Selection of spore-specific aptamers for Geobacillus stearothermophilus, a food spoilage bacterium

Due to their ability to form extremely heat resistant spores, anaerobic bacteria are responsible for frequent food spoilage. The development of rapid and specific methods for the detection and quantification of spore contamination is therefore of major interest. In this paper, we describe for the first time the selection of aptamers specific to spores of Geobacillus stearothermophilus (Gbs), which induce flat sour spoilage in vegetable cans. Eighteen Spore-SELEX cycles were performed including 4 counter-selections with 12 bacteria commonly found in cannery. To optimise candidate amplification, PCR in emulsion was performed, and high-throughput sequencing analysis was applied to follow candidate evolution. Sequencing of aptamers from cycle 18 revealed 43 overrepresented sequences whose copy number exceeds 0.15% of the total obtained sequences. Within this group, the A01 aptamer presented a much higher enrichment with a relative abundance of 17.71%. Affinity and specificity for Gbs spores of the 10 most abundant candidates at cycle 18 were confirmed by PCR assay based on aptamerspore complex formation and filtration step. Obtaining these aptamers is the starting point for the future development of biosensors dedicated to the detection of Gbs spores.

Automated summary

Anaerobic bacteria, due to their ability to form heat resistant spores, commonly cause food spoilage. This study focuses on the development of a method for the detection and quantification of spore contamination by selecting specific aptamers for Geobacillus stearothermophilus (Gbs) spores. Through multiple selection cycles and high-throughput sequencing analysis, 43 overrepresented sequences were identified, with the A01 aptamer showing the highest enrichment. PCR assay confirmed the affinity and specificity of the top 10 candidates for Gbs spores.