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.
Why participate in the DTU Genomic Proficiency Test?
The proficiency test (PT) represents an important tool for the evaluation and production of reliable laboratory results of consistently good quality within the area of DNA preparation, sequencing, and analysis in relation to paired end sequences. Participation in the DTU Genomic PT supports the further development of the PT and allows for relevant feedback on your own performance.
What is the DTU Genomic 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 include assessing (1a) the laboratory’s DNA preparation and sequencing procedures and (1b) the laboratory’s sequencing output.
The PT focuses on Salmonella enterica, Escherichia coli and Campylobacter coli, 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 Salmonella enterica strains, two Escherichia coli strains and two Campylobacter coli strains. Participants will be requested to identify the Multi Locus Sequence Type (MLST) of the strains, and - if the laboratory performs this type of analysis routinely - the antimicrobial resistance genes present in the strains. The reads must be submitted using a File Transfer Protocol (FTP) site.
1b) Perform whole-genome-sequencing of pre-prepared DNA (each vial contains a minimum of 2 µg DNA) delivered by the PT organisers of the same six bacterial strains mentioned in clause 1a. For clause 1b, participants will also be requested to identify the Multi Locus Sequence Type (MLST) of the strains, and - if the laboratory performs this type of analysis routinely - the antimicrobial resistance genes present in the strains. The reads must be submitted using a File Transfer Protocol (FTP) site.
Technologies covered
Paired end sequences must be submitted for analysis.
Assessment of single end sequences or long reads sequences (e.g., ONT) is not offered as part of the present PT.
Who can participate?
EJP CARE partner institutes, laboratories belonging to the Fleming Fund project, SEQAFRICA, and laboratories belonging to the EURL-AR network are invited to participate.
Costs for participation?
For EJP CARE partner institutes and laboratories belonging to the Fleming Fund project, SEQAFRICA, there is no participation fee for the DTU Genomic Proficiency Test 2021. 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 2021 has ended.
Protocol and further information
The protocol including appendices is available for download via this website (see link to the right).
Additional information relevant for participants will be sent directly by email.
Timeline
The bacterial isolates and the DNA was shipped from National Food Institute DTU in October 2021. The PT material will be sent as ‘UN3373 Biological Substance Category B’ (without temperature control).
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 Salmonella enterica strains, two Escherichia coli strains and two Campylobacter strains (note: some of these strains may be carbapenemase-producing).
By 4 March 2022 (updated deadline), results must be submitted as described in the protocol. 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.
Contact
If you have questions or comments to the DTU Genomic PT 2021, please contact the DTU Genomic PT Coordinator Susanne Karlsmose Pedersen (suska@food.dtu.dk).