Whole-genome sequencing analysis to identify antimicrobial resistance regions and virulence factors in Mycobacterium tuberculosis isolates from the Amhara Region, Ethiopia
Abstract
Tuberculosis caused by Mycobacterium tuberculosis complex is a significant global health burden, with drug-resistant TB, especially multidrug-resistant TB, causing severe challenges to treatment. In Ethiopia, a high TB-burden country, drug resistance has continued spreading. However, some studies indicate genetic diversity, transmission dynamics, and resistance-conferring mutations by using targeted amplification, there are limited reports of whole genome sequencing analysis to uncover the antimicrobial resistance and virulent genes. Based on that, the objective of this project was to identify antimicrobial resistance regions and characterize virulence factors in M. tuberculosis isolates through in silico whole-genome sequence analysis. A FASTQ file of 45 M. tuberculosis isolates whole genome sequence was downloaded from the SAR database. Following quality control using FASTQC coupled with MultiQC and trimming with Trimmomatic, de novo assembly was conducted using SPAdes. The Burrows-Wheeler Aligner was used for mapping against the M. tuberculosis H37Rv reference genome, followed by variant calling with FreeBayes. In silico spoligotyping was performed using SpoTyping, and drug resistance mutations were identified with TB-Profiler and validated using Mykrobe. Virulence factors were detected through ABRicate and the Virulence Factor Database. STRING was used to network the virulent genes. All statistical analyses were performed using R software. This study revealed the most…
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