Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential

Publication: Research - peer-reviewJournal article – Annual report year: 2011

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Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential. / Grønlund, Hugo Ahlm; Riber, Leise; Vigre, Håkan; Löfström, Charlotta; Folling, Liselotte; Huehn, Stephan; Malorny, Burkhard; Rådström, Peter; Rudi, Knut; Hoorfar, Jeffrey.

In: International Journal of Food Microbiology, Vol. 145, No. Supplement 1, 03.2011, p. S79-S85.

Publication: Research - peer-reviewJournal article – Annual report year: 2011

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Author

Grønlund, Hugo Ahlm; Riber, Leise; Vigre, Håkan; Löfström, Charlotta; Folling, Liselotte; Huehn, Stephan; Malorny, Burkhard; Rådström, Peter; Rudi, Knut; Hoorfar, Jeffrey / Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential.

In: International Journal of Food Microbiology, Vol. 145, No. Supplement 1, 03.2011, p. S79-S85.

Publication: Research - peer-reviewJournal article – Annual report year: 2011

Bibtex

@article{569bdb5566f84ac7b0f680b33c652809,
title = "Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential",
keywords = ", Salmonella, Genotyping, Microarray, Comparative study, Standardization",
publisher = "Elsevier BV",
author = "Grønlund, {Hugo Ahlm} and Leise Riber and Håkan Vigre and Charlotta Löfström and Liselotte Folling and Stephan Huehn and Burkhard Malorny and Peter Rådström and Knut Rudi and Jeffrey Hoorfar",
year = "2011",
doi = "10.1016/j.ijfoodmicro.2010.08.007",
volume = "145",
number = "Supplement 1",
pages = "S79--S85",
journal = "International Journal of Food Microbiology",
issn = "0168-1605",

}

RIS

TY - JOUR

T1 - Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential

A1 - Grønlund,Hugo Ahlm

A1 - Riber,Leise

A1 - Vigre,Håkan

A1 - Löfström,Charlotta

A1 - Folling,Liselotte

A1 - Huehn,Stephan

A1 - Malorny,Burkhard

A1 - Rådström,Peter

A1 - Rudi,Knut

A1 - Hoorfar,Jeffrey

AU - Grønlund,Hugo Ahlm

AU - Riber,Leise

AU - Vigre,Håkan

AU - Löfström,Charlotta

AU - Folling,Liselotte

AU - Huehn,Stephan

AU - Malorny,Burkhard

AU - Rådström,Peter

AU - Rudi,Knut

AU - Hoorfar,Jeffrey

PB - Elsevier BV

PY - 2011/3

Y1 - 2011/3

N2 - Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variationamong different isolates in order to control pathogen-induced infections. Microarray technology is a promising diagnostic tool that provides genomic information onmany genes simultaneously. However, standardization of DNA microarray analysis is needed before it can be used as a routine method for characterizing Salmonella isolates across borders and laboratories. A comparative study was designed inwhich the agreement of data fromaDNA microarray assay used for typing Salmonella spp. between two different labs was assessed. The study was expected to reveal the possibility of obtaining the same results in different labs using different equipment in order to evaluate the reproducibility of the microarray technique as a first step towards standardization. The low-density array contains 281 57–60-mer oligonucleotide probes for detecting a wide range of specific genomic marker genes associated with antibiotic resistance, cell envelope structures,mobile genetic elements and pathogenicity. Several critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer,wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four-factorial experiment and statistical measures of inter-lab consistency and agreementwere performed based on the kappa coefficient. A high level of agreement (kappa=0.7–1.0) in microarray results was obtained even when employing different printing and hybridization facilities, different procedures for purifying genomicDNA and different wash buffers. However, less agreement (Kappa=0.2–0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly criticalwhen transferring a standard microarray assay between laboratories. In conclusion, this study indicates that DNA microarray assays can be reproduced in at least two different facilities, which is a pre-requisite for the development of standard guidelines.

AB - Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variationamong different isolates in order to control pathogen-induced infections. Microarray technology is a promising diagnostic tool that provides genomic information onmany genes simultaneously. However, standardization of DNA microarray analysis is needed before it can be used as a routine method for characterizing Salmonella isolates across borders and laboratories. A comparative study was designed inwhich the agreement of data fromaDNA microarray assay used for typing Salmonella spp. between two different labs was assessed. The study was expected to reveal the possibility of obtaining the same results in different labs using different equipment in order to evaluate the reproducibility of the microarray technique as a first step towards standardization. The low-density array contains 281 57–60-mer oligonucleotide probes for detecting a wide range of specific genomic marker genes associated with antibiotic resistance, cell envelope structures,mobile genetic elements and pathogenicity. Several critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer,wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four-factorial experiment and statistical measures of inter-lab consistency and agreementwere performed based on the kappa coefficient. A high level of agreement (kappa=0.7–1.0) in microarray results was obtained even when employing different printing and hybridization facilities, different procedures for purifying genomicDNA and different wash buffers. However, less agreement (Kappa=0.2–0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly criticalwhen transferring a standard microarray assay between laboratories. In conclusion, this study indicates that DNA microarray assays can be reproduced in at least two different facilities, which is a pre-requisite for the development of standard guidelines.

KW - Salmonella

KW - Genotyping

KW - Microarray

KW - Comparative study

KW - Standardization

U2 - 10.1016/j.ijfoodmicro.2010.08.007

DO - 10.1016/j.ijfoodmicro.2010.08.007

JO - International Journal of Food Microbiology

JF - International Journal of Food Microbiology

SN - 0168-1605

IS - Supplement 1

VL - 145

SP - S79-S85

ER -