bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Eight Methods To Detect Vancomycin Resistance in Enterococci
Authors: Endtz Hubert P. , Van Den Braak Nicole , Van Belkum Alex , Goessens Wil H. , Kreft Deborah , Stroebel A. Barnard , Verbrugh Henri A. 
Published: December 2019

ABSTRACT

A collection of genetically unrelated vancomycin-resistant enterococci (VRE) including 50
vanA
, 15
vanB
, 50
vanC1
, and 30
vanC2
VRE were used to evaluate the accuracy of eight currently available susceptibility test methods (agar dilution, disk diffusion, E-test, agar screen plate, Vitek GPS-TA and GPS-101, and MicroScan overnight and rapid panels).
vanA
VRE were detected by all methods.
vanB
VRE were often not detected by Vitek GPS-TA and MicroScan rapid (sensitivities, 47 and 53%, respectively), though the new Vitek GPS-101 was found to be a significant improvement. E-test and the agar screen were the only two methods detecting all VRE, including the
vanC1/C2
VRE.
Genus Level Identification of Mycobacteria from Clinical Specimens by Using an Easy-To-Handle
Mycobacterium
-Specific PCR Assay
Authors: Stauffer Fritz , Haber Heinrich , Rieger Armin , Mutschlechner Robert , Hasenberger Petra , Tevere Vincent J. , Young Karen K. Y. 
Published: December 2019

ABSTRACT

An easy-to-handle
Mycobacterium
-specific PCR assay for detection of the presence of a wide range of mycobacterial species in clinical samples was evaluated. The performance of the genus probe was compared with the performance of probes specific for
Mycobacterium tuberculosis
and
Mycobacterium avium
and with that of standard culture. In addition, the utility of an internal control in monitoring amplification inhibitors was studied. Of 545 respiratory and 325 nonrespiratory specimens (a total of 870 specimens), 58 (6.7%) showed the presence of amplification inhibitors, as determined by a negative result for the internal control. Of these 58 specimens, 31 (53%) were stool specimens; other material, even citrate blood after lysis of erythrocytes, did not pose a problem with regard to inhibition of PCR amplification. Eighty-one of the remaining 812 specimens had a positive
Mycobacterium
culture result. Of these culture-positive specimens, 58 (71.6%) showed a positive result with the
Mycobacterium
genus-specific probe. Seventy-two samples had a positive result with the
Mycobacterium
-specific probe but a negative culture result. Of these 72 samples, 26 samples were regarded as true positive, either because the
M. tuberculosis
- or
M. avium
-specific probe was also positive at the same time or because other specimens from the same patient taken at the same time were culture positive. The sensitivity of the
Mycobacterium
-specific probe was 78.5% and the specificity was 93.5%. This study showed that pretesting of clinical specimens for mycobacteria to the genus level with a
Mycobacterium
-specific probe offers the routine clinical laboratory the possibility of detecting tuberculous and nontuberculous mycobacteria with one test. Furthermore, specimens testing positive with the genus-specific probe can be immediately identified with species-specific probes.
Method for Reduction of Inhibition in a
Mycobacterium tuberculosis
-Specific Ligase Chain Reaction DNA Amplification Assay
Authors: Leckie Gregor W. , Erickson Dwight D. , He Qizhi , Facey Ingrid E. , Lin Bor-Chian , Cao Jianli , Halaka Folim G. 
Published: December 2019

ABSTRACT

The present study describes the identification of inhibitors of a
Mycobacterium tuberculosis
-specific gap ligase chain reaction (LCR) DNA amplification assay as well as a method for their removal. A major contributor to inhibition was deduced to be a calcium phosphate precipitate, CaHPO
4
. The precipitate forms during
N
-acetyl-
l
-cysteine–sodium hydroxide (NALC-NaOH) decontamination, digestion, and concentration of respiratory specimens. The solubility product of CaHPO
4
precipitate at pH 7.8, the pH at which gap LCR is optimized, indicates that the precipitate releases an amount of phosphate ions sufficient to inhibit amplification. A method for removal of the precipitate was identified. The precipitate is dissociated by exposing it to a mildly acidic (pH 4.1) buffer during the first of two centrifugation steps; the inhibitory phosphate ions are removed by the centrifugation steps. When 100 NALC-NaOH respiratory sediments were tested by gap LCR, none of the sediments were inhibitory when the acidic buffer was used while 24 samples were inhibitory when TE buffer, pH 7.8, was used. In another study, when the acidic buffer wash was applied to 1,440 NALC-NaOH respiratory sediments, only 10 sediments were found to be inhibitory. None of the inhibited sediments were culture positive for
M. tuberculosis
. This work demonstrates that when inhibition mechanisms are identified, relatively simple protocols can be used to obtain low inhibition rates and to allow the use of larger volume equivalents in amplification reactions.
Diversity of DNA Fingerprints of
Mycobacterium tuberculosis
Isolates in the United States
Authors: Yang Zhenhua , Barnes Peter F. , Chaves Fernando , Eisenach Kathleen D. , Weis Stephen E. , Bates Joseph H. , Cave M. Donald 
Published: December 2019

ABSTRACT

To investigate the diversity of IS
6110
fingerprints of
Mycobacterium tuberculosis
isolates in the United States and to determine if matching IS
6110
fingerprints represent recent interstate tuberculosis transmission, we performed restriction fragment length polymorphism analysis of
M. tuberculosis
isolates from 1,326 patients in three geographically separated states. Seven hundred ninety-five different IS
6110
fingerprint patterns were generated, and pattern diversity was similar in each state. Ninety-six percent of the fingerprint patterns were observed in only one state, demonstrating that most IS
6110
fingerprint patterns are confined to a single geographic location. Of the IS
6110
fingerprint patterns that were shared by isolates from more than one state, most isolates with 1 to 5 IS
6110
copies were separable by pTBN12 fingerprinting whereas those with >15 copies were not. One high-copy-number
M. tuberculosis
strain had identical IS
6110
and pTBN12 fingerprints and included 57 isolates from three states. Epidemiological data demonstrated significant recent transmission of tuberculosis within each city but not among the states. This suggests that identical fingerprints of isolates from geographically separate locations most likely reflect interstate tuberculosis transmission in the past, with subsequent intrastate spread of disease. Further evaluation of
M. tuberculosis
strains that cause outbreaks in different geographic locations will provide insight into the epidemiological and bacteriological factors that facilitate the spread of tuberculosis.
Evaluation of Four Methods for Rapid Identification of
Staphylococcus aureus
from Blood Cultures
Authors: Speers David J. , Olma Thomas R. , Gilbert Gwendolyn L. 
Published: December 2019

ABSTRACT

The identification of
Staphylococcus aureus
directly from blood cultures is clinically relevant, but it requires a test that is both rapid and reliable. Previously, biochemical, immunological, tube coagulase, and thermostable-endonuclease methods have shown variable sensitivity and specificity. Testing directly from blood culture broth has not been described for the latex kit Staphaurex Plus (Murex Diagnostics Ltd.), and the modified conventional tests have not been used with the newer, continuously monitored blood culture systems. In addition, the commercial RAPIDEC staph kit (bioMerieux Vitek, Inc.) has been used to detect
S. aureus
directly from the Vital blood culture system (bioMerieux, Marcy l’Etoile, France), but its performance has not been evaluated with other continuously monitored systems. A total of 201 clinical blood cultures (BACTEC 9240 culture system; Johnston Laboratories, Inc.) in which a Gram stain showed gram-positive cocci resembling staphylococci were evaluated prospectively. The Staphaurex Plus kit, the tube coagulase test, the thermostable-endonuclease test, and the RAPIDEC staph kit were compared. The sensitivities were 23, 92, 85, and 98% and the specificities were 99, 100, 93, and 100%, respectively. The RAPIDEC staph kit was the most reliable test, with a diagnostic accuracy comparable to that of the best published results for any of the rapid tests. However, it was the most expensive of the tests and relatively labor-intensive. The tube coagulase test was also sensitive, the simplest to perform, and inexpensive.
Comparison of Culture- and Non-Culture-Based Methods for Quantification of Viral Load and Resistance to Antiretroviral Drugs in Patients Given Zidovudine Monotherapy
Authors: Tedder Richard S. , Kaye Steve , Loveday Clive , Weller Ian V. D. , Jeffries Don , Norman Jane , Weber Jonathan , Bourelly Michel , Foxall Russell , Babiker Abdel , Darbyshire Janet H. 
Published: December 2019

ABSTRACT
Virological assays for human immunodeficiency virus type 1 load and drug resistance can broadly be divided into culture-based and molecular biology-based methods. Culture-based methods give a direct measure of infectious virus load and phenotypic drug resistance, whereas molecular biology-based methods are indirect, assaying nucleic acid levels to determine virus load and point mutations associated with drug resistance. We have compared culture-based and non-culture-based methods for patients enrolled in a placebo-controlled trial of zidovudine (the Concorde Trial). Virus loads were assayed by culture of peripheral blood mononuclear cells (PBMCs) or quantitative PCR, and drug resistance was assayed in culture or in a quantitative, PCR-based point mutation assay. The rates of detection of viremia and drug resistance were higher by PCR than by culture for this population of subjects. Comparison of the virus loads by the two measures showed a good correlation for virus loads in PBMCs but a poor correlation for virus loads in plasma. The latter result probably reflected the inaccuracies of culture in assaying plasma with the low infectious virus titers seen in the study population. The concordance of phenotypic and genotypic drug resistance methods was high, with all phenotypically resistant isolates having at least one resistance-associated mutation and with no mutations being found in a drug-sensitive isolate. Genomic resistance scores (weighted sums of levels of resistance mutations) showed good correlations with the levels of phenotypic resistance, and both resistance measures were observed to increase as the duration of exposure to drug increased. Overall, non-culture-based methods were shown to correlate well with culture-based methods and offer a low-cost, high-throughput alternative. However, culture-based methods remain the final arbiters of infectious virus load and phenotypic drug resistance and are unlikely to be superseded entirely.
Molecular Typing of
Staphylococcus aureus
Based on PCR Restriction Fragment Length Polymorphism and DNA Sequence Analysis of the Coagulase Gene
Authors: Hookey John V. , Richardson Judith F. , Cookson Barry D. 
Published: December 2019

ABSTRACT

A typing procedure for
Staphylococcus aureus
was developed based on improved PCR amplification of the coagulase gene and restriction fragment length polymorphism (RFLP) analysis of the product. All coagulase-positive staphylococci produced a single PCR amplification product of either 875, 660, 603, or 547 bp. Those strains of epidemic methicillin-resistant
S. aureus
16 (EMRSA-16) studied all gave a product of 547 bp. PCR products were digested with
Alu
I and
Cfo
I, and the fragments were separated by gel electrophoresis. Ten distinct RFLP patterns were found among 85 isolates of methicillin-resistant
S. aureus
(MRSA) and 10 propagating strains (PS) of methicillin-sensitive
S. aureus
(MSSA) examined. RFLP patterns 1, 2, and 3 were specific to strains of EMRSA-3, -15, and -16, respectively. By contrast, RFLP patterns 4 and 5 were seen with a heterogeneous collection of strains, together with drug-resistant forms of
S. aureus
isolated in Europe and four propagating strains used for the international phage set. RFLP pattern 6 was given by the Airedale isolate and PS 95. RFLP pattern 7 encompassed EMRSA-2 (isolate 331), PS 94, and PS 96. An isolate from Germany gave RFLP pattern 8. Eight strains of MSSA gave patterns similar to those of methicillin-resistant strains (RFLP patterns 3, 4, 5, 6, and 7), but two, PS 42E and PS 71, gave unique RFLP patterns 9 and 10, respectively. The coagulase gene PCR products for 24 isolates of MRSA and two isolates of MSSA were sequenced for both strands. The sequences were aligned, and evolutionary lineages were inferred based on pairwise distances between isolates.
Development of PCR Assays for Species- and Type-Specific Identification of
Pasteurella multocida
Isolates
Authors: Townsend Kirsty M. , Frost Alan J. , Lee Chiang W. , Papadimitriou John M. , Dawkins Hugh J. S. 
Published: December 2019

ABSTRACT

Genomic subtractive hybridization of closely related
Pasteurella multocida
isolates has generated clones useful in distinguishing hemorrhagic septicemia-causing type B strains from other
P. multocida
serotypes. Oligonucleotide primers designed during the sequencing of these clones have proved valuable in the development of PCR assays for rapid species- and type-specific detection of
P. multocida
and of type B:2 in particular. This study demonstrated that the primer pair designed from the sequence of the clone 6b (KTT72 and KTSP61) specifically amplified a DNA fragment from types B:2, B:5, and B:2,5
P. multocida
and that the primers KMT1T7 and KMT1SP6 produced an amplification product unique to all
P. multocida
isolates analyzed. It was also shown that PCR amplification performed directly on bacterial colonies or cultures represents an extremely rapid, sensitive method of
P. multocida
identification.
Rising Levels of Human Cytomegalovirus (HCMV) Antigenemia during Initial Antiviral Treatment of Solid-Organ Transplant Recipients with Primary HCMV Infection
Authors: Gerna Giuseppe , Zavattoni Maurizio , Percivalle Elena , Grossi Paolo , Torsellini Maria , Revello M. Grazia 
Published: December 2019

ABSTRACT

In 7 of 18 solid-organ transplant recipients with primary human cytomegalovirus (HCMV) infection, HCMV antigenemia levels were unexpectedly found to rise significantly (
P
= 0.018) during a mean time of 7.3 ± 3.2 days after initiation of specific antiviral treatment, whereas corresponding levels of viremia dropped significantly (
P
= 0.043). Thus, shifting to an alternative antiviral drug based solely on increasing antigenemia levels is not justified in this group of patients.
Detection of JC Virus in Cerebrospinal Fluid (CSF) Samples from Patients with Progressive Multifocal Leukoencephalopathy but Not in CSF Samples from Patients with Herpes Simplex Encephalitis, Enteroviral Meningitis, or Multiple Sclerosis
Authors: Bogdanovic G. , Priftakis P. , Hammarin A.-L. , Söderström M. , Samuelson A. , Lewensohn-Fuchs I. , Dalianis T. 
Published: December 2019

ABSTRACT
JC virus (JCV) DNA was detected in cerebrospinal fluid (CSF) samples from patients with progressive multifocal leukoencephalopathy (PML) but not in CSF samples from patients with herpes simplex encephalitis, enteroviral meningitis, or multiple sclerosis. This suggests that inflammatory processes in the brain do not necessarily reactivate JCV, which further supports the proposal that the presence of JCV DNA in the CSF is diagnostic for PML.
Different Hepatitis C Virus (HCV) RNA Load Profiles Following Seroconversion among Injecting Drug Users without Correlation with HCV Genotype and Serum Alanine Aminotransferase Levels
Authors: Beld Marcel , Penning Maarten , McMorrow Martin , Gorgels Jozef , van den Hoek Anneke , Goudsmit Jaap 
Published: December 2019

ABSTRACTHepatitis C virus (HCV) infection often persists in association with chronic hepatitis. Different factors have been proposed to determine the clinical outcome of HCV infection. The aim of this study was to examine three different factors of HCV infection among injecting drug users. Nineteen untreated HCV seroconverters were tested longitudinally for the presence of HCV RNA by reverse transcriptase (RT) PCR, and results were quantified by the branched-DNA (bDNA) assay. HCV genotypes were determined with the first sample taken after HCV seroconversion. To assess the natural course of infection, serum alanine aminotransferase (ALT) levels were measured at three stages in every individual. The concordance between bDNA and RT-PCR was 98.9%. Three distinct patterns were found, according to the HCV RNA load after seroconversion during a mean follow-up period of 5 years (range, 1 to 8 years). HCV genotype 1a was predominant (52.6%). There was a significant increase in serum ALT levels (mean 55.5 U/liter) in the early phase of HCV infection, compared with basal serum ALT levels before HCV seroconversion and at the end of the follow-up period. Three distinct HCV RNA load profiles were found, without apparent relationship to genotype and serum ALT levels in the first 5 years of HCV infection.
Taxonomic Relationships among Spotted Fever Group Rickettsiae as Revealed by Antigenic Analysis with Monoclonal Antibodies
Authors: Xu Wenbin , Raoult Didier 
Published: December 2019

ABSTRACTThe spotted fever group (SFG) is made up of more than 20 different rickettsial species and strains. Study of the taxonomic relationships among the group has been attempted by phenotypic, genotypic, and phylogenetic analyses. In this study, we determined taxonomic relationships among the SFG rickettsiae by comparative analysis of immunogenic epitopes reactive against a panel of monoclonal antibodies. A total of 98 monoclonal antibodies, which were directed against epitopes on the major immunodominant proteins or on the lipopolysaccharide-like antigens of strains ofRickettsia africae,Rickettsia conorii,Rickettsia massiliae,Rickettsia akari,Rickettsia sibirica, andRickettsia slovaca, were used in the study. The distribution and expression of the epitopes among 29 SFG rickettsiae andRickettsia belliiwere assessed by determination of reaction titers in a microimmunofluorescence assay. The results were scored as numerical taxonomic data, and cluster analysis was used to construct a dendrogram. The architecture of this dendrogram was consistent with previous taxonomic studies, and the implications of this and other findings are discussed.
Emergence of Multidrug Resistance in Ubiquitous and Dominant
Pseudomonas aeruginosa
Serogroup O:11
Authors: Tassios Panayotis T. , Gennimata Vassiliki , Maniatis Anthony N. , Fock Caroline , Legakis Nicholas J. , Group The Greek Pseudomonas aeruginosa Study 
Published: December 2019

ABSTRACT

The serotypes of 88 nonreplicate nosocomial
Pseudomonas aeruginosa
isolates from 11 Greek hospitals were studied in relation to their antibiotic susceptibilities. Rates of resistance to β-lactams, aminoglycosides, and quinolones ranged from 31 to 65%, except for those to ceftazidime (15%) and imipenem (21%). Four serotypes were dominant: O:12 (25% of isolates), O:1 (17%), O:11 (16%), and O:6 (10%). Multidrug resistance rates in the major serogroups O:12 (91%) and O:11 (79%) were higher than those in serogroups O:1 (40%) and O:6 (43%). Further typing with respect to pulsed-field gel electrophoresis patterns following
Xba
I digestion of genomic DNA discriminated the isolates into 74 types. Pulsed-field gel electrophoresis revealed that the ubiquitous O:12 group was genetically homogeneous, since 95% of strains belonged to two clusters of genotypic similarity, while the O:11 strains, present in 8 of the 11 hospitals, were distributed among five such clusters. Therefore, apart from the already reported O:12 multidrug-resistant European clone, an O:11 population, characterized by a serotype known to be dominant in the environment and the hospital in several parts of the world, but previously not associated with multidrug resistance to antibiotics, has progressed to a multidrug-resistant state.
Diversity of
Helicobacter pylori vacA
and
cagA
Genes and Relationship to VacA and CagA Protein Expression, Cytotoxin Production, and Associated Diseases
Authors: Rudi Jochen , Kolb Christof , Maiwald Matthias , Kuck Dirk , Sieg Andreas , Galle Peter R. , Stremmel Wolfgang 
Published: December 2019

ABSTRACT

The vacuolating cytotoxin and the cytotoxin-associated protein, encoded by
vacA
and
cagA
, respectively, are important virulence determinants of
Helicobacter pylori
. Sixty-five
H. pylori
strains were isolated from dyspeptic patients (19 with peptic ulcer disease, 43 with chronic gastritis, and 3 with gastric cancer) and studied for differences in the
vacA
and
cagA
genes and their relationship to VacA and CagA expression, cytotoxin activity, and the clinical outcome of infection. By PCR, fifty-four (83.1%) of 65 strains had the
vacA
signal sequence genotype s1 and only 10 (15.4%) had the type s2. After primer modification, the
vacA
middle-region types m1 and m2 were detected in 24 (36.9%) and 41 (63.1%) strains, respectively. The combinations s1-m2 (31 [47.7%]) and s1-m1 (23 [35.4%]) occurred more frequently than s2-m2 (10 [15.4%]) (
P
= 0.01). No strain with the combination s2-m1 was found. All 19 patients with peptic ulcers harbored type s1 strains, in contrast to 32 (74.4%) of 43 patients with gastritis (
P
= 0.02). The
vacA
genotype s1 was associated with the presence of
cagA
(
P
< 0.0001), VacA expression (
P
< 0.0001), and cytotoxin activity (
P
= 0.003). The
cagA
gene was detectable in 48 (73.8%) of 65 isolates and present in 16 (84.2%) of 19 ulcer patients and 29 (67.4%) of 43 patients with gastritis (
P
= 0.17). The
vacA
genotypes of German
H. pylori
isolates are identical to those previously reported.
H. pylori
strains of
vacA
type s1 are associated with the occurrence of peptic ulceration and the presence of
cagA
, cytotoxin activity, and VacA expression.
Flow Cytometric Determination of Ganciclovir Susceptibilities of Human Cytomegalovirus Clinical Isolates
Authors: McSharry James M. , Lurain Nell S. , Drusano George L. , Landay Alan , Manischewitz Jody , Nokta Mostafa , O’Gorman Maurice , Shapiro Howard M. , Weinberg Adriana , Reichelderfer Patricia , Crumpacker Clyde 
Published: December 2019

ABSTRACT

A flow cytometric assay has been developed for the measurement of susceptibilities to ganciclovir of laboratory strains and clinical isolates of human cytomegalovirus (HCMV). The assay uses fluorochrome-labeled monoclonal antibodies to HCMV immediate-early and late antigens to identify HCMV-infected cells and flow cytometry to detect and quantitate the number of antigen-positive cells. By this assay, the 50 and 90% inhibitory concentrations (IC
50
and IC
90
, respectively) of ganciclovir for the AD169 strain of HCMV were 1.7 and 9.2 μM, respectively, and the IC
50
for the ganciclovir-resistant D6/3/1 derivative of the AD169 strain was greater than 12 μM. The ganciclovir susceptibilities of 17 HCMV clinical isolates were also determined by flow cytometric analysis of the effect of ganciclovir on late-antigen synthesis in HCMV-infected cells. The average IC
50
of ganciclovir for drug-sensitive HCMV clinical isolates was 3.79 μM (±2.60). The plaque-reduction assay for these clinical isolates yielded an average IC
50
of 2.80 μM (±1.46). Comparison of the results of the flow cytometry assays with those obtained from the plaque-reduction assays demonstrated acceptable bias and precision. Flow cytometric and plaque-reduction analysis of cells infected with ganciclovir-resistant clinical isolates failed to show a reduction in the percentage of late-antigen-positive cells or PFU, even at 96 μM ganciclovir. The flow cytometric assay for determining ganciclovir susceptibility of HCMV is quantitative, and objective, and potentially automatable, and its results are reproducible among laboratories.