Current microscopy systems for the imaging of micro-organisms are expensive because of their optimized design for resolution maximization and aberration correction. In situations where such an optimization is not needed, for instance to merely detect the presence of pathogens in liquids, a potential approach is to use highly-refractive spheres in combination with low-magnification objectives to increase the resolution and the sensitivity of the optical sensing system in a cost-effective fashion. Here, we report a study on highly-refractive dielectric mm-size spheres that are partially-embedded in polymeric membranes of mismatched refractive index. We computed the transformation that the sphere mediates on the light originating from the sample towards the optical detector, and show its enhanced-detection potential. We then propose a method to easily fabricate microfluidic chips with custom designs and precise location of dielectric spheres for enhanced imaging of micro-organisms. Our technique is based on the creation of polymeric membranes with partially-embedded spheres by spin-coating of polydimethylsiloxane pre-polymer on micro-structured Si wafers, followed by manual positioning of the dielectric spheres and polymer cross-linking. We applied this concept to the detection of living fluorescent bacteria in a water flow by creating a microfluidic chip with suitable design to confine the bacteria in the imaging region of the sphere. Based on the fluorescence-image analysis, we quantified the net contrast gain provided by the sphere for short exposure time, showing its potential for fast imaging. This fabrication method combines the flexibility of microfluidic handling with the optical enhancement of low-magnification systems and has potential for use in flow cytometry applications.