bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Vitek GNI and GNI+ Cards for Identification of Gram-Negative Bacteria
Authors: Bourbeau Paul P. , Heiter Barbara J. 
Published: December 2019

ABSTRACT

The GNI+ card has been developed by bioMerieux Vitek as an improvement over the GNI card for the identification of certain species of aerobic and facultative anaerobic bacteria. In this study, we tested 304 organisms from 30 different species on both the GNI and GNI+ cards. The GNI card correctly identified 285 (93.8%) of the isolates tested, and the GNI+ card correctly identified 287 (94.4%) of the isolates tested. The average time to reporting was 4.1 h for the GNI+ card compared to 5.7 h for the GNI card (
P
< 0.001). Overall, the GNI and GNI+ cards were comparable in identifying the organisms in this study while the GNI+ card gave substantially faster final test results.
Detection of
Pneumocystis carinii
DNA in Blood Specimens from Human Immunodeficiency Virus-Infected Patients by Nested PCR
Authors: Rabodonirina Meja , Cotte Laurent , Boibieux André , Kaiser Karine , Mayençon Martine , Raffenot Didier , Trepo Christian , Peyramond Dominique , Picot Stéphane 
Published: December 2019

ABSTRACT

The detection of
Pneumocystis carinii
DNA in blood by PCR could be useful for studying the natural history of pneumocystosis and could also be a noninvasive diagnostic method. The results of previous studies are nevertheless conflicting. In our study, we compared three commercially available DNA extraction kits (GeneReleaser, QIAamp Tissue Kit, and ReadyAmp Genomic DNA Purification System) and proteinase K and proteinase K-phenol-chloroform treatments for the extraction of
P. carinii
DNA from dilutions of a
P. carinii
f. sp.
hominis
cyst suspension mixed with human whole blood. A rapid and simple nested PCR protocol which amplifies a portion of the mitochondrial large-subunit rRNA gene was applied to all the extraction products. The QIAmp Tissue Kit was the most effective kit for the isolation of amplification-ready
P. carinii
DNA and was used with nested PCR for the testing of whole-blood specimens from 35 immunocompetent control patients and 84 human immunodeficiency virus (HIV)-infected patients investigated for pulmonary disease and/or fever. In HIV-infected patients,
P. carinii
DNA was detected by nested PCR in blood samples from 3 of 14 patients with microscopically proven
P. carinii
pneumonia, 7 of 22 patients who were considered to be colonized with
P. carinii
, and 9 of 48 patients who were neither infected nor colonized with
P. carinii. P. carinii
DNA was not detected in blood specimens from the 35 immunocompetent patients.
P. carinii
DNA in blood might represent viable
P. carinii
organisms or DNA complexes released from pulmonary phagocytes. In conclusion,
P. carinii
DNA may be detected in whole blood from HIV-infected patients, but the nature and the meaning of the circulating form of
P. carinii
remain to be established.
Influence of Incubation Time, Inoculum Size, and Glucose Concentrations on Spectrophotometric Endpoint Determinations for Amphotericin B, Fluconazole, and Itraconazole
Authors: Nguyen M. Hong , Yu Christine Y. 
Published: December 2019

ABSTRACT

We addressed the influence of the incubation time (24 h versus 48 h), starting inoculum size (standard inoculum size, ∼10
3
CFU/ml, versus large inoculum size, ∼10
4
CFU/ml), and supplementation with 2% glucose of RPMI 1640 medium on the spectrophotometric determination of the MICs of amphotericin B, fluconazole, and itraconazole. We compared the MICs determined spectrophotometrically with those determined by the standard broth macrodilution method (National Committee for Clinical Laboratory Standards approved guideline M27-A). The agreement between the results of the spectrophotometric and standard methods for amphotericin B testing was 100%; this agreement was independent of the inoculum size and incubation time. On the other hand, the agreement for the results for fluconazole testing and itraconazole testing was dependent on the inoculum size and incubation time. With large inoculum size, excellent agreement can be achieved at 24 h. With standard inoculum size, acceptable agreement can be achieved only at 48 h. In contrast to previous observations, the addition of 2% glucose did not have any significant impact on the growth density at 24 h, nor did it improve the agreement with the standard method. Furthermore, supplemental glucose might falsely elevate the MIC at 48 h.
Nucleic Acid-Based Cross-Linking Assay for Detection and Quantification of Hepatitis B Virus DNA
Authors: Lai Vicky C. H. , Guan Richard , Wood Michael L. , Lo Su Kong , Yuen Man-Fung , Lai Ching-Lung 
Published: December 2019

ABSTRACT

A nucleic acid photo-cross-linking technology was used to develop a direct assay for the quantification of hepatitis B virus (HBV) DNA levels in serum. Cross-linker-modified DNA probes complementary to the viral genomes of the major HBV subtypes were synthesized and used in an assay that could be completed in less than 6 h. The quantification range of the assay, as determined by testing serial dilutions of Eurohep HBV reference standards and cloned HBV DNA, was 5 × 10
5
to 3 × 10
9
molecules of HBV DNA/ml of serum. Within-run and between-run coefficients of variation (CVs) for the assay were 4.3 and 4.0%, respectively. The assay was used to determine HBV DNA levels in 302 serum samples, and the results were compared to those obtained after testing the same samples with the Chiron branched-DNA (bDNA) assay for HBV DNA. Of the samples tested, 218 were positive for HBV DNA by both assays and 72 gave results below the cutoff for both assays. Of the remaining 12 samples, 10 were positive for HBV DNA by the cross-linking assay only; the 2 other samples were positive by the bDNA assay only. Twenty-eight samples had to be retested by the bDNA assay (CV, >20% between the results obtained from the testing of each sample in duplicate), whereas only three samples required retesting by the cross-linking assay. The correlation between the HBV DNA levels, as measured by the two tests, was very high (
r
= 0.902;
P
= 0.01). We conclude that the cross-linking assay is a sensitive and reproducible method for the detection and quantification of HBV DNA levels in serum.
Usefulness of Leifson Staining Method in Diagnosis of
Helicobacter pylori
Infection
Authors: Piccolomini Raffaele , Di Bonaventura Giovanni , Neri Matteo , Di Girolamo Arturo , Catamo Giovanni , Pizzigallo Eligio 
Published: December 2019

ABSTRACT

The Leifson staining method was used to diagnose
Helicobacter pylori
infection and was compared to histology, culture, and the rapid urease test (RUT). Histology gave the best sensitivity (98%), compared to Leifson staining (97%), culture (92%), and RUT (85%) (
P
< 0.005). Leifson staining is a sensitive, rapid, economical method for diagnosis of
H. pylori
infection in dyspeptic patients.
E Test versus Agar Dilution for Antimicrobial Susceptibility Testing of Viridans Group Streptococci
Authors: Rosser S. J. , Alfa M. J. , Hoban S. , Kennedy J. , Harding G. K. 
Published: December 2019

ABSTRACT
Viridans group streptococci (VGS) are commonly isolated from the blood of hospitalized patients. The E test represents a convenient method for determining the MICs for VGS, but for this purpose it has not been well validated against reference methods. In this study, 180 unselected VGS isolates were identified to a species level, and the MICs of penicillin, cefuroxime, cefotaxime, and vancomycin were determined by both agar dilution and the E test. Available data regarding demographic and laboratory variables for each VGS bacteremic episode were collected, the significance of each VGS isolate was assessed, and the associations between and among laboratory and clinical variables were investigated. Among all VGS isolates, 68.3% (median of three runs) were found to be fully susceptible to penicillin by agar dilution. The E test and agar dilution showed average agreements (within ±1 dilution) of 92.2% for penicillin, 95.7% for cefuroxime 91.3% for cefotaxime, and 86.7% for vancomycin. Agreements over serial E tests and serial agar dilutions were excellent for β-lactam agents (intraclass correlation coefficients, >0.9) but less impressive for vancomycin. Very major error rates for the E test were ≤0.7%, and combined major and minor error rates were within acceptable limits for all antimicrobial agents tested. Lysis-centrifugation culture methods were more often associated with clinically insignificant VGS isolates; otherwise, no associations between clinical and laboratory variables were noted.
Molecular Epidemiology of Outbreaks of Gastroenteritis Associated with Small Round-Structured Viruses in East Anglia, United Kingdom, During the 1996–1997 Season
Authors: Maguire Alison J. , Green Jon , Brown David W. G. , Desselberger Ulrich , Gray James J. 
Published: December 2019

ABSTRACT
During the winter season from November 1996 to May 1997, 550 fecal specimens were submitted from 94 outbreaks of gastroenteritis occurring in East Anglia, United Kingdom. These specimens were tested for the presence of small round-structured viruses (SRSVs) by electron microscopy, reverse transcriptase PCR, or both methods. SRSVs were shown to be associated with 64 of 94 (68%) of these outbreaks, of which 16 (25%) outbreaks occurred at a single location (Southend) within the region. Twenty-four specimens from 13 of the 16 SRSV-positive outbreaks occurring in Southend were available for genomic analysis, in which divergence within the RNA polymerase region of the SRSV genome was investigated. A further 27 specimens from 17 other SRSV-associated outbreaks, occurring at different locations within East Anglia but at the same time as those at Southend, were also studied. Fifty of the total of 51 (98%) specimens studied were shown to belong to genogroup II, and within this genogroup, 49 of 50 (98%) specimens were shown to be Grimsby-like viruses, with only one Mexico-like strain. Furthermore, phylogenetic analysis of the Grimsby-like viruses indicated clusterings according to the geographical location of the outbreak. One specimen contained a virus belonging to genogroup I, and this had the greatest sequence identity (83%) with Southampton virus.
Use of PCR in Detection of
Mycobacterium avium
Complex (MAC) Bacteremia: Sensitivity of the Assay and Effect of Treatment for MAC Infection on Concentrations of Human Immunodeficiency Virus in Plasma
Authors: MacGregor Rob Roy , Dreyer Kimberly , Herman Steve , Hocknell Peter K. , Nghiem Lan , Tevere Vincent J. , Williams Amy L. 
Published: December 2019

ABSTRACT

We evaluated the sensitivity and specificity of a PCR-based qualitative test for the rapid diagnosis of
Mycobacterium avium-M. intracellulare
complex (MAC) bacteremia in patients with AIDS disease. Eleven subjects with newly culture-proven MAC bacteremia had the following tests performed at biweekly intervals during the first 8 weeks of therapy: blood culture,
Mycobacterium
-specific PCR, and quantitative human immunodeficiency virus (HIV) viral-load testing.
Mycobacterium
genus-specific biotinylated primers were used to amplify a sequence of approximately 582 nucleotides within the 16S rRNA genes of
M. avium
and
M. intracellulare
. Detection of the amplified product was performed with an oligonucleotide probe-coated microwell plate combined with an avidin-horseradish peroxidase–tetramethylbenzidine conjugate-substrate system. While not as sensitive as BACTEC culture, PCR detected 17 of 18 specimens which grew ≥40 organisms/ml (94.4% sensitivity) and 9 of 16 specimens which grew ≤40 organisms/ml (56.3% sensitivity). No clear change in HIV viremia occurred in response to successful treatment of patients’ MAC bacteremia. Use of the PCR test allowed detection of MAC bacteremia in 1 day, with a sensitivity similar to those of quantitative blood culture techniques, and it may prove useful for rapid screening of suspected cases. HIV viremia was unaffected by 8 weeks of MAC therapy.
Evaluation of New Quantitative Assays for Diagnosis and Monitoring of Cytomegalovirus Disease in Human Immunodeficiency Virus-Positive Patients
Authors: Pellegrin Isabelle , Garrigue Isabelle , Binquet Christine , Chene Genevieve , Neau Didier , Bonot Pascal , Bonnet Fabrice , Fleury Herve , Pellegrin Jean-Luc 
Published: December 2019

ABSTRACT
Cobas Amplicor CMV Monitor (CMM) and Quantiplex CMV bDNA 2.0 (CMV bDNA 2.0), two new standardized and quantitative assays for the detection of cytomegalovirus (CMV) DNA in plasma and peripheral blood leukocytes (PBLs), respectively, were compared to the CMV viremia assay, pp65 antigenemia assay, and the Amplicor CMV test (P-AMP). The CMV loads were measured in 384 samples from 58 human immunodeficiency virus (HIV) type 1-infected, CMV-seropositive subjects, including 13 with symptomatic CMV disease. The assays were highly concordant (agreement, 0.88 to 0.97) except when the CMV load was low. Quantitative results for plasma and PBLs were significantly correlated (Spearman ρ = 0.92). For PBLs, positive results were obtained 125 days before symptomatic CMV disease by CMV bDNA 2.0 and 124 days by pp65 antigenemia assay, whereas they were obtained 46 days before symptomatic CMV disease by CMM and P-AMP. At the time of CMV disease diagnosis, the sensitivity, specificity, and positive and negative predictive values of CMV bDNA 2.0 were 92.3, 97.8, 92.3, and 97.8%, respectively, whereas they were 92.3, 93.3, 80, and 97.8%, respectively, for the pp65 antigenemia assay; 84.6, 100, 100, and 95.7%, respectively, for CMM; and 76.9, 100, 100, and 93.8%, respectively, for P-AMP. Considering the entire follow-up, the sensitivity, specificity, and positive and negative predictive values of CMV bDNA 2.0 were 92.3, 73.3, 52.1, and 97.1%, respectively, whereas they were 100, 55.5, 39.4, and 100%, respectively, for the pp65 antigenemia assay; 92.3, 86.7, 66.7, and 97.5%, respectively, for CMM; and 84.6, 91.1, 73.3, and 95.3%, respectively, for P-AMP. Detection of CMV in plasma is technically easy and, despite its later positivity (i.e., later than in PBLs), can provide enough information sufficiently early so that HIV-infected patients can be effectively treated. In addition, these standardized quantitative assays accurately monitor the efficacy of anti-CMV treatment.
Role of Genotypic Analysis of the Thymidine Kinase Gene of Herpes Simplex Virus for Determination of Neurovirulence and Resistance to Acyclovir
Authors: Lee N. Y. , Tang Y.-W. , Espy M. J. , Kolbert C. P. , Rys P. N. , Mitchell P. S. , Day S. P. , Henry S. L. , Persing D. H. , Smith T. F. 
Published: December 2019

ABSTRACT

Mutations in the thymidine kinase (TK) gene of herpes simplex virus (HSV) have been associated with resistance to acyclovir (ACY) and possible recognition of neurotropic strains. We sequenced a 335-bp segment of the TK gene to determine the frequency of mutations in HSV strains recovered from dermal, genital, and cerebrospinal fluid (CSF) specimens (
n
= 200; 102 HSV type 1 [HSV-1] 98 HSV-2 strains). Four polymorphic sites were detected in HSV-1 strains; C513T, A528G, C575T, and C672T. Among the polymorphisms, only C575T resulted in a change of amino acid sequence (residue 192, Ala→Val). For HSV-2 strains, only one polymorphism (G420T) which resulted in an amino acid substitution (residue 139, Leu→Phe) was detected. Phenotypic determination of resistance to ACY by a plaque reduction assay of 48 HSV isolates was not correlated with the sequence results of 11 strains in that 7 of these with genotypic polymorphisms were susceptible to the drug in vitro. In addition, of 32 ACY-resistant HSV strains, 28 (87.5%) had no polymorphisms detected in the 335-bp amplicon of the TK gene. There was no statistical difference in the frequency of polymorphisms according to the source of the specimens. We conclude that the detection of nucleic acid polymorphisms in a previously implicated 335-bp segment of the TK gene cannot be interpreted as indicative of either ACY resistance or neurotropism of HSV strains from dermal, genital, and CSF sources.
Genotyping of Epidemic Methicillin-Resistant
Staphylococcus aureus
Phage Type 15 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis
Authors: Grady Ruth , Desai Meeta , O’Neill Gael , Cookson Barry , Stanley John 
Published: December 2019

ABSTRACT

Fluorescent amplified-fragment length polymorphism (FAFLP) analysis was investigated for its ability to identify and subtype isolates of an epidemic methicillin-resistant phage type of
Staphylococcus aureus
, EMRSA-15. These isolates were also characterized by PCR-restriction fragment length polymorphism (PCR-RFLP) of the coagulase gene and pulsed-field gel electrophoresis (PFGE). For FAFLP, DNA was double digested with restriction enzymes
Apa
I plus
Taq
I or
Eco
RI plus
Mse
I. Site-specific adaptors were ligated to one or the other set of restriction fragments, and PCR amplification was carried out with adaptor-specific primers. Amplified fragments separated on an ABI 377 automated sequencer and analyzed with Genescan version 2.1 software generated FAFLP profiles for all the isolates. The presence or absence of fragments was scored, similarity coefficients were calculated, and UPGMA (unweighted pair group method using arithmatic averages) cluster analysis was performed. Either enzyme-primer combination readily differentiated EMRSA-15 from other methicillin-resistant
S. aureus
(MRSA) isolates and also revealed heterogeneity within the phage type. The discriminatory power of FAFLP was high. By combining both enzyme-primer data sets, 24 isolates were divided into 11 profiles. PCR-RFLP did not discriminate among these EMRSA-15 isolates. PFGE could discriminate well between isolates but was not as reproducible as FAFLP. All
S. aureus
and MRSA isolates in this study were typeable by FAFLP, which was easy to perform, robust, and reproducible, with evident potential to subtype MRSA for purposes of hospital infection control.
Study of Restriction Fragment Length Polymorphism Analysis and Spoligotyping for Epidemiological Investigation of
Mycobacterium bovis
Infection
Authors: Costello Eamon , O’Grady Donnacha , Flynn Orla , O’Brien Rory , Rogers Mark , Quigley Frances , Egan John , Griffin John 
Published: December 2019

ABSTRACT

Restriction fragment length polymorphism (RFLP) analysis with probes derived from the insertion element IS
6110
, the direct repeat sequence, and the polymorphic GC-rich sequence (PGRS) and a PCR-based typing method called spacer oligonucleotide typing (spoligotyping) were used to strain type
Mycobacterium bovis
isolates from the Republic of Ireland. Results were assessed for 452 isolates which were obtained from 233 cattle, 173 badgers, 33 deer, 7 pigs, 5 sheep, and 1 goat. Eighty-five strains were identified by RFLP analysis, and 20 strains were identified by spoligotyping. Twenty percent of the isolates were the most prevalent RFLP type, while 52% of the isolates were the most prevalent spoligotype. Both the prevalent RFLP type and the prevalent spoligotype were identified in isolates from all animal species tested and had a wide geographic distribution. Isolates of some RFLP types and some spoligotypes were clustered in regions consisting of groups of adjoining counties. The PGRS probe gave better differentiation of strains than the IS
6110
or DR probes. The majority of isolates from all species carried a single IS
6110
copy. In four RFLP types IS
6110
polymorphism was associated with deletion of fragments equivalent in size to one or two direct variable repeat sequences. The same range and geographic distribution of strains were found for the majority of isolates from cattle, badgers, and deer. This suggests that transmission of infection between these species is a factor in the epidemiology of
M. bovis
infection in Ireland.
Serodiagnosis of Epstein-Barr Virus Infection by Using Recombinant Viral Capsid Antigen Fragments and Autologous Gene Fusion
Authors: Hinderer Walter , Lang Dieter , Rothe Markus , Vornhagen Rolf , Sonneborn Hans H. , Wolf Hans 
Published: December 2019

ABSTRACT

Using recombinant 15- to 30-kDa fragments and fusion with glutathione
S
-transferase (GST), we investigated the seroreactivity of three large structural proteins of Epstein-Barr virus (EBV), p150 (BcLF1, capsid), p143 (BNRF1, tegument), and gp125 (BALF4, membrane) in Western blots. None of 13 fragments tested, however, was qualified for diagnostic application. In contrast, the two small viral capsid antigens (VCA), p18 (BFRF3) and p23 (BLRF2), demonstrated sensitive (100%) EBV-specific immunoglobulin G (IgG) reactivities. While p18 additionally showed maximum sensitivity for IgM detection, the IgM sensitivity of p23 was restricted (44%). An autologous fusion protein, p23-p18, which consists N-terminally of full-length p23, followed by the carboxy half of p18, was constructed. This antigen was subjected to indirect VCA enzyme-linked immunosorbent assays (ELISAs), for IgG and IgM, as well as to a μ-capture (μc) IgM ELISA. All assays were found to be 100% specific when EBV-negative sera were tested. Using sera from previously infected individuals, the p23-p18 fusion revealed an improved IgG sensitivity of 99% compared to sensitivities of 97 and 93% for the single antigens p18 and p23, respectively. The sensitivity and specificity of the indirect IgM ELISA with samples of primary and past infections, respectively, were 100%. The μc principle for IgM overcame completely the interference by rheumatoid factors. Compared to the specificity of the indirect IgM version, the specificity with sera collected from rheumatoid arthritis patients increased from 48 to 100%. In summary, the p23-p18 IgG and μc IgM ELISAs showed excellent performances and are promising new diagnostic tests for the detection of EBV-specific antiviral capsid antibodies.
Case of
Staphylococcus schleiferi
Endocarditis and a Simple Scheme To Identify Clumping Factor-Positive Staphylococci
Authors: Leung Michael J. , Nuttall Nichalas , Mazur Margaret , Taddei Tania L. , McComish Michael , Pearman John W. 
Published: December 2019

ABSTRACT

Staphylococcus schleiferi
is a coagulase-negative staphylococcus infrequently reported as a human pathogen. We report a case of prosthetic valve endocarditis attributed to this organism, contrast it to another
Staphylococcus
species that gives similar clumping factor results (
S. lugdunensis
), and propose a simple, effective identification scheme for identification of clumping factor-positive staphylococci.
Cost-Effective Methods for Isolation of
Salmonella enterica
in the Clinical Laboratory
Authors: Kelly Sinead , Cormican Martin , Parke Leanne , Corbett-Feeney Geraldine , Flynn John 
Published: December 2019

ABSTRACT

Data from 8,717 fecal specimens indicate that primary inoculation of xylose lysine deoxycholate (XLD) agar may enhance the speed, but not the sensitivity, of isolation of
Salmonella enterica
over that achieved with Selenite enrichment only. Plating of Selenite broth onto both brilliant green and XLD agar offers no advantage over plating onto XLD alone.
Adenovirus Strains of Subgenus D Associated with Nosocomial Infection as New Etiological Agents of Epidemic Keratoconjunctivitis in Japan
Authors: Takeuchi Satoshi , Itoh Norihiko , Uchio Eiichi , Tanaka Keico , Kitamura Noriko , Kanai Hikaru , Isobe Kazumi , Aoki Koki , Ohno Shigeaki 
Published: December 2019

ABSTRACT
Adenovirus strains of a new type were isolated from patients with epidemic keratoconjunctivitis. They were not completely neutralized by any antiserum against adenovirus prototypes. PCR followed by restriction endonuclease analysis demonstrated that they were type 8. PCR followed by sequencing revealed a high homology rate between them and type 9.