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Applied and Environmental Microbiology, June 2006, p. 3879-3886, Vol. 72, No. 6
0099-2240/06/$08.00+0     doi:10.1128/AEM.02266-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Comparison of Methods of Extracting Salmonella enterica Serovar Enteritidis DNA from Environmental Substrates and Quantification of Organisms by Using a General Internal Procedural Control

M. M. Klerks,1* A. H. C. van Bruggen,2 C. Zijlstra,1 and M. Donnikov3

Plant Research International BV, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands,1 Biological Farming Systems, Wageningen University and Research Centre, Marijkeweg 22, 6709 PG Wageningen, The Netherlands,2 Center for Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia3

Received 26 September 2005/ Accepted 20 March 2006

This paper compares five commercially available DNA extraction methods with respect to DNA extraction efficiency of Salmonella enterica serovar Enteritidis from soil, manure, and compost and uses an Escherichia coli strain harboring a plasmid expressing green fluorescent protein as a general internal procedural control. Inclusion of this general internal procedural control permitted more accurate quantification of extraction and amplification of S. enterica serovar Enteritidis in these samples and reduced the possibility of false negatives. With this protocol it was found that the optimal extraction method differed for soil (Mobio soil DNA extraction kit), manure (Bio101 soil DNA extraction kit), and compost (Mobio fecal DNA extraction kit). With each method, as little as 1.2 x 103 to 1.8 x 103 CFU of added serovar Enteritidis per 100 mg of substrate could be detected by direct DNA extraction and subsequent S. enterica-specific TaqMan PCR. After bacterial enrichment, as little as 1 CFU/100 mg of original substrate was detected. Finally, the study presents a more accurate molecular analysis for quantification of serovar Enteritidis initially present in soil or manure using DNA extraction and TaqMan PCR.

* Corresponding author. Mailing address: Plant Research International BV, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Phone: 31 317 476 156. Fax: 31 317 410 113. E-mail: Michel.Klerks{at}wur.nl.

Applied and Environmental Microbiology, June 2006, p. 3879-3886, Vol. 72, No. 6
0099-2240/06/$08.00+0     doi:10.1128/AEM.02266-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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