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other·research methods, infectious disease, epidemiology, public health·PMC10483428

Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities

Microbial Genomics · 10 authors, 5 centres

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The central result was that most laboratories delivered high-quality sequence data, with two identified as overall underperforming, and specific quality control metrics (N50 and number of contigs) were proposed as indicators for high-sequencing quality.

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Performance was evaluated based on quality control (QC) metrics, single nucleotide polymorphism (SNP) analysis, and multilocus sequence typing (MLST) prediction. The results showed most laboratories produced high-quality data, with only two identified as overall underperforming due to serious sequencing problems. Limitations include the exclusion of data based on genome size deviation and the inability to assess metrics reliant on a reference genome for routine QC. The findings underscore the importance of systematic QC procedures for ensuring reliable WGS data for surveillance and outbreak investigation.

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research methods

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ORIGINAL PAPER

PMC10483428

Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities

Microbial Genomics

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ABSTRACT

The global surveillance and outbreak investigation of antimicrobial resistance (AMR) is amidst a paradigm shift from traditional biology to bioinformatics. This is due to developments in whole-genome-sequencing (WGS) technologies, bioinformatics tools, and reduced costs. The increased use of WGS is accompanied by challenges such as standardization, quality control (QC), and data sharing. Thus, there is global need for inter-laboratory WGS proficiency test (PT) schemes to evaluate laboratories' capacity to produce reliable genomic data. Here, we present the results of the first iteration of the Genomic PT (GPT) organized by the Global Capacity Building Group at the Technical University of Denmark in 2020. Participating laboratories sequenced two isolates and corresponding DNA of Salmonella enterica , Escherichia coli and Campylobacter coli , using WGS methodologies routinely employed at their laboratories. The participants' ability to obtain consistently good-quality WGS data was assessed based on several QC WGS metrics. A total of 21 laboratories from 21 European countries submitted WGS and meta-data. Most delivered high-quality sequence data with only two laboratories identified as overall underperforming. The QC metrics, N50 and number of contigs, were identified as good indicators for high-sequencing quality. We propose QC thresholds for N50 greater than 20 000 and 25 000 for Campylobacter coli and Escherichia coli, respectively, and number of contigs >200 bp greater than 225, 265 and 100 for Salmonella enterica , Escherichia coli and Campylobacter coli , respectively. The GPT2020 results confirm the importance of systematic QC procedures, ensuring the submission of reliable WGS data for surveillance and outbreak investigation to meet the requirements of the paradigm shift in methodology.

CITATION EXPORT

Thea Kristensen, Lauge Holm Sørensen, Susanne Karlsmose Pedersen et al.. Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities. Microbial Genomics. (2023). https://doi.org/10.1099/mgen.0.001076

AUTHORS

10 · 5 CENTRES

Thea Kristensen, Lauge Holm Sørensen, Susanne Karlsmose Pedersen, Jacob Dyring Jensen, Hanne Mordhorst, Niamh Lacy-Roberts, Oksana Lukjancenko, Yan Luo, Maria Hoffmann, Rene S. Hendriksen

1 National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
2 Department of Plant and Environmental Sciences, Section for Organismal Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
3 National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
4 Clinical Microbiomics, Copenhagen, Denmark
5 Center for Food and Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA