bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Evaluation of Initial and New Versions of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for Direct Detection of
Mycobacterium tuberculosis
in Respiratory and Nonrespiratory Specimens
Authors: Gamboa Fredy , Fernandez Gregorio , Padilla Eduardo , Manterola José M. , Lonca Joan , Cardona Pere Joan , Matas Lurdes , Ausina Vicente 
Published: December 2019

ABSTRACT

We evaluated the initial version of the Amplified Mycobacterium Tuberculosis Direct Test (Gen-Probe) (AMTDT 1) and the new version of AMTDT (AMTDT 2) for the detection of
Mycobacterium tuberculosis
directly from respiratory and nonrespiratory samples and compared the results with those of culture and staining methods. The assays were applied to 410 respiratory and 272 nonrespiratory samples collected from 515 patients. The combination of the culture results and clinical diagnosis was considered to be the “gold standard.” Ninety-five respiratory specimens were collected from 67 patients with a diagnosis of pulmonary tuberculosis (TB) and 68 nonrespiratory specimens were collected from 61 patients with a diagnosis of extrapulmonary TB. With respiratory specimens, the sensitivity, specificity, and positive and negative predictive values were 83, 100, 100, and 96%, respectively, for AMTDT 1 and 94.7, 100, 100, and 98.4%, respectively, for AMTDT 2. With nonrespiratory specimens, the sensitivity, specificity, and positive and negative predictive values were 83, 100, 100, and 94%, respectively, for AMTDT 1 and 86.8, 100, 100, and 98.4%, respectively, for AMTDT 2. The overall results of AMTDT 1 and AMTDT 2 were concordant for 97% (661 of 682) of the samples. Statistically significant differences in sensitivities were found between AMTDT 1 and AMTDT 2 with respiratory specimens. It was concluded that although both nucleic acid amplification methods are rapid, sensitive, and specific for the detection of
M. tuberculosis
complex in all types of clinical samples, AMTDT 2 appeared to be more sensitive than AMTDT 1 when applied to smear-negative specimens. In contrast AMTDT 2 is more susceptible than AMTDT 1 to inhibitory substances in the amplification reaction. The turnaround time of AMTDT 2 is shorter (3.5 h) than that for AMTDT 1 (5 h).
Immunosorbent Assay Based on Recombinant Hemagglutinin Protein Produced in a High-Efficiency Mammalian Expression System for Surveillance of Measles Immunity
Authors: Bouche Fabienne , Ammerlaan Wim , Berthet Francoise , Houard Sophie , Schneider Francois , Muller Claude P. 
Published: December 2019

ABSTRACT

Recombinant hemagglutinin (H) protein of the measles virus (MV) was produced in mammalian cells with a high-yield expression system based on the Semliki Forest virus replicon. Crude membrane preparations of H protein-transfected BHK-21 cells were used to coat microtiter plates to measure specific immunoglobulin G antibodies in 228 serologically defined serum samples mainly from measles late-convalescent adults. The titers by the enzyme-linked immunosorbent assay for the H protein (H-ELISA) closely correlated with neutralization test (NT) titers (
R
2
= 0.66), hemagglutination inhibition test (HI) titers (
R
2
= 0.64), with the titers from a certified commercial ELISA based on whole MV-infected cells (MV-ELISA;
R
2
= 0.45). The correlations described above were better than those of the commercial MV-ELISA titers with the NT (
R
2
= 0.52) or HI (
R
2
= 0.48) titers. By using the 2nd International Standard for anti-measles serum, the detection level of the assay corresponds to 215 mIU/ml for undiluted serum, which corresponds to the estimated threshold for protective immunity. The specificity, accuracy, and positive predictive value were, in general, better for the H-ELISA than for a commercial MV-ELISA, independent of whether HI, NT, or HI and NT were used as “gold standards.” In contrast, the H-ELISA proved to be slightly less sensitive than the MV-ELISA (sensitivities, 98.6 versus 99.5%, respectively;
P
was not significant). The assays did not differ significantly in the number of serum samples with positive HI and NT results (
n
= 212) which measured false negative (H-ELISA, 2 of 212 [0.94%]; MV-ELISA, 1 of 212 [0.47%]), but the H-ELISA detected significantly more measles-susceptible individuals than the MV-ELISA (10 of 11 versus 3 of 11, respectively;
P
< 0.05) among the individuals whose sera had negative HI and NT results. Our data demonstrate that the H-protein preparation that we describe could be a cost-effective alternative to current whole-virus-based ELISAs for surveillance for immunity to measles and that such an assay could be more efficient in detecting susceptibility to measles. Furthermore, unlike whole MV-based antigens, H-protein would also be suitable for use in the development of a simple field test for the diagnosis of measles.
Electrophoretic Karyotypes and Genome Sizing of the Pathogenic Fungus
Paracoccidioides brasiliensis
Authors: Nogueira Cano Maria Isabel , Cisalpino Patrícia Silva , Galindo Ivan , Ramírez José Luiz , Mortara Renato Arruda , da Silveira José Franco 
Published: December 2019

ABSTRACT

Here we present the karyotype analysis and genome sizing of
Paracoccidioides brasiliensis
, a pathogen refractory to conventional genetic analysis. We have established pulsed-field gel electrophoresis (PFGE) conditions to resolve the high-molecular-weight chromosomal bands of two clinical isolates of
P. brasiliensis
. Both isolates showed four megabase-sized bands, ranging from 2.0 to 10.0 Mbp. Significant differences in chromosome sizes and in the chromosomal location of genes for the gp43 antigen and chitin synthase were found. Different technical approaches were employed to estimate the DNA content and to define the ploidy of
P. brasiliensis
. An estimated genome size in the range of 45.7 to 60.9 Mbp was provided by the analysis of data generated by measuring the amplitude of fluorescence intensity of DAPI (4′,6-diamidino-2-phenylindole)-stained nuclei (by confocal microscopy). The nuclear genome size estimated by confocal microscopy is twice that estimated by the average sum of the molecular weight of chromosome-sized DNA molecules by PFGE, suggesting that each separated
P. brasiliensis
chromosomal band is diploid.
PCR Methods for Rapid Identification and Characterization of
Actinobacillus seminis
Strains
Authors: Appuhamy S. , Coote J. G. , Low J. C. , Parton R. 
Published: December 2019

ABSTRACT

Twenty-four isolates of
Actinobacillus seminis
were typed by PCR ribotyping, repetitive extragenic palindromic element (REP)-based PCR, and enterobacterial repetitive intergenic consensus (ERIC)-based PCR. Five types were distinguished by REP-PCR, and nine types were distinguished by ERIC-PCR. PCR ribotyping produced the simplest pattern and could be useful for identification of
A. seminis
and for its differentiation from related species. REP- and ERIC-PCR could be used for strain differentiation in epidemiological studies of
A. seminis.
Optochin Revisited: Defining the Optimal Type of Blood Agar for Presumptive Identification of
Streptococcus pneumoniae
Authors: Gardam M. A. , Miller M. A. 
Published: December 2019

ABSTRACT

To determine the optimal media for optochin susceptibility testing of
Streptococcus pneumoniae
, we measured inhibition zones for 72
S. pneumoniae
and 22
Streptococcus viridans
isolates on three blood-containing media. Because 15.3, 0, and 22.2% of
S. pneumoniae
organisms were misidentified on Columbia agar, Trypticase soy agar (TSA), and Mueller-Hinton agar, respectively, each containing sheep blood, we recommend that TSA-sheep blood agar be used.
Molecular Evidence that a Distinct
Vibrio cholerae
O1 Biotype El Tor Strain in Calcutta May Have Spread to the African Continent
Authors: Sharma Charu , Ghosh Amit , Dalsgaard A. , Forslund Anita , Ghosh R. K. , Bhattacharya S. K. , Nair G. Balakrish 
Published: December 2019

ABSTRACT

We present molecular evidence that a distinct genotype of
Vibrio cholerae
O1 which appeared in Calcutta, India, in September 1993 and which is characterized by a unique ribotype that is not found in the standardized ribotyping scheme of
V. cholerae
and that shows a specific pulsed-field gel electrophoresis profile may have spread to the west African country of Guinea-Bissau where it was responsible for an epidemic of cholera which began in October 1994 and continued into 1996.
Culture-Confirmed Reinfection of a Person with Different Strains of
Borrelia burgdorferi
Sensu Stricto
Authors: Golde William T. , Robinson-Dunn Barbara , Stobierski Mary Grace , Dykhuizen Daniel , Wang Ing-Nang , Carlson Vernette , Stiefel Harlan , Shiflett Susan , Campbell Grant L. 
Published: December 2019

ABSTRACT

In recent years, the utility of serum-based diagnostic testing for Lyme disease has improved substantially; however, recovery by culture of the bacterium from skin biopsies of suspected patients is still the only definitive laboratory test. Reinfection of patients has been assumed to occur but as yet has not been documented by serial isolates from the same person. We present a case of culture-confirmed reinfection of a patient in Menominee County, Michigan.
Borrelia burgdorferi
was isolated from the skin punch biopsy specimens during each episode of erythema migrans (EM) and was subjected to molecular strain typing, genetic analysis of two outer surface protein genes, protein profile analysis, and serum antibody response testing. Results show that these isolates are distinct strains of the bacterium and that the two episodes of EM were caused by independent infections. This report describes the documented, culture-confirmed reinfection of a human by two different strains of
B. burgdorferi.
Characterization of Staphylococci with Reduced Susceptibilities to Vancomycin and Other Glycopeptides
Authors: Tenover Fred C. , Lancaster Michael V. , Hill Bertha C. , Steward Christine D. , Stocker Sheila A. , Hancock Gary A. , O’Hara Caroline M. , Clark Nancye C. , Hiramatsu Keiichi 
Published: December 2019

ABSTRACT

During the last several years a series of staphylococcal isolates that demonstrated reduced susceptibility to vancomycin or other glycopeptides have been reported. We selected 12 isolates of staphylococci for which the vancomycin MICs were ≥4 μg/ml or for which the teicoplanin MICs were ≥8 μg/ml and 24 control strains for which the vancomycin MICs were ≤2 μg/ml or for which the teicoplanin MICs were ≤4 μg/ml to determine the ability of commercial susceptibility testing procedures and vancomycin agar screening methods to detect isolates with reduced glycopeptide susceptibility. By PCR analysis, none of the isolates with decreased glycopeptide susceptibility contained known vancomycin resistance genes. Broth microdilution tests held a full 24 h were best at detecting strains with reduced glycopeptide susceptibility. Disk diffusion did not differentiate the strains inhibited by 8 μg of vancomycin per ml from more susceptible isolates. Most of the isolates with reduced glycopeptide susceptibility were recognized by MicroScan conventional panels and Etest vancomycin strips. Sensititre panels read visually were more variable, although with some of the panels MICs of 8 μg/ml were noted for these isolates. Vitek results were 4 μg/ml for all strains for which the vancomycin MICs were ≥4 μg/ml. Vancomycin MICs on Rapid MicroScan panels were not predictive, giving MICs of either ≤2 or ≥16 μg/ml for these isolates. Commercial brain heart infusion vancomycin agar screening plates containing 6 μg of vancomycin per ml consistently differentiated those strains inhibited by 8 μg/ml from more susceptible strains. Vancomycin-containing media prepared in-house showed occasional growth of susceptible strains,
Staphylococcus aureus
ATCC 29213, and on occasion,
Enterococcus faecalis
ATCC 29212. Thus, strains of staphylococci with reduced susceptibility to glycopeptides, such as vancomycin, are best detected in the laboratory by nonautomated quantitative tests incubated for a full 24 h. Furthermore, it appears that commercial vancomycin agar screening plates can be used to detect these isolates.
Immunoglobulin M Capture Assay for Serologic Confirmation of Early Lyme Disease: Analysis of Immune Complexes with Biotinylated
Borrelia burgdorferi
Sonicate Enhanced with Flagellin Peptide Epitope
Authors: Brunner Michael , Stein Stanley , Mitchell Paul D. , Sigal Leonard H. 
Published: December 2019

ABSTRACT

We previously reported on the efficacy of the enzyme-linked immunoglobulin M capture immune complex (IC) biotinylated antigen assay (EMIBA) for the seroconfirmation of early Lyme disease and active infection with
Borrelia burgdorferi
. In earlier work we identified non-cross-reacting epitopes of a number of
B. burgdorferi
proteins, including flagellin. We now report on an improvement in the performance of EMIBA with the addition of a biotinylated form of a synthetic non-cross-reacting immunodominant flagellin peptide to the biotinylated
B. burgdorferi
B31 sonicate antigen source with the avidin-biotinylated peroxidase complex detection system used in our recently developed indirect IgM-capture immune complex-based assay (EMIBA). As in our previous studies, the enzyme-linked immunosorbent assay (ELISA) reactivities of antibodies liberated from circulating ICs (by EMIBA) were compared with those of antibodies in unprocessed serum (antibodies found free in the serum, thus as an IgM-capture ELISA, but not EMIBA, because the antibodies were not liberated from ICs), the sample usually used in standard ELISAs and Western blot assays. The addition of the flagellin epitope enhanced the ELISA signal obtained with untreated sera from many Lyme disease patients but not from healthy controls. In tests with both free antibodies and ICs, with or without the addition of the flagellin epitope to the sonicate, we found the most advantageous combination was IC as the source of antibodies and sonicate plus the flagellin epitope as the antigen. In a blinded study of sera obtained from patients with early and later-phase Lyme disease, EMIBA with the enhanced antigenic preparation compared favorably with other serologic assays, especially for the confirmation of early disease.
Mycobacterium tuberculosis
Infection in a Green-Winged Macaw (
Ara chloroptera
): Report with Public Health Implications
Authors: Washko Rita M. , Hoefer Heidi , Kiehn Timothy E. , Armstrong Donald , Dorsinville Guy , Frieden Thomas R. 
Published: December 2019

ABSTRACT

Mycobacterium tuberculosis
was isolated from the eyelid, skin, tongue, and lungs of a green-winged macaw (
Ara chloroptera
). Two persons living in the same household were culture positive for pulmonary tuberculosis 3 to 4 years before tuberculosis was diagnosed in the bird. Although humans have not been shown to acquire tuberculosis from birds, an infected bird may be a sentinel for human infection.
Intravitam Diagnosis of Human Rabies by PCR Using Saliva and Cerebrospinal Fluid
Authors: Crepin P. , Audry L. , Rotivel Y. , Gacoin A. , Caroff C. , Bourhy H. 
Published: December 2019

ABSTRACTAn optimized reverse transcription (RT)-PCR protocol for the intravitam detection of rabies virus genomic RNA was tested with clinical samples obtained from 28 patients suspected of having rabies, 9 of whom were confirmed to have had rabies by postmortem examination. RT-PCR using saliva combined with an immunofluorescence assay performed with skin biopsy samples allowed detection of rabies in the nine patients.
Development of a Monoclonal Antibody to a
Ureaplasma urealyticum
Serotype 9 Antigen
Authors: Naessens Anne , Cheng Xiaoxing , Lauwers Sabine , Robertson Janet A. 
Published: December 2019

ABSTRACT

We produced a monoclonal antibody (MAb) to
Ureaplasma urealyticum
Vancouver, the serotype 9 standard strain. By immunoblotting, this MAb showed a single, 85-kDa band with the homologous serotype and a minor, 100-kDa band with serotype 2 but did not react with any other serotype standard strain. Clinical isolates of
U. urealyticum
were tested with this MAb and with two sets of polyclonal antisera against the 14 serotype standard strains. The use of MAb 9-2H9 correctly identified certain serotype 9 strains but did not react with wild-type strains lacking the serotype 9 determinant.
Bile-Esculin Test for Presumptive Identification of Enterococci and Streptococci: Effects of Bile Concentration, Inoculation Technique, and Incubation Time
Authors: Chuard C. , Reller L. B. 
Published: December 2019

ABSTRACT

The bile-esculin test is used to differentiate enterococci and group D streptococci from non-group D viridans group streptococci. The effects on test performance of the concentration of bile salts, inoculum, and duration of incubation were examined with 110 strains of enterococci, 30 strains of
Streptococcus bovis
, and 110 strains of non-group D viridans group streptococci. Optimal sensitivity (>99%) and specificity (97%) of the bile-esculin test can be obtained with a bile concentration of 40%, a standardized inoculum of 10
6
CFU, and incubation for 24 h.
Molecular Identification of
Gemella
Species from Three Patients with Endocarditis
Authors: La Scola Bernard , Raoult Didier 
Published: December 2019

ABSTRACT

Gemella morbillorum
and
Gemella haemolysans
are opportunistic pathogens which cause endocarditis and other severe infections. We report on three patients with endocarditis, one with endocarditis caused by
G. haemolysans
and two with endocarditis caused by
G. morbillorum
. The paucity of reports concerning these bacteria is probably related to the difficulties associated with their identification. For example, one of the strains reported in this study was originally sent to our laboratory with a preliminary characterization as a short “gram-negative” coccobacillus, highlighting the specific problem associated with Gram staining of these bacteria. The usefulness of 16S rRNA gene amplification, partial sequencing, and comparison of the nucleotide sequence to those in databases when standard phenotypic identification schemes are not helpful is emphasized. We also suggest that the use of simple tests, such as testing susceptibility to vancomycin for gram-negative bacteria and colistin for gram-positive bacteria, could prevent misinterpretation of Gram staining in gram-variable bacteria such as
Gemella
spp.
Differentiation of
Mycobacterium ulcerans
,
M. marinum
, and
M. haemophilum
: Mapping of Their Relationships to
M. tuberculosis
by Fatty Acid Profile Analysis, DNA-DNA Hybridization, and 16S rRNA Gene Sequence Analysis
Authors: Tønjum T. , Welty D. B. , Jantzen E. , Small P. L. 
Published: December 2019

ABSTRACT

Although
Mycobacterium ulcerans
,
M. marinum
, and
M. haemophilum
are closely related, their exact taxonomic placements have not been determined. We performed gas chromatography of fatty acids and alcohols, as well as DNA-DNA hybridization and 16S rRNA gene sequence analysis, to clarify their relationships to each other and to
M. tuberculosis. M. ulcerans
and
M. marinum
were most closely related to one another, and each displayed very strong genetic affinities to
M. tuberculosis
; they are actually the two mycobacterial species outside the
M. tuberculosis
complex most closely related to
M. tuberculosis
.
M. haemophilum
was more distinct from
M. ulcerans
and
M. marinum
, and it appeared to be as related to these two species as to
M. tuberculosis
. These results are important with regard to the development of diagnostic and epidemiological tools such as species-specific DNA probes and PCR assays for
M. ulcerans
,
M. marinum
, and
M. haemophilum
. In addition, the finding that
M. ulcerans
and
M. marinum
are more closely related to
M. tuberculosis
than are other pathogenic mycobacterial species suggests that they may be evaluated as useful models for studying the pathogenesis of
M. tuberculosis
.
M. marinum
may be particularly useful in this regard since strains of this species grow much more rapidly than
M. tuberculosis
and yet can cause systemic disease in immunocompromised hosts.
Comparative Evaluation of FUNGITEST and Broth Microdilution Methods for Antifungal Drug Susceptibility Testing of
Candida
Species and
Cryptococcus neoformans
Authors: Davey Kate G. , Holmes Ann D. , Johnson Elizabeth M. , Szekely Adrien , Warnock David W. 
Published: December 2019

ABSTRACT

The FUNGITEST method (Sanofi Diagnostics Pasteur, Paris, France) is a microplate-based procedure for the breakpoint testing of six antifungal agents (amphotericin B, flucytosine, fluconazole, itraconazole, ketoconazole, and miconazole). We compared the FUNGITEST method with a broth microdilution test, performed according to National Committee for Clinical Laboratory Standards document M27-A guidelines, for determining the in vitro susceptibilities of 180 isolates of
Candida
spp. (50
C. albicans
, 50
C. glabrata
, 10
C. kefyr
, 20
C. krusei
, 10
C. lusitaniae
, 20
C. parapsilosis
, and 20
C. tropicalis
isolates) and 20 isolates of
Cryptococcus neoformans
. Overall, there was 100% agreement between the methods for amphotericin B, 95% agreement for flucytosine, 84% agreement for miconazole, 83% agreement for itraconazole, 77% agreement for ketoconazole, and 76% agreement for fluconazole. The overall agreement between the methods exceeded 80% for all species tested with the exception of
C. glabrata
(71% agreement). The poorest agreement between the results for individual agents was seen with
C. glabrata
(38% for fluconazole, 44% for ketoconazole, and 56% for itraconazole) and
C. tropicalis
(50% for miconazole). The FUNGITEST method misclassified as susceptible 2 of 12 (16.6%) fluconazole-resistant isolates, 2 of 10 (20%) itraconazole-resistant isolates, and 4 of 8 (50%) ketoconazole-resistant isolates of several
Candida
spp. Further development of the FUNGITEST procedure will be required before it can be recommended as an alternative method for the susceptibility testing of
Candida
spp. or
C. neoformans.
Identification of a New DNA Region Specific for Members of
Mycobacterium tuberculosis
Complex
Authors: Magdalena Juana , Vachée Anne , Supply Philip , Locht Camille 
Published: December 2019

ABSTRACT

The successful use of DNA amplification for the detection of tuberculous mycobacteria crucially depends on the choice of the target sequence, which ideally should be present in all tuberculous mycobacteria and absent from all other bacteria. In the present study we developed a PCR procedure based on the intergenic region (IR) separating two genes encoding a recently identified mycobacterial two-component system named SenX3-RegX3. The
senX3-regX3
IR is composed of a novel type of repetitive sequence, called mycobacterial interspersed repetitive units (MIRUs). In a survey of 116
Mycobacterium tuberculosis
strains characterized by different IS
6110
restriction fragment length polymorphisms, 2
Mycobacterium africanum
strains, 3
Mycobacterium bovis
strains (including 2 BCG strains), and 1
Mycobacterium microti
strain, a specific PCR fragment was amplified in all cases. This collection included
M. tuberculosis
strains that lack IS
6110
or
mtp40
, two target sequences that have previously been used for the detection of
M. tuberculosis
. No PCR fragment was amplified when DNA from other organisms was used, giving a sensitivity of 100% and a specificity of 100% in the confidence limit of this study. The numbers of MIRUs were found to vary among strains, resulting in six different groups of strains on the basis of the size of the amplified PCR fragment. However, the vast majority of the strains (approximately 90%) fell within the same group, containing two 77-bp MIRUs followed by one 53-bp MIRU.