The widespread adoption of Connected and Automated Vehicles (CAVs) is being propelled, not only in the realm of private vehicles but also within transit systems. This development serves to enhance urban transport activities, rendering transportation more appealing to passengers. The present study aims to identify and examine the safety effects of testing different operational speed shuttle bus services in various future mobility conditions. To investigate impacts of autonomous shuttle bus services and to further examine their operational speed, the microscopic simulation method was performed. Specifically, four sets of simulation scenarios were comprised: a baseline scenario representing the current conditions and three operational speed scenarios (15 km/h, 30 km/h and 45 km/h) for an autonomous shuttle service. Each one of these sets included eleven CAV market penetration rates (MPRs) of CAVs of the general traffic (ranging from 0 to 100% in 10% increments). By analyzing the trajectory data extracted from microsimulation, traffic conflicts were identified and further analyzed by developing Mixed-Effects Multinomial Logit Regression models (ME-MLMs) in order to associate conflict type taking into account network characteristics as well as traffic conditions. Several aspects were determined as statistical significant parameters influencing type of conflict. The analysis yielded several significant findings that provide quantitative measurements and assessments of the effects observed, enabling a better understanding of the safety implications associated with the widespread adoption of automated services.