Profil Resistansi Tetrasiklin dan Karakteristik Genom Isolat Pseudomonas sp. Asal Air Irigasi Pertanian

Abstract

Pseudomonas sp. merupakan salah satu bakteri yang dapat ditemukan di air. Air irigasi pertanian menjadi salah satu sumber kontaminan mikroorganisme yang berpeluang memiliki sifat resistansi antibiotik, salah satunya adalah tetrasiklin. Paparan tetrasiklin yang berlebihan dapat menyebabkan bakteri menjadi resistan. Deteksi keberadaan mikroorganisme serta gen-gen terkait penting dilakukan untuk menduga potensi, salah satu caranya dengan analisis Whole Genome Sequencing (WGS). Penelitian ini bertujuan untuk melihat profil resistansi tetrasiklin isolat bakteri asal air irigasi pertanian dan mengarakterisasi genomik dari isolat Pseudomonas sp. Penelitian ini terdiri dari dua bagian, yaitu bagian 1 uji resistansi isolat bakteri (n=19) terhadap tetrasiklin menggunakan metode disc diffusion test (Kirby-Bauer), dan uji konfirmasi isolat bakteri tersebut menggunakan real-time PCR. Bagian kedua yaitu karakterisasi genomik dengan Whole Genome Sequencing (WGS) menggunakan GeneMind, GenoLab M, dan analisis data sekuens menggunakan tools bioinformatika yaitu Galaxy, Proksee, TYGS, RAST, CARD dan BAGEL4. Hasil penelitian menunjukkan bahwa sebanyak 4 dari 19 isolat (21,05%) resistan tetrasiklin, 1 dari 19 isolat (5,26%) intermediet dan 14 dari 19 isolat sensitif (73,68%) tetrasiklin. Semua isolat tidak memiliki gen invA yang berarti bukan kelompok patogen enterik Salmonella. Hasil bagian 2 menunjukkan bahwa isolat H.1.2 teridentifikasi sebagai Pseudomonas peradeniyensis berdasarkan %ANI, dDDH, pohon filogenetik dan %GC. Isolat H.1.2 memiliki 45 gen yang berasosiasi dengan virulensi dan 4 gen stres berdasarkan ABRicate dan AMRFinderPlus. Isolat tersebut memiliki gen mexE (abriTAMR), dan yajC (CARD) dengan mekanisme adaptasi yang umum, serta tidak menunjukkan resistansi antibiotik. Isolat H.1.2 memiliki gen bacteriocin-like yaitu gen colicin dan pyocin berdasarkan BAGEL4. Selain itu, tidak ada plasmid yang terdeteksi pada isolat H.1.2 berdasarkan PlasmidFinder.

Pseudomonas sp. is a bacterial group commonly found in water. Agricultural irrigation water represents a potential source of microbial contamination, including microorganisms that may harbor antibiotic resistance properties, particularly against tetracycline. Excessive exposure to tetracycline can promote the development of bacterial resistance. Therefore, the detection of microorganisms and resistance-related genes is essential for assessing potential risks, one of which can be achieved through Whole Genome Sequencing (WGS) analysis. This study aimed to determine the tetracycline resistance profile of bacterial isolates obtained from irrigation water and to characterize the genomic features of Pseudomonas sp. isolates. This study consisted of two parts. The first part involved tetracycline resistance testing of bacterial isolates (n=19) using the disc diffusion method (Kirby-Bauer), followed by confirmation of the isolates using real-time PCR. The second part focused on genomic characterization through Whole Genome Sequencing (WGS) using the GeneMind, GenoLab M platform, with sequence data analyzed using bioinformatics tools including Galaxy, Proksee, TYGS, RAST, CARD, and BAGEL4. The results showed that 4 out of 19 isolates (21,05%) were resistant to tetracycline, 1 isolate (5,26%) exhibited intermediate resistance, and 14 isolates (73,68%) were sensitive to tetracycline. None of the isolates harbored the invA gene, indicating the absence of Salmonella enteric pathogens strains. Genomic analysis revealed that isolate H.1.2 was identified as Pseudomonas peradeniyensis based on %ANI, digital DNA-DNA hybridization (dDDH), phylogenetic tree, and %GC content. Isolate H.1.2 harbored 45 virulence-associated genes and four stress-related genes based on ABRicate and AMRFinderPlus analyses. This isolate contained the mexE (abriTAMR) and yajC (CARD) genes, which are associated with general adaptive mechanisms, but did not exhibit antibiotic resistance phenotypes. Additionally, isolate H.1.2 possessed bacteriocin-like genes, including colicin and pyocin, as identified by BAGEL4. No plasmids were detected in isolate H.1.2 based on PlasmidFinder.