A comparative study of anthropogenic antimicrobial pollution on Australia’s little penguins

This thesis presents a synthesis of the literature on antimicrobial resistance (AMR) in wildbirds, in order to ascertain whether there are any traits, physiological or ecological, that are associated with the acquisition and retention of resistant organisms in wild birds. Major knowledge gaps were identified in types of bird species and bacterial species targeted for investigating AMR in wild birds. This was particularly evident in the Australian context. In Australia, the little penguin (Eudyptula minor) is an iconic marine bird that spends the majority of its life at sea. The life history of the little penguin potentially increases the species’ opportunity for exposure to resistant organisms present in the marine environment, making these birds an ideal study species for the investigation of the dissemination of antimicrobial resistance. Little penguin colonies in Australia are widely distributed, with mainland and island colonies ranging from New South Wales on the East coast to Western Australia. These colonies experience differing levels of human influences ranging from isolated off-shore islands to mainland sites highly frequented by tourists. There are also several little penguin colonies in captive institutions in Australia, enabling comparison of resistant determinants between wild and captive little penguins. After identifying the little penguin as a key species to investigate in the dissemination of antimicrobial resistance from humans to wild birds, the aim of this study was to examine the bacterial community of wild and captive little penguins to determine if the class 1 integron, a mobile element that confers antibiotic resistance, was present in their faecal microbiota. In addition, two Gram-negative bacterial species of clinical relevance, Escherichia coli and Klebsiella pneumoniae, were genetically characterised and assessed for the presence of class 1 integrons to elucidate if the bacterial species harbouring the class 1 integrons are human associated. Understanding the presence of organisms carrying resistance traits in the host is an important step towards understanding if human antimicrobial pollution is contributing to the decline seen in little penguin colonies across Australia, as such acquisition may affect little penguin health. Defining alterations caused by the acquisition of resistance determinants could thus help shape conservation practices for future management of the little penguin.