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

中文翻译：

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GenoMycAnalyzer：基于网络的工具，用于分枝杆菌基因组的物种和耐药性预测

耐药结核病（TB）是全球公共卫生的主要威胁。全基因组测序 (WGS) 是物种鉴定和耐药性预测的有用工具，许多临床实验室正在转向 WGS 作为常规诊断工具。然而，需要用户友好且高置信度的自动化生物信息学工具来快速识别结核分枝杆菌复合体（MTBC）和非结核分枝杆菌（NTM），检测耐药性并进一步指导治疗选择。我们开发了 GenoMycAnalyzer，这是一款基于网络的软件，集成了识别 MTBC 和 NTM 物种、谱系和 spoligotype 预测、变异调用、注释、耐药性测定和数据可视化的功能。使用经过表型 DST (pDST) 的 5,473 个 MTBC 分离株评估 GenoMycAnalyzer 基因型药物敏感性测试 (gDST) 的准确性。 GenoMycAnalyzer 数据库旨在使用世界卫生组织突变目录预测 15 种抗结核药物的 gDST。与 pDST 相比，GenoMycAnalyzer 对一线药物的敏感性范围为利福平 95.9%（95% CI 94.8–96.7%）至吡嗪酰胺 79.6%（95% CI 76.9–82.2%），而二线药物的有效率为 98.2%（95% CI 90.1–100.0%）至 74.9%（95% CI 69.3–80.0%）卷曲霉素。值得注意的是，四个抗性基因的大量缺失的整合增加了 gDST 敏感性。 GenoMycAnalyzer 的药物敏感性特异性范围为阿米卡星 98.7%（95% CI 97.8–99.3%）到乙硫异烟胺 79.5%（95% CI 76.4–82.3%）。集成的 Kraken2 软件识别出 1,284 种分枝杆菌，准确度为 98.8%。 GenoMycAnalyzer 还完美预测了 1,935 个 MTBC 的谱系和 54 个 MTBC 的 spoligotype。 GenoMycAnalyzer 提供基于网络和图形用户界面，可以帮助无法访问高性能计算系统或生物信息学技能有限的生物学家。通过简化 WGS 数据的解释，GenoMycAnalyzer 有可能对结核病管理产生重大影响，并为全球抗击这种传染病的努力做出贡献。 GenoMycAnalyzer 可从 http://www.mycochase.org 获取。