Comparison between swabbing devices in order to analyze the microbial flora found on surfaces of community kitchens by classical microbiology and 16S rRNA amplicon sequencing

Background
The work in community kitchens involves several manual steps which justifies accurate control of surfaces to prevent foodborne illnesses. Different sampling methods have been proposed to isolate bacteria from surfaces. However, recovery efficiencies of these methods are very different and not always comparable.

Objectives
The aim of this study is to evaluate different sampling methods to detect the presence of pathogenic bacteria on surfaces in contact with foods. The recovery efficiency was examined by classical microbiology an culture-independent metagenomic analysis.

Methods
To mimic surfaces which can be found in community kitchens, sterile polypropylene stainless steel surfaces and cutting boards were spiked with serial dilutions of Escherichia coli, Salmonella enterica and Bacillus cereus. They were left to dry for 1-2 hours before collection of the surviving bacteria with different moistened swabs, including commercial swabs (sponges-HS10NB2G, Sponge-Sticks-SSL100; 3M) and cotton and gauze pads. Different solutions were tested to moisten the swabs (physiological water (0,85% NaCl), Maximum Recovery Diluent and quarter-strength Ringer solution). Bacterial population analysis was performed by classical methods and metagenomics.

Conclusions
Important differences on bacterial survival were observed depending on their nature and the solution used to collect them from the surfaces. Maximum Recovery Diluent and cotton pads showed the best results in relation with bacteria recovery and required technical skills. Metagenomic analysis showed a higher detection sensibility than classical microbiology. However, preliminary results showed that both methods are necessary to improve the detection of pathogens in surfaces.