Understanding sepsis-causing pathogens using wastewater surveillance

Mathias, Jordan 2025. Understanding sepsis-causing pathogens using wastewater surveillance. PhD Thesis, Cardiff University. Item availability restricted.

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Abstract

At the time of writing this thesis, we stand at an unusual precipice within the discipline of Microbiology. On the one hand, we appreciate the importance of our relationships with ‘good’ bacteria, and DNA sequencing allows us to differentiate within a bacterial genus. On the other hand, misinformation, misunderstanding and scientific scepticism against microbiology and immunology are at an all-time high in the wake of the COVID-19 pandemic. Within academic institutions and popular science literature, our attitudes toward microbes and our place in the biosphere are becoming increasingly nuanced. Inspired by the macro-biological tales of rewilding programs such as the reintroduction of wolves to Yellowstone National Park (Smith and Peterson 2021), scientists are also inspired to rewild our own micro-biology. The rise of inflammatory disorders within high-income countries and our increasingly remote ways of interacting with our surroundings have led scientists to suggest that we are currently in a state of dysbiosis with our usual microbiology (known as the old-friends hypothesis) (Rook 2023). It is currently believed that a more diverse microbiome helps train our immune system throughout development, and the loss of these microbes is a key factor in the rise of inflammatory disorders. The work on helminths (Loke and Lim 2015), bacteriophages (Bragg et al. 2014), Helicobacter pylori (Haesebrouck et al. 2009), natural births vs. caesarean (Ríos-Covian et al. 2021), and faecal transplants (Doll et al. 2022) are a testament to these shifting attitudes. Regrettably, the subtlety of this needed shift in thinking is lost on some sections of society. The reduction in our own microbial diversity is likely due to excessive use of disinfectants, irradiated and ultra-processed foods, and to a higher proportion of people living in cities (removed from nature) than ever before. These overly hygienic and sterilised practices are being confused with beneficial advances in healthy hygiene, such as handwashing. Simply put, laymen confuse the message of ‘being too clean’. The issue is further complicated by the zeitgeisty thinking that if something is natural, then it is also good (known as the nature fallacy). Therefore, the advances made by microbiology are conceding ground to attitudes of anti-vaccination, anti-hygiene, and anti-Pasteurisation. Currently, vaccine hesitancy is increasing (Lazarus et al. 2023) and ironically, the practice of handwashing has seen a significant reduction since the COVID-19 pandemic (HandbookLive 2021), although reports are conflicting (Heard 2021). More recently, the trend of consuming raw milk is gaining popularity. These ill-informed attitudes are stunning when we consider that historically, 1 in 4 Europeans would die of tuberculosis (TB) and likely one of the significant sources of TB was unpasteurised milk. Therefore, 2025 is truly a time of revolutionary thinking in microbiology, but simultaneously, more than ever, we need better public education and outreach to bridge the chasm in understanding between the academic institutes and the general public. In this thesis, I plan to contribute to this newly nuanced field of microbiology by highlighting the importance of individual bacterial strains. Namely, Escherichia coli and Staphylococcus aureus. The two most clinically relevant bacteria in terms of human infection (both in terms of antibiotic resistance and non-resistant infections) (Ikuta et al. 2022). In a new world of widely available whole-genome sequencing, genotypic data reveal that our issues of disease, pathogenicity, and antibiotic resistance are not only species-specific but, more importantly, strain specific. Additionally, the burden of these problems is often limited to a tiny handful of specific strains. Understanding this further will help us to reshape our microbial world to our advantage.

Item Type:	Thesis (PhD)
Date Type:	Completion
Status:	Unpublished
Schools:	Schools > Medicine
Date of First Compliant Deposit:	18 May 2026
Last Modified:	18 May 2026 09:20
URI:	https://orca.cardiff.ac.uk/id/eprint/187026

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