The SeqNet.org initiative is a dynamic Europe-wide network of laboratories for DNA sequence-based typing of microbial pathogens, especially Staphylococcus aureus. SeqNet.org (http://www.SeqNet.org) aims to ensure that unambiguous, electronic, portable and easily comparable typing data for local infection control and for national and European-wide surveillance of sentinel microorganisms, such as methicillin resistant S. aureus (MRSA) are generated. Producing high quality typing data is necessary for cross-border comparisons and for relating local data to a European-wide epidemiological context.

SeqNet.org, which currently involves 30 laboratories from 20 European countries (Table), was founded in November 2004. Its main objective is to establish European standards for sequence-based typing of microbial pathogens and thereby create a common European nomenclature for identification and tracing of important pathogens.

To test the concept, sequence typing of S. aureus Protein A (spa) was chosen as a typing method. It has been shown that spa typing is stable [1, 2], fast [3, 4], and discriminatory [3, 5]. Furthermore, it is affordable for most European laboratories.

The objectives of SeqNet are:

The SeqNet.org central database server
In addition to the quality feature, 30 laboratories have been synchronising their data since 2004 within the network. This data is the basis for a virtual laboratory network for typing of MRSA. Using a special bioinformatics tool [4], the laboratory typing data are synchronised via the internet, ensuring a universal nomenclature. New spa repeats and spa types detected by one laboratory are given a preliminary name (eg, txAA or txAB) in the local database, which after synchronisation with the central database are then matched automatically with spa types found by other participants. If the repeat succession is new, the t-number is finally assigned for all future detection of this spa type. If the repeat succession has already been described and synchronised by another laboratory, the preliminary name in the local database of the inquiring laboratory is automatically changed to the pre-existing denomination. That means that the same repeat succession, provisionally designated txAA and txAB from two different laboratories, are both automatically and immediately changed during synchronisation by the StaphType software into t002 and designated as such for future identification.

Currently, the 30 SeqNet.org laboratories (Table) and 34 other submitting laboratories have synchronised more than 1040 spa types, 90 spa repeats, and 11000 S. aureus, 92% of which are MRSA. The complete dataset of the strain records is available for 8943 isolates. Currently, 69% of all submissions are sent to the central server from 13 German laboratories, but other countries including Denmark, Sweden, Norway, Austria, Belgium and the United Kingdom, also synchronise their data.

Network of typing networks
Recently, a BURP (‘based upon repeat patterns’) algorithm module (Ridom StaphType) was released, making it possible to group the spa types by means of their relatedness. Preliminary results show a correlation of spa clonal complexes (CC) with MLST CC and PFGE groups of about 95% [Witte W, personal communication, 12 October 2005], so that spa typing generated within the SeqNet.org network seems to be highly concordant with PFGE and MLST results. A direct link to the mlst.net database has been established. For example, MRSA isolates belonging to MLST type ST80 are often associated in Europe with the Panton-Valentine Leukocidin (PVL) coding gene (lukS-lukF) [6]. These isolates so far correspond to spa type t044 and its variants t376 and t455. Broader use of spa typing could make associations between specific virulence markers and spa types apparent, which might be then useful as surrogate markers for virulence and could be used for risk assessment and early-warning algorithms [4]. The SeqNet.org laboratory network delivers the tools to detect the cross-border spreading of MRSA and enables participating countries to establish local, national and international early warning systems. Moreover, the SeqNet.org typing data can already be used for trend analysis and early warning algorithms.

Other laboratories are welcome to join this initiative. The results of the certification trial and the common standard for external and internal quality control will be published in the near future. As the participating laboratories are able to store very detailed information about the isolates and their origin, SeqNet.org will decide, in collaboration with other networks and institutions interested in the SeqNet.org data (eg EARSS, national reference laboratories), how the data should flow nationally and internationally (eg, via the national reference laboratories) and if further data should be synchronised (MLST types, specimen, source, etc.).

Table. The 30 laboratories and institutions in Europe participating in SeqNet.org