Comparison of individual and pooled samples for quantification of antimicrobial resistance genes in swine feces by high-throughput qPCR

Julie Clasen, Anders Mellerup, John Elmerdahl Olsen, Øystein Angen, Sven Anders Folkesson, Nils Toft, Anna Camilla Birkegård

    Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsResearchpeer-review

    Abstract

    There is a considerable societal interest in the careful monitoring of antimicrobial resistance (AMR) levels in human and animal populations. Sampling and data analysis can be both costly and time consuming. Optimization of sample pooling procedures is therefore important to reduce costs and analysis times. The objective of this study was to estimate how many individual fecal samples are needed to pool to get a representative sample for quantification of AMR-genes in a Danish pig herd. 20 individual fecal samples were collected from one section in a Danish pig herd. One to five rectal fecal samples were taken from each pen with respect to the number of pigs in the pen. A total of 48 pools were made of increasing number of individual samples. The levels of 9 different AMR-genes were quantified using dynamic qPCR arrays on the BioMark HD system(Fluidigm®).DNA was extracted using the Maxwell® 16 Blood DNA Purification Kit (Promega). DNA concentrations were diluted to 40 ng/μl. The efficiency of the primers was determined using standard curves. Obtained results were normalized with 16S ribosomal DNA. There were large variations in the levels of AMR-genes between individual samples. As the number of samples in a pool increased a decrease in sample variation was observed. A steady state in the sample variation was seen when pooling five or more samples. No significant difference was found between pools of five samples and pools of more. There were a significant difference between pools of five or more samples and pools of less (p < 0.0001). In order to quantify the level of AMR-genes pools of five individual samples will give a result representative of the pig herd. The findings of this study could be used in planning of observational studies.
    Original languageEnglish
    Title of host publicationProceedings of the Annual Scientific Conference and the Annual General Meeting of the European College of Veterinary Public Health
    EditorsBojan Blagojevic
    Place of PublicationBelgrade, Serbia
    PublisherEuropean College of Veterinary Public Health
    Publication date2015
    Pages27-27
    Article numberP15
    Publication statusPublished - 2015
    EventAnnual General Meeting of the European College of Veterinary Public Health 2015 - Belgrade, Serbia
    Duration: 7 Oct 20159 Oct 2015

    Conference

    ConferenceAnnual General Meeting of the European College of Veterinary Public Health 2015
    CountrySerbia
    CityBelgrade
    Period07/10/201509/10/2015

    Fingerprint Dive into the research topics of 'Comparison of individual and pooled samples for quantification of antimicrobial resistance genes in swine feces by high-throughput qPCR'. Together they form a unique fingerprint.

    Cite this