Bachelor of Science (Honours)
School of Earth, Atmospheric and Life Sciences
Yerbury, Maddison, Metagenomic analysis facilitates ontogenetic investigations of microbiota composition and antimicrobial resistance in silver gull (Chroicocephalus novaehollandiae) chicks, Bachelor of Science (Honours), School of Earth, Atmospheric and Life Sciences, University of Wollongong, 2021.
The proliferation of antimicrobial resistance (AMR) in recent decades has been fuelled by the development, overconsumption and misuse of antibiotic therapeutics and non-medical antimicrobials. The evolution of AMR-bacteria is predominantly underpinned by the horizontal transfer of antimicrobial resistance genes (ARGs), which allows AMR to be transferred between bacterial species and accumulate within bacteria, even in the absence of antimicrobial selection pressures. It has been speculated that avian wildlife, in particular waterbird species such as gulls, act as reservoirs of AMR, facilitating the propagation of AMR-bacteria that can then be transmitted into humans. The current thesis, therefore, investigated whether silver gull (Chroiocephalus novaehollandiae) chicks may play a role in the evolution and proliferation of AMR-bacteria. Firstly, numerous DNA extraction protocols were trialled to optimise the extraction of DNA from multi-species microbiota samples. Metagenomic sequencing and analysis were then conducted for 60 temporal multi-species microbiota samples from 23 silver gull chicks, which had been subcultured for Enterobacteriaceae, a subpopulation of the microbiome enriched in AMR-associated bacteria. The data were examined in order to characterise bacterial and AMR composition and to analyse ontogenetic shifts in the microbiome to assess if the silver gull chick microbiome has the ability to accumulate and maintain AMR. Metagenomic analysis revealed a diverse Gammaproteobacterial community of 125 species and 30 genera, and the majority of species were of a genus containing pathogenic and AMR-associated species. Additionally, metagenomic analysis detected a large ARG pool, with 115 ARGs identified across all samples. These ARGs were dominated by Beta-lactams and Aminoglycoside resistance phenotypes, which are the most commonly used antibiotics in Australia. Ontogenetic analyses further showed that both bacterial and AMR profiles were in constant flux and varied between samples and within individual chicks. Additionally, both richness and composition measures for bacterial species and ARGs were significantly correlated, such that the ARG profile within a sample was correlated to the bacterial profile. The high diversity of AMR-associated bacteria and ARGs found in these samples indicates that the silver gull microbiome may act as an ‘ecological sponge’ of AMR-bacterial contamination in the environment, which transiently colonise the gut. Moreover, these findings indicate that ARGs are not accumulated and do not persist over time but are brought in with the transient bacteria they are associated with. The current thesis, therefore, concludes that silver gull chicks do not contribute to the proliferation and evolution of AMR-bacteria, and further, do not act as a 6 reservoir to support the propagation of AMR-bacteria. Moreover, this thesis presents the first longitudinal metagenomic study to examine the dynamic nature of the microbiome and AMR in a wildlife host. Future studies should investigate potential sources of the AMR contamination reflected in this silver gull population, and explore potential reservoirs of AMR, including wildlife populations and the non-human environment.
Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.