Abstract

Whole-genome sequencing (WGS) has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupled with epidemiological and environmental investigations, it delivers ultimate resolution for tracing sources of epidemic infections. To ascertain the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritized diseases in the European Union (EU)/European Economic Area (EEA), two surveys were conducted in 2015 and 2016. The surveys were designed to determine the national public health reference laboratories’ access to WGS and operational WGS-based typing capacity for national surveillance of selected foodborne pathogens, antimicrobial-resistant pathogens, and vaccine-preventable diseases identified as priorities for European genomic surveillance. Twenty-eight and twenty-nine out of the 30 EU/EEA countries participated in the survey in 2015 and 2016, respectively. National public health reference laboratories in 22 and 25 countries had access to WGS-based typing for public health applications in 2015 and 2016, respectively. Reported reasons for limited or no access were lack of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was limited. By mid-2016, half of the EU/EEA countries were using WGS analysis either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame as well as bioinformatics analysis varied by pathogen/resistance issue and country. Core genome multilocus allelic profiling, also called cgMLST, was the most frequently used annotation approach for typing bacterial genomes suggesting potential bioinformatics pipeline compatibility. Further capacity development for WGS-based typing is ongoing in many countries and upon consolidation and harmonization of methods should enable pan-EU data exchange for genomic surveillance in the medium-term subject to the development of suitable data management systems and appropriate agreements for data sharing.

Highlights

  • In the European Union (EU), surveillance of 53 communicable diseases, healthcare-associated infections and antimicrobial resistance is conducted jointly by the European Centre for Disease Prevention and Control (ECDC) and the member states based on national case notification in accordance with EU case-definitions which are combining clinical and laboratory criteria [1]

  • Fulfilling its mandate to collate, appraise, and disseminate information for public health action, ECDC is committed to foster the integration of Whole-genome sequencing (WGS)-based typing for infectious disease surveillance and outbreak investigations at European level [6, 12]

  • We have undertaken to monitor the transition to nextgeneration sequencing (NGS) technologies through annual surveys with our public health partners across the EU/Economic Area (EEA)

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Summary

Introduction

In the European Union (EU), surveillance of 53 communicable diseases, healthcare-associated infections and antimicrobial resistance is conducted jointly by the European Centre for Disease Prevention and Control (ECDC) and the member states based on national case notification in accordance with EU case-definitions which are combining clinical and laboratory criteria [1]. WGSderived resistome prediction for Mycobacterium tuberculosis was found to be 93% accurate to detect and characterize multidrugresistant (MDR) tuberculosis cases with a median reporting of 21 days and at 7% lower cost than culture-based methods [9]. Despite these advantages, current costs of implementation of NGS and lack of expertise as well as the need for adapting epidemiological investigation methods may limit its use by public health laboratories [8, 10]. Further harmonization for bioinformatic analysis, smart information technology solutions for WGS data storage and sharing, and trained staff with new skill mix are fundamental elements to translate genomic epidemiology into real-life infection control and prevention [5, 8, 13]

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