To prevent the spread of hospital-acquired infections, embodiments described herein monitor mobile device usage in clinical settings (by a physician, nurse, etc.) to characterize potential pathogenic contamination of the mobile device, the user's hands, and the surfaces in contact with the device. Our method considers the physical properties of how the device is handled and held during use, as well as the location and setting before, during, and after use to estimate potential contamination and transmission of pathogens. A system can use the estimation, along with knowledge (e.g., of the user's upcoming schedule) to alert them of potential contamination hazards and suggest when to avoid mobile device use as well as when to sanitize the device and user's hands.