bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Use of a New Chromogenic Agar in Detection of Urinary Tract Pathogens
Authors: Samra Z. , Heifetz M. , Talmor J. , Bain E. , Bahar J. 
Published: December 2019

ABSTRACT

CHROMagar Orientation, a new chromogenic medium, was evaluated for the detection and differentiation of gram-positive and gram-negative pathogenic microorganisms in 900 urine samples from hospitalized patients. Performance characteristics of the medium were evaluated in comparison to those of 5% sheep blood and MacConkey agars by direct inoculation of the urine samples on the three media. Four gram-negative and two gram-positive strains as well as one yeast control strain from the American Type Culture Collection were used to ensure quality control. CHROMagar Orientation succeeded in detecting all the urine pathogens that were detected by the reference media, including gram-negative bacilli, staphylococci, streptococci, and yeasts. Colony color and morphology on CHROMagar Orientation accurately differentiated
Escherichia coli
,
Proteus mirabilis
,
Proteus vulgaris
,
Pseudomonas aeruginosa
, and
Acinetobacter
spp. Owing to the similarity in the pigmentation produced by
Klebsiella
,
Enterobacter
, and
Citrobacter
isolates, the medium failed to distinguish among them; however, these isolates were easily recognized as coliforms because of their metallic blue coloration. Staphylococci were clearly perceptible:
S. aureus
and
S. epidermidis
grow in regular-size colonies that range from opaque white to yellowish, and
S. saprophyticus
produces opaque pink colonies. All streptococcus strains, including those from groups B and C, were detected. They grow as undifferentiated flat dry diffused colonies, and additional tests were required for identification. Enterococci were easily discriminated by their strong turquoise pigmentation and their typical growth on the agar’s surface. Yeast grow in typical creamy wet convex colonies. The accuracy of antibiotic susceptibility determinations according to standard methods was also tested by picking isolates directly from CHROMagar Orientation. The results showed excellent correlation with those obtained with microorganisms picked from reference media. Owing to the ease in differentiating mixed flora on CHROMagar Orientation, antimicrobic susceptibility tests were performed directly from primary isolates in all cases without the need for subcultures.
Short-Term Follow-Up by Serology of Patients Given Antibiotic Treatment for
Helicobacter pylori
Infection
Authors: Laheij R. J. F. , Witteman E. M. , Bloembergen P. , de Koning R. W. , Jansen J. B. M. J. , Verbeek A. L. M. 
Published: December 2019

ABSTRACT

Helicobacter pylori
serology and in particular enzyme-linked immunosorbent assays for the measurement of immunoglobulin G (IgG) antibody titers form an accurate means of diagnosing
H. pylori
infection in patients before treatment.
H. pylori
serology is of limited value in monitoring treatment because of the slow decline in antibody titers. In the present study we aimed to measure the most suitable moment after antibiotic treatment at which serology should be used to monitor treatment. Sixty-four patients who had nonulcer dyspepsia and
H. pylori
infection and who underwent upper gastrointestinal endoscopy because of persistent dyspeptic symptoms were included in the study.
H. pylori
cure was confirmed by histology and culture 5 weeks after the completion of the antibiotic treatment. Serological examination was performed before therapy and at 5 weeks, 10 weeks, and 1 year after the completion of antibiotic treatment. Diagnostic performance was assessed by receiver-operating characteristic analysis. The areas under the receiver-operating characteristic curves of the
H. pylori
antibody titers at 5 weeks, 10 weeks, and 1 year after the completion of treatment were 0.53 (95% confidence interval [CI], 0.36 to 0.69), 0.60 (95% CI, 0.43 to 0.76), and 0.78 (95% CI, 0.63 to 0.93), respectively. The areas under the receiver-operating characteristic curves of the changes in
H. pylori
IgG antibody titers at 5 weeks, 10 weeks, and 1 year after the completion of treatment in comparison with the pretreatment titers were 0.85 (95% CI, 0.72 to 0.97), 0.96 (95% CI, 0.89 to 1.0), and 1.0 (95% CI, not estimable), respectively. We conclude that serology forms a useful means of monitoring treatment in patients with nonulcer dyspepsia and
H. pylori
infection as early as 10 weeks and maybe even sooner after the completion of treatment for the infection.
Use of Roche AMPLICOR
Mycobacterium tuberculosis
PCR in Early Diagnosis of Tuberculous Meningitis
Authors: Bonington Alec , Strang J. I. George , Klapper Paul E. , Hood Steven V. , Rubombora William , Penny Miranda , Willers Rose , Wilkins Edmund G. L. 
Published: December 2019

ABSTRACT

Several nucleic acid-based amplification tests are available for the detection of
Mycobacterium tuberculosis
, but few data are available on their use in the diagnosis of tuberculous meningitis (TBM). We performed a prospective study to assess the Roche AMPLICOR
Mycobacterium tuberculosis
PCR test (TB AMPLICOR) for use in the diagnosis of TBM and compared it with direct Ziehl-Neelsen staining of smears, radiometric culture for
M. tuberculosis
, and clinical and cerebrospinal fluid (CSF) findings. Eighty-three CSF specimens collected from 69 patients with suspected meningitis in South Africa were tested by TB AMPLICOR. On the basis of clinical and laboratory findings, 40 of these patients were treated for TBM and 29 patients were not treated for TBM. Ten CSF samples from 10 patients were positive by TB AMPLICOR. Seven of these 10 patients were classified as having definite TBM, 2 were classified as having probable TBM, and 1 was classified as having possible TBM. The sensitivity of TB AMPLICOR for detecting cases of definite and probable TBM in patients from whom CSF specimens had been collected less than 10 days into antituberculosis treatment was 60.0%. Specimens from all 29 patients not treated for TBM were negative by the TB AMPLICOR, giving a 100% specificity. TB AMPLICOR is therefore more sensitive than the combination of Ziehl-Neelsen staining of smears and radiometric culture for
M. tuberculosis
and is a rapid and highly specific diagnostic test for TBM.
Use of Ligase Chain Reaction with Urine versus Cervical Culture for Detection of
Chlamydia trachomatis
in an Asymptomatic Military Population of Pregnant and Nonpregnant Females Attending Papanicolaou Smear Clinics
Authors: Gaydos Charlotte A. , Howell M. Rene , Quinn Thomas C. , Gaydos Joel C. , McKee Kelly T. 
Published: December 2019

ABSTRACT

Ligase chain reaction (LCR) (Abbott Laboratories, Abbott Park, Ill.) with first-catch urine specimens was used to detect
Chlamydia trachomatis
infections in 465 asymptomatic military women attending clinics for routine Papanicolaou smear tests. Results were compared to results of cervical culture to determine the sensitivity of the urine LCR and the possible presence of inhibitors of amplification in pregnant and nonpregnant women. Discrepant results for LCR and culture were resolved by direct fluorescent antibody staining of culture sediments, two different PCR assays, and LCR for the outer membrane protein 1 gene. The prevalence of
Chlamydia
in specimens by urine LCR was 7.3% compared to 5% by culture. For 434 women with matching specimens, there were 11 more specimens positive by LCR than were positive by culture, of which all but one were determined to be true positives. There were four culture-positive, LCR-negative specimens, all from nonpregnant women. The sensitivity, specificity, and positive and negative predictive values of urine LCR after discrepant results were resolved were 88.6, 99.7, 96.9, and 99.0%, respectively. The sensitivity of culture was 71.4%. From the 148 pregnant women (prevalence by LCR, 6.8%), there were no patients who were cervical culture positive and urine LCR negative to indicate the presence in pregnant women of inhibitors of LCR. Additionally, a subset of 55 of the LCR-negative frozen urine specimens from pregnant women that had been previously processed in LCR buffer were inoculated with 5 cell culture inclusion forming units of
C. trachomatis
each and retested by LCR; all tested positive, indicating the absence of inhibitors of LCR in urine from these pregnant women. The use of LCR testing of urine specimens from asymptomatic women, whether pregnant or not, offers a sensitive and easy method to detect
C. trachomatis
infection in women.
Comparative Evaluation of National Committee for Clinical Laboratory Standards Broth Macrodilution and Agar Dilution Screening Methods for Testing Fluconazole Susceptibility of
Cryptococcus neoformans
Authors: Kirkpatrick William R. , McAtee Robert K. , Revankar Sanjay G. , Fothergill Annette W. , McCarthy Dora I. , Rinaldi Michael G. , Patterson Thomas F. 
Published: December 2019

ABSTRACT

A simple screening method for fluconazole susceptibility of
Cryptococcus neoformans
using 2% dextrose Sabouraud dextrose agar (SabDex) with fluconazole was compared to the National Committee for Clinical Laboratory Standards (NCCLS) broth macrodilution method. By this method, fluconazole-susceptible
C. neoformans
isolates are significantly smaller on medium with fluconazole than on fluconazole-free medium. Isolates with decreased susceptibility have normal-size colonies on medium containing fluconazole. The 48-h NCCLS broth macrodilution MICs (NCCLS MICs) for isolates with normal-size colonies on 8- or 16-μg/ml fluconazole plates were predicted to be ≥8 or ≥16 μg/ml, respectively. On medium with 16 μg of fluconazole per ml, all strains (84 of 84) for which the NCCLS MICs were <16 μg/ml were correctly predicted, as were all isolates (7 of 7) for which the MICs were ≥16 μg/ml. Agar dilution appears to be an effective screening method for fluconazole resistance in
C. neoformans.
Evaluation of Murex CMV DNA Hybrid Capture Assay for Detection and Quantitation of Cytomegalovirus Infection in Patients following Allogeneic Stem Cell Transplantation
Authors: Hebart Holger , Gamer Daphne , Loeffler Juergen , Mueller Claudia , Sinzger Christian , Jahn Gerhard , Bader Peter , Klingebiel Thomas , Kanz Lothar , Einsele Hermann 
Published: December 2019

ABSTRACT

Murex hybrid capture DNA assay (HCS) is a solution hybridization antibody capture assay for detection and quantitation of cytomegalovirus (CMV) DNA in leukocytes. To determine whether CMV HCS is sensitive enough to initiate and monitor antiviral therapy after allogeneic stem cell transplantation (SCT), 51 consecutive SCT recipients were prospectively screened for the appearance of CMV infection by HCS, PCR, and culture assays from blood samples. Preemptive antiviral therapy was initiated after the second positive PCR result in all patients, as previously reported, and HCS was not considered for clinical decision making. A total of 417 samples were analyzed. Of these, 21 samples were found to be positive by PCR and HCS, 88 samples were PCR positive but HCS negative, and 308 were negative by both assays. Concordance of results between PCR and HCS and between HCS and blood culture was observed in 78.9 and 95.9% of the samples assayed, respectively. PCR was found to be more sensitive than HCS, and HCS was more sensitive than the blood culture assay (
P
< 0.0001). Four patients with symptomatic CMV infection were PCR positive prior to the onset of CMV-related symptoms, whereas HCS detected CMV DNA in three patients prior to and one at onset of CMV disease. The numbers of genomes per milliliter of blood were higher in patients with symptomatic CMV infection than in those with asymptomatic CMV infection (
P
= 0.06). None of the HCS-negative patients developed CMV disease. Thus, all patients with CMV disease were correctly identified by HCS; however, the lower sensitivity limit of the HCS assay may still be insufficient to allow diagnosis of CMV infection early enough to prevent CMV disease in patients following allogeneic SCT.
Simultaneous Detection and Identification of Human Parainfluenza Viruses 1, 2, and 3 from Clinical Samples by Multiplex PCR
Authors: Echevarría Juan E. , Erdman Dean D. , Swierkosz Ella M. , Holloway Brian P. , Anderson Larry J. 
Published: December 2019

ABSTRACT

Reverse transcription (RT)-PCR assays have been widely described for use in the diagnosis of human parainfluenza viruses (HPIVs) and other respiratory virus pathogens. However, these assays are mostly monospecific, requiring separate amplifications for each HPIV type. In the present work, we describe multiplex RT-PCR assays that detect and differentiate HPIV serotypes 1, 2, and 3 in a combined reaction. Specifically, a mixture of three pairs of primers to conserved regions of the hemagglutinin-neuraminidase gene of each HPIV serotype was used for primary amplification, yielding amplicons with similar sizes. For typing, a second amplification was performed with a mixture of nested primers, yielding amplicons with sizes easily differentiated by agarose gel electrophoresis. A modified single-amplification RT-PCR assay with fluorescence-labeled nested primers, followed by analysis of the labeled products on an automated sequencing gel, was also evaluated. Fifteen temporally and geographically diverse HPIV isolates from the Centers for Disease Control and Prevention archives and 26 of 30 (87%) previously positive nasopharyngeal specimens (8 of 10 positive for HPIV serotype 1 [HPIV1], 9 of 10 positive for HPIV2, and 9 of 10 positive for HPIV3) were positive and were correctly typed by both assays. Negative results were obtained with naso- or oropharyngeal specimens and/or culture isolates of 33 unrelated respiratory tract pathogens, including HPIV4, enterovirus, rhinovirus, respiratory syncytial virus, adenovirus, influenza virus, and
Streptococcus pneumoniae
. Our multiplex RT-PCR assays provide sensitive, specific, and simplified tools for the rapid diagnosis of HPIV infections.
Simplified Quantitative Assay System for Measuring Activities of Drugs against IntracellularLegionella pneumophila
Authors: Higa Futoshi , Kusano Nobuchika , Tateyama Masao , Shinzato Takashi , Arakaki Noriko , Kawakami Kazuyoshi , Saito Atsushi 
Published: December 2019

ABSTRACTWe developed a new simple assay for the quantitation of the activities of drugs against intracellularLegionella pneumophila. The cells of a murine macrophage-like cell line (J774.1 cells) allowed the intracellular growth and replication of the bacteria, which ultimately resulted in cell death. The infected J774.1 cell monolayers in 96-well microplates were first treated with antibiotics and were further cultured for 72 h. The number of viable J774.1 cells in each well was quantified by a colorimetric assay with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and an enzyme-linked immunosorbent assay reader. The number of growing bacteria in each well was also determined by counting the numbers of CFU on buffered charcoal yeast extract-α agar plates. Viable J774.1 cell counts, determined by the colorimetric assay, were inversely proportional to the number of intracellular replicating bacteria. The minimum extracellular concentrations (MIECs) of 24 antibiotics causing inhibition of intracellular growth ofL. pneumophilawere determined by the colorimetric assay system. The MIECs of beta-lactams and aminoglycosides were markedly higher than the MICs in buffered yeast extract-α broth. The MIECs of macrolides, fluoroquinolones, rifampin, and minocycline were similar to the respective MICs. According to their intracellular activities, clarithromycin and sparfloxacin were the most potent among the macrolides or fluoroquinolones tested in this study. Our results indicated that the MTT assay system allows comparative and quantitative evaluations of the intracellular activities of antibiotics and efficient processing of a large number of samples.
Apparent Increased Prevalence of High-Level Aminoglycoside-Resistant
Enterococcus durans
Resulting from False Identification by a Semiautomated Software System
Authors: Tsakris Athanassios , Woodford Neil , Pournaras Spyros , Kaufmann Mary , Douboyas John 
Published: December 2019

ABSTRACT

Identification of enterococci by using a semiautomated system (PASCO; Difco Laboratories, Detroit, Mich.) in the AHEPA University Hospital, Thessaloniki, Greece, revealed a high proportion of
Enterococcus durans
, particularly among isolates highly resistant to gentamicin and streptomycin. When 14 isolates were further tested by a conventional biochemical scheme and by PCR, all were reidentified as
Enterococcus faecalis
. Antibiotic resistance and pulsed-field gel electrophoresis patterns showed that unrelated strains were misidentified.
Comparison of the Rapid Yeast Plus Panel with the API20C Yeast System for Identification of Clinically Significant Isolates of
Candida
Species
Authors: Heelan Judith S. , Sotomayor Edgar , Coon Kimberly , D’Arezzo Julia B. 
Published: December 2019

ABSTRACT

The RapID Yeast Plus system (Innovative Diagnostic Systems, Norcross, Ga.) is a qualitative micromethod employing conventional tests and single-substrate chromogenic tests and having a 4-h incubation period. This system was compared with the API20C (bioMerieux Vitek, Hazelwood, Mo.) system, a 24- to 72-h carbohydrate assimilation method. One hundred thirty-three clinical yeast isolates, including 57 of
Candida albicans
, 26 of
Candida tropicalis
, 23 of
Candida glabrata
, and 27 of other yeasts, were tested by both methods. When discrepancies occurred, isolates were further tested by the Automated Yeast Biochemical Card (bioMerieux Vitek). Germ tube production and microscopic morphology were used as needed to definitively identify yeast isolates. The RapID Yeast Plus system correctly identified 125 yeast isolates, with an overall accuracy of 94% (125 of 133). Excellent correlation was found in the recognition of the three yeasts most commonly isolated from human sources. The test was 99% (105 of 106 isolates) accurate with
C. albicans
,
C. tropicalis
, and
C. glabrata
. The RapID Yeast Plus system compares favorably with the API20C system and provides a simple, accurate alternative to conventional assimilation methods for the rapid identification of the most commonly encountered isolates of
Candida
species.
Survey of
Klebsiella pneumoniae
Strains Producing Extended-Spectrum β-Lactamases: Prevalence of SHV-12 and SHV-2a in Korea
Authors: Kim Jungmin , Kwon Youngmi , Pai Hyunjoo , Kim Jong-Won , Cho Dong-Taek 
Published: December 2019

ABSTRACT

Fifty-three clinical isolates of extended-spectrum β-lactamase (ESBL)-producing
Klebsiella pneumoniae
collected from three hospitals in Korea were investigated for phenotypical and genotypical characterizations. Among these, 39 strains (74%) were shown by isoelectric focusing to carry SHV-type β-lactamases: 27 strains showed the pI 8.2 β-lactamase, and another 12 strains showed the pI 7.6 β-lactamase. The SHV gene of each of these strains was amplified by PCR, followed by nucleotide sequencing analysis. The gene of the pI 8.2 β-lactamase was found to be identical to the sequences encoding SHV-12, and the gene of the pI 7.6 β-lactamase was identical to the sequences encoding SHV-2a. A total of eight cefoxitin-resistant strains were found to have the plasmid-mediated AmpC-type β-lactamase, with a pI of 8.0, and this was confirmed to be CMY-1 β-lactamase by PCR and hybridization analysis. Noteworthy in this study is the fact that SHV-12 and SHV-2a have been the most commonly identified SHV-type ESBLs in Korea.
Detection of
Leptospira
DNA in Patients with Aseptic Meningitis by PCR
Authors: Romero Eliete C. , Billerbeck Ana E. C. , Lando Valéria S. , Camargo Eide D. , Souza Candida C. , Yasuda Paulo H. 
Published: December 2019

ABSTRACT
Samples of cerebrospinal fluid from 103 patients with aseptic meningitis were tested by PCR for detection of leptospires, and the results were compared with those of the microscopic agglutination test (MAT) and an enzyme-linked immunosorbent assay for detection of immunoglobulin M (ELISA-IgM). Of these samples, 39.80% were positive by PCR and 8.74 and 3.88% were positive by MAT and ELISA-IgM, respectively.
Comparison of DNA Enzyme Immunoassay and Line Probe Assays (Inno-LiPA HCV I and II) for Hepatitis C Virus Genotyping
Authors: Le Pogam S. , Dubois F. , Christen R. , Raby C. , Cavicchini A. , Goudeau A. 
Published: December 2019

ABSTRACT
Two methods for genotyping hepatitis C virus (DNA enzyme immunoassay [DEIA] and line probe assay [Inno-LiPA HCV I and II]) were compared on 120 samples and of these 87% were assigned to the same subtype by both assays. There were 15 subtyping discrepancies which involved 5% of type 1 isolates and 90% of type 2 isolates. Amplified products from the core and 5′ untranslated regions (UTR) were sequenced to resolve conflicts. Type 1 discordant samples had a guanosine at position −99 in the 5′ UTR, a characteristic of genotype 1b, and a core region typical of subtype 1a. The eight isolates classified as 2a/2c by LiPA and as subtype 2c by DEIA belonged to type 2.
Sensitivities and Specificities of Premier
E. coli
O157 and Premier EHEC Enzyme Immunoassays for Diagnosis of Infection with Verotoxin (Shiga-Like Toxin)-Producing
Escherichia coli
Authors: Mackenzie A. M. R. , Lebel P. , Orrbine E. , Rowe P. C. , Hyde L. , Chan F. , Johnson W. , McLaine P. N. ,   The Synsorb Pk Study Investigators
Published: December 2019

ABSTRACT

This study describes the performance of two rapid enzyme immunoassays, Premier
E. coli
O157 and Premier EHEC (Meridian Diagnostics Inc., Cincinnati, Ohio) for the detection in stools of
Escherichia coli
O157 and verotoxins (Shiga-like toxins), respectively. Both tests were performed on stools from 876 children presenting to eight emergency departments with diarrhea. Standard culture, including
E. coli
O157:H7 isolation, was performed, and paired sera were taken for anti-O157-lipopolysaccharide antibody determination. Stools from patients enrolled in the study, and those yielding discordant results, were sent to a reference laboratory for repeat testing and further investigation, including cytotoxicity and non-O157 verotoxin-producing
E. coli
culture. Results were classified as field results (obtained in the eight site laboratories) and resolved results (obtained after repeat testing in the central laboratory). The “gold standard” for sensitivity of both tests and for specificity of Premier
E. coli
O157 was isolation of
E. coli
O157:H7 or a fourfold anti-O157 antibody rise. Specimens positive by the Premier EHEC test and negative for
E. coli
O157 culture were examined for non-O157 verotoxin-producing
E. coli
. The field sensitivity of Premier
E. coli
O157 was 86%, that of Premier EHEC was 89%, and the specificity of Premier
E. coli
O157 was 98%. Ten of 13 discordant Premier
E. coli
O157 results were reassigned as true results after repeat testing. Ten non-O157 verotoxin-producing
E. coli
isolates were recovered from Premier EHEC-positive,
E. coli
O157 culture-negative stools. Only one specimen gave an unequivocally false-positive Premier EHEC result. Both tests are highly sensitive and are specific if correctly performed. The Premier EHEC test will be particularly valuable as a practical routine test for the detection of non-O157 verotoxin-producing
E. coli.