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  • Publication
    Monitoring and control of Cronobacter sakazakii in Irish dairy powder processing facilities
    (University College Dublin. School of Biosystems and Food Engineering, 2022)
    Cronobacter sakazakii is a pathogen widely associated with powdered infant formula (PIF). However, there is a broadening concern in the dairy powder industry relating to Cronobacter sakazakii, particularly if the dairy ingredients are subsequently used in PIF products. The first objective of this thesis was to use whole genome sequencing in an extensive monitoring programme for Cronobacter sakazakii in an Irish dairy process facility. A yearlong surveillance programme of a large-scale Irish milk protein concentrate processing facility detected a significant amount of Cronobacter sakazakii. Subsequent sequencing and species identification confirmed that all 88 positive isolates were Cronobacter sakazakii strains. Phylogenetic analysis demonstrated frequent genetically similar isolates among the strains recovered indicating that they most likely came from the same individual initial contamination event. In all nine separate genetically similar groups were identified pointing to potentially multiple contamination events in the process facility before / during the monitoring period. Phylogenetic analysis coupled with temporal and spatial analysis of the isolates also indicated a significant amount of persistence of strains in the process facility. The second major objective was to identify the occurrence of thermal tolerant regions in the genome of Cronobacter sakazakii strains recovered from Irish dairy process facilities and to undertake laboratory thermal inactivation studies to confirm that presence of the thermal tolerant region confers enhanced thermal tolerance to the strain. Of 114 isolates examined, 56 isolates contained the shorter thermal tolerant gene island as present in Cronobacter sakazakii, strain SP291. Thermal inactivation studies confirmed that in general, the short thermal tolerant region found in Cronobacter sakazakii strains recovered from Irish dairy process facilities confers enhanced thermal tolerance to strains containing the genomic region. Overall, the thesis demonstrated the utility of using whole genome sequencing as a ‘fingerprinting’ tool in pathogen monitoring programmes in food process facilities and demonstrated that increasingly, genomic data can be used to predict phenotypic behaviour such as thermal tolerance.