Comparison between swabbing devices in order to analyse the microbial flora found on surfaces by classical microbiology and 16S rDNA amplicon sequencing

The work in community kitchens involves several steps bearing the risk of transmitting pathogenic microorganisms from static or dynamic surfaces to the food. This study aimed at comparing the recovery efficiency of different sampling devices in terms of culture methods and culture-independent 16S rDNA amplicon sequencing for characterising the microbial flora. In order to mimic surfaces found in community kitchens, sterile stainless steel and polypropylene surfaces were spiked with a two-fold raw chicken meat dilution and several concentrations of Escherichia coli, Salmonella Enteritidis and Bacillus cereus, respectively. The ideal swab for kitchen analyses should recover the highest number of viable bacteria with the highest population diversity. Classical culture method showed that recovery was possible with all swabs, but that Sponge-Sticks had the highest recovery rates. The 16S rDNA amplicon sequencing revealed a high relative abundance of Bacillus genus in cotton pad, gauze pad and Sponge-Stick samples and low proportions of Salmonella genus in all samples. Analysis of Escherichia genus results was problematic for molecular analyses as it appeared as a source of DNA contamination of the reagents used during library creation. Furthermore, it was possible to decipher bias populations in the sponge samples (from neutralising buffer) and in controls (due to low amounts of DNA), allowing the exclusion of those in the following analyses, if needed. In the end, these results attest the similarity of population diversity in cotton pad, gauze pad and Sponge-Stick samples, leaving the final choice to the operator.