The PIBnet initiative is a large collaborative program that aims at reinforcing microbial strain collection management and characterization approaches and technologies. It involves National Reference Centers, WHO-collaborative centers, biological resources centers and other microbiological expertise laboratories, together with the Center for Bioinformatics, Biostatistics and Integrative Biology and the Biomics center.
Within this large concerted effort, a priority is to promote whole genome sequencing (WGS) as a rapid and accurate characterization approach of microbial agents for population biology, epidemiological surveillance and outbreak detection. The target volume is 10 000 genomes per year to be sequenced and analyzed within 3 workdays. On the bioinformatics level, this requires implementing fast data treatment tools, genotyping strategies and automated methods to extract medically relevant information from genomic sequences (resistome, virulome).