Dear ReSeqTB users
We appreciate your support and ReSeqTB have enjoyed hosting your collective data regarding drug resistance for the larger TB community over the last several years. Unfortunately, we have not been able to secure funding to keep the resource available and updated. As a result we will need to shut the site down by Q12021. Please feel free to download existing data for your research projects. We will be connecting with data contributors separately with next steps regarding their data. The ReSeqTB platform was transferred to the World Health Organization in 2018 and is being used to support sequencing for the surveillance of drug resistant TB and ultimately the clinical diagnosis of drug-resistant TB.
Web-based WGS tools
- TBProfiler: tbdr.lshtm.ac.uk
- Coll F, McNerney R, Preston MD, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome medicine 2015; 7(1): 51.
- GenTB: gentb.hms.harvard.edu
- PATRIC: www.patricbrc.org
- PhyResSE: bioinf.fz-borstel.de/mchips/phyresse/
- Feuerriegel S, Schleusener V, Beckert P, et al. PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole Genome Sequencing Data. Journal of clinical microbiology 2015; 53(6): 1908-14.
Tools that can be run off-line
- TGS-TB: gph.niid.go.jp/tgs-tb/
- Tsuyoshi Sekizuka,Akifumi Yamashita,Yoshiro Murase, et al. TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing
- Published: November 13, 2015 doi.org/10.1371/journal.pone.0142951
- Mykrobe predictor: www.mykrobe.com
- Bradley, P., Gordon, N., Walker, T. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 6, 10063 (2015). doi.org/10.1038/ncomms10063
Bioinformatics tools for experts
- MTBseq:
- a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates PMID: 30479891
- The full source code with accompanying documentation and usage guidelines is provided at github.com/ngs-fzb/MTBseq_source.
- ResFinder:
- Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. The Journal of antimicrobial chemotherapy 2012; 67(11): 2640-4
- The full source code with accompanying documentation and usage guidelines is provided at cge.cbs.dtu.dk/services/ResFinder/
The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb. It provides a standardized and validated whole genome sequencing (WGS) analysis pipeline and a “one stop� source of curated, aggregated, clinically relevant genetic and associated metadata for global Mtb strains.
Having these standardized and validated data easily accessible under one platform will accelerate the development of rapid drug susceptibility tests for TB and will significantly improve diagnosis of drug resistant disease in TB patients.
This initiative is led by a collaborative partnership which includes the Bill & Melinda Gates Foundation (BMGF), Critical Path Institute (C-Path), Foundation for Innovative New Diagnostics (FIND), World Health Organization (WHO), US Centers for Disease Control and Prevention (CDC), New Diagnostics Working Group (NDWG), and the National Institute of Allergy and Infectious Diseases (NIAID).
Isolates Collected Over Time
Major Lineages
Global
**Note: Location information is not yet available for some isolates
