Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015-2016

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.

Keywords: antimicrobial resistance; food and waterborne infections; genomic epidemiology; outbreak investigation; public health laboratory capacity; public health surveillance; vaccine-preventable diseases; whole-genome sequencing.

Figure 1

Number of EU/EEA countries with capability to use whole-genome sequencing (WGS)-based typing (dark tone) or planning to use it by 2018 (light tone) as of mid-2015 (orange bars) and mid-2016 (blue bars) applied to outbreak investigations (A) or surveillance (B), by disease group and pathogen.

Figure 2

Use of whole-genome sequencing (WGS)-based typing of human pathogens in Public Health Reference Laboratories for routine national surveillance by country in the EU/EEA, 2015–16. Dark blue: WGS-based typing used routinely of at least one human pathogen; light blue: national plan in place/in progress for WGS-based typing for surveillance of at least one human pathogen by 2018; orange: no use in 2016 nor national plan for use by 2018; dark gray: no information. (A) 2015 data, cross-validated with EULabCap report (15) and (B) 2016 data.