Analisis Keberadaan Gen Antimicrobial Resistance (AMR) dan Identifikasi Molekuler pada Isolat Streptomyces dari Limbah Organik di PIAT UGM

Aksanti Lutfi Dellasari, Prof. Dr. Ir. Siti Subandiyah, M.Agr.Sc.

2026 | Skripsi | ILMU HAMA & PENYAKIT TUMBUHAN

Senyawa antimikroba memegang peran penting dalam kehidupan manusia sebagai agen pengendali patogen penyebab penyakit. Namun, penggunaan senyawa antimikroba secara masif dan berlebihan dalam berbagai sektor, termasuk pertanian dan peternakan telah mendorong munculnya fenomena antimicrobial resistance (AMR). Gen AMR dapat tersebar dengan cepat melalui 2 mekanisme utama, yaitu vertical gene transfer (VGT) dan horizontal gene transfer (HGT). Tanah dan pupuk kandang diketahui merupakan reservoir utama bagi gen AMR. Sebagai bakteri tanah, Streptomyces berpotensi berperan sebagai agen penyebaran gen AMR di lingkungan. Penelitian ini bertujuan untuk mendeteksi keberadaan gen AMR pada isolat Streptomyces yang berasal dari sampel limbah organik di PIAT UGM serta melakukan identifikasi molekuler pada isolat pembawa gen AMR. Deteksi gen AMR dilakukan menggunakan metode multiplex PCR dan PCR konvensional dengan primer spesifik untuk 7 gen resistensi, yaitu cmIV, blaOXY, mcr-1, aac-Iva, vanTC_2, ermX_2, dan tetX5. Identifikasi molekuler didasarkan pada hasil sekuensing gen trpB. Hasil penelitian menunjukkan bahwa seluruh isolat yang diuji mengandung gen AMR dengan komposisi gen yang bervariasi pada masing-masing isolat. Gen mcr-1, tetX5, dan ermX_2 terdeteksi pada seluruh isolat uji. Gen aac-Iva, blaOXY, dan cmIV tidak terdeteksi pada sebagian kecil isolat (1-2 isolat), sedangkan gen vanTC_2 terdeteksi pada 3 isolat. Seluruh isolat berpotensi mengalami multidrug resistance (MDR) karena mengandung > 1 gen resistensi. Isolat WTP-1 diketahui memiliki hubungan kekerabatan yang dekat dengan Streptomyces sp. WAC00288 dan Streptomyces cinereoruber strain ATCC 19740.

Antimicrobial compounds play an essential role in controlling disease-causing pathogens. However, the excessive and widespread use of antimicrobials in various sectors, including agriculture and livestock production, has accelerated the emergence of antimicrobial resistance (AMR). AMR genes can spread rapidly through vertical gene transfer (VGT) and horizontal gene transfer (HGT), with soil and manure acting as major environmental reservoirs. As soil-dwelling bacteria, Streptomyces spp. have the potential to contribute to the dissemination of AMR genes in the environment. This study aimed to detect AMR genes in Streptomyces isolates obtained from organic waste samples at PIAT UGM and to perform molecular identification of AMR gene–carrying isolates. AMR gene detection was conducted using multiplex PCR and conventional PCR targeting 7 resistance genes, namely cmIV, blaOXY, mcr-1, aac-Iva, vanTC_2, ermX_2, and tetX5. Molecular identification was based on sequencing of the trpB genes. The results showed that all tested isolates harbored AMR genes, with varying gene compositions among isolates. The mcr-1, tetX5, and ermX_2 genes were detected in all isolates. The aac-Iva, blaOXY, and cmIV genes were not detected in a small number of isolates (1–2 isolates), whereas the vanTC_2 gene was detected in three isolates. All isolates exhibited potential multidrug resistance (MDR) due to the presence of more than one resistance gene. Isolate WTP-1 showed a close phylogenetic relationship with Streptomyces sp. WAC00288 and Streptomyces cinereoruber strain ATCC 19740.

Kata Kunci : Antimicrobial resistance (AMR), Streptomyces, gen resistensi antibiotik, limbah organik, PCR