Use of a whole genome sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study

Abstract

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 cross-border 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 WGS-based 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.

FIGURE 1

Percentage of multidrug-resistant (MDR)-tuberculosis (TB) coverage per European Union/European Economic Area country in 2018. The number of MDR-TB cases among all laboratory-confirmed TB cases notified to the European Centre for Disease Prevention and Control in 2018 was used as reference. The map was generated using the online tool available at www.mapchart.net/.

FIGURE 2

a, b) Lineage distribution of the 2151 rifampicin-resistant (RR)/multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) isolates included in the EUSeqMyTB study. Lineages: 1: East-African Indian (EAI) (includes EAI and EAI Manila); 2: East-Asian (includes 2.2.1 Beijing and 2.1 East-Asian non-Beijing); 3: Delhi-CAS; 4.1: Euro-American (includes 4.1 and 4.1.2: Euro-American; 4.1.1: X-type; and 4.1.2.1: Haarlem); 4.2: Euro-American (includes 4.2 and 4.2.2: Euro-American; 4.2.1: Ural; and 4.2.2.1: TUR); 4.3: LAM; 4.4 (includes 4.4.1.1: S-type); 4.5: Euro-American; 4.6: Euro-American; 4.7: mainly T; 4.8: mainly T; 4.9: H37Rv-like; 5: West-Africa 1.

FIGURE 3

Map showing the percentage of rifampicin-resistant/multidrug-resistant tuberculosis cases of foreign origin in cross-border clusters per European Union/European Economic Area country. The map was generated using the online tool available at www.mapchart.net/.

FIGURE 4

Minimum spanning tree of a) snpCL1, b) snpCL3 and c) snpCL8. The numbers on the branches indicate the genetic distance in single nucleotide polymorphism (SNP) differences to the nearest isolate. SNP differences between distant isolates can be reconstituted by summing the number of SNPs on the branches. Different colours indicate the different European Union/European Economic Area countries where the strains were isolated.