Identifying risks associated with organic soil amendments: microbial contamination in compost and manure amendments

The application of animal manures to agricultural land as a soil organic amendment has been identified as an important route by which foodborne pathogens can enter the human food chain. Knowledge of the presence and incidence of key foodborne pathogens in manure is a vital first step in the establishment of sound and effective guidelines for management and prevention of contamination by manure. The work described in this thesis attempts to determine the persistence of pathogens when raw manures are directly applied to agricultural soils, and treated under thermophilic composting conditions. Results from this study indicated that the current conditions suggested by typical food safety guidelines are sufficient to reduce the population of enteric bacteria to levels that minimise risks associated with culturable cells in raw manure and finished compost. However, E. coli cells have the potential to enter a viable but non-culturable (VBNC) state and are undetected by culture-based monitoring methods, thus providing a false impression of the innate risk of the product. Prc, bamB and tolA, which are responsible for stabilising the cell membrane, were found to be essential genes required for surviving heat treatment at 55°C. In addition, the presence of relA and oxyR suggested that E. coli may use the VBNC state as an adaptive strategy for long-term survival to withstand multiple stresses, including heat stress. Entering the VBNC state with a strengthen cell envelope may help E. coli to survive prolonged heating during standard composting conditions. Successful resuscitation from the VBNC state was achieved in the presence of cell-free supernatant from actively growing E. coli MG1655. These results underline the importance of considering VBNC cells when evaluating the sanitary effect of the composting process. VBNC cells in composts could facilitate the persistence of pathogens in manure-amended soil and thus pose a risk of microbial contamination of fresh produce