Distribution and fate of antimicrobial resistance genes in riverine systems and coastal waters: implications for public health

Antimicrobial resistance genes (ARGs) are increasingly recognized as a significant global threat to human and environmental health, with aquatic systems serving as critical reservoirs of these genes. Faecal contamination, primarily from urban streams and wastewater discharges, has been identified as a major contributor to ARG dissemination in freshwater and coastal environments. While much focus has been placed on water quality, the role of sediments in harbouring and preserving ARGs remains underexplored, despite their potential to act as long-term reservoirs under favourable conditions. This PhD research investigates the abundance, distribution, and persistence of ARGs and faecal contamination in interconnected environments, focusing on the polluted Elm Park Stream, Merrion Strand seawater, and beach sediments, including surface and underlying sediment layers of Merrion Strand, which are impacted by discharges from this polluted stream. Chapters 5 and 6 explore foundational aspects of microbial communities and sediment characteristics, helping to understand how ARGs persist and spread. Chapter 5 highlights the distinct microbiomes present across freshwater, seawater, beach sand and sediment layers, emphasizing how microbial communities change in these different environments. This was analysed using next-generation sequencing using the MiSeq Illumina platform, targeting the V3-V4 region of the 16S rRNA gene to provide a detailed view of bacterial diversity and composition. Chapter 6 focuses on the sedimentology of Merrion Strand, analysing sand characteristics to understand how sediment properties influence bacterial persistence. Building on these insights, Chapters 4 and 7 examine the presence of faecal pollution and ARGs, revealing remarkably increased levels of faecal indicator bacteria (FIB) and ARGs in surface environments. Chapter 7 further identifies the presence of five ARGs at depth, suggesting that sediments may act as long-term reservoirs for ARGs and potentially facilitate horizontal gene transfer (HGT). horizontal gene transfer (HGT). Nanopore sequencing of ARG amplicons products was applied to examine the allelic diversity of ARGs across all environments and to investigate whether horizontal gene transfer (HGT) occurred. This analysis revealed that some ARGs can be traced back to Elm Park Stream, others are linked to external sources, and certain ARGs are unique to deeper sediment layers. Single nucleotide polymorphism (SNPs) analyses identified potential HGT between bacterial populations, providing insights into ARG exchange across interconnected environments. This thesis demonstrates that sediments play a pivotal role in the persistence and dissemination of ARGs, presenting a risk to public health.