This proficiency test is provided to facilitate harmonization and standardization in whole genome sequencing and data analysis, with the aim to produce comparable data for monitoring and research purposes.
What is the DTU Genomic Proficiency test (PT)? ?
The PT assesses laboratory’s DNA preparation, sequencing procedures and sequencing output.
DTU Genomic PT 2024 focuses on Escherichia coli, Staphylococcus aureus, and Enterococcus (E. faecium and/or E. faecalis) and allows for sign-up for each species separately. It covers DNA extraction, purification, library-preparation, and whole-genome-sequencing of six bacterial cultures; two E. coli strains, two S. aureus strains, and two Enterococcus strains.
Participating laboratories will need to report results from WGS-based identification of bacterial species, prediction of Multi-Locus Sequence Types (MLST), detection of plasmid replicon types, detection of genes and chromosomal point mutations mediating antimicrobial resistance (AMR) towards antimicrobials relevant for monitoring, and in silico prediction of AMR profile. Participating laboratories can choose to apply any tools they find suitable for the analyses.
Moreover, participants will need to submit the obtained FASTQ files using ScienceData for the purpose of evaluation of the sequence quality.
Why participate in the DTU Genomic PT?
The DTU Genomic PT is an important tool to evaluate your laboratory’s capacity to conduct WGS-based analysis and promotes the production of reliable and accurate results of consistently good quality. Moreover, participating laboratories will be able to identify strengths and weaknesses in their technical and analytical setup and implement appropriate actions for improvement of their performance in WGS-based resistome profiling and identification of pathogens.
Technologies covered
Paired end sequences based on short read technology must be submitted for analysis.
Assessment of long reads sequences (e.g., ONT) is not offered as part of the present PT.
Who can participate?
Laboratories connected to the Fleming Fund project, SeqAfrica (including SARA and PGI), and laboratories belonging to the EURL-AR network are invited to participate.
Costs for participation?
For laboratories connected to the Fleming Fund project, SeqAfrica, there is no participation fee for the DTU Genomic Proficiency Test 2024. Laboratories belonging to the EURL-AR network will be contacted directly to clarify the costs for participation. All participating laboratories are expected to cover expenses related to the handling and sequencing of the test strains as part of their participation in the proficiency test.
How to participate?
Sign-up for the DTU Genomic PT 2024 here: https://ec.europa.eu/eusurvey/runner/9eee5f58-f14f-439b-1019-0250ec705800
Protocol and further information
The protocol including appendices are now available for download.
Additional information relevant for participants will be sent directly by email.
If your institution requires a permit in order to receive a UN3373 shipment from Denmark, please apply for an import permit to receive the following bacterial cultures (according to your level of participation): UN3373, Biological Substance, Category B: Two E. coli strains, two S. aureus strains and two Enterococcus strains (note: some of these strains may be carbapenemase-producing). In order to minimize delays, we ask you to send a valid import permit to the PT coordinator (see below) as soon as possible.
Each participating laboratory will receive an individual summary of its performance. An overall summary of the results will be published. Individual results will be anonymized, and only the PT-organizers will have access to your laboratory’s results. Due to the anonymity of results, authors and co-authors of publication(s) will be those who have contributed to the preparation and execution of the proficiency test.
Timeline
Deadline for sign-up: 23 August 2024
Test material (bacterial isolates) will be shipped from National Food Institute DTU mid-October 2024.
The PT material will be sent as ‘UN3373 Biological Substance Category B’ (without temperature control).
Deadline for result submission will be 15 January 2025 at 4 pm.
Contact
If you have questions or comments to the DTU Genomic PT 2024, please contact the DTU Genomic PT Coordinator Joana Mourão (joam@food.dtu.dk).