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  • 1
    Language: English
    In: Journal of clinical microbiology, 2018-08, Vol.56 (8)
    Description: This multicenter study evaluated the performance of the Cepheid Xpert Carba-R assay, a qualitative PCR test designed for the rapid detection of , , , , and carbapenem resistance genes from bacterial isolates grown on blood agar or MacConkey agar. The results were compared to those obtained from bidirectional DNA sequence analysis of nucleic acid extracted from pure colonies. Isolates of , , and that tested as either intermediate or resistant to a carbapenem antibiotic were analyzed. A total of 467 isolates were evaluated, including prospectively collected clinical isolates, frozen isolates, and a group of contrived broth specimens sent by a central reference laboratory. The assay was run on the GeneXpert platform and took 48 min, with less than 1 min of hands-on time. Compared to the results of the reference methods, the overall sensitivity of the assay was 100% (95% confidence interval [CI], 99.0 to 100%) for isolates grown on both blood and MacConkey agars. Overall specificity was 98.1% (95% CI, 93.1 to 99.8%) and 97.1% (95% CI, 91.7 to 99.4%) for blood and MacConkey agars, respectively. This platform, previously demonstrated to be effective for the detection of carbapenemase genes in rectal swabs, is also adequate for the detection of these genes in bacterial colonies isolated from blood and MacConkey agars.
    Subject(s): Index Medicus
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 2
    Language: English
    In: Journal of clinical microbiology, 2017-06, Vol.55 (6), p.1915-1919
    Description: is a significant pathogen for which first-line treatment is becoming less effective due to increased resistance to macrolides. As conventional culture and antimicrobial susceptibility testing is not feasible for routine detection of this pathogen, molecular markers such as detection of mutations in the 23S rRNA gene have been described to predict resistance. Recently, a novel multiplex quantitative PCR (qPCR) assay, ResistancePlus MG, has been described for the simultaneous detection of and macrolide resistance. In the current study, the clinical performance of the assay was evaluated on 1,089 consecutive urine and anogenital swab samples in symptomatic and asymptomatic male and female patients. Overall, 6.0% were positive for , with 63.1% having macrolide resistance-associated mutations. Compared to the laboratory-validated qPCR method targeting the 16S rRNA gene and Sanger sequencing to determine 23S rRNA mutations, the sensitivity and specificity of detection were 98.5% and 100% and for detection of macrolide resistance mutations were 100.0% and 96.2%, respectively. This assay offers a considerable advantage in clinical settings for testing by making the results of macrolide resistance and mutation analyses simultaneously available, which is increasingly important with escalating macrolide resistance.
    Subject(s): Molecular Diagnostic Techniques - methods ; Prospective Studies ; Anal Canal - microbiology ; Humans ; Real-Time Polymerase Chain Reaction - methods ; Drug Resistance, Bacterial ; Mycoplasma Infections - diagnosis ; Male ; DNA, Bacterial - chemistry ; DNA, Ribosomal - chemistry ; Mycoplasma genitalium - genetics ; RNA, Ribosomal, 23S - genetics ; Sensitivity and Specificity ; Macrolides - pharmacology ; Female ; Mycoplasma genitalium - drug effects ; Urine - microbiology ; DNA, Ribosomal - genetics ; Multiplex Polymerase Chain Reaction - methods ; Mycoplasma Infections - microbiology ; DNA, Bacterial - genetics ; Mycoplasma genitalium - isolation & purification ; RNA, Ribosomal, 16S - genetics ; Anti-Bacterial Agents - pharmacology ; Microbial Sensitivity Tests - methods ; Genitalia - microbiology ; Index Medicus ; NAAT ; 23S rRNA ; multiplex assay ; Mycoplasma genitalium ; qPCR ; diagnostic ; Bacteriology ; sensitivity and specificity ; macrolide resistance
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 3
    Language: English
    In: Journal of clinical microbiology, 2017-03, Vol.55 (3), p.724-734
    Description: serotype 35B is a nonvaccine serotype associated with high rates of penicillin nonsusceptibility. An increase in the proportion of multidrug-resistant (MDR) 35B isolates has recently been reported. The genetic events contributing to the emergence of MDR serotype 35B are unknown. The sequence type (ST) composition of 78 serotype 35B isolates obtained from pediatric patients with invasive pneumococcal disease from 1994 to 2014 and 48 isolates from pediatric patients with otitis media (noninvasive) from 2011 to 2014 was characterized by multilocus sequence typing (MLST). The most common STs were ST558 (69.2%), ST156 (10.3%), and ST452 (3.8%). Two major clonal complexes (CC), CC558 and CC156, were identified by eBURST analysis. Overall, 91% (71/78) of isolates were penicillin nonsusceptible and 16.7% (13/78) were MDR. Among all invasive serotype 35B isolates, MDR isolates increased significantly, from 2.9% (1/35) to 27.9% (12/43) ( = 0.004), after the 13-valent pneumococcal conjugate vaccine (PCV13) was introduced. All CC156 isolates were identified after the introduction of PCV13 (0/35 [0%] before versus 9/43 [20.9%] after; = 0.003) and were MDR. All CC156 isolates had similar antimicrobial susceptibility patterns; in contrast, high variability in antimicrobial susceptibility was observed among CC558 isolates. The distributions of CC558 and CC156 among invasive and noninvasive isolates were not different. The increased prevalence of MDR serotype 35B after the introduction of PCV13 was directly associated with the emergence of ST156. Genotyping suggests that capsular switching has occurred between MDR vaccine serotypes belonging to ST156 (e.g., 9V, 14, and 19A) and serotype 35B.
    Subject(s): United States - epidemiology ; Streptococcus pneumoniae - classification ; Streptococcus pneumoniae - drug effects ; Prevalence ; Prospective Studies ; Humans ; Serogroup ; Child, Preschool ; Genotype ; Infant ; Male ; Pneumococcal Vaccines - administration & dosage ; Multilocus Sequence Typing ; Pneumococcal Infections - epidemiology ; Streptococcus pneumoniae - isolation & purification ; Drug Resistance, Multiple, Bacterial ; Adolescent ; Bacterial Capsules - genetics ; Pneumococcal Vaccines - immunology ; Female ; Pneumococcal Infections - microbiology ; Child ; Index Medicus ; multidrug resistance ; pneumococcus ; otitis media ; pneumococcal disease ; pneumococcal vaccine ; serotype 35B ; Bacteriology ; Streptococcus pneumoniae
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 4
    Language: English
    In: Journal of clinical microbiology, 2018-06, Vol.56 (6), p.e00319-18
    Description: We have previously demonstrated that culturing periprosthetic tissue in blood culture bottles (BCBs) improves sensitivity compared to conventional agar and broth culture methods for diagnosis of prosthetic joint infection (PJI). We have also shown that prosthesis sonication culture improves sensitivity compared to periprosthetic tissue culture using conventional agar and broth methods. The purpose of this study was to compare the diagnostic accuracy of tissue culture in BCBs (subsequently referred to as tissue culture) to prosthesis sonication culture (subsequently referred to as sonicate fluid culture). We studied 229 subjects who underwent arthroplasty revision or resection surgery between March 2016 and October 2017 at Mayo Clinic in Rochester, Minnesota. Using the Infectious Diseases Society of America (IDSA) PJI diagnostic criteria (omitting culture criteria) as the gold standard, the sensitivity of tissue culture was similar to that of the sonicate fluid culture (66.4% versus 73.1%, = 0.07) but was significantly lower than that of the two tests combined (66.4% versus 76.9%, 〈 0.001). Using Bayesian latent class modeling, which assumes no gold standard for PJI diagnosis, the sensitivity of tissue culture was slightly lower than that of sonicate fluid culture (86.3% versus 88.7%) and much lower than that of the two tests combined (86.3% versus 99.1%). In conclusion, tissue culture in BCBs reached sensitivity similar to that of prosthesis sonicate fluid culture for diagnosis of PJI, but the two tests combined had the highest sensitivity without compromising specificity. The combination of tissue culture in BCBs and sonicate fluid culture is recommended to achieve the highest level of microbiological diagnosis of PJI.
    Subject(s): Index Medicus
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 5
    Language: English
    In: Journal of clinical microbiology, 2017-12, Vol.55 (12), p.3513-3529
    Description: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) sample preparation methods, including the direct, on-plate formic acid, and ethanol/formic acid tube extraction methods, were evaluated for their ability to render highly pathogenic organisms nonviable and safe for handling in a biosafety level 2 laboratory. Of these, the tube extraction procedure was the most successful, with none of the tested strains surviving this sample preparation method. Tube extracts from several agents of bioterrorism and their near neighbors were analyzed in an eight-laboratory study to examine the utility of the Bruker Biotyper and Vitek MS MALDI-TOF MS systems and their diagnostic (IVD), research-use-only, and Security-Relevant databases, as applicable, to accurately identify these agents. Forty-six distinct strains of , , , , , , , , , and were extracted and distributed to participating laboratories for analysis. A total of 35 near-neighbor isolates were also analyzed.
    Subject(s): Index Medicus ; clinical laboratory ; pathogenic organisms ; MALDI-TOF ; biothreat agents ; Bacteriology ; public health
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 6
    Language: English
    In: The Plant cell, 2010-04-01, Vol.22 (4), p.1344-1357
    Description: Plants constantly adjust their repertoire of plasma membrane proteins that mediates transduction of environmental and developmental signals as well as transport of ions, nutrients, and hormones. The importance of regulated secretory and endocytic trafficking is becoming increasingly clear; however, our knowledge of the compartments and molecular machinery involved is still fragmentary. We used immunogold electron microscopy and confocal laser scanning microscopy to trace the route of cargo molecules, including the BRASSINOSTEROID INSENSITIVE1 receptor and the REQUIRES HIGH BORON1 boron exporter, throughout the plant endomembrane system. Our results provide evidence that both endocytic and secretory cargo pass through the trans-Golgi network/early endosome (TGN/EE) and demonstrate that cargo in late endosomes/multivesicular bodies is destined for vacuolar degradation. Moreover, using spinning disc microscopy, we show that TGN/EEs move independently and are only transiently associated with an individual Golgi stack.
    Subject(s): Receptors ; Endocytosis ; Boron ; Cell walls ; Plants ; Freight ; Plant cells ; Endosomes ; Seedlings ; Golgi apparatus ; cell-wall pectins ; by-2 cells ; boron transporter ; root-cells ; homotypic fusion ; plant-cells ; prevacuolar compartments ; atpase activity ; endoplasmic-reticulum ; brefeldin-a ; Arabidopsis Proteins - metabolism ; Protein Kinases - metabolism ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; trans-Golgi Network - metabolism ; Antiporters - metabolism ; Multivesicular Bodies - metabolism ; Arabidopsis - metabolism ; Protein Transport ; Arabidopsis thaliana ; Physiological aspects ; Research ; Plant physiology ; Index Medicus
    ISSN: 1040-4651
    E-ISSN: 1532-298X
    Source: American Society of Plant Biologists
    Source: HighWire Press (Free Journals)
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 7
    Language: English
    In: Journal of clinical microbiology, 2018-03, Vol.56 (3)
    Subject(s): Singapore ; Blood Culture ; Genes, Bacterial - genetics ; Bacteremia - diagnosis ; Flavobacteriaceae - genetics ; Flavobacteriaceae - drug effects ; Sequence Analysis, DNA ; Bacteremia - microbiology ; Genetic Variation ; Microbial Sensitivity Tests ; Flavobacteriaceae - isolation & purification ; Flavobacteriaceae Infections - blood ; Genome, Bacterial - genetics ; DNA, Bacterial - genetics ; Drug Resistance, Multiple, Bacterial ; Sensitivity and Specificity ; RNA, Ribosomal, 16S - genetics ; Bacteriological Techniques ; Anti-Bacterial Agents - pharmacology ; Retrospective Studies ; Index Medicus
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 8
    Language: English
    In: Journal of clinical microbiology, 2020-12-17, Vol.59 (1)
    Subject(s): Index Medicus
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: Hellenic Academic Libraries Link
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 9
    Language: English
    In: Journal of clinical microbiology, 2020-03-25, Vol.58 (4)
    Description: We assessed the ceftazidime-avibactam disk diffusion breakpoints that provide the lowest discrepancy error rates by testing an isolate collection with ceftazidime-avibactam MIC values near the breakpoints. Isolates (  = 112) were susceptibility tested by broth microdilution and disk diffusion methods in 3 laboratories. Current disk diffusion breakpoints (≥21/≤20 mm for susceptible/resistant) provided the lowest error rates, but confirmatory MIC testing is indicated for isolates with inhibition zones of 20 to 22 mm.
    Subject(s): Index Medicus
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 10
    Language: English
    In: Journal of clinical microbiology, 2020-03-25, Vol.58 (4)
    Description: Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Ten microbiology laboratories throughout the United States collected residual, deidentified positive blood culture samples for analysis. Five laboratories tested both clinical and contrived samples with the BCID-GP Panel. Comparator identification methods included each laboratory's SOC, which included matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and automated identification systems as well as targeted PCR/analytically validated real-time PCR (qPCR) with bidirectional sequencing. A total of 2,342 evaluable samples (1,777 clinical and 565 contrived) were tested with the BCID-GP Panel. The overall sample accuracy for on-panel organisms was 89% before resolution of discordant results. For pathogenic Gram-positive targets ( group, spp., , , spp., , , , spp., , spp., , group, , and ), positive percent agreement (PPA) and negative percent agreement (NPA) ranged from 93.1% to 100% and 98.8% to 100%, respectively. For contamination rule-out targets ( group, , , , and ), PPA and NPA ranged from 84.5% to 100% and 99.9% to 100%, respectively. Positive percent agreement and NPA for the Pan and Pan Gram-Negative targets were 92.4% and 95.7% for the former and 99.9% and 99.6% for the latter. The PPAs for resistance markers were as follows: , 97.2%; , 100%; , 96.8%; and , 100%. Negative percent agreement ranged from 96.6% to 100%. In conclusion, the ePlex BCID-GP Panel compares favorably to SOC and targeted molecular methods for the identification of 20 Gram-positive pathogens and four antimicrobial resistance genes in positive blood culture bottles. This panel detects a broad range of pathogens and mixed infections with yeast and Gram-negative organisms from the same positive blood culture bottle.
    Subject(s): Index Medicus
    ISSN: 0095-1137
    E-ISSN: 1098-660X
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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