A metagenomic investigation of antibiotic resistance in non-clinical environments
S. Pillay (TU Delft - Pattern Recognition and Bioinformatics)
Marcel J T Reinders – Promotor (TU Delft - Pattern Recognition and Bioinformatics)
Thomas Abeel – Promotor (TU Delft - Pattern Recognition and Bioinformatics)
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Abstract
Antimicrobial resistance (AMR), termed a "silent pandemic" has caused 4.95 million deaths in 2019, with numbers expected to rise. AMR spans human, animal, and environmental sectors, requiring a One Health approach to address this multifaceted global challenge. This dissertation focuses on the under-represented non-clinical sectors and employs the use of metagenomic data to advance AMR research.
The primary focus in AMR research has been on clinical settings, overlooking animals and the environment and leaving data gaps in resource-limited regions. The world of AMR and metagenomic data is first introduced followed by an in-depth review of AMR in non-clinical sectors and the information metagenomic data can provide. The emphasis is on bioinformatic tools, databases, and workflows to support researchers utilising metagenomic data for AMR studies in these sectors.
Moving forward, the wastewater treatment process, including the neglected upstream and downstream freshwater systems, is examined, to assess the microbiome, resistome and mobilome at each stage. Specific differences within every wastewater treatment plant process sector and their role in AMR transmission are identified. Inspired by the natural baseline of antibiotic resistance in soil, a comparative study of the composition of the microbiome, resistome and mobilome in different soil types, from natural to rural soils, is then further presented. Given the limited information on resistance patterns and the effects of geographical and anthropogenic factors, the influence of antibiotic resistance in different soil types is then further explored.
The swine industry, as the largest consumer of antibiotics, raises concerns about the effects of antibiotic use on the gut microbiome of animals. Antibiotics can impact animal health and promote the transmission of AMR to other non-clinical sectors and humans. How antibiotic use affects the fecal microbiome of pigs raised with and without antibiotics is examined to understand the dynamics of antibiotic resistance in the swine industry.
The burden of AMR, particularly in low- and middle-income countries, where resources for infectious disease surveillance are limited, was the inspiration to propose a method for generating metagenomic data in-field and in resource-limited settings, offering a cost-effective solution for outbreak monitoring and pathogen detection.
The main goal of this dissertation is to highlight the under-represented sectors, their significant role in AMR and to promote global inclusivity.