 
Published: December 2019

ABSTRACT

Enterotoxigenic
Bacteroides fragilis
(ETBF) strains are associated with diarrheal disease in children. These strains produce a zinc metalloprotease enterotoxin, or fragilysin, that can be detected by a cytotoxicity assay with HT-29 cells. Recently, three different isoforms or variants of the enterotoxin gene, designated
bft-1
,
bft-2
, and
bft-3
, have been identified and sequenced. We used restriction fragment length polymorphism analysis of the PCR-amplified enterotoxin gene to detect the isoforms
bft-1
and
bft-2
or
bft-3
borne by ETBF. By sequencing the portion of the
bft
gene corresponding to the mature toxin in some strains and applying allele-specific PCR for strains categorized as
bft-2
or
bft-3
, we found in our collection two strains harboring
bft-3
, a variant that had been described for isolates from East Asia. Analysis of 66 ETBF strains from different sources showed that
bft-1
is the most frequent allele, being present in 65% of isolates; it is largely predominant in isolates from feces of adults, while
bft-2
is present in isolates from feces of children. This association is statistically significant (
P
, 0.0064). Sixteen strains were examined by Southern hybridization using, as probes, the
bft
and second metalloprotease genes, both included in a pathogenicity islet. Five strains were found to harbor double copies of both genes, suggesting that the whole islet was duplicated. Four of these strains, harboring
bft-1
(three strains) or
bft-2
(one strain), were found to produce a large amount of biologically active toxin, as determined by a cytotoxicity assay with HT-29 cells. The strains harboring
bft-3
, either in a single copy or in double copies, produced the smallest amount of toxin in our collection.
Prevalence of Vancomycin-Resistant Enterococci in Fecal Samples from Hospitalized Patients and Nonhospitalized Controls in a Cattle-Rearing Area of France
Authors: Gambarotto Karine , Ploy Marie-Cécile , Turlure Pascal , Grélaud Carole , Martin Christian , Bordessoule Dominique , Denis Francois 
Published: December 2019

ABSTRACT

Vancomycin-resistant enterococci (VRE) have emerged as nosocomial pathogens over the last decade, but little is known about their epidemiology. We report on the prevalence of VRE fecal colonization on the basis of a prospective study among patients hospitalized in a hematology intensive care unit and among nonhospitalized subjects living in the local community. A total of 243 rectal swabs from hematology patients and 169 stool samples from the control group were inoculated onto bile-esculin agar plates with and without 6 mg of vancomycin per liter and into an enrichment bile-esculin broth supplemented with 4 mg of vancomycin per liter. A total of 37% of the hospitalized patients and 11.8% of the subjects from the community were found to be VRE carriers. A total of 65 VRE strains were isolated: 12 (18.5%)
E. faecium
, 46 (70.7%)
E. gallinarum
, and 7 (10.8%)
E. casseliflavus
strains. No
E. faecalis
strains were detected. All the
E. faecium
strains were of the
vanA
genotype. Molecular typing by pulsed-field gel electrophoresis revealed a different pattern for each
vanA
VRE strain that originated from an individual subject. To our knowledge, this is the first study to be carried out in a cattle-rearing region of France. It reports a higher VRE prevalence than that reported in previous European or U.S. studies. A partial explanation is the use of an enrichment broth step which enabled detection of strains which would otherwise have been missed, but the fact that subjects and patients were recruited from a predominantly agricultural area where vancomycin-related antibiotics have recently been used in animal husbandry could also contribute to the high levels of VRE in patients and subjects alike.
PCR-Based Assay To Quantify Human Immunodeficiency Virus Type 1 DNA in Peripheral Blood Mononuclear Cells
Authors: Christopherson Cindy , Kidane Yorda , Conway Brian , Krowka John , Sheppard Haynes , Kwok Shirley 
Published: December 2019

ABSTRACT

An assay that quantifies the amount of human immunodeficiency virus type 1 (HIV-1) DNA in peripheral blood mononuclear cells has been developed. PCR amplification of the HIV-1 DNA is performed in the presence of an internal quantitation standard, and colorimetric detection of the amplified product is performed with microwell plates. The copies of HIV-1 DNA are normalized to total genomic DNA input. The assay has an analytical sensitivity of 10 input copies per amplification reaction and a three-log detection range. In an analysis of sequential samples from patients on combination therapy, HIV-1 DNA was quantifiable for all individuals tested, including those with undetectable plasma HIV-1 RNA. In a separate study, a comparison of HIV-1 DNA levels was made with a group of long-term survivors and progressors. The mean HIV-1 DNA levels were lower in the long-term survivors than in the progressors (
P
, 0.04). The mean HIV-1 RNA levels were also lower, but the difference was not statistically significant (
P
, 0.164). A quantitative DNA assay will provide an additional tool to gain insight into the natural history of infection and the continued efficacy of potent antiretroviral therapies.
Line Probe Assay for Monitoring Drug Resistance in Hepatitis B Virus-Infected Patients during Antiviral Therapy
Authors: Stuyver Lieven , Van Geyt Caroline , De Gendt Sija , Van Reybroeck Georges , Zoulim Fabien , Leroux-Roels Geert , Rossau Rudi 
Published: December 2019

ABSTRACT
Since the introduction of antiviral compounds such as lamivudine and famciclovir in the treatment schedules of patients with chronic hepatitis B virus (HBV) infection, the accumulation of a variety of mutations in the HBV polymerase gene has been observed. The selection of these mutations is generally considered the cause of viral nonresponsiveness and treatment failure. Therefore, the detection of these mutations is of clinical importance. Previously genotyped HBV strains isolated from treated and untreated patients were amplified with primers specific for the HBV polymerase region from amino acids 465 to 562. Amplified products were cloned into plasmid vectors. The clones were used as reference strains. A set of 38 highly specific oligonucleotide probes covering three different codon positions, L528M, M552V/I, and V/L/M555I, were selected. These probes were applied as 19 different lines on a membrane strip. The strips were then hybridized with PCR fragments from the reference panel, revealing the amino acids at the three codon positions simultaneously for each clone. PCR products generated from two patients infected with HBV genotypes A and C, respectively, and treated with nucleoside analogs were analyzed on these strips. A gradual increase in genetic HBV polymerase complexity was observed in follow-up samples compared to that in pretreatment samples. Additional analysis of HBV polymerase DNA fragments in recombinant plasmid clones demonstrated the existence of (i) clones with double mutations, (ii) clones with single mutations at either codon 528, 552, or 555, and (iii) the simultaneous occurrence of two or more viral populations within one sample. This line probe assay detected the complex quasispecies nature of HBV and provided some insight into the dynamics of resistance mutations.
Application of 16S rRNA Gene Sequencing To Identify
Bordetella hinzii
as the Causative Agent of Fatal Septicemia
Authors: Kattar M. M. , Chavez J. F. , Limaye A. P. , Rassoulian-Barrett S. L. , Yarfitz S. L. , Carlson L. C. , Houze Y. , Swanzy S. , Wood B. L. , Cookson B. T. 
Published: December 2019

ABSTRACT

We report on the first case of fatal septicemia caused by
Bordetella hinzii
. The causative organism exhibited a biochemical profile identical to that of
Bordetella avium
with three commercial identification systems (API 20E, API 20 NE, and Vitek GNI+ card). However, its cellular fatty acid profile was not typical for either
B. avium
or previously reported strains of
B. hinzii
. Presumptive identification of the patient's isolate was accomplished by traditional biochemical testing, and definitive identification was achieved by 16S rRNA gene sequence analysis. Phenotypic features useful in distinguishing
B. hinzii
from
B. avium
were production of alkali from malonate and resistance to several antimicrobial agents.
Genotypic Stability of Cold-Adapted Influenza Virus Vaccine in an Efficacy Clinical Trial
Authors: Cha Tai-An , Kao Kevin , Zhao Jackie , Fast Patricia E. , Mendelman Paul M. , Arvin Ann 
Published: December 2019

ABSTRACT
An investigational live influenza virus vaccine, FluMist, contains three cold-adapted H1N1, H3N2, and B influenza viruses. The vaccine viruses are 6/2 reassortants, in which the hemagglutinin (HA) and neuraminidase (NA) genes are derived from the circulating wild-type viruses and the remaining six genes are derived from the cold-adapted master donor strains. The six genes from the cold-adapted master donor strains ensure the attenuation, and the HA and NA genes from the wild-type viruses confer the ability to induce protective immunity against contemporary influenza strains. The genotypic stability of this vaccine was studied by employing clinical samples collected during an efficacy trial. Viruses present in the nasal and throat swab specimens and in supernatants after culturing the specimens were detected and subtyped by multiplex reverse transcriptase (RT)-PCR. Complete genotypes of these detected viruses were determined by a combination of RT-PCR and restriction fragment length polymorphism, multiplex RT-PCR and fluorescent single-strand conformation polymorphism, and nucleic acid sequencing analysis. The FluMist vaccine appeared to be genotypically stable after replication in the human host. All viruses detected during the 2-week postvaccination period were shed vaccine viruses and had maintained the 6/2 genotype.
Simultaneous Approach for Nonculture PCR-Based Identification and Serogroup Prediction of
Neisseria meningitidis
Authors: Taha Muhamed-Kheir 
Published: December 2019

ABSTRACT

A nonculture PCR-based method to characterize
Neisseria meningitidis
was used to test 225 clinical specimens. PCR correctly identified and predicted the serogroups of
N. meningitidis
of culture-proven meningococcal diseases and confirmed this diagnosis in 35% of suspected samples. This approach could be useful when culture fails to isolate
N. meningitidis
.
Clinical Evaluation of the BDProbeTec ET System for Rapid Detection of
Mycobacterium tuberculosis
Authors: Bergmann John S. , Keating William E. , Woods Gail L. 
Published: December 2019

ABSTRACT

The performance of the BDProbeTec ET system (BD Biosciences, Sparks, Md.) for direct detection of
Mycobacterium tuberculosis
complex (MTBC) in respiratory specimens was evaluated by comparing results to those of conventional mycobacterial culture performed with the BACTEC 460 TB system and Middlebrook 7H11 biplates. Patients known to have been on antituberculous therapy were excluded from the analysis. Of 600 evaluable specimens (4 specimens were excluded from the analysis due to failure of the internal amplification control [IAC]) from 332 patients, 57 grew mycobacteria; 16 were MTBC (from 12 patients), and 41 were nontuberculous mycobacteria. Of the 16 MTBC culture-positive specimens, 12 were smear positive and 4 were smear negative. BDProbeTec ET detected 14 of the 16 MTBC culture-positive specimens, resulting in initial overall sensitivity, specificity, and positive and negative predictive values of 87.5, 99.0, 70.0, and 99.7%, respectively. After resolution of discrepancies by review of medical records and retesting of samples yielding discordant MTBC culture and BDProbeTec ET results, the revised overall sensitivity, specificity, and positive and negative predictive values of the BDProbeTec ET were respectively 93.8, 99.8, 93.8, and 99.8% by specimen and 91.7, 99.7, 91.7, and 99.7% by patient. The BDProbeTec ET System offers the distinct advantage of including an IAC in the specimen well. These data suggest that the test performance is very good, especially for smear-positive samples. However, the number of patients with tuberculosis in our study, especially those with smear-negative disease, was small; therefore, additional studies are needed.