Patho-NGen-Trace Outlook

Even after the end of funding the successful Patho-NGen-Trace consortium will remain functional and active, as its mission is not yet over. The consortium created and validated the microbial genome-wide gene by gene allele calling approach that is termed in the meantime by many molecular epidemiologists either as core genome MLST (cgMLST) when done with a gene-set that is shared by all/most isolates of the species under study or whole genome MLST (wgMLST) when done with the pan-genome genes of the species. Like MLST the wg/cgMLST approach enables for a global and public nomenclature that is required for a successful integrated cross-border and –sectional infectious disease surveillance (ONE Health). Although Patho-NGen-Trace already published a microbial typing ontology (TypON) and established public wg/cgMLST reference databases (pubMLST based on BIGSdb and Ridom further harmonization work - e.g., implemented common application programming interfaces (API) - is needed to establish a federated, inter-operable, and sustainable microbial genomic nomenclature system. Therefore, watch out for further exciting achievements of the consortium in the near future.