We routinely characterize bacteria and fungi under appropritae BSL1, 2 or 3 conditions. Most of the characterization assays are quality control assays, performed upon deposit and/or before distribution of a strain. However, some characterization assays are performed only on request and aim to further characterize specific strains, in the context of research collaborations.
Colony Forming Units are measured automatically. Numbers of total and viable bacteria per volume unit are measured with an automatic counting method based on membrane integrity.
Bruker MALDI-TOF MS is performed for authentication Quality Control of all incoming strains. We follow CLSI M58 standards.
Paired end 150bp reads Illumina sequencing is performed by the Institut Pasteur P2M sequencing platform. Illumina sequencing is performed on all incoming strains for authentication Quality Control.
Double stranded DNA is quantified by spectrofluorometry. Genome copy numbers are quantified by digital PCR, based on single copy genes.
For genomes <10Mb, QC bioinformatic analysis of a single genome sequence is performed for identification and contextualisation of sequences of concern. Curation of data in existing cgMLST databases is also performed. For genomes <10Mb, multiple genome-based analysis is performed for comparative genomics (phylogeny, ANI). We also offer support to strain collections through private genomic databases and analytical web tools.
