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Title: On the phylogeny, detection and behaviour of Clostridial pathogens in the soil
Author: Palmer, Joseph Samuel
ISNI:       0000 0004 7971 3782
Awarding Body: University of Nottingham
Current Institution: University of Nottingham
Date of Award: 2019
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Clostridial pathogens are the aetiological agents for various human and animal diseases. Their presence in soils, manure and other organic wastes can give rise to multiple routes of infection via ingestion, inhalation or contamination of wounds, crops or silage with soil containing vegetative cells or spores. More qualitative and quantitative data are needed on the distribution, abundance and behaviour of these pathogens in agricultural soils to better manage risk. This project investigated how various soil and land-management factors affect the prevalence and survival of key pathogenic Clostridia in the soil. A multidisciplinary approach was used to develop molecular tools for clostridial diagnostics. For accurate strain identification, single and multi-gene markers were used to produce an updated phylogeny for members of the Class Clostridia, indicating examples of misnamed and misclassified strains. For rapid, simultaneous detection of Clostridia, proof-of-concept for an automated multiplex ribosomal intergenic spacer analysis (AMRISA) protocol was devised, and its utility demonstrated on agricultural soils collected from sites in north-east Scotland. Clinically important Clostridia were identified in soils across farms, including Paeniclostridium sordellii and Clostridium novyi, which were prevalent in all soils. Farm management type, season and grazing levels affected the clostridial community, with Pn. sordellii prevalence and relative abundance highest under dairy and beef regimes. C. novyi abundance was highest in the winter. Permanent waterlogging had a pronounced effect on pathogen abundance, although short-term changes in soil moisture had little observable effect. Microcosm studies indicated that Clostridioides difficile, C. perfringens and C. sporogenes were more persistent when spiked into drier soils compared to soils with higher moisture contents. Future work should increase pathogen surveillance on farms and identify the effect of other soil characteristics on pathogen behaviour, to understand disease epidemiology and establish appropriate risk-aversion practices.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QR100 Microbial ecology