German network set up for bacteria surveillance

Three German organizations have created a consortium to monitor bacterial pathogens and detect outbreaks faster.

The University of Münster, Research Center Borstel and the Robert Koch Institute formed the miGenomeSurv network (microbial genome-based surveillance of infectious agents).

This network is based on national reference laboratories, where infectious agents relevant to the population are characterized microbiologically and via genome analysis. Genome sequencing methods provide DNA fingerprints and other characteristics of the bacteria allowing surveillance and cluster detection.

The initial focus includes Enterohemorrhagic E. coli (EHEC) and Listeria monocytogenes and submitted samples dated from early 2019, reaching almost 3,000 by the second quarter of 2021.

A detailed fingerprint of a pathogen is needed to identify or exclude any similarities between strains. This helps investigators recognize if the pathogens involved are similar and if they have already been seen elsewhere or earlier.

“In order to improve infection control, molecular surveillance of infectious agents is essential,” said professor Lothar H. Wieler, president of the Robert Koch Institute.

Pathogens’ unique signature
In 2011, the German public health system faced a foodborne outbreak of E. coli O104:H4, which caused one of the largest outbreaks of EHEC infections resulting in 2,987 illnesses, 855 cases of severe kidney failure and 53 deaths. Fenugreek sprouts from Egypt were identified as most likely vehicle of infection.

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

A database with restricted access automatically triggers outbreak early warnings by sending emails to data submitters in the case of close genomic matches between samples.

In the consortium, a common language, called nomenclature, is defined for the numerous lineages of detected pathogens.

This is based on the genome sequence and of a core genome (cg) – multi-locus sequence type (MLST) calculated from the genome data. As a result, the genetic material of the pathogen is translated into a standardized numerical code.

This allows the exchange of data between participating laboratories, with other national and international partners and institutions such as the European Centre for Disease Prevention and Control (ECDC) and public health services responsible for measures such as outbreak management.

“Easy-to-use bioinformatics tools help to give each pathogen a unique signature,” said professor Dag Harmsen, from the University of Münster.

Similar existing groups include the GenomeTrakr Network, Global Microbial Identifier consortium and PulseNet International.

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