Numerical shape optimisation is becoming an essential tool in aeronautic design. Highfidelity optimisation with many design variables will require gradient-based optimisation, adjoint methods can compute gradients very efficiently. CAD models are used on every stage of engineering product development from design to manufacturing. Ideally, the CAD system is kept inside the optimisation loop to maintain a consistent CAD model during the optimisation, as often practised in gradient-free optimisation. However, typical commercial CAD systems do not offer derivative computation, and standard CAD parametrisations may not define a suitable design space for the optimisation. In this work, we use the automatically differentiated (AD) version of Open Cascade Technology (OCCT) CAD-kernel, which robustly provides accurate derivatives with respect to CAD parameters. The kernel is used to handle implicit CAD parametrisations, e.g. move control points of NURBS surfaces, automatically re-parametrise these surfaces, compute intersections between them and perform corresponding mesh morphing. We apply the differentiated CAD tool and parametrisation to high-fidelity aerodynamic shape optimisation of the NASA CRM wing-body intersection and exercise the CAD method for the pylon-nacelle modification.