METAGENOMIC ANALYSIS OF BACTERIA IN NASOPHARYNGEAL SWABS SAMPLES OF ASYMPTOMATIC AND MILD SYMPTOMS OF COVID-19 PATIENTS IN WEST JAVA

• Main Author: Izzati Ginting, Nurul
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/77017
• Institution: Institut Teknologi Bandung

The COVID-19 pandemic is caused by SARS-CoV-2, which transmitted through droplets and aerosols in the upper respiratory system. The nasopharyngeal microbiome is crucial in combating pathogens that enter this system. SARS-CoV-2 infection disrupts the host immune response, leading to bacterial coinfection and microbial dysbiosis. In mild cases, symptoms range from fever to loss of smell, while asymptomatic cases have no consistent symptoms. Bacterial colonization can contribute to clinical complications such as decreased lung function and pneumonia. Research on microbial dysbiosis and bacterial co-pathogens due to SARS-CoV-2 infection is limited in Indonesia. In this regard, this research aims to analyze the difference of bacterial community found in nasopharyngeal swabs of Asymptomatic (n=3), Mild (n=5), and recovered SARS-CoV-2 as control (n=3), which are collected by Labkes Jabar. The swab samples were extracted by QIAamp Viral RNA Mini Kit (QIAGEN, Germany) with library preparation using Ribo-ZeroTMPlus and sequenced by Illumina NextSeq 550 by using the approach shotgun metagenomic to generate raw reads. Quality control of raw reads done by FASTQC and CUTADAPT to generate clean reads. Furthermore, pre-processing step with BOWTIE2 was used to eliminate the Homo sapiens sequence employing database GRCh38 to generate dehosted reads. Dehosted reads were used for taxonomical analysis and functional analysis using Kraken2-employed database Minikraken1 and HUMAnN3-employed database ChocoPhlan, respectively. Subsequently, statistical analysis of bacterial diversity and abundance differential data visualization was conducted by RStudio and Excel. The results of ????-diversity analysis using the Shannon Index indicate higher species diversity in the control group compared to the infected groups. The comparison of microbial diversity among sample groups was analyzed through ????-diversity using Bray Curtis calculations in Principle Coordinate Analysis (PCoA), showing two main clusters: the control group cluster separated from the cluster of infected groups. The highest bacterial relative abundance in both infected groups was observed in Burkholderia spp. Further analysis with DESeq2 (p-value < 0.1; LFC ± 2.0) revealed a significant increase in the abundance of Burkholderia spp. and Pseudomonas spp. in both infected groups compared to the control group. Functional analysis of microbial pathways using DESeq2 (p-value < 0.5; LFC ± 2.0) revealed increased activity associated with nucleotide biosynthesis, which was higher in the Mild group. Specifically, ethanolamine utilization was revealed in the Mild group. This research can provide valuable insights into SARS-CoV-2 co-infection potential in Indonesia, improving prognosis accuracy and treatment effectiveness.