Global microbial identifier

For genotyping of microorganisms for medical diagnosis, or other purposes, scientists may use a wide variety of DNA profiling techniques, such as polymerase chain reaction, pulsed-field gel electrophoresis or multilocus sequence typing. A complication of this broad variety of techniques is the difficulty to standardize between techniques, laboratories and microorganisms, which may be overcome using the complete DNA code of the genome generated by whole genome sequencing.{{cite journal|last=Shendure|first=J|title= Next-generation DNA sequencing|journal=Nature Biotechnology|year=2008|volume=26|issue=10|pages=1135–1145|doi=10.1038/nbt1486|pmid=18846087|s2cid=6384349}} For straightforward diagnostic identification, the whole genome sequencing information of a microbiological sample is fed into a global genomic database and compared using BLAST procedures to the genomes already present in the database.{{Cite web|url=http://www.genomicepidemiology.org/|title=Center for Genomic Epidemiology|website=www.genomicepidemiology.org}} In addition, whole genome sequencing data may be used to back calculate to the different pre-whole genome sequencing genotyping methods, so previous collected valuable information is not lost.{{cite journal|last=Inouye|first=M|title=Short read sequence typing (SRST):multi-locus sequence types from short reads|journal=BMC Genomics|year=2012|volume=13|pages=388|doi=10.1186/1471-2164-13-338|pmid=22827703|pmc=3460743|display-authors=etal|doi-access=free}}{{cite journal|last=Larsen|first=MV|title=Multilocus sequence typing of total-genome-sequenced bacteria|journal=Journal of Clinical Microbiology|year=2012|volume=50|pages=1355–1366|doi=10.1128/JCM.06094-11|pmid=22238442|issue=4|pmc=3318499|display-authors=etal}} For the global microbial identifier the genomic information is coupled to a wide spectrum of metadata about the specific microbial clone and includes important clinical and epidemiological information such as the global finding places, treatment options and antimicrobial resistance, making it a general microbiological identification tool. This makes personalized treatment of microbial disease possible as well as real-time tracing systems for global surveillance of infectious diseases for food safety and serving human health.{{citation needed|date=August 2022}}

The initiative for building the database arose in 2011 and when several preconditions were met: 1) whole genome sequencing has become mature and serious alternative for other genotyping techniques,{{cite journal|last=Zankari|first=E|title=Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing|journal=Journal of Antimicrobial Chemotherapy|year=2013|pmid=23233485|doi=10.1093/jac/dks496|volume=68|issue=4|pages=771–7|display-authors=etal|doi-access=free}}{{cite journal|last=Dunne|first=WM|title= Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory|journal=European Journal of Clinical Microbiology and Infectious Diseases|year=2012|volume=31|issue=8|pages=1719–17126|doi=10.1007/s10096-012-1641-7|pmid=22678348|s2cid=11511739|display-authors=etal}} 2) the price of whole genome sequencing has started falling dramatically and in some cases below the price of traditional identifications, 3) vast amounts of IT resources and a fast Internet have become available, and 4) there is the idea that via a cross sectoral and One Health approach infectious diseases may be better controlled.{{cite book|last=Current Topics in Microbiology and Immunology, Vol 366|title=One Health: The Human-Animal-Environment Interfaces in Emerging Infectious Diseases|year=2013|publisher=Springer|isbn=978-3-540-70961-9|pages=280|url=https://www.springer.com/biomed/virology/book/978-3-642-35845-6?detailsPage=authorsAndEditors#|editor=Mackenzie, J.S. |editor2=Jeggo, M. |editor3=Daszak, P. |editor4=Richt, J}}{{cite book|author1=Wielinga, PR |author2=Schlundt, J |chapter=Food Safety: At the Center of a One Health Approach for Combating Zoonoses |title=One Health: The Human-Animal-Environment Interfaces in Emerging Infectious Diseases |series=Current Topics in Microbiology and Immunology |year=2013|volume=366 |pmid=22763857|doi=10.1007/82_2012_238|pages=3–17|doi-broken-date=1 November 2024 |pmc=7121890|isbn=978-3-642-35845-6 }}

Starting the second millennium, many microbiological laboratories, as well as national health institutes, started genome sequencing projects for sequencing the infectious agents collections they had in their biobanks.{{cite web|last= A summary of genomic databases|title= Bacterial genome databases|url= http://phobos.ramapo.edu/~pbagga/binf/binf_res/bioinfo_gndb_bact.htm }}{{cite web|last= WGS projects info by EBI|title= WGS projects|url= http://www.ebi.ac.uk/genomes/wgs.html }} Thereby generating private databases and sending model genomes to global nucleotide databases such as GenBank of the National Center for Biotechnology Information{{cite web|last= Genome Browser NCBI|title= Genome information by organism |url= https://www.ncbi.nlm.nih.gov/genome/browse/}} or the nucleotide database of the EMBL.{{cite web|last= Genome Browser EMBL|title= Access to Completed Genomes|url= http://www.ebi.ac.uk/genomes/}} This created a wealth of genomic information and independent databases for eukaryotic as well as prokaryotic genomes.{{cite web|last= Microbial Genomes Database|title=MBGD|url= http://mbgd.genome.ad.jp/}}{{Cite web|url=https://www.ebi.ac.uk/2can|title=2Can Support Portal < EMBL-EBI|website=www.ebi.ac.uk}}{{cite web|last= DOE's Joint Genome Institute Integrated Microbial Genomes (IMG) |title= IMG DOEs JGI|url=http://img.jgi.doe.gov/cgi-bin/w/main.cgi}} The need to further integrate these databases and to harmonize data collection, and to link the genomic data to metadata for optimal prevention of infectious diseases, was generally recognized by the scientific community.{{cite journal|last=Aarestrup|first=F|title=Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response|journal=Emerging Infectious Diseases|year=2012|volume=18|issue=11|pages=e1|doi=10.3201/eid/1811.120453|pmid=23092707|pmc=3559169|display-authors=etal}} In 2011, several infectious disease control centers and other organizations took the initiative of a series of international scientific- and policy-meetings, to develop a common platform and to better understand the potentials of an interactive microbiological genomic database. The first meeting was in Brussels, September 2011,{{cite journal|last=Kupferschmidt|first=K|title=Epidemiology. Outbreak detectives embrace the genome era.|journal=Science|year=2011|volume=333|issue=6051|pages=1818–1819|pmid=21960605|doi=10.1126/science.333.6051.1818}}{{Cite web|url=http://www.food.dtu.dk/upload/f%C3%B8devareinstituttet/food.dtu.dk/publikationer/2011/consensus%20report%20perspectives%20of%20a%20global,%20real-time.pdf|title=Consensus report of an expert meeting 1-2 September 2011, Brussels, Belgium.}} followed by meetings in Washington (March 2012) and Copenhagen{{Cite web|url=https://www.globalmicrobialidentifier.org/News-and-Events|title=News & Events - Global Microbial Identifier|website=www.globalmicrobialidentifier.org}} (February 2013). In addition to experts from around the globe, Intergovernmental Organizations have been included in the action, notably the World Health Organization and the World Organisation for Animal Health.{{citation needed|date=August 2022}}

A detailed roadmap{{Cite web|url=http://www.globalmicrobialidentifier.org/~/media/Sites/gmi/About/roadmap-draft2.ashx|title=GMI development plan}} for the development of the database was set up with the following general timeline:

:2010 - 2012: Development of pilot systems.

:2011 - 2013: International structural start-up, with the formation of an international core group, analysis of the present and future landscape to build the database, and diplomacy efforts to bring the relevant groups together.

:2012 - 2016: Development of a robust IT-backbone for the database, and development of novel genome analysis algorithms and software.

:2017 - 2020: Construction of a global solution, including the creation of networks and regional hubs.

Current members:

• Eric Brown, Food and Drug Administration, USA
• Amy Cawthorne, World Health Organization, Switzerland
• Jørgen Schlundt, Nanyang Technological University, Singapore.
• David J. Lipman, National Center for Biotechnology Information, USA.
• Alisdair Wotherspoon, Food Standards Agency, United Kingdom.
• Pathom Sawanpanyalert, Ministry of Public Health, Thailand.
• David Heyman, Health Protection Agency, United Kingdom.
• Marion Koopmans, Erasmus University Medical Center, Netherlands National Institute for Public Health and the Environment.
• Masami T. Takeuchi, Food and Agriculture Organization
• Vincenco Caporale, World Organization of Animal Health

Former members:

• Steven M. Musser, Food and Drug Administration, USA.
• Angelik Tritscher, World Health Organization, Switzerland.

• Human Microbiome Project
• Whole genome sequencing
• DNA profiling
• Personal Genome Project
• List of sequenced eukaryotic genomes
• List of sequenced bacterial genomes
• List of sequenced archaeal genomes
• Predictive medicine
• Personalized medicine
• DNA database
• Integrated Microbial Genomes

{{Reflist|colwidth=30em}}

• [https://archive.today/20130415020311/http://www.g-m-i.org/About.aspx Global Microbial Identifier project page]
• [https://web.archive.org/web/20130313102854/http://100kgenome.vetmed.ucdavis.edu/ 100K Foodborne Pathogen Genome Project]
• [http://www.genomicepidemiology.org/ Genomic Epidemiology pilot database]
• [http://www.noronet.nl/ Norovirus database]

Category:Applied genetics

Category:Microbiology

Category:Biological databases

Category:Pathogen genomics

Category:Public health

Category:Epidemiology