Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR

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Standard

Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR. / Clasen, Julie; Mellerup, Anders; Olsen, John Elmerdahl; Angen, Øystein; Folkesson, Anders; Halasa, Tariq; Toft, Nils; Birkegard, Anna Camilla.

I: Veterinary Microbiology, Bind 189, 30.06.2016, s. 46-51.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Clasen, J, Mellerup, A, Olsen, JE, Angen, Ø, Folkesson, A, Halasa, T, Toft, N & Birkegard, AC 2016, 'Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR', Veterinary Microbiology, bind 189, s. 46-51. https://doi.org/10.1016/j.vetmic.2016.04.017

APA

Clasen, J., Mellerup, A., Olsen, J. E., Angen, Ø., Folkesson, A., Halasa, T., Toft, N., & Birkegard, A. C. (2016). Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR. Veterinary Microbiology, 189, 46-51. https://doi.org/10.1016/j.vetmic.2016.04.017

Vancouver

Clasen J, Mellerup A, Olsen JE, Angen Ø, Folkesson A, Halasa T o.a. Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR. Veterinary Microbiology. 2016 jun 30;189:46-51. https://doi.org/10.1016/j.vetmic.2016.04.017

Author

Clasen, Julie ; Mellerup, Anders ; Olsen, John Elmerdahl ; Angen, Øystein ; Folkesson, Anders ; Halasa, Tariq ; Toft, Nils ; Birkegard, Anna Camilla. / Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR. I: Veterinary Microbiology. 2016 ; Bind 189. s. 46-51.

Bibtex

@article{6a23cd4b593b49b783a350d946f2660d,
title = "Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR",
abstract = "The primary objective of this study was to determine the minimum number of individual fecal samples to pool together in order to obtain a representative sample for herd level quantification of antimicrobial resistance (AMR) genes in a Danish pig herd, using a novel high-throughput qPCR assay. The secondary objective was to assess the agreement between different methods of sample pooling. Quantification of AMR was achieved using a high-throughput qPCR method to quantify the levels of seven AMR genes (ermB,ermF, sulI, sulII, tet(M), tet(O) and tet(W)). A large variation in the levels of AMR genes was found between individual samples. As the number of samples in a pool increased, a decrease in sample variation was observed. It was concluded that the optimal pooling size is five samples, as an almost steady state in the variation was observed when pooling this number of samples. Good agreement between different pooling methods was found and the least time-consuming method of pooling, by transferring feces from each individual sample to a tube using a 10 mu l inoculation loop and adding 3.5 ml of PBS, approximating a 10% solution, can therefore be used in future studies. ",
keywords = "Pooling, Antimicrobial resistance gene, Pig, High-throughput qPCR, Sample size, Herd level",
author = "Julie Clasen and Anders Mellerup and Olsen, {John Elmerdahl} and {\O}ystein Angen and Anders Folkesson and Tariq Halasa and Nils Toft and Birkegard, {Anna Camilla}",
year = "2016",
month = jun,
day = "30",
doi = "10.1016/j.vetmic.2016.04.017",
language = "English",
volume = "189",
pages = "46--51",
journal = "Veterinary Microbiology",
issn = "0378-1135",
publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR

AU - Clasen, Julie

AU - Mellerup, Anders

AU - Olsen, John Elmerdahl

AU - Angen, Øystein

AU - Folkesson, Anders

AU - Halasa, Tariq

AU - Toft, Nils

AU - Birkegard, Anna Camilla

PY - 2016/6/30

Y1 - 2016/6/30

N2 - The primary objective of this study was to determine the minimum number of individual fecal samples to pool together in order to obtain a representative sample for herd level quantification of antimicrobial resistance (AMR) genes in a Danish pig herd, using a novel high-throughput qPCR assay. The secondary objective was to assess the agreement between different methods of sample pooling. Quantification of AMR was achieved using a high-throughput qPCR method to quantify the levels of seven AMR genes (ermB,ermF, sulI, sulII, tet(M), tet(O) and tet(W)). A large variation in the levels of AMR genes was found between individual samples. As the number of samples in a pool increased, a decrease in sample variation was observed. It was concluded that the optimal pooling size is five samples, as an almost steady state in the variation was observed when pooling this number of samples. Good agreement between different pooling methods was found and the least time-consuming method of pooling, by transferring feces from each individual sample to a tube using a 10 mu l inoculation loop and adding 3.5 ml of PBS, approximating a 10% solution, can therefore be used in future studies.

AB - The primary objective of this study was to determine the minimum number of individual fecal samples to pool together in order to obtain a representative sample for herd level quantification of antimicrobial resistance (AMR) genes in a Danish pig herd, using a novel high-throughput qPCR assay. The secondary objective was to assess the agreement between different methods of sample pooling. Quantification of AMR was achieved using a high-throughput qPCR method to quantify the levels of seven AMR genes (ermB,ermF, sulI, sulII, tet(M), tet(O) and tet(W)). A large variation in the levels of AMR genes was found between individual samples. As the number of samples in a pool increased, a decrease in sample variation was observed. It was concluded that the optimal pooling size is five samples, as an almost steady state in the variation was observed when pooling this number of samples. Good agreement between different pooling methods was found and the least time-consuming method of pooling, by transferring feces from each individual sample to a tube using a 10 mu l inoculation loop and adding 3.5 ml of PBS, approximating a 10% solution, can therefore be used in future studies.

KW - Pooling

KW - Antimicrobial resistance gene

KW - Pig

KW - High-throughput qPCR

KW - Sample size

KW - Herd level

U2 - 10.1016/j.vetmic.2016.04.017

DO - 10.1016/j.vetmic.2016.04.017

M3 - Journal article

C2 - 27259826

VL - 189

SP - 46

EP - 51

JO - Veterinary Microbiology

JF - Veterinary Microbiology

SN - 0378-1135

ER -

ID: 165744539