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Firman Fajar Perdhana
Universitas Mataram
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Journal : West Science Nature and Technology

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In Silico Design of Multiplex PCR Primers for the Detection of Foodborne Pathogens in Fermented Shrimp Paste (Terasi) from Lombok Island: In Silico PCR and Primer Verification Unsunnidhal, Lalu; Perdhana, Firman Fajar; Ariyana, Mutia Devi
West Science Nature and Technology Vol. 3 No. 02 (2025): West Science Nature and Technology
Publisher : Westscience Press

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.58812/wsnt.v3i02.1813

Abstract

Fermented shrimp paste (terasi) is a traditional food product produced by micro, small, and medium enterprises (MSMEs) in Lombok Island, Indonesia. Due to its fermentation and handling processes, terasi is susceptible to contamination by foodborne pathogens. The Indonesian Food and Drug Authority has identified specific bacterial pathogens that pose a risk of contamination in shrimp paste, necessitating accurate and efficient detection methods. Molecular detection using polymerase chain reaction (PCR) is known for its high specificity and sensitivity, as well as its rapid processing time and cost-effectiveness. However, conventional PCR can only detect a single target pathogen in one reaction, limiting its efficiency in screening multiple contaminants simultaneously. This study aims to design and optimize Multiplex PCR primers for detecting multiple foodborne pathogens in terasi through an in-silico approach, followed by In Silico PCR verification to assess primer specificity and efficiency. Target pathogens include Salmonella spp., Staphylococcus aureus and Vibrio cholerae. DNA target sequences were retrieved from the National Center for Biotechnology Information (NCBI) database, and primer design was conducted using Primer3Plus software. The designed primer sets were validated using Primer-BLAST (NCBI), and in-silico PCR was performed to verify amplification efficiency and specificity. The designed primer set has been successfully obtained and evaluated using In Silico PCR and Primer-BLAST (NCBI), confirming its specificity to the target genes. These results demonstrate that the primers can be effectively used as a molecular detection tool for foodborne pathogens. The optimized conditions and validated primer set are expected to contribute to molecular-based food safety detection methods, particularly for Indonesian fermented food products.
Co-Authors A Yuniastuti Adriani, Ika Reskiana Afni, Nur' Ahmad Alamsyah Amaliah, Wenny Amaliyah, Wenny Amaro, Moegiratul Amro, Moegiratul Anggraini, Ines Marisya Dwi Antesty, Sella Apriani, Tindih Ardo, Laela Aridho, Mulia Ariyanti, Baiq Haulia Baiq Rien Handayani, Baiq Rien Cicilia, Siska Devi Ariyana, Mutia Dilla Afriansyah Dody Handito, Dody Elya Antariksana Bachmida Febriandito, Muhammad ‘Aidil Gunawan, Rendi Hijayanti, Yatmi Idayanti, Fitri Inayati, Fitri Iqlima Khaerunnisa Kirtiyani, Ni Kadek Ayu Astiti Laily, Alfu Lalu Unsunnidhal Lestari, Risna Lingga Gita Dwikasari, Lingga Gita Lumbessy, Salnida Yuniarti Made Gendis Putri Pertiwi Made Gendis Putri Pertiwi Marisya Dwi Anggraini, Ines Mi’raj Fuadi Moegiratul Amaro Murad Mutia Devi Ariyana Mutia Devi Ariyana, Mutia Devi Namira, Afrisha Sekar Ningsi Ningsi NK Dewi Novia Rahayu Oki Saputra OKI SAPUTRA Pertiwi, Made Gendis Putri Putri Sulhana El Fiesha Balqis Putri, Mey Rizka R. Qabul Dinanta Utama Rasyda, Riezka Zuhriatika Ratih Dewanti -Hariyadi Raudatul Jannah Rini Nofrida Rizal Fahmi S., Ince Siti Wardatullatifah Sabilillah, Rizki Muhammad Ibnu Sella Antesty Setyaning Pawestri Sri Widyastuti Sukma, Dinda Galuh Tri Isti Rahayu Tri Isti Rahayu, Tri Isti Unsunnidhal, Lalu Vrisco Harjanto Wardatullatifah , Ince Siti Wati, Husnul Wati, Nila Susila Weriningsih, Wiharyani Wiharyani Werdiningsih Yarfaryh, Uswatun Hasanah Yasa, I Wayan Sweca Yeni Sulastri Yesica Marcelina Romauli Sinaga Zahra, Khoiruz Zalila, Nurfatin Zuhdia, Lalu Diani Zuhdia, Lulu Diani Zuhriatika Rasyda, Riezka