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Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential
DTU Technical University of Denmark, Denmark.ORCID iD: 0000-0001-6492-1245
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2011 (English)In: International Journal of Food Microbiology, ISSN 0168-1605, E-ISSN 1879-3460, Vol. 145, no SUPPL. 1, p. S79-S85Article in journal (Refereed) Published
Abstract [en]

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 variation among different isolates in order to control pathogen-induced infections. Microarray technology is a promising diagnostic tool that provides genomic information on many 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 in which the agreement of data from a DNA 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 agreement were 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 genomic DNA 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 critical when 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. © 2010 Elsevier B.V.

Place, publisher, year, edition, pages
2011. Vol. 145, no SUPPL. 1, p. S79-S85
Keywords [en]
Comparative study, Genotyping, Microarray, Salmonella, Standardization, genomic DNA, article, DNA microarray, evaluation, genotype, laboratory, microarray analysis, nonhuman, oligonucleotide probe, parameter, reproducibility, Food Microbiology, Humans, Laboratory Techniques and Procedures, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Bacteria (microorganisms)
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Natural Sciences
Identifiers
URN: urn:nbn:se:ri:diva-39025DOI: 10.1016/j.ijfoodmicro.2010.08.007Scopus ID: 2-s2.0-79953044976OAI: oai:DiVA.org:ri-39025DiVA, id: diva2:1324767
Note

 Funding details: Nordisk komité for jordbruks- og matforskning, 036272, 125; Funding text 1: Pia Engelsmann is acknowledged for excellent technical assistance. This study was financially supported by the Nordic Joint Committee for Agricultural Research (NKJ, project no. 125) and the European Union-funded integrated project BIOTRACER (contract no. 036272 ) under the 6th RTD Framework.

Available from: 2019-06-14 Created: 2019-06-14 Last updated: 2019-06-14Bibliographically approved

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Löfström, Charlotta

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