GenoMycAnalyzer: a web-based tool for species and drug resistance prediction for Mycobacterium genomes

• DOI: 10.1186/s12864-024-10320-3
• Publication Date: 2024-04-20T08:02:30Z
• Authors: Doyoung Kim; Jeong-Ih Shin; In Young Yoo; Sungjin Jo; Jiyon Chu; Woo Young Cho; Seung-Hun Shin; Yeun-Jun Chung; Yeon-Joon Park; Seung-Hyun Jung
• Keywords: Mycobacterium tuberculosis complex; Capreomycin; Ethionamide; Pyrazinamide; Amikacin

Abstract Background Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) useful tool for species identification and drug resistance prediction, many clinical laboratories are transitioning WGS as routine diagnostic tool. However, user-friendly high-confidence automated bioinformatics tools needed rapidly identify M. complex (MTBC) non-tuberculous mycobacteria (NTM), detect resistance, further guide treatment options. Results We developed GenoMycAnalyzer, web-based software that integrates functions identifying MTBC NTM species, lineage spoligotype variant calling, annotation, drug-resistance determination, data visualization. The accuracy of GenoMycAnalyzer genotypic susceptibility testing (gDST) was evaluated using 5,473 isolates underwent phenotypic DST (pDST). database built predict the gDST 15 antituberculosis drugs World Health Organization mutational catalogue. Compared pDST, sensitivity susceptibilities by first-line ranged from 95.9% rifampicin (95% CI 94.8–96.7%) 79.6% pyrazinamide 76.9–82.2%), whereas those second-line 98.2% levofloxacin 90.1–100.0%) 74.9% capreomycin 69.3–80.0%). Notably, integration large deletions four resistance-conferring genes increased sensitivity. specificity 98.7% amikacin 97.8–99.3%) 79.5% ethionamide 76.4–82.3%). incorporated Kraken2 identified 1,284 mycobacterial with an 98.8%. also perfectly predicted lineages 1,935 spoligotypes 54 MTBC. Conclusions offers both graphical user interfaces, which can help biologists limited access high-performance computing systems or skills. By streamlining interpretation data, has potential significantly impact TB management contribute efforts combat this infectious disease. available at http://www.mycochase.org .