bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urinary Tract Infections Associated with Nontyphoidal
Salmonella
Serogroups
Authors: Abbott Sharon L. , Portoni Barbara A. , Janda J. Michael 
Published: December 2019

ABSTRACT

In an analysis of over 23,000 nontyphoidal strains of
Salmonella
submitted to the Microbial Diseases Laboratory between 1992 and 1996, two groups (C
1
and E) were significantly recovered more often from the urinary tract than stool compared to more common groups such as B and D. An analysis of >60 urine isolates from 1996 suggests that most of these represent true urinary tract infections, as opposed to colonization or fecal contamination, by virtue of being isolated in pure culture and in high concentrations (>100,000 CFU/ml).
Characterization of Blood Culture Isolates of
Streptococcus dysgalactiae
subsp.
equisimilis
Possessing Lancefield's Group A Antigen
Authors: Brandt Claudia M. , Haase Gerhard , Schnitzler Norbert , Zbinden Reinhard , Lütticken Rudolf 
Published: December 2019

ABSTRACT

For three human blood culture isolates of beta-hemolytic streptococci with Lancefield's serogroup A antigen, phylogenetic analysis of the 16S rRNA genes confirmed biochemical identification as
Streptococcus dysgalactiae
subsp.
equisimilis
. Genes encoding M or M-like proteins, which are considered to be major virulence determinants in streptococci, were detected in all of these strains. Our data clearly demonstrate that for beta-hemolytic streptococci, the species assignment should not be based on the results of serogrouping alone.
Quantitative Analysis of mRNA as a Marker for Viability of
Mycobacterium tuberculosis
Authors: Hellyer T. J. , DesJardin L. E. , Hehman G. L. , Cave M. D. , Eisenach K. D. 
Published: December 2019

ABSTRACT

Numerous assays which use conserved DNA or rRNA sequences as targets for amplification have been described for the diagnosis of tuberculosis. However, these techniques have not been applied successfully to the monitoring of therapeutic efficacy owing to the persistence of amplifiable nucleic acid beyond the point at which smears and cultures become negative. Semiquantitative analysis of rRNA has been used to reduce the time required for antimicrobial susceptibility testing of
Mycobacterium tuberculosis
, although growth for up to 5 days in the presence of some drugs is still required to discriminate resistant strains. The purpose of the present study was to determine whether quantitative analysis of
M. tuberculosis
mRNA could be used to assess bacterial viability and to illustrate the application of this technique to rapid determination of drug susceptibility. Levels of mRNA encoding the 85B protein (α-antigen), IS
6110
DNA, and 16S rRNA were compared in parallel cultures of
M. tuberculosis
that were treated with either no drug, 0.2 μg of isoniazid per ml, or 1 μg of rifampin per ml. Exposure of sensitive strains to isoniazid or rifampin for 24 h reduced the levels of 85B mRNA to <4 and <0.01%, respectively, of those present in control cultures without drug. In contrast, the levels of IS
6110
DNA and 16S rRNA did not diminish over the same period. Strains which were resistant to either isoniazid or rifampin demonstrated no reduction in 85B mRNA in the presence of the drug to which they were nonresponsive. Quantitative analysis of 85B mRNA offers a potentially useful tool for the rapid determination of
M. tuberculosis
drug susceptibility and for the monitoring of therapeutic efficacy.
Usefulness of Spoligotyping in Molecular Epidemiology of
Mycobacterium bovis
-Related Infections in South America
Authors: Zumárraga Martín J. , Martin Carlos , Samper Sofia , Alito Alicia , Latini Omar , Bigi Fabiana , Roxo Eliana , Cicuta María Elena , Errico Francisco , Ramos Miguel Castro , Cataldi Angel , van Soolingen Dick , Romano María Isabel 
Published: December 2019

ABSTRACT

Two hundred twenty-four
Mycobacterium bovis
isolates, mainly from South American countries, were typed by spoligotyping, and 41 different spoligotypes were identified. A total of 202
M. bovis
isolates (90%) were grouped into 19 different clusters. The largest cluster contained 96 isolates (42.8%) on the basis of the most frequently observed spoligotype, spoligotype 34. Nineteen
M. bovis
isolates from humans in Argentina had spoligotypes and polymorphic GC-rich repetitive sequence (PGRS) types that represented the most common types found among isolates from cattle. All five isolates from Uruguay and three of the six isolates from Paraguay had spoligotypes that were also detected for isolates from Argentina. The spoligotypes of isolates from Brazil, Costa Rica, and Mexico and of some of the isolates from Paraguay could not be found in Argentina. A total of 154
M. bovis
isolates were selected in order to compare the discriminative power of spoligotyping and restriction fragment length polymorphism (RFLP) analysis with direct repeat (DR) and PGRS probes. By spoligotyping, 31 different types were found, while
Alu
I-digested DR probe-associated RFLP analysis identified 42 types, and RFLP analysis with the PGRS probe also detected 42 types; these were partly independent of the DR types. By combining the results obtained by spoligotyping and by RFLP analysis with the DR and PGRS probes, 88 different types were obtained. Although the differentiation of
M. bovis
by spoligotyping was less discriminatory than differentiation by RFLP analysis with the DR and PGRS probes, spoligotyping is easier to perform and its results are easier to interpret. Therefore, for the purpose of typing of
M. bovis
isolates, spoligotyping could be performed first and the isolates could be grouped into clusters and then analyzed by RFLP analysis with the DR and PGRS probes.
Development of a Firefly Luciferase-Based Assay for Determining Antimicrobial Susceptibility ofMycobacterium aviumsubsp.paratuberculosis
Authors: Williams Stephanie L. , Harris N. Beth , Barletta Raúl G. 
Published: December 2019

ABSTRACTParatuberculosis (Johne’s disease) is a fatal disease of ruminants for which no effective treatment is available. Presently, no drugs againstMycobacterium aviumsubsp.paratuberculosis(M. paratuberculosis), the causative agent of Johne’s disease, are approved for use in livestock. Additionally,M. paratuberculosishas been linked to a human chronic granulomatous ileitis (Crohn’s disease). To assist in the evaluation of antimicrobial agents with potential activity againstM. paratuberculosis, we have developed a firefly luciferase-based assay for the determination of drug susceptibilities. The microorganism used wasM. paratuberculosisK-10(pYUB180), a clinical isolate carrying a plasmid with the firefly luciferase gene. The MICs determined by the broth macrodilution method were as follows: amikacin, 2 μg/ml; Bay y 3118, 0.015 μg/ml; clarithromycin, 1.25 μg/ml;d-cycloserine, 25 μg/ml; ethambutol, 20 μg/ml; and rifabutin, 0.5 μg/ml. The strain was resistant to isoniazid and kanamycin. The results obtained by the luciferase assay were identical or fell within 1 doubling dilution. These results suggest that a combination of amikacin, clarithromycin, and rifabutin may be the most efficacious therapy for the treatment ofM. paratuberculosisinfections and that the use of fluoroquinolone class of antibiotics deserves further consideration. We demonstrate that the luciferase drug susceptibility assay is reliable forM. paratuberculosisand gives results within 7 days, whereas the broth macrodilution method requires 14 days.
High-Throughput Real-Time Reverse Transcription-PCR Quantitation of Hepatitis C Virus RNA
Authors: Martell María , Gómez Jordi , Esteban Juan I. , Sauleda Silvia , Quer Josep , Cabot Beatriz , Esteban Rafael , Guardia Jaime 
Published: December 2019

ABSTRACT

We describe a rapid and reproducible method for assessment of the hepatitis C virus (HCV) load in serum samples. The method combines Taqman technology (Roche) and the ABI Prism 7700 (Perkin Elmer) real-time sequence detection system. We have optimized a single-tube reverse transcription-PCR (RT-PCR) that contains a dual-labeled fluorogenic probe to quantify the 5′ noncoding region (5′ NCR) of HCV. The probe contains a fluorescent reporter at the 5′ end and a fluorescent quencher at the 3′ end. The use of such a probe combined with the 5′-3′ nuclease activity of
Taq
polymerase allows direct quantitation of the PCR product by the detection of a fluorescent reporter released in the course of the exponential phase of the PCR. For accurate quantitation of the number of copies of HCV in samples containing unknown quantities, we have used serial dilutions of a synthetic 5′ NCR RNA standard of HCV that was previously quantified with an isotopic tracer. The method has a 5-log dynamic range (10
3
to 10
7
). The coefficient of regression of the standard curve was, on average, 0.98. The intra-assay and the interassay coefficients of variation of the threshold cycle were 1% and 6.2%, respectively. Seventy-nine RNA samples from the sera of infected patients were quantified by this method. Comparison of the results with those obtained by other quantitation methods (the Quantiplex 2.0 branched-DNA assay and the Superquant assay from the National Genetics Institute) revealed a significant correlation with all of the results. The mean values were also statistically comparable. In conclusion, the high sensitivity, simplicity, and reproducibility of the real-time HCV RNA quantitation which allows the screening of large numbers of samples, combined with its wide dynamic range, make this method especially suitable for monitoring of the viral load during therapy and tailoring of treatment schedules.
Clinical Evaluation of an In-House Reverse Transcription-Competitive PCR for Quantitation of Human Immunodeficiency Virus Type 1 RNA in Plasma
Authors: Zazzi Maurizio , Romano Laura , Catucci Marinunzia , Venturi Giulietta , De Milito Angelo , Valensin Pier E. 
Published: December 2019

ABSTRACT

An in-house reverse transcription (RT)-competitive PCR (RT-cPCR) for the quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma samples was developed and validated. The procedure involves (i) extraction of RNA with spin columns, (ii) ready-to-use bead-mediated RT, (iii) competitive PCR in a microtiter plate, (iv) agarose gel electrophoresis of the reaction products, and (v) densitometric analysis of the digitized image of the gel. Quadruplicate tests and dilution studies showed that the sensitivity and intertest coefficient of variability of the RT-cPCR are comparable to those of the reference AMPLICOR HIV-1 MONITOR test. The results obtained by the two assays with a panel of 45 clinical samples were in good agreement (mean difference, 0.36 ± 0.25 log units). Analysis of 1,982 clinical samples by the in-house RT-cPCR yielded the typical range of plasma HIV-1 RNA levels with the expected inverse correlation between CD4 counts and HIV-1 RNA titers. In addition, testing of plasma from 36 subjects at weeks 0 and 4 with respect to the time of initiation of protease inhibitor therapy detected a significant decrease in HIV-1 viremia. The mean reduction in the HIV-1 RNA level was 0.914 log unit for those receiving saquinavir (
P
= 0.0210), 1.584 log units for those receiving indinavir (
P
= 0.0047), and 1.904 log units for those receiving ritonavir (
P
< 0.0001). The in-house RT-cPCR assay is simple to develop and perform and allows quantitation of HIV-1 RNA in 100 to 200 samples per operator per week. Since the cost is 1/8 to 1/10 of those of reference commercial assays, this procedure could be conveniently used in medium-scale laboratories.
Evaluation of a Colorimetric PCR-Based Assay To Diagnose
Plasmodium falciparum
Malaria in Travelers
Authors: Zhong Kathleen J. Y. , Kain Kevin C. 
Published: December 2019

ABSTRACT

New diagnostic tests are needed to facilitate the diagnosis of
Plasmodium falciparum
malaria in the returned traveler. We performed a blinded evaluation of a nonisotopic colorimetric PCR-based assay (Digene SHARP Signal System) and compared the results with those obtained by microscopy and nested PCR for the detection of
P. falciparum
malaria in 150 febrile travelers. By using nested PCR as the reference standard, the colorimetric assay had a sensitivity of 100% and a specificity of 95.4% for the detection of
P. falciparum
. This PCR-based nonisotopic assay is a rapid, sensitive, and specific method for the detection of falciparum malaria in returned travelers.
Rapid Detection of a
Schistosoma mansoni
Circulating Antigen Excreted in Urine of Infected Individuals by Using a Monoclonal Antibody
Authors: Attallah Abdelfattah M. , Ismail Hisham , El Masry Samir A. , Rizk Hassan , Handousa Aia , El Bendary Mahmoud , Tabll Ashraf , Ezzat Farouk 
Published: December 2019

ABSTRACT

Schistosoma
circulating antigens were used to indicate the infection intensity and to assess cure. An immunoglobulin G2a (IgG2a) mouse monoclonal antibody was used in a fast dot-enzyme-linked immunosorbent assay (ELISA; FDA) for rapid and simple diagnosis of schistosomiasis in the field. Seven hundred Egyptians were parasitologically examined for
Schistosoma mansoni
and other parasitic infections. A rectal biopsy was done as a “gold standard” for individuals showing no
S. mansoni
eggs in their feces. Egg counts were obtained by the Kato smear method for only 100 of 152 individuals with eggs in their feces. Specific anti-schistosome IgG antibodies were evaluated in sera by ELISA. Urine samples from the 700 individuals were tested by FDA for detection of the circulating antigen. The assay showed a sensitivity of 93% among 433 infected individuals and a specificity of 89% among 267 noninfected individuals. FDA showed the highest efficiency of antigen detection (91%) compared with the efficiency of antibody detection by ELISA (75%) and stool analysis (60%). In addition, FDA detected infected patients with 20 eggs/g of feces. Also, the sensitivity of FDA ranged from 90 to 94% among samples from patients with different clinical stages of schistosomiasis. All the assay steps can be completed within 30 min at room temperature for 96 urine samples. The monoclonal antibody identified a 74-kDa antigen in different antigenic extracts of
S. mansoni
and
Schistosoma haematobium
and in the urine of infected individuals. In addition, a 30-kDa degradation product was identified only in the urine samples. On the basis of these results, FDA should be used as a rapid tool for the sensitive and specific diagnosis of
Schistosoma
infection.
Pulsed-Field Gel Electrophoresis Is More Efficient than Ribotyping and Random Amplified Polymorphic DNA Analysis in Discrimination ofPasteurella haemolyticaStrains
Authors: Kodjo Angeli , Villard Laurence , Bizet Chantal , Martel Jean-Louis , Sanchis Richard , Borges Evelyne , Gauthier Dominique , Maurin Françoise , Richard Yves 
Published: December 2019

ABSTRACTOne hundred thirty-three strains ofPasteurella haemolyticaof both biotypes (90 and 43 strains of biotypes A and T, respectively) and almost all the serotypes were subjected to ribotyping, random amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE) analysis for epidemiological purposes. A total of 15 patterns recorded as ribotypes HA to HO were found for theP. haemolyticabiotype A strains, with ribotypes HA, HC, and HD being encountered most often (66 strains [74%]); and 20 ribotypes, designated HA′ to HT′, that were clearly distinct from those observed for biotype A strains were observed for strains of biotype T. RAPD analysis generated a total of 44 (designated Rp1 to Rp44) and 15 (designated Rp1′ to Rp 15′) unique RAPD patterns for biogroup A and biogroup T, respectively. Analysis of the data indicated that a given combined ribotype-RAPD pattern could be observed for biotype A strains of different serotypes, whatever the zoological or geographic origin, whereas this was not the case for biotype T strains. PFGE appeared to be more efficient in strain discrimination since selected strains from various zoological or geographical origins harboring the same ribotype-RAPD group were further separated into unique entities.
Stability of
Mycobacterium tuberculosis
IS
6110
Restriction Fragment Length Polymorphism Patterns and Spoligotypes Determined by Analyzing Serial Isolates from Patients with Drug-Resistant Tuberculosis
Authors: Niemann Stefan , Richter Elvira , Rüsch-Gerdes Sabine 
Published: December 2019

ABSTRACT

The stability of
Mycobacterium tuberculosis
IS
6110
fingerprint patterns and spoligotypes has been assessed by analyzing serial isolates from patients with drug-resistant tuberculosis. Altogether, 165
M. tuberculosis
isolates obtained from 56 patients have been analyzed. The time spans between the first and the last or a changed isolate from one patient ranged from 1 to 772 days. Among the 56 patients, 5 (9%) were infected with isolates with changes in their IS
6110
fingerprint patterns. According to the total number of strains analyzed, 5% of the subsequent isolates showed variations in their IS
6110
restriction fragment length polymorphism patterns compared to the pattern of the first isolates. Up to 10 isolates from one patient sampled at time intervals of up to 772 days with no changes in their IS
6110
patterns have been analyzed. A statistically significant correlation could be found between changes in insertion sequence (IS) patterns and the increased time intervals over which the isolates were obtained, whereas changes in IS patterns are not correlated to changes in the drug resistance of the isolates. In contrast to the observed variations in IS
6110
fingerprint patterns, no changes in the spoligotypes of the isolates analyzed could be found. In conclusion, our results confirm that the IS
6110
fingerprint patterns of
M. tuberculosis
isolates have high degrees of stability. Compared to IS
6110
, the direct repeat (DR) region, which is the basis for spoligotyping, has a lower rate of change. Partial deletions, e.g., deletions induced by homologous recombination between the repetitive DR elements, could not be detected in this study.
Molecular and Phenotypic Characterization of Genotypic
Candida albicans
Subgroups and Comparison with
Candida dubliniensis
and
Candida stellatoidea
Authors: McCullough Michael J. , Clemons Karl V. , Stevens David A. 
Published: December 2019

ABSTRACT

There have been increased reports of the isolation of unusual genotypic groups of
Candida albicans
(groups C and D) based on a well-defined genotypic method; this method uses cellular DNA digested with the
Eco
RI enzyme and the restriction fragment length polymorphisms (RFLPs) generated by agarose gel electrophoresis. The aim of the present study was to use additional molecular tools to characterize these unusual strains and to compare them with authentic strains of
C. dubliniensis
, a recently delineated species, and type I
C. stellatoidea
. The RFLPs of PCR products generated from the intergenic transcribed spacer (ITS) region did not differentiate among
C. albicans
genotypes A, B, and C and type I
C. stellatoidea
. However, this method did differentiate the
C. albicans
genotype D strains, which were identical to
C. dubliniensis
. The RFLPs generated by
Hae
III digestion of the PCR products of the V3 region of the 25S rRNA gene (rDNA) could differentiate the same groups as RFLP analysis of the PCR amplicon of the ITS region.
C. albicans
genotype B isolates have been shown to have a transposable intron in the 25S rDNA, whereas genotype A isolates do not;
C. dubliniensis
strains also have an intron that is larger than that in genotype B
C. albicans
strains but that is in the same location. PCR designed to span this region resulted in a single product for
C. albicans
genotype A (450 bp), B (840 bp), type 1
C. stellatoidea
(840 bp), and
C. dubliniensis
(1,080 bp), whereas the
C. albicans
genotype C isolates had two major products (450 and 840 bp). All
C. albicans
genotype D isolates gave a PCR product identical to that given by
C. dubliniensis
. These results indicate that those strains previously designated
C. albicans
genotype D are in fact
C. dubliniensis
, that no differences were found between type 1
C. stellatoidea
and
C. albicans
genotype B strains, and that the
C. albicans
genotype C strains appear to have the transposable intron incompletely inserted throughout the ribosomal repeats in their genomes. The results of the antifungal susceptibility testing of 105 of these strains showed that, for fluconazole, strains of
C. dubliniensis
were significantly more susceptible than strains of each of the
C. albicans
genotypes (genotypes A, B, and C). The flucytosine susceptibility results indicated that strains of
C. albicans
genotype A were significantly less susceptible than either
C. albicans
genotype B or
C. albicans
genotype C strains. These results indicate that there is a correlation between the
Candida
groups and antifungal susceptibility.
Comparison of NucliSens and Roche Monitor Assays for Quantitation of Levels of Human Immunodeficiency Virus Type 1 RNA in Plasma
Authors: Dyer John R. , Pilcher Christopher D. , Shepard Robin , Schock Jody , Eron Joseph J. , Fiscus Susan A. 
Published: December 2019

ABSTRACT
We compared the performance of Organon Teknika’s NucliSens and Roche Diagnostic Systems’ Monitor quantitative human immunodeficiency type 1 RNA assays. Both had similar linearity and sensitivity over most of the dynamic range of the assays, although the Monitor assay was superior at the low range of RNA values while the NucliSens assay was more consistent at higher RNA values. NucliSens generally showed less interassay variability.
Comparison of Randomly Amplified Polymorphic DNA Analysis and Pulsed-Field Gel Electrophoresis for Typing of
Moraxella catarrhalis
Strains
Authors: Vu-Thien Hoang , Dulot Carole , Moissenet Didier , Fauroux Brigitte , Garbarg-Chenon Antoine 
Published: December 2019

ABSTRACT

Randomly amplified polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) for the analysis of 13
Moraxella catarrhalis
isolates, 11 successive strains isolated from sputa of five children and 2 isolates obtained the same day from twins, were compared. RAPD and PFGE both yielded nine types from the 13 isolates, showing a chronic colonization with one strain in three patients and a successive colonization with different strains in two patients. The promising results obtained with RAPD should be confirmed with a larger number of strains, but RAPD seems as suitable as PFGE for the typing of
M. catarrhalis
.
Detection of
Cryptosporidium parvum
in Horses: Thresholds of Acid-Fast Stain, Immunofluorescence Assay, and Flow Cytometry
Authors: Cole D. J. , Snowden K. , Cohen N. D. , Smith R. 
Published: December 2019

ABSTRACT

Feces collected from three asymptomatic horses and seeded with
Cryptosporidium parvum
oocysts (10
1
to 10
6
/g of feces) were evaluated by acid-fast staining (AF), an immunofluorescent antibody (IFA) technique, and flow cytometry. The thresholds of detection were 5 × 10
5
oocysts/g of feces for the IFA and AF techniques and 5 × 10
4
oocysts/g for flow cytometry.