In silico and in vitro analysis primers for antibiotic resistance gene of bacteria

Eva Ayuntya, Kiky Martha Ariesaka, Wahyu Prihanta, Husamah Husamah, Fendy Hardian Permana, Moh Mirza Nuryady

Abstract


The prevalence of Extended-Spectrum Beta-Lactamase (ESBL) occurs due to excessive use of antibiotics, resulting in antibiotic resistance. Research on ESBL has been conducted in several Indonesian cities, such as Surabaya, Malang, and Jakarta which identified the presence of ESBL bacterial isolates. Limited information about blaCTX-M and blaVEB primer data in in silico analysis such as primer length, GC base content, melting temperature, and organisms attached to the gene, is an important thing that needs further research, because in silico data will affect the annealing temperature in the in vitro process using Polymerase Chain Reaction (PCR). The purpose of this study was to determine that blaCTX-M and blaVEB primers can be used to detect the presence of ESBL genes from amplification results in PCR. In silico primer analysis was carried out using BLAST primers from the NCBI website which would then be continued through in vitro primer analysis using PCR to see the presence of DNA bands. The results of in silico research showed that there were 27 organisms detected in the blaCTX-M gene and 37 organisms in the blaVEB gene. The results of in vitro analysis on blaCTX-M primers can be amplified at ± 400 bp, while blaVEB cannot be amplified. 


Keywords


blaCTX-M; blaVEB; ESBL; primer analysis

Full Text:

PDF

References


Adikara, I. J., Wirajana, I., & Yowani, S. C. (2016). Optimasi suhu annealing tiga regio berbeda isolat multidrug resistance Mycobacterium tuberculosis dengan Metode Multiplex Polymerase Chain Reaction. Jurnal Veteriner Desember, 17(4), 535–539.

Al-Ouqaili, M. T., Khalaf, E. A., & Al-Kubaisy, S. H. (2020). DNA Sequence Analysis of BlaVEB Gene Encoding Multi-drug Resistant and Extended-spectrum β-lactamases Producer Isolates of and. The Open Microbiology Journal, 14(1), 40–47.

Bahi, R. R. R., Mappa, M. R., & Gonibala, A. P. (2023). Sosialisasi Penggunaan Antibiotik yang Bijak untuk Mencegah Resistensi Obat. Jurnal Pengabdian Kepada Masyarakat Nusantara, 4(2), 775–782.

Buchori, A., Firmansah, H., Anika, M., Ratnawati, S., Ulfa, U. T., & Zendrato, Y. (2023). Komparasi metode ekstraksi DNA menggunakan daun padi. Agriculture and Biological Technology, 1(1), 40–50.

Cahyadi, M., Taufik, I. M., Pramono, A., & Abdurrahman, Z. H. (2019). Development of mitochondrial 12S rRNA gene for identification of dog and rat in beef using multiplex PCR. Journal of the Indonesian Tropical Animal Agriculture, 44(1), 10–18.

Efrilia, D., Carolia, N., Mustofa, S., & Oktarlina, R. Z. (2023). Metode Gyssens Sebagai Pilihan Utama Dalam Evaluasi Kualitatif Penggunaan Antibiotik di Indonesia. Medula, 13(1), 1–15.

Gach, M. W., Lazarus, G., Simadibrata, D. M., Sinto, R., Saharman, Y. R., Limato, R., Nelwan, E. J., Van Doorn, H. R., Karuniawati, A., & Hamers, R. L. (2024). Antimicrobial resistance among common bacterial pathogens in Indonesia: a systematic review. The Lancet Regional Health, 26.

Gunawan, S., Tjandra, O., & Halim, S. (2021). Edukasi Mengenai Penggunaan Antibiotik yang Rasional di Lingkungan SMK Negeri 1 Tambelang Bekasi. Jurnal Bakti Masyarakat Indonesia, 4(1), 156–164.

Hassan, M., Gaber, A., Alsanie, W., El-Hallous, E., Mohamed, A., Alharthi, A., & Ibrahim, A. (2018). Phylogeny and Detection of blaTEM, blaSHV, blaCTX-M Genes in Escherichia coli Isolates from Patients with Urinary Tract Infections in Taif Hospitals, Saudi Arabia. Annual Research & Review in Biology, 25(1), 1–8. https://doi.org/10.9734/arrb/2018/39689

Korir, R., Anzala, O., Jaoko, W., Bii, C., & Keter, L. (2017). Multidrug-resistant bacterial isolates recovered from herbal medicinal products sold in Nairobi, Kenya. The East African Health Research Journal, 1(1), 40–46.

Kuntaman, K., Santoso, S., Mertaniasih, N. M., Lestari, E. S., Farida, H., Hapsari, R., Firmanti, S. C., As, N., Santosaningsih, D., Purwono, P. B., Kusumaningrum, D., Sakit, R., Soetomo, S., Mikrobiologi, D., Kedokteran, F., Brawijaya, U., & Anwar, S. (2018). The Sensitivity Pattern of Extended Spectrum Beta Lactamase-

Producing Bacteria Against Six Antibiotics that Routinely Used in Clinical Setting. In Artikel Penelitian J Indon Med Assoc.

Lestari, D., Triana, A., & Prasetyorini, T. (2022). Profile Keberadaaan Extended Spectrum Beta Lactamase Berdasarkan Jenis Bakteri, Jenis Spesimen, dan Sumber Ruangan. Jurnal Kesehatan Saintika Meditory, 5(1), 1–12.

Lukey, N. M., & Abbas, F. M. (2021). Genotypic detection of GES and VEB extended spectrum βlactamase among aerobic Gram-negative bacteria isolated from diabetic foot ulcers . Earth and Environmental Science, 790(1), 1–12.

Maharani, Y. R., Yuniarti, N., & Puspitasari, I. (2021). Prevalensi Bakteri Extended-Spectrum Beta-Lactamase dan Evaluasi Kesesuaian Antibiotik Definitif pada Pasien Rawat Inap di RSUP Dr Soeradji Tirtonegoro Klaten. Majalah Farmaseutik, 17(2), 165–167.

Miranti, K. A., Wahyuni, S., Permana, T. I., Fatmawati, D., & Nuryady, M. M. (2023). Desain Primer Spesifik Vektor Dengue Aedes aegypti Berdasarkan DNA Pengkode ITS-1, 5.8S Ribosomal RNA, dan ITS-2. Jurnal Veteriner, 24(1), 76–82.

Nova, T. D., Yurnalis, Y. , & Sari, A. K. (2016). Keragaman genetik gen hormon pertumbuhan (gh| mboii) pada itik sikumbang janti menggunakan penciri pcr-rflp. Jurnal Peternakan Indonesia (Indonesian Journal of Animal Science), 18(1), 44–52.

Nuryady, M. M., Husamah, H., Miharja, F. J., Hindun, I., & Patmawati, P. (2020). Desain dan optimasi primer gen pengkode MRPA Trypanosoma evansi dan penerapan pada pembelajaran biologi molekuler. Jurnal Penelitian Dan Pengkajian Ilmu Pendidikan: E-Saintika, 4(2), 223–233.

Oktaviani, N. (2018). Identifikasi Bakteri Pada Air Limbah Pencucian Pembuatan Batik di Pekalongan Selatan. Pena: Jurnal Ilmu Pengetahuan Dan Teknolog, 32(2), 59–67.

Ramadhani, A., & Saadah, S. (2020). Efek antibakteri ekstrak daun cengkeh (Syzygium aromaticum) terhadap Escherichia coli dan Staphylococcus aureus. Jurnal Bioteknologi Dan Biosains Indonesia, 7(2), 203–214.

Ranjabar, R., & Sami, M. (2017). Genetic Investigation of Beta-Lactam Associated Antibiotic Resistance Among Escherichia Coli Strains Isolated from Water Sources. The Open Microbiology Journal, 11(1), 203–210. https://doi.org/10.2174/1874285801711010203

Safitri, Y., Gultom, W. R., Tobing, D. A. L., & Sianturi, D. R. (2024). Potensi Escherichia Coli Sebagai Resistansi Antibiotik. Jurnal Matematika, Ilmu Pengetahuan Alam, Kebumian Dan Angkasa, 2(5), 8–20.

Sales, A. J., Naebi, S., Bannazadeh-Baghi, H., & Saki, M. (2021). Antibiotic Resistance Pattern and Prevalence of blaOXA-51, bla NDM, bla VIM, bla PER, bla VEB, bla CTX, tetA and tetB Genes in Acinetobacter baumannii Isolated from Clinical Specimens of Hospitals in Tabriz city, Iran. Journal of Clinical Research in Paramedical Sciences, 10(2).

Sasmito, D. E. K., Kurniawan, R., & Muhimmah, I. (2014). arakteristik primer pada Polymerase Chain Reaction (PCR) untuk sekuensing DNA: Mini Review. Seminar Nasional Informatika Medis , 93–102.

Siswanto, T., Sianipar, N. F., Warnars, H. L. H. S., & Prabowo, H. (2022). Algorithm Model Determination of DNA Primer Design For The Success PCR Process. International Journal of Emerging Technology and Advanced Engineering, 12(7), 101–107.

Sunarti, R. N. (2016). Uji kualitas air minum isi ulang disekitar kampus uin Raden Fatah Palembang. Bioilmi: Jurnal Pendidikan, 2(1), 40–50.

Sutandhio et al. (2017). Distribusi Dan Pola Kepekaan Enterobacteriaceae Dari Spesimen Urin Di Rsud Dr. Soetomo Surabaya Periode Januari – Juni 2015. Jurnal Widya Medika, 3(1), 1–8.

Tabar, M., Shiva, M., & Rabeeh, I. A. I. (2016). Detection of ctx-M gene in ESBL-producing E. coli strains isolated from urinary tract infection in Semnan, Iran. Electronic Physician, 8(7), 2686–2690. https://doi.org/10.19082/2686

Wibisono, F. J., Sumiarto, B., Untari, T., Effendi, M., Permatasari, D. A., & Permatasari, D. A. (2020). CTX Gene of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli on Broilers in Blitar, Indonesia. Systematic Reviews in Pharmacy, 11(3), 396–403.

Wijaya, V. P. (2014). Antibacterial power Village Fowl Egg Albumen (Gallus domesticus) and Kate chicken (Gallus Bantam) against fecal Coliform Bacteria Species at Eggshell Egg. Jurnal Pendidikan Sains Universitas Negeri Malang, 1(4), 356–374.




DOI: http://dx.doi.org/10.30821/biolokus.v8i2.4313

Refbacks

  • There are currently no refbacks.


Copyright (c) 2025 Jurnal Biolokus: Jurnal Penelitian Pendidikan Biologi dan Biologi

indexed by :