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)?
This proficiency test is provided to facilitate harmonization and standardization in whole genome sequencing and data analysis of paired end sequencing, with the aim to produce comparable data for monitoring and research purposes.
The PT consists of two parts and includes assessing (1a) the laboratory’s DNA preparation and sequencing procedures and (1b) the laboratory’s sequencing output.
DTU Genomic PT 2023 focuses on Escherichia coli, Salmonella enterica, and Staphylococcus aureus, and allows for sign-up for each species separately. Note that item 1a and item 1b are parallel; i.e. when signing up for 1a for one species, participation in 1b is expected.
The two items consist of
1a) DNA extraction, purification, library-preparation, and whole-genome-sequencing of six bacterial cultures; two Escherichia coli strains, two Salmonella enterica strains, and two Staphylococcus aureus strains.
1b) Perform whole-genome-sequencing of pre-prepared DNA (each vial contains approximately 1 µg DNA) delivered by the PT organisers of the same six bacterial strains mentioned in clause 1a.
For items 1a and 1b, participating laboratories will be requested 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, for items 1a and 1b, participants will be requested to submit FASTQ files using ScienceData for the purpose of evaluation of the sequence quality.
Why participate in the DTU Genomic PT?
The DTU Genomic PT represents an important tool for the evaluation of capacity for 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, 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 2023. 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 as regards the handling and sequencing of the test strains and DNA in relation to their participation in the proficiency test.
How to participate?
Sign-up for the DTU Genomic PT 2023 via this link.
Protocol and further information
The protocol including appendices will be made available for download via this website.
Additional information relevant for participants will be sent directly by email.
In order to minimize delays, we ask you to send a valid import permit to the PT coordinator (see below). Therefore, if relevant for your institution in order to receive a UN3373 shipment from Denmark, please apply for an import permit to receive the following bacterial cultures or DNA (according to your level of participation): UN3373, Biological Substance, Category B: Two E. coli strains, two Salmonella enterica strains and two S. aureus (note: some of these strains may be carbapenemase-producing).
Each participating laboratory will receive an individual summary of the obtained 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. Authors and co-authors of publication(s) will be those who have contributed to the preparation and execution of the proficiency test. Due to the anonymity of results, the individual participating laboratories will not be acknowledged in the publications.
Timeline
Deadline for sign-up: 22 September 2023
Test material (bacterial isolates and DNA) will be shipped from National Food Institute DTU mid-October 2023.
The PT material will be sent as ‘UN3373 Biological Substance Category B’ (without temperature control).
Results must be submitted electronically no later than 12 December 2023 at 4 pm CET
Contact
If you have questions or comments to the DTU Genomic PT 2023, please contact the DTU Genomic PT Coordinator Susanne Karlsmose Pedersen (suska@food.dtu.dk).