Comparative genomic analysis of T.whipplei strains reveals that diversity is mainly related to the WiSP proteins

In this work we analyzed the genomic diversity of several Tropheryma whipplei strains by microarray based-comparative genomic hybridization. Fifteen clinical isolates originating from biopsy samples recovered from different countries were compared with the T. whipplei Twist strain. For each isolate, the genes were defined as either present or absent/divergent using the GACK analysis software. Genomic changes were then further characterized by PCR and sequencing. Obtained results revealed a limited genetic variation between these T. whipplei isolates with at most 2.24 % of the probes exhibiting differential hybridization against the Twist strain. The main variation was found in genes encoding for the WiSP family proteins supporting the view of these membrane proteins as key actors of immune evasion. This work also evidenced a 19.2 kb-pair deletion within T. whipplei DIG15 strain. This deletion takes place in the same region as the large genomic rearrangement previously described between Twist and TW08/27 which can thus be considered as a major hot-spot for intra-specific T. whipplei differentiation. Analysis of this deleted region confirmed the role of WND-domains in generating T. whipplei diversity Keywords: Comparative genomic hybridization *15 test strains (Endo5, Endo7, Slow1B, Slow2, ART1, Neuro1, Neuro2, Dig7, Dig9, Dig10, DigADP11, Dig Neuro14, Dig15, DigMusc17, DigNeuro18) *1 reference strain (T. whipplei strain Twist) *3 biological replicates per condition *4 technical replicates per microarray *Dual-labeling using a reference design: reference sample labeled with Cy5-dCTP and test sample labeled with Cy3-dCTP