Karakterisasi Genom Bakteri Paenibacillus woosongensis dari Limbah Rumah Sakit di Jakarta Timur

Abstract

Karakterisasi genom bakteri dari limbah rumah sakit penting untuk menilai potensi adaptasi metabolik dan risiko reservoir zat antimikroba akibat dari perubahan karakter yang terjadi. Penelitian ini bertujuan mengonfirmasi identitas genomik serta mengidentifikasi gen fungsional, resistome serta virulome pada isolat limbah rumah sakit. Metode penelitian dimulai dengan sampling isolat dari titik outlet limbah rumah sakit, lalu DNA diekstraksi menggunakan DNA mini kit dan dikualifikasi melalui spektrofotometer NanoDrop, elektroforesis dan Quantus fluorometer. Kemudian, sampel dilakukan sequencing dengan PromethION 2 Solo dan hasilnya dianalisis dengan tools bioinformatika melalui platform UseGalaxy. Hasil penelitian mengonfirmasi genom isolat dengan kualitas baik (Q10>75,6%; contig tunggal; GC content 49,69%; coverage 68x) dan berkerabat dekat dengan satu strain Paenibacillus sp. (ANI, dDDH, AF melampaui ambang batas) dan dua strain P. woosongensis (dDDH mendekati 70%). Anotasi fungsional mendeteksi ratusan gen CAZyme, gen respons stres, gen biodegradasi dan mobile genetic elements. Terdapat gen resistensi yang terdiri dari gen vanY/vanW/vanT, qacJ dan LlmA. Faktor virulensi menunjukkan dominasi gen adherence, akuisisi besi, hlyIII dan ndk Kesimpulan menunjukkan isolat berpotensi sebagai biodegradator sekaligus reservoir resistensi/virulensi adaptif terhadap tekanan seleksi ekosistem rumah sakit.

Genomic characterization of bacteria from hospital wastewater is important for assessing their potential for metabolic adaptation and risk as reservoirs for antimicrobial substances due to changes in their characteristics. This study aims to confirm genomic identity and identify functional genes, antibiotic resistance genes, and virulence factors in hospital wastewater isolates. Research method began with sampling isolates from hospital wastewater outlets, followed by DNA extraction using DNA Mini Kit and quantification with NanoDrop spectrophotometer, electrophoresis, and Quantus fluorometer. The samples sequenced using the PromethION 2 Solo, and the results were analyzed using bioinformatics tools with UseGalaxy platform. The results confirmed high-quality genome for the isolate (Q10 > 75,6%; single contig; GC content 49.69%; coverage 68x) that is closely related to one strain Paenibacillus sp. (ANI, dDDH, AF passed threshold) dan two strain P. woosongensis. (dDDH close to 70%) .Functional annotation detect hundreds of CAZyme genes, stress response genes, biodegradation genes and mobile genetic elements. There are resistance genes, included vanY/vanW/vanT, qacJ and LlmA genes. Virulence factor show dominance of adherence, iron acquisition, hlyIII and ndk genes. In conclusion, the isolate has potential to serve as a biodegradator and a reservoir of adaptive resistance/virulence against the selective pressures of hospital ecosystem.