Network uses "genetic fingerprint" to monitor bacterial pathogens and to expedite the detection of outbreaks.

In a modern and global society, the mobility of humans and animals, and the transport of goods and food are on a permanent high. Infectious diseases and their causative agents have always followed trade and travel routes and the contact points involved. This is impressively illustrated by the current SARS-CoV2 pandemic. Further in 2011, the German public health system was confronted with a food-borne outbreak of a pathogen - an E. coli EHEC O104: H4 variant - which caused one of the largest outbreaks of EHEC infections resulting in 2,987 cases of diarrhea, 855 cases of severe kidney failure and 53 deaths.

The identification of the source of infection is usually essential for successful outbreak control. If the infection source is not identified quickly, such outbreaks can go on for long periods of time and across different locations, making the identification of the causative agent very difficult.

However - how do you recognize that the pathogens involved are "similar"? What does "similar” mean, and how can we identify whether a pathogen has already been observed elsewhere or earlier? How exactly can pathogens be traced? For this, a detailed "fingerprint" of the pathogen is needed which identifies or excludes any similarities.

"In order to improve infection control, molecular surveillance of infectious agents is essential", says Professor L. H. Wieler, President and Head of the Robert Koch Institute. To provide suitable instruments a consortium has been initiated by partners from three German organizations: the University of Münster, the Research Center Borstel and the Robert Koch Institute to form the network "miGenomeSurv" (microbial genome-based surveillance of infectious agents). This network is based on national reference laboratories, where - according to their mandate - infectious agents relevant to the population are characterized not just microbiologically but also via genome analysis. Genome sequencing methods provide "fingerprints" and other characteristics of the bacteria allowing surveillance and cluster detection.

In the context of "miGenomeSurv", a common language (nomenclature) is defined for the numerous lineages of detected pathogens. "Easy-to-use bioinformatic tools help to give each pathogen a unique signature", explains Professor Dag Harmsen of the University of Münster. This particularly important aspect is based on the genome sequence and of a so-called core genome (cg) –MLST type calculated from the genome data. As a result, the genetic material of the pathogen is translated into a standardized numerical code. This allows an easy exchange of data between the participating laboratories, with other national and international partners and institutions such as the ECDC and the public health service responsible for implementing measures such as outbreak management. The genomic profiles and other project data are published in a summarized form on the network’s website at www.miGenomeSurv.org.

The consortium will first concentrate on the following high-priority organisms:

• enterohaemorrhagic Escherichia coli (EHEC)
• Listeria monocytogenes
• multi-resistant Mycobacterium tuberculosis, M. bovis / caprae
• Vancomycin-resistant enterococci (VRE).

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