The GMI initiative- and its working groups

Michael Fam Chair Professor

Food Science and Technology

Jørgen Schlundt

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Database(s) in the

Cloud

Diagn

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Whole

Genome

Sequencing

Patient /

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Food &

Disease

Surveillanc

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Global

Prevention

GMI – The idea

Global Microbial IdentifierA global system will enable three major lines of

action:

• Simple identification of all microorganisms in clinical (or other) settings, enabling reduction of total time (and cost) for characterization down to typical time needed to obtain the original isolate

• A total database of unique sequences of all relevant microbiological strains globally, enabling real-time global surveillance of disease developments

• A backbone of Microbial DNA sequences to be used for deep sequencing analyses from different sources (gut, sewage, environment, food?)

Virus – Bacteria – ParasitesSame - Samewww.globalmicrobialidentifier.org

GMI Steering Committee

Eric Brown, Food and Drug Administration (FDA), USAVincenco Caporale, World Organization of Animal Health (OIE)Amy Cawthorne, World Health Organization (WHO), SwitzerlandPaul Cook, Food Standards Agency (FSA), UKDavid Heymann, Health Protection Agency, UKMarion Koopmans, Erasmus Medical Centre, NetherlandsDavid J. Lipman, Nat. Center for Biol. Information (NCBI), USAPathom Sawanpanyalert, Ministry of Public Health, ThailandJørgen Schlundt, Nanyang Technological University, SingaporeMasami T. Takeuchi, Food and Agriculture Organization (FAO)Jianguo XU, National Institute for CDC, China

GMI - according to the Charter

GMI consists of The Platform (organizing body, including e.g. the Steering Committee and the Working Groups) and The Community Network (all individuals and organizations that subscribe to the GMI Website by filling in a profile)The Work Groups Four WGs – originally five

Structuring of GMI must aim to continue to minimize bureaucracy whilst maximizing the flexibility that has characterized GMI thus far.

WG1: Political challenges, outreach and building a global networkChair: Jorgen Schlundt, Co-chair: Pathom SawanpanyalertDeveloping a long-term plan to shape political level involvement in GMI development at the global, regional and national level.Attempting to establish a functional link to political level decision makers in several countries or regional, international organizations.Initiate a coherent system for international discussion of relevant themes, e.g. › global health diplomacy, › coordination between different sectors, › sensitivity of metadata, › open access database of genome sequences, › sharing of strains over borders, › intellectual property rights (IPR), and › funding.

WG2: Repository and storage of sequence and meta-dataChair: Bill Klimke, Co-chair: Guy CoachraneDeveloping a format to capture ”Minimum Data for Matching (MDM)”, consisting of reads and minimum metadata. 

The MDM may or may not be accompanied by assemblies and/or annotation and/or additional metadata.

Ideally, any MDM provided for purposes of searching the GMI databases should immediately also become a deposit available for searching by later submitters.

The search and analytical layers may be provided by INSDC members or by other parties (International Nucleotide Sequence Database Collaboration)

Aiming for a centrally controlled searching and reporting protocol that official sites adhere to and to whom relevant agencies submit

WG3: Analytical approachesChair: Marion Koopmans, Co-chair: Marc Allard

Providing guidance for the development of analytical tools for the optimal functioning of the GMI platform.

Develop a global platform (database, linked databases) that facilitates the application of NGS in research, clinical and public health settings worldwide

Define requirements for GMI functioning from the perspective of end-users (clinical, public health, food safety, research) in terms of applications (identification, outbreak detection etc.) and priority targets/diseases

Map current analytical options and solutions against the needs of GMI end-users, to identify possible R&D and implementation gaps and to identify projects that may fill those gaps

WG4: Ring trials and quality assuranceChair: Rene Hendriksen, Co-chairs: James Pettengill, Errol Strain

Aiming for all laboratories globally to conduct NGS on bacteria and virus to the highest degree of quality

Establishing a proficiency testing (PT) WGS infrastructure for GMI and other partners to ensure high quality and reliable data.

Roll out of PT focusing on testing the quality of sequencing bacterial DNA as well as cluster analysis on sets of genomes

Initiate virus pilot PT scheme initially focusing on identification of virus in matrices from metagenomics sequencing data

WG5: Pilot Projects

Steering Committee decided “to retire working group 5 and discuss a new communication outreach effort at the GMI9 meeting.”

WG 1-4 are suggested to initiate such discussions in the Break-out sessions