Tesis

Profil Mikrobiota Usus pada Pasien COVID-19 dengan dan tanpa Diare = Gut microbiome profile in COVID-19 patients with and without diarrhea.

Pendahuluan: COVID-19 adalah suatu sindrom pernapasan akut yang disebabkan oleh Novel Severe Acure Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). COVID-19 terutama menginfeksi saluran pernapasan dan mengakibatkan gejala pada berbagai tingkat keparahan pasien setelah infeksi, seperti demam, malaise, batuk kering, sesak napas, mialgia, nyeri tenggorokan, sakit kepala, diare, mual, muntah, dan pilek/ rinorea. Sekitar 5%–33% pasien COVID-19 memiliki gejala gastrointestinal (GI), termasuk diare, mual, dan muntah. Mikrobiota usus mempunyai fungsi protektif dan berperan penting dalam proses metabolisme saluran cerna. Mikrobiota usus dapat mengalami perubahan komposisi dan keragaman yang dikenal dengan istilah disbiosis. Disbiosis dapat diketahui dengan profil mikrobiota usus yang dapat dilihat dari perbedaan keragaman dan komposisi mikrobiota usus. Penelitian ini bertujuan memotret profil mikrobiota usus pada pasien COVID-19 dengan dan tanpa diare. Metode: Penelitian ini dilakukan dari Juli 2022 sampai Februari 2023 di RSUPN dr. Cipto Mangunkusumo dengan bentuk studi deskriptif potong lintang. Pasien COVID-19 akan diambil spesimen dari swab rektal, kemudian akan dilakukan ekstraksi DNA dilanjutkan sekuensing gen 16S menggunakan metode Metagenome Next Generation Sequencing. Data sekuensing dianalisis menggunakan program bioinformatika untuk memperoleh keragaman dan komposisi mikrobiota. Data yang dikumpulkan kemudian dianalisis untuk mengatahui profil mikrobiota usus pada pasien COVID-19 dengan dan tanpa diare. Hasil: Total terdapat 24 subjek penelitian, ditemukan kelompok COVID-19 dengan diare lebih banyak terjadi pada anak-anak (58.3%), sedangkan dewasa lebih banyak COVID-19 tanpa diare (58,3%). Pada penelitian ditemukan 5 filum terbanyak dari keseluruhan sampel yaitu Proteobacteria, Firmicutes, Fusobacteria, Bacteroidota, dan Verrucomicrobia. Genus Anaerococcus, Prevotella, Faecalibacterium, dan Bifidobacterium lebih tinggi pada pasien COVID-19 tanpa diare, sedangkan genus Enterococcus, Bacteroides, Escherichia, dan Klebsiella lebih tinggi pada pasien COVID-19 dengan diare. Analisis keragaman alfa yaitu Chao 1 (1079.42 ± 416.31 vs 1078.2 ± 416.67, p > 0,05), Shannon (3.69 ± 1.17 vs 3.70 ± 1.12, p > 0,05), dan Simpson (0.85 ± 0.25 vs 0, .85 ± 0.24, p > 0,05) menandai bahwa richness dan evenness mikrobiota usus relatif serupa dikedua kelompok. Analisis keragaman beta dengan analisis PCoA menunjukkan terdapat perbedaan signifikan (PERMANOVA: p < 0,05; ANOSIM: p < 0,05) dalam komposisi mikrobiota usus antara pasien COVID-19 dengan dan tanpa diare. Kesimpulan: Tidak terdapat perbedaan keragaman alfa, namun terdapat perbedaan keragaman beta dan komposisi mikrobiota usus pada pasien COVID-19 dengan dan tanpa diare.
Kata kunci: COVID-19, diare, mikrobiota usus, kelimpahan relatif, keragaman, komposisi


Introduction: COVID-19 is an acute respiratory syndrome caused by the Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). COVID-19 primarily infects the respiratory tract and results in symptoms of varying severity in patients following infection, including fever, malaise, dry cough, dyspnea, myalgia, sore throat, headache, diarrhea, nausea, vomiting, and rhinorrhea. Approximately 5%–33% of COVID-19 patients present with gastrointestinal (GI) symptoms, including diarrhea, nausea, and vomiting. The gut microbiota serves a protective function and plays a crucial role in gastrointestinal metabolic processes. The gut microbiota can undergo changes in composition and diversity, a phenomenon known as dysbiosis. Dysbiosis can be identified through gut microbiota profiling, which examines differences in diversity and composition of the gut microbiota. This study aims to characterize the gut microbiota profile in COVID-19 patients with and without diarrhea. Methods: This study was conducted from July 2022 to February 2023 at Dr. Cipto Mangunkusumo Hospital using a descriptive cross-sectional design. Rectal swab specimens were collected from COVID-19 patients, followed by DNA extraction and 16S gene sequencing using the Metagenome Next Generation Sequencing method. Sequencing data were analyzed using bioinformatics software to determine microbiota diversity and composition. The collected data were subsequently analyzed to characterize the gut microbiota profile in COVID-19 patients with and without diarrhea. Results: A total of 24 research subjects were included. COVID-19 with diarrhea was found to occur more frequently in children (58.3%), while adults more commonly presented with COVID-19 without diarrhea (58.3%). The study identified the five most abundant phyla across all samples: Proteobacteria, Firmicutes, Fusobacteria, Bacteroidota, and Verrucomicrobia. The genera Anaerococcus, Prevotella, Faecalibacterium, and Bifidobacterium were more abundant in COVID- 19 patients without diarrhea, while the genera Enterococcus, Bacteroides, Escherichia, and Klebsiella were more abundant in COVID-19 patients with diarrhea. Alpha diversity analysis including Chao 1 (1079.42 ± 416.31 vs 1078.2 ± 416.67, p > 0.05), Shannon (3.69 ± 1.17 vs 3.70 ± 1.12, p > 0.05), and Simpson (0.85 ± 0.25 vs 0.85 ± 0.24, p > 0.05) indices indicated that the richness and evenness of gut microbiota were relatively similar between the two groups. Beta diversity analysis using PCoA revealed significant differences (PERMANOVA: p < 0.05; ANOSIM: p < 0.05) in gut microbiota composition between COVID-19 patients with and without diarrhea. Conclusion: No differences were observed in alpha diversity; however, significant differences in beta diversity and gut microbiota composition were found between COVID-19 patients with and without diarrhea.
Keywords: COVID-19, diarrhea, gut microbiota, relative abundance, diversity, composition