Antibiotic-associated diarrhoea (AAD) often occurs following the unintended disruption of the protective gut microbiota by antibiotic treatment, leading to infection with opportunistic pathogens. The most common infectious cause of AAD is Clostridium difficile, which is associated with approximately 25% of all AAD cases. Although several other clinically important bacterial species have also been associated with AAD, infectious aetiologies other than C. difficile are not often screened for, and in the majority of AAD cases, the aetiology remains undetermined. Despite the current worldwide interest in gut health and the role that the normal microbiota play in maintaining homeostasis, little is known about infections that result from perturbations to the microbiota for pathogens other than C. difficile. In this study, we identified new infectious aetiologies of AAD by employing clinical screening of faecal samples from patients with C. difficile-negative AAD. Using this approach, we isolated several bacterial pathogens including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli, and using a novel mouse model of non-C. difficile AAD infection, we have demonstrated the capacity of these isolates to cause gut damage. Using immunostaining, we have also analysed the damage caused by these isolates by observing specific markers in the gastrointestinal mucosa of infected mice, including the adherens junction proteins E-cadherin and β-catenin, and have defined how this damage occurs differentially in varying sections of the small and large intestine. The results of this project highlight the diverse range of bacteria that can cause AAD and offer new insights into the mechanisms of disease pathogenesis for these organisms, which will be a key to the future development of improved strategies for diagnosis, prevention and treatment. Furthermore, the use of these new mouse models will provide a platform that can be used to rationally test the efficacy of new therapeutic agents for preventing or treating AAD.