GMI is a global, visionary taskforce of scientists and other stakeholders who share an aim of applying novel genomic technologies and informatics tools to improve global patient diagnostics, surveillance and research, by developing needs- and end-user-based data exchange and analysis tools for characterization of all microbial organisms and microbial communities.
Why participate in the GMI 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 (e.g. clustering).
What is the GMI 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 the GMI initiative.
The GMI PT 2016 is supported by COMPARE, which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 643476. In addition, the GMI PT 2016 is supported by FDA GenomeTrakr and Microbiologics®.
The GMI working group 4 (WG4) steered by the US FDA, Microbiologics, and Technical University of Denmark has prepared this proficiency test. The PT consists of three parts, each of which are optional, and include assessing (1a) the laboratory’s DNA preparation and sequencing procedures, (1b) the laboratory’s sequencing output, and (2) the laboratory’s procedure to identify variant sites within whole genome sequence data and cluster and distinguish samples based on those variants.
The proficiency test focuses on Campylobacter coli and C. jejuni, Listeria monocytogenes and Klebsiella pneumoniae, 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 three items consist of
1a) DNA extraction, purification, library-preparation, and whole-genome-sequencing of six bacterial cultures; one Campylobacter coli and one C. jejuni strain, two Listeria monocytogenes strains and two Klebsiella pneumoniae strains. Participants will be requested to submit reads using batch-upload via a web-interface 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 delivered by GMI Working Group 4 of the same six bacterial strains mentioned in clause 1a.
2) Variant detection and phylogenetic/clustering analysis of three datasets each including fastq data from circa 20 genomes of Campylobacter jejuni, Listeria monocytogenes and Klebsiella pneumoniae. Note: If performing a reference based approach for variant detection, the reference applied for the analysis must be the species specific reference indicated in the proficiency test protocol.
For your information, this GMI PT 2016 is the second PT provided by the GMI initiative and will follow the same set-up as the one organized in 2015. Note, however, the GMI PT 2015 focused at Salmonella enterica, Escherichia coli and Staphylococcus aureus. The outcome of the GMI PT 2015 indicated that some of the applied quality markers could be species dependent. Therefore the GMI PT organizers selected the organisms Campylobacter coli and C. jejuni, Listeria monocytogenes and Klebsiella pneumoniae for the 2016 PT.
Who should participate?
All laboratories of the GMI community performing whole-genome-sequencing and/or phylogenetic/clustering analysis are invited to participate, in particular, laboratories frequently submitting data to NCBI, EBI and DDBJ.
Priority will be given to educational institutions and public health institutions. Private companies will not be accepted as participants. Should the sign up list exceed the number of participants that culture and DNA-material has been prepared for, participants will be included on a first come, first served basis.
Costs for participation?
There is no participation fee in the GMI proficiency test. The participating laboratories are, however, expected to cover all expenses as regards the handling and sequencing of the test strains and DNA in relation to their participation in the proficiency test. In addition, laboratories are expected to cover the expenses for parcel shipment if possible. Should a laboratory not be able to cover all expenses, they should notify the PT Coordinator in an email, as there might be limited funding available for this purpose.
The PT material will be sent as ‘UN3373 Biological Substance Category B’ (without temperature control). The courier selected to handle the bacterial cultures and DNA shipment must be able to handle UN3373 in your country, e.g. you could look into one of the following couriers which we have previously had good experience with: DHL, DHL Global Forwarding, Fedex, TNT or World Courier. We ask, also, that you provide your courier import account number in the sign-up form or directly to the PT Coordinator (please find contact information below). We need this information already at this stage to save time and resources.
Note: DHL distinguish between export account numbers and import account numbers; for the purpose of sending you the GMI PT bacterial cultures and DNA, we need your DHL import account number, i.e. the first digits must be 95 or 96, and the number must have 9 digits.
Participating laboratories are responsible for all costs related to taxes or custom fees applied by their country as well as those related to the analysis.
How to participate?
Sign-up to the GMI Proficiency Test 2016 has ended.
Protocol
The protocol including appendices is available for download.
Additional information relevant for participants will be sent directly by email or post.
Discussion forum
Note that a web‐based discussion forum (https://foros.isciii.es/viewforum.php?f=7) is available for participants in the GMI PT 2016. The forum allows you to discuss issues relating to the analysis with other PT‐participants. Appendix 4 of the protocol presents detailed information on the PT discussion forum.
Timeline
The bacterial isolates and the DNA will be shipped from DTU Food in October 2016. At this time, the data-files will also be available for download.
In order to minimize delays, we ask you to send a valid import permit to the PT coordinator. Please apply for a permit to receive the following bacterial cultures or DNA (according to your level of participation): UN3373, Biological Substance, Category B: two Campylobacter strains, two Listeria monocytogenes strains, two Klebsiella pneumoniae strains (note: these strains are carbapenemase-producing).
Deadline for submission of results
By 13 January 2017 (new extended deadline), 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 GMI PT 2016, please contact the GMI PT Coordinator Susanne Karlsmose Pedersen (suska@food.dtu.dk)