Exploring the diversity of human-associated microbes and antimicrobial resistance in three species of Australian pinniped pups

Abstract

Contamination of coastal marine environments with human-associated microbes and antibiotic resistance genes is continually increasing, impacting marine ecosystems and the wildlife species therein. Australian fur seals (Arctocephalus pusillus doriferus), long-nosed fur seals (Arctocephalus forsteri) and Australian sea lions (Neophoca cinerea) inhabit numerous coastal and offshore sites along the Australian coastline. The overarching aim of this thesis was to investigate the presence of human-associated Escherichia coli, an indicator of faecal contamination, and class 1 integrons, genetic determinants of antimicrobial resistance, in neonatal pinniped pups. Faecal samples were collected from A. p. doriferus, A. forsteri and N. cinerea pups from eight breeding colonies between 2016-2021. Escherichia coli was cultured from faecal swabs and DNA was subsequently extracted from E. coli isolates and a subset of faecal swabs. Phylotype diversity was not significantly different across species or breeding colonies and the human-associated E. coli B2 phylotype was the most prevalent phylotype across all species. Class 1 integrons were isolated from E. coli (n=36, 4.52%) and faecal DNA (n=15, 4.85%) in A. p. doriferus (n=40) and N. cinerea (n=11) pups but were absent in A. forsteri pups. Finally, the faecal microbiota of endangered N. cinerea pups was characterised to investigate the impact of anthelmintic treatment to eliminate hookworm infection on the composition of the gut microbiota. Topical treatment did not significantly change the microbial composition, suggesting that it is a safe and minimally invasive management strategy to aid in the conservation of endangered N. cinerea pups. The high prevalence of human-associated E. coli in addition to the detection of antimicrobial resistance genes highlights the imperative for ongoing monitoring and surveillance of microbes in marine sentinel species.