Use of a whole genome sequencingbased approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: An ECDC pilot study

Elisa Tagliani*, Richard Anthony, Thomas A. Kohl, Albert De Neeling, Vladyslav Nikolayevskyy, Csaba Ködmön, Florian P. Maurer, Stefan Niemann, Dick Van Soolingen, Marieke J. Van Der Werf, Daniela Maria Cirillo

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


Whole genome sequencing (WGS) can be used for molecular typing and characterisation of Mycobacterium tuberculosis complex (MTBC) strains. We evaluated the systematic use of a WGS-based approach for MTBC surveillance involving all European Union/European Economic Area (EU/EEA) countries and highlight the challenges and lessons learnt to be considered for the future development of a WGS-based surveillance system. WGS and epidemiological data of patients with rifampicin-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) were collected from EU/EEA countries between January 2017 and December 2019. WGS-based genetic relatedness analysis was performed using a standardised approach including both core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data comparability. A total of 2218 RR/MDR-MTBC isolates were collected from 25 countries. Among these, 56 crossborder clusters with increased likelihood of recent transmission (5 SNPs distance) comprising 316 RR/ MDR-MTBC isolates were identified. The cross-border clusters included between two and 30 resistant isolates from two to six countries, demonstrating different RR/MDR-TB transmission patterns in Western and Eastern EU countries. This pilot study shows that a WGS-based surveillance system is not only feasible but can efficiently elucidate the dynamics of in-country and cross-border RR/MDR-TB transmission across EU/EEA countries. Lessons learnt from this study highlight that the establishment of an EU/EEA centralised WGSbased surveillance system for TB will require strengthening of national integrated systems performing prospective WGS surveillance and the development of clear procedures to facilitate international collaboration for the investigation of cross-border clusters.

Original languageEnglish
Article number57
JournalEuropean Respiratory Journal
Issue number1
Publication statusPublished - 1 Jan 2021

Bibliographical note

Funding Information:
Support statement: This project was funded by the European Centre for Disease Prevention and Control (framework contact ECDC/2017/012). The funder of the study was involved in the revision of the manuscript. Funding information for this article has been deposited with the Crossref Funder Registry.

Publisher Copyright:
© 2021 European Respiratory Society. All rights reserved.

Copyright 2021 Elsevier B.V., All rights reserved.


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