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  1. Article ; Online: Express Yourself: Quantitative Real-Time PCR Assays for Rapid Chromosomal Antimicrobial Resistance Detection in Pseudomonas aeruginosa.

    Madden, Danielle E / Olagoke, Olusola / Baird, Timothy / Neill, Jane / Ramsay, Kay A / Fraser, Tamieka A / Bell, Scott C / Sarovich, Derek S / Price, Erin P

    Antimicrobial agents and chemotherapy

    2022  Volume 66, Issue 5, Page(s) e0020422

    Abstract: The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then ... ...

    Abstract The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then validated two multiplex quantitative real-time PCR (qPCR) assays to simultaneously detect differential expression of the resistance-nodulation-division efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM, the AmpC β-lactamase, and the porin OprD, which are commonly associated with chromosomally encoded AMR. Next, qPCRs were tested on 15 sputa from 11 participants with P. aeruginosa respiratory infections to determine AMR profiles
    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/metabolism ; Carbapenems/therapeutic use ; Cystic Fibrosis/complications ; Drug Resistance, Bacterial ; Humans ; Membrane Transport Proteins/genetics ; Microbial Sensitivity Tests ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa ; Real-Time Polymerase Chain Reaction
    Chemical Substances Anti-Bacterial Agents ; Bacterial Outer Membrane Proteins ; Bacterial Proteins ; Carbapenems ; Membrane Transport Proteins
    Language English
    Publishing date 2022-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/aac.00204-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei.

    Madden, Danielle E / Webb, Jessica R / Steinig, Eike J / Currie, Bart J / Price, Erin P / Sarovich, Derek S

    EBioMedicine

    2020  Volume 63, Page(s) 103152

    Abstract: Background: Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in accurately and comprehensively detecting AMR across the spectrum ... ...

    Abstract Background: Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in accurately and comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens.
    Methods: Using 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA, CARD, ResFinder, and AMRFinderPlus) for detecting clinically relevant AMR in this pathogen. B. pseudomallei was chosen due to limited treatment options, high fatality rate, and AMR caused exclusively by chromosomal mutation (i.e. single-nucleotide polymorphisms [SNPs], insertions-deletions [indels], copy-number variations [CNVs], inversions, and functional gene loss). Due to poor performance with existing tools, we developed ARDaP (Antimicrobial Resistance Detection and Prediction) to identify the spectrum of AMR-conferring determinants in B. pseudomallei.
    Findings: CARD, ResFinder, and AMRFinderPlus failed to identify any clinically-relevant AMR in B. pseudomallei; ARIBA identified AMR encoded by SNPs and indels that were manually added to its database. However, none of these tools identified CNV, inversion, or gene loss determinants, and ARIBA could not differentiate AMR determinants from natural genetic variation. In contrast, ARDaP accurately detected all SNP, indel, CNV, inversion, and gene loss AMR determinants described in B. pseudomallei (n≈50). Additionally, ARDaP accurately predicted three previously undescribed determinants. In mixed strain data, ARDaP identified AMR to as low as ~5% allelic frequency.
    Interpretation: Existing AMR software packages are inadequate for chromosomal AMR detection due to an inability to detect resistance conferred by CNVs, inversions, and functional gene loss. ARDaP overcomes these major shortcomings. Further, ARDaP enables AMR prediction from mixed sequence data down to 5% allelic frequency, and can differentiate natural genetic variation from AMR determinants. ARDaP databases can be constructed for any microbial species of interest for comprehensive AMR detection.
    Funding: National Health and Medical Research Council (BJC, EPP, DSS); Australian Government (DEM, ES); Advance Queensland (EPP, DSS).
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Burkholderia pseudomallei/drug effects ; Burkholderia pseudomallei/genetics ; Burkholderia pseudomallei/isolation & purification ; Computational Biology/methods ; Drug Resistance, Bacterial ; Genes, Bacterial ; Genome, Bacterial ; Genomics/methods ; Humans ; Melioidosis/drug therapy ; Melioidosis/microbiology ; Microbial Sensitivity Tests ; Mutation ; Sequence Analysis, DNA ; Whole Genome Sequencing
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2020-12-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2020.103152
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 7090: Show issues Location:
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  3. Article ; Online: Rapid fluoroquinolone resistance detection in

    Madden, Danielle E / McCarthy, Kate L / Bell, Scott C / Olagoke, Olusola / Baird, Timothy / Neill, Jane / Ramsay, Kay A / Kidd, Timothy J / Stewart, Adam G / Subedi, Shradha / Choong, Keat / Fraser, Tamieka A / Sarovich, Derek S / Price, Erin P

    Journal of medical microbiology

    2022  Volume 71, Issue 10

    Abstract: Background. ...

    Abstract Background.
    MeSH term(s) Fluoroquinolones/pharmacology ; Pseudomonas aeruginosa ; DNA Gyrase/genetics ; Drug Resistance, Bacterial/genetics ; Real-Time Polymerase Chain Reaction ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Australia ; Mutation
    Chemical Substances Fluoroquinolones ; DNA Gyrase (EC 5.99.1.3) ; Anti-Bacterial Agents
    Language English
    Publishing date 2022-10-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 218356-0
    ISSN 1473-5644 ; 0022-2615
    ISSN (online) 1473-5644
    ISSN 0022-2615
    DOI 10.1099/jmm.0.001593
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 634: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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    ab Jg. 2022: Lesesaal (EG)

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