EUSeqMyTB to set standards and build capacity for whole genome sequencing for tuberculosis in the EU

Abstract

2 ECDC, WHO Regional Office for Europe. Tuberculosis surveillance and monitoring in Europe 2018-2016 data. Stockholm: European Centre for Disease prevention and Control (ECDC), 2018. 3 Kendall EA, Fofana MO, Dowdy DW. Burden of transmitted multidrug resistance in epidemics of tuberculosis: a transmission modelling analysis. Lancet Respir Med 2015; 3: 963-72. 4 Walker TM, Kohl TA, Omar SV, et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

“…Using this dataset, the EUSeqMyTB consortium showed that existing pipelines could confidently distinguish linked from unlinked cases, especially when the SNP distances are high, as is often the case in low burden settings 12 . This comparison was 259 undertaken as part of an effort to standardise WGS for monitoring MDR-TB cross border 260 transmission in Europe 15 .…”

“…. Rapid, reliable, and increasingly affordable 105 WGS technologies, can now guide all components of TB control: diagnosis, treatment, 106 surveillance and contact tracing 5,6 (Fig. 1).…”

“…Individual (sub)species of human and animal Mtbc 107 lineages can be identified, [7][8][9] and drug resistance profiles can be predicted, especially well for 108 1 st line drugs 2 , enabling prompt, appropriate initiation of treatment and monitoring the 109 acquisition of drug resistance 10 . TB outbreaks can be identified with high resolution [11][12][13] , including across borders, 14,15 and diseases control measures implemented. The analysis of the 111 emergence, spread, genetic makeup, and evolution of particular outbreak strains, e.g.…”

“…The World Health Organization (WHO) is already using WGS for drug resistance surveillance 19 and is scheduled to evaluate sequencing technologies for routine genotypic drug susceptibility testing in 2019 1 . As WGS-guided individualized treatment 20 and WGS-based surveillance systems 15 are being implemented in several countries (e.g. the UK and the 118 Netherlands) with more to come, accurate methods and standardized reporting are vital.…”

Precision tuberculosis control by genome sequencing: Benefit and challenges of a new standard

“…Several large-scale projects are ongoing to set guidelines/standards and ensure better (inter)national integration of WGS-based systems [ 10 ]. The obvious obstacle of the implementation in low resource, high-incidence settings is also being tackled e.g.…”