Four laboratories encountered issues during a proficiency test for Listeria monocytogenes whole genome assembly, according to a European Centre for Disease Prevention and Control (ECDC) report.
The aim was to help national public health reference labs performing whole genome sequencing-based typing to generate good quality and comparable genome assemblies for Listeria monocytogenes.
Assemblies can be used for analyses including whole and core genome multilocus sequence typing (wg/cgMLST) data. Good quality assemblies are needed to produce wg/cgMLST data that are comparable between labs. Reporting labs should ensure their assembly pipeline is concordant to avoid issues with comparability and potentially affecting outbreak detection and verification, according to the ECDC report.
The ECDC supports integration of whole genome sequencing (WGS) data into surveillance and multi-country outbreak investigations of foodborne diseases including listeriosis.
Ten of 14 participants in the 2018 review had at least one concordant pipeline, and the other four were assisted after the proficiency test to identify root cause of the issue and improve results. Labs not having a concordant assembly pipeline should consider updating it to avoid issues with outbreak detection and in the meantime share raw reads with ECDC.
The four labs that had problems were given feedback regarding the possible causes. Two of them have since updated their pipeline and generated concordant results. For the third lab, the cause is dependent on a software upgrade and this could be the case for the fourth lab.
The 14 participants submitted assembled genomes for 15 sets of raw sequence reads. More than one assembly pipeline was allowed per participant, and results per pipeline were compared to the reference assembly generated by ECDC on several quality metrics.
Sixteen organizations, including 14 public health national reference labs, the European Food Safety Authority (EFSA) and ANSES (French Agency for Food, Environmental and Occupational Health and Safety) as the European Union Reference Laboratory (EURL) for Listeria monocytogenes, provided results for 29 assembly pipelines.
For the Illumina reads, the reference assemblies were found to be appropriate. For Ion Torrent reads, it was not possible to establish concordance.
For European surveillance of listeriosis, ECDC will only accept from labs assemblies generated by a concordant pipeline as verified according to the methodology in the report.
Moving WGS forward
Meanwhile, an ECDC report last month proposed to prioritize implementation of WGS depending on disease and public health application.
It outlined implementation options for medium-term integration of molecular/genomic typing information into EU-level surveillance and multi-country outbreak investigations.
Pace of WGS uptake varies between pathogens, diseases and European Union countries. ECDC is supporting nations in the gradual use of sequence-based typing so they can participate in joint response and surveillance operations with member states.
WGS-based typing use for routine surveillance of at least one human pathogen increased from no countries in 2013 to 20 in 2017. Survey results indicate by the end of this year, 29 member states intend to use WGS-based typing for public health surveillance of at least one pathogen with implementation common for Listeria monocytogenes.
From November 2015 to June 2018, ECDC helped investigate 41 presumptive multi-country foodborne outbreaks caused by Salmonella enterica, Listeria monocytogenes or Shiga-toxin producing E. coli (STEC). As part of this work, more than 2,000 bacterial genomes were sequenced. Investigations confirmed 31 multi-country outbreaks and identified the food source for 12 outbreaks.
The proposed framework revises the list of priority pathogens and diseases for medium-term integration in 2019 to 2021. Over this period, ECDC plans to prepare for and/or implement support to multi-country outbreak investigations, continuous EU surveillance, and sentinel surveillance.
Campylobacter spp., hepatitis A virus, Legionella spp., Listeria monocytogenes, Salmonella enterica, and STEC are listed in the support to multi-country outbreak investigations through sequence-based typing category.
Listeria monocytogenes, Salmonella enterica, and STEC are also part of the EU-wide sequence-based continuous surveillance category.
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