Cell SELEX-based DNA aptamer selection targeting Streptococcus agalactiae using high-throughput sequencing: toward multifunctional applications in aquaculture

Nguyen, Dung Ho My; Khianchaikhan, Kamolwan; Longya, Apinya; Laopichienpong, Nararat; Lao, Thuan Duc; Sukkarun, Pimwarang

doi:10.30466/vrf.2025.2065775.4838

Cell SELEX-based DNA aptamer selection targeting Streptococcus agalactiae using high-throughput sequencing: toward multifunctional applications in aquaculture

Document Type : Original Article

Authors

Dung Ho My Nguyen ¹

Kamolwan Khianchaikhan ²

Apinya Longya ²

Nararat Laopichienpong ²

Thuan Duc Lao ³

Pimwarang Sukkarun ⁴

¹ Center for Life Science Research – CELI, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam

² Department of Research and Development, Queen Saovabha Memorial Institute, Bangkok, Thailand

³ Department of Pharmaceutical and Medical Biotechnology, Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam

⁴ Faculty of Veterinary Science, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat, Thailand

https://doi.org/10.30466/vrf.2025.2065775.4838

Abstract

Streptococcus agalactiae is a Gram-positive bacterial pathogen accountable for disease outbreaks in tilapia, resulting in substantial economic losses in aquaculture. In this study, a 10-round whole-cell Systemic Evolution of Ligands by Exponential Enrichment procedure was conducted to isolate and characterize single-stranded DNA aptamers with specific binding affinity to S. agalactiae. The enriched single-stranded DNA libraries were sequenced by high-throughput sequencing, yielding a total of 180,987 reads, of which 126,933 included unique aptamer sequences. The most frequent sequences were selected for further analysis. Among them, SA1 had the highest frequency, with 231 reads, whereas SA2 showed a lower number of 16 reads. These findings underscored the validity of combining whole-cell Systemic Evolution of Ligands by Exponential Enrichment, high-throughput sequencing and aptamer-structure analysis to explore the interaction between aptamers and bacterial cell surfaces. The selected aptamers not only showed promise for the detection of S. agalactiae but also served as molecular probes for identifying surface-exposed proteins, studying host-pathogen interactions and guiding targeted drug delivery in aquaculture-related applications.

Keywords

Aptamer

Aquatic pathogens

High-throughput sequencing

Streptococcus agalactiae

Whole-cell SELEX