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.

Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food‐ and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries

“…The study of virulence factors was particularly important for E. coli, as also observed by Revez and colleagues (Revez et al, 2017), while WGS-serotyping as well as the detection of resistance genes were mostly used for characterising Salmonella spp. and E. coli isolates.…”

“…VTEC, Campylobacter spp., L. monocytogenes, Coagulase Positive Staphylococci, others) and antimicrobial resistant isolates from animals, food, feed and their environment. Similar surveys have also been launched by ECDC to collect information from the European public health sector laboratories (Revez et al, 2017).…”

“…This has been recognised by the European Commission (EC), the European Food Safety Authority (EFSA), and the European Centre for Disease Prevention and Control (ECDC). ECDC has started collecting information on the use of WGS in public health laboratories since 2015 2,3 (Revez et al, 2017).…”

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

“…Many recent evaluations on the use of NGS for the determination of AMR have emphasised the difficulty of establishing a curated knowledge base on drug resistance genetic determinants to be used as a reference database in NGS data analysis 2, 13, 55 . The same problem is mirrored in the design of a benchmark that would ensure all determinants are correctly detected.…”

“…Focusing on the bioinformatics step, an important shared challenge is the need to correctly and reliably identify the known genomic determinants of AMR from a set of NGS reads produced from sequencing a sample. The ECDC study reported the requirement for sufficient bioinformatics expertise as one of the important hurdles to a more general implementation of NGS for routine testing 2 . This observation has also been expressed in recent case studies and reviews 7– 11 .…”