P052

1:Swiss Tropical and Public Health Institute; 2:University of Basel

The Mycobacterium tuberculosis complex (MTBC) causes tuberculosis (TB) disproportionally in resource limited countries. Whole-genome sequencing (WGS) has been key in improving our understanding of drug resistance and of transmission of the MTBC. Yet, the need for expertise guiding WGS implementation and the lack of bioinformatic expertise, are main obstacles hindering the implementation of WGS in low resource settings. We built GOMA (Galaxy Open-source MTBC Genomic Analysis), a bioinformatics pipeline designed to perform DNA variant detection, drug-resistance prediction, MTBC lineage detection, transmission inference and phylogenetic analysis. The pipeline was implemented on the Galaxy platform (https://usegalaxy.eu) and is free, cloud-based, accessible thought a web-browser and graphical user interfaces, and does not require programming skills. GOMA processes Illumina short reads and can handle single or multiple samples in one run. Its accuracy has been tested using a variety of previously characterized WGS representing; all the human-adapted lineages (L1-L10) and the main animal-adapted MTBC lineages, a wide range of drug-resistant MTBC profiles, and strains involved or not in recent transmission chains. GOMA could accurately detect; i) the main human and animal-adapted MTBC lineages, including mixed infections and contaminations, ii) drug-resistance conferring mutations defined by the WHO and iii) MTBC isolates involved in transmission chains according to several genetic distance thresholds. In summary, we created a pipeline that can aid genomic epidemiology of small-scale projects without the need for a high-performance computing facilities or hardware, nor programming knowledge. Being hosted on the open-source platform Galaxy, this pipeline will benefit especially low-income high-burden TB settings.