About the GMI Proficiency Test 2017

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 2017 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 2017 is supported by FDA GenomeTrakr.

The GMI working group 4 (WG4) steered by the US FDA 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 Salmonella enterica, Escherichia coli 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 three 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 Staphylococcus aureus 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 S. enterica, E. coli and S. aureus. 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 2017 is the third PT provided by the GMI initiative and will follow the same set-up as the one organized in 2016.

Many of the quality control markers evaluated in the PT scheme appeared to be genus-depended, therefore the GMI PT organizers decided to revisit the bacterial genera selected for the PT in 2015, i.e. two strains of each of the genera Salmonella enterica spp enterica, Escherichia coli and Staphylococcus aureus were selected for the wet-lab component in 2017. The relevance of these genera was indicated to be high in the GMI end-user survey. Moreover, these genera are not expected to pose difficulties in sequencing and analysis due to the limited number of repeats and rearrangement in the sequences. The Salmonella as well as the E. coli strains were selected based on the emerging antimicrobial threats in terms of resistance to colistin and carbapenemases. In addition, the GMI PT organizers selected two S. aureus strains (MRSA) isolated from humans. They belong to two different clonal complexes, one believed to have been associated with infections in both humans and animals and one livestock associated phenotype. In addition, one expresses resistance to linezolid.

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. 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 for the GMI Proficiency Test 2017 is closed.

The deadline for sign-up was 09 June 2017.

Protocol

The protocol including appendices is available for download. There is also a Quick Start protocol.

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 2017. 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 August 2017. 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 Salmonella enterica strains, two Escherichia coli strains and two Staphylococcus aureus strains (note: some of these strains are carbapenemase-producing).

Deadline for submission of results

By 31 January 2018, 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.