The genomic epidemiological database for global identification of microorganisms or global microbial identifier is a platform for storing

whole genome sequencing Whole genome sequencing (WGS), also known as full genome sequencing or just genome sequencing, is the process of determining the entirety of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's ...

data of

microorganisms A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in ...

, for the identification of relevant

genes In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

and for the comparison of

genomes A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

to detect and track-and-trace

infectious disease An infection is the invasion of tissue (biology), tissues by pathogens, their multiplication, and the reaction of host (biology), host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmis ...

outbreaks and emerging

pathogens In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ. The term ...

. The database holds two types of information: 1) genomic information of

, linked to, 2)

metadata Metadata (or metainformation) is "data that provides information about other data", but not the content of the data itself, such as the text of a message or the image itself. There are many distinct types of metadata, including: * Descriptive ...

of those microorganism such as

epidemiological Epidemiology is the study and analysis of the distribution (who, when, and where), patterns and Risk factor (epidemiology), determinants of health and disease conditions in a defined population, and application of this knowledge to prevent dise ...

details. The database includes all genera of microorganisms:

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

viruses A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almo ...

parasites Parasitism is a close relationship between species, where one organism, the parasite, lives (at least some of the time) on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The en ...

and

fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...

Technology

For

genotyping Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using bioassay, biological assays and comparing it to another individual's sequence or a reference seq ...

of microorganisms for

medical diagnosis Medical diagnosis (abbreviated Dx, Dx, or Ds) is the process of determining which disease or condition explains a person's symptoms and signs. It is most often referred to as a diagnosis with the medical context being implicit. The information ...

, or other purposes, scientists may use a wide variety of

DNA profiling DNA profiling (also called DNA fingerprinting and genetic fingerprinting) is the process of determining an individual's deoxyribonucleic acid (DNA) characteristics. DNA analysis intended to identify a species, rather than an individual, is cal ...

techniques, such as

polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed st ...

, pulsed-field gel electrophoresis or

multilocus sequence typing Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. The first MLST scheme ...

. 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 Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

code of the genome generated by whole genome sequencing. 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. 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. 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

information such as the global finding places, treatment options and

antimicrobial resistance Antimicrobial resistance (AMR or AR) occurs when microbes evolve mechanisms that protect them from antimicrobials, which are drugs used to treat infections. This resistance affects all classes of microbes, including bacteria (antibiotic resista ...

, 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 infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable dise ...

for

food safety Food safety (or food hygiene) is used as a scientific method/discipline describing handling, food processing, preparation, and food storage, storage of food in ways that prevent foodborne illness. The occurrence of two or more cases of a simi ...

and serving

human health Health has a variety of definitions, which have been used for different purposes over time. In general, it refers to physical and emotional well-being, especially that associated with normal functioning of the human body, absent of disease, pain ...

The initiative

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, 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 The Internet (or internet) is the Global network, global system of interconnected computer networks that uses the Internet protocol suite (TCP/IP) to communicate between networks and devices. It is a internetworking, network of networks ...

have become available, and 4) there is the idea that via a cross sectoral and One Health approach infectious diseases may be better controlled. 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 A biobank is a type of biorepository that stores biological samples (usually human) for use in research. Biobanks have become an important resource in medical research, supporting many types of contemporary research like genomics and personalize ...

. Thereby generating private databases and sending model genomes to global nucleotide databases such as

GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...

of the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

or the nucleotide database of the

EMBL The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 29 member states, two prospect member states, and one associate member state. EMBL was created in ...

. This created a wealth of genomic information and independent databases for

eukaryotic The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

as well as

prokaryotic A prokaryote (; less commonly spelled procaryote) is a single-celled organism whose cell lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Greek (), meaning 'before', and (), meaning 'nut' ...

genomes. 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. 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, followed by meetings in Washington (March 2012) and Copenhagen (February 2013). In addition to experts from around the globe, Intergovernmental Organizations have been included in the action, notably the

World Health Organization The World Health Organization (WHO) is a list of specialized agencies of the United Nations, specialized agency of the United Nations which coordinates responses to international public health issues and emergencies. It is headquartered in Gen ...

and the

World Organisation for Animal Health The World Organisation for Animal Health (WOAH), formerly the (OIE), is an intergovernmental organisation founded in 1924, coordinating, supporting and promoting animal disease control. The primary objective of WOAH is to control epizootic dis ...

Development plan

A detailed roadmap 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.

Steering committee

Current members: * Eric Brown,

Food and Drug Administration The United States Food and Drug Administration (FDA or US FDA) is a List of United States federal agencies, federal agency of the United States Department of Health and Human Services, Department of Health and Human Services. The FDA is respo ...

, USA * Amy Cawthorne,

, Switzerland * Jørgen Schlundt,

Nanyang Technological University Nanyang Technological University (NTU) is a public research university in Singapore. Founded in 1981, it is also the second oldest autonomous university in the country. The university is organised across numerous colleges and schools, includi ...

, Singapore. * David J. Lipman,

, USA. * Alisdair Wotherspoon,

Food Standards Agency The Food Standards Agency is a non-ministerial government department of the Government of the United Kingdom. It is responsible for protecting public health in relation to food in England, Wales and Northern Ireland. It is led by a board appoin ...

, United Kingdom. * Pathom Sawanpanyalert, Ministry of Public Health, Thailand. * David Heyman,

Health Protection Agency The Health Protection Agency (HPA) was a non-departmental public body in England. It was set up by the UK government in 2003 to protect the public from threats to their health from infectious diseases and environmental hazards. The HPA's role w ...

, United Kingdom. * Marion Koopmans, Erasmus University Medical Center,

Netherlands National Institute for Public Health and the Environment The National Institute for Public Health and the Environment ( or simply RIVM) is a Dutch research institute that is an independent agency of the Ministry of Health, Welfare and Sport. RIVM performs tasks to promote public health and a safe liv ...

. * Masami T. Takeuchi,

Food and Agriculture Organization The Food and Agriculture Organization of the United Nations; . (FAO) is a specialized agency of the United Nations that leads international efforts to defeat hunger and improve nutrition and food security. Its Latin motto, , translates ...

* Vincenco Caporale, World Organization of Animal Health Former members: * Steven M. Musser,

, USA. * Angelik Tritscher,

, Switzerland.

References

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External links