About the DTU Genomic Proficiency Test 2020

This inter-laboratory performance 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.

What is the DTU Genomic PT?
This inter-laboratory performance 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.

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 C. jejuni, 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 and C. jejuni strains. Participants will be requested to submit reads using File Transfer Protocol (FTP) and optionally also identify the Multi Locus Sequence Type (MLST) of the strains as well as the resistance genes present in the strains if the laboratory performs this type of analysis routinely.

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.

The DTU Genomic PT 2020 is based on the same setup as the three PTs previously provided by the Global Microbial Identifier (GMI) initiative.

How to participate?
Should you be interested in signing up to participate, please contact the DTU Genomic PT Coordinator (see below).
Deadline for sign-up: 31 January 2020.

Protocol and further information
The protocol including appendices will be made available for download via this website: http://www.globalsurveillance.eu/
The protocol will be available when the test materials is shipped from DTU.

Additional information relevant for participants will be sent directly by email.

Timeline
The bacterial isolates and the DNA will be shipped from DTU Food in May 2020. 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). 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).

Deadline for submission of results
By 30 September 2020, results must be submitted as described in the protocol. Individual results will be anonymized, and only the PT-organizers will have access to your laboratory’s results. Each participating laboratory will receive an individual summary of the obtained performance. An overall report summarizing the results will be published and possibly subsequently in a peer-reviewed publication. Authors and co-authors of the publications 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 2020, please contact the DTU Genomic PT Coordinator Susanne Karlsmose Pedersen (suska@food.dtu.dk).

 

Contact

Susanne Karlsmose Pedersen
Research assistant
National Food Institute
+45 35 88 66 01
https://www.globalsurveillance.eu/Projects/Genomic-Proficiency-Test-2020
7 APRIL 2020