bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of
Mycobacterium tuberculosis
Complex in Sputum Specimens by the Automated Roche Cobas Amplicor Mycobacterium Tuberculosis Test
Authors: Rajalahti Iiris , Vuorinen Pauli , Nieminen Markku M. , Miettinen Ari 
Published: December 2019

ABSTRACT

Three hundred twenty-four sputum specimens from 151 patients with suspected active pulmonary tuberculosis were tested for the presence of the
Mycobacterium tuberculosis
complex with auramine fluorochrome stain and automated PCR assay (Roche Cobas Amplicor Mycobacterium Tuberculosis Test [MTB]). The results were compared with those of the conventional Löwenstein-Jensen tube culture and the BACTEC radiometer liquid culture. A total of 76 specimens from 32 patients were culture positive for
M. tuberculosis
. In addition, 37 specimens from 15 patients were smear and culture positive for other
Mycobacterium
species but negative by the present nucleic acid amplification method and thus were not included in the comparison. Compared with culture, the sensitivities, specificities, and positive and negative predictive values for acid-fast smear were 67, 98, 93, and 91% and those for the Cobas Amplicor MTB were 83, 99, 97, and 95%, respectively. When three consecutive sputum specimens per patient could be obtained, the sensitivity of the Cobas Amplicor MTB improved to 91%, whereas the sensitivity of the acid-fast smear remained unchanged.
Bordetella parapertussis
Infection in Children: Epidemiology, Clinical Symptoms, and Molecular Characteristics of Isolates
Authors: Mastrantonio Paola , Stefanelli P. , Giuliano M. , Rojas Y. Herrera , Ciofi degli Atti M. , Anemona A. , Tozzi A. E. 
Published: December 2019

ABSTRACT

The clinical trial conducted in Italy to evaluate the efficacy of acellular pertussis vaccines provided an opportunity to estimate the frequency of clinical infections with
Bordetella parapertussis
and to compare the clinical characteristics of children suffering from
Bordetella pertussis
illness with those of children with
B. parapertussis
illness. This study dealt with 76
B. parapertussis
infections diagnosed from a population of 15,601 children participating in the follow-up of suspected cases of pertussis. An overall incidence of 2.1 cases of laboratory-confirmed parapertussis per 1,000 person-years was observed. Children affected by
B. parapertussis
infections showed a less severe clinical picture both in the duration of symptoms and in the percentage of patients affected, even when compared with vaccinated children with pertussis. To characterize the isolated strains, we performed assays for susceptibility to erythromycin and sulfamethoxazole-trimethoprim, and we examined the genomic DNAs by pulsed-field gel electrophoresis. The results showed a high degree of genetic stability among
B. parapertussis
strains regardless of time of collection and geographical distribution.
Growth and Survival ofHelicobacter pyloriin Defined Medium and Susceptibility to Brij 78
Authors: Albertson N. , Wenngren I. , Sjöström J.-E. 
Published: December 2019

ABSTRACTThe gastrointestinal pathogenHelicobacter pylorirequires supplementation with either fetal calf serum (FCS), bovine serum albumin (BSA), or (2,6-dimethyl)-β-cyclodextrin (CD) for growth in a complex or defined medium. Because the availability of medium in which all components were chemically defined would facilitate metabolic studies ofH. pylori, growth of the type strain, ATCC 43504, was compared in a defined medium with different growth additives. The dependency ofH. pylorigrowth on FCS or BSA in a defined medium could partially be replaced by dependency on CD and cholesterol when the last two components were both added to the defined medium. Growth and cell yield were not affected by the addition of glucose, but the culture viability (numbers of CFU per milliliter was extended. Because therapeutic antifoams are used to relieve gastrointestinal symptoms we studied whether the unique susceptibility ofH. pylorito the emulsifier polyoxyethylene-20-stearylether (Brij 78) was growth dependent or medium specific. The bactericidal activity exerted in buffer at pH 5 was independent of the preculture medium, and a 5-h exposure of the bacteria to 1.28 to 2.56 μg of Brij 78 per ml reduced the numbers of viable bacteria by >5 log10. The MICs (0.16 to 0.32 μg/ml) were lower than the corresponding minimal bactericidal concentrations in different growth media and were affected by FCS or BSA. In conclusion, CD plus cholesterol promotes the growth ofH. pyloriin a serum-free defined medium in which glucose enhances cell viability. The antibacterial activity exerted by Brij 78 is neither growth dependent nor medium specific.
Recombinant Mouse-Human Chimeric Antibodies as Calibrators in Immunoassays That Measure Antibodies toToxoplasma gondii
Authors: Hackett John , Hoff-Velk Jane , Golden Alan , Brashear Jeff , Robinson John , Rapp Margaret , Klass Michael , Ostrow David H. , Mandecki Wlodek 
Published: December 2019

ABSTRACTIn the present study, we examined the feasibility of using recombinant antibodies containing murine variable regions and human constant regions as calibrators or controls in immunoassays. As a model system, we chose the Abbott IMx Toxo immunoglobulin M (IgM) and Toxo IgG assays designed to detect antibodies toToxoplasma gondii. Two mouse monoclonal antibodies were selected based on their reactivity to theT. gondiiantigens P30 and P66. Heavy- and light-chain variable-region genes were cloned from both hybridomas and transferred into immunoglobulin expression vectors containing human kappa and IgG1 or IgM constant regions. The constructs were stably transfected into Sp2/0-Ag14 cells. In the IMx Toxo IgG assay, immunoreactivity of the anti-P30 chimeric IgG1 antibody paralleled that of the positive human plasma-derived assay calibrators. Signal generated with the anti-P66 chimeric IgG1 antibody was observed to plateau below the maximal reactivity observed for the assay calibrator. Examination of the IgM chimeric antibodies in the IMx Toxo IgM assay revealed that both the anti-P30 and anti-P66 antibodies matched the assay index calibrator manufactured with human Toxo IgM-positive plasma. When evaluated with patient samples, the correlation between results obtained with the chimeric antibody calibrators and the positive human plasma calibrators was ≥0.985. These data demonstrate that chimeric mouse-human antibodies are a viable alternative to high-titer positive human plasma for the manufacture of calibrators and controls for diagnostic assays.
Phylogenetic Placement of Rickettsiae from the TicksAmblyomma americanumandIxodes scapularis
Authors: Weller Susan J. , Baldridge Gerald D. , Munderloh Ulrike G. , Noda Hiroaki , Simser Jason , Kurtti Timothy J. 
Published: December 2019

ABSTRACTA rickettsial isolate (isolate MOAa) belonging to the spotted fever group (SFG) was obtained from the lone star tickAmblyomma americanum. We used PCR to characterize the genes for the rickettsial outer membrane proteins rOmpA and rOmpB. We sequenced the PCR products (domains I of both therompAgene and therompBgene) of MOAa and WB-8-2, another rickettsial isolate fromA. americanum. To place MOAa and WB-8-2 and two other nonpathogenic isolates (Rickettsia rickettsiiHlp2 andRickettsia montanaM5/6) with respect to their putative sister species, we included them in a phylogenetic analysis of 9Rickettsiaspecies and 10Rickettsiastrains. Our phylogenetic results implied three evolutionary lineages of SFG rickettsiae and that WB-8-2 and MOAa were most closely related toR. montana. New World isolates were not the most closely related to each other (they did not form a clade). Rather, our results supported four independent origins (introductions) of rickettsiae into North America from different Old World regions. The results of our phylogenetic analysis did not support the hypothesis of a stable coevolution of rickettsiae and their tick hosts. Finally, we examined therompAgene of a nonpathogenic rickettsial symbiont isolated from the tickIxodes scapularis. In a phylogenetic analysis, the symbiont was placed as the sister toR. montanaand its isolates. The relationship of this symbiont toR. montanaraised questions as to the potential origin of pathogenic SFG rickettsiae from nonpathogenic tick symbionts, or vice versa.
Computerized Analysis of Restriction Fragment Length Polymorphism Patterns: Comparative Evaluation of Two Commercial Software Packages
Authors: Gerner-Smidt P. , Graves L. M. , Hunter Susan , Swaminathan B. 
Published: December 2019

ABSTRACT

Two computerized restriction fragment length polymorphism pattern analysis systems, the BioImage system and the GelCompar system (Molecular Analyst Fingerprinting Plus in the United States), were compared. The two systems use different approaches to compare patterns from different gels. In GelCompar, a standard reference pattern in one gel is used to normalize subsequent gels containing lanes with the same reference pattern. In BioImage, the molecular sizes of the fragments are calculated from size standards present in each gel. The molecular size estimates obtained with the two systems for 12 restriction fragments of phage λ were between 97 and 101% of their actual sizes, with a standard deviation of less than 1% of the average estimated size for most fragments. At the window sizes used for analysis, the GelCompar system performed somewhat better than BioImage in identifying visually identical patterns generated by electrophoretic separation of
Hha
I-restricted DNA of
Listeria monocytogenes
. Both systems require the user to make critical decisions in the analysis. It is very important to visually verify that the systems are finding all bands in each lane and that no artifacts are being detected; both systems allow manual editing. It is also important to verify results obtained in the pattern matching or clustering portions of the analysis.
Effects of Following National Committee for Clinical Laboratory Standards and Deutsche Industrie Norm-Medizinische Mikrobiologie Guidelines, Country of Isolate Origin, and Site of Infection on Susceptibility of
Escherichia coli
to Amoxicillin-Clavulanate (Augmentin)
Authors: Simpson I. , Durodie J. , Knott S. , Shea B. , Wilson J. , Machka K. 
Published: December 2019

ABSTRACT

Amoxicillin-clavulanate (Augmentin), as a combination of two active agents, poses extra challenges over single agents in establishing clinically relevant breakpoints for in vitro susceptibility tests. Hence, reported differences in amoxicillin-clavulanate percent susceptibilities among
Escherichia coli
isolates may reflect localized resistance problems and/or methodological differences in susceptibility testing and breakpoint criteria. The objectives of the present study were to determine the effects of (i) methodology, e.g., those of the National Committee for Clinical Laboratory Standards (NCCLS) and the Deutsche Industrie Norm-Medizinische Mikrobiologie (DIN), (ii) country of origin (Spain, France, and Germany), and (iii) site of infection (urinary tract, intra-abdominal sepsis, or other site[s]) upon the incidence of susceptibility to amoxicillin-clavulanate in 185 clinical isolates of
E. coli
. Cefuroxime and cefotaxime were included for comparison. The use of NCCLS methodology resulted in different distribution of amoxicillin-clavulanate MICs than that obtained with the DIN methodology, a difference highlighted by the 10% more strains found to be within the 8- to 32-μg/ml MIC range. This difference reflects the differing amounts of clavulanic acid present. NCCLS and DIN methodologies also produce different MIC distributions for cefotaxime but not for cefuroxime. Implementation of NCCLS and DIN breakpoints produced markedly different incidences of strains that were found to be susceptible, intermediate or resistant to amoxicillin-clavulanate. A total of 86.5% strains were found to be susceptible to amoxicillin-clavulanate by the NCCLS methodology, whereas only 43.8% were found to be susceptible by the DIN methodology. Similarly, 4.3% of the strains were found to be resistant by NCCLS guidelines compared to 21.1% by the DIN guidelines. The use of DIN breakpoints resulted in a fivefold-higher incidence of strains categorized as resistant to cefuroxime. There were no marked differences due to country of origin upon the MIC distributions for amoxicillin-clavulanate, cefuroxime, or cefotaxime, as determined with the NCCLS guidelines. Isolates from urinary tract and intra-abdominal infections were generally more resistant to amoxicillin-clavulanate than were isolates from other sites of infection.
Buffered Plate Antigen Test as a Screening Test for Diagnosis of Human Brucellosis
Authors: Lucero Nidia E. , Bolpe Jorge E. 
Published: December 2019

ABSTRACT
Brucellosis in Argentina is currently investigated in bank donor blood by the standard plate agglutination test (PAT). This study evaluated the buffered plate antigen test (BPA), now used to screen for bovine brucellosis, as a screen for human disease. Of 57 sera from patients with culture-confirmed brucellosis, 100% were detected with the BPA. Of 142 sera positive by rose bengal (RB) and complement fixation (CF), from patients with clinical evidence of brucellosis, the BPA detected 100%. Of 307 sera from a nonsymptomatic population that were RB and CF negative, the BPA detected 99.67% of the negative sera. The data indicate that the BPA is satisfactory compared to the other agglutination tests employed. It is an inexpensive and practical screening test and reduces the nonspecific reactions detected by the PAT.
Evaluation of a Membrane Filter Assay System, Ortho HCV Ab Quik Pack, for Detection of Anti-Hepatitis C Virus Antibody
Authors: Kodama Takanari , Ichiyama Satoshi , Sato Kumiko , Nada Toshi , Nakashima Nobuo 
Published: December 2019

ABSTRACT
A simple membrane immunoassay assay system, Quik Pack, for the detection of hepatitis C virus antibody was compared with two enzyme-linked immunosorbent assays (ELISAs) in a study of 600 serum samples. Quik Pack exhibited excellent sensitivity and specificity: 96.0 and 99.7%, respectively, versus the ELISA-2 and 99.7 and 99.4%, respectively, versus the ELISA-3.
Molecular Typing of Environmental and Patient Isolates of
Aspergillus fumigatus
from Various Hospital Settings
Authors: Chazalet Valérie , Debeaupuis Jean-Paul , Sarfati Jacqueline , Lortholary Jacques , Ribaud Patricia , Shah Pramod , Cornet Muriel , Thien Hoang Vu , Gluckman Eliane , Brücker Gilles , Latgé Jean-Paul 
Published: December 2019

ABSTRACT

Fingerprinting of more than 700 clinical and environmental isolates of
Aspergillus fumigatus
from four differential hospital settings was undertaken with a dispersed repeated DNA sequence. The analysis of the environmental isolates showed that the airborne
A. fumigatus
population is extremely diverse, with 85% of the strains being represented as a single genotype isolated once. The remaining 15% of the strains were isolated several times and were able to persist for several months in the same hospital environment. No strains were found to be associated with a specific location inside the hospital, and identical strains were isolated from different buildings of the hospital and outdoors. Isolation of the same strain both from patients and from the environment of the same hospital is highly suggestive of a nosocomial infection. The characteristics of the environmental fungal population explains the two main results obtained from the typing of the clinical isolates: (i) the absence of a common strain responsible for an invasive aspergillosis outbreak results from the extreme diversity of the environmental population of
A. fumigatus
in contact with the patients, and (ii) patients hospitalized in different wards of the same hospital can be infected with the same strain since every patient might inhale the same spore population.
Production and Characterization ofEhrlichia risticii, the Agent of Potomac Horse Fever, from Snails (Pleuroceridae:Jugaspp.) in Aquarium Culture and Genetic Comparison to Equine Strains
Authors: Reubel Gerhard H. , Barlough Jeffrey E. , Madigan John E. 
Published: December 2019

ABSTRACTWe report on the production and characterization ofEhrlichia risticii, the agent of Potomac horse fever (PHF), from snails (Pleuroceridae:Jugaspp.) maintained in aquarium culture and compare it genetically to equine strains. Snails were collected from stream waters on a pasture in Siskiyou County, Calif., where PHF is enzootic and were maintained for several weeks in freshwater aquaria in the laboratory. Upon exposure to temperatures above 22°C the snails released trematode cercariae tentatively identified as virgulate cercariae. Fragments of three different genes (genes for 16S rRNA, thegroESLheat shock operon, and the 51-kDa major antigen) were amplified from cercaria lysates by PCR and sequenced. Genetic information was also obtained fromE. risticiistrains from horses with PHF. The PCR positivity of snail secretions was associated with the presence of trematode cercariae. Sequence analysis of the three genes indicated that the source organism closely resembledE. risticii, and the sequences of all three genes were virtually identical to those of the genes of an equineE. risticiistrain from a property near the snail collection site. Phylogenetic analyses of the three genes indicated the presence of geographicalE. risticiistrain clusters.
Use of Tests for Acidification of Methyl-α-
d
-Glucopyranoside and Susceptibility to Efrotomycin for Differentiation of Strains of
Enterococcus
and Some Related Genera
Authors: Carvalho Maria Da Glória S. , Teixeira Lúcia M. , Facklam Richard R. 
Published: December 2019

ABSTRACT

A total of 107
Enterococcus
strains, 10
Vagococcus fluvialis
strains, and 8
Lactococcus garvieae
strains were tested for acidification of methyl-α-
d
-glucopyranoside (MGP) and susceptibility to 100-μg efrotomycin (EFRO) disks. All 26 strains of
Enterococcus casseliflavus
, including 3 nonmotile and 2 nonpigmented strains, acidified MGP and were resistant to EFRO. All 22 strains of
Enterococcus gallinarum
, including 5 nonmotile strains, also acidified MGP and were resistant to EFRO. None of the 26 strains of
Enterococcus faecium
acidified MGP, and all were susceptible to EFRO. Although all 12
Enterococcus faecalis
strains were also negative in the MGP test, they were resistant to EFRO. Other enterococcal strains gave variable results. All 10 strains of
V. fluvialis
and all 8 strains of
L. garvieae
gave positive and negative results, respectively, in the MGP test and were, respectively, resistant and susceptible to EFRO. These results indicate that tests of the production of acid from MGP and susceptibility to EFRO can be used as adjunct tests in the identification of typical and atypical strains of enterococci in the clinical microbiology laboratory.
Rapid Extraction of Genomic DNA from Medically Important Yeasts and Filamentous Fungi by High-Speed Cell Disruption
Authors: Müller Frank-Michael C. , Werner Katherine E. , Kasai Miki , Francesconi Andrea , Chanock Stephen J. , Walsh Thomas J. 
Published: December 2019

ABSTRACT

Current methods of DNA extraction from different fungal pathogens are often time-consuming and require the use of toxic chemicals. DNA isolation from some fungal organisms is difficult due to cell walls or capsules that are not readily susceptible to lysis. We therefore investigated a new and rapid DNA isolation method using high-speed cell disruption (HSCD) incorporating chaotropic reagents and lysing matrices in comparison to standard phenol-chloroform (PC) extraction protocols for isolation of DNA from three medically important yeasts (
Candida albicans
,
Cryptococcus neoformans
, and
Trichosporon beigelii
) and two filamentous fungi (
Aspergillus fumigatus
and
Fusarium solani
). Additional extractions by HSCD were performed on
Saccharomyces cerevisiae
,
Pseudallescheria boydii
, and
Rhizopus arrhizus
. Two different inocula (10
8
and 10
7
CFU) were compared for optimization of obtained yields. The entire extraction procedure was performed on as many as 12 samples within 1 h compared to 6 h for PC extraction. In comparison to the PC procedure, HSCD DNA extraction demonstrated significantly greater yields for 10
8
CFU of
C. albicans
,
T. beigelii
,
A. fumigatus
, and
F. solani
(
P
≤ 0.005), 10
7
CFU of
C. neoformans
(
P
≤ 0.05), and 10
7
CFU of
A. fumigatus
(
P
≤ 0.01). Yields were within the same range for 10
8
CFU of
C. neoformans
and 10
7
CFU of
C. albicans
for both HSCD extraction and PC extraction. For 10
7
CFU of
T. beigelii
, PC extraction resulted in a greater yield than did HSCD (
P
≤ 0.05). Yields obtained from 10
8
and 10
7
CFU were significantly greater for filamentous fungi than for yeasts by the HSCD extraction procedure (
P
< 0.0001). By the PC extraction procedure, differences were not significant. For all eight organisms, the rapid extraction procedure resulted in good yield, integrity, and quality of DNA as demonstrated by restriction fragment length polymorphism, PCR, and random amplified polymorphic DNA. We conclude that mechanical disruption of fungal cells by HSCD is a safe, rapid, and efficient procedure for extracting genomic DNA from medically important yeasts and especially from filamentous fungi.
Comparison of Culture and PCR for Detection of
Burkholderia cepacia
in Sputum Samples of Patients with Cystic Fibrosis
Authors: Whitby Paul W. , Dick Hani L. N. , Campbell Preston W. , Tullis D. Elizabeth , Matlow Anne , Stull Terrence L. 
Published: December 2019

ABSTRACT

We investigated the utility of PCR to detect
Burkholderia cepacia
directly in sputum samples at two cystic fibrosis (CF) centers serving children and adults. Following liquefaction of the sputa by using
N
-acetyl-
l
-cysteine, DNA was isolated and analyzed by PCRs with three different primer pairs directed toward bacterial rRNA loci. Two primer pairs were putatively specific for
B. cepacia
. The other pair, which universally amplifies a band from all bacteria, served as a control. Sputum samples were obtained from 219 patients and analyzed independently by culture and by PCR to detect
B. cepacia
. The analyses were performed blinded with respect to each other. The results of the PCR with sputa demonstrated that the primers directed to the 16S loci demonstrated approximately 95% concordance with culture results and were more specific than those amplifying the 16S to 23S spacer region. In addition, the 16S primer pair putatively identified
B. cepacia
in seven patients whose sputa were culture negative at this time. Of these culture-negative patients, five had sputum samples that were culture positive for
B. cepacia
either prior or subsequent to this study. The results of this study indicate the utility of PCR as a diagnostic method for the rapid identification of
B. cepacia
in sputum samples of CF patients. We anticipate that improvements in our taxonomic understanding may allow the design of more specific primers for detection of each species of the
B. cepacia
complex in sputum samples.